{ "_3dmet": { "comment": "Website has been down since 2023/2024", "deprecated": true, "description": "3DMET is a database collecting three-dimensional structures of natural metabolites.", "example": "B00162", "homepage": "http://www.3dmet.dna.affrc.go.jp/", "keywords": [ "chemical", "life science", "metabolite", "metabolomics", "structure" ], "mappings": { "biocontext": "3DMET", "edam": "2635", "fairsharing": "FAIRsharing.5ab0n7", "integbio": "nbdc00351", "miriam": "3dmet", "n2t": "3dmet", "prefixcommons": "3dmet", "wikidata": "P2796" }, "name": "3D Metabolites", "pattern": "^B\\d{5}$", "preferred_prefix": "_3dmet", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/aao:$1" } ], "publications": [ { "doi": "10.1186/2041-1480-5-21", "pmc": "PMC4089931", "pubmed": "25009735", "title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon", "year": 2014 }, { "doi": "10.1142/9789812772435_0035", "pubmed": "17992749", "title": "An anatomical ontology for amphibians", "year": 2007 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/AAO_$1", "uri_format": "http://purl.obolibrary.org/obo/AAO_$1" }, "abcam": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "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", "wikidata.entity": "Q29123382" }, "name": "Abcam", "preferred_prefix": "abcam", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "uri_format": "https://www.abcam.com/$1.html" }, "abcd": { "contact": { "email": "Pierre.Cosson@unige.ch", "name": "Pierre Cosson", "orcid": "0000-0002-4881-0358" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "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/", "keywords": [ "immunology", "molecular biology" ], "mappings": { "cellosaurus": "ABCD", "fairsharing": "FAIRsharing.Z8OKi5", "uniprot": "DB-0236", "wikidata.entity": "Q110998933" }, "name": "AntiBodies Chemically Defined database", "preferred_prefix": "abcd", "publications": [ { "doi": "10.1093/nar/gkz714", "pmc": "PMC6943046", "pubmed": "31410491", "title": "The ABCD database: a repository for chemically defined antibodies", "year": 2020 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "uri_format": "https://web.expasy.org/abcd/ABCD_$1" }, "abm": { "contributor_extras": [ { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. 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It provides unique identifiers for antibody sequences, including both immunoglobulin and single-chain variable fragment sequences. These are are critical for immunological studies, and allows users to search and retrieve antibody sequences based on sequence similarity and specificity, and other biological properties.", "example": "81d0ea69a9ab134f6ba68314e982171a367d3ab739c85c5ba49701dd02170ed3", "github_request_issue": 1362, "homepage": "https://absd.pasteur.cloud", "name": "AntiBody Sequence Database", "pattern": "^[a-f0-9]{64}$", "preferred_prefix": "absd", "publications": [ { "doi": "10.1093/nargab/lqae171", "pmc": "PMC11655285", "pubmed": "39703430", "title": "AntiBody Sequence Database", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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This collection references C. elegans genes and expression.", "example": "aap-1", "homepage": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm", "keywords": [ "dna", "gene", "rna" ], "mappings": { "biocontext": "ACEVIEW.WORM", "miriam": "aceview.worm", "n2t": "aceview.worm", "prefixcommons": "aceview.worm" }, "name": "Aceview Worm", "pattern": "^[a-z0-9-]+$", "preferred_prefix": "aceview.worm", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/addgene:$1" } ], "publications": [ { "doi": "10.1093/nar/gku893", "pmc": "PMC4384007", "pubmed": "25392412", "title": "The Addgene repository: an international nonprofit plasmid and data resource", "year": 2014 }, { "doi": "10.1038/505272a", "pubmed": "24429608", "title": "Repositories share key research tools", "year": 2014 }, { "doi": "10.1038/nbt.2177", "pubmed": "22491276", "title": "Addgene provides an open forum for plasmid sharing", "year": 2012 } ], "twitter": "Addgene", "uri_format": "http://addgene.org/$1" }, "addicto": { "contact": { "email": "robertwest100@gmail.com", "github": "robertjwest", "name": "Robert J. 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This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining.", "download_owl": "http://purl.obolibrary.org/obo/ado.owl", "example": "0000001", "homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO", "keywords": [ "alzheimer's disease", "health science", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "ADO", "bioportal": "ADO", "fairsharing": "FAIRsharing.ckd4rf", "obofoundry": "ado", "ols": "ado", "ontobee": "ADO", "wikidata.entity": "Q54887745" }, "name": "Alzheimer's Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ADO", "providers": [ { "code": "legacy", "description": "Legacy URI used before switching to OBO PURLs", "homepage": "http://scai.fraunhofer.de", "name": "Legacy", "uri_format": "http://scai.fraunhofer.de/AlzheimerOntology#$1" } ], "publications": [ { "doi": "10.1016/j.jalz.2013.02.009", "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_$1", "version": "2023-09-20" }, "adw": { "contact": { "email": "adw_geeks@umich.edu", "name": "Animal Diversity Web technical staff" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "deprecated": true, "description": "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology.", "download_owl": "http://aber-owl.net/media/ontologies/ADW/2/adw.owl", "example": "Lycalopex_vetulus", "homepage": "http://www.animaldiversity.org", "keywords": [ "anatomy", "life science", "obo", "ontology", "taxonomic classification" ], "mappings": { "aberowl": "ADW", "agroportal": "ADW", "biocontext": "ADW", "bioportal": "ADW", "fairsharing": "FAIRsharing.t9fvdn", "miriam": "adw", "n2t": "adw", "obofoundry": "adw", "wikidata.entity": "Q114677837" }, "name": "Animal natural history and life history", "pattern": "^[A-Z_a-z]+$", "preferred_prefix": "ADW", "rdf_uri_format": "http://purl.obolibrary.org/obo/ADW_$1", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "uri_format": "https://animaldiversity.org/accounts/$1" }, "aeo": { "appears_in": [ "ehdaa2" ], "contact": { "email": "J.Bard@ed.ac.uk", "name": "Jonathan Bard" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "deprecated": true, "description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology", "download_obo": "http://purl.obolibrary.org/obo/aeo.obo", "download_owl": "http://purl.obolibrary.org/obo/aeo.owl", "example": "0001017", "homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology/", "keywords": [ "anatomy", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "AEO", "bartoc": "181", "biocontext": "AEO", "bioportal": "AEO", "fairsharing": "FAIRsharing.93ee19", "obofoundry": "aeo", "ols": "aeo", "ontobee": "AEO", "wikidata.entity": "Q81661532" }, "name": "Anatomical Entity Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "AEO", "publications": [ { "doi": "10.3389/fgene.2012.00018", "pmc": "PMC3278863", "pubmed": "22347883", "title": "The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs", "year": 2012 } ], "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" ], "uri_format": "http://purl.obolibrary.org/obo/AEO_$1", "version": "2022-09-13" }, "aeon": { "contact": { "email": "philip.stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "contributor": { "email": "philip.stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "description": "The academic event ontology, currently still in development and thus unstable, is an OBO compliant reference ontology for describing academic events such as conferences, workshops or seminars and their series. It is being developed as part of the [ConfIDent project](https://projects.tib.eu/confident/) to allow RDF representations of the academic events and series stored and curated in the [ConfIDent platform](https://www.confident-conference.org/index.php/main_page).", "download_owl": "https://raw.githubusercontent.com/tibonto/aeon/main/aeon.owl", "example": "0000001", "github_request_issue": 617, "homepage": "https://tibonto.github.io/aeon/", "keywords": [ "educational science", "history", "ontology", "social sciences", "tib" ], "license": "CC-BY-4.0", "mappings": { "tib": "aeon" }, "name": "Academic Event Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "aeon", "repository": "https://github.com/tibonto/aeon", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://purl.obolibrary.org/obo/AEON_$1" }, "aero": { "contact": { "email": "mcourtot@gmail.com", "name": "Melanie Courtot", "orcid": "0000-0002-9551-6370" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "deprecated": true, "description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events", "download_owl": "http://purl.obolibrary.org/obo/aero.owl", "example": "0000125", "homepage": "http://purl.obolibrary.org/obo/aero", "keywords": [ "adverse reaction", "biomedical science", "electronic health record", "health science", "medicine", "obo", "ontology", "preclinical studies" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "AERO", "biocontext": "AERO", "bioportal": "AERO", "fairsharing": "FAIRsharing.rycy2x", "obofoundry": "aero", "ols": "aero", "wikidata.entity": "Q55118235" }, "name": "Adverse Event Reporting Ontology", "pattern": "^\\d{7}$", "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_$1" }, "affy.probeset": { "description": "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration.", "example": "243002_at", "homepage": "http://bio2rdf.org", "mappings": { "biocontext": "AFFY.PROBESET", "miriam": "affy.probeset", "n2t": "affy.probeset", "togoid": "AffyProbeset" }, "name": "Affymetrix Probeset", "pattern": "^\\d{4,}((_[asx])?_at)?$", "preferred_prefix": "affy.probeset", "uri_format": "http://bio2rdf.org/affymetrix:$1" }, "afo": { "contact": { "email": "more.info@allotrope.org", "name": "Allotrope Foundation" }, "description": "Allotrope Merged Ontology Suite", "download_owl": "http://purl.allotrope.org/voc/afo/merged/REC/2025/12/merged-without-qudt-and-inferred", "homepage": "https://www.allotrope.org/", "keywords": [ "agricultural engineering", "agriculture", "biology", "chemistry", "environmental science", "food", "food chemistry", "forest management", "nfdi4cat", "nfdi4chem", "nfdi4ing", "ontology", "veterinary medicine" ], "license": "http://purl.allotrope.org/voc/copyright", "mappings": { "aberowl": "AFO", "bioportal": "AFO", "fairsharing": "FAIRsharing.595710", "ols": "afo", "ontobee": "AFO", "tib": "afo" }, "name": "Allotrope Merged Ontology Suite", "no_own_terms": true, "preferred_prefix": "afo", "uri_format": "https://purl.allotrope.org/voc/afo/merged/REC/2025/03/merged-without-qudt-and-inferred$1", "version": "2025-12-01" }, "afpo": { "contact": { "email": "mcmelek@msn.com", "github": "Melek-C", "name": "Melek Chaouch", "orcid": "0000-0001-5868-4204" }, "description": "AfPO is an ontology that can be used in the study of diverse populations across Africa. It brings together publicly available demographic, anthropological and genetic data relating to African people in a standardised and structured format. The AfPO can be employed to classify African study participants comprehensively in prospective research studies. It can also be used to classify past study participants by mapping them using a language or ethnicity identifier or synonyms.", "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": { "aberowl": "AFPO", "bioportal": "AFPO", "obofoundry": "afpo", "ols": "afpo", "ontobee": "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", "version": "2024-03-21" }, "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=$1" }, "aftol.taxonomy": { "contact": { "email": "davem@umn.edu", "name": "David J. McLaughlin" }, "contributor_extras": [ { "email": "laylamichan@ciencias.unam.mx", "github": "lmichan", "name": "Layla Michán Aguirre", "orcid": "0000-0002-5798-662X" } ], "deprecated": true, "description": "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species.", "example": "959", "homepage": "https://aftol.umn.edu", "mappings": { "biocontext": "AFTOL.TAXONOMY", "miriam": "aftol.taxonomy", "n2t": "aftol.taxonomy" }, "name": "Assembling the Fungal Tree of Life - Taxonomy", "pattern": "^\\d+$", "preferred_prefix": "aftol.taxonomy", "uri_format": "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1" }, "agilent.probe": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699.", "example": "A_24_P98555", "homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt", "keywords": [ "transcriptomics" ], "name": "Agilent Probe", "pattern": "^A_\\d+_.+$", "preferred_prefix": "agilent.probe", "references": [ "http://www.cs.tau.ac.il/cgi-bin/cgiwrap/click/get.cgi/conversionFiles/conversion_human_14850_agilent2entrez.txt" ] }, "agricola": { "appears_in": [ "chebi", "pmc" ], "contact": { "email": "judith.blake@jax.org", "github": "judyblake", "name": "Judith A Blake", "orcid": "0000-0001-8522-334X" }, "contributor_extras": [ { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, { "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.", "example": "IND608186955", "example_extras": [ "GUA85008832" ], "homepage": "http://agricola.nal.usda.gov/", "mappings": { "biocontext": "AGRICOLA", "go": "AGRICOLA_ID", "miriam": "agricola", "n2t": "agricola", "wikidata.entity": "Q4651693" }, "name": "Agricultural Online Access", "pattern": "^(IND|GUA)\\d+$", "preferred_prefix": "agricola", "providers": [ { "code": "usda", "description": "This endpoint no longer works but is maintained for legacy purposes", "homepage": "https://agricola.nal.usda.gov", "name": "USDA Legacy Endpoint", "uri_format": "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1" } ], "publications": [ { "doi": "10.1093/nar/gkz813", "pmc": "PMC6943066", "pubmed": "31552413", "title": "Alliance of Genome Resources Portal: unified model organism research platform", "year": 2020 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "synonyms": [ "AGR", "AGRICOLA_ID" ], "uri_format": "https://europepmc.org/article/AGR/$1" }, "agrkb": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor": { "email": "smoxon@lbl.gov", "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" }, "description": "The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations.\n\nThe Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location:\n\n- [ZFIN](https://zfin.org) - Zebrafish Information Network\n- [WormBase](https://wormbase.org)\n- [MGI](https://www.mgi.org) - Mouse Genome Informatics\n- [RGD](https://rgd.mcw.edu) - Rat Genome Database\n- [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database\n- [FlyBase](https://flybase.org)\n- [Xenbase](https://www.xenbase.org)", "example": "100000000000001", "github_request_issue": 359, "homepage": "https://www.alliancegenome.org", "keywords": [ "model organism database" ], "mappings": { "biolink": "AGRKB", "uniprot": "DB-0266" }, "name": "Alliance of Genome Resources Knowledge Base", "pattern": "^[1-9][0-9]{14}$", "preferred_prefix": "agrkb", "publications": [ { "doi": "10.1093/nar/gkz813", "pubmed": "31552413" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.alliancegenome.org/accession/$1" }, "agro": { "contact": { "email": "m.a.laporte@cgiar.org", "github": "marieALaporte", "name": "Marie-Angélique Laporte", "orcid": "0000-0002-8461-9745" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "depends_on": [ "bfo", "envo", "foodon", "go", "iao", "ncbitaxon", "obi", "pato", "peco", "po", "ro", "to", "uo", "xco" ], "description": "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities", "download_obo": "https://raw.githubusercontent.com/KrishnaTO/agro/master/agro.obo", "download_owl": "http://purl.obolibrary.org/obo/agro.owl", "example": "00020007", "homepage": "https://github.com/AgriculturalSemantics/agro", "keywords": [ "agriculture", "agronomy", "cropping systems", "dataplant", "farming systems research", "obo", "ontology", "plant breeding" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "AGRO", "agroportal": "AGRO", "biocontext": "AGRO", "bioportal": "AGRO", "fairsharing": "FAIRsharing.m40bhw", "obofoundry": "agro", "ols": "agro", "ontobee": "AGRO", "tib": "agro", "wikidata.entity": "Q81661533" }, "name": "Agronomy Ontology", "pattern": "^\\d{8}$", "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_$1", "version": "2022-11-02" }, "agrovoc": { "banana": "c_", "comment": "The download page for the [rdf](https://data.apps.fao.org/catalog/dataset/agrovoc-2025-07/resource/b5571fb6-7098-4866-b053-87b550e4624a) resource states it's available under CC-BY-4.0, though this information is not widely accesible on the website.", "contact": { "email": "alex.skrenchuk@stanford.edu", "name": "Alex Skrenchuk" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages.", "download_rdf": "https://agrovoc.fao.org/latestAgrovoc/agrovoc_core.rdf.zip", "example": "2842", "homepage": "https://data.apps.fao.org/catalog/organization/agrovoc", "keywords": [ "agricultural products", "agriculture", "agronomy", "aquaculture", "botany", "climate", "data management", "environmental science", "fisheries science", "food", "food security", "forest management", "knowledge and information systems", "nutritional science", "ontology", "water management" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "AGROVOC", "agroportal": "AGROVOC", "bartoc": "305", "bioportal": "AGROVOC", "ecoportal": "AGROVOC", "fairsharing": "FAIRsharing.anpj91", "wikidata": "P8061", "wikidata.entity": "Q292649" }, "name": "Agronomy Vocabulary", "pattern": "^[a-z0-9]+$", "preferred_prefix": "agrovoc", "publications": [ { "doi": "10.4060/cb2838en", "title": "AGROVOC", "year": 2021 }, { "doi": "10.3390/engproc2021009017", "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", "title": "AGROVOC: The linked data concept hub for food and agriculture", "year": 2022 } ], "rdf_uri_format": "http://aims.fao.org/aos/agrovoc/$1", "references": [ "http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_core.nt.zip", "http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_lod.nt.zip", "https://en.wikipedia.org/wiki/AGROVOC" ], "twitter": "FAOAIMS", "uri_format": "http://aims.fao.org/aos/agrovoc/c_$1" }, "agsc": { "contact": { "email": "srvoss@uky.edu", "name": "Stephen Randal Voss", "orcid": "0000-0002-8332-3176" }, "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. 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It also defines general categories for post-secondary education (vocational, professional and life-long learning).", "example": "Pre-K", "example_extras": [ "1", "2", "K" ], "homepage": "http://purl.org/ASN/scheme/ASNEducationLevel/", "keywords": [ "education level", "open educational resources" ], "name": "U.S. Education Level Vocabulary", "preferred_prefix": "ans.educationlevel", "uri_format": "http://purl.org/ASN/scheme/ASNEducationLevel/$1" }, "antibodyregistry": { "contact": { "email": "abandrowski@ncmir.ucsd.edu", "github": "bandrow", "name": "Anita Bandrowski", "orcid": "0000-0002-5497-0243" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.", "example": "493771", "homepage": "http://antibodyregistry.org/", "keywords": [ "antibody", "reagent", "unique identifiers" ], "logo": "https://www.antibodyregistry.org/assets/logo.svg", "mappings": { "biocontext": "ANTIBODYREGISTRY", "integbio": "nbdc01696", "miriam": "antibodyregistry", "n2t": "antibodyregistry", "rrid": "AB", "wikidata.entity": "Q111182712" }, "name": "Antibody Registry", "pattern": "^\\d{6}$", "preferred_prefix": "antibodyregistry", "publications": [ { "doi": "10.1093/nar/gkac927", "pmc": "PMC9825422", "pubmed": "36370112", "title": "The Antibody Registry: ten years of registering antibodies", "year": 2023 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "uri_format": "http://antibodyregistry.org/AB_$1" }, "antifam": { "contact": { "email": "agb@ebi.ac.uk", "name": "Alex Bateman", "orcid": "0000-0002-6982-4660" }, "contributor": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "AntiFam is a database of spurious protein families that have been removed from Pfam due to incorrect hidden Markov model prediction.", "example": "ANF00001", "github_request_issue": 1523, "homepage": "https://www.ebi.ac.uk/interpro/entry/antifam", "mappings": { "uniprot": "DB-0275" }, "name": "AntiFam", "pattern": "^ANF\\d{5}$", "preferred_prefix": "antifam", "publications": [ { "doi": "10.1093/database/bas003", "pmc": "PMC3308159", "pubmed": "22434837", "title": "AntiFam: a tool to help identify spurious ORFs in protein annotation", "year": 2012 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.ebi.ac.uk/interpro/entry/antifam/$1" }, "antweb": { "description": "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures.", "example": "casent0106247", "homepage": "http://www.antweb.org/", "keywords": [ "anatomy", "classification", "life science" ], "mappings": { "biocontext": "ANTWEB", "fairsharing": "FAIRsharing.yk38tw", "integbio": "nbdc01710", "miriam": "antweb", "n2t": "antweb", "ncbi": "AntWeb", "prefixcommons": "antweb", "wikidata": "P5299" }, "name": "AntWeb", "pattern": "^casent\\d+(\\-D\\d+)?$", "preferred_prefix": "antweb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/antweb:$1" } ], "publications": [ { "doi": "10.1038/424242b", "pubmed": "12867945", "title": "Ants join online colony to boost conservation efforts", "year": 2003 } ], "uri_format": "http://www.antweb.org/specimen.do?name=$1" }, "anzctr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "The Australian New Zealand Clinical Trials Registry (ANZCTR) is an online register of clinical trials being undertaken in Australia, New Zealand and elsewhere. The ANZCTR includes trials from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies.\n\nIn 2007 the ANZCTR was one of the first three trial registries to be recognised by the World Health Organization International Clinical Trials Registry Platform (WHO ICTRP) as a Primary Registry. WHO recognises registries as Primary Registries if they fulfil certain criteria with respect to data content, quality and validity, accessibility, unique identification, technical capacity and administration. The ANZCTR contributes data to the WHO ICTRP, which was developed in 2007. Trials from all ICTRP Primary Registries can be searched at: www.who.int/trialsearch. (from website)", "example": "ACTRN12623000498695", "homepage": "https://anzctr.org.au", "mappings": { "wikidata.entity": "Q65242932" }, "name": "Australian New Zealand Clinical Trials Registry", "pattern": "^ACTRN\\d+$", "preferred_prefix": "anzctr", "providers": [ { "code": "redirect", "description": "Australian New Zealand Clinical Trials Registry (redirect)", "homepage": "https://anzctr.org.au", "name": "Australian New Zealand Clinical Trials Registry (redirect)", "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=$1" }, "aop": { "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "International repository of Adverse Outcome Pathways.", "example": "98", "homepage": "https://aopwiki.org/", "mappings": { "biocontext": "AOP", "miriam": "aop", "n2t": "aop", "wikidata.entity": "Q111254792" }, "name": "AOPWiki", "pattern": "^\\d+$", "preferred_prefix": "aop", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "uri_format": "https://aopwiki.org/aops/$1" }, "aop.events": { "description": "International repository of Adverse Outcome Pathways.", "example": "3", "homepage": "https://aopwiki.org/", "mappings": { "biocontext": "AOP.EVENTS", "miriam": "aop.events", "n2t": "aop.events" }, "name": "AOPWiki (Key Event)", "pattern": "^\\d+$", "preferred_prefix": "aop.events", "uri_format": "https://aopwiki.org/events/$1" }, "aop.relationships": { "description": "International repository of Adverse Outcome Pathways.", "example": "5", "homepage": "https://aopwiki.org/", "mappings": { "biocontext": "AOP.RELATIONSHIPS", "miriam": "aop.relationships", "n2t": "aop.relationships" }, "name": "AOPWiki (Key Event Relationship)", "pattern": "^\\d+$", "preferred_prefix": "aop.relationships", "uri_format": "https://aopwiki.org/relationships/$1" }, "aop.stressor": { "description": "International repository of Adverse Outcome Pathways.", "example": "9", "homepage": "https://aopwiki.org/", "mappings": { "biocontext": "AOP.STRESSOR", "miriam": "aop.stressor", "n2t": "aop.stressor" }, "name": "AOPWiki (Stressor)", "pattern": "^\\d+$", "preferred_prefix": "aop.stressor", "uri_format": "https://aopwiki.org/stressors/$1" }, "aopo": { "comment": "There's no associated primary publication to my knowledge. The class and property CURIE format strings are somewhat inconsistent, but all conform to http://aopkb.org/aop_ontology#AdverseOutcomePathway, http://aopkb.org/aop_ontology#has_key_event or http://aopkb.org/aop_ontology#hasProcess. It is not indexed in the OLS but supports the AOP-WIKI RDF (see https://doi.org/10.1089/aivt.2021.0010 or https://aopwiki.rdf.bigcat-bioinformatics.org/).", "contact": { "github": "DataSciBurgoon", "name": "Lyle Burgoon", "orcid": "0000-0003-4977-5352" }, "contributor": { "email": "javier.millanacosta@maastrichtuniversity.nl", "github": "jmillanacosta", "name": "Javier Millán Acosta", "orcid": "0000-0001-5608-781X" }, "description": "The AOPO provides classes and relationships for the semantic representation of the Adverse Outcome Pathway framework.", "download_owl": "https://github.com/DataSciBurgoon/aop-ontology/raw/refs/heads/master/aopo.owl", "example": "AdverseOutcomePathway", "github_request_issue": 1744, "homepage": "https://github.com/DataSciBurgoon/aop-ontology", "keywords": [ "adverse outcome pathway", "ontology" ], "license": "Apache-2.0", "name": "Adverse Outcome Pathway Ontology", "pattern": "^[A-Za-z_]+$", "preferred_prefix": "aopo", "publications": [ { "doi": "10.1089/aivt.2017.0017", "pmc": "PMC6060416", "pubmed": "30057931", "title": "Creating a Structured Adverse Outcome Pathway Knowledgebase via Ontology-Based Annotations", "year": 2017 } ], "repository": "https://github.com/DataSciBurgoon/aop-ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://aopkb.org/aop_ontology#$1" }, "apaonto": { "contact": { "email": "awalker@apa.org", "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" ], "mappings": { "aberowl": "APAONTO", "bioportal": "APAONTO", "fairsharing": "FAIRsharing.gkw1w8", "wikidata.entity": "Q111194686" }, "name": "Psychology Ontology", "preferred_prefix": "apaonto", "references": [ "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#$1" }, "apd": { "contact": { "email": "gwang@unmc.edu", "name": "Guangshun Wang", "orcid": "0000-0002-4841-7927" }, "deprecated": true, "description": "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides.", "example": "01001", "homepage": "http://aps.unmc.edu/AP/", "keywords": [ "biology", "protein" ], "mappings": { "biocontext": "APD", "fairsharing": "FAIRsharing.ctwd7b", "miriam": "apd", "n2t": "apd", "prefixcommons": "apd", "re3data": "r3d100012901" }, "name": "Antimicrobial Peptide Database", "pattern": "^\\d{5}$", "preferred_prefix": "apd", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/apd:$1" } ], "publications": [ { "doi": "10.1093/nar/gkv1278", "pmc": "PMC4702905", "pubmed": "26602694", "title": "APD3: the antimicrobial peptide database as a tool for research and education", "year": 2015 }, { "doi": "10.1093/nar/gkn823", "pmc": "PMC2686604", "pubmed": "18957441", "title": "APD2: the updated antimicrobial peptide database and its application in peptide design", "year": 2008 }, { "doi": "10.1093/nar/gkh025", "pmc": "PMC308759", "pubmed": "14681488", "title": "APD: the Antimicrobial Peptide Database", "year": 2004 } ], "uri_format": "http://aps.unmc.edu/AP/database/query_output.php?ID=$1" }, "aphidbase.transcript": { "contact": { "email": "fabrice.legeai@rennes.inra.fr", "name": "Fabrice Legeai", "orcid": "0000-0002-6472-4839" }, "description": "AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information.", "example": "ACYPI000159", "homepage": "http://www.aphidbase.com/aphidbase", "keywords": [ "genome" ], "mappings": { "biocontext": "APHIDBASE.TRANSCRIPT", "miriam": "aphidbase.transcript", "n2t": "aphidbase.transcript", "prefixcommons": "aphidbase" }, "name": "AphidBase Transcript", "pattern": "^ACYPI\\d{6}(-RA)?$", "preferred_prefix": "aphidbase.transcript", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/aphidbase:$1" } ], "publications": [ { "doi": "10.1111/j.1365-2583.2009.00930.x", "pmc": "PMC4372297", "pubmed": "20482635", "title": "AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome", "year": 2010 } ], "uri_format": "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1" }, "apid.interactions": { "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.", "example": "P01116", "homepage": "http://cicblade.dep.usal.es:8080/APID/", "mappings": { "biocontext": "APID.INTERACTIONS", "miriam": "apid.interactions", "n2t": "apid.interactions", "wikidata.entity": "Q111047825" }, "name": "APID Interactomes", "pattern": "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$", "preferred_prefix": "apid.interactions", "provides": "uniprot", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "uri_format": "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1" }, "apo": { "contact": { "email": "stacia@stanford.edu", "github": "srengel", "name": "Stacia R Engel", "orcid": "0000-0001-5472-917X" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "A structured controlled vocabulary for the phenotypes of Ascomycete fungi.", "download_obo": "http://purl.obolibrary.org/obo/apo.obo", "download_owl": "http://purl.obolibrary.org/obo/apo.owl", "example": "0000184", "homepage": "http://www.yeastgenome.org/", "keywords": [ "cell biology", "genomics", "life cycle stage", "life science", "morphology", "mutation", "obo", "ontology", "phenomics", "phenotype", "study design" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "APO", "biocontext": "APO", "bioportal": "APO", "fairsharing": "FAIRsharing.dyqz3y", "obofoundry": "apo", "ols": "apo", "ontobee": "APO", "wikidata.entity": "Q81661535" }, "name": "Ascomycete phenotype ontology", "pattern": "^\\d{7}$", "preferred_prefix": "APO", "publications": [ { "doi": "10.1093/database/bap001", "pmc": "PMC2790299", "pubmed": "20157474", "title": "New mutant phenotype data curation system in the Saccharomyces Genome Database", "year": 2009 } ], "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": "http://purl.obolibrary.org/obo/APO_$1", "version": "2026-01-12" }, "apollosv": { "appears_in": [ "scdo" ], "contact": { "email": "hoganwr@gmail.com", "github": "hoganwr", "name": "William Hogan", "orcid": "0000-0002-9881-1017" }, "description": "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.", "download_obo": "https://github.com/ApolloDev/apollo-sv/raw/refs/heads/main/apollo_sv.obo", "download_owl": "http://purl.obolibrary.org/obo/apollo_sv.owl", "example": "00000443", "homepage": "https://github.com/ApolloDev/apollo-sv", "keywords": [ "biomedical science", "ecology", "epidemiology", "infection process", "obo", "ontology", "pathogen", "population genetics" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "APOLLO_SV", "bioportal": "APOLLO-SV", "fairsharing": "FAIRsharing.ngv2xx", "obofoundry": "apollo_sv", "ols": "apollo_sv", "ontobee": "APOLLO_SV" }, "name": "Apollo Structured Vocabulary", "pattern": "^\\d{8}$", "preferred_prefix": "APOLLO_SV", "providers": [ { "code": "conflated", "description": "This might be resulting from properties in Apollo SV actually trying to use appropriate identifiers", "homepage": "http://purl.obolibrary.org", "name": "OBO PURL in Parts", "uri_format": "http://purl.obolibrary.org/obo/apollo_sv/dev/apollo_sv.owl#APOLLO_SV_$1" } ], "publications": [ { "doi": "10.1186/s13326-016-0092-y", "pmc": "PMC4989460", "pubmed": "27538448", "title": "The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation", "year": 2016 }, { "pmc": "PMC3900155", "pubmed": "24551417", "title": "Apollo: giving application developers a single point of access to public health models using structured vocabularies and Web services", "year": 2013 } ], "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_$1", "version": "2024-12-24" }, "arachnoserver": { "contact": { "email": "glenn.king@imb.uq.edu.au", "name": "Glenn King", "orcid": "0000-0002-2308-2200" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information.", "example": "AS000060", "homepage": "http://www.arachnoserver.org/", "keywords": [ "drug", "life science", "protein" ], "mappings": { "biocontext": "ARACHNOSERVER", "edam": "2578", "fairsharing": "FAIRsharing.c54ywe", "integbio": "nbdc01221", "miriam": "arachnoserver", "n2t": "arachnoserver", "prefixcommons": "arachnoserver", "re3data": "r3d100012902", "uniprot": "DB-0145", "wikidata.entity": "Q4783563" }, "name": "ArachnoServer", "pattern": "^AS\\d{6}$", "preferred_prefix": "arachnoserver", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/arachnoserver:$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/btx661", "pubmed": "29069336", "title": "ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins", "year": 2018 }, { "doi": "10.1093/nar/gkq1058", "pmc": "PMC3013666", "pubmed": "21036864", "title": "ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures", "year": 2010 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/1141" ], "uri_format": "http://www.arachnoserver.org/toxincard.html?id=$1" }, "araport": { "contact": { "email": "hello@vivekkrish.com", "github": "vivekkrish", "name": "Vivek Krishnakuma", "orcid": "0000-0002-5227-0200" }, "description": "Website with general information about Arabidopsis and functionalities such as a genomic viewer", "example": "AT5G05330", "homepage": "https://www.araport.org/", "mappings": { "integbio": "nbdc02433", "miriam": "tair.name", "ncbi": "Araport", "pathguide": "768", "uniprot": "DB-0221" }, "name": "Arabidopsis Information Portal", "pattern": "^AT.G[0-9]{5}$", "preferred_prefix": "araport", "publications": [ { "doi": "10.1093/nar/gku1200", "pmc": "PMC4383980", "pubmed": "25414324", "title": "Araport: the Arabidopsis information portal", "year": 2014 } ], "uri_format": "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1" }, "archdb": { "contact": { "email": "narcis.fernandez@gmail.com", "name": "Narcis Fernandez-Fuentes", "orcid": "0000-0002-6421-1080" }, "description": "ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al.", "example": "39421", "homepage": "http://sbi.imim.es/archdb", "keywords": [ "classification", "life science", "protein" ], "mappings": { "fairsharing": "FAIRsharing.tp9z4q", "integbio": "nbdc01795", "prefixcommons": "archdb" }, "name": "ArchDB", "preferred_prefix": "archdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/archdb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkt1189", "pmc": "PMC3964960", "pubmed": "24265221", "title": "ArchDB 2014: structural classification of loops in proteins", "year": 2013 }, { "doi": "10.1093/nar/gkh002", "pmc": "PMC308737", "pubmed": "14681390", "title": "ArchDB: automated protein loop classification as a tool for structural genomics", "year": 2004 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop=$1" }, "ardb": { "deprecated": true, "description": "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. 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The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels.", "example": "A10BA02", "homepage": "http://www.whocc.no/atc_ddd_index/", "keywords": [ "approved drug", "atc code", "biomedical science", "chemical", "chemical biology", "drug", "ontology", "pharmacological family classification", "pharmacology" ], "mappings": { "aberowl": "ATC", "bartoc": "449", "biocontext": "ATC", "bioportal": "ATC", "edam": "3103", "fairsharing": "FAIRsharing.1a27h8", "hl7": "2.16.840.1.113883.6.73", "miriam": "atc", "n2t": "atc", "prefixcommons": "atc", "togoid": "Atc", "wikidata": "P267", "wikidata.entity": "Q192093" }, "name": "Anatomical Therapeutic Chemical Classification System", "pattern": "^[A-Z](\\d+([A-Z]{1,2}(\\d+)?)?)?$", "preferred_prefix": "atc", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/atc:$1" }, { "code": "bioportal.purl", "description": "BioPortal assigned additional PURLs for ATC codes", "homepage": "http://purl.bioontology.org/ontology/ATC", "name": "BioPortal", "uri_format": "http://purl.bioontology.org/ontology/ATC/$1" } ], "publications": [ { "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", "pubmed": "11214783", "title": "Different versions of the anatomical therapeutic chemical classification system and the defined daily dose--are drug utilisation data comparable?", "year": 2000 } ], "synonyms": [ "ATC_code", "ATTC" ], "uri_format": "http://www.whocc.no/atc_ddd_index/?code=$1" }, "atcc": { "description": "The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences.", "example": "11303", "example_extras": [ "ccl-1", "ccl-1.4" ], "homepage": "https://www.lgcstandards-atcc.org", "keywords": [ "epidemiology", "life science", "virology" ], "mappings": { "biocontext": "ATCC", "cellosaurus": "ATCC", "fairsharing": "FAIRsharing.j0ezpm", "hl7": "2.16.840.1.113883.6.77", "miriam": "atcc", "n2t": "atcc", "ncbi": "ATCC" }, "name": "American Type Culture Collection", "pattern": "^([a-zA-Z]+-)?\\d+(\\.\\d)?$", "preferred_prefix": "atcc", "synonyms": [ "ATCC", "ATCC number", "ATCC(dna)", "ATCC(in host)" ], "uri_format": "https://www.atcc.org/products/$1" }, "atcvet": { "description": "The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use.", "example": "QJ51RV02", "homepage": "http://www.whocc.no/atcvet/atcvet_index/", "mappings": { "biocontext": "ATCVET", "miriam": "atcvet", "n2t": "atcvet" }, "name": "Anatomical Therapeutic Chemical Vetinary", "pattern": "^Q[A-Z0-9]+$", "preferred_prefix": "atcvet", "uri_format": "http://www.whocc.no/atcvet/atcvet_index/?code=$1" }, "atfdb.family": { "description": "The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found.", "example": "CUT", "homepage": "https://guolab.wchscu.cn/AnimalTFDB4", "mappings": { "biocontext": "ATFDB.FAMILY", "miriam": "atfdb.family", "n2t": "atfdb.family" }, "name": "Animal TFDB Family", "pattern": "^\\w+$", "preferred_prefix": "atfdb.family", "uri_format": "https://guolab.wchscu.cn/AnimalTFDB4//#/family_summary/TF/$1" }, "ato": { "contact": { "email": "david.c.blackburn@gmail.com", "name": "David Blackburn", "orcid": "0000-0002-1810-9886" }, "deprecated": true, "description": "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource", "download_obo": "http://aber-owl.net/media/ontologies/ATO/2/ato.obo", "example": "0000000", "homepage": "http://www.amphibanat.org", "keywords": [ "obo", "ontology", "taxonomic classification", "taxonomy" ], "mappings": { "aberowl": "ATO", "biocontext": "ATO", "bioportal": "ATO", "fairsharing": "FAIRsharing.ayjdsm", "obofoundry": "ato", "wikidata.entity": "Q114677879" }, "name": "Amphibian taxonomy", "pattern": "^\\d{7}$", "preferred_prefix": "ATO", "rdf_uri_format": "http://purl.obolibrary.org/obo/ATO_$1", "uri_format": "http://purl.obolibrary.org/obo/ATO_$1" }, "atol": { "contact": { "email": "pylebail@rennes.inra.fr", "name": "Pierre-Yves LeBail", "orcid": "0000-0002-8310-5195" }, "description": "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production.", "download_owl": "http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=atol.owl", "example": "0002233", "homepage": "http://www.atol-ontology.com", "keywords": [ "agriculture", "animal husbandry", "life science", "livestock", "ontology", "phenotype" ], "mappings": { "aberowl": "ATOL", "agroportal": "ATOL", "bioportal": "ATOL", "fairsharing": "FAIRsharing.wsfk5z", "ols": "atol" }, "name": "Animal Trait Ontology for Livestock", "pattern": "^\\d{7}$", "preferred_prefix": "atol", "uri_format": "http://opendata.inra.fr/ATOL/ATOL_$1", "version": "2018-09-13" }, "atomistic": { "description": "An EMMO-based domain ontology for atomistic and electronic modelling.", "example": "08fd7117-66ac-5b6d-b65e-34a826675877", "homepage": "https://github.com/emmo-repo/domain-atomistic", "keywords": [ "engineering", "nfdi4ing" ], "license": "CC-BY-4.0", "mappings": { "tib": "atomistic" }, "name": "Atomistic", "preferred_prefix": "atomistic", "repository": "https://github.com/emmo-repo/domain-atomistic", "uri_format": "https://w3id.org/emmo/domain/atomistic#$1" }, "autdb": { "deprecated": true, "description": "AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder.", "example": "ADA", "homepage": "http://autism.mindspec.org/autdb/", "mappings": { "biocontext": "AUTDB", "miriam": "autdb", "n2t": "autdb" }, "name": "AutDB", "pattern": "^[A-Z]+[A-Z-0-9]{2,}$", "preferred_prefix": "autdb", "uri_format": "http://autism.mindspec.org/GeneDetail/$1" }, "authenticus": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ID of a researcher in Authenticus website", "example": "P-008-GD6", "homepage": "https://www.authenticus.pt", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P7834" }, "name": "Authenticus ID", "pattern": "^[A-Z]-[0-9A-Z]{3}-[0-9A-Z]{3}$", "preferred_prefix": "authenticus", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://www.authenticus.pt/$1" }, "authorea.author": { "description": "identifier for an author on the Authorea writing service", "example": "229233", "homepage": "https://www.authorea.com", "mappings": { "wikidata": "P5039" }, "name": "Authorea author ID", "pattern": "^[1-9]\\d*$", "preferred_prefix": "authorea.author", "uri_format": "https://www.authorea.com/users/$1" }, "babelon": { "contact": { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, "contributor": { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, "description": "Babelon is a simple standard for managing ontology translations and language profiles. Profiles are managed as TSV files, see for example https://github.com/obophenotype/hpo-translations/tree/main/babelon. The goal of Babelon as a data model and vocabulary is to capture the minimum data required to capture important metadata such as confidence and precision of translation.", "example": "translation_language", "github_request_issue": 903, "homepage": "https://monarch-initiative.github.io/babelon/", "license": "MIT", "name": "Babelon", "pattern": "^[a-z][a-z0-9_]+[a-z0-9]$", "preferred_prefix": "babelon", "repository": "https://github.com/monarch-initiative/babelon", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://w3id.org/babelon/$1" }, "bacdive": { "contact": { "email": "lorenz.reimer@dsmz.de", "name": "Lorenz Reimer", "orcid": "0000-0002-7805-0660" }, "description": "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity.", "example": "131392", "homepage": "https://bacdive.dsmz.de/", "keywords": [ "biodiversity", "life science", "microbiology" ], "mappings": { "fairsharing": "FAIRsharing.aSszvY", "miriam": "bacdive", "n2t": "bacdive", "re3data": "r3d100013060", "wikidata": "P2946" }, "name": "BacDive", "pattern": "^[0-9]+$", "preferred_prefix": "bacdive", "publications": [ { "doi": "10.1093/nar/gky879", "pmc": "PMC6323973", "pubmed": "30256983", "title": "BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis", "year": 2019 }, { "doi": "10.1016/j.jbiotec.2017.05.004", "pubmed": "28487186", "title": "Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase", "year": 2017 }, { "doi": "10.1093/nar/gkv983", "pmc": "PMC4702946", "pubmed": "26424852", "title": "BacDive--The Bacterial Diversity Metadatabase in 2016", "year": 2015 }, { "doi": "10.1093/nar/gkt1058", "pmc": "PMC3965005", "pubmed": "24214959", "title": "BacDive--the Bacterial Diversity Metadatabase", "year": 2013 } ], "uri_format": "https://bacdive.dsmz.de/strain/$1" }, "bacmap.biog": { "description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information.", "example": "1050", "homepage": "http://bacmap.wishartlab.com/", "mappings": { "biocontext": "BACMAP.BIOG", "miriam": "bacmap.biog", "n2t": "bacmap.biog" }, "name": "BacMap Biography", "pattern": "^\\d+$", "preferred_prefix": "bacmap.biog", "uri_format": "http://bacmap.wishartlab.com/organisms/$1" }, "bacmap.map": { "description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information.", "example": "AP011135", "homepage": "http://bacmap.wishartlab.com/", "mappings": { "biocontext": "BACMAP.MAP", "miriam": "bacmap.map", "n2t": "bacmap.map" }, "name": "BacMap Map", "pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$", "preferred_prefix": "bacmap.map", "uri_format": "http://bacmap.wishartlab.com/maps/$1/index.html" }, "bactibase": { "contact": { "email": "ismail.fliss@fsaa.ulaval.ca", "name": "Ismail Fliss", "orcid": "0000-0002-8467-9414" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria.", "example": "BAC045", "homepage": "http://bactibase.hammamilab.org", "keywords": [ "life science", "protein" ], "mappings": { "fairsharing": "FAIRsharing.5f5mfm", "prefixcommons": "bactibase", "re3data": "r3d100012755" }, "name": "Bactibase", "preferred_prefix": "bactibase", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/bactibase:$1" } ], "publications": [ { "doi": "10.1186/1471-2180-10-22", "pmc": "PMC2824694", "pubmed": "20105292", "title": "BACTIBASE second release: a database and tool platform for bacteriocin characterization", "year": 2010 }, { "doi": "10.1186/1471-2180-7-89", "pmc": "PMC2211298", "pubmed": "17941971", "title": "BACTIBASE: a new web-accessible database for bacteriocin characterization", "year": 2007 } ], "uri_format": "http://bactibase.hammamilab.org/$1" }, "bams": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions.", "homepage": "https://bams1.org", "name": "Brain Architecture Knowledge Management System Neuroanatomical Ontology", "preferred_prefix": "bams", "references": [ "https://www.frontiersin.org/articles/10.3389/neuro.11.002.2008/full" ] }, "bao": { "contact": { "email": "bao@miamiedu.onmicrosoft.com", "name": "Caty Chung" }, "description": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.", "download_owl": "http://www.bioassayontology.org/bao/bao_complete.owl", "example": "0002989", "homepage": "http://bioassayontology.org", "keywords": [ "assay", "biochemistry", "biological_process", "biomedical science", "cell", "chemical and environmental engineering", "chemical entity", "dataplant", "life science", "life sciences, biology", "molecular entity", "nfdi4cat", "ontology", "protein", "reagent", "target" ], "mappings": { "aberowl": "BAO", "biocontext": "BAO", "bioportal": "BAO", "fairsharing": "FAIRsharing.mye76w", "miriam": "bao", "n2t": "bao", "ols": "bao", "ontobee": "BAO", "tib": "bao" }, "name": "BioAssay Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "bao", "publications": [ { "doi": "10.1186/2041-1480-5-s1-s5", "pmc": "PMC4108877", "pubmed": "25093074", "title": "Evolving BioAssay Ontology (BAO): modularization, integration and applications", "year": 2014 }, { "doi": "10.1371/journal.pone.0049198", "pmc": "PMC3498356", "pubmed": "23155465", "title": "Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO)", "year": 2012 }, { "doi": "10.1186/1471-2105-12-257", "pmc": "PMC3149580", "pubmed": "21702939", "title": "BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results", "year": 2011 }, { "doi": "10:1371/journal.pone.0049198", "pubmed": "10", "title": "Digitoxin metabolism by rat liver microsomes", "year": 1975 } ], "repository": "https://github.com/BioAssayOntology/BAO", "synonyms": [ "BAO" ], "uri_format": "http://www.bioassayontology.org/bao#BAO_$1", "version": "2.8.18a" }, "bartoc": { "contact": { "email": "voss@gbv.de", "github": "nichtich", "name": "Jakob Voß", "orcid": "0000-0002-7613-4123" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "voss@gbv.de", "github": "nichtich", "name": "Jakob Voß", "orcid": "0000-0002-7613-4123" } ], "description": "The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries.\nThe main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO).", "example": "241", "homepage": "https://bartoc.org", "keywords": [ "knowledge and information systems", "ontology and terminology" ], "license": "PDDL 1.0", "mappings": { "bartoc": "2054", "fairsharing": "FAIRsharing.f1777e", "wikidata": "P2689" }, "name": "Basic Register of Thesauri, Ontologies & Classifications", "owners": [ { "name": "Verbundzentrale des GBV", "partnered": false, "ror": "048vdhs48" } ], "pattern": "^[1-9][0-9]*$", "preferred_prefix": "bartoc", "rdf_uri_format": "http://bartoc.org/en/node/$1", "references": [ "https://github.com/biopragmatics/bioregistry/issues/783" ], "repository": "https://github.com/gbv/bartoc.org", "uri_format": "https://bartoc.org/en/node/$1" }, "battinfo": { "description": "A battery interface domain ontology based on EMMO.", "example": "74ed2670_657d_4f0b_b0a6_3f13bc2e9c17", "homepage": "https://big-map.github.io/BattINFO/index.html", "keywords": [ "electrical engineering", "engineering", "nfdi4ing" ], "mappings": { "tib": "battinfo" }, "name": "Battery Interface Ontology", "preferred_prefix": "battinfo", "repository": "https://github.com/BIG-MAP/BattINFO", "uri_format": "https://w3id.org/emmo/domain/battery#battery_$1" }, "bbkg": { "deprecated": true, "description": "Blue Brain Project's published data as knowledge graphs and Web Studios.", "example": "topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a", "homepage": "https://portal.bluebrain.epfl.ch", "mappings": { "miriam": "bbkg" }, "name": "Blue Brain Project Knowledge Graph", "pattern": "^[-\\w]+(?:\\/[-\\w]+)(?:\\/\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b)$", "preferred_prefix": "bbkg", "uri_format": "https://bbp.epfl.ch/nexus/web/studios/public/$1" }, "bbtp": { "deprecated": true, "description": "Input data and analysis results for the paper \"Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 ).", "example": "f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a", "homepage": "https://portal.bluebrain.epfl.ch", "mappings": { "miriam": "bbtp" }, "name": "Blue Brain Project Topological sampling Knowledge Graph", "pattern": "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$", "preferred_prefix": "bbtp", "uri_format": "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1" }, "bcbc": { "description": "One of the many goals of the BCBC was to develop and maintain databases of useful research resources. A total of 813 different scientific resources were generated and submitted by BCBC investigators over the 14 years it existed. Information pertaining to 495 selected resources, judged to be the most scientifically-useful, has been converted into a static catalog, as shown below. In addition, the metadata for these 495 resources have been transferred to dkNET in the form of RDF descriptors, and all genomics data have been deposited to either ArrayExpress or GEO. 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This collection references individual models.", "example": "iECABU_c1320", "homepage": "http://bigg.ucsd.edu/models", "keywords": [ "metabolic model", "pathway" ], "license": "http://bigg.ucsd.edu/license#license", "logo": "https://lh3.googleusercontent.com/proxy/vQjhtm8lVovH27pBaBSbAx_50uQbOvjubQM4s-R3-6JLiEzlozInmDfqGpp7OwbbkwxbTwfqie4g1GSGOG-vryt20uzT", "mappings": { "biocontext": "BIGG.MODEL", "miriam": "bigg.model", "n2t": "bigg.model" }, "name": "BiGG Model", "pattern": "^[a-z_A-Z0-9]+$", "preferred_prefix": "bigg.model", "uri_format": "http://bigg.ucsd.edu/models/$1" }, "bigg.reaction": { "contact": { "email": "zaking@ucsd.edu", "github": "zakandrewking", "name": "Zachary King", "orcid": "0000-0003-1238-1499" }, "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. 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"contact": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Manually curated collections of resources stored in the bioregistry", "example": "0000001", "homepage": "https://bioregistry.io/collection", "keywords": [ "registry" ], "name": "Bioregistry Collections", "pattern": "^\\d{7}$", "preferred_prefix": "bioregistry.collection", "uri_format": "https://bioregistry.io/collection/$1" }, "bioregistry.registry": { "contact": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Bioregistry's meta-registry", "example": "miriam", "homepage": "https://bioregistry.io/metaregistry/", "keywords": [ "data integration", "data science", "metaregistry", "registry" ], "name": "Bioregistry Metaregistry", "preferred_prefix": "bioregistry.registry", "uri_format": "https://bioregistry.io/metaregistry/$1" }, "bioregistry.schema": { "contact": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Schema for the export of the Bioregistry as RDF", "example": "0000001", "homepage": "https://bioregistry.io/schema", "keywords": [ "registry" ], "name": "Bioregistry Schema", "pattern": "^\\d{7}$", "preferred_prefix": "bioregistry.schema", "uri_format": "https://bioregistry.io/schema/#$1" }, "biorxiv": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The bioRxiv is a preprint server for biology", "example": "2022.07.08.499378", "example_extras": [ "000091", "000091v1", "2022.07.08.499378v2" ], "homepage": "https://biorxiv.org", "keywords": [ "preprints", "publishing" ], "mappings": { "go": "bioRxiv", "wikidata": "P3951" }, "name": "bioRxiv", "pattern": "^(\\d{4}\\.\\d{2}\\.\\d{2}\\.)?\\d{6,8}(v\\d{1,3})?$", "preferred_prefix": "biorxiv", "providers": [ { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/biorxiv/$1" } ], "rdf_uri_format": "http://dx.doi.org/10.1101/$1", "uri_format": "https://www.biorxiv.org/content/10.1101/$1" }, "biosample": { "contact": { "email": "mizrachi@ncbi.nlm.nih.gov", "name": "Ilene Karsch-Mizrachi", "orcid": "0000-0002-0289-7101" }, "description": "The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation.", "example": "SAMEA2397676", "homepage": "https://www.ebi.ac.uk/biosamples/", "keywords": [ "biology", "biomaterial", "cell", "cell line", "dna", "gold standard", "rna", "stem cell" ], "mappings": { "biocontext": "BIOSAMPLE", "cellosaurus": "BioSamples", "fairsharing": "FAIRsharing.qr6pqk", "miriam": "biosample", "n2t": "biosample", "re3data": "r3d100012828", "rrid": "SAMN", "togoid": "Biosample" }, "name": "BioSample", "pattern": "^SAM[NED](\\w)?\\d+$", "preferred_prefix": "biosample", "providers": [ { "code": "ddbj", "description": "BioSample at DNA Data Bank of Japan", "homepage": "https://www.ddbj.nig.ac.jp/biosample", "name": "BioSample at DNA Data Bank of Japan", "uri_format": "https://ddbj.nig.ac.jp/search/entry/biosample/$1" }, { "code": "ncbi", "description": "BioSample at NCBI", "homepage": "http://www.ncbi.nlm.nih.gov/biosample", "name": "BioSample at NCBI", "uri_format": "http://www.ncbi.nlm.nih.gov/biosample?term=$1" } ], "publications": [ { "doi": "10.1093/nar/gkr1163", "pmc": "PMC3245069", "pubmed": "22139929", "title": "BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata", "year": 2011 } ], "synonyms": [ "biosamples" ], "uri_format": "https://www.ebi.ac.uk/biosamples/sample/$1" }, "bioschemas": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. It does this by encouraging people in the life sciences to use Schema.org markup in their websites so that they are indexable by search engines and other services. Bioschemas encourages the consistent use of markup to ease the consumption of the contained markup across many sites. This structured information then makes it easier to discover, collate, and analyse distributed resources. [from BioSchemas.org]", "download_rdf": "https://bioschemas.org/types/bioschemas_types.ttl", "example": "Dataset", "homepage": "https://bioschemas.org", "mappings": { "biolink": "bioschemas" }, "name": "BioSchemas", "preferred_prefix": "bioschemas", "providers": [ { "code": "biothings", "uri_format": "https://discovery.biothings.io/view/bioschemastypes/$1" }, { "code": "draft", "description": "BioSchemas makes a difference between its draft and released terms by putting them in different namespaces. This causes problems when consuming it, so this URI format maps them all into a unified semantic space", "homepage": "https://bioschemas.org", "name": "BioSchemas Draft", "uri_format": "https://bioschemas.org/draft_terms/$1" }, { "code": "term", "uri_format": "https://bioschemas.org/terms/$1" }, { "code": "w3id", "uri_format": "https://w3id.org/bioschemas/terms/$1" } ], "repository": "https://github.com/BioSchemas/specifications", "synonyms": [ "bioschema", "bioschemas_draft" ], "twitter": "bioschemas", "uri_format": "https://bioschemas.org/profiles/$1" }, "biosimulations": { "description": "BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools.", "example": "Yeast-cell-cycle-Irons-J-Theor-Biol-2009", "homepage": "https://icahn.mssm.edu/", "mappings": { "miriam": "biosimulations", "re3data": "r3d100013361" }, "name": "biosimulations", "pattern": "^[a-zA-Z0-9_-]{3,}$", "preferred_prefix": "biosimulations", "uri_format": "https://biosimulations.org/projects/$1" }, "biosimulators": { "contact": { "email": "karr@mssm.edu", "name": "Jonathan Karr", "orcid": "0000-0002-2605-5080" }, "description": "BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML).", "example": "vcell", "homepage": "https://biosimulators.org/", "keywords": [ "computational biology", "systems biology" ], "mappings": { "fairsharing": "FAIRsharing.pwEima", "miriam": "biosimulators", "re3data": "r3d100013432" }, "name": "BioSimulators", "pattern": "^[a-zA-Z0-9-_]+$", "preferred_prefix": "biosimulators", "repository": "https://github.com/biosimulators/Biosimulators/issues/new/choose", "uri_format": "https://biosimulators.org/simulators/$1" }, "biostudies": { "contact": { "email": "ugis@ebi.ac.uk", "name": "Ugis Sarkans", "orcid": "0000-0001-9227-8488" }, "description": "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.", "example": "S-EPMC6266652", "homepage": "https://www.ebi.ac.uk/biostudies/", "keywords": [ "biomedical science", "life science" ], "mappings": { "fairsharing": "FAIRsharing.mtjvme", "integbio": "nbdc02279", "miriam": "biostudies", "n2t": "biostudies", "re3data": "r3d100012627" }, "name": "BioStudies database", "pattern": "^S-[A-Z]{4}[\\-\\_A-Z\\d]+$", "preferred_prefix": "biostudies", "publications": [ { "doi": "10.1093/nar/gkx965", "pmc": "PMC5753238", "pubmed": "29069414", "title": "The BioStudies database-one stop shop for all data supporting a life sciences study", "year": 2018 }, { "doi": "10.15252/msb.20156658", "pmc": "PMC4704487", "pubmed": "26700850", "title": "The BioStudies database", "year": 2015 } ], "uri_format": "https://www.ebi.ac.uk/biostudies/studies/$1" }, "biosystems": { "contact": { "email": "lewis.geer@nih.gov", "name": "Aron Marchler-Bauer", "orcid": "0000-0003-1516-0712" }, "contributor_extras": [ { "email": "egon.willighagen@gmail.com", "github": "egonw", "name": "Egon Willighagen", "orcid": "0000-0001-7542-0286" } ], "deprecated": true, "description": "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources.", "example": "001", "homepage": "https://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html", "keywords": [ "biology", "molecules", "pathways", "systems biology" ], "mappings": { "biocontext": "BIOSYSTEMS", "fairsharing": "FAIRsharing.w2eeqr", "integbio": "nbdc00379", "miriam": "biosystems", "n2t": "biosystems", "prefixcommons": "biosystems", "re3data": "r3d100011033" }, "name": "BioSystems", "pattern": "^\\d+$", "preferred_prefix": "biosystems", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/biosystems:$1" } ], "publications": [ { "doi": "10.1093/nar/gkp858", "pmc": "PMC2808896", "pubmed": "19854944", "title": "The NCBI BioSystems database", "year": 2009 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/biosystems/$1" }, "biotools": { "contact": { "email": "haiiu@dtu.dk", "github": "hansioan", "name": "Hans Ienasescu", "orcid": "0000-0001-9727-2544" }, "description": "BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research.", "example": "bioregistry", "homepage": "https://bio.tools/", "keywords": [ "bioinformatics", "biology", "biomedical science" ], "mappings": { "biocontext": "BIOTOOLS", "fairsharing": "FAIRsharing.63520c", "miriam": "biotools", "n2t": "biotools", "re3data": "r3d100013668" }, "name": "BioTools", "pattern": "^[-A-Za-z0-9\\_]*$", "preferred_prefix": "biotools", "publications": [ { "doi": "10.1093/nar/gkv1116", "pmc": "PMC4702812", "pubmed": "26538599", "title": "Tools and data services registry: a community effort to document bioinformatics resources", "year": 2015 } ], "repository": "http://github.com/bio-tools/biotoolsregistry/", "uri_format": "https://bio.tools/$1" }, "biotop": { "contact": { "email": "stefan.schulz@medunigraz.at", "github": "steschu63", "name": "Stefan Schulz", "orcid": "0000-0001-7222-3287" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network", "download_owl": "https://raw.githubusercontent.com/BioTopOntology/biotop/master/biotop.owl", "example": "attachedTo", "github_request_issue": 1312, "homepage": "http://purl.org/biotop", "keywords": [ "biology", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "BIOTOP", "bioportal": "BIOTOP", "lov": "biotop" }, "name": "BioTop", "preferred_prefix": "biotop", "publications": [ { "doi": "10.1093/bioinformatics/btp194", "pmc": "PMC2687948", "pubmed": "19478019", "title": "Alignment of the UMLS semantic network with BioTop: methodology and assessment", "year": 2009 }, { "doi": "10.1093/bioinformatics/btn158", "pmc": "PMC2718636", "pubmed": "18586729", "title": "The ontology of biological taxa", "year": 2008 } ], "repository": "https://github.com/BioTopOntology/biotop", "uri_format": "http://purl.org/biotop/biotop.owl#$1" }, "biozil": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Redistributor of bilogics and biomedical supplies", "example": "ls-c35719-120", "homepage": "https://www.biozol.de/en", "keywords": [ "biologics", "life sciences", "vendor" ], "name": "BIOZIL", "preferred_prefix": "biozil", "uri_format": "https://www.biozol.de/en/product/$1" }, "birnlex": { "comment": "Part of the NeuroLex namespace now", "contact": { "email": "wbug@ncmir.ucsd.edu", "name": "William Bug" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design.", "download_owl": "http://aber-owl.net/media/ontologies/BIRNLEX/1/birnlex.owl", "example": "2023", "homepage": "https://bioportal.bioontology.org/ontologies/BIRNLEX", "keywords": [ "anatomy", "biomedical science", "disease", "ontology", "study design" ], "mappings": { "aberowl": "BIRNLEX", "bioportal": "BIRNLEX", "fairsharing": "FAIRsharing.jedbbt" }, "name": "Biomedical Informatics Research Network Lexicon", "pattern": "^\\d+$", "preferred_prefix": "birnlex", "providers": [ { "code": "bioportal.purl", "description": "Pseudo-BioPortal PURL assigned to BirnLex", "homepage": "http://bioontology.org/projects/ontologies/birnlex", "name": "BioPortal", "uri_format": "http://bioontology.org/projects/ontologies/birnlex#$1" } ], "uri_format": "http://uri.neuinfo.org/nif/nifstd/birnlex_$1" }, "biro": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively.", "example": "BibliographicRecord", "homepage": "http://www.sparontologies.net/ontologies/biro", "keywords": [ "spar", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.99da5f", "lov": "biro" }, "name": "Bibliographic Reference Ontology", "preferred_prefix": "BiRO", "repository": "https://github.com/sparontologies/biro", "twitter": "sparontologies", "uri_format": "http://purl.org/spar/biro/$1" }, "bitbucket": { "description": "Bitbucket is a Git-based source code repository hosting service owned by Atlassian.", "example": "andreadega/systems-biology-compiler", "homepage": "https://www.atlassian.com/", "keywords": [ "knowledge and information systems", "software engineering", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.fc3431", "miriam": "bitbucket", "re3data": "r3d100013478" }, "name": "Bitbucket", "pattern": "^[0-9A-Za-z-_\\.]+/[0-9A-Za-z-_\\.]+$", "preferred_prefix": "bitbucket", "uri_format": "https://bitbucket.org/$1" }, "bitterdb.cpd": { "description": "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds.", "example": "46", "homepage": "http://bitterdb.agri.huji.ac.il/dbbitter.php", "mappings": { "biocontext": "BITTERDB.CPD", "miriam": "bitterdb.cpd", "n2t": "bitterdb.cpd" }, "name": "BitterDB Compound", "pattern": "^\\d+$", "preferred_prefix": "bitterdb.cpd", "uri_format": "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1" }, "bitterdb.rec": { "description": "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors.", "example": "1", "homepage": "http://bitterdb.agri.huji.ac.il/dbbitter.php", "mappings": { "biocontext": "BITTERDB.REC", "miriam": "bitterdb.rec", "n2t": "bitterdb.rec" }, "name": "BitterDB Receptor", "pattern": "^\\d+$", "preferred_prefix": "bitterdb.rec", "uri_format": "http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1" }, "bko": { "comment": "This resource also uses SBO terms and resolves them, e.g., http://www.sbgnbricks.org/BKO/full/entry/all/SBO:0000177/.", "contact": { "email": "adrienrougny@gmail.com", "github": "adrienrougny", "name": "Adrien Rougny", "orcid": "0000-0002-2118-035X" }, "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way.", "download_owl": "http://aber-owl.net/media/ontologies/BKO/1/bko.owl", "example": "0000204", "github_request_issue": 283, "homepage": "http://www.sbgnbricks.org/", "keywords": [ "ontology" ], "mappings": { "aberowl": "BKO", "bioportal": "BKO" }, "name": "SBGN Bricks data and ontology", "pattern": "^\\d+$", "preferred_prefix": "bko", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1" }, "blastrule": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "BlastRules (identifiers starting with the “NBR” prefix) are a type of evidence for functional classification of proteins based on BLAST (Basic Local Alignment Search Tool). A BlastRule consists of one or more 'model' proteins with known biological function, and BLAST identity and coverage cutoffs. Any protein aligning to a model protein above the cutoffs is considered a BlastRule hit. [from homepage]", "example": "NBR016799", "github_request_issue": 1522, "homepage": "https://www.ncbi.nlm.nih.gov/genome/annotation_prok/evidence/", "name": "BlastRule", "pattern": "^NBR\\d+$", "preferred_prefix": "blastrule", "references": [ "https://ftp.ncbi.nlm.nih.gov/pub/blastrules/" ], "uri_format": "https://www.ncbi.nlm.nih.gov/genome/annotation_prok/evidence/$1" }, "bmbf.glossary": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A german-language glossary provides you with definitions of the terms used in the portal in the fields of education, science, research and innovation and is updated regularly.", "example": "G1", "homepage": "https://www.datenportal.bmbf.de/portal/de/glossary.html", "name": "German Federal Ministry of Education and Research Glossary", "preferred_prefix": "bmbf.glossary", "uri_format": "https://www.datenportal.bmbf.de/portal/de/$1.html" }, "bmont": { "contact": { "email": "alpha.tom.kodamullil@scai.fraunhofer.de", "github": "akodamullil", "name": "Alpha Tom Kodamullil", "orcid": "0000-0001-9896-3531" }, "description": "An application ontology that represents comprehensive knowledge involving a variety of fields of medical and biological aspects.", "download_owl": "http://purl.obolibrary.org/obo/bmont/releases/2025-06-20/bmont.owl", "example": "0000006", "homepage": "https://github.com/SCAI-BIO/BiomarkerOntology", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "BMONT", "bioportal": "BMONT", "obofoundry": "bmont", "ols": "bmont", "ontobee": "BMONT" }, "name": "Biomarker Ontology", "preferred_prefix": "BMONT", "rdf_uri_format": "http://purl.obolibrary.org/obo/BMONT_$1", "repository": "https://github.com/SCAI-BIO/BiomarkerOntology", "uri_format": "http://purl.obolibrary.org/obo/BMONT_$1" }, "bmrb.entry": { "contact": { "email": "markley@nmrfam.wisc.edu", "name": "John L. 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The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy.", "example": "15000", "homepage": "https://bmrb.io/", "keywords": [ "structural biology" ], "mappings": { "fairsharing": "FAIRsharing.p06nme", "integbio": "nbdc00380", "miriam": "bmrb", "re3data": "r3d100010191", "uniprot": "DB-0256" }, "name": "Biological Magnetic Resonance Data Bank", "pattern": "^(bmr|bmse|bmst)?[0-9]{1,6}$", "preferred_prefix": "bmrb.entry", "publications": [ { "doi": "10.1093/nar/gkac1050", "pubmed": "36478084" }, { "doi": "10.1007/s10858-008-9221-y", "pmc": "PMC2268728", "pubmed": "18288446", "title": "BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions", "year": 2008 }, { "doi": "10.1093/nar/gkm957", "pmc": "PMC2238925", "pubmed": "17984079", "title": "BioMagResBank", "year": 2007 } ], "synonyms": [ "bmrb" ], "uri_format": "https://bmrb.io/data_library/summary/index.php?bmrbId=$1" }, "bmrb.restraint": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. 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As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae.", "example": "S7000002168151102", "homepage": "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/", "mappings": { "biocontext": "BROAD", "miriam": "broad", "n2t": "broad" }, "name": "Broad Fungal Genome Initiative", "pattern": "^S\\d+$", "preferred_prefix": "broad", "uri_format": "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1" }, "bs": { "comment": "An alernative vocabulary that has been aligned and integrated in Sequence Ontology (SO).", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. 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It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments.", "example": "288", "homepage": "http://bugs.sgul.ac.uk/E-BUGS", "mappings": { "biocontext": "BUGBASE.EXPT", "miriam": "bugbase.expt", "n2t": "bugbase.expt" }, "name": "BugBase Expt", "pattern": "^\\d+$", "preferred_prefix": "bugbase.expt", "uri_format": "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?action=view&expt_id=$1" }, "bugbase.protocol": { "deprecated": true, "description": "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. 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The taxonomy of building components is based on the proposed by the IFC 4.1 standard.", "download_owl": "http://aber-owl.net/media/ontologies/building/1/building.owl", "example": "AirConditioningUnit", "homepage": "https://bimerr.iot.linkeddata.es/def/building/", "keywords": [ "architecture", "civil engineering", "digital planning and construction", "fid baudigital", "nfdi4ing", "ontology" ], "mappings": { "aberowl": "building", "tib": "building" }, "name": "Building Ontology", "preferred_prefix": "building", "uri_format": "http://bimerr.iot.linkeddata.es/def/building#$1" }, "bykdb": { "contact": { "email": "cozzone@ibcp.fr", "name": "Alain J. Cozzone" }, "description": "The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information.", "example": "A0A009HB13", "homepage": "https://bykdb.lyon.inserm.fr/BYKdb/BYKdbIndex", "keywords": [ "domain", "life science", "microbial", "sequence" ], "mappings": { "biocontext": "BYKDB", "fairsharing": "FAIRsharing.jr30xc", "miriam": "bykdb", "n2t": "bykdb", "prefixcommons": "bykdb" }, "name": "Bacterial Tyrosine Kinase Database", "pattern": "^[A-Z0-9]+$", "preferred_prefix": "bykdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/bykdb:$1" } ], "provides": "uniprot", "publications": [ { "doi": "10.1016/s0378-1119(97)00554-4", "pubmed": "9434192", "title": "Characterization of a bacterial gene encoding an autophosphorylating protein tyrosine kinase", "year": 1997 }, { "doi": "10.1093/nar/gkr915", "pmc": "PMC3245071", "pubmed": "22080550", "title": "BYKdb: the Bacterial protein tYrosine Kinase database", "year": 2011 }, { "doi": "10.1007/s00726-009-0237-8", "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", "pubmed": "18772155", "title": "Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature", "year": 2008 } ], "uri_format": "https://bykdb.lyon.inserm.fr/data/html/annotated/$1.html" }, "c4o": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date.", "example": "InTextReferencePointer", "homepage": "http://www.sparontologies.net/ontologies/c4o", "keywords": [ "spar", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.beb855", "lov": "c4o" }, "name": "Citation Counting and Context Characterisation Ontology", "preferred_prefix": "C4O", "repository": "https://github.com/sparontologies/c4o", "twitter": "sparontologies", "uri_format": "http://purl.org/spar/c4o/$1" }, "cabi": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Research and learning in agriculture, the environment and the applied life sciences", "example": "20000614040", "github_request_issue": 1313, "homepage": "https://www.cabidigitallibrary.org", "name": "CABI Digital Library", "pattern": "^\\d+$", "preferred_prefix": "cabi", "uri_format": "https://www.cabi.org/cabebooks/ebook/$1" }, "cabri": { "contact": { "email": "paolo.romano@hsanmartino.it", "name": "Paolo Romano", "orcid": "0000-0003-4694-3883" }, "description": "CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it.", "example": "dsmz_mutz-id:ACC 291", "homepage": "http://www.cabri.org/", "keywords": [ "applied microbiology", "medical microbiology", "microbiology", "molecular biology", "molecular microbiology", "virology" ], "mappings": { "biocontext": "CABRI", "edam": "2380", "fairsharing": "FAIRsharing.qx2rvz", "miriam": "cabri", "n2t": "cabri", "ncbi": "CABRI" }, "name": "Common Access to Biological Resources and Information Project", "pattern": "^([A-Za-z]+)?(\\_)?([A-Za-z-]+)\\:([A-Za-z0-9 ]+)$", "preferred_prefix": "cabri", "providers": [ { "code": "", "description": "CABRI Cell Lines catalogue in Brussels (SRS)", "homepage": "http://www.be.cabri.org/", "name": "CABRI Cell Lines catalogue in Brussels (SRS)", "uri_format": "http://www.be.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]" } ], "publications": [ { "doi": "10.1002/cfg.376", "pmc": "PMC2447341", "pubmed": "18629057", "title": "Interoperability of CABRI Services and Biochemical Pathways Databases", "year": 2004 }, { "doi": "10.2165/00822942-200594030-00002", "pubmed": "16231959", "title": "The role of informatics in the coordinated management of biological resources collections", "year": 2005 } ], "uri_format": "http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]" }, "cadsr": { "description": "The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR.", "example": "3771992", "homepage": "https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki", "mappings": { "miriam": "cadsr", "n2t": "cadsr" }, "name": "Cancer Data Standards Registry and Repository", "pattern": "^[0-9]*$", "preferred_prefix": "cadsr", "uri_format": "https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1]" }, "caloha": { "contact": { "email": "Paula.Duek@sib.swiss", "github": "paulacalipho", "name": "Paula Duek Roggli", "orcid": "0000-0002-0819-0473" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins.", "download_obo": "https://raw.githubusercontent.com/calipho-sib/controlled-vocabulary/master/caloha.obo", "example": "TS-0001", "homepage": "https://github.com/calipho-sib/controlled-vocabulary", "keywords": [ "anatomy", "human", "ontology", "physiology" ], "license": "CC-BY-4.0", "name": "CALIPHO Group Ontology of Human Anatomy", "pattern": "^TS-\\d+$", "preferred_prefix": "caloha", "providers": [ { "code": "biopragmatics", "description": "A static site generated from the CALOHA OBO flat file", "homepage": "https://biopragmatics.github.io/providers", "name": "Biopragmatics Browser", "uri_format": "https://biopragmatics.github.io/providers/caloha/$1" } ], "references": [ "https://twitter.com/neXtProt_news/status/1350105997633867781", "https://github.com/biopragmatics/bioregistry/issues/721" ], "repository": "https://github.com/calipho-sib/controlled-vocabulary", "twitter": "neXtProt_news", "uri_format": "https://www.nextprot.org/term/$1" }, "cameo": { "contact": { "email": "torsten.schwede@unibas.ch", "name": "Torsten Schwede", "orcid": "0000-0003-2715-335X" }, "description": "The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB.", "example": "2019-08-03_00000089_1", "homepage": "https://cameo3d.org", "keywords": [ "life science" ], "mappings": { "biocontext": "CAMEO", "fairsharing": "FAIRsharing.dq34p2", "miriam": "cameo", "n2t": "cameo" }, "name": "Continuous Automated Model Evaluation", "pattern": "^[0-9\\-_]+$", "preferred_prefix": "cameo", "publications": [ { "doi": "10.1093/database/bat031", "pmc": "PMC3889916", "pubmed": "23624946", "title": "The Protein Model Portal--a comprehensive resource for protein structure and model information", "year": 2013 } ], "uri_format": "https://www.cameo3d.org/sp/targets/target/$1" }, "cao": { "contact": { "email": "williams.antony@epa.gov", "name": "Antony Williams", "orcid": "0000-0002-2668-4821" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology developed as part of the Chemical Analysis Metadata Project (ChAMP) as a resource to semantically annotate standards developed using the ChAMP platform. (source: CAO ontology)", "download_owl": "https://champ.stuchalk.domains.unf.edu/images/ontology/cao.owl", "example": "000064", "homepage": "https://champ.stuchalk.domains.unf.edu", "keywords": [ "annotation", "characterisation data heat", "chemistry", "gene", "genetics", "life science", "nfdi4cat", "ontology", "orthologous", "phylogenetics", "polypeptide region", "protein", "transcript", "transport and kinetic data" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "CAO", "bartoc": "20701", "bioportal": "CAO", "fairsharing": "FAIRsharing.wp0134", "ols": "cao", "tib": "cao" }, "name": "Chemical Analysis Ontology", "pattern": "^\\d+$", "preferred_prefix": "cao", "publications": [ { "doi": "10.1126/science.278.5338.631", "pubmed": "9381173", "title": "A genomic perspective on protein families", "year": 1997 } ], "repository": "https://github.com/stuchalk/chemical-analysis-ontology", "uri_format": "http://champ-project.org/images/ontology/cao.owl#CAO_$1", "version": "0.2" }, "caps": { "description": "CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps.", "example": "434", "homepage": "http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home", "mappings": { "biocontext": "CAPS", "miriam": "caps", "n2t": "caps" }, "name": "CAPS-DB", "pattern": "^\\d+$", "preferred_prefix": "caps", "uri_format": "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1" }, "carnegie.stage": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "One of the 23 stages of embryo development", "example": "20", "github_request_issue": 1325, "homepage": "https://embryology.med.unsw.edu.au/embryology/index.php/Carnegie_Stages", "name": "Carnegie Stage", "pattern": "^\\d+$", "preferred_prefix": "carnegie.stage", "uri_format": "https://embryology.med.unsw.edu.au/embryology/index.php/Carnegie_Stages#Stage_$1" }, "caro": { "appears_in": [ "aism", "colao", "ehdaa2", "gallont", "lepao", "pco" ], "contact": { "email": "haendel@ohsu.edu", "github": "mellybelly", "name": "Melissa Haendel", "orcid": "0000-0001-9114-8737" }, "deprecated": true, "description": "The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies.", "download_json": "http://purl.obolibrary.org/obo/caro.json", "download_obo": "http://purl.obolibrary.org/obo/caro.obo", "download_owl": "http://purl.obolibrary.org/obo/caro.owl", "example": "0000000", "homepage": "https://github.com/obophenotype/caro/", "keywords": [ "anatomy", "annotation", "life science", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "CARO", "biocontext": "CARO", "bioportal": "CARO", "fairsharing": "FAIRsharing.3kcgmr", "go": "CARO", "obofoundry": "caro", "ols": "caro", "ontobee": "CARO", "wikidata.entity": "Q55118319" }, "name": "Common Anatomy Reference Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CARO", "providers": [ { "code": "obo.1", "description": "This incorrect encoding was found inside IDO-COVID-19", "homepage": "http://purl.obolibrary.org", "name": "Nonstandard OBO PURL", "uri_format": "http://purl.obolibrary.org/obo/ido.owl/CARO_$1" } ], "publications": [ { "doi": "10.1007/978-1-84628-885-2_16", "title": "CARO – The Common Anatomy Reference Ontology", "year": 2008 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CARO_$1", "repository": "https://github.com/obophenotype/caro", "uri_format": "http://purl.obolibrary.org/obo/CARO_$1", "version": "2023-03-15" }, "cas": { "contact": { "email": "ajacobs@cas.org", "name": "Andrea Jacobs", "orcid": "0000-0001-9316-9400" }, "description": "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information.", "example": "50-00-0", "homepage": "https://commonchemistry.cas.org/", "keywords": [ "chemical", "chemical entity", "physical chemistry", "structure" ], "logo": "https://upload.wikimedia.org/wikipedia/en/2/2a/Chemical_Abstracts_Service_logo.svg", "mappings": { "biocontext": "CAS", "cheminf": "000446", "edam": "1002", "fairsharing": "FAIRsharing.r7Kwy7", "go": "CAS", "hl7": "2.16.840.1.113883.6.61", "miriam": "cas", "n2t": "cas", "prefixcommons": "cas", "wikidata": "P231" }, "name": "CAS Registry Number", "pattern": "^\\d{1,7}\\-\\d{2}\\-\\d$", "preferred_prefix": "cas", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cas:$1" }, { "code": "hoelzel", "description": "Vendor page", "homepage": "https://www.hoelzel-biotech.com", "name": "Hölzel Diagnostika", "uri_format": "https://www.hoelzel-biotech.com/de/casinfo/cas/index/number/$1" }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/cas/$1" } ], "publications": [ { "doi": "10.1021/acs.jcim.2c00268", "pmc": "PMC9199008", "pubmed": "35559614", "title": "CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community", "year": 2022 } ], "synonyms": [ "CASID", "CAS_RN", "SECONDARY_CAS_RN", "cas_id" ], "uri_format": "https://commonchemistry.cas.org/detail?cas_rn=$1" }, "casspc": { "comment": "Jim Balhoff said that Catalog of Fishes does not publish their data in a machine readable format, but a long time ago they sent a CSV dump to help in the development of TTO and VTO. These ontologies are effectively retired and CASSPC terms are only also used in Phenoscape. Note that the github request issue is not correct, since this was made on a commit (but, fishbase is related).", "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "contributor_extras": [ { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } ], "deprecated": true, "example": "5359", "github_request_issue": 149, "homepage": "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp", "mappings": { "go": "CASSPC" }, "name": "Eschmeyer's Catalog of Fishes", "pattern": "^\\d+$", "preferred_prefix": "casspc", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "CASGEN" ], "uri_format": "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1" }, "cath": { "contact": { "email": "c.orengo@ucl.ac.uk", "name": "Christine Orengo", "orcid": "0000-0002-7141-8936" }, "description": "CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence.", "example": "1.10.8.10", "homepage": "http://www.cathdb.info", "keywords": [ "biology", "classification", "evolutionary biology", "protein", "structure" ], "mappings": { "biocontext": "CATH", "edam": "2700", "fairsharing": "FAIRsharing.xgcyyn", "integbio": "nbdc01888", "miriam": "cath", "n2t": "cath", "prefixcommons": "cath", "re3data": "r3d100012629" }, "name": "CATH Protein Structural Domain Superfamily", "pattern": "^[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+$", "preferred_prefix": "cath", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cath:$1" } ], "publications": [ { "doi": "10.1016/s0969-2126(97)00260-8", "pubmed": "9309224", "title": "CATH--a hierarchic classification of protein domain structures", "year": 1997 }, { "doi": "10.1093/nar/gkae1087", "pubmed": "39565206", "title": "CATH v4.4: major expansion of CATH by experimental and predicted structural data", "year": 2024 }, { "doi": "10.1093/nar/gkaa1079", "pmc": "PMC7778904", "pubmed": "33237325", "title": "CATH: increased structural coverage of functional space", "year": 2021 }, { "doi": "10.1093/nar/gky1097", "pmc": "PMC6323983", "pubmed": "30398663", "title": "CATH: expanding the horizons of structure-based functional annotations for genome sequences", "year": 2019 }, { "doi": "10.1093/nar/gkx1069", "pmc": "PMC5753370", "pubmed": "29112716", "title": "Gene3D: Extensive prediction of globular domains in proteins", "year": 2018 }, { "doi": "10.1093/nar/gkw1098", "pmc": "PMC5210570", "pubmed": "27899584", "title": "CATH: an expanded resource to predict protein function through structure and sequence", "year": 2016 }, { "doi": "10.1093/bioinformatics/btw473", "pmc": "PMC5018379", "pubmed": "27477482", "title": "Functional classification of CATH superfamilies: a domain-based approach for protein function annotation", "year": 2016 }, { "doi": "10.1016/j.biochi.2015.08.004", "pmc": "PMC4678953", "pubmed": "26253692", "title": "The history of the CATH structural classification of protein domains", "year": 2015 }, { "doi": "10.1093/nar/gku947", "pmc": "PMC4384018", "pubmed": "25348408", "title": "CATH: comprehensive structural and functional annotations for genome sequences", "year": 2014 }, { "pubmed": "11788987", "title": "The CATH protein family database: a resource for structural and functional annotation of genomes", "year": 2002 } ], "twitter": "CATHDatabase", "uri_format": "http://www.cathdb.info/cathnode/$1" }, "cath.domain": { "description": "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains.", "example": "1cukA01", "homepage": "http://www.cathdb.info/", "mappings": { "biocontext": "CATH.DOMAIN", "edam": "1040", "miriam": "cath.domain", "n2t": "cath.domain" }, "name": "CATH domain", "pattern": "^\\w+$", "preferred_prefix": "cath.domain", "uri_format": "http://www.cathdb.info/domain/$1" }, "cath.superfamily": { "description": "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification.", "example": "1.10.10.200", "homepage": "http://www.cathdb.info/", "mappings": { "biocontext": "CATH.SUPERFAMILY", "miriam": "cath.superfamily", "n2t": "cath.superfamily" }, "name": "CATH superfamily", "part_of": "cath", "pattern": "^\\d+(\\.\\d+(\\.\\d+(\\.\\d+)?)?)?$", "preferred_prefix": "cath.superfamily", "uri_format": "http://www.cathdb.info/cathnode/$1" }, "cattleqtldb": { "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs.", "example": "4685", "homepage": "https://www.animalgenome.org/QTLdb", "keywords": [ "dna", "genome" ], "mappings": { "biocontext": "CATTLEQTLDB", "miriam": "cattleqtldb", "n2t": "cattleqtldb", "prefixcommons": "cattleqtldb" }, "name": "Animal Genome Cattle QTL", "part_of": "qtldb", "pattern": "^\\d+$", "preferred_prefix": "cattleqtldb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cattleqtldb:$1" } ], "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" }, "cazy": { "contact": { "email": "nicolas.terrapon@univ-amu.fr", "github": "gandarath", "name": "Nicolas Terrapon", "orcid": "0000-0002-3693-6017" }, "description": "The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. 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For more information on describing licenses in RDF and attaching those descriptions to digital works, see [ccREL](https://wiki.creativecommons.org/CC_REL) in the [Creative Commons wiki](https://wiki.creativecommons.org/).", "download_rdf": "https://creativecommons.org/schema.rdf", "example": "Work", "homepage": "https://creativecommons.org/ns", "keywords": [ "law", "metadata", "nfdi4ing" ], "license": "CC0-1.0", "mappings": { "aberowl": "CC", "lov": "cc", "tib": "ccrel", "zazuko": "cc" }, "name": "Creative Commons Rights Expression Language", "pattern": "^\\w+$", "preferred_prefix": "cc", "synonyms": [ "ccrel" ], "twitter": "cc_opensource", "uri_format": "https://creativecommons.org/ns#$1" }, "cc.legacy": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "A precursor that was later replaced with the Creative Commons Rights Expression Language (ccREL)", "download_rdf": "https://web.resource.org/cc/schema.rdf", "example": "License", "github_request_issue": 1639, "homepage": "https://web.resource.org/cc/", "keywords": [ "license", "schema" ], "name": "Creative Commons Schema", "preferred_prefix": "cc.legacy", "uri_format": "http://web.resource.org/cc/$1" }, "ccdc": { "description": "The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC.", "example": "1829126", "homepage": "https://www.ccdc.cam.ac.uk/", "mappings": { "miriam": "ccdc" }, "name": "CCDC Number", "pattern": "^\\d{6,7}$", "preferred_prefix": "ccdc", "uri_format": "https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG" }, "ccds": { "contact": { "email": "murphyte@ncbi.nlm.nih.gov", "github": "murphyte", "name": "Terence D. Murphy", "orcid": "0000-0001-9311-9745" }, "description": "The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations.", "example": "CCDS12976", "example_extras": [ "CCDS12976.1" ], "homepage": "http://www.ncbi.nlm.nih.gov/CCDS/", "keywords": [ "gene", "life science", "protein" ], "mappings": { "biocontext": "CCDS", "fairsharing": "FAIRsharing.46s4nt", "integbio": "nbdc00023", "miriam": "ccds", "n2t": "ccds", "prefixcommons": "ccds", "togoid": "Ccds", "uniprot": "DB-0187" }, "name": "Consensus CDS", "pattern": "^CCDS\\d+(\\.\\d+)?$", "preferred_prefix": "ccds", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/ccds:$1" } ], "publications": [ { "doi": "10.1093/nar/gkx1031", "pubmed": "29126148" }, { "doi": "10.1101/gr.080531.108", "pmc": "PMC2704439", "pubmed": "19498102", "title": "The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes", "year": 2009 } ], "uri_format": "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1" }, "ccf": { "contact": { "email": "katy@indiana.edu", "github": "katyb", "name": "Katy Börner", "orcid": "0000-0002-3321-6137" }, "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. 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All relationships between anatomical structures and from cell types to anatomical structures are valid Uberon and CL relationships. The Spatial Ontology defines the shape, size, location, and rotation of experimental tissue and data major anatomical structures in the 3D Reference Object Library. The Specimen Ontology captures the sex, age, and other information on donors that provided tissue data used in the construction of the HRA.", "download_owl": "http://aber-owl.net/media/ontologies/CCF/16/ccf.owl", "example": "extraction_set", "github_request_issue": 879, "homepage": "https://bioportal.bioontology.org/ontologies/CCF", "keywords": [ "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "CCF", "bioportal": "CCF", "ols": "ccf", "re3data": "r3d100012657" }, "name": "Human Reference Atlas Common Coordinate Framework Ontology", "pattern": "^\\S+$", "preferred_prefix": "ccf", "rdf_uri_format": "http://purl.org/ccf/$1", "repository": "https://github.com/hubmapconsortium/ccf-ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://bioportal.bioontology.org/ontologies/CCF/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fccf%2F$1" }, "ccle": { "contact": { "email": "wsellers@broadinstitute.org", "name": "William R. Sellers", "orcid": "0000-0002-3539-9803" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Datasets around different cancer cell lines generated by the Broad Institute and Novartis", "example": "BT20_BREAST", "homepage": "https://www.cbioportal.org/study/summary?id=ccle_broad_2019", "keywords": [ "cancer cell line", "cell", "cell line" ], "license": "ODbL-1.0", "logo": "https://sites.broadinstitute.org/files/files/ccle/files/cclelogo_200h_4.jpg", "mappings": { "cellosaurus": "CCLE" }, "name": "Cancer Cell Line Encyclopedia Cells", "preferred_prefix": "ccle", "publications": [ { "doi": "10.1016/j.cell.2019.12.023", "pmc": "PMC7339254", "pubmed": "31978347", "title": "Quantitative Proteomics of the Cancer Cell Line Encyclopedia", "year": 2020 }, { "doi": "10.1038/s41586-019-1186-3", "pmc": "PMC6697103", "pubmed": "31068700", "title": "Next-generation characterization of the Cancer Cell Line Encyclopedia", "year": 2019 } ], "synonyms": [ "ccle.cell" ], "uri_format": "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1" }, "cco": { "banana": "CCO", "contact": { "email": "kuiper@bio.ntnu.no", "github": "makuintnu", "name": "Martin Kuiper", "orcid": "0000-0002-1171-9876" }, "description": "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process.", "download_obo": "https://www.bio.ntnu.no/ontology/CCO/cco.obo", "download_owl": "https://www.bio.ntnu.no/ontology/CCO/cco.owl", "example": "0000003", "homepage": "http://www.semantic-systems-biology.org/apo", "keywords": [ "cell", "cell cycle", "functional genomics", "genomics", "life science", "molecular_function", "obo", "ontology", "proteomics" ], "mappings": { "aberowl": "CCO", "bartoc": "20461", "biocontext": "CCO", "bioportal": "CCO", "fairsharing": "FAIRsharing.xhwrnr", "miriam": "cco", "n2t": "cco", "ols": "cco", "prefixcommons": "cco" }, "name": "Cell Cycle Ontology", "namespace_in_lui": true, "pattern": "^\\w+$", "preferred_prefix": "cco", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cco:$1" } ], "publications": [ { "doi": "10.1186/gb-2009-10-5-r58", "pmc": "PMC2718524", "pubmed": "19480664", "title": "The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process", "year": 2009 } ], "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:$1" }, "ccrid": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Cell line databases/resources", "example": "4201PAT-CCTCC00348", "homepage": "http://www.cellresource.cn", "mappings": { "cellosaurus": "CCRID" }, "name": "National Experimental Cell Resource Sharing Platform", "preferred_prefix": "ccrid", "uri_format": "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1" }, "ccso": { "contact": { "email": "merocknyxta@gmail.com", "github": "vkreations", "name": "Evangelos Katis" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "CCSO is an educational ontology acting as a data model for concepts and entities within an academic setting, enabling also the annotation of potentially available resources. The ontology aims to conceptualize educational entities within Curriculum and Syllabus with appropriate coverage and quality, in order to support rich services on top for improving curriculum management and automatically enabling syllabus semantic processes. (from homepage)", "download_owl": "https://vkreations.github.io/CCSO/CCSO_071owl.owl", "example": "AcademicStaff", "homepage": "https://vkreations.github.io/CCSO/", "keywords": [ "curricula", "curriculum", "education", "oer", "oers", "ontology", "open educational resources" ], "license": "GPL-3.0", "name": "Curriculum Course Syllabus Ontology", "preferred_prefix": "ccso", "rdf_uri_format": "https://w3id.org/ccso/ccso#$1", "repository": "https://github.com/Vkreations/CCSO", "uri_format": "https://w3id.org/ccso/ccso#$1" }, "cdao": { "contact": { "email": "balhoff@renci.org", "github": "balhoff", "name": "Jim Balhoff", "orcid": "0000-0002-8688-6599" }, "description": "a formalization of concepts and relations relevant to evolutionary comparative analysis", "download_owl": "http://purl.obolibrary.org/obo/cdao.owl", "example": "0000072", "homepage": "https://github.com/evoinfo/cdao", "keywords": [ "bioinformatics", "biomedical science", "evolution", "evolutionary biology", "life science", "molecular biology", "obo", "ontology", "phylogenetics", "taxonomy" ], "license": "CC0-1.0", "mappings": { "aberowl": "CDAO", "agroportal": "CDAO", "biocontext": "CDAO", "bioportal": "CDAO", "fairsharing": "FAIRsharing.kay31r", "obofoundry": "cdao", "ols": "cdao", "ontobee": "CDAO", "wikidata.entity": "Q55118328" }, "name": "Comparative Data Analysis Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CDAO", "publications": [ { "doi": "10.4137/ebo.s2320", "pmc": "PMC2747124", "pubmed": "19812726", "title": "Initial implementation of a comparative data analysis ontology", "year": 2009 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CDAO_$1", "repository": "https://github.com/evoinfo/cdao", "uri_format": "http://purl.obolibrary.org/obo/CDAO_$1", "version": "2024-01-25" }, "cdd": { "description": "The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution.", "example": "cd00400", "homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd", "keywords": [ "earth science", "geology", "protein", "structure" ], "mappings": { "biocontext": "CDD", "edam": "2666", "fairsharing": "FAIRsharing.ea287c", "go": "CDD", "integbio": "nbdc00401", "miriam": "cdd", "n2t": "cdd", "ncbi": "CDD", "prefixcommons": "cdd", "re3data": "r3d100012041", "uniprot": "DB-0214" }, "name": "Conserved Domain Database at NCBI", "pattern": "^(cd)?\\d{5}$", "preferred_prefix": "cdd", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cdd:$1" } ], "publications": [ { "doi": "10.1093/nar/gkac1096", "pubmed": "36477806" }, { "doi": "10.1093/nar/gku1221", "pmc": "PMC4383992", "pubmed": "25414356", "title": "CDD: NCBI's conserved domain database", "year": 2014 }, { "doi": "10.1093/nar/gkn845", "pmc": "PMC2686570", "pubmed": "18984618", "title": "CDD: specific functional annotation with the Conserved Domain Database", "year": 2008 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1" }, "cdno": { "contact": { "email": "landreshdz@gmail.com", "github": "LilyAndres", "name": "Liliana Andres Hernandez", "orcid": "0000-0002-7696-731X" }, "depends_on": [ "bfo", "chebi", "envo", "pato", "ro" ], "description": "The CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. These terms are intended primarily to be associated with datasets that quantify concentration of chemical nutritional components derived from samples taken from any stage in the production of food raw materials (including from crops, livestock, fisheries) and through processing and supply chains. Additional knowledge associated with these dietary sources may be represented by terms that describe functional, physical and other attributes. Whilst recognising that dietary nutrients within food substrates may be present as complex and dynamic physical and chemical structures or mixtures, CDNO focuses on components typically quantified in an analytical chemistry laboratory. The primary CDNO class ‘dietary nutritional component’ contains hierarchical sets of terms organised to reflect commonly used classifications of chemical food composition. This class does not represent an exhaustive classification of chemical components, but focuses on structuring terms according to widely accepted categories. This class is independent of, but may be used in conjunction with, classes that describe ‘analytical methods’ for quantification, ‘physical properties’ or ‘dietary function’. Quantification data may be used and reported in research literature, to inform food composition tables and labelling, or for supply chain quality assurance and control. More specifically, terms within the ‘nutritional component concentration’ class may be used to represent quantification of components described in the ‘dietary nutritional component’ class. Concentration data are intended to be described in conjunction with post-composed metadata concepts, such as represented by the Food Ontology (FoodOn) ‘Food product by organism’, which derives from some food or anatomical entity and a NCBI organismal classification ontology (NCBITaxon) entity. The common vocabulary and relationships defined within CDNO should facilitate description, communication and exchange of material entity-derived nutritional composition datasets typically generated by analytical laboratories. The organisation of the vocabulary is structured to reflect common categories variously used by those involved in crop, livestock or other organismal production, associated R&D and breeding, as well as the food processing and supply sector, and nutritionists, inlcuding compilers and users of food composition databases. The CDNO therefore supports characterisation of genetic diversity and management of biodiversity collections, as well as sharing of knowledge relating to dietary composition between a wider set of researchers, breeders, farmers, processors and other stakeholders. Further development of the functional class should also assist in understanding how interactions between organismal genetic and environmental variation contribute to human diet and health in the farm to fork continuum.", "download_obo": "http://purl.obolibrary.org/obo/cdno.obo", "download_owl": "http://purl.obolibrary.org/obo/cdno.owl", "example": "0000013", "homepage": "https://cdno.info/", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "CDNO", "agroportal": "CDNO", "bioportal": "CDNO", "obofoundry": "cdno", "ols": "cdno", "ontobee": "CDNO", "wikidata.entity": "Q111272479" }, "name": "Compositional Dietary Nutrition Ontology", "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", "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/CompositionalDietaryNutritionOntology/cdno", "uri_format": "http://purl.obolibrary.org/obo/CDNO_$1", "version": "2025-06-09" }, "cdpd": { "description": "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN).", "example": "63250", "homepage": "https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/drug-product-database.html", "mappings": { "biocontext": "CDPD", "miriam": "cdpd", "n2t": "cdpd" }, "name": "Canadian Drug Product Database", "pattern": "^\\d+$", "preferred_prefix": "cdpd", "uri_format": "https://health-products.canada.ca/dpd-bdpp/info?lang=eng&code=$1" }, "cdt": { "appears_in": [ "ohd" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment.\n\nNote that CDT codes should look like D2150 but for some reason the ontology conversion that is reused across OBO rewrites them as CPT_000 + the four numbers without the leading D.", "download_owl": "https://raw.githubusercontent.com/oral-health-and-disease-ontologies/ohd-ontology/f19378ff192b6f9ea16133e85671e8359fc371cd/src/ontology/archive/CDTCodes%20as%20Classes_pruned.owl", "example": "1000001", "homepage": "https://www.ada.org/publications/CDT", "keywords": [ "ontology" ], "mappings": { "bartoc": "20299", "hl7": "2.16.840.1.113883.6.116" }, "name": "Current Dental Terminology", "pattern": "^\\d{7}$", "preferred_prefix": "cdt" }, "ceds.element": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Common Entity Data Standards (CEDS) Domain Entity Schema (DES) provides a hierarchy of domains, entities, categories, and elements. It is intended for use primarily by people as an index to search, map, and organize elements in a logical way. [from homepage]", "example": "000254", "homepage": "https://ceds.ed.gov/domainEntitySchema.aspx", "name": "Common Entity Data Standards - Domain Entity Schema", "pattern": "^\\d+$", "preferred_prefix": "ceds.element", "uri_format": "https://ceds.ed.gov/element/$1" }, "ceds.learning_resource_type": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A vocabulary for learning resource types", "example": "AlternateAssessment", "homepage": "https://ceds.ed.gov/element/000928", "keywords": [ "educational resources", "learning materials", "open educational resources" ], "name": "CEDS Learning Resource Type", "preferred_prefix": "ceds.learning_resource_type", "uri_format": "https://ceds.ed.gov/element/000928#$1" }, "cell_biolabs": { "description": "Cell line collections (Providers)", "example": "AKR-270", "homepage": "https://www.cellbiolabs.com", "mappings": { "cellosaurus": "Cell_Biolabs" }, "name": "Cell Biolabs cell line products", "preferred_prefix": "cell_biolabs", "uri_format": "https://www.cellbiolabs.com/search?keywords=$1" }, "cell_model_passport": { "description": "Cell line databases/resources", "example": "SIDM01262", "homepage": "https://cellmodelpassports.sanger.ac.uk/", "mappings": { "cellosaurus": "Cell_Model_Passport" }, "name": "Sanger Cell Model Passports", "preferred_prefix": "cell_model_passport", "uri_format": "https://cellmodelpassports.sanger.ac.uk/passports/$1" }, "cellbank.australia": { "description": "CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world.", "example": "ab-1-ha", "homepage": "https://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/", "mappings": { "cellosaurus": "CBA" }, "name": "CellBank Australia", "preferred_prefix": "cellbank.australia", "uri_format": "https://www.cellbankaustralia.com/$1.html" }, "cellimage": { "contact": { "email": "dorloff@ncmir.ucsd.edu", "name": "David N. Orloff", "orcid": "0000-0001-7594-0820" }, "description": "The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.", "example": "24801", "homepage": "http://cellimagelibrary.org/", "keywords": [ "cell biology", "image", "life science" ], "mappings": { "biocontext": "CELLIMAGE", "fairsharing": "FAIRsharing.8t18te", "miriam": "cellimage", "n2t": "cellimage", "prefixcommons": "cellimage", "re3data": "r3d100000023" }, "name": "Cell Image Library", "pattern": "^\\d+$", "preferred_prefix": "cellimage", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cellimage:$1" } ], "publications": [ { "doi": "10.1093/nar/gks1257", "pmc": "PMC3531121", "pubmed": "23203874", "title": "The cell: an image library-CCDB: a curated repository of microscopy data", "year": 2012 } ], "twitter": "CellImageLibrar", "uri_format": "http://cellimagelibrary.org/images/$1" }, "cellopub": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Cellosaurus identifeirs for publications, like Pubmed", "example": "CLPUB00496", "homepage": "https://web.expasy.org/cellosaurus/", "mappings": { "cellosaurus": "CelloPub" }, "name": "Cellosaurus Publication", "pattern": "^CLPUB\\d+$", "preferred_prefix": "cellopub", "uri_format": "https://web.expasy.org/cellosaurus/cellopub/$1" }, "cellosaurus": { "banana": "CVCL", "banana_peel": "_", "contact": { "email": "Amos.Bairoch@sib.swiss", "github": "AmosBairoch", "name": "Amos Bairoch", "orcid": "0000-0003-2826-6444" }, "description": "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.", "download_obo": "https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo", "example": "0440", "homepage": "https://cellosaurus.org", "keywords": [ "cell lines", "controlled vocabularies", "life science", "ontologies", "ontology", "thesaurus" ], "license": "CC-BY-4.0", "logo": "https://www.cellosaurus.org/images/cellosaurus/cellosaurus.png", "mappings": { "biocontext": "CELLOSAURUS", "cellosaurus": "Cellosaurus", "fairsharing": "FAIRsharing.hkk309", "integbio": "nbdc02180", "miriam": "cellosaurus", "n2t": "cellosaurus", "re3data": "r3d100013293", "rrid": "CVCL", "togoid": "Cellosaurus", "wikidata": "P3289", "wikidata.entity": "Q21014462" }, "mastodon": "cellosaurus@fediscience.org", "name": "Cellosaurus", "pattern": "^[A-Z0-9]{4}$", "preferred_prefix": "cellosaurus", "providers": [ { "code": "legacy", "description": "The legacy URI for the Cellosaurus website, updated on August 30, 2022 [ref](https://twitter.com/Cellosaurus/status/1564658792691810305).", "homepage": "https://web.expasy.org/cellosaurus", "name": "Legacy Endpoint", "uri_format": "https://web.expasy.org/cellosaurus/CVCL_$1" }, { "code": "nextprot", "description": "The neXtProt endpoint for exploring Cellosaurus", "homepage": "https://www.nextprot.org/", "name": "neXtProt Cellosaurus Browser", "uri_format": "https://www.nextprot.org/term/CVCL_$1" }, { "code": "obo", "description": "Incorrectly encoded OBO PURL - do not use!", "homepage": "http://purl.obolibrary.org", "name": "OBO PURL", "uri_format": "http://purl.obolibrary.org/obo/Cellosaurus#CVCL_$1" }, { "code": "obo.incorrect", "description": "OBO PURL generated by incorrectly configured OBO file - this is not registered in OBO Foundry.", "homepage": "http://purl.obolibrary.org", "name": "OBO (Incorrect)", "uri_format": "http://purl.obolibrary.org/obo/Cellosaurus#CVCL_$1" } ], "publications": [ { "doi": "10.1002/ijc.32639", "pubmed": "31444973", "title": "CLASTR: The Cellosaurus STR similarity search tool - A precious help for cell line authentication", "year": 2019 }, { "doi": "10.7171/jbt.18-2902-002", "pmc": "PMC5945021", "pubmed": "29805321", "title": "The Cellosaurus, a Cell-Line Knowledge Resource", "year": 2018 } ], "repository": "https://github.com/calipho-sib/cellosaurus", "synonyms": [ "CVCL" ], "twitter": "cellosaurus", "uri_format": "https://www.cellosaurus.org/CVCL_$1" }, "cellosaurus.resource": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The set of prefixes used in the Cellosaurus resource", "example": "4DN", "homepage": "https://web.expasy.org/cellosaurus/", "keywords": [ "cell lines", "cells", "registry" ], "name": "Cellosaurus Registry", "preferred_prefix": "cellosaurus.resource", "uri_format": "https://bioregistry.io/metaregistry/cellosaurus/$1" }, "cellrepo": { "description": "The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines", "example": "82", "homepage": "https://www.cellrepo.com/", "mappings": { "miriam": "cellrepo" }, "name": "Cell Version Control Repository", "pattern": "^[0-9]+$", "preferred_prefix": "cellrepo", "uri_format": "https://www.cellrepo.com/repositories/$1" }, "cellxgene.collection": { "contact": { "email": "acarr@chanzuckerberg.com", "github": "ambrosejcarr", "name": "Ambrose Carr", "orcid": "0000-0002-8457-2836" }, "contributor": { "email": "robert.j.allaway@gmail.com", "github": "allaway", "name": "Robert Allaway", "orcid": "0000-0003-3573-3565" }, "description": "Assigns identifiers to collections of datasets indexed by CELLxGENE.\n\nCELLxGENE is an interactive data visualization and exploration tool developed by the Chan Zuckerberg Initiative that enables researchers to analyze and share single-cell genomics datasets. It provides a user-friendly interface for biologists and computational scientists to interrogate gene expression patterns across different cell types.", "example": "436154da-bcf1-4130-9c8b-120ff9a888f2", "github_request_issue": 1541, "homepage": "https://cellxgene.cziscience.com/collections", "license": "CC-BY-4.0", "name": "Chan Zuckerberg CELLxGENE Collection", "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$", "preferred_prefix": "cellxgene.collection", "publications": [ { "doi": "10.1093/nar/gkae1142", "pmc": "PMC11701654", "pubmed": "39607691", "title": "CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://cellxgene.cziscience.com/collections/$1" }, "cellxgene.dataset": { "contact": { "email": "acarr@chanzuckerberg.com", "github": "ambrosejcarr", "name": "Ambrose Carr", "orcid": "0000-0002-8457-2836" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Assigns identifiers to datasets indexed by CELLxGENE, such those resulting from scRNA-seq experiments", "example": "f72958f5-7f42-4ebb-98da-445b0c6de516", "github_request_issue": 1541, "homepage": "https://cellxgene.cziscience.com", "name": "Chan Zuckerberg CELLxGENE Dataset", "preferred_prefix": "cellxgene.dataset", "publications": [ { "doi": "10.1093/nar/gkae1142", "pmc": "PMC11701654", "pubmed": "39607691", "title": "CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data", "year": 2024 } ], "uri_format": "https://cellxgene.cziscience.com/e/$1" }, "cemo": { "contact": { "email": "n.queralt_rosinach@lumc.nl", "github": "NuriaQueralt", "name": "Núria Queralt Rosinach", "orcid": "0000-0003-0169-8159" }, "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "The covid-19 epidemiology and monitoring ontology (cemo) provides a common ontological model to make epidemiological quantitative data for monitoring the covid-19 outbreak machine-readable and interoperable to facilitate its exchange, integration and analysis, to eventually support evidence-based rapid response.", "download_json": "https://raw.githubusercontent.com/cthoyt/covid19-epidemiology-ontology/add-artifacts/owl/cemo.json", "download_owl": "https://raw.githubusercontent.com/NuriaQueralt/covid19-epidemiology-ontology/main/owl/cemo.owl", "example": "secondary_attack_rate", "github_request_issue": 593, "homepage": "https://github.com/NuriaQueralt/covid19-epidemiology-ontology", "keywords": [ "ontology" ], "license": "CC0-1.0", "name": "The COVID-19 epidemiology and monitoring ontology", "pattern": "^[0-9a-z_-]+$", "preferred_prefix": "cemo", "providers": [ { "code": "obo", "description": "This represents misconfigured base IRIs, even though this ontology isn't an OBO Foundry ontology", "homepage": "http://purl.obolibrary.org/obo/", "name": "Legacy OBO PURL", "uri_format": "http://purl.obolibrary.org/obo/cemo.owl#$1" } ], "repository": "https://github.com/NuriaQueralt/covid19-epidemiology-ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://biopragmatics.github.io/providers/cemo/$1" }, "ceph": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "deprecated": true, "description": "An anatomical and developmental ontology for cephalopods", "download_obo": "https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo", "download_owl": "http://purl.obolibrary.org/obo/ceph.owl", "example": "0000109", "homepage": "https://github.com/obophenotype/cephalopod-ontology", "keywords": [ "anatomy", "fisheries science", "life cycle", "obo", "ontology", "zoology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "CEPH", "biocontext": "CEPH", "bioportal": "CEPH", "fairsharing": "FAIRsharing.p58bm4", "obofoundry": "ceph", "ols": "ceph", "ontobee": "CEPH", "wikidata.entity": "Q104030182" }, "name": "Cephalopod Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CEPH", "rdf_uri_format": "http://purl.obolibrary.org/obo/CEPH_$1", "repository": "https://github.com/obophenotype/cephalopod-ontology", "uri_format": "http://purl.obolibrary.org/obo/CEPH_$1", "version": "2016-01-12" }, "cert": { "description": "Ontology for Certificates and crypto stuff.", "example": "Certificate", "homepage": "http://www.w3.org/ns/auth/cert#", "keywords": [ "quality" ], "mappings": { "lov": "cert", "zazuko": "cert" }, "name": "The Cert Ontology", "preferred_prefix": "cert" }, "cessda": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A vocabulary service for the social sciences, covering the Data Documentation Initiative (DDI) is an international standard for describing data produced by surveys and other observational methods in the social, behavioural, economic, and health sciences.", "example": "TopicClassification", "homepage": "https://vocabularies.cessda.eu", "keywords": [ "registry" ], "name": "Consortium of European Social Science Data Archives Vocabulary", "preferred_prefix": "cessda", "uri_format": "https://vocabularies.cessda.eu/vocabulary/$1" }, "cessda.cdcpublishernames": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Names of organisations providing metadata for CESSDA Data Catalogue.", "example": "AUSSDA", "homepage": "https://vocabularies.cessda.eu/vocabulary/CdcPublisherNames", "license": "CC-BY-4.0", "name": "CDC Publisher Names", "owners": [ { "name": "Consortium of European Social Science Data Archives", "partnered": false, "ror": "02wg9xc72" } ], "preferred_prefix": "cessda.cdcpublishernames", "uri_format": "https://vocabularies.cessda.eu/vocabulary/CdcPublisherNames?lang=en#code_$1", "version": "6.0.0" }, "cessda.cessdadatacataloguecollections": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This vocabulary holds the definitions and descriptions of the collections included in the CESSDA Data Catalogue.", "example": "BY-COVID", "homepage": "https://vocabularies.cessda.eu/vocabulary/CESSDADataCatalogueCollections", "license": "CC-BY-4.0", "name": "CESSDA Data Catalogue Collections", "owners": [ { "name": "Consortium of European Social Science Data Archives", "partnered": false, "ror": "02wg9xc72" } ], "preferred_prefix": "cessda.cessdadatacataloguecollections", "uri_format": "https://vocabularies.cessda.eu/vocabulary/CESSDADataCatalogueCollections?lang=en#code_$1", "version": "1.0.0" }, "cessda.cessdapersistentidentifiertypes": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Lists the types of persistent identifiers that CESSDA accepts as study level PIDs in its data catalogue.", "example": "ARK", "homepage": "https://vocabularies.cessda.eu/vocabulary/CessdaPersistentIdentifierTypes", "license": "CC-BY-4.0", "name": "CESSDA Persistent Identifier Types", "owners": [ { "name": "Consortium of European Social Science Data Archives", "partnered": false, "ror": "02wg9xc72" } ], "preferred_prefix": "cessda.cessdapersistentidentifiertypes", "uri_format": "https://vocabularies.cessda.eu/vocabulary/CessdaPersistentIdentifierTypes?lang=en#code_$1", "version": "1.0.0" }, "cessda.countrynamesandcodes": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ISO 3166-1 alpha-2 country codes and names.", "example": "AF", "homepage": "https://vocabularies.cessda.eu/vocabulary/CountryNamesAndCodes", "license": "CC-BY-4.0", "name": "Country Names and Codes", "owners": [ { "name": "Consortium of European Social Science Data Archives", "partnered": false, "ror": "02wg9xc72" } ], "preferred_prefix": "cessda.countrynamesandcodes", "uri_format": "https://vocabularies.cessda.eu/vocabulary/CountryNamesAndCodes?lang=en#code_$1", "version": "1.1.0" }, "cessda.topicclassification": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A typology of main themes or subjects of data.", "example": "Demography", "homepage": "https://vocabularies.cessda.eu/vocabulary/TopicClassification", "license": "CC-BY-4.0", "name": "CESSDA Topic Classification", "owners": [ { "name": "Consortium of European Social Science Data Archives", "partnered": false, "ror": "02wg9xc72" } ], "preferred_prefix": "cessda.topicclassification", "uri_format": "https://vocabularies.cessda.eu/vocabulary/TopicClassification?lang=en#code_$1", "version": "4.2.3" }, "cgd": { "contact": { "email": "gsherloc@stanford.edu", "name": "Gavin Sherlock", "orcid": "0000-0002-1692-4983" }, "description": "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.", "example": "CAL0003079", "homepage": "http://www.candidagenome.org/", "keywords": [ "eukaryotic", "genome", "life science", "nucleotide" ], "mappings": { "biocontext": "CGD", "fairsharing": "FAIRsharing.j7j53", "go": "CGD", "integbio": "nbdc00391", "miriam": "cgd", "n2t": "cgd", "ncbi": "CGD", "prefixcommons": "cgd", "re3data": "r3d100010617", "uniprot": "DB-0126" }, "name": "Candida Genome Database", "pattern": "^CAL\\d{7}$", "preferred_prefix": "cgd", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cgd:$1" } ], "publications": [ { "doi": "10.1093/nar/gkw924", "pmc": "PMC5210628", "pubmed": "27738138", "title": "The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data", "year": 2016 }, { "doi": "10.1093/nar/gkr945", "pmc": "PMC3245171", "pubmed": "22064862", "title": "The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata", "year": 2011 }, { "doi": "10.1093/nar/gki003", "pmc": "PMC539957", "pubmed": "15608216", "title": "The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information", "year": 2005 } ], "uri_format": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1" }, "cghdb": { "description": "Cell line databases/resources", "example": "300165/p13898_2106T", "homepage": "https://web.archive.org/web/20190222051223/http://www.cghtmd.jp/CGHDatabase/index_e.jsp", "mappings": { "cellosaurus": "CGH-DB" }, "name": "CGH Data Base", "preferred_prefix": "cghdb" }, "cgnc": { "contact": { "email": "fionamcc@arizona.edu", "name": "Fiona M McCarthy", "orcid": "0000-0003-2175-5464" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)", "example": "10087", "homepage": "http://birdgenenames.org", "keywords": [ "gene" ], "license": "CC-BY-4.0", "logo": "https://birdgenenames.org/img/CGNC.png", "mappings": { "cellosaurus": "CGNC", "prefixcommons": "cgnc", "re3data": "r3d100012429" }, "name": "Chicken Gene Nomenclature Consortium", "pattern": "^\\d+$", "preferred_prefix": "cgnc", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cgnc:$1" } ], "publications": [ { "doi": "10.1186/1471-2164-10-s2-s5", "pmc": "PMC2966335", "pubmed": "19607656", "title": "The Chicken Gene Nomenclature Committee report", "year": 2009 } ], "synonyms": [ "BirdBase", "CGNC" ], "uri_format": "http://birdgenenames.org/cgnc/GeneReport?id=$1" }, "cgsc": { "contact": { "email": "kelly.hughes@utah.edu", "name": "Kelly T. 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The terms can be retrieved from ACTION_TYPE table in ChEMBL's SQL dump and are used to annotate the DRUG_MECHANISM table. Because these aren't really identifiers, they are transformed by lowercasing and replacing spaces with dashes to form 'identifiers'. The pattern in the Bioregistry record contains an enumeration of the 33 allowed values as of ChEMBL v35.", "example": "activator", "example_extras": [ "cross-linking-agent", "negative-allosteric-modulator" ], "homepage": "https://www.ebi.ac.uk/chembl", "license": "CC-BY-SA-3.0", "logo": "https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5LCdi4mEW56jpmM0YDjEwLtGUUy2F9I7m02I9hygI0OPugnZKlTrAgfBtug5yJS5RbpCXifID0pzA5Wxdc6un1UjCCtOJcvlkeoAFgzQspvplZcstYNwx8lBtvlYY8WJ-kLj-I891VIAO/s1600/Screenshot+2018-12-20+at+10.30.09.png", "name": "ChEMBL mechanism", "part_of": "chembl", "pattern": "^activator|agonist|allosteric-antagonist|antagonist|antisense-inhibitor|binding-agent|blocker|chelating-agent|cross-linking-agent|degrader|disrupting-agent|exogenous-gene|exogenous-protein|hydrolytic-enzyme|inhibitor|inverse-agonist|methylating-agent|modulator|negative-allosteric-modulator|negative-modulator|opener|other|oxidative-enzyme|partial-agonist|positive-allosteric-modulator|positive-modulator|proteolytic-enzyme|reducing-agent|releasing-agent|rnai-inhibitor|sequestering-agent|stabiliser|substrate|vaccine-antigen$", "preferred_prefix": "chembl.mechanism" }, "chembl.target": { "contact": { "email": "dmendez@ebi.ac.uk", "github": "nclopezo", "name": "David Mendez Lopez", "orcid": "0000-0002-0294-5484" }, "description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.", "example": "CHEMBL3467", "homepage": "https://www.ebi.ac.uk/chembldb/", "keywords": [ "cell", "cell line", "protein", "protein complex" ], "license": "CC-BY-SA-3.0", "logo": "https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5LCdi4mEW56jpmM0YDjEwLtGUUy2F9I7m02I9hygI0OPugnZKlTrAgfBtug5yJS5RbpCXifID0pzA5Wxdc6un1UjCCtOJcvlkeoAFgzQspvplZcstYNwx8lBtvlYY8WJ-kLj-I891VIAO/s1600/Screenshot+2018-12-20+at+10.30.09.png", "mappings": { "biocontext": "CHEMBL.TARGET", "cellosaurus": "ChEMBL-Targets", "miriam": "chembl.target", "n2t": "chembl.target", "togoid": "ChemblTarget" }, "name": "ChEMBL target", "pattern": "^CHEMBL\\d+$", "preferred_prefix": "chembl.target", "synonyms": [ "ChEMBL-Targets" ], "uri_format": "https://www.ebi.ac.uk/chembl/target/inspect/$1" }, "chembl.tissue": { "contact": { "email": "dmendez@ebi.ac.uk", "github": "nclopezo", "name": "David Mendez Lopez", "orcid": "0000-0002-0294-5484" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Tissues used to annotate cells and cell lines, cross-referenced to EFO, BTO, UBERON, and CALOHA", "example": "CHEMBL3559721", "homepage": "https://www.ebi.ac.uk/chembl", "logo": "https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5LCdi4mEW56jpmM0YDjEwLtGUUy2F9I7m02I9hygI0OPugnZKlTrAgfBtug5yJS5RbpCXifID0pzA5Wxdc6un1UjCCtOJcvlkeoAFgzQspvplZcstYNwx8lBtvlYY8WJ-kLj-I891VIAO/s1600/Screenshot+2018-12-20+at+10.30.09.png", "name": "ChEMBL tissue", "part_of": "chembl", "pattern": "^CHEMBL\\d+$", "preferred_prefix": "chembl.tissue", "references": [ "https://chembl.blogspot.com/2018/03/chembl-tissues-increasing-depth-breadth.html" ] }, "chemdb": { "contact": { "email": "pfbaldi@uci.edu", "name": "Pierre Baldi", "orcid": "0000-0001-8752-4664" }, "description": "ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds.", "example": "3966782", "homepage": "http://cdb.ics.uci.edu/", "keywords": [ "biochemistry", "biomedical science", "life science", "preclinical studies", "small molecule", "systems biology" ], "mappings": { "biocontext": "CHEMDB", "fairsharing": "FAIRsharing.dstf7h", "miriam": "chemdb", "n2t": "chemdb", "prefixcommons": "chemdb" }, "name": "ChemDB", "pattern": "^\\d+$", "preferred_prefix": "chemdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/chemdb:$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/btm341", "pubmed": "17599932", "title": "ChemDB update--full-text search and virtual chemical space", "year": 2007 }, { "doi": "10.1093/bioinformatics/bti683", "pubmed": "16174682", "title": "ChemDB: a public database of small molecules and related chemoinformatics resources", "year": 2005 } ], "uri_format": "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1" }, "chemfont.chemical": { "contact": { "email": "david.wishart@ualberta.ca", "github": "DavidWishartLab", "name": "David S. Wishart", "orcid": "0000-0002-3207-2434" }, "contributor": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "The Chemical Functional Ontology (ChemFOnt) is a hierarchical, OWL-compatible ontology describing the functions and actions of biologically important chemicals including primary metabolites, secondary metabolites, natural products, food chemicals, synthetic food additives, drugs, herbicides, pesticides and environmental chemicals. The identifiers in this semantic space correspond to individual chemicals.", "example": "CFc000239295", "github_request_issue": 1617, "homepage": "https://www.chemfont.ca/chemicals", "keywords": [ "chemical", "ontology" ], "name": "ChemFOnt Chemical", "pattern": "^CFc\\d{9}$", "preferred_prefix": "chemfont.chemical", "publications": [ { "doi": "10.1093/nar/gkac919", "pmc": "PMC9825615", "pubmed": "36305829", "title": "ChemFOnt: the chemical functional ontology resource", "year": 2023 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.chemfont.ca/chemicals/$1" }, "chemfont.ontology": { "contact": { "email": "david.wishart@ualberta.ca", "github": "DavidWishartLab", "name": "David S. Wishart", "orcid": "0000-0002-3207-2434" }, "contributor": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "The Chemical Functional Ontology (ChemFOnt) is a hierarchical, OWL-compatible ontology describing the functions and actions of biologically important chemicals including primary metabolites, secondary metabolites, natural products, food chemicals, synthetic food additives, drugs, herbicides, pesticides and environmental chemicals. The identifiers in this semantic space correspond to entries in the ChemFOnt ontology that are used to organize individual chemicals. Terms can be looked up using the following URL (https://www.chemfont.ca/ontology_browse/term_info/18), but not directly by ID", "download_owl": "https://www.chemfont.ca/system/downloads/1.0/chemfont.owl.zip", "example": "CFo000000197", "github_request_issue": 1617, "homepage": "https://www.chemfont.ca/ontology_browse", "keywords": [ "chemical", "ontology" ], "name": "ChemFOnt Ontology", "pattern": "^CFo\\d{9}$", "preferred_prefix": "chemfont.ontology", "publications": [ { "doi": "10.1093/nar/gkac919", "pmc": "PMC9825615", "pubmed": "36305829", "title": "ChemFOnt: the chemical functional ontology resource", "year": 2023 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "chemicalbook": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A hybrid chemical enyclopedia and supplier advertizing system for chemicals.", "example": "CB82546919", "github_request_issue": 1311, "homepage": "https://www.chemicalbook.com", "name": "Chemical Book", "preferred_prefix": "chemicalbook", "synonyms": [ "ChemicalBookNo" ], "uri_format": "https://www.chemicalbook.com/ChemicalProductProperty_IN_$1.htm" }, "chemidplus": { "description": "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.", "example": "57-27-2", "homepage": "https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp", "keywords": [ "biomedical science", "chemistry", "molecules", "structure" ], "mappings": { "biocontext": "CHEMIDPLUS", "edam": "2658", "fairsharing": "FAIRsharing.5949vn", "integbio": "nbdc01837", "miriam": "chemidplus", "n2t": "chemidplus", "prefixcommons": "chemidplus" }, "name": "ChemIDplus", "pattern": "^\\d+\\-\\d+\\-\\d+$", "preferred_prefix": "chemidplus", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/chemidplus:$1" } ], "publications": [ { "doi": "10.1300/j115v21n01_04", "pubmed": "11989279", "title": "ChemIDplus-super source for chemical and drug information", "year": 2002 }, { "doi": "10.1300/J115v21n01_04", "title": "ChemIDplus-super source for chemical and drug information." } ], "synonyms": [ "ChemIDplus" ], "uri_format": "https://chem.nlm.nih.gov/chemidplus/rn/$1" }, "cheminf": { "appears_in": [ "proco" ], "banana": "CHEMINF", "contact": { "email": "egon.willighagen@gmail.com", "github": "egonw", "name": "Egon Willighagen", "orcid": "0000-0001-7542-0286" }, "description": "The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals.", "download_owl": "https://github.com/semanticchemistry/semanticchemistry/raw/master/ontology/cheminf.owl", "example": "000410", "homepage": "https://github.com/semanticchemistry/semanticchemistry", "keywords": [ "biochemistry", "chemistry", "life science", "molecular entity", "nfdi4cat", "nfdi4chem", "obo", "ontology", "structure" ], "license": "CC0-1.0", "mappings": { "aberowl": "CHEMINF", "bartoc": "20702", "biocontext": "CHEMINF", "bioportal": "CHEMINF", "fairsharing": "FAIRsharing.sjhvyy", "miriam": "cheminf", "obofoundry": "cheminf", "ols": "cheminf", "ontobee": "CHEMINF", "tib": "cheminf", "wikidata.entity": "Q55118298" }, "name": "Chemical Information Ontology", "namespace_in_lui": true, "pattern": "^\\d{6}$", "preferred_prefix": "CHEMINF", "providers": [ { "code": "semanticscience", "description": "Legacy URLs before conversion of CHEMINF to OBO PURLs", "homepage": "http://semanticscience.org", "name": "Semantic Science", "uri_format": "http://semanticscience.org/resource/CHEMINF_$1" } ], "publications": [ { "doi": "10.1371/journal.pone.0025513", "pmc": "PMC3184996", "pubmed": "21991315", "title": "The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web", "year": 2011 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CHEMINF_$1", "repository": "https://github.com/semanticchemistry/semanticchemistry", "uri_format": "http://purl.obolibrary.org/obo/CHEMINF_$1", "version": "2.1.0" }, "chempro.competitor": { "contact": { "email": "zhufeng@zju.edu.cn", "name": "Feng Zhu", "orcid": "0000-0001-8069-0053" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for compounds that compete with probes for binding to target proteins.", "example": "LDCM0160", "github_request_issue": 1424, "homepage": "https://chemprosquare.idrblab.net", "name": "ChemPro Competitor", "pattern": "^LDCM\\d+$", "preferred_prefix": "chempro.competitor", "publications": [ { "doi": "10.1093/nar/gkae943", "pmc": "PMC11701659", "pubmed": "39436046", "title": "Chem(Pro)2: the atlas of chemoproteomic probes labelling human proteins", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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This prefix provides identifiers for chemoproteomic probes used to label human proteins in living cells.", "example": "LDPC0032", "github_request_issue": 1424, "homepage": "https://chemprosquare.idrblab.net", "name": "ChemPro Probe", "pattern": "^LDPC\\d+$", "preferred_prefix": "chempro.probe", "publications": [ { "doi": "10.1093/nar/gkae943", "pmc": "PMC11701659", "pubmed": "39436046", "title": "Chem(Pro)2: the atlas of chemoproteomic probes labelling human proteins", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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This prefix provides identifiers for human proteins that interact with chemoproteomic probes.", "example": "LDTP03903", "github_request_issue": 1424, "homepage": "https://chemprosquare.idrblab.net", "name": "ChemPro Target", "pattern": "^LDTP\\d+$", "preferred_prefix": "chempro.target", "publications": [ { "doi": "10.1093/nar/gkae943", "pmc": "PMC11701659", "pubmed": "39436046", "title": "Chem(Pro)2: the atlas of chemoproteomic probes labelling human proteins", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://chemprosquare.idrblab.net/data/target/details/$1" }, "chemrof": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A data model for managing information about chemical entities, ranging from atoms through molecules to complex mixtures.", "download_owl": "https://raw.githubusercontent.com/chemkg/chemrof/main/schema/owl/chemrof.owl.ttl", "example": "FullySpecifiedAtom", "homepage": "https://chemkg.github.io/chemrof/", "keywords": [ "chemistry", "nfdi4chem", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "CHEMROF", "bioportal": "CHEMROF", "tib": "chemrof" }, "name": "Chemical Entity Materials and Reactions Ontological Framework", "preferred_prefix": "ChEMROF", "rdf_uri_format": "https://w3id.org/chemrof/$1", "repository": "https://github.com/chemkg/chemrof", "uri_format": "https://chemkg.github.io/chemrof/$1" }, "chemspider": { "contact": { "email": "pencehe@oneonta.edu", "name": "Harry E. Pence", "orcid": "0000-0002-0412-9018" }, "description": "ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources.", "example": "56586", "homepage": "http://www.chemspider.com/", "keywords": [ "chemistry", "life science", "molecules", "structure" ], "mappings": { "biocontext": "CHEMSPIDER", "cheminf": "000405", "edam": "1173", "fairsharing": "FAIRsharing.96f3gm", "integbio": "nbdc01863", "miriam": "chemspider", "n2t": "chemspider", "prefixcommons": "chemspider", "re3data": "r3d100010205", "wikidata": "P661" }, "name": "ChemSpider", "pattern": "^\\d+$", "preferred_prefix": "chemspider", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/chemspider:$1" } ], "publications": [ { "doi": "10.1021/ed100697w", "title": "ChemSpider: An Online Chemical Information Resource", "year": 2010 } ], "rdf_uri_format": "http://rdf.chemspider.com/$1", "synonyms": [ "ChemSpiderID", "Chemspider" ], "twitter": "ChemSpider", "uri_format": "http://www.chemspider.com/Chemical-Structure.$1.html" }, "chickenqtldb": { "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs.", "example": "14362", "homepage": "https://www.animalgenome.org/QTLdb", "keywords": [ "dna", "genome" ], "mappings": { "biocontext": "CHICKENQTLDB", "miriam": "chickenqtldb", "n2t": "chickenqtldb", "prefixcommons": "chickenqtldb" }, "name": "Animal Genome Chicken QTL", "part_of": "qtldb", "pattern": "^\\d+$", "preferred_prefix": "chickenqtldb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/chickenqtldb:$1" } ], "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" }, "chictr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Established in 2005 by professor Wu Taixiang and Li Youping team, West China Hospital, Sichuan University, and the Ministry of Health of China assigned it to be the representative of China to join WHO ICTRP in 2007. The Chinese Clinical Trial Registry provides the services include register for trials, consultation for trial design, central randomization for an allocation sequence, peer review for draft articles and training for peer reviewers. (from website)", "example": "ChiCTR2300070727", "homepage": "https://www.chictr.org.cn", "logo": "https://www.chictr.org.cn/images/top.jpg", "name": "Chinese Clinical Trial Registry", "pattern": "^ChiCTR(-[A-Z]+-)?\\d+$", "preferred_prefix": "chictr", "references": [ "https://www.chictr.org.cn/showproj.html?proj=187605" ] }, "chiro": { "contact": { "email": "vasilevs@ohsu.edu", "github": "nicolevasilevsky", "name": "Nicole Vasilevsky", "orcid": "0000-0001-5208-3432" }, "depends_on": [ "chebi", "go", "hp", "mp", "ncbitaxon", "pr", "uberon" ], "description": "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.", "download_obo": "http://purl.obolibrary.org/obo/chiro.obo", "download_owl": "http://purl.obolibrary.org/obo/chiro.owl", "homepage": "https://github.com/obophenotype/chiro", "keywords": [ "chemistry", "nfdi4chem", "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "CHIRO", "bioportal": "CHIRO", "obofoundry": "chiro", "ols": "chiro", "ontobee": "CHIRO", "tib": "chiro", "wikidata.entity": "Q113006226" }, "name": "ChEBI Integrated Role Ontology", "no_own_terms": true, "preferred_prefix": "CHIRO", "publications": [ { "doi": "10.26434/chemrxiv.12591221", "title": "Extension of Roles in the ChEBI Ontology", "year": 2020 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CHIRO_$1", "repository": "https://github.com/obophenotype/chiro", "uri_format": "http://purl.obolibrary.org/obo/chiro#$1", "version": "2015-11-23" }, "chmo": { "appears_in": [ "rbo", "scdo" ], "contact": { "email": "batchelorc@rsc.org", "github": "batchelorc", "name": "Colin Batchelor", "orcid": "0000-0001-5985-7429" }, "description": "CHMO, the chemical methods ontology, describes methods used to", "download_obo": "http://purl.obolibrary.org/obo/chmo.obo", "download_owl": "http://purl.obolibrary.org/obo/chmo.owl", "example": "0002902", "homepage": "https://github.com/rsc-ontologies/rsc-cmo", "keywords": [ "assay", "chemistry", "chromatography", "dataplant", "electron microscopy", "mass spectrometry assay", "nfdi4cat", "nfdi4chem", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "CHMO", "bartoc": "20703", "biocontext": "CHMO", "bioportal": "CHMO", "fairsharing": "FAIRsharing.9j4wh2", "obofoundry": "chmo", "ols": "chmo", "ontobee": "CHMO", "tib": "chmo", "wikidata.entity": "Q55118301" }, "name": "Chemical Methods Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CHMO", "rdf_uri_format": "http://purl.obolibrary.org/obo/CHMO_$1", "repository": "https://github.com/rsc-ontologies/rsc-cmo", "uri_format": "http://purl.obolibrary.org/obo/CHMO_$1", "version": "2025-10-21" }, "chr": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor": { "email": "jhc@lbl.gov", "github": "caufieldjh", "name": "Harry Caufield", "orcid": "0000-0001-5705-7831" }, "description": "The Chromosome Ontology is an automatically derived ontology of chromosomes and chromosome parts.", "download_json": "https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.json", "download_obo": "https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.obo", "download_owl": "https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.owl", "example": "10090-chr10qC", "github_request_issue": 1265, "homepage": "https://github.com/monarch-initiative/monochrom", "keywords": [ "ontology" ], "license": "BSD-3", "mappings": { "aberowl": "CHR", "biocontext": "CHR", "bioportal": "CHR" }, "name": "Chromosome Ontology", "preferred_prefix": "CHR", "repository": "https://github.com/monarch-initiative/monochrom", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "cido": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "description": "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.", "download_owl": "https://github.com/CIDO-ontology/cido/raw/master/cido.owl", "example": "0000005", "homepage": "https://github.com/cido-ontology/cido", "keywords": [ "bioinformatics", "covid-19", "disease", "drug", "drug discovery", "drug interaction", "drug repositioning", "epidemiology", "infection process", "obo", "ontology", "virology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "CIDO", "bioportal": "CIDO", "fairsharing": "FAIRsharing.aVmpKl", "obofoundry": "cido", "ols": "cido", "ontobee": "CIDO", "wikidata.entity": "Q110998476" }, "name": "Coronavirus Infectious Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CIDO", "publications": [ { "doi": "10.1186/s13326-022-00279-z", "pmc": "PMC9585694", "pubmed": "36271389", "title": "A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology", "year": 2022 }, { "doi": "10.1038/s41597-020-0523-6", "pmc": "PMC7293349", "pubmed": "32533075", "title": "CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis", "year": 2020 } ], "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": "2024-02-16" }, "cidoc.crm": { "contact": { "email": "patrick.le-boeuf@bnf.fr", "name": "Patrick Le Bœuf" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The CIDOC Conceptual Reference Model (CRM) is a theoretical and practical tool for information integration in the field of cultural heritage. It can help researchers, administrators and the public explore complex questions with regards to our past across diverse and dispersed datasets. The CIDOC CRM achieves this by providing definitions and a formal structure for describing the implicit and explicit concepts and relationships used in cultural heritage documentation and of general interest for the querying and exploration of such data. Such models are also known as formal ontologies. These formal descriptions allow the integration of data from multiple sources in a software and schema agnostic fashion. [from homepage]", "download_owl": "http://aber-owl.net/media/ontologies/CIDOC-CRM/2/cidoc-crm.owl", "example": "E1", "homepage": "https://cidoc-crm.org", "keywords": [ "anthropology", "coypu", "cultural studies", "culture", "digital planning and construction", "fid baudigital", "history", "humanities and social science", "nfdi4culture", "ontology" ], "logo": "https://cidoc-crm.org/sites/default/files/logo3.png", "mappings": { "aberowl": "CIDOC-CRM", "bioportal": "CIDOC-CRM", "fairsharing": "FAIRsharing.9xcr4z", "tib": "cidoc", "zazuko": "crm" }, "name": "CIDOC Conceptual Reference Model", "preferred_prefix": "cidoc.crm", "uri_format": "http://www.cidoc-crm.org/cidoc-crm/$1" }, "cienciavitae": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier of scientific author in www.cienciavitae.pt", "example": "0C1F-DA6C-4B02", "homepage": "https://www.ciencia-id.pt", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P7893" }, "name": "CIÊNCIAVITAE ID", "pattern": "^([0-9A-F]{4}-){2}[0-9A-F]{4}$", "preferred_prefix": "cienciavitae", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://www.cienciavitae.pt/$1" }, "cio": { "contact": { "email": "frederic.bastian@unil.ch", "github": "fbastian", "name": "Frédéric Bastian", "orcid": "0000-0002-9415-5104" }, "description": "An ontology to capture confidence information about annotations.", "download_obo": "http://purl.obolibrary.org/obo/cio.obo", "download_owl": "http://purl.obolibrary.org/obo/cio.owl", "example": "0000040", "homepage": "https://github.com/BgeeDB/confidence-information-ontology", "keywords": [ "annotation", "biology", "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "CIO", "biocontext": "CIO", "bioportal": "CIO", "fairsharing": "FAIRsharing.e3t0yw", "obofoundry": "cio", "ols": "cio", "ontobee": "CIO", "wikidata.entity": "Q81661853" }, "name": "Confidence Information Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CIO", "publications": [ { "doi": "10.1093/database/bav043", "pmc": "PMC4425939", "pubmed": "25957950", "title": "The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations", "year": 2015 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CIO_$1", "repository": "https://github.com/BgeeDB/confidence-information-ontology", "uri_format": "http://purl.obolibrary.org/obo/CIO_$1", "version": "2015-03-10" }, "citedcat": { "contact": { "email": "andrea.perego@jrc.ec.europa.eu", "github": "andrea-perego", "name": "Andrea Perego", "orcid": "0000-0001-9300-2694" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A vocabuarly for describing the background and methodology for the design of the DataCite profile of DCAT-AP (CiteDCAT-AP), as well as the defined mappings.", "download_rdf": "https://ec-jrc.github.io/datacite-to-dcat-ap/citedcat-ap.ttl", "example": "isSupplementedBy", "homepage": "https://ec-jrc.github.io/datacite-to-dcat-ap/", "keywords": [ "catalogs", "methods" ], "mappings": { "lov": "citedcat" }, "name": "DataCite to DCAT-AP Mapping", "preferred_prefix": "citedcat", "rdf_uri_format": "https://w3id.org/citedcat-ap/$1", "uri_format": "https://w3id.org/citedcat-ap/$1" }, "citexplore": { "contact": { "email": "maria.taboada@usc.es", "name": "Maria Taboada", "orcid": "0000-0002-2353-596X" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes.", "example": "C6155", "homepage": "https://www.ebi.ac.uk/citexplore/", "keywords": [ "biomedical science", "brain", "disease", "genetics", "lipid", "phenotype", "preclinical studies" ], "mappings": { "fairsharing": "FAIRsharing.619eqr", "prefixcommons": "citexplore" }, "name": "CiteXplore", "preferred_prefix": "citexplore", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/citexplore:$1" } ], "publications": [ { "doi": "10.1097/mol.0b013e328362df13", "pubmed": "23759795", "title": "Cerebrotendinous xanthomatosis", "year": 2013 } ], "references": [ "https://www.embl.de/aboutus/communication_outreach/media_relations/2006/061127_hinxton/" ], "synonyms": [ "CTX" ], "uri_format": "https://europepmc.org/article/CTX/$1" }, "cito": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology that enables characterization of the nature or type of citations, both factually and rhetorically.", "download_owl": "https://github.com/SPAROntologies/cito/raw/refs/heads/master/docs/current/cito.owl", "example": "sharesAuthorInstitutionWith", "homepage": "http://www.sparontologies.net/ontologies/cito", "keywords": [ "knowledge and information systems", "ontology", "spar", "tib" ], "mappings": { "fairsharing": "FAIRsharing.b220d4", "lov": "cito", "tib": "cito" }, "name": "Citation Typing Ontology", "preferred_prefix": "CiTO", "publications": [ { "doi": "10.1016/j.websem.2012.08.001", "title": "FaBiO and CiTO: Ontologies for describing bibliographic resources and citations", "year": 2012 } ], "repository": "https://github.com/sparontologies/cito", "twitter": "sparontologies", "uri_format": "http://purl.org/spar/cito/$1" }, "civic.aid": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC.", "example": "3", "homepage": "https://civicdb.org/", "license": "CC0-1.0", "logo": "https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png", "mappings": { "miriam": "civic.aid" }, "name": "CIViC Assertion", "pattern": "^[0-9]+$", "preferred_prefix": "civic.aid", "synonyms": [ "civic.assertion" ], "uri_format": "https://civicdb.org/links/assertions/$1" }, "civic.did": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement.", "example": "46", "homepage": "https://civicdb.org/", "license": "CC0-1.0", "logo": "https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png", "mappings": { "miriam": "civic.did" }, "name": "CIViC Disease", "pattern": "^[0-9]+$", "preferred_prefix": "civic.did", "synonyms": [ "civic.disease" ], "uri_format": "https://civicdb.org/links/diseases/$1" }, "civic.eid": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract).", "example": "1199", "homepage": "https://civicdb.org/", "license": "CC0-1.0", "logo": "https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png", "mappings": { "miriam": "civic.eid" }, "name": "CIViC Evidence", "pattern": "^[0-9]+$", "preferred_prefix": "civic.eid", "synonyms": [ "civic.evidence" ], "uri_format": "https://civicdb.org/links/evidence/$1" }, "civic.gid": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus on emphasizing the clinical relevance from a molecular perspective rather than describing the biological function of the gene unless necessary to contextualize its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes, specific treatments for the gene’s associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis", "example": "272", "homepage": "https://civicdb.org/", "keywords": [ "gene" ], "license": "CC0-1.0", "logo": "https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png", "mappings": { "miriam": "civic.gid", "wikidata": "P11277" }, "name": "CIViC gene", "pattern": "^[0-9]+$", "preferred_prefix": "civic.gid", "synonyms": [ "civic.gene" ], "uri_format": "https://civicdb.org/links/gene/$1" }, "civic.mpid": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "CIViC Molecular Profiles are combinations of one or more CIViC variants. Most Molecular Profiles are “Simple” Molecular Profiles comprised of a single variant. In most cases, these can be considered equivalent to the CIViC concept of a Variant. However, increasingly clinical significance must be considered in the context of multiple variants simultaneously. Complex Molecular Profiles in CIViC allow for curation of such variant combinations. Regardless of the nature of the Molecular Profile (Simple or Complex), it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional clinical relevance to be entered in CIViC.", "example": "559", "homepage": "https://civicdb.org/", "license": "CC0-1.0", "logo": "https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png", "mappings": { "miriam": "civic.mpid" }, "name": "CIViC Molecular Profile", "pattern": "^[0-9]+$", "preferred_prefix": "civic.mpid", "synonyms": [ "civic.molecularprofile" ], "uri_format": "https://civicdb.org/links/molecular_profile/$1" }, "civic.sid": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source.", "example": "62", "homepage": "https://civicdb.org/", "license": "CC0-1.0", "logo": "https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png", "mappings": { "miriam": "civic.sid" }, "name": "CIViC Source", "pattern": "^[0-9]+$", "preferred_prefix": "civic.sid", "synonyms": [ "civic.source" ], "uri_format": "https://civicdb.org/links/sources/$1" }, "civic.tid": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant.", "example": "14", "homepage": "https://civicdb.org/", "license": "CC0-1.0", "logo": "https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png", "mappings": { "miriam": "civic.tid" }, "name": "CIViC Therapy", "pattern": "^[0-9]+$", "preferred_prefix": "civic.tid", "synonyms": [ "civic.therapy" ], "uri_format": "https://civicdb.org/links/drugs/$1" }, "civic.vgid": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "Variant Groups in CIViC provide user-defined grouping of Variants within and between genes based on unifying characteristics. CIViC curators are required to define a cohesive rationale for grouping these variants together, summarize their relevance to cancer diagnosis, prognosis or treatment and highlight any treatments or cancers of particular relevance", "example": "16", "homepage": "https://civicdb.org/", "license": "CC0-1.0", "logo": "https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png", "mappings": { "miriam": "civic.vgid" }, "name": "CIViC Variant Group", "pattern": "^[0-9]+$", "preferred_prefix": "civic.vgid", "synonyms": [ "civic.variantgroup" ], "uri_format": "https://civicdb.org/links/variant_group/$1" }, "civic.vid": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making.", "example": "12", "homepage": "https://civicdb.org/", "license": "CC0-1.0", "logo": "https://civic.readthedocs.io/en/latest/_images/CIViC_logo_for-light-bg_LG_v5a1.png", "mappings": { "miriam": "civic.vid", "wikidata": "P3329" }, "name": "CIViC variant", "pattern": "^[0-9]+$", "preferred_prefix": "civic.vid", "synonyms": [ "civic.variant" ], "uri_format": "https://civicdb.org/links/variant/$1" }, "cl": { "appears_in": [ "clo", "ecao", "ehdaa2", "go", "mco", "pcl", "uberon", "xpo" ], "banana": "CL", "contact": { "email": "do12@sanger.ac.uk", "github": "dosumis", "name": "David Osumi-Sutherland", "orcid": "0000-0002-7073-9172" }, "contributor_extras": [ { "github": "anitacaron", "name": "Anita Caron", "orcid": "0000-0002-6523-4866" } ], "depends_on": [ "go", "ncbitaxon", "omo", "pato", "pr", "ro", "uberon" ], "description": "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.", "download_json": "http://purl.obolibrary.org/obo/cl.json", "download_obo": "https://github.com/obophenotype/cell-ontology/raw/master/cl.obo", "download_owl": "http://purl.obolibrary.org/obo/cl.owl", "example": "0000062", "homepage": "https://obophenotype.github.io/cell-ontology/", "keywords": [ "anatomy", "annotation", "cell", "cell biology", "immunogenetics", "immunology", "life science", "morphology", "obo", "omics", "ontology" ], "license": "CC-BY-4.0", "logo": "https://obofoundry.org/images/CL-logo.jpg", "mappings": { "aberowl": "CL", "agroportal": "CL", "biocontext": "CL", "bioportal": "CL", "cellosaurus": "CL", "fairsharing": "FAIRsharing.j9y503", "go": "CL", "miriam": "cl", "n2t": "cl", "obofoundry": "cl", "ols": "cl", "ontobee": "CL", "prefixcommons": "cl", "wikidata": "P7963", "wikidata.entity": "Q55118285" }, "name": "Cell Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "CL", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cl:$1" }, { "code": "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" } ], "publications": [ { "doi": "10.1186/s13326-016-0088-7", "pmc": "PMC4932724", "pubmed": "27377652", "title": "The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability", "year": 2016 }, { "doi": "10.1186/1471-2105-12-6", "pmc": "PMC3024222", "pubmed": "21208450", "title": "Logical development of the cell ontology", "year": 2011 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CL_$1", "repository": "https://github.com/obophenotype/cell-ontology", "twitter": "CellOntology", "uri_format": "http://purl.obolibrary.org/obo/CL_$1", "version": "2025-12-17" }, "clao": { "contact": { "email": "lagonzalezmo@unal.edu.co", "github": "luis-gonzalez-m", "name": "Luis González-Montaña", "orcid": "0000-0002-9136-9932" }, "depends_on": [ "ro" ], "description": "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).", "download_obo": "http://purl.obolibrary.org/obo/clao.obo", "download_owl": "http://purl.obolibrary.org/obo/clao.owl", "example": "0000088", "homepage": "https://github.com/luis-gonzalez-m/Collembola", "keywords": [ "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "CLAO", "bioportal": "CLAO", "obofoundry": "clao", "ols": "clao", "ontobee": "CLAO", "wikidata.entity": "Q111274067" }, "name": "Collembola Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CLAO", "rdf_uri_format": "http://purl.obolibrary.org/obo/CLAO_$1", "repository": "https://github.com/luis-gonzalez-m/Collembola", "uri_format": "http://purl.obolibrary.org/obo/CLAO_$1", "version": "2021-09-27" }, "clarin.clavas": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Representation of languages", "example": "CDB-00133756-001", "homepage": "https://vocabularies.clarin.eu/clavas/ISO639-3/en/", "keywords": [ "language" ], "name": "CLAVAS: ISO 639-3 Language Codes", "preferred_prefix": "clarin.clavas", "uri_format": "http://cdb.iso.org/lg/$1" }, "clarin.concept": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Concepts for encoding bibliometric information", "example": "CCR_C-3784_55fa12c9-35ad-7b55-b7a5-f9926c801952", "homepage": "https://vocabularies.clarin.eu/clavas/ccr/en/", "name": "CLARIN Concept Registry", "preferred_prefix": "clarin.concept", "uri_format": "http://hdl.handle.net/11459/$1" }, "classyfire": { "banana": "C", "comment": "There's a mismatch between the MIRIAM URI format string, which has a C prefix in front of class identifiers and the ontology which does not use them.", "description": "ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API.", "download_obo": "http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip", "example": "0004828", "homepage": "http://classyfire.wishartlab.com/", "keywords": [ "ontology" ], "mappings": { "miriam": "classyfire" }, "name": "ClassyFire", "pattern": "^\\d{7}$", "preferred_prefix": "classyfire", "synonyms": [ "CHEMONTID", "chemont" ], "uri_format": "http://classyfire.wishartlab.com/tax_nodes/C$1" }, "clb": { "description": "ChecklistBank is an index and repository for taxonomic and nomenclatural datasets", "example": "1010", "homepage": "https://www.checklistbank.org", "mappings": { "miriam": "clb" }, "name": "ChecklistBank", "pattern": "^[0-9]+(LR)?$", "preferred_prefix": "clb", "uri_format": "https://www.checklistbank.org/dataset/$1" }, "cldb": { "description": "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories.", "example": "cl3603", "homepage": "http://bioinformatics.hsanmartino.it/hypercldb/indexes.html", "mappings": { "biocontext": "CLDB", "cellosaurus": "CLDB", "miriam": "cldb", "n2t": "cldb" }, "name": "Cell Line Database", "pattern": "^(cl|tum)\\d+$", "preferred_prefix": "cldb", "synonyms": [ "hypercldb" ], "uri_format": "http://bioinformatics.hsanmartino.it/hypercldb/$1.html" }, "clingen.affiliation": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ClinGen is a National Institutes of Health (NIH)-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This prefix provides identifiers for a panel of experts performing variant pathogenecity evaluation.", "example": "40135", "github_request_issue": 1314, "homepage": "https://clinicalgenome.org/affiliation", "name": "ClinGen Clinical Genome Expert Panel", "preferred_prefix": "clingen.affiliation", "uri_format": "https://clinicalgenome.org/affiliation/$1/" }, "clingen.allele": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "smoxon@lbl.gov", "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" } ], "description": "ClinGen is a National Institutes of Health (NIH)-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This prefix provides and maintains identifiers for alleles.", "example": "CA981206459", "homepage": "https://reg.clinicalgenome.org", "keywords": [ "alleles", "genetics", "mutations" ], "mappings": { "biolink": "CAID" }, "name": "ClinGen Allele Registry", "pattern": "^CA\\d+$", "preferred_prefix": "clingen.allele", "references": [ "https://github.com/biopragmatics/bioregistry/issues/647" ], "synonyms": [ "CAID", "clingene" ], "uri_format": "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1" }, "clingen.curation": { "banana": "CCID", "banana_peel": ":", "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "ClinGen is a National Institutes of Health (NIH)-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This prefix provides identifiers for curations representing evidence aggregation and expert panel assertions based on standardized evaluation procedures", "example": "004126", "github_request_issue": 1414, "homepage": "https://search.clinicalgenome.org/kb/gene-validity", "name": "ClinGen Curation", "pattern": "^\\d{6}$", "preferred_prefix": "clingen.curation", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://search.clinicalgenome.org/CCID:$1" }, "clinicaltrials": { "contact": { "email": "register@clinicaltrials.gov", "name": "ClinicalTrials.gov Helpdesk" }, "description": "ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries", "example": "NCT00222573", "homepage": "https://clinicaltrials.gov/", "keywords": [ "disease", "drug", "human" ], "license": "https://clinicaltrials.gov/about-site/terms-conditions#availability", "logo": "https://clinicaltrials.gov/assets/images/ctg-header-logo.svg", "mappings": { "biocontext": "CLINICALTRIALS", "miriam": "clinicaltrials", "n2t": "clinicaltrials", "prefixcommons": "clinicaltrials", "wikidata": "P3098" }, "name": "ClinicalTrials.gov", "pattern": "^NCT\\d{8}$", "preferred_prefix": "clinicaltrials", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/clinicaltrials:$1" }, { "code": "smartpatients", "description": "Smart Patients is an online community for patients and their families. Join us to talk with other patients about the latest research for your condition.", "homepage": "https://www.smartpatients.com", "name": "Smart Patients", "uri_format": "https://www.smartpatients.com/trials/$1" } ], "synonyms": [ "NCT", "clinicaltrial", "ctgov" ], "uri_format": "https://www.clinicaltrials.gov/study/$1" }, "clinvar.record": { "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession.", "example": "RCV000033555.3", "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", "mappings": { "biocontext": "CLINVAR.RECORD", "miriam": "clinvar.record", "n2t": "clinvar.record" }, "name": "ClinVar Record", "pattern": "^RCV\\d+(\\.\\d+)?$", "preferred_prefix": "clinvar.record", "uri_format": "http://www.ncbi.nlm.nih.gov/clinvar/$1" }, "clinvar.submission": { "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession.", "example": "SCV000151292", "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", "mappings": { "biocontext": "CLINVAR.SUBMISSION", "miriam": "clinvar.submission", "n2t": "clinvar.submission" }, "name": "ClinVar Submission", "pattern": "^SCV\\d+(\\.\\d+)?$", "preferred_prefix": "clinvar.submission", "uri_format": "http://www.ncbi.nlm.nih.gov/clinvar?term=$1" }, "clinvar.submitter": { "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs).", "example": "26957", "homepage": "https://www.ncbi.nlm.nih.gov/clinvar/", "mappings": { "miriam": "clinvar.submitter" }, "name": "ClinVar Submitter", "pattern": "^\\d+$", "preferred_prefix": "clinvar.submitter", "uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1" }, "clinvar.variation": { "contact": { "email": "maglott@ncbi.nlm.nih.gov", "name": "Donna R. Maglott", "orcid": "0000-0001-7451-4467" }, "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier.", "example": "12345", "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", "keywords": [ "biomedical science", "clinical studies", "genomics", "preclinical studies" ], "mappings": { "biocontext": "ClinVarVariant", "biolink": "CLINVAR", "cellosaurus": "ClinVar", "fairsharing": "FAIRsharing.wx5r6f", "hl7": "2.16.840.1.113883.6.319", "integbio": "nbdc01514", "miriam": "clinvar", "n2t": "clinvar", "re3data": "r3d100013331", "togoid": "Clinvar", "wikidata": "P1929" }, "name": "ClinVar Variation", "pattern": "^\\d+$", "preferred_prefix": "clinvar.variation", "publications": [ { "doi": "10.1093/nar/gkt1113", "pmc": "PMC3965032", "pubmed": "24234437", "title": "ClinVar: public archive of relationships among sequence variation and human phenotype", "year": 2013 } ], "synonyms": [ "clinvar", "clinvar.variant" ], "uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1" }, "clm": { "contact": { "email": "davidos@ebi.ac.uk", "github": "dosumis", "name": "David Osumi-Sutherland", "orcid": "0000-0002-7073-9172" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This ontology integrates cell type markers for cells in the Cell Ontology from various sources along with details of marker context (anatomical context, assay), confidence (where available) and provenance. [from repository]", "download_json": "https://github.com/Cellular-Semantics/CellMark/raw/refs/heads/main/clm.json", "download_obo": "https://github.com/Cellular-Semantics/CellMark/raw/refs/heads/main/clm.obo", "download_owl": "https://github.com/Cellular-Semantics/CellMark/raw/refs/heads/main/clm.owl", "example": "1000003", "github_request_issue": 1551, "homepage": "https://github.com/Cellular-Semantics/CellMark", "keywords": [ "ontology" ], "name": "Cell Markers Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CLM", "repository": "https://github.com/Cellular-Semantics/CellMark", "uri_format": "http://purl.obolibrary.org/obo/CLM_$1" }, "clo": { "appears_in": [ "mco" ], "contact": { "email": "zhengj2007@gmail.com", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "depends_on": [ "cl", "doid", "ncbitaxon", "uberon" ], "description": "The Cell Line Ontology is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.", "download_owl": "http://purl.obolibrary.org/obo/clo.owl", "example": "0000091", "homepage": "https://github.com/CLO-Ontology/CLO", "keywords": [ "cell", "cell biology", "cell line", "life science", "morphology", "obo", "ontology" ], "license": "CC-BY-3.0", "logo": "https://avatars.githubusercontent.com/u/12410534", "mappings": { "aberowl": "CLO", "biocontext": "CLO", "bioportal": "CLO", "cellosaurus": "CLO", "fairsharing": "FAIRsharing.4dvtcz", "miriam": "clo", "obofoundry": "clo", "ols": "clo", "ontobee": "CLO", "prefixcommons": "clo", "wikidata": "P2158", "wikidata.entity": "Q21039006" }, "name": "Cell Line Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CLO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/clo:$1" }, { "code": "bioportal", "description": "Our vision is that all biomedical knowledge and data are disseminated on the Internet using principled ontologies in such a way that the knowledge and data are semantically interoperable and useful for furthering biomedical science and clinical care. Our mission is to create software and support services for the application of principled ontologies in biomedical science and clinical care, ranging from tools for application developers to software for end-users.", "homepage": "https://bioportal.bioontology.org", "name": "Center for Biomedical Informatics Research, Stanford", "uri_format": "https://bioportal.bioontology.org/ontologies/CLO/?p=classes&conceptid=http://purl.obolibrary.org/obo/CLO_$1" } ], "publications": [ { "doi": "10.1186/2041-1480-5-37", "pmc": "PMC4387853", "pubmed": "25852852", "title": "CLO: The cell line ontology", "year": 2014 }, { "doi": "10.1186/gb-2005-6-2-r21", "pmc": "PMC551541", "pubmed": "15693950", "title": "An ontology for cell types", "year": 2005 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CLO_$1", "repository": "https://github.com/CLO-Ontology/CLO", "synonyms": [ "CLO" ], "uri_format": "http://purl.obolibrary.org/obo/CLO_$1", "version": "2.1.188" }, "cls": { "description": "Cell line collections (Providers)", "example": "300108/p3934_A-172", "homepage": "https://www.cytion.com/", "mappings": { "cellosaurus": "CLS" }, "name": "Cell Lines Service", "preferred_prefix": "cls", "uri_format": "https://www.cytion.com/$1" }, "clyh": { "contact": { "email": "lucas.leclere@obs-banyuls.fr", "github": "Leclere-L", "name": "Lucas Leclere", "orcid": "0000-0002-7440-0467" }, "depends_on": [ "iao", "ro", "uberon" ], "description": "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica.", "download_obo": "http://purl.obolibrary.org/obo/clyh.obo", "download_owl": "http://purl.obolibrary.org/obo/clyh.owl", "example": "1000100", "homepage": "https://github.com/EBISPOT/clyh_ontology", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "CLYH", "bioportal": "CLYH", "obofoundry": "clyh", "ols": "clyh", "ontobee": "CLYH", "wikidata.entity": "Q111274068" }, "name": "Clytia hemisphaerica Development and Anatomy Ontology", "pattern": "^\\d+$", "preferred_prefix": "CLYH", "rdf_uri_format": "http://purl.obolibrary.org/obo/CLYH_$1", "repository": "https://github.com/EBISPOT/clyh_ontology", "uri_format": "http://purl.obolibrary.org/obo/CLYH_$1", "version": "2020-05-29" }, "cmecs": { "contact": { "email": "kate.rose@noaa.gov", "name": "Kate Rose" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard.", "download_owl": "http://aber-owl.net/media/ontologies/CMECS/2/cmecs.owl", "example": "595", "homepage": "https://cmecscatalog.org/cmecs", "keywords": [ "ecology", "marine ecology", "ontology" ], "mappings": { "aberowl": "CMECS", "bioportal": "CMECS", "ecoportal": "CMECS" }, "name": "Costal and Marine Ecological Classification Standard", "pattern": "^\\d+$", "preferred_prefix": "cmecs", "rdf_uri_format": "https://w3id.org/CMECS/CMECS_$1", "references": [ "http://www.natureserve.org/sites/default/files/publications/files/cmecs_version_06-2012_final.pdf" ], "repository": "https://github.com/NOAA-OCM/cmecs", "uri_format": "https://cmecscatalog.org/cmecs/classification/unit/$1.html" }, "cmf": { "contact": { "email": "engelsta@ohsu.edu", "name": "Mark Engelstad", "orcid": "0000-0001-5889-4463" }, "deprecated": true, "description": "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain", "homepage": "https://code.google.com/p/craniomaxillofacial-ontology/", "keywords": [ "obo", "ontology" ], "mappings": { "aberowl": "CMF", "biocontext": "CMF", "obofoundry": "cmf", "ontobee": "CMF", "wikidata.entity": "Q114677881" }, "name": "CranioMaxilloFacial ontology", "preferred_prefix": "CMF", "rdf_uri_format": "http://purl.obolibrary.org/obo/CMF_$1", "uri_format": "http://purl.obolibrary.org/obo/CMF_$1" }, "cmo": { "appears_in": [ "scdo" ], "contact": { "email": "jrsmith@mcw.edu", "github": "jrsjrs", "name": "Jennifer Smith", "orcid": "0000-0002-6443-9376" }, "description": "Morphological and physiological measurement records generated from clinical and model organism research and health programs.", "download_obo": "http://purl.obolibrary.org/obo/cmo.obo", "download_owl": "http://purl.obolibrary.org/obo/cmo.owl", "example": "0001350", "homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html", "keywords": [ "biomedical science", "disease", "electronic health record", "life science", "model organisms", "obo", "ontology", "phenotype", "preclinical studies" ], "license": "CC0-1.0", "logo": "http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif", "mappings": { "aberowl": "CMO", "biocontext": "CMO", "bioportal": "CMO", "fairsharing": "FAIRsharing.dq78pn", "obofoundry": "cmo", "ols": "cmo", "ontobee": "CMO", "wikidata.entity": "Q81661570" }, "name": "Clinical measurement ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CMO", "publications": [ { "doi": "10.1186/2041-1480-4-26", "pmc": "PMC3882879", "pubmed": "24103152", "title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications", "year": 2013 }, { "doi": "10.3389/fgene.2012.00087", "pmc": "PMC3361058", "pubmed": "22654893", "title": "Three ontologies to define phenotype measurement data", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CMO_$1", "repository": "https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology", "twitter": "ratgenome", "uri_format": "http://purl.obolibrary.org/obo/CMO_$1", "version": "2.263" }, "cmpo": { "contact": { "email": "jupp@ebi.ac.uk", "name": "Simon Jupp", "orcid": "0000-0002-0643-3144" }, "description": "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations.", "download_owl": "http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl", "example": "0000435", "homepage": "http://www.ebi.ac.uk/cmpo", "keywords": [ "bioimaging", "cell", "cell biology", "cellular_component", "imaging", "microscopy", "ontology", "phenomics", "phenotype" ], "mappings": { "aberowl": "CMPO", "bioportal": "CMPO", "fairsharing": "FAIRsharing.knp11s", "ols": "cmpo" }, "name": "Cellular Microscopy Phenotype Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "cmpo", "publications": [ { "doi": "10.1186/s13326-016-0074-0", "pmc": "PMC4870745", "pubmed": "27195102", "title": "The cellular microscopy phenotype ontology", "year": 2016 } ], "repository": "https://github.com/EBISPOT/CMPO", "twitter": "EBIOLS", "uri_format": "http://www.ebi.ac.uk/cmpo/CMPO_$1", "version": "2017-12-19" }, "cncb.gwh": { "contact": { "email": "baoym@big.ac.cn", "name": "Yiming Bao", "orcid": "0000-0002-9922-9723" }, "contributor": { "email": "palayoor.n@northeastern.edu", "github": "nalikapalayoor", "name": "Nalika Palayoor", "orcid": "0009-0008-8406-631X" }, "description": "The China National Center for Bioinformation's (CNCB) Genome Warehouse (GWH) is a public repository holding genetic information for a wide range of species including humans, plants, animals, and microorganisms. Identifiers in this resource correspond to genomes of various species. The goal of the resource is to make genomic data accessible to researchers in areas like precision medicine and biotechnology.", "example": "167047", "github_request_issue": 1452, "homepage": "https://ngdc.cncb.ac.cn/gwh/browse/genome", "name": "CNCB Genome Warehouse", "pattern": "^\\d{6}$", "preferred_prefix": "cncb.gwh", "publications": [ { "doi": "10.1093/gpbjnl/qzaf010", "pubmed": "39977364", "title": "The Updated Genome Warehouse: Enhancing Data Value, Security, and Usability to Address Data Expansion", "year": 2025 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://ngdc.cncb.ac.cn/gwh/Genome/$1/show" }, "cnrs": { "comment": "Motivated to add because of appearance in ROR", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for an academic research group issued by the CNRS", "example": "UMR7315", "example_extras": [ "UPS76" ], "homepage": "https://annuaire.cnrs.fr", "mappings": { "wikidata": "P4550" }, "name": "French National Center for Scientific Research - Research Group Identifier", "pattern": "^(UMR|UMS|UMI|UPR|URA|USR|GDR|EA|FR|SNC|ERL|FRC|FRE|IFR|MOY|UPS)\\d+$", "preferred_prefix": "cnrs", "uri_format": "https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin?&p_lab=$1&p_origine_appel=u" }, "cnt": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This vocabulary is intended to provide a flexible framework within different usage scenarios to semantically represent any type of content, be it on the Web or in local storage media. For example, it can be used by web quality assurance tools such as web accessibility evaluation tools to record a representation of the assessed web content, including text, images, or other types of formats. In many cases, it can be used together with HTTP Vocabulary in RDF 1.0, which allows quality assurance tools to record the HTTP headers that have been exchanged between a client and a server. This is particularly useful for quality assurance testing, conformance claims, and reporting languages like the W3C Evaluation And Report Language (EARL). [from homepage]", "example": "Content", "homepage": "https://www.w3.org/TR/Pointers-in-RDF/#ref-content", "keywords": [ "rdf" ], "mappings": { "bartoc": "17875", "lov": "cnt", "zazuko": "cnt" }, "name": "Representing Content in RDF", "preferred_prefix": "cnt", "rdf_uri_format": "http://www.w3.org/2011/content#$1", "uri_format": "http://www.w3.org/2011/content#$1", "version": "2011" }, "co_320": { "contact": { "email": "j.detras@cgiar.org", "name": "Jeffrey A. Detras", "orcid": "0000-0002-6680-578X" }, "description": "Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables", "example": "0000618", "homepage": "https://cropontology.org/ontology/CO_320/Rice", "keywords": [ "agriculture", "botany", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_320", "cropoct": "CO_320", "fairsharing": "FAIRsharing.2jkxp5", "ols": "co_320" }, "name": "Rice ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_320", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_320:$1", "version": "2019-10-09" }, "co_321": { "contact": { "email": "r.shrestha2@cgiar.org", "name": "Rosemary Shrestha", "orcid": "0000-0002-9399-8003" }, "description": "July 2018", "example": "0000449", "homepage": "https://cropontology.org/ontology/CO_321/Wheat", "keywords": [ "agriculture", "food", "life science", "phenotype" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_321", "cropoct": "CO_321", "fairsharing": "FAIRsharing.czzmpg", "ols": "co_321" }, "name": "Wheat ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_321", "publications": [ { "doi": "10.1093/aobpla/plq008", "pmc": "PMC3000699", "pubmed": "22476066", "title": "Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature", "year": 2010 } ], "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_321:$1", "version": "2019-10-09" }, "co_322": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Maize Trait Dictionary in template 5 - CIMMYT- September 2016", "example": "0000773", "homepage": "https://cropontology.org/ontology/CO_322/Maize", "keywords": [ "agriculture", "botany", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_322", "cropoct": "CO_322", "fairsharing": "FAIRsharing.eeyne8", "ols": "co_322" }, "name": "Maize ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_322", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_322:$1", "version": "2019-10-09" }, "co_323": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Fawzy Nawar" }, "description": "ICARDA - TDv5 - Sept 2018", "example": "0000252", "homepage": "https://cropontology.org/ontology/CO_323/Barley", "keywords": [ "agriculture", "botany", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_323", "cropoct": "CO_323", "fairsharing": "FAIRsharing.f69084", "ols": "co_323" }, "name": "Barley ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_323", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_323:$1", "version": "2019-11-20" }, "co_324": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Sorghum TDv5 - Oct 2019", "example": "0000111", "homepage": "https://cropontology.org/ontology/CO_324/Sorghum", "keywords": [ "agriculture", "botany", "food", "phenotype" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_324", "cropoct": "CO_324", "fairsharing": "FAIRsharing.dxx0c", "ols": "co_324" }, "name": "Sorghum ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_324", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_324:$1", "version": "2019-10-09" }, "co_325": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019", "example": "0000519", "homepage": "https://cropontology.org/ontology/CO_325/Banana", "keywords": [ "agriculture", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_325", "cropoct": "CO_325", "fairsharing": "FAIRsharing.gdszhh", "ols": "co_325" }, "name": "Banana ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_325", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_325:$1", "version": "2019-10-09" }, "co_326": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Draft version", "example": "0000254", "homepage": "https://cropontology.org/ontology/CO_326/Coconut", "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_326", "cropoct": "CO_326", "ols": "co_326" }, "name": "Coconut ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_326", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_326:$1" }, "co_327": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016", "example": "0000095", "homepage": "http://www.cropontology.org/ontology/CO_327/Pearl%20millet", "keywords": [ "agriculture", "botany", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_327", "cropoct": "CO_327", "fairsharing": "FAIRsharing.4e3qh9", "ols": "co_327" }, "name": "Pearl millet ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_327", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_327:$1" }, "co_330": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "CIP - potato ontology - december 2018", "example": "0000106", "homepage": "https://cropontology.org/ontology/CO_330/Potato", "keywords": [ "agriculture", "botany", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_330", "cropoct": "CO_330", "fairsharing": "FAIRsharing.4fa657", "ols": "co_330" }, "name": "Potato ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_330", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_330:$1", "version": "2019-10-09" }, "co_331": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Vilma Hualla Mamani", "orcid": "0000-0003-0595-5271" }, "description": "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019", "example": "0000088", "homepage": "http://www.cropontology.org/ontology/CO_331/Sweet%20Potato", "keywords": [ "agriculture", "botany", "food", "life science" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_331", "cropoct": "CO_331", "fairsharing": "FAIRsharing.4g5qcw", "ols": "co_331" }, "name": "Sweet Potato ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_331", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_331:$1" }, "co_333": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017.", "example": "3000045", "homepage": "http://www.cropontology.org/ontology/CO_333/Beet%20Ontology", "keywords": [ "agriculture", "botany", "food", "life science", "phenotype", "plant breeding", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_333", "cropoct": "CO_333", "fairsharing": "FAIRsharing.af5655", "ols": "co_333" }, "name": "Beet Ontology ontology", "pattern": "^\\d+$", "preferred_prefix": "CO_333", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_333:$1" }, "co_334": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016", "example": "0000070", "homepage": "https://cropontology.org/ontology/CO_334/Cassava", "keywords": [ "agriculture", "botany", "food", "nutritional science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_334", "cropoct": "CO_334", "fairsharing": "FAIRsharing.v06c4q", "ols": "co_334" }, "name": "Cassava ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_334", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_334:$1", "version": "2019-10-09" }, "co_335": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "CIAT Common bean trait dictionary - version August 2014", "example": "0000189", "homepage": "http://www.cropontology.org/ontology/CO_335/Common%20Bean", "keywords": [ "agriculture", "botany", "food" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_335", "cropoct": "CO_335", "fairsharing": "FAIRsharing.a14123", "ols": "co_335" }, "name": "Common Bean ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_335", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_335:$1" }, "co_336": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Soybean Trait Dictionary in template v5 - IITA - July 2015", "example": "0000339", "homepage": "https://cropontology.org/ontology/CO_336/Soybean", "keywords": [ "agriculture", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_336", "cropoct": "CO_336", "fairsharing": "FAIRsharing.j75srj", "ols": "co_336" }, "name": "Soybean ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_336", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_336:$1" }, "co_337": { "contact": { "email": "tm.shah@cgiar.org", "name": "Trushar Shah", "orcid": "0000-0002-0091-7981" }, "description": "Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015", "example": "0000054", "homepage": "https://cropontology.org/ontology/CO_337/Groundnut", "keywords": [ "agriculture", "botany", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_337", "cropoct": "CO_337", "fairsharing": "FAIRsharing.ge8y23", "ols": "co_337" }, "name": "Groundnut ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_337", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_337:$1", "version": "2019-10-09" }, "co_338": { "contact": { "email": "tm.shah@cgiar.org", "name": "Trushar Shah", "orcid": "0000-0002-0091-7981" }, "description": "Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015", "example": "0000138", "homepage": "https://cropontology.org/ontology/CO_338/Chickpea", "keywords": [ "agriculture", "botany", "food", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_338", "cropoct": "CO_338", "fairsharing": "FAIRsharing.js20q3", "ols": "co_338" }, "name": "Chickpea ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_338", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_338:$1", "version": "2019-10-09" }, "co_339": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Lentil Trait Dictionary in template v5 - ICARDA - July 2015", "example": "0000032", "homepage": "https://cropontology.org/ontology/CO_339/Lentil", "keywords": [ "agriculture", "botany", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_339", "cropoct": "CO_339", "fairsharing": "FAIRsharing.ry1ezg", "ols": "co_339" }, "name": "Lentil ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_339", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_339:$1", "version": "2019-10-09" }, "co_340": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Cowpea Trait Dictionary in template v5 - IITA - August 2015", "example": "0000639", "homepage": "https://cropontology.org/ontology/CO_340/Cowpea", "keywords": [ "agriculture", "botany", "food", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_340", "cropoct": "CO_340", "fairsharing": "FAIRsharing.31apg2", "ols": "co_340" }, "name": "Cowpea ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_340", "publications": [ { "doi": "10.3389/fphys.2012.00326", "pmc": "PMC3429094", "pubmed": "22934074", "title": "Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice", "year": 2012 } ], "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_340:$1", "version": "2019-10-09" }, "co_341": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015", "example": "0000140", "homepage": "https://cropontology.org/ontology/CO_341/Pigeonpea", "keywords": [ "agriculture", "botany", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_341", "cropoct": "CO_341", "fairsharing": "FAIRsharing.ehe3yp", "ols": "co_341" }, "name": "Pigeonpea ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_341", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_341:$1", "version": "2019-11-18" }, "co_343": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "version 2019 - pvs", "example": "0100010", "homepage": "https://cropontology.org/ontology/CO_343/Yam", "keywords": [ "agriculture", "botany", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_343", "cropoct": "CO_343", "fairsharing": "FAIRsharing.7e9cff", "ols": "co_343" }, "name": "Yam ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_343", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_343:$1", "version": "2019-10-09" }, "co_345": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Brachiaria (forages) ontology TD v5 - Version Oct 2016", "example": "0000127", "homepage": "https://cropontology.org/ontology/CO_345/Brachiaria", "keywords": [ "agriculture", "botany", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_345", "cropoct": "CO_345", "fairsharing": "FAIRsharing.9e9683", "ols": "co_345" }, "name": "Brachiaria ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_345", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_345:$1", "version": "2019-10-09" }, "co_346": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "oct 2016", "example": "0000199", "homepage": "https://cropontology.org/ontology/CO_346/Mungbean", "keywords": [ "agriculture", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_346", "cropoct": "CO_346", "fairsharing": "FAIRsharing.fgd5gq", "ols": "co_346" }, "name": "Mungbean ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_346", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_346:$1", "version": "2019-10-09" }, "co_347": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "March 2017 version ", "example": "0000108", "homepage": "http://www.cropontology.org/ontology/CO_347/Castor%20bean", "keywords": [ "agriculture", "botany", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_347", "cropoct": "CO_347", "fairsharing": "FAIRsharing.qrrvyk", "ols": "co_347" }, "name": "Castor bean ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_347", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_347:$1" }, "co_348": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France).", "example": "1100107", "homepage": "https://cropontology.org/ontology/CO_348/Brassica", "keywords": [ "agriculture", "botany", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_348", "cropoct": "CO_348", "fairsharing": "FAIRsharing.af7a2d", "ols": "co_348" }, "name": "Brassica ontology", "pattern": "^\\d+$", "preferred_prefix": "CO_348", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_348:$1", "version": "2019-11-29" }, "co_350": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Jean-Luc Jannink", "orcid": "0000-0003-4849-628X" }, "description": "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo", "example": "0000215", "homepage": "https://cropontology.org/ontology/CO_350/Oat", "keywords": [ "agriculture", "botany", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_350", "cropoct": "CO_350", "fairsharing": "FAIRsharing.35e1c3", "ols": "co_350" }, "name": "Oat ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_350", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_350:$1", "version": "2019-10-09" }, "co_356": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Eric Duchêne" }, "description": "Grape Ontology including OIV and bioversity descriptors. INRA July 2017", "example": "4000027", "homepage": "https://cropontology.org/ontology/CO_356/Vitis", "keywords": [ "agriculture", "botany", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_356", "cropoct": "CO_356", "fairsharing": "FAIRsharing.c7f4d7", "ols": "co_356" }, "name": "Vitis ontology", "pattern": "^\\d+$", "preferred_prefix": "CO_356", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_356:$1", "version": "2019-11-29" }, "co_357": { "contact": { "email": "celia.michotey@inrae.fr", "name": "Célia Michotey", "orcid": "0000-0003-1877-1703" }, "description": "This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE.", "example": "1000290", "homepage": "http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology", "keywords": [ "botany", "life science", "phenotype" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_357", "cropoct": "CO_357", "fairsharing": "FAIRsharing.2b04ae", "ols": "co_357" }, "name": "Woody Plant Ontology ontology", "pattern": "^\\d+$", "preferred_prefix": "CO_357", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_357:$1" }, "co_358": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Cotton ontology from CottonGen database - June 2019", "example": "0000139", "homepage": "https://cropontology.org/ontology/CO_358/Cotton", "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_358", "cropoct": "CO_358", "ols": "co_358" }, "name": "Cotton ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_358", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_358:$1", "version": "2020-01-03" }, "co_359": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "December 2019", "example": "0000947", "homepage": "https://cropontology.org/ontology/CO_359/Sunflower", "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_359", "cropoct": "CO_359", "ols": "co_359" }, "name": "Sunflower ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_359", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_359:$1" }, "co_360": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Sugar Kelp trait ontology", "example": "0000071", "homepage": "http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait", "keywords": [ "botany", "life science", "marine environment", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_360", "cropoct": "CO_360", "fairsharing": "FAIRsharing.1c1738", "ols": "co_360" }, "name": "Sugar Kelp trait ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_360", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_360:$1" }, "co_365": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "developed by ICARDA - Dec 2018", "example": "0000205", "homepage": "https://cropontology.org/ontology/CO_365/Fababean", "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_365", "cropoct": "CO_365", "ols": "co_365" }, "name": "Fababean ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_365", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_365:$1", "version": "2019-10-15" }, "co_366": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "version Dec 2019", "example": "0000072", "homepage": "http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut", "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_366", "cropoct": "CO_366", "ols": "co_366" }, "name": "Bambara groundnut ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_366", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_366:$1" }, "co_367": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Quinoa Ontology database of the Crop Ontology (CO_367) of the Generation Challenge Program (GCP) describe traits variables of Quinoa Germinate Database http://germinate.quinoadb.org. Quinoa Phenotyping Consortium Creation Date 23.05.2021", "example": "0000004", "homepage": "http://cropontology.org/term/CO_367:ROOT", "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_367", "cropoct": "CO_367" }, "name": "Quinoa Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_367", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_367:$1" }, "co_370": { "contact": { "email": "ekaterina.chuprikova@eurac.edu", "name": "Ekaterina Chuprikova", "orcid": "0000-0002-8981-0442" }, "description": "Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales. This project has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 894215.", "example": "0000890", "homepage": "http://cropontology.org/term/CO_370:ROOT", "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_370", "cropoct": "CO_370" }, "name": "Apple Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_370", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_370:$1" }, "cob": { "contact": { "email": "bpeters@lji.org", "github": "bpeters42", "name": "Bjoern Peters", "orcid": "0000-0002-8457-6693" }, "description": "COB brings together key terms from a wide range of OBO projects to improve interoperability.", "download_owl": "http://purl.obolibrary.org/obo/cob.owl", "example": "0000080", "homepage": "https://obofoundry.org/COB/", "keywords": [ "dataplant", "life sciences, biology", "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "COB", "bioportal": "COB", "obofoundry": "cob", "ols": "cob", "ontobee": "COB", "tib": "cob", "wikidata.entity": "Q113006456" }, "name": "Core Ontology for Biology and Biomedicine", "pattern": "^\\d{7}$", "preferred_prefix": "COB", "rdf_uri_format": "http://purl.obolibrary.org/obo/COB_$1", "repository": "https://github.com/OBOFoundry/COB", "uri_format": "http://purl.obolibrary.org/obo/COB_$1", "version": "2025-12-12" }, "coconut": { "comment": "@mSorok is the dev of the resource, hope I got it right!", "contributor": { "email": "adriano.rutz@ik.me", "github": "adafede", "name": "Adriano Rutz", "orcid": "0000-0003-0443-9902" }, "description": "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a \"flat\" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties.", "example": "CNP0171505", "example_extras": [ "CNP0018459.2" ], "github_request_issue": 221, "homepage": "https://coconut.naturalproducts.net", "keywords": [ "chemistry", "natural producs", "organic chemistry" ], "mappings": { "re3data": "r3d100014517" }, "name": "COlleCtion of Open Natural ProdUcTs", "pattern": "^CNP\\d{7}(\\.\\d+)?$", "preferred_prefix": "coconut", "publications": [ { "doi": "10.1093/nar/gkae1063", "pubmed": "39588778", "title": "COCONUT 2.0: a comprehensive overhaul and curation of the collection of open natural products database", "year": 2024 }, { "doi": "10.1186/s13321-020-00478-9", "pmc": "PMC7798278", "pubmed": "33423696", "title": "COCONUT online: Collection of Open Natural Products database", "year": 2021 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://coconut.naturalproducts.net/compound/coconut_id/$1" }, "codata.rdmt": { "contact": { "email": "laura@codata.org", "name": "Laura Molloy" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The goal of the CODATA Research Data Management Terminology is to gather the key terms needed for a common understanding of the research data management domain. The RDMT was revised by the CODATA RDM Terminology Working Group, shared for public review, and then confirmed and finalised in 2023.\n\nThe RDMT grew out of the CASRAI Research Data Management Glossary, which was intended as a practical reference for individuals and groups concerned with the improvement of research data management (RDM). In 2020, CASRAI requested that CODATA assume responsibility for the curation of this valued resource. \n\nTo that end, the RDM Terminology Working Group uses a lightweight and pragmatic biennial process to review the resource now restructured as the CODATA RDM Terminology and suggest any edits, additions and removals that are required in order to develop and improve this important reference resource.", "example": "aggregated-data", "homepage": "https://vocabs.ardc.edu.au/viewById/685", "mappings": { "ecoportal": "CODATA-RDMT" }, "name": "CODATA Research Data Management Terminology", "preferred_prefix": "codata.rdmt", "references": [ "https://zenodo.org/records/10626170" ], "uri_format": "https://terms.codata.org/rdmt/$1" }, "codelink": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release).", "example": "GE86325", "homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt", "keywords": [ "microarray", "transcriptomics" ], "name": "GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray", "pattern": "^GE\\d+$", "preferred_prefix": "codelink", "references": [ "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-8060/A-GEOD-8060.adf.txt", "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt" ] }, "coexistence": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "COEXISTENCE - Thesaurus of intersectionality and decolonial issues: black studies, gender, sexuality and feminist studies", "example": "163", "github_request_issue": 1310, "homepage": "https://mamoura.eci.ufmg.br", "name": "COEXISTENCE", "pattern": "^\\d+$", "preferred_prefix": "coexistence", "uri_format": "https://mamoura.eci.ufmg.br/tematres/vocab/index.php?tema=$1" }, "cog.category": { "contact": { "email": "cogs@ncbi.nlm.nih.gov", "name": "Michael Y Galperin", "orcid": "0000-0002-2265-5572" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Higher-level classifications of COG Pathways", "example": "K", "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/", "keywords": [ "pathways" ], "name": "COG Categories", "preferred_prefix": "cog.category", "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1" }, "cog.cluster": { "contact": { "email": "cogs@ncbi.nlm.nih.gov", "name": "Michael Y Galperin", "orcid": "0000-0002-2265-5572" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems.", "example": "COG0001", "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/", "keywords": [ "genome", "life science", "protein" ], "mappings": { "biolink": "COG", "fairsharing": "FAIRsharing.djsbw2", "go": "COG_Cluster", "miriam": "cog", "prefixcommons": "cog", "togoid": "Cog" }, "name": "Cluster of orthologous genes", "pattern": "^COG\\d+$", "preferred_prefix": "cog.cluster", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cog:$1" } ], "publications": [ { "doi": "10.1126/science.278.5338.631", "pubmed": "9381173", "title": "A genomic perspective on protein families", "year": 1997 }, { "doi": "10.1093/nar/gku1223", "pmc": "PMC4383993", "pubmed": "25428365", "title": "Expanded microbial genome coverage and improved protein family annotation in the COG database", "year": 2014 } ], "synonyms": [ "COG_Cluster", "cog" ], "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1" }, "cog.pathway": { "contact": { "email": "cogs@ncbi.nlm.nih.gov", "name": "Michael Y Galperin", "orcid": "0000-0002-2265-5572" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera.", "example": "NAD%20biosynthesis", "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/pathways", "mappings": { "go": "COG_Pathway" }, "name": "COG Pathways", "preferred_prefix": "cog.pathway", "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1" }, "cohd": { "comment": "not really sure where the source is. this also links to a system called athena. I was not able to figure out what COHD stands for.", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012", "homepage": "https://github.com/MIT-LCP/mimic-omop", "keywords": [ "clinical data", "clinical trials", "health", "health sciences" ], "name": "MIMIC III Database", "no_own_terms": true, "preferred_prefix": "cohd", "repository": "https://github.com/MIT-LCP/mimic-omop" }, "cohesindb.binding": { "contact": { "email": "rnakato@iqb.u-tokyo.ac.jp", "name": "Ryuichiro Nakato", "orcid": "0000-0003-3019-5817" }, "contributor": { "email": "maaya.m466@gmail.com", "github": "maayamanoj466", "name": "Maaya Manoj", "orcid": "0009-0000-6974-6386" }, "description": "Contains identifiers of cohesin binding sites in human cells from CohesinDB. CohesinDB includes 2043 epigenomics, transcriptomics and 3D genomics datasets from 530 studies involving 176 cell types. Each cohesin object is annotated with locus, cell type, classification, function, 3D genomics and cis-regulatory information.", "example": "CDBP00415501", "github_request_issue": 1646, "homepage": "https://cohesindb.iqb.u-tokyo.ac.jp", "keywords": [ "binding site", "cohesin", "protein" ], "name": "CohesinDB - cohesin site", "pattern": "^CDBP00\\d{6}$", "preferred_prefix": "cohesindb.binding", "publications": [ { "doi": "10.1093/nar/gkac795", "pmc": "PMC9825609", "pubmed": "36162821", "title": "CohesinDB: a comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells", "year": 2023 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://cohesindb.iqb.u-tokyo.ac.jp/browsepeak/eachpeak/$1" }, "cohesindb.gene": { "contact": { "email": "rnakato@iqb.u-tokyo.ac.jp", "name": "Ryuichiro Nakato", "orcid": "0000-0003-3019-5817" }, "contributor": { "email": "maaya.m466@gmail.com", "github": "maayamanoj466", "name": "Maaya Manoj", "orcid": "0009-0000-6974-6386" }, "description": "Contains identifiers for genes that are part of cohesin regulated CRMs (cis-regulatory modules) from CohesinDB. CohesinDB includes 2043 epigenomics, transcriptomics and 3D genomics datasets from 530 studies involving 176 cell types. Each identifier represents a single cohesin-related CRM. Each cohesin object is annotated with locus, cell type, classification, function, 3D genomics and cis-regulatory information.", "example": "CDBG00009781", "github_request_issue": 1646, "homepage": "https://cohesindb.iqb.u-tokyo.ac.jp", "keywords": [ "gene" ], "name": "CohesinDB gene", "pattern": "^CDBG000\\d{5}$", "preferred_prefix": "cohesindb.gene", "publications": [ { "doi": "10.1093/nar/gkac795", "pmc": "PMC9825609", "pubmed": "36162821", "title": "CohesinDB: a comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells", "year": 2023 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://cohesindb.iqb.u-tokyo.ac.jp/browsegene/eachgene/$1" }, "cohesindb.loops": { "contact": { "email": "rnakato@iqb.u-tokyo.ac.jp", "name": "Ryuichiro Nakato", "orcid": "0000-0003-3019-5817" }, "contributor": { "email": "maaya.m466@gmail.com", "github": "maayamanoj466", "name": "Maaya Manoj", "orcid": "0009-0000-6974-6386" }, "description": "Contains identifiers of cohesin-related chromatin loops from CohesinDB. CohesinDB includes 2043 epigenomics, transcriptomics and 3D genomics datasets from 530 studies involving 176 cell types. Each identifier represents a single cohesin-related chromatin loop. Each cohesin object is annotated with locus, cell type, classification, function, 3D genomics and cis-regulatory information.", "example": "CDBL00540805", "github_request_issue": 1646, "homepage": "https://cohesindb.iqb.u-tokyo.ac.jp", "keywords": [ "chromatin loop", "cohesin", "interaction", "protein" ], "name": "CohesinDB - cohesin-related chromatin loop", "pattern": "^CDBL00\\d{6}$", "preferred_prefix": "cohesindb.loops", "publications": [ { "doi": "10.1093/nar/gkac795", "pmc": "PMC9825609", "pubmed": "36162821", "title": "CohesinDB: a comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells", "year": 2023 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://cohesindb.iqb.u-tokyo.ac.jp/browseloop/eachloop/$1" }, "coi": { "contact": { "email": "coi@bot.uc.pt", "name": "COI Catalogue" }, "contributor": { "email": "shah.tanay2@northeastern.edu", "github": "tanayshah2", "name": "Tanay Shah", "orcid": "0009-0001-1912-5132" }, "description": "COI Catalogue is a herbarium with c. 800.000 specimens, organised in separate collections due to the research priorities over the years.", "example": "63812", "github_request_issue": 1145, "homepage": "https://coicatalogue.uc.pt/index.php", "name": "COI Catalogue", "preferred_prefix": "coi", "publications": [ { "doi": "10.1038/s41597-024-03520-9", "pmc": "PMC11193818", "pubmed": "38909064", "title": "O armário: Fruiting phenology data for 4,462 plant taxa in Portugal (1926-2013)", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://coicatalogue.uc.pt/index.php?t=specimen&COINumber=$1" }, "col": { "description": "Identifier of a taxon or synonym in the Catalogue of Life", "example": "4QHKG", "homepage": "https://www.checklistbank.org", "mappings": { "bartoc": "1915", "miriam": "col", "wikidata.entity": "Q38840" }, "name": "Catalogue of Life", "pattern": "^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$", "preferred_prefix": "col", "providers": [ { "code": "col", "description": "The Catalogue of Life website providing a view onto the latest release of the COL Checklist.", "homepage": "https://www.catalogueoflife.org", "name": "Catalogue of Life (COL)", "uri_format": "https://www.catalogueoflife.org/data/taxon/$1" } ], "uri_format": "https://www.checklistbank.org/dataset/3LR/taxon/$1" }, "col.taiwan": { "contributor": { "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" }, "description": "Identifier (name code) for a taxon in the catalogue of life in taiwan", "example": "431472", "github_request_issue": 466, "homepage": "http://taibnet.sinica.edu.tw/home.php", "mappings": { "wikidata": "P3088" }, "name": "Catalogue of Life in Taiwan", "pattern": "^[1-9]\\d{5}$", "preferred_prefix": "col.taiwan", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1" }, "colao": { "contact": { "email": "entiminae@gmail.com", "github": "JCGiron", "name": "Jennifer C. Giron", "orcid": "0000-0002-0851-6883" }, "depends_on": [ "aism", "bfo", "bspo", "caro", "pato", "ro", "uberon" ], "description": "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research.", "download_obo": "http://purl.obolibrary.org/obo/colao.obo", "download_owl": "http://purl.obolibrary.org/obo/colao.owl", "example": "0000000", "homepage": "https://github.com/insect-morphology/colao", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "COLAO", "bioportal": "COLAO", "obofoundry": "colao", "ols": "colao", "ontobee": "COLAO", "wikidata.entity": "Q113009128" }, "name": "Coleoptera Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "COLAO", "rdf_uri_format": "http://purl.obolibrary.org/obo/COLAO_$1", "repository": "https://github.com/insect-morphology/colao", "uri_format": "http://purl.obolibrary.org/obo/COLAO_$1", "version": "2024-06-21" }, "collagenmutdb": { "description": "This database aims to record all published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP, FKBP10, LEPRE1 and PPIB genes.", "example": "COL3A1", "homepage": "http://www.le.ac.uk/genetics/collagen/", "keywords": [ "gene" ], "mappings": { "prefixcommons": "cmd" }, "name": "Collagen Mutation Database", "preferred_prefix": "collagenmutdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cmd:$1" } ], "provides": "hgnc.symbol", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://eds.gene.le.ac.uk/home.php?select_db=$1" }, "colonatlas": { "description": "Cell line databases/resources", "example": "ALA", "homepage": "http://www.coloncanceratlas.org", "mappings": { "cellosaurus": "ColonAtlas" }, "name": "Colorectal Cancer Atlas", "preferred_prefix": "colonatlas", "uri_format": "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1" }, "combine.specifications": { "description": "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network.", "example": "sed-ml.level-1.version-1", "homepage": "https://co.mbine.org/standards/", "mappings": { "biocontext": "COMBINE.SPECIFICATIONS", "miriam": "combine.specifications", "n2t": "combine.specifications" }, "name": "COMBINE specifications", "pattern": "^\\w+(\\-|\\.|\\w)*$", "preferred_prefix": "combine.specifications", "uri_format": "https://github.com/combine-org/combine-specifications/blob/main/specifications/$1.md" }, "come": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif.", "example": "MOL000160", "homepage": "https://www.flymine.org/come", "keywords": [ "protein" ], "mappings": { "prefixcommons": "come" }, "name": "The Bioinorganic Motif Database", "preferred_prefix": "come", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/come:$1" } ], "synonyms": [ "COMe" ], "uri_format": "https://www.flymine.org/come/entry?gn=$1" }, "commoncoreontology": { "contact": { "email": "mpjensen@buffalo.edu", "github": "mark-jensen", "name": "Mark Jensen", "orcid": "0000-0001-9228-8838" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Common Core Ontologies (CCO) comprise twelve ontologies that are designed to represent and integrate taxonomies of generic classes and relations across all domains of interest.\n\nCCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained by the BFO framework, from which it inherits much of its basic semantic relationships.", "example": "DirectiveInformationContentEntity", "homepage": "http://www.ontologyrepository.com", "keywords": [ "engineering", "nfdi4ing", "ontology", "upper-level ontology" ], "license": "CC-BY-4.0", "mappings": { "tib": "cco" }, "name": "Common Core Ontologies", "preferred_prefix": "commoncoreontology", "repository": "https://github.com/CommonCoreOntology/CommonCoreOntologies", "uri_format": "http://www.ontologyrepository.com/CommonCoreOntologies/$1" }, "complexportal": { "contact": { "email": "sbalu@ebi.ac.uk", "github": "CP-SB", "name": "Sucharitha Balu", "orcid": "0000-0001-7456-0594" }, "description": "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases.", "example": "CPX-263", "homepage": "https://www.ebi.ac.uk/complexportal", "keywords": [ "protein complex" ], "license": "CC0-1.0", "logo": "https://www.ebi.ac.uk/complexportal/assets/images/logo.png", "mappings": { "biocontext": "COMPLEXPORTAL", "biolink": "ComplexPortal", "go": "ComplexPortal", "miriam": "complexportal", "n2t": "complexportal", "re3data": "r3d100013295", "uniprot": "DB-0228", "wikidata": "P7718" }, "name": "Complex Portal", "pattern": "^CPX-[0-9]+$", "preferred_prefix": "complexportal", "publications": [ { "doi": "10.1093/nar/gkae1085", "pmc": "PMC11701666", "pubmed": "39558156", "title": "Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes", "year": 2025 }, { "doi": "10.1093/nar/gky1001", "pubmed": "30357405" }, { "doi": "10.1093/nar/gku975", "pmc": "PMC4384031", "pubmed": "25313161", "title": "The complex portal--an encyclopaedia of macromolecular complexes", "year": 2014 } ], "synonyms": [ "ComplexPortal" ], "uri_format": "https://www.ebi.ac.uk/complexportal/complex/$1" }, "comptox": { "description": "The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks.", "example": "DTXSID2021028", "homepage": "https://comptox.epa.gov/dashboard", "mappings": { "biocontext": "COMPTOX", "miriam": "comptox", "n2t": "comptox", "wikidata": "P3117" }, "name": "DSSTox substance", "pattern": "^DTXSID\\d+$", "preferred_prefix": "comptox", "uri_format": "https://comptox.epa.gov/dashboard/$1" }, "compulyeast": { "deprecated": true, "description": "Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record.", "example": "O08709", "homepage": "http://compluyeast2dpage.dacya.ucm.es/", "keywords": [ "protein" ], "mappings": { "biocontext": "COMPULYEAST", "fairsharing": "FAIRsharing.rbjs3e", "miriam": "compulyeast", "n2t": "compulyeast", "prefixcommons": "compluyeast2dpage" }, "name": "Compluyeast-2D-DB", "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$", "preferred_prefix": "compulyeast", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/compluyeast2dpage:$1" } ], "provides": "uniprot", "uri_format": "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1" }, "condo": { "description": "The COnCEPT upper-level Design Ontology (COnDO).", "example": "AestheticFunction", "homepage": "https://github.com/OntoRep/COnCEPT", "keywords": [ "engineering", "nfdi4ing" ], "mappings": { "tib": "condo" }, "name": "The COnCEPT upper-level Design Ontology", "preferred_prefix": "condo", "uri_format": "http://www.w3id.org/Concept/Ontology/COnDO#$1" }, "conference": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The conference-ontology is a new self-contained ontology for modelleing knowledge about conferences. The conference-ontology adopts best ontology design practices (e.g., Ontology Design Patterns, ontology reuse and interlinking) and guarantees interoperability with SWC ontology and all other pertinent vocabularies. (from homepage)", "download_owl": "https://w3id.org/scholarlydata/ontology/conference-ontology.owl", "example": "isDocumentRelatedTo", "homepage": "http://www.scholarlydata.org/ontology/doc/", "keywords": [ "ontology" ], "license": "CC-BY-3.0", "name": "Conference Ontology", "preferred_prefix": "conference", "uri_format": "https://w3id.org/scholarlydata/ontology/conference-ontology.owl#$1" }, "confident.event": { "contact": { "email": "philip.stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating.", "example": "37af84f2-bfd7-4653-b608-eaff44febba6", "github_request_issue": 519, "homepage": "https://www.confident-conference.org/index.php/Category:Event", "keywords": [ "conferences", "meetings", "metascience" ], "name": "ConfIDent Event", "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$", "preferred_prefix": "confident.event", "uri_format": "https://www.confident-conference.org/index.php/Event:$1" }, "confident.series": { "contact": { "email": "philip.stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating.", "example": "AAC", "github_request_issue": 519, "homepage": "https://www.confident-conference.org/index.php/Category:Event_Series", "keywords": [ "conferences", "grouping", "meetings", "metascience" ], "name": "ConfIDent Event Series", "preferred_prefix": "confident.series", "uri_format": "https://www.confident-conference.org/index.php/Event_Series:$1" }, "conoserver": { "contact": { "email": "d.craik@imb.uq.edu.au", "name": "David Craik", "orcid": "0000-0003-0007-6796" }, "description": "ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails.", "example": "2639", "homepage": "http://www.conoserver.org/", "keywords": [ "life science", "neurophysiology", "statistics", "synthetic biology" ], "mappings": { "biocontext": "CONOSERVER", "fairsharing": "FAIRsharing.y00hz4", "miriam": "conoserver", "n2t": "conoserver", "uniprot": "DB-0156" }, "name": "ConoServer", "pattern": "^\\d+$", "preferred_prefix": "conoserver", "publications": [ { "doi": "10.1093/nar/gkr886", "pmc": "PMC3245185", "pubmed": "22058133", "title": "ConoServer: updated content, knowledge, and discovery tools in the conopeptide database", "year": 2011 }, { "doi": "10.1016/j.toxicon.2010.03.002", "pubmed": "20211197", "title": "Conopeptide characterization and classifications: an analysis using ConoServer", "year": 2010 }, { "doi": "10.1093/bioinformatics/btm596", "pubmed": "18065428", "title": "ConoServer, a database for conopeptide sequences and structures", "year": 2007 }, { "doi": "10.1021/cb700091j", "pubmed": "17649970", "title": "Chemical modification of conotoxins to improve stability and activity", "year": 2007 }, { "doi": "10.1152/physrev.00020.2003", "pubmed": "14715910", "title": "Conus venoms: a rich source of novel ion channel-targeted peptides", "year": 2004 } ], "uri_format": "http://www.conoserver.org/?page=card&table=protein&id=$1" }, "conso": { "contact": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases.", "example": "CONSO00010", "homepage": "https://pharmacome.github.io/conso/", "keywords": [ "biology", "life science", "neurodegeneration", "neuroscience", "ontology" ], "name": "Curation of Neurodegeneration Supporting Ontology", "pattern": "^CONSO\\d{5}$", "preferred_prefix": "conso", "uri_format": "https://pharmacome.github.io/conso/$1" }, "cora": { "description": "This is the OWL implementation of CORA in IEEE 1872-2015. It only includes the taxonomy of concepts and relations, with some few axioms reggarding disjointness, property characteristics and property ranges/domains. The OWL implementation is an underspecified version of the SUO-KIF implementation in IEEE 1872-2015. That is, the set of allowed models of the SUO-KIF implementation is a proper subset of the allowed models by the OWL implementation. Concept definitions in natural language and othe clarifications can be found in the IEEE 1872-2015 standard.", "example": "-bare#CollectiveRoboticSystem", "homepage": "https://github.com/srfiorini/IEEE1872-owl", "keywords": [ "engineering", "nfdi4ing" ], "mappings": { "tib": "cora" }, "name": "Core Ontology for Robotics and Automation", "preferred_prefix": "cora", "uri_format": "http://purl.org/ieee1872-owl/cora$1" }, "coral.como": { "contact": { "email": "JMChandonia@lbl.gov", "github": "jmchandonia", "name": "John-Marc Chandonia", "orcid": "0000-0002-5153-9079" }, "contributor": { "email": "JMChandonia@lbl.gov", "github": "jmchandonia", "name": "John-Marc Chandonia", "orcid": "0000-0002-5153-9079" }, "description": "The Context and Measurement Ontology (COMO) contains ontological terms to describe the context for various types of experimental data and measurements. It is useful in its current state for several different environmental microbiology projects. This ontology is used in multiple CORAL (Contextual Ontology-based Repository Analysis Library) deployments.", "download_obo": "https://raw.githubusercontent.com/jmchandonia/CORAL/refs/heads/main/example/pedometer/ontologies/context_measurement_ontology.obo", "example": "0000001", "github_request_issue": 1360, "homepage": "https://github.com/jmchandonia/CORAL", "keywords": [ "ontology" ], "license": "AGPL-3.0-only", "name": "Contextual Ontology-based Repository Analysis Library - Context and Measurement Ontology", "pattern": "^\\d+$", "preferred_prefix": "coral.como", "publications": [ { "doi": "10.1093/gigascience/giac089", "pmc": "PMC9575582", "pubmed": "36251274", "title": "CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis", "year": 2022 } ], "repository": "https://github.com/jmchandonia/CORAL", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "cordis.article": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).", "example": "436605", "homepage": "https://cordis.europa.eu/", "name": "CORDIS Article", "pattern": "^\\d+$", "preferred_prefix": "cordis.article", "uri_format": "https://cordis.europa.eu/article/id/$1" }, "cordis.project": { "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. 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These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world.", "example": "GM17027", "homepage": "http://ccr.coriell.org/", "mappings": { "biocontext": "Coriell", "cellosaurus": "Coriell", "go": "CORIELL", "miriam": "coriell", "n2t": "coriell" }, "name": "Coriell Institute for Medical Research", "pattern": "^[A-Z]{2}\\d+$", "preferred_prefix": "coriell", "uri_format": "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1" }, "corrdb": { "contact": { "email": "zhu@iastate.edu", "name": "Zhiliang Hu", "orcid": "0000-0002-6704-7538" }, "description": "A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies.", "example": "37232", "homepage": "https://www.animalgenome.org", "keywords": [ "animal genetics", "genetics", "life science", "systems biology" ], "mappings": { "fairsharing": "FAIRsharing.IziuCK", "miriam": "corrdb", "re3data": "r3d100011496" }, "name": "CorrDB", "pattern": "^[0-9]+$", "preferred_prefix": "corrdb", "uri_format": "https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1" }, "corum": { "contact": { "email": "andreas.ruepp@helmholtz-muenchen.de", "name": "Andreas Ruepp", "orcid": "0000-0003-1705-3515" }, "description": "The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded.", "example": "100", "homepage": "https://mips.helmholtz-muenchen.de/corum", "keywords": [ "bioinformatics", "biology", "protein" ], "mappings": { "biocontext": "CORUM", "fairsharing": "FAIRsharing.ohbpNw", "go": "CORUM", "miriam": "corum", "n2t": "corum", "pathguide": "322", "prefixcommons": "corum", "uniprot": "DB-0224" }, "name": "Comprehensive Resource of Mammalian protein complexes", "pattern": "^\\d+$", "preferred_prefix": "corum", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/corum:$1" } ], "publications": [ { "doi": "10.1093/nar/gkae1033", "pubmed": "39526397", "title": "CORUM in 2024: protein complexes as drug targets", "year": 2024 }, { "doi": "10.1093/nar/gkac1015", "pubmed": "36382402" }, { "doi": "10.1093/nar/gky973", "pmc": "PMC6323970", "pubmed": "30357367", "title": "CORUM: the comprehensive resource of mammalian protein complexes-2019", "year": 2019 } ], "uri_format": "https://mips.helmholtz-muenchen.de/corum/?complex_id=$1" }, "cosmic.cell": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer", "example": "906801", "homepage": "https://cancer.sanger.ac.uk/cell_lines/", "mappings": { "cellosaurus": "Cosmic" }, "name": "COSMIC Cell Lines", "pattern": "^\\d+$", "preferred_prefix": "cosmic.cell", "uri_format": "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1" }, "cosmic.gene": { "contact": { "email": "jt6@sanger.ac.uk", "github": "jgtate", "name": "John G Tate", "orcid": "0000-0002-8315-6574" }, "description": "COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes.", "example": "BRAF", "homepage": "http://cancer.sanger.ac.uk/cosmic/", "keywords": [ "biomedical science", "genetics" ], "mappings": { "biocontext": "COSMIC", "edam": "3264", "fairsharing": "FAIRsharing.s5zmbp", "miriam": "cosmic", "n2t": "cosmic" }, "name": "COSMIC Gene", "pattern": "^[A-Z0-9][A-Z0-9-]*$", "preferred_prefix": "cosmic.gene", "provides": "hgnc.symbol", "publications": [ { "doi": "10.1093/nar/gky1015", "pmc": "PMC6323903", "pubmed": "30371878", "title": "COSMIC: the Catalogue Of Somatic Mutations In Cancer", "year": 2019 }, { "doi": "10.1093/nar/gku1075", "pmc": "PMC4383913", "pubmed": "25355519", "title": "COSMIC: exploring the world's knowledge of somatic mutations in human cancer", "year": 2014 }, { "doi": "10.1093/nar/gkq929", "pmc": "PMC3013785", "pubmed": "20952405", "title": "COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer", "year": 2010 }, { "doi": "10.1038/sj.bjc.6601894", "pmc": "PMC2409828", "pubmed": "15188009", "title": "The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website", "year": 2004 } ], "synonyms": [ "cosmic" ], "uri_format": "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1" }, "covid19": { "contact": { "email": "dylan.mcgagh@magd.ox.ac.uk", "name": "Dylan McGagh", "orcid": "0000-0002-6772-2775" }, "description": "Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease.", "download_owl": "http://aber-owl.net/media/ontologies/COVID19/3/covid19.owl", "example": "SFB_COVID19_MW286762", "homepage": "https://covid19.sfb.uit.no", "keywords": [ "ontology" ], "mappings": { "aberowl": "COVID19", "bioportal": "COVID19", "miriam": "covid19" }, "name": "COVID-19 Surveillance Ontology", "pattern": "^\\w+_COVID19_[-\\w]+$", "preferred_prefix": "covid19", "uri_format": "https://covid19.sfb.uit.no/api/records/$1" }, "covoc": { "contact": { "email": "zmp@ebi.ac.uk", "github": "zoependlington", "name": "Zoë May Pendlington", "orcid": "0000-0002-4071-8397" }, "description": "The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.", "download_json": "https://github.com/EBISPOT/covoc/releases/download/current/covoc.json", "download_obo": "https://github.com/EBISPOT/covoc/releases/download/current/covoc.obo", "download_owl": "https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl", "example": "0010034", "homepage": "https://github.com/EBISPOT/covoc", "keywords": [ "ontology" ], "mappings": { "ols": "covoc" }, "name": "CoVoc Coronavirus Vocabulary", "pattern": "^\\d{7}$", "preferred_prefix": "covoc", "repository": "https://github.com/EBISPOT/covoc", "uri_format": "http://purl.obolibrary.org/obo/COVOC_$1", "version": "2022-10-26" }, "coypu": { "description": "Ontology to describe companies and their supply network, employees, products, production materials, industries, events and relations.", "example": "AbductionOrForcedDisappearance", "homepage": "https://gitlab.com/coypu-project/coy-ontology", "keywords": [ "coypu", "economics" ], "mappings": { "tib": "coy" }, "name": "CoyPu Ontology", "preferred_prefix": "coypu", "uri_format": "https://schema.coypu.org/global#$1" }, "coypu.emdat": { "description": "Crisis and hazard related taxonomy developed by CRED for disaster preparedness and humanitarian actions at national and international level.", "example": "Air", "homepage": "https://schema.coypu.org/em-dat/1.0", "keywords": [ "coypu", "earth sciences", "life sciences, biology" ], "mappings": { "tib": "emdat" }, "name": "EM-DAT Disaster Classification Ontology", "preferred_prefix": "coypu.emdat", "uri_format": "https://schema.coypu.org/em-dat#$1" }, "coypu.gta": { "description": "An ontology for modeling global trade alerts, mainly inspired by the Global Trade Alerts repository.", "example": "AffectedCommercialFlow", "homepage": "https://schema.coypu.org/gta/1.0", "keywords": [ "coypu", "economics" ], "mappings": { "tib": "gta" }, "name": "Global Trade Alerts Ontology", "preferred_prefix": "coypu.gta", "uri_format": "https://schema.coypu.org/gta#$1" }, "coypu.ta": { "description": "An ontology for modeling trade agreements", "example": "CustomsUnion", "homepage": "https://schema.coypu.org/ta/1.0", "keywords": [ "coypu", "economics" ], "mappings": { "tib": "ta" }, "name": "Trade Agreement Ontology", "preferred_prefix": "coypu.ta", "uri_format": "https://schema.coypu.org/ta#$1" }, "coypu.tiva": { "description": "An ontology for modeling international trade flows.", "example": "hasExport", "homepage": "https://gitlab.com/coypu-project/coy-ontology/", "keywords": [ "coypu", "economics" ], "mappings": { "tib": "tiva" }, "name": "OECD TIVA Ontology", "preferred_prefix": "coypu.tiva", "uri_format": "https://schema.coypu.org/vtf#$1" }, "cp": { "appears_in": [ "cl" ], "comment": "Part of cell ontology but deprecated, see https://github.com/obophenotype/cell-ontology/issues/572", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "name": "Cellular Phenotypes", "preferred_prefix": "cp" }, "cpc": { "description": "The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). 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No provider of outpatient services gets paid without reporting the proper CPT® codes. 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It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.", "example": "D053716", "homepage": "http://ctdbase.org/", "mappings": { "biocontext": "CTD.DISEASE", "biolink": "CTD.DISEASE", "miriam": "ctd.disease", "n2t": "ctd.disease" }, "name": "CTD Disease", "pattern": "^D\\d+$", "preferred_prefix": "ctd.disease", "provides": "mesh", "uri_format": "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1" }, "ctd.gene": { "contact": { "email": "apdavis3@ncsu.edu", "name": "Allan Peter Davis", "orcid": "0000-0002-5741-7128" }, "description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. 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The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.", "example": "101", "homepage": "http://ctdbase.org/", "mappings": { "biocontext": "CTD.GENE", "biolink": "CTD.GENE", "miriam": "ctd.gene", "n2t": "ctd.gene", "uniprot": "DB-0140" }, "name": "CTD Gene", "pattern": "^\\d+$", "preferred_prefix": "ctd.gene", "provides": "ncbigene", "publications": [ { "doi": "10.1093/nar/gkaa891", "pmc": "PMC7779006", "pubmed": "33068428", "title": "Comparative Toxicogenomics Database (CTD): update 2021", "year": 2021 } ], "uri_format": "http://ctdbase.org/detail.go?type=gene&acc=$1" }, "cteno": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "depends_on": [ "ro", "uberon" ], "description": "An anatomical and developmental ontology for ctenophores (Comb Jellies)", "download_obo": "https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo", "download_owl": "http://purl.obolibrary.org/obo/cteno.owl", "example": "0000047", "homepage": "https://github.com/obophenotype/ctenophore-ontology", "keywords": [ "anatomy", "developmental biology", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "CTENO", "biocontext": "CTENO", "bioportal": "CTENO", "fairsharing": "FAIRsharing.mgxgza", "obofoundry": "cteno", "ols": "cteno", "ontobee": "CTENO", "wikidata.entity": "Q81661576" }, "name": "Ctenophore Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CTENO", "rdf_uri_format": "http://purl.obolibrary.org/obo/CTENO_$1", "repository": "https://github.com/obophenotype/ctenophore-ontology", "uri_format": "http://purl.obolibrary.org/obo/CTENO_$1", "version": "2016-10-19" }, "ctis": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This website supports the undertaking and oversight of clinical trials in the European Union (EU) and European Economic Area (EEA). It is part of a broad initiative to transform the EU/EEA clinical trials environment in support of large clinical trials in multiple European countries, to the benefit of medical innovation and patients. (from homepage)", "example": "2023-503698-40-00", "homepage": "https://euclinicaltrials.eu/", "name": "Clinical Trials Information System", "pattern": "^\\d{4}-\\d+-\\d+-\\d+$", "preferred_prefix": "ctis", "uri_format": "https://euclinicaltrials.eu/app/#/view/$1" }, "cto": { "contact": { "email": "alpha.tom.kodamullil@scai.fraunhofer.de", "github": "akodamullil", "name": "Dr. Alpha Tom Kodamullil", "orcid": "0000-0001-9896-3531" }, "description": "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials.", "download_owl": "http://purl.obolibrary.org/obo/cto.owl", "example": "0000022", "homepage": "https://github.com/ClinicalTrialOntology/CTO/", "keywords": [ "biomedical science", "disease", "neurobiology", "obo", "ontology", "preclinical studies" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "CTO", "bioportal": "CTO", "fairsharing": "FAIRsharing.qp211a", "obofoundry": "cto", "ols": "cto", "ontobee": "CTO", "wikidata.entity": "Q113009139" }, "name": "Clinical Trials Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CTO", "publications": [ { "pubmed": "35992013", "title": "CTO: a Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView", "year": 2020 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CTO_$1", "repository": "https://github.com/ClinicalTrialOntology/CTO", "uri_format": "http://purl.obolibrary.org/obo/CTO_$1", "version": "1.0.0" }, "ctri": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The mission of the Clinical Trials Registry-India (CTRI) is to ensure that all clinical trials conducted in India are prospectively registered, i.e. before the enrolment of the first participant. Additionally, post-marketing surveillance studies, BA/BE studies as well as clinical studies as part of PG thesis are also expected to be registered in the CTRI. (from homepage)\n\nNote that the identifier in this semantic space is not the one used in the webpages", "example": "CTRI/2023/04/052053", "homepage": "https://ctri.nic.in", "name": "India Clinical Trials Registry", "pattern": "^CTRI/\\d{4}/\\d{2,3}/\\d+$", "preferred_prefix": "ctri", "references": [ "https://www.ctri.nic.in/Clinicaltrials/pmaindet2.php?trialid=82487" ], "uri_format": "https://trialsearch.who.int/Trial2.aspx?TrialID=$1" }, "cubedb": { "comment": "website down as of 2021-10-04", "deprecated": true, "description": "Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available.", "example": "AKR", "homepage": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html", "mappings": { "biocontext": "CUBEDB", "integbio": "nbdc02094", "miriam": "cubedb", "n2t": "cubedb" }, "name": "Cube db", "pattern": "^[A-Za-z_0-9]+$", "preferred_prefix": "cubedb", "uri_format": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/" }, "cutg": { "description": "Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank.", "example": "9606", "homepage": "http://www.kazusa.or.jp/codon/", "keywords": [ "dna", "gene" ], "mappings": { "prefixcommons": "cutg" }, "name": "Codon Usage Tabulated from GenBank", "preferred_prefix": "cutg", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cutg:$1" } ], "provides": "ncbitaxon", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=$1" }, "cvdo": { "contact": { "email": "paul.fabry@usherbrooke.ca", "github": "pfabry", "name": "Paul Fabry", "orcid": "0000-0002-3336-2476" }, "description": "An ontology to describe entities related to cardiovascular diseases", "download_owl": "http://purl.obolibrary.org/obo/cvdo.owl", "example": "0000546", "homepage": "https://github.com/OpenLHS/CVDO", "keywords": [ "cardiology", "cardiovascular disease", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "CVDO", "biocontext": "CVDO", "bioportal": "CVDO", "fairsharing": "FAIRsharing.2basyz", "obofoundry": "cvdo", "ols": "cvdo", "ontobee": "CVDO", "wikidata.entity": "Q55118269" }, "name": "Cardiovascular Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CVDO", "rdf_uri_format": "http://purl.obolibrary.org/obo/CVDO_$1", "repository": "https://github.com/OpenLHS/CVDO", "uri_format": "http://purl.obolibrary.org/obo/CVDO_$1", "version": "2024-05-17" }, "cvx": { "contact": { "email": "iisinfo@cdc.gov", "name": "IIS Helpdesk" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The CDC's National Center of Immunization and Respiratory Diseases (NCIRD) developed and maintains the CVX (vaccine administered) code set. The table below has the most up to date values. It includes both active and inactive vaccines available in the US. CVX codes for inactive vaccines allow transmission of historical immunization records.", "example": "54", "homepage": "https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx", "keywords": [ "vaccine" ], "logo": "https://www2.cdc.gov/TemplatePackage/4.0/assets/imgs/logo/logo-notext.svg", "mappings": { "hl7": "2.16.840.1.113883.6.59" }, "name": "Vaccine administered code set", "pattern": "^\\d+$", "preferred_prefix": "cvx", "uri_format": "https://biopragmatics.github.io/providers/cvx/$1" }, "d1id": { "description": "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences.", "example": "00030692-0FE1-4A1B-955E-A2E55D659267", "homepage": "https://www.dataone.org", "mappings": { "biocontext": "D1ID", "miriam": "d1id", "n2t": "d1id" }, "name": "DataONE", "pattern": "^\\S+$", "preferred_prefix": "d1id", "uri_format": "https://cn.dataone.org/cn/v2/resolve/%7B$1%7D" }, "dai.thesauri": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A thesaurus of terms useful for digital archaeology", "example": "_fe65f286", "homepage": "http://thesauri.dainst.org/en.html", "name": "German Archaeological Institute Thesaurus", "preferred_prefix": "dai.thesauri", "uri_format": "http://thesauri.dainst.org/en/concepts/$1" }, "dailymed": { "description": "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read.", "example": "973a9333-fec7-46dd-8eb5-25738f06ee54", "homepage": "https://dailymed.nlm.nih.gov/dailymed/", "mappings": { "biocontext": "DAILYMED", "miriam": "dailymed", "n2t": "dailymed", "prefixcommons": "dailymed" }, "name": "DailyMed", "pattern": "^[A-Za-z0-9-]+$", "preferred_prefix": "dailymed", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/dailymed:$1" } ], "uri_format": "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1" }, "dalia.community": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A UUID for a community indexed in the Data Liteacy Alliance (DALIA) web application", "example": "bead62a8-c3c2-46d6-9eb1-ffeaba38d5bf", "github_request_issue": 1616, "homepage": "https://search.dalia.education", "name": "DALIA Community", "pattern": "^[A-Za-z0-9]{8}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{12}$", "preferred_prefix": "dalia.community", "uri_format": "https://search.dalia.education/communities/$1" }, "dalia.oer": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A UUID for an open educational resource indexed in the Data Liteacy Alliance (DALIA) web application", "example": "69aebdfe-73f6-4bac-85d7-047dd8cec076", "github_request_issue": 1616, "homepage": "https://search.dalia.education", "name": "DALIA Open Educational Resource", "pattern": "^[A-Za-z0-9]{8}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{12}$", "preferred_prefix": "dalia.oer", "uri_format": "https://search.dalia.education/items/$1" }, "daml.pt": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A representation of the periodic table of the elements in OWL, with both elements and a hierarchical classification. This is from the DARPA Agent Markup Language (DAML) project, which has been inactive since the mid 2000's.", "download_owl": "https://www.daml.org/2003/01/periodictable/PeriodicTable.owl", "example": "Be", "example_extras": [ "Metallic", "Non-metallic" ], "github_request_issue": 1419, "homepage": "https://www.daml.org/2003/01/periodictable/", "keywords": [ "ontology" ], "name": "DAML Periodic Table of the Elements", "preferred_prefix": "daml.pt", "uri_format": "http://www.daml.org/2003/01/periodictable/PeriodicTable#$1" }, "dandi": { "contact": { "email": "yoh@dartmouth.edu", "name": "Yaroslav Halchenko", "orcid": "0000-0003-3456-2493" }, "description": "DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable).\nDANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data.\nThese data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.", "example": "000017", "homepage": "https://dandiarchive.org/", "keywords": [ "neurophysiology" ], "mappings": { "fairsharing": "FAIRsharing.f2c119", "miriam": "dandi", "re3data": "r3d100013638" }, "name": "Distributed Archives for Neurophysiology Data Integration", "pattern": "^\\d{6}(\\/\\d+\\.\\d+\\.\\d+)?$", "preferred_prefix": "dandi", "repository": "https://github.com/dandi/dandiarchive", "twitter": "dandiarchive", "uri_format": "https://dandiarchive.org/dandiset/$1" }, "darc": { "contact": { "email": "daniel.wilson@uni-hamburg.de", "name": "Daniel N. Wilson", "orcid": "0000-0003-3816-3828" }, "deprecated": true, "description": "DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.", "example": "1250", "homepage": "http://darcsite.genzentrum.lmu.de/darc/index.php", "keywords": [ "life science" ], "mappings": { "biocontext": "DARC", "fairsharing": "FAIRsharing.evfe2s", "miriam": "darc", "n2t": "darc" }, "name": "Database of Aligned Ribosomal Complexes", "pattern": "^\\d+$", "preferred_prefix": "darc", "publications": [ { "doi": "10.1093/nar/gkr824", "pmc": "PMC3245104", "pubmed": "22009674", "title": "The DARC site: a database of aligned ribosomal complexes", "year": 2011 } ], "uri_format": "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1" }, "dashr.expression": { "description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression.", "example": "hsa-mir-200a", "homepage": "https://dashr1.lisanwanglab.org/show-expression-table.php?start=0", "mappings": { "biocontext": "DASHR.EXPRESSION", "miriam": "dashr.expression", "n2t": "dashr.expression" }, "name": "DASHR expression", "pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$", "preferred_prefix": "dashr.expression", "uri_format": "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable" }, "dashr.rna": { "contact": { "email": "dashr@lisanwanglab.org", "name": "Li-San Wang", "orcid": "0000-0002-3684-0031" }, "description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records.", "example": "hsa-mir-200a", "homepage": "http://lisanwanglab.org/DASHR/", "keywords": [ "life science" ], "mappings": { "biocontext": "DASHR", "fairsharing": "FAIRsharing.ztvs34", "miriam": "dashr", "n2t": "dashr" }, "name": "Database of small human noncoding RNAs", "pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$", "preferred_prefix": "dashr.rna", "publications": [ { "doi": "10.1093/nar/gkv1188", "pmc": "PMC4702848", "pubmed": "26553799", "title": "DASHR: database of small human noncoding RNAs", "year": 2015 } ], "synonyms": [ "dashr" ], "uri_format": "http://lisanwanglab.org/DASHR/entry/$1" }, "datacite": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF.", "download_owl": "http://aber-owl.net/media/ontologies/DATACITE/3/datacite.owl", "example": "AgentIdentifierScheme", "homepage": "http://www.sparontologies.net/ontologies/datacite", "keywords": [ "ontology", "subject agnostic" ], "mappings": { "aberowl": "DATACITE", "bioportal": "DATACITE", "fairsharing": "FAIRsharing.c06f1e" }, "name": "DataCite Ontology", "preferred_prefix": "DataCite", "repository": "https://github.com/sparontologies/datacite", "twitter": "datacite", "uri_format": "http://purl.org/spar/datacite/$1" }, "datacommons": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A large RDF store built from American governmental data. This semantic space has a mixture of direct terms and subspaces.", "example": "Gene", "homepage": "https://datacommons.org", "mappings": { "biolink": "dcid" }, "name": "Data Commons", "preferred_prefix": "datacommons", "repository": "https://github.com/datacommonsorg/website", "synonyms": [ "dcid" ], "uri_format": "https://datacommons.org/browser/$1" }, "datanator.gene": { "description": "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.", "example": "K00973", "homepage": "https://datanator.info/", "mappings": { "miriam": "datanator.gene" }, "name": "Datanator Gene", "pattern": "^K[0-9]+$", "preferred_prefix": "datanator.gene", "uri_format": "https://www.datanator.info/gene/$1" }, "datanator.metabolite": { "description": "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.", "example": "OUYCCCASQSFEME-MRVPVSSYSA-N", "homepage": "https://datanator.info/", "mappings": { "miriam": "datanator.metabolite" }, "name": "Datanator Metabolite", "pattern": "^[A-Z\\-]+$", "preferred_prefix": "datanator.metabolite", "uri_format": "https://www.datanator.info/metabolite/$1" }, "datanator.reaction": { "description": "\tDatanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.", "example": "XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N", "homepage": "https://icahn.mssm.edu/", "mappings": { "miriam": "datanator.reaction" }, "name": "Datanator Reaction", "pattern": "^.*?--%3E.*?$", "preferred_prefix": "datanator.reaction", "uri_format": "https://datanator.info/reaction/$1" }, "datf": { "deprecated": true, "description": "DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals.", "example": "AT1G01030.1", "homepage": "http://datf.cbi.pku.edu.cn/", "keywords": [ "regulation" ], "mappings": { "biocontext": "DATF", "miriam": "datf", "n2t": "datf", "pathguide": "518", "prefixcommons": "datf" }, "name": "Database of Arabidopsis Transcription Factors", "pattern": "^AT[1-5]G\\d{5}(\\.\\d+)?$", "preferred_prefix": "datf", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/datf:$1" } ], "uri_format": "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1" }, "dbamp": { "banana": "dbAMP", "banana_peel": "_", "contact": { "email": "leetzongyi@nycu.edu.tw", "name": "Tzong-Yi Lee", "orcid": "0000-0001-8475-7868" }, "contributor": { "email": "ji.kang@northeastern.edu", "github": "kanghosaeyo", "name": "Kangho Ji", "orcid": "0009-0009-3402-8013" }, "description": "Identifiers represent antimicrobial peptides in the Database of Antimicrobial Peptides (dbAMP) which is an open-access, manually curated database of antimicrobial peptides (AMPs).", "example": "28463", "github_request_issue": 1714, "homepage": "https://awi.cuhk.edu.cn/dbAMP/", "keywords": [ "antimicrobial peptides" ], "logo": "https://awi.cuhk.edu.cn/dbAMP/assets/img/dbAMPv2.svg", "mappings": { "integbio": "nbdc02467" }, "name": "Database of Anti-Microbial Peptides", "pattern": "^\\d{5}$", "preferred_prefix": "dbamp", "providers": [ { "code": "abpdb", "description": "Antimicrobial Peptide Database (ABPDB) is a comprehensive database that aggregates antimicrobial peptide data from DRAMP and dbAMP.", "homepage": "http://www.acdb.plus/ABPDB/", "name": "AntiBacterial Peptides DataBase", "publications": [ { "doi": "10.1109/tcbbio.2025.3582844", "pubmed": "40811252", "title": "ABPDB: a Database of Antibacterial Peptides", "year": 2025 } ], "uri_format": "http://www.acdb.plus/ABPDB/abp-search.php?keywords=dbAMP$1" } ], "publications": [ { "doi": "10.1109/tcbbio.2025.3582844", "pubmed": "40811252", "title": "ABPDB: a Database of Antibacterial Peptides", "year": 2025 }, { "doi": "10.1093/nar/gkae1019", "pmc": "PMC11701527", "pubmed": "39540425", "title": "dbAMP 3.0: updated resource of antimicrobial activity and structural annotation of peptides in the post-pandemic era", "year": 2025 }, { "doi": "10.1093/nar/gkab1080", "pmc": "PMC8690246", "pubmed": "34850155", "title": "dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data", "year": 2022 }, { "doi": "10.1093/nar/gky1030", "pmc": "PMC6323920", "pubmed": "30380085", "title": "dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data", "year": 2019 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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It does not include basal transcription factors or chromatin-associated proteins.", "example": "0045310", "homepage": "http://www.transcriptionfactor.org/", "keywords": [ "genome", "regulation" ], "mappings": { "biocontext": "DBD", "edam": "2716", "miriam": "dbd", "n2t": "dbd", "pathguide": "496", "prefixcommons": "dbd" }, "name": "Transcription Factor Database", "pattern": "^\\d+$", "preferred_prefix": "dbd", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/dbd:$1" } ], "uri_format": "http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD" }, "dbest": { "contact": { "email": "tmjlowe@ucsc.edu", "name": "Todd M Lowe", "orcid": "0000-0003-3253-6021" }, "description": "The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms.", "example": "BP100000", "homepage": "https://www.ncbi.nlm.nih.gov/nucest", "keywords": [ "bioinformatics", "dna", "life science" ], "mappings": { "biocontext": "DBEST", "edam": "1105", "fairsharing": "FAIRsharing.v9fya8", "integbio": "nbdc00413", "miriam": "dbest", "n2t": "dbest", "ncbi": "dbEST", "prefixcommons": "dbest", "re3data": "r3d100010648" }, "name": "EST database maintained at the NCBI.", "pattern": "^([A-Z]+)?\\d+(\\.\\d+)?$", "preferred_prefix": "dbest", "providers": [ { "code": "", "description": "dbEST through DNA Data Bank of Japan (DDBJ)", "homepage": "http://www.ddbj.nig.ac.jp/", "name": "dbEST through DNA Data Bank of Japan (DDBJ)", "uri_format": "https://getentry.ddbj.nig.ac.jp/getentry/na/$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/dbest:$1" }, { "code": "ebi", "description": "dbEST through European Nucleotide Archive (ENA)", "homepage": "https://www.ebi.ac.uk/ena", "name": "dbEST through European Nucleotide Archive (ENA)", "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" } ], "publications": [ { "doi": "10.1038/ng0893-332", "pubmed": "8401577", "title": "dbEST--database for \"expressed sequence tags\"", "year": 1993 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/nucest/$1" }, "dbg2introns": { "contact": { "email": "zimmerly@ucalgary.ca", "name": "Steven John Zimmerly" }, "deprecated": true, "description": "The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank.", "example": "Cu.me.I1", "homepage": "http://webapps2.ucalgary.ca/~groupii/", "keywords": [ "dna" ], "mappings": { "biocontext": "DBG2INTRONS", "miriam": "dbg2introns", "n2t": "dbg2introns", "prefixcommons": "mgiid" }, "name": "DBG2 Introns", "pattern": "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$", "preferred_prefix": "dbg2introns", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/mgiid:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr1043", "pmc": "PMC3245105", "pubmed": "22080509", "title": "Database for bacterial group II introns", "year": 2011 } ], "uri_format": "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1" }, "dbgap": { "contact": { "email": "feolo@ncbi.nlm.nih.gov", "github": "mfeolo", "name": "Michael Feolo", "orcid": "0000-0002-1650-5156" }, "description": "The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype.", "example": "phs000768.v2.p1", "homepage": "https://www.ncbi.nlm.nih.gov/gap/", "keywords": [ "biomedical science", "epigenetics", "genetics" ], "mappings": { "biocontext": "DBGAP", "cellosaurus": "dbGAP", "fairsharing": "FAIRsharing.88v2k0", "integbio": "nbdc00414", "miriam": "dbgap", "n2t": "dbgap" }, "name": "Database of Genotypes and Phenotypes", "pattern": "^phs[0-9]{6}(.v\\d+.p\\d+)?$", "preferred_prefix": "dbgap", "publications": [ { "doi": "10.1093/nar/gkt1211", "pmc": "PMC3965052", "pubmed": "24297256", "title": "NCBI's Database of Genotypes and Phenotypes: dbGaP", "year": 2013 }, { "doi": "10.1038/ng1007-1181", "pmc": "PMC2031016", "pubmed": "17898773", "title": "The NCBI dbGaP database of genotypes and phenotypes", "year": 2007 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1" }, "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", "uri_format": "https://dblp.org/pid/$1" }, "dbmhc": { "appears_in": [ "cellosaurus" ], "deprecated": true, "description": "Cell line databases/resources", "example": "48439", "homepage": "https://www.ncbi.nlm.nih.gov/gv/mhc/", "mappings": { "cellosaurus": "dbMHC", "integbio": "nbdc01831" }, "name": "Database of human Major Histocompatibility Complex", "pattern": "^\\d+$", "preferred_prefix": "dbmhc" }, "dbo": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki.", "example": "careerPrizeMoney", "github_request_issue": 515, "homepage": "https://dbpedia.org/ontology", "keywords": [ "dbpedia", "ontology" ], "mappings": { "zazuko": "dbo" }, "name": "DBPedia Ontology", "preferred_prefix": "dbo", "uri_format": "https://dbpedia.org/ontology/$1" }, "dbpedia.property": { "appears_in": [ "fovt" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Properties in DBPedia.", "example": "insertion", "github_request_issue": 1420, "homepage": "http://dbpedia.org/property", "name": "DBPedia Property", "preferred_prefix": "dbpedia.property", "uri_format": "http://dbpedia.org/property/$1" }, "dbpedia.resource": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A semi-automatically generated knowledgebase", "example": "Grenada", "github_request_issue": 1315, "homepage": "https://dbpedia.org", "mappings": { "re3data": "r3d100011713" }, "name": "DBPedia Resource", "preferred_prefix": "dbpedia.resource", "synonyms": [ "dbpedia", "dbr" ], "uri_format": "http://dbpedia.org/resource/$1" }, "dbprobe": { "deprecated": true, "description": "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.", "example": "1000000", "homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe", "keywords": [ "nucleotide" ], "mappings": { "biocontext": "DBPROBE", "edam": "2719", "miriam": "dbprobe", "n2t": "dbprobe", "ncbi": "dbProbe", "prefixcommons": "dbprobe" }, "name": "NCBI Probe database Public registry of nucleic acid reagents", "pattern": "^\\d+$", "preferred_prefix": "dbprobe", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/dbprobe:$1" } ], "uri_format": "https://www.ncbi.nlm.nih.gov/probe/?term=$1" }, "dbsnp": { "contact": { "email": "pruitt@ncbi.nlm.nih.gov", "name": "Kim Dixon Pruitt", "orcid": "0000-0001-7950-1374" }, "description": "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.", "example": "rs121909098", "homepage": "https://www.ncbi.nlm.nih.gov/snp/", "keywords": [ "genome", "life science" ], "mappings": { "biocontext": "dbSNP", "cellosaurus": "dbSNP", "edam": "1106", "fairsharing": "FAIRsharing.edxb58", "go": "dbSNP", "hl7": "2.16.840.1.113883.6.284", "integbio": "nbdc00206", "miriam": "dbsnp", "n2t": "dbsnp", "ncbi": "dbSNP", "prefixcommons": "dbsnp", "re3data": "r3d100010652", "togoid": "Dbsnp", "uniprot": "DB-0013", "wikidata": "P6861" }, "name": "dbSNP Reference SNP number", "pattern": "^rs\\d+$", "preferred_prefix": "dbsnp", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/dbsnp:$1" }, { "code": "sib", "description": "SNP2TFBS", "homepage": "https://epd.expasy.org/", "name": "SNP2TFBS", "uri_format": "https://epd.expasy.org/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1" } ], "publications": [ { "doi": "10.1093/nar/gkaa892", "pubmed": "33095870" }, { "doi": "10.1093/nar/gkl1031", "pmc": "PMC1781113", "pubmed": "17170002", "title": "Database resources of the National Center for Biotechnology Information", "year": 2006 }, { "doi": "10.1093/nar/29.1.308", "pmc": "PMC29783", "pubmed": "11125122", "title": "dbSNP: the NCBI database of genetic variation", "year": 2001 } ], "repository": "https://github.com/ncbi/dbsnp/tree/master/tutorials", "uri_format": "https://www.ncbi.nlm.nih.gov/snp/$1" }, "dbvar.study": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Studies in dbVar.", "example": "nstd102", "homepage": "https://www.ncbi.nlm.nih.gov/dbvar", "name": "Database of Genomic Structural Variation - Study", "preferred_prefix": "dbvar.study", "synonyms": [ "dbvar.studies" ], "uri_format": "https://www.ncbi.nlm.nih.gov/dbvar/studies/$1" }, "dbvar.variant": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Variants in dbVar.", "example": "nsv3875336", "homepage": "https://www.ncbi.nlm.nih.gov/dbvar", "name": "Database of Genomic Structural Variation - Variant", "preferred_prefix": "dbvar.variant", "synonyms": [ "dbvar.variants" ], "uri_format": "https://www.ncbi.nlm.nih.gov/dbvar/variants/$1" }, "dc": { "contact": { "email": "kdurante@stanford.edu", "name": "Kim Durante", "orcid": "0000-0001-9052-2854" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.\n\n**Deprecation Notice**: While the `/elements/1.1/` namespace will be supported indefinitely, DCMI gently encourages use of the `/terms/` namespace (i.e., `dcterms`) ([source](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3)).", "download_owl": "http://aber-owl.net/media/ontologies/dcelements/1/dcelements.owl", "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": { "aberowl": "dcelements", "biocontext": "dc", "bioportal": "DC", "fairsharing": "FAIRsharing.3nx7t", "lov": "dce", "ols": "dc", "zazuko": "dc11" }, "name": "Dublin Core Elements (1.1)", "preferred_prefix": "dc", "synonyms": [ "dc.elements", "dc11", "dce", "dcelem", "elements" ], "uri_format": "http://purl.org/dc/elements/1.1/$1" }, "dc_cl": { "contact": { "email": "Lindsay.Cowell@utsouthwestern.edu", "name": "Lindsay Cowell", "orcid": "0000-0003-1617-8244" }, "deprecated": true, "example": "0000003", "homepage": "http://www.dukeontologygroup.org/Projects.html", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "DC_CL", "obofoundry": "dc_cl" }, "name": "Dendritic cell", "pattern": "^\\d{7}$", "preferred_prefix": "DC_CL", "rdf_uri_format": "http://purl.obolibrary.org/obo/DC_CL_$1", "uri_format": "http://purl.obolibrary.org/obo/DC_CL_$1" }, "dcam": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A metadata model for Dublin Core metadata", "example": "domainIncludes", "github_request_issue": 1677, "homepage": "https://www.dublincore.org/specifications/dublin-core/abstract-model/2007-06-04/", "keywords": [ "general & upper", "metadata model", "schema", "semantic web" ], "logo": "https://www.dublincore.org/images/dcmi_logo_v802.svg", "mappings": { "lov": "dcam", "zazuko": "dcam" }, "name": "Dublin Core Metadata Initiative Abstract Model", "preferred_prefix": "dcam", "rdf_uri_format": "http://purl.org/dc/dcam/$1", "uri_format": "http://purl.org/dc/dcam/$1" }, "dcat": { "contact": { "email": "kdurante@stanford.edu", "name": "Kim Durante", "orcid": "0000-0001-9052-2854" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web", "download_owl": "http://www.w3.org/ns/dcat3", "download_rdf": "https://www.w3.org/ns/dcat.ttl", "example": "Dataset", "homepage": "https://www.w3.org/ns/dcat", "keywords": [ "computer science", "data management", "ess", "ontology", "subject agnostic", "tib", "w3c rec" ], "mappings": { "aberowl": "DCAT", "biocontext": "dcat", "biolink": "dcat", "bioportal": "DCAT", "fairsharing": "FAIRsharing.h4j3qm", "lov": "dcat", "ols": "dcat", "tib": "dcat3", "zazuko": "dcat" }, "name": "Data Catalog", "preferred_prefix": "dcat", "repository": "https://github.com/w3c/dxwg/", "uri_format": "http://www.w3.org/ns/dcat#$1", "version": "3" }, "dcterms": { "contact": { "email": "futo@stanford.edu", "name": "Michelle Futornick" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.", "download_owl": "http://aber-owl.net/media/ontologies/dcterms/1/dcterms.owl", "download_rdf": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_terms.ttl", "example": "title", "homepage": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/", "keywords": [ "digital planning and construction", "ess", "fid baudigital", "metadata", "metadata standardization", "nfdi4ing", "ontology", "resource metadata", "subject agnostic" ], "mappings": { "aberowl": "dcterms", "biocontext": "dcterms", "biolink": "dct", "bioportal": "DCTERMS", "fairsharing": "FAIRsharing.9vtwjs", "lov": "dcterms", "ols": "dcterms", "tib": "dcterms", "zazuko": "dcterms" }, "name": "Dublin Core Metadata Initiative Terms", "preferred_prefix": "dcterms", "synonyms": [ "dc.terms", "dct", "terms" ], "uri_format": "http://purl.org/dc/terms/$1" }, "dctypes": { "contact": { "email": "kdurante@stanford.edu", "name": "Kim Durante" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.", "download_owl": "http://aber-owl.net/media/ontologies/DCMITYPE/4/dcmitype.owl", "example": "Collection", "homepage": "https://dublincore.org/specifications/dublin-core/dcmi-terms/", "keywords": [ "ontology" ], "mappings": { "aberowl": "DCMITYPE", "biocontext": "dctypes", "bioportal": "DCMITYPE", "zazuko": "dcmitype" }, "name": "Dublin Core Types", "preferred_prefix": "dctypes", "synonyms": [ "dcmitype", "dcmitypes" ], "uri_format": "http://purl.org/dc/dcmitype/$1" }, "ddanat": { "contact": { "email": "pfey@northwestern.edu", "github": "pfey03", "name": "Petra Fey", "orcid": "0000-0002-4532-2703" }, "description": "A structured controlled vocabulary of anatomies of the slime-mold Dictyostelium discoideum.", "download_obo": "http://purl.obolibrary.org/obo/ddanat.obo", "download_owl": "http://purl.obolibrary.org/obo/ddanat.owl", "example": "0000006", "homepage": "http://dictybase.org/", "keywords": [ "anatomy", "cell", "life science", "obo", "ontology", "slime-mould" ], "license": "CC0-1.0", "logo": "http://dictybase.org/inc/images/logo.gif", "mappings": { "aberowl": "DDANAT", "biocontext": "DDANAT", "bioportal": "DDANAT", "fairsharing": "FAIRsharing.z656ab", "go": "DDANAT", "obofoundry": "ddanat", "ols": "ddanat", "ontobee": "DDANAT", "prefixcommons": "ddanat", "wikidata.entity": "Q81661582" }, "name": "Dictyostelium discoideum anatomy", "pattern": "^\\d{7}$", "preferred_prefix": "DDANAT", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/ddanat:$1" } ], "publications": [ { "doi": "10.1186/1471-2164-9-130", "pmc": "PMC2323390", "pubmed": "18366659", "title": "An anatomy ontology to represent biological knowledge in Dictyostelium discoideum", "year": 2008 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/DDANAT_$1", "repository": "https://github.com/dictyBase/migration-data", "twitter": "dictybase", "uri_format": "http://purl.obolibrary.org/obo/DDANAT_$1" }, "ddc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Dewey Decimal Classification (DDC) system, devised by library pioneer Melvil Dewey in the 1870s and owned by OCLC since 1988, provides a dynamic structure for the organization of library collections. Now in its 23rd edition, and available in print and Web versions, the DDC is the world's most widely used library classification system.", "example": "325.4", "example_extras": [ "3", "32", "325", "325.4-325.9" ], "homepage": "http://www.oclc.org/dewey/", "mappings": { "bartoc": "241", "wikidata.entity": "Q48460" }, "name": "Dewey Decimal Classification", "pattern": "^(([0-9][0-9]?|[0-9]{3}(-[0-9]{3})?|[0-9]{3}(-[0-9]{3}(:[0-9]+)?)?|[0-9]{3}\\.[0-9]+(-[0-9]{3}\\.[0-9]+(:[0-9]+)?)?|T[1-9][A-Z]?--[0-9]+(-T[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?|[1-9][A-Z]?--[0-9]+(-[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?)?)$", "preferred_prefix": "ddc" }, "ddi": { "contact": { "email": "soldatova.larisa@gmail.com", "name": "Larisa Soldatova", "orcid": "0000-0001-6489-3029" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A set of controlled vocabularies in the Data Documentation Initiative, each of which has its own code.", "download_owl": "http://aber-owl.net/media/ontologies/DDI/2/ddi.owl", "example": "Instrument", "github_request_issue": 1632, "homepage": "https://rdf-vocabulary.ddialliance.org/", "keywords": [ "biomedical science", "drug discovery", "ontology", "registry" ], "mappings": { "aberowl": "DDI", "bioportal": "DDI", "fairsharing": "FAIRsharing.pf2qyq" }, "name": "Data Documentation Initiative Vocabulary", "preferred_prefix": "ddi", "uri_format": "http://rdf-vocabulary.ddialliance.org/lifecycle#$1" }, "ddi.aggregationmethod": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Identifies the type of aggregation used to combine related categories, usually within a common branch of a hierarchy, to provide information at a broader level than the level at which detailed observations are taken. (From: The OECD Glossary of Statistical Terms)", "example": "Sum", "homepage": "https://vocabularies.cessda.eu/vocabulary/AggregationMethod", "license": "CC-BY-4.0", "name": "Aggregation Method", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.aggregationmethod", "uri_format": "https://vocabularies.cessda.eu/vocabulary/AggregationMethod?lang=en#code_$1", "version": "1.1.2" }, "ddi.analysisunit": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Describes the entity being analyzed in the study or variable. This vocabulary can also be used to describe the unit of observation, which is the unit being observed, or from which data are collected. The unit of observation can be the same as, or different from the unit of analysis.", "example": "Individual", "homepage": "https://vocabularies.cessda.eu/vocabulary/AnalysisUnit", "license": "CC-BY-4.0", "name": "Analysis Unit", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.analysisunit", "uri_format": "https://vocabularies.cessda.eu/vocabulary/AnalysisUnit?lang=en#code_$1", "version": "2.1.3" }, "ddi.characterset": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Standard set of characters upon which many character encodings are based (Wikipedia).", "example": "ASCII", "homepage": "https://vocabularies.cessda.eu/vocabulary/CharacterSet", "license": "CC-BY-4.0", "name": "Character Set", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.characterset", "uri_format": "https://vocabularies.cessda.eu/vocabulary/CharacterSet?lang=en#code_$1", "version": "1.0.0" }, "ddi.commonalitytype": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Describes the degree of similarity between two items or schemes (collections of items).", "example": "Identical", "homepage": "https://vocabularies.cessda.eu/vocabulary/CommonalityType", "license": "CC-BY-4.0", "name": "Commonality Type", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.commonalitytype", "uri_format": "https://vocabularies.cessda.eu/vocabulary/CommonalityType?lang=en#code_$1", "version": "1.0.2" }, "ddi.contributorrole": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A 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"https://vocabularies.cessda.eu/vocabulary/DataSourceType?lang=en#code_$1", "version": "1.0.2" }, "ddi.datatype": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Identifies the type of data, which has a bearing on the acceptable data values, the operations that can be performed with the data, and the ways in which the data are stored.", "example": "String", "homepage": "https://vocabularies.cessda.eu/vocabulary/DataType", "license": "CC-BY-4.0", "name": "Data Type", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.datatype", "uri_format": "https://vocabularies.cessda.eu/vocabulary/DataType?lang=en#code_$1", "version": "1.1.2" }, "ddi.datetype": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Specifies the type of date.", "example": "DateTime", "homepage": "https://vocabularies.cessda.eu/vocabulary/DateType", "license": "CC-BY-4.0", "name": "Date Type", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.datetype", "uri_format": "https://vocabularies.cessda.eu/vocabulary/DateType?lang=en#code_$1", "version": "1.1.2" }, "ddi.generaldataformat": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Describes the physical format(s) of the data documented in the logical product(s) of a study unit.", "example": "Numeric", "homepage": "https://vocabularies.cessda.eu/vocabulary/GeneralDataFormat", "license": "CC-BY-4.0", "name": "General Data Format", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.generaldataformat", "uri_format": 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life cycle that is considered significant enough to document.", "example": "StudyProposal", "homepage": "https://vocabularies.cessda.eu/vocabulary/LifecycleEventType", "license": "CC-BY-4.0", "name": "Lifecycle Event Type", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.lifecycleeventtype", "uri_format": "https://vocabularies.cessda.eu/vocabulary/LifecycleEventType?lang=en#code_$1", "version": "1.0.2" }, "ddi.modeofcollection": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The procedure, technique, or mode of inquiry used to attain the data.", "example": "Interview", "homepage": "https://vocabularies.cessda.eu/vocabulary/ModeOfCollection", "license": "CC-BY-4.0", "name": "Mode Of Collection", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.modeofcollection", "uri_format": "https://vocabularies.cessda.eu/vocabulary/ModeOfCollection?lang=en#code_$1", "version": "5.0.0" }, "ddi.numerictype": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Specifies the type of numeric data.", "example": "Integer", "homepage": "https://vocabularies.cessda.eu/vocabulary/NumericType", "license": "CC-BY-4.0", "name": "Numeric Type", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.numerictype", "uri_format": "https://vocabularies.cessda.eu/vocabulary/NumericType?lang=en#code_$1", "version": "1.1.0" }, "ddi.responseunit": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Indicates the entity that provided the information carried by the variable.", "example": "Self", "homepage": "https://vocabularies.cessda.eu/vocabulary/ResponseUnit", "license": "CC-BY-4.0", "name": "Response Unit", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.responseunit", "uri_format": "https://vocabularies.cessda.eu/vocabulary/ResponseUnit?lang=en#code_$1", "version": "1.0.2" }, "ddi.samplingprocedure": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A typology of sampling methods.", "example": "TotalUniverseCompleteEnumeration", "homepage": "https://vocabularies.cessda.eu/vocabulary/SamplingProcedure", "license": "CC-BY-4.0", "name": "Sampling Procedure", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.samplingprocedure", "uri_format": "https://vocabularies.cessda.eu/vocabulary/SamplingProcedure?lang=en#code_$1", "version": "2.0.1" }, "ddi.softwarepackage": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Indicates the statistical software package used in the production/processing/dissemination of the data. Data collection software is not covered in this list.", "example": "AcaStat", "homepage": "https://vocabularies.cessda.eu/vocabulary/SoftwarePackage", "license": "CC-BY-4.0", "name": "Software Package", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.softwarepackage", "uri_format": "https://vocabularies.cessda.eu/vocabulary/SoftwarePackage?lang=en#code_$1", "version": "1.0.1" }, "ddi.summarystatistictype": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Specifies the type of summary statistic. Summary statistics are a single number representation of the characteristics of a set of values.", "example": "ArithmeticMean", "homepage": "https://vocabularies.cessda.eu/vocabulary/SummaryStatisticType", "license": "CC-BY-4.0", "name": "Summary Statistic Type", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.summarystatistictype", "uri_format": "https://vocabularies.cessda.eu/vocabulary/SummaryStatisticType?lang=en#code_$1", "version": "2.1.2" }, "ddi.timemethod": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Describes the time dimension of the data collection.", "example": "Longitudinal", "homepage": "https://vocabularies.cessda.eu/vocabulary/TimeMethod", "license": "CC-BY-4.0", "name": "Time Method", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.timemethod", "uri_format": "https://vocabularies.cessda.eu/vocabulary/TimeMethod?lang=en#code_$1", "version": "1.2.3" }, "ddi.timezone": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Time zone specification as an offset from UTC (Coordinated Universal Time) in terms of hours and minutes.", "example": "-12:00", "homepage": "https://vocabularies.cessda.eu/vocabulary/TimeZone", "license": "CC-BY-4.0", "name": "Time Zone", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.timezone", "uri_format": "https://vocabularies.cessda.eu/vocabulary/TimeZone?lang=en#code_$1", "version": "1.0.0" }, "ddi.typeofaddress": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Identifies the type of address entered as contact information for an individual or an organization.", "example": "Mailing", "homepage": "https://vocabularies.cessda.eu/vocabulary/TypeOfAddress", "license": "CC-BY-4.0", "name": "Type of Address", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.typeofaddress", "uri_format": "https://vocabularies.cessda.eu/vocabulary/TypeOfAddress?lang=en#code_$1", "version": "1.1.0" }, "ddi.typeofconceptgroup": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Specifies the rationale for creating a concept group.", "example": "Administrative", "homepage": "https://vocabularies.cessda.eu/vocabulary/TypeOfConceptGroup", "license": "CC-BY-4.0", "name": "Type of Concept Group", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.typeofconceptgroup", "uri_format": "https://vocabularies.cessda.eu/vocabulary/TypeOfConceptGroup?lang=en#code_$1", "version": "1.0.2" }, "ddi.typeoffrequency": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Indicates the frequency of data collection events.", "example": "Continuous", "homepage": "https://vocabularies.cessda.eu/vocabulary/TypeOfFrequency", "license": "CC-BY-4.0", "name": "Type of Frequency", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.typeoffrequency", "uri_format": "https://vocabularies.cessda.eu/vocabulary/TypeOfFrequency?lang=en#code_$1", "version": "1.0.2" }, "ddi.typeofinstrument": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Includes a typology of 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"https://vocabularies.cessda.eu/vocabulary/TypeOfNote?lang=en#code_$1", "version": "1.1.1" }, "ddi.typeoftelephone": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Identifies the type of telephone entered as contact information for an individual or an organization.", "example": "Fixed", "homepage": "https://vocabularies.cessda.eu/vocabulary/TypeOfTelephone", "license": "CC-BY-4.0", "name": "Type of Telephone", "owners": [ { "name": "Data Documentation Initiative Alliance", "partnered": false, "ror": "015em2733" } ], "preferred_prefix": "ddi.typeoftelephone", "uri_format": "https://vocabularies.cessda.eu/vocabulary/TypeOfTelephone?lang=en#code_$1", "version": "1.0.0" }, "ddi.typeoftranslationmethod": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A typology of methods used to translate 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including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety.", "example": "DDInter20", "github_request_issue": 492, "homepage": "http://ddinter.scbdd.com", "keywords": [ "chemistry", "drugs", "relationships" ], "license": "CC BY-NC-SA 4.0", "name": "Curated Drug-Drug Interactions Database - Drug", "pattern": "^DDInter\\d+$", "preferred_prefix": "ddinter.drug", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://ddinter.scbdd.com/ddinter/drug-detail/$1" }, "ddinter.interaction": { "contact": { "email": "oriental-cds@163.com", "name": "Dongsheng Cao", "orcid": "0000-0003-3604-3785" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Ddinter is a comprehensive, professional, and open-access database 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"https://raw.githubusercontent.com/obophenotype/dicty-phenotype-ontology/master/ddpheno.obo", "download_owl": "http://purl.obolibrary.org/obo/ddpheno.owl", "example": "0001417", "homepage": "http://dictybase.org/", "keywords": [ "anatomy", "developmental biology", "life science", "microbe-host interaction phenotype", "microbial ecology", "obo", "ontology", "phenomics", "phenotype", "soil science" ], "license": "CC0-1.0", "mappings": { "aberowl": "DDPHENO", "biocontext": "DDPHENO", "bioportal": "DDPHENO", "fairsharing": "FAIRsharing.9c1p18", "obofoundry": "ddpheno", "ols": "ddpheno", "ontobee": "DDPHENO", "wikidata.entity": "Q81661585" }, "name": "Dictyostelium discoideum phenotype ontology", "pattern": "^\\d{7}$", "preferred_prefix": "DDPHENO", "publications": [ { "doi": "10.1387/ijdb.190226pf", "pmc": "PMC7409682", "pubmed": "31840793", "title": "dictyBase and the Dicty Stock Center (version 2.0) - a progress report", "year": 2019 }, { "doi": "10.1007/978-1-62703-302-2_4", "pmc": "PMC3762881", "pubmed": "23494302", "title": "One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/DDPHENO_$1", "repository": "https://github.com/obophenotype/dicty-phenotype-ontology", "twitter": "dictybase", "uri_format": "http://purl.obolibrary.org/obo/DDPHENO_$1", "version": "2023-08-26" }, "debio": { "contact": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON.", "download_json": "https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.json", "download_obo": "https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.obo", "download_owl": "https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.owl", "example": "0000001", "homepage": "https://biopragmatics.github.io/debio", "keywords": [ "ontology" ], "name": "Decentralized Biomedical Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "debio", "providers": [ { "code": "obo2", "description": "Because it's not possible to configure the base URI with ROBOT/OWLAPI, this pops out", "homepage": "http://purl.obolibrary.org", "name": "Placeholder OBO PURL", "uri_format": "http://purl.obolibrary.org/obo/debio_$1" } ], "synonyms": [ "DeBiO" ], "uri_format": "https://biopragmatics.github.io/debio/$1" }, "decipher": { "contact": { "email": "ganesh.swaminathan@sanger.ac.uk", "name": "Jawahar Swaminathan", "orcid": "0000-0002-0215-4084" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms", "example": "1", "homepage": "https://www.deciphergenomics.org/", "keywords": [ "biomedical science", "life science" ], "mappings": { "biocontext": "DECIPHER", "fairsharing": "FAIRsharing.l8Sf5x" }, "name": "DECIPHER CNV Syndromes", "pattern": "^\\d+$", "preferred_prefix": "decipher", "publications": [ { "doi": "10.1093/nar/gkt937", "pmc": "PMC3965078", "pubmed": "24150940", "title": "DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation", "year": 2013 }, { "doi": "10.1016/j.ajhg.2009.03.010", "pmc": "PMC2667985", "pubmed": "19344873", "title": "DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources", "year": 2009 } ], "uri_format": "https://www.deciphergenomics.org/syndrome/$1" }, "degradome": { "description": "The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced.", "example": "Ax1", "homepage": "http://degradome.uniovi.es/", "mappings": { "biocontext": "DEGRADOME", "miriam": "degradome", "n2t": "degradome" }, "name": "Degradome Database", "pattern": "^[AMCST][0-9x][0-9]$", "preferred_prefix": "degradome", "uri_format": "http://degradome.uniovi.es/cgi-bin/protease/$1" }, "deims.activity": { "contact": { "email": "christoph.wohner@umweltbundesamt.at", "github": "stopopol", "name": "Christoph Wohner", "orcid": "0000-0002-0655-3699" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Activities in DEIMS SDR", "example": "7dfd3f10-d410-45a4-983d-8fbd6dfbc374", "github_request_issue": 1381, "homepage": "https://deims.org", "license": "CC-BY-NC-4.0", "name": "Dynamic Ecological Information Management System - Site and Dataset Registry - Activity", "pattern": "^[0-9a-f\\-]+$", "preferred_prefix": "deims.activity", "providers": [ { "code": "api", "description": "A first-party API endpoint for an activity in DEIMS-SDR", "homepage": "https://deims.org/api", "name": "DEIMS-SDR API", "uri_format": "https://deims.org/api/activities/$1" } ], "publications": [ { "doi": "10.1016/j.ecoinf.2022.101708", "pmc": "PMC9461184", "pubmed": "36105745", "title": "Designing and implementing a data model for describing environmental monitoring and research sites", "year": 2022 }, { "doi": "10.1016/j.ecoinf.2020.101158", "title": "Towards interoperable research site documentation – Recommendations for information models and data provision", "year": 2020 }, { "doi": "10.1016/j.ecoinf.2019.01.005", "title": "DEIMS-SDR – A web portal to document research sites and their associated data", "year": 2019 } ], "uri_format": "https://deims.org/activity/$1" }, "deims.dataset": { "contact": { "email": "christoph.wohner@umweltbundesamt.at", "github": "stopopol", "name": "Christoph Wohner", "orcid": "0000-0002-0655-3699" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Datasets in DEIMS SDR", "example": "bb0754dd-7e69-4b29-b348-3f8017f73d6b", "github_request_issue": 1381, "homepage": "https://deims.org", "license": "CC-BY-NC-4.0", "name": "Dynamic Ecological Information Management System - 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Site and Dataset Registry - Network", "pattern": "^[0-9a-f\\-]+$", "preferred_prefix": "deims.network", "publications": [ { "doi": "10.1016/j.ecoinf.2022.101708", "pmc": "PMC9461184", "pubmed": "36105745", "title": "Designing and implementing a data model for describing environmental monitoring and research sites", "year": 2022 }, { "doi": "10.1016/j.ecoinf.2020.101158", "title": "Towards interoperable research site documentation – Recommendations for information models and data provision", "year": 2020 }, { "doi": "10.1016/j.ecoinf.2019.01.005", "title": "DEIMS-SDR – A web portal to document research sites and their associated data", "year": 2019 } ], "uri_format": "https://deims.org/networks/$1" }, "deims.sensor": { "contact": { "email": "christoph.wohner@umweltbundesamt.at", "github": "stopopol", "name": "Christoph Wohner", "orcid": "0000-0002-0655-3699" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Sensors in DEIMS SDR", "example": "2af339dd-a956-471f-9406-b0f74bacd579", "github_request_issue": 1381, "homepage": "https://deims.org", "license": "CC-BY-NC-4.0", "name": "Dynamic Ecological Information Management System - Site and Dataset Registry - Sensor", "pattern": "^[0-9a-f\\-]+$", "preferred_prefix": "deims.sensor", "providers": [ { "code": "api", "description": "A first-party API endpoint for a sensor in DEIMS-SDR", "homepage": "https://deims.org/api", "name": "DEIMS-SDR API", "uri_format": "https://deims.org/api/sensors/$1" } ], "publications": [ { "doi": "10.1016/j.ecoinf.2022.101708", "pmc": "PMC9461184", "pubmed": "36105745", "title": "Designing and implementing a data model for describing environmental monitoring and research sites", "year": 2022 }, { "doi": "10.1016/j.ecoinf.2020.101158", "title": "Towards interoperable research site documentation – Recommendations for information models and data provision", "year": 2020 }, { "doi": "10.1016/j.ecoinf.2019.01.005", "title": "DEIMS-SDR – A web portal to document research sites and their associated data", "year": 2019 } ], "uri_format": "https://deims.org/sensors/$1" }, "deims.site": { "comment": "This is an important resource for us in fields like environmental genomics. We frequently want to link metagenome samples to sites to make it easier to pull in environmental data to explore connections between environments, gene functions, community structure, etc. I will try and reach out to establish contacts with them", "contact": { "email": "christoph.wohner@umweltbundesamt.at", "github": "stopopol", "name": "Christoph Wohner", "orcid": "0000-0002-0655-3699" }, "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "DEIMS-SDR (Dynamic Ecological Information Management System - Site and dataset registry) is an information management system powered by eLTER. It allows you to discover long-term ecosystem research sites around the globe, along with the data gathered at those sites and the people and networks associated with them. DEIMS-SDR describes a wide range of sites, providing a wealth of information, including each site’s location, ecosystems, facilities, parameters measured and research themes. It is also possible to access a growing number of datasets and data products associated with the sites.", "example": "0e39569d-ff81-4b78-9c34-b07309504d80", "github_request_issue": 1381, "homepage": "https://deims.org/", "license": "CC-BY-NC-4.0", "name": "Dynamic Ecological Information Management System - Site and dataset registry", "pattern": "^[0-9a-f\\-]+$", "preferred_prefix": "deims.site", "providers": [ { "code": "api", "description": "A first-party API endpoint for a site in DEIMS-SDR", "homepage": "https://deims.org/api", "name": "DEIMS-SDR API", "uri_format": "https://deims.org/api/sites/$1" } ], "publications": [ { "doi": "10.1016/j.ecoinf.2022.101708", "pmc": "PMC9461184", "pubmed": "36105745", "title": "Designing and implementing a data model for describing environmental monitoring and research sites", "year": 2022 }, { "doi": "10.1016/j.ecoinf.2020.101158", "title": "Towards interoperable research site documentation – Recommendations for information models and data provision", "year": 2020 }, { "doi": "10.1016/j.ecoinf.2019.01.005", "title": "DEIMS-SDR – A web portal to document research sites and their associated data", "year": 2019 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "deims.id" ], "uri_format": "https://deims.org/$1" }, "deims.taxonomy": { "contact": { "email": "christoph.wohner@umweltbundesamt.at", "github": "stopopol", "name": "Christoph Wohner", "orcid": "0000-0002-0655-3699" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Taxonomy in DEIMS SDR", "example": "21157", "github_request_issue": 1381, "homepage": "https://deims.org", "license": "CC-BY-NC-4.0", "name": "Dynamic Ecological Information Management System - Site and Dataset Registry - Taxonomy", "pattern": "^\\d+$", "preferred_prefix": "deims.taxonomy", "publications": [ { "doi": "10.1016/j.ecoinf.2022.101708", "pmc": "PMC9461184", "pubmed": "36105745", "title": "Designing and implementing a data model for describing environmental monitoring and research sites", "year": 2022 }, { "doi": "10.1016/j.ecoinf.2020.101158", "title": "Towards interoperable research site documentation – Recommendations for information models and data provision", "year": 2020 }, { "doi": "10.1016/j.ecoinf.2019.01.005", "title": "DEIMS-SDR – A web portal to document research sites and their associated data", "year": 2019 } ], "uri_format": "https://deims.org/taxonomy/term/$1" }, "deo": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology that provides a structured vocabulary for rhetorical elements within documents (e.g., Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix). It is imported by DoCO.", "example": "Reference", "homepage": "http://www.sparontologies.net/ontologies/deo", "keywords": [ "spar", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.39fd58", "lov": "deo" }, "name": "Discourse Elements Ontology", "preferred_prefix": "DEO", "publications": [ { "doi": "10.3233/sw-150177", "title": "The Document Components Ontology (DoCO)", "year": 2016 } ], "repository": "https://github.com/sparontologies/deo", "twitter": "sparontologies", "uri_format": "http://purl.org/spar/deo/$1" }, "depmap": { "contact": { "email": "vazquez@broadinstitute.org", "name": "Francisca Vazquez", "orcid": "0000-0002-2857-4685" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells.", "example": "ACH-000001", "homepage": "https://depmap.org/portal", "keywords": [ "cancer cell line", "cell", "cell line" ], "license": "CC-BY-4.0", "logo": "https://target-discovery.depmap.org/img/depmaplogo.png", "mappings": { "cellosaurus": "DepMap" }, "name": "DepMap Cell Lines", "pattern": "^ACH-\\d+$", "preferred_prefix": "depmap", "publications": [ { "doi": "10.1038/s41568-024-00763-x", "pubmed": "39468210", "title": "The present and future of the Cancer Dependency Map", "year": 2025 } ], "uri_format": "https://depmap.org/portal/cell_line/$1" }, "depod": { "contact": { "email": "depod@embl.de", "name": "General Enquiries", "orcid": "0000-0003-3562-7869" }, "description": "The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources.", "example": "PTPN1", "homepage": "http://www.depod.bioss.uni-freiburg.de", "keywords": [ "life science" ], "mappings": { "biocontext": "DEPOD", "fairsharing": "FAIRsharing.q9j2e3", "miriam": "depod", "n2t": "depod", "pathguide": "584", "re3data": "r3d100011936", "uniprot": "DB-0190" }, "name": "Human Dephosphorylation Database", "pattern": "^[A-Z0-9]+$", "preferred_prefix": "depod", "provides": "hgnc.symbol", "publications": [ { "doi": "10.1093/database/baz133", "pmc": "PMC6911163", "pubmed": "31836896", "title": "The human DEPhOsphorylation Database DEPOD: 2019 update", "year": 2019 }, { "doi": "10.1093/nar/gku1009", "pmc": "PMC4383878", "pubmed": "25332398", "title": "The human DEPhOsphorylation database DEPOD: a 2015 update", "year": 2014 }, { "doi": "10.1126/scisignal.2003203", "pubmed": "23674824", "title": "Elucidating human phosphatase-substrate networks", "year": 2013 } ], "uri_format": "http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1" }, "dermo": { "contact": { "email": "pns12@hermes.cam.ac.uk", "github": "PaulNSchofield", "name": "Paul Schofield", "orcid": "0000-0002-5111-7263" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders", "download_obo": "http://aber-owl.net/media/ontologies/DERMO/10/dermo.obo", "example": "0000000", "homepage": "https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x", "keywords": [ "dermatology", "disease", "ontology" ], "mappings": { "aberowl": "DERMO", "bioportal": "DERMO", "fairsharing": "FAIRsharing.k008w7" }, "name": "Human Dermatological Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "dermo", "publications": [ { "doi": "10.1186/s13326-016-0085-x", "pmc": "PMC4907256", "pubmed": "27296450", "title": "DermO; an ontology for the description of dermatologic disease", "year": 2016 } ], "repository": "https://github.com/dermatology-ontology/dermatology", "uri_format": "http://purl.obolibrary.org/obo/DERMO_$1" }, "destatis.subject": { "description": "A vocabulary of university course subjects", "example": "01", "homepage": "https://github.com/VIVO-DE/destatis_faecherklassifikation", "keywords": [ "educational science", "subject", "tib" ], "mappings": { "tib": "destf" }, "name": "Destatis subject classification", "preferred_prefix": "destatis.subject", "repository": "https://github.com/VIVO-DE/destatis_faecherklassifikation", "uri_format": "https://onto.tib.eu/destf/cs/$1" }, "dev.ga4ghdos": { "description": "Assists in resolving data across cloud resources.", "example": "23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00", "homepage": "http://github.com/ga4gh/data-object-service-schemas", "mappings": { "biocontext": "DEV.GA4GHDOS", "miriam": "dev.ga4ghdos", "n2t": "dev.ga4ghdos" }, "name": "Development Data Object Service", "pattern": "^[a-zA-Z0-9\\-:#\\.]+$", "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. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/doi:$1" }, { "code": "doi_http", "description": "An alternate provider from the DOI website using HTTP", "homepage": "https://www.doi.org", "name": "Digital Object Identifier", "uri_format": "http://doi.org/$1" }, { "code": "dx_doi_http", "description": "An alternate provider from the DOI website using HTTP", "homepage": "https://www.doi.org", "name": "Digital Object Identifier", "uri_format": "http://dx.doi.org/$1" }, { "code": "dx_doi_https", "description": "An alternate provider from the DOI website using HTTPS", "homepage": "https://www.doi.org", "name": "Digital Object Identifier", "uri_format": "https://dx.doi.org/$1" }, { "code": "miriam_legacy", "description": "A legacy MIRIAM URI that does not follow the standard pattern", "homepage": "https://identifiers.org", "name": "Legacy MIRIAM URI", "uri_format": "http://identifiers.org/DOI/$1" }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/doi/$1" } ], "publications": [ { "doi": "10.1000/292", "title": "DOI URI Scheme", "year": 2024 } ], "rdf_uri_format": "http://dx.doi.org/$1", "references": [ "https://github.com/biopragmatics/bioregistry/issues/287", "https://github.com/biopragmatics/bioregistry/pull/316" ], "uri_format": "https://doi.org/$1" }, "doid": { "appears_in": [ "clo", "scdo" ], "banana": "DOID", "contact": { "email": "lynn.schriml@gmail.com", "github": "lschriml", "name": "Lynn Schriml", "orcid": "0000-0001-8910-9851" }, "description": "The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts.", "download_json": "http://purl.obolibrary.org/obo/doid.json", "download_obo": "https://github.com/DiseaseOntology/HumanDiseaseOntology/raw/main/src/ontology/doid.obo", "download_owl": "http://purl.obolibrary.org/obo/doid.owl", "example": "0110974", "homepage": "https://disease-ontology.org", "keywords": [ "biomedical science", "classification", "disease", "disease course", "disease phenotype", "genetic disorder", "human", "infection process", "life science", "mental health", "obo", "ontology" ], "license": "CC0-1.0", "logo": "https://disease-ontology.org/media/images/DO_logo_teal.png", "mappings": { "aberowl": "DOID", "bartoc": "576", "biocontext": "DOID", "bioportal": "DOID", "fairsharing": "FAIRsharing.8b6wfq", "integbio": "nbdc00261", "miriam": "doid", "n2t": "doid", "obofoundry": "doid", "ols": "doid", "ontobee": "DOID", "prefixcommons": "do", "togoid": "Doid", "wikidata": "P699", "wikidata.entity": "Q5282129" }, "name": "Human Disease Ontology", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "DOID", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/do:$1" }, { "code": "hdo", "description": "Human Disease Ontology at Northwestern University", "homepage": "http://disease-ontology.org/", "name": "Human Disease Ontology at Northwestern University", "uri_format": "http://disease-ontology.org/term/DOID:$1" }, { "code": "purl", "description": "Legacy PURLs for DOID, including the redundant DOID_", "homepage": "http://purl.org/obo/owl/", "name": "Legacy PURL", "uri_format": "http://purl.org/obo/owl/DOID#DOID_$1" }, { "code": "purl2", "description": "Legacy PURLs for DOID, not including the redundant DOID_", "homepage": "http://purl.org/obo/owl/", "name": "Legacy PURL", "uri_format": "http://purl.org/obo/owl/DOID#$1" } ], "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", "pubmed": "34755882", "title": "The Human Disease Ontology 2022 update", "year": 2022 }, { "doi": "10.1093/bib/bbab191", "pmc": "PMC8195003", "pubmed": "34015823", "title": "COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model", "year": 2021 }, { "doi": "10.7554/elife.52614", "pmc": "PMC7077981", "pubmed": "32180547", "title": "Wikidata as a knowledge graph for the life sciences", "year": 2020 }, { "doi": "10.1093/nar/gky1036", "pmc": "PMC6323956", "pubmed": "30407590", "title": "ECO, the Evidence & Conclusion Ontology: community standard for evidence information", "year": 2019 }, { "doi": "10.1093/nar/gky1032", "pmc": "PMC6323977", "pubmed": "30407550", "title": "Human Disease Ontology 2018 update: classification, content and workflow expansion", "year": 2019 }, { "doi": "10.1242/dmm.032839", "pmc": "PMC5897730", "pubmed": "29590633", "title": "Disease Ontology: improving and unifying disease annotations across species", "year": 2018 }, { "doi": "10.1093/database/baw015", "pmc": "PMC4795929", "pubmed": "26989148", "title": "Wikidata as a semantic framework for the Gene Wiki initiative", "year": 2016 }, { "doi": "10.1016/j.ajhg.2015.05.020", "pmc": "PMC4572507", "pubmed": "26119816", "title": "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease", "year": 2015 }, { "doi": "10.1007/s00335-015-9576-9", "pmc": "PMC4602048", "pubmed": "26093607", "title": "The Disease Ontology: fostering interoperability between biological and clinical human disease-related data", "year": 2015 }, { "doi": "10.1093/database/bav032", "pmc": "PMC4385274", "pubmed": "25841438", "title": "Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis", "year": 2015 }, { "doi": "10.1093/nar/gku1011", "pmc": "PMC4383880", "pubmed": "25348409", "title": "Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data", "year": 2014 }, { "doi": "10.1093/nar/gkr972", "pmc": "PMC3245088", "pubmed": "22080554", "title": "Disease Ontology: a backbone for disease semantic integration", "year": 2011 }, { "doi": "10.1186/1471-2164-10-s1-s6", "pmc": "PMC2709267", "pubmed": "19594883", "title": "Annotating the human genome with Disease Ontology", "year": 2009 }, { "doi": "10.1093/bioinformatics/btp193", "pmc": "PMC2687947", "pubmed": "19478018", "title": "From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations", "year": 2009 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/DOID_$1", "repository": "https://github.com/DiseaseOntology/HumanDiseaseOntology", "synonyms": [ "do" ], "twitter": "diseaseontology", "uri_format": "http://purl.obolibrary.org/obo/DOID_$1", "version": "2025-12-23" }, "dolce": { "comment": "This resource doesn't exist anymore", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering) is a foundational ontology developed as part of the WonderWeb Foundational Ontologies Library (WFOL). The development of this library has been guided by the need of a reliable set of foundational ontologies that can serve as 1) astarting point for building other ontologies, 2) a reference point for easy and rigorous comparisons among different ontological approaches, and 3) a rigorous basis for analyzing, harmonizing and integrating existing ontologies and metadata standards (by manually mapping them into some general module(s) in the library). DOLCE is the first module of WFOL and it is not a candidate for a universal standard ontology. Rather, it is intended as a starting point for comparing and elucidating the relationships with the other modules of the library, and also for clarifying the hidden assumptions underlying existing ontologies or linguistic resources such as WordNet. As reflected by its acronym, DOLCE has a clear cognitive bias, in the sense that it aims at capturing the ontological categories underlying natural language and human commonsense. DOLCE is an ontology that focuses on particulars in the sense that its domain of discourse is restricted to them. The project is complete, though the ontology remains available for use.", "homepage": "http://www.loa.istc.cnr.it/dolce/overview.html", "keywords": [ "classification", "computer science", "knowledge and information systems", "linguistics", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.ae8hpt" }, "name": "Descriptive Ontology for Linguistic and Cognitive Engineering", "preferred_prefix": "dolce" }, "dome": { "contact": { "email": "silvio.tosatto@unipd.it", "github": "silvio-tosatto", "name": "Silvio Tosatto", "orcid": "0000-0003-4525-7793" }, "contributor": { "email": "palayoor.n@northeastern.edu", "github": "nalikapalayoor", "name": "Nalika Palayoor", "orcid": "0009-0008-8406-631X" }, "description": "The DOME registry is a curated set of papers related to machine learning methods in biology, each with its own unique DOME identifier.", "example": "dfyn1yvtz3", "github_request_issue": 1374, "homepage": "https://registry.dome-ml.org", "mappings": { "miriam": "dome" }, "name": "DOME Registry", "pattern": "^[a-z0-9]{10}$", "preferred_prefix": "dome", "publications": [ { "doi": "10.1093/gigascience/giae094", "pmc": "PMC11633452", "pubmed": "39661723", "title": "DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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It includes operons for RNA genes.", "example": "1398574", "homepage": "http://csbl.bmb.uga.edu/DOOR/operon.php", "keywords": [ "dna" ], "mappings": { "biocontext": "DOOR", "miriam": "door", "n2t": "door", "prefixcommons": "door", "re3data": "r3d100014113" }, "name": "Database for Prokaryotic Operons", "pattern": "^\\d+$", "preferred_prefix": "door", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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This datatype provides access to specific models.", "example": "57", "homepage": "http://doqcs.ncbs.res.in/", "keywords": [ "model" ], "mappings": { "biocontext": "DOQCS.MODEL", "miriam": "doqcs.model", "n2t": "doqcs.model", "prefixcommons": "doqcs.model" }, "name": "Database of Quantitative Cellular Signaling: Model", "pattern": "^\\d+$", "preferred_prefix": "doqcs.model", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/doqcs.model:$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/btf860", "pubmed": "12584128", "title": "The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks", "year": 2003 } ], "uri_format": "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1" }, "doqcs.pathway": { "contact": { "email": "bhalla@ncbs.res.in", "github": "upibhalla", "name": "Upinder S. Bhalla", "orcid": "0000-0003-1722-5188" }, "description": "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways.", "example": "131", "homepage": "http://doqcs.ncbs.res.in/", "keywords": [ "pathway" ], "mappings": { "biocontext": "DOQCS.PATHWAY", "miriam": "doqcs.pathway", "n2t": "doqcs.pathway", "prefixcommons": "doqcs.pathway" }, "name": "Database of Quantitative Cellular Signaling: Pathway", "pattern": "^\\d+$", "preferred_prefix": "doqcs.pathway", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/doqcs.pathway:$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/btf860", "pubmed": "12584128", "title": "The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks", "year": 2003 } ], "uri_format": "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1" }, "dpbo": { "contact": { "email": "k.dumschott@fz-juelich.de", "github": "kdumschott", "name": "Kathryn Dumschott", "orcid": "0000-0002-9905-4011" }, "contributor": { "email": "h.doerpholz@fz-juelich.de", "github": "Hannah-Doerpholz", "name": "Hannah Dörpholz", "orcid": "0000-0002-0476-9699" }, "description": "With the DataPLANT biology ontology (DPBO), DataPLANT provides an intermediate ontology that acts as a broker and bridge between the individual researcher/domain experts and main ontology providers. DPBO enables easy and agile collection of missing vocabulary as well as relationships between terms for (meta)data annotation using DataPLANT’s Swate tool.", "download_obo": "https://raw.githubusercontent.com/nfdi4plants/nfdi4plants_ontology/refs/heads/main/dpbo.obo", "example": "0010015", "github_request_issue": 1466, "homepage": "https://www.nfdi4plants.org/", "keywords": [ "dataplant", "life sciences, biology", "ontology" ], "license": "CC-BY-4.0", "mappings": { "tib": "dpbo" }, "name": "DataPLANT Biology Ontology", "pattern": "^\\d+$", "preferred_prefix": "dpbo", "publications": [ { "doi": "10.11588/heibooks.1288.c18067", "title": "DataPLANT - Harnessing the Power of Ontologies for FAIR Research Data Management", "year": 2023 } ], "repository": "https://github.com/nfdi4plants/nfdi4plants_ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://purl.org/nfdi4plants/ontology/dpbo/DPBO_$1" }, "dpo": { "comment": "DPO is a subset of terms from FBcv", "contact": { "email": "cp390@cam.ac.uk", "github": "Clare72", "name": "Clare Pilgrim", "orcid": "0000-0002-1373-1705" }, "description": "An ontology of commonly encountered and/or high level Drosophila phenotypes.", "download_json": "http://purl.obolibrary.org/obo/dpo.json", "download_obo": "http://purl.obolibrary.org/obo/dpo.obo", "download_owl": "http://purl.obolibrary.org/obo/dpo.owl", "homepage": "http://purl.obolibrary.org/obo/fbcv", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "DPO", "bioportal": "DPO", "obofoundry": "dpo", "ols": "dpo", "ontobee": "DPO" }, "name": "Drosophila Phenotype Ontology", "no_own_terms": true, "part_of": "fbcv", "preferred_prefix": "DPO", "publications": [ { "doi": "10.1186/2041-1480-4-30", "pmc": "PMC3816596", "pubmed": "24138933", "title": "The Drosophila phenotype ontology", "year": 2013 } ], "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_$1", "version": "2026-01-13" }, "dpv": { "contact": { "email": "mike.adams@bbsrc.ac.uk", "name": "Michael J. Adams" }, "description": "Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene.", "example": "100", "homepage": "http://www.dpvweb.net/", "keywords": [ "classification", "gene", "people", "security" ], "mappings": { "biocontext": "DPV", "integbio": "nbdc02410", "lov": "dpv", "miriam": "dpv", "n2t": "dpv", "prefixcommons": "dpvweb" }, "name": "Description of Plant Viruses", "pattern": "^\\d+$", "preferred_prefix": "dpv", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/dpvweb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkj023", "pmc": "PMC1347386", "pubmed": "16381892", "title": "DPVweb: a comprehensive database of plant and fungal virus genes and genomes", "year": 2006 } ], "uri_format": "https://www.dpvweb.net/dpv/showdpv/?dpvno=$1" }, "dpvocab": { "comment": "The resource itself specifies a preferred prefix of `dpv` but this is already claimed in Bioregistry by the Description of Plant Viruses (https://bioregistry.io/registry/dpv). See also license discussion at https://github.com/w3c/dpv/issues/195.", "contact": { "email": "me@harshp.com", "github": "coolharsh55", "name": "Harshvardhan J. Pandit", "orcid": "0000-0002-5068-3714" }, "contributor": { "email": "jhc@lbl.gov", "github": "caufieldjh", "name": "Harry Caufield", "orcid": "0000-0001-5705-7831" }, "contributor_extras": [ { "email": "b.gyori@northeastern.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" }, { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, { "email": "arthit@gmail.com", "github": "bact", "name": "Arthit Suriyawongkul", "orcid": "0000-0002-9698-1899" } ], "description": "The Data Privacy Vocabulary provides an ontology (classes and properties) and taxonomies of concepts to represent information regarding how personal data is processed in the form of an ontology or a knowledge graph.", "example": "Duration", "github_request_issue": 1241, "homepage": "https://w3c.github.io/dpv/2.0/dpv", "keywords": [ "ess", "law", "nfdi4ing" ], "license": "W3C-20150513", "mappings": { "tib": "dpv" }, "name": "Data Privacy Vocabulary", "preferred_prefix": "dpvocab", "publications": [ { "doi": "10.48550/arxiv.2404.13426", "title": "Data Privacy Vocabulary (DPV) -- Version 2", "year": 2024 }, { "doi": "10.1007/978-3-030-33246-4_44", "title": "Creating a Vocabulary for Data Privacy", "year": 2019 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/1250" ], "repository": "https://github.com/w3c/dpv", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://w3id.org/dpv#$1" }, "dqv": { "description": "The Data Quality Vocabulary (DQV) is seen as an extension to DCAT to cover the quality of the data, how frequently is it updated, whether it accepts user corrections, persistence commitments etc. When used by publishers, this vocabulary will foster trust in the data amongst developers.", "example": "QualityAnnotation", "homepage": "https://www.w3.org/TR/vocab-dqv/", "keywords": [ "quality" ], "mappings": { "lov": "dqv", "zazuko": "dqv" }, "name": "Data Quality Vocabulary", "preferred_prefix": "dqv" }, "dragondb.allele": { "comment": "Deprecated because the website is dead", "deprecated": true, "description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information.", "example": "cho", "homepage": "http://www.antirrhinum.net/", "mappings": { "biocontext": "DRAGONDB.ALLELE", "miriam": "dragondb.allele", "n2t": "dragondb.allele" }, "name": "DragonDB Allele", "pattern": "^\\w+$", "preferred_prefix": "dragondb.allele", "uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele" }, "dragondb.dna": { "comment": "Deprecated because the website is dead", "deprecated": true, "description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information.", "example": "3hB06", "homepage": "http://www.antirrhinum.net/", "mappings": { "biocontext": "DRAGONDB.DNA", "miriam": "dragondb.dna", "n2t": "dragondb.dna" }, "name": "DragonDB DNA", "pattern": "^\\d\\w+$", "preferred_prefix": "dragondb.dna", "uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA" }, "dragondb.locus": { "comment": "Deprecated because the website is dead", "deprecated": true, "description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information.", "example": "DEF", "homepage": "http://www.antirrhinum.net/", "mappings": { "biocontext": "DRAGONDB.LOCUS", "miriam": "dragondb.locus", "n2t": "dragondb.locus" }, "name": "DragonDB Locus", "pattern": "^\\w+$", "preferred_prefix": "dragondb.locus", "uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus" }, "dragondb.protein": { "comment": "Deprecated because the website is dead", "deprecated": true, "description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information.", "example": "AMDEFA", "homepage": "http://www.antirrhinum.net/", "mappings": { "biocontext": "DRAGONDB.PROTEIN", "miriam": "dragondb.protein", "n2t": "dragondb.protein" }, "name": "DragonDB Protein", "pattern": "^\\w+$", "preferred_prefix": "dragondb.protein", "uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide" }, "dramp": { "contact": { "email": "zhengh18@hotmail.com", "name": "Heng Zheng", "orcid": "0000-0002-1810-5842" }, "contributor": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "Identifiers repesent antimicrobial peptides in the Data Repository of Antimicrobial Peptides (DRAMP) database which is an open-access, manually curated database of antimicrobial peptides (AMPs).", "example": "DRAMP00005", "github_request_issue": 1705, "homepage": "http://dramp.cpu-bioinfor.org", "keywords": [ "antimicrobial peptides" ], "name": "Data Repository of Antimicrobial Peptides", "pattern": "^DRAMP\\d{5}$", "preferred_prefix": "dramp", "providers": [ { "code": "abpdb", "description": "Antimicrobial Peptide Database (ABPDB) is a comprehensive database that aggregates antimicrobial peptide data from multiple sources including DRAMP, providing streamlined access to antimicrobial peptide information.", "homepage": "http://www.acdb.plus/ABPDB/", "name": "AntiBacterial Peptides DataBase", "publications": [ { "doi": "10.1109/tcbbio.2025.3582844", "pubmed": "40811252", "title": "ABPDB: a Database of Antibacterial Peptides", "year": 2025 } ], "uri_format": "http://www.acdb.plus/ABPDB/abp-search.php?keywords=$1" } ], "publications": [ { "doi": "10.1109/tcbbio.2025.3582844", "pubmed": "40811252", "title": "ABPDB: a Database of Antibacterial Peptides", "year": 2025 }, { "doi": "10.1093/nar/gkae1046", "pmc": "PMC11701585", "pubmed": "39526377", "title": "DRAMP 4.0: an open-access data repository dedicated to the clinical translation of antimicrobial peptides", "year": 2025 }, { "doi": "10.1093/nar/gkab651", "pmc": "PMC8728287", "pubmed": "34390348", "title": "DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides", "year": 2022 }, { "doi": "10.1038/s41597-019-0154-y", "pmc": "PMC6692298", "pubmed": "31409791", "title": "DRAMP 2.0, an updated data repository of antimicrobial peptides", "year": 2019 }, { "doi": "10.1038/srep24482", "pmc": "PMC4830929", "pubmed": "27075512", "title": "DRAMP: a comprehensive data repository of antimicrobial peptides", "year": 2016 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://dramp.cpu-bioinfor.org/browse/All_Information.php?id=$1" }, "drao": { "contact": { "email": "allyson.lister@oerc.ox.ac.uk", "github": "allysonlister", "name": "Allyson Lister", "orcid": "0000-0002-7702-4495" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A project supporting the DRAO application ontology, a hierarchy of specific research domains and descriptors which imports subsets of terms from over 40 publicly-available terminologies. (from repository)", "download_obo": "https://github.com/FAIRsharing/domain-ontology/raw/refs/heads/master/DRAO.obo", "download_owl": "https://github.com/FAIRsharing/domain-ontology/raw/refs/heads/master/DRAO.owl", "example": "0000001", "homepage": "http://www.fairsharing.org", "keywords": [ "agriculture", "biomedical science", "classification", "computer science", "earth science", "environmental science", "fair", "humanities", "life science", "metadata standardization", "natural science", "ontology", "resource metadata" ], "license": "CC-BY-4.0", "mappings": { "fairsharing": "FAIRsharing.FSIfv8" }, "name": "Domain Resource Application Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "drao", "repository": "https://github.com/FAIRsharing/domain-ontology", "uri_format": "http://www.fairsharing.org/ontology/domain/DRAO_$1" }, "drc.filenumber": { "contributor": { "email": "egon.willighagen@maastrichtuniversity.nl", "github": "egonw", "name": "Egon Willighagen", "orcid": "0000-0001-7542-0286" }, "description": "Dutch Research Council file numbers are used for approved grants.", "example": "osf232097", "github_request_issue": 1460, "homepage": "https://www.nwo.nl/en/", "name": "Dutch Research Council File Number", "preferred_prefix": "drc.filenumber", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.nwo.nl/en/projects/$1" }, "drduke": { "description": "identifier for chemicals linked to information on occurrence in plants", "example": "19", "homepage": "https://phytochem.nal.usda.gov/phytochem/search/list", "mappings": { "wikidata": "P10074" }, "name": "Dr. Duke's Phytochemical and Ethnobotanical Databases chemical", "preferred_prefix": "drduke", "uri_format": "https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1" }, "drks": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The German Clinical Trials Register (DRKS) is the German WHO primary registry. It is competent for the registration of all patient-oriented clinical trials conducted in Germany. The DRKS now contains well over 14,000 studies. Currently, around 2,000 studies are added annually. (from website)", "example": "DRKS00031815", "homepage": "http://drks.de", "name": "German Clinical Trials Register", "pattern": "^DRKS\\d+$", "preferred_prefix": "drks", "providers": [ { "code": "alt1", "description": "German Language Provider", "first_party": true, "homepage": "http://drks.de", "name": "German Language Provider", "uri_format": "https://drks.de/search/de/trial/$1" }, { "code": "alt2", "description": "Legacy Provider", "first_party": true, "homepage": "http://drks.de", "name": "Legacy Provider", "uri_format": "http://drks.de/en/trial/$1" } ], "uri_format": "https://drks.de/search/en/trial/$1" }, "dron": { "appears_in": [ "scdo" ], "contact": { "email": "hoganwr@gmail.com", "github": "hoganwr", "name": "William Hogan", "orcid": "0000-0002-9881-1017" }, "description": "An ontology to support comparative effectiveness researchers studying claims data.", "download_json": "http://purl.obolibrary.org/obo/dron.json", "download_obo": "http://purl.obolibrary.org/obo/dron.obo", "download_owl": "http://purl.obolibrary.org/obo/dron.owl", "example": "00023232", "homepage": "https://github.com/ufbmi/dron", "keywords": [ "approved drug", "biomedical science", "drug", "obo", "ontology", "small molecule" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "DRON", "biocontext": "DRON", "bioportal": "DRON", "fairsharing": "FAIRsharing.w5ntfd", "obofoundry": "dron", "ols": "dron", "ontobee": "DRON", "wikidata.entity": "Q81661592" }, "name": "The Drug Ontology", "pattern": "^\\d{8}$", "preferred_prefix": "DRON", "publications": [ { "doi": "10.1186/s13326-017-0121-5", "pmc": "PMC5335794", "pubmed": "28253937", "title": "Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request", "year": 2017 }, { "doi": "10.1186/s13326-016-0048-2", "pmc": "PMC4836073", "pubmed": "27096073", "title": "An accurate and precise representation of drug ingredients", "year": 2016 }, { "doi": "10.1186/2041-1480-4-44", "pmc": "PMC3931349", "pubmed": "24345026", "title": "Building a drug ontology based on RxNorm and other sources", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/DRON_$1", "repository": "https://github.com/mcwdsi/dron", "uri_format": "http://purl.obolibrary.org/obo/DRON_$1", "version": "2025-12-19" }, "drsanv0": { "description": "This namespace is used for GA4GH Data Repository Service (DRS) access to the USA National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI), Genomic Analysis, Visualization and Informatics Lab-space (AnVIL) program data. AnVIL is a cloud-based genomic data sharing and analysis platform which facilitates integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by the National Institutes of Health (NIH) or by other agencies that support human genomics research. ", "example": "v2_1b0f158a-86e2-3887-b990-89e3cf2d9082", "homepage": "https://www.genome.gov/", "mappings": { "miriam": "drs.anv0" }, "name": "AnVIL DRS", "pattern": "^v2_[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$", "preferred_prefix": "drsanv0", "uri_format": "https://data.terra.bio/ga4gh/drs/v1/objects/$1" }, "drsc": { "description": "The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene.", "example": "DRSC05221", "homepage": "http://flyrnai.org/", "mappings": { "biocontext": "DRSC", "miriam": "drsc", "n2t": "drsc" }, "name": "Drosophila RNAi Screening Center", "pattern": "^DRSC\\d+$", "preferred_prefix": "drsc", "uri_format": "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1" }, "drugbank": { "contact": { "email": "david.wishart@ualberta.ca", "github": "DavidWishartLab", "name": "David S. Wishart", "orcid": "0000-0002-3207-2434" }, "description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information.", "example": "DB14938", "homepage": "http://www.drugbank.ca", "keywords": [ "biomedical science", "drug", "life science", "protein" ], "logo": "https://upload.wikimedia.org/wikipedia/commons/thumb/f/fd/Drugbank_logo.svg/1280px-Drugbank_logo.svg.png", "mappings": { "bartoc": "18377", "biocontext": "DrugBank", "cellosaurus": "DrugBank", "cheminf": "000406", "edam": "2326", "fairsharing": "FAIRsharing.353yat", "integbio": "nbdc01071", "miriam": "drugbank", "n2t": "drugbank", "pathguide": "221", "prefixcommons": "drugbank", "re3data": "r3d100010544", "togoid": "Drugbank", "uniprot": "DB-0019", "wikidata": "P715", "wikidata.entity": "Q1122544" }, "name": "DrugBank", "pattern": "^DB\\d{5}$", "preferred_prefix": "drugbank", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/drugbank:$1" } ], "publications": [ { "doi": "10.1093/nar/gkad976", "pubmed": "37953279" }, { "doi": "10.1093/nar/gkt1068", "pmc": "PMC3965102", "pubmed": "24203711", "title": "DrugBank 4.0: shedding new light on drug metabolism", "year": 2013 }, { "doi": "10.1093/nar/gkq1126", "pmc": "PMC3013709", "pubmed": "21059682", "title": "DrugBank 3.0: a comprehensive resource for 'omics' research on drugs", "year": 2010 }, { "doi": "10.1093/nar/gkm958", "pmc": "PMC2238889", "pubmed": "18048412", "title": "DrugBank: a knowledgebase for drugs, drug actions and drug targets", "year": 2007 }, { "doi": "10.1093/nar/gkj067", "pmc": "PMC1347430", "pubmed": "16381955", "title": "DrugBank: a comprehensive resource for in silico drug discovery and exploration", "year": 2006 } ], "synonyms": [ "DRUGBANK_ID", "DrugBank" ], "twitter": "DrugBankDB", "uri_format": "https://go.drugbank.com/drugs/$1" }, "drugbank.bioentity": { "contact": { "email": "david.wishart@ualberta.ca", "github": "DavidWishartLab", "name": "David S. Wishart", "orcid": "0000-0002-3207-2434" }, "description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database.", "example": "BE0000048", "homepage": "http://www.drugbank.ca/targets", "logo": "https://upload.wikimedia.org/wikipedia/commons/thumb/f/fd/Drugbank_logo.svg/1280px-Drugbank_logo.svg.png", "mappings": { "biocontext": "DRUGBANKV4.TARGET", "miriam": "drugbankv4.target", "n2t": "drugbankv4.target" }, "name": "DrugBank Target v4", "pattern": "^BE\\d{7}$", "preferred_prefix": "drugbank.bioentity", "synonyms": [ "drugbank.target", "drugbankv4.target" ], "uri_format": "https://go.drugbank.com/bio_entities/$1" }, "drugbank.category": { "contact": { "email": "david.wishart@ualberta.ca", "github": "DavidWishartLab", "name": "David S. Wishart", "orcid": "0000-0002-3207-2434" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Close to 5K Categorizations for drugs, similar to ATCC.", "example": "DBCAT000600", "homepage": "https://go.drugbank.com/categories", "keywords": [ "chemistry", "drugs", "metascience", "topics" ], "logo": "https://upload.wikimedia.org/wikipedia/commons/thumb/f/fd/Drugbank_logo.svg/1280px-Drugbank_logo.svg.png", "name": "DrugBank Drug Category", "pattern": "^DBCAT\\d+$", "preferred_prefix": "drugbank.category", "uri_format": "https://www.drugbank.ca/categories/$1" }, "drugbank.condition": { "contact": { "email": "david.wishart@ualberta.ca", "github": "DavidWishartLab", "name": "David S. Wishart", "orcid": "0000-0002-3207-2434" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Indications and other conditions in drugbank", "example": "DBCOND0066902", "homepage": "https://go.drugbank.com", "logo": "https://upload.wikimedia.org/wikipedia/commons/thumb/f/fd/Drugbank_logo.svg/1280px-Drugbank_logo.svg.png", "name": "DrugBank Condition", "pattern": "^DBCOND\\d+$", "preferred_prefix": "drugbank.condition", "uri_format": "https://go.drugbank.com/indications/$1" }, "drugbank.metabolite": { "contact": { "email": "david.wishart@ualberta.ca", "github": "DavidWishartLab", "name": "David S. Wishart", "orcid": "0000-0002-3207-2434" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Metabolites in drugbank", "example": "DBMET02292", "homepage": "https://go.drugbank.com", "logo": "https://upload.wikimedia.org/wikipedia/commons/thumb/f/fd/Drugbank_logo.svg/1280px-Drugbank_logo.svg.png", "name": "DrugBank Metabolite", "pattern": "^DBMET\\d+$", "preferred_prefix": "drugbank.metabolite", "uri_format": "https://go.drugbank.com/metabolites/$1" }, "drugbank.reaction": { "contact": { "email": "david.wishart@ualberta.ca", "github": "DavidWishartLab", "name": "David S. Wishart", "orcid": "0000-0002-3207-2434" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Reactions in drugbank", "example": "1537", "homepage": "https://go.drugbank.com", "logo": "https://upload.wikimedia.org/wikipedia/commons/thumb/f/fd/Drugbank_logo.svg/1280px-Drugbank_logo.svg.png", "name": "DrugBank Reaction", "pattern": "^\\d+$", "preferred_prefix": "drugbank.reaction", "uri_format": "https://go.drugbank.com/reactions/$1" }, "drugbank.salt": { "contact": { "email": "david.wishart@ualberta.ca", "github": "DavidWishartLab", "name": "David S. Wishart", "orcid": "0000-0002-3207-2434" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets.", "example": "DBSALT001211", "homepage": "http://www.drugbank.ca", "keywords": [ "chemical", "compound", "salt", "small molecule" ], "logo": "https://upload.wikimedia.org/wikipedia/commons/thumb/f/fd/Drugbank_logo.svg/1280px-Drugbank_logo.svg.png", "name": "DrugBank Salts", "pattern": "^DBSALT\\d{6}$", "preferred_prefix": "drugbank.salt", "uri_format": "https://go.drugbank.com/salts/$1" }, "drugcentral": { "contact": { "email": "toprea@salud.unm.edu", "name": "Tudor Oprea", "orcid": "0000-0002-6195-6976" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action.", "example": "307", "homepage": "http://drugcentral.org", "keywords": [ "biomedical science", "drug development", "drug discovery", "drug repositioning", "pharmacology", "pharmacy" ], "license": "CC-BY-SA-4.0", "logo": "https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcTV8USVHMzllhzTb3yLIUbEA9qKRR4Sub2QDA&s", "mappings": { "biolink": "DrugCentral", "fairsharing": "FAIRsharing.3me82d", "integbio": "nbdc02192", "miriam": "drugcentral", "uniprot": "DB-0239", "wikidata": "P11198" }, "name": "Drug Central", "pattern": "^\\d+$", "preferred_prefix": "drugcentral", "publications": [ { "doi": "10.1093/nar/gkac1085", "pubmed": "36484092" }, { "doi": "10.1093/nar/gky963", "pmc": "PMC6323925", "pubmed": "30371892", "title": "DrugCentral 2018: an update", "year": 2019 }, { "doi": "10.1093/nar/gkw993", "pmc": "PMC5210665", "pubmed": "27789690", "title": "DrugCentral: online drug compendium", "year": 2016 } ], "synonyms": [ "Drug_Central" ], "uri_format": "http://drugcentral.org/drugcard/$1" }, "dsm4": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]", "example": "315.1", "example_extras": [ "291.89" ], "homepage": "https://en.wikipedia.org/wiki/Diagnostic_and_Statistical_Manual_of_Mental_Disorders#DSM-IV-TR_(2000)", "mappings": { "hl7": "2.16.840.1.113883.6.126", "wikidata": "P663", "wikidata.entity": "Q3078495" }, "name": "Diagnostic and Statistical Manual of Mental Disorders (4th Edition)", "pattern": "^\\d+\\.\\d+$", "preferred_prefix": "dsm4", "synonyms": [ "dsm-iv" ] }, "dsm5": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]", "example": "312.33", "homepage": "https://en.wikipedia.org/wiki/DSM-5", "mappings": { "hl7": "2.16.840.1.113883.6.344", "wikidata": "P1930" }, "name": "Diagnostic and Statistical Manual of Mental Disorders (5th Edition)", "pattern": "^\\d{3}\\.\\d{2}$", "preferred_prefix": "dsm5", "references": [ "https://archive.org/details/diagnosticstatis0005unse" ], "synonyms": [ "dsm-v" ] }, "dsmz": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). The following designations are used as part of local unique identifiers:\n\n- `PC`: positive control\n- `NC`: negative control\n- `AS`: antiserum\n- `PV`: plant viruses\n- `RT`: recommended test\n- `ACC`: human or animal cell line\n- `DSM`: microorganism cell line", "example": "ACC-1", "example_extras": [ "AS-0753", "DSM-2", "PC-0754", "PV-0998", "RT-0753" ], "homepage": "https://www.dsmz.de", "mappings": { "cellosaurus": "DSMZCellDive", "re3data": "r3d100010219" }, "name": "Deutsche Sammlung von Mikroorganismen und Zellkulturen", "pattern": "^(ACC|DSM|NC|PC|RT|AS|PV)-\\d+$", "preferred_prefix": "dsmz", "synonyms": [ "DSMZCellDive" ], "uri_format": "https://www.dsmz.de/collection/catalogue/details/culture/$1" }, "dso": { "contact": { "email": "evan@epatters.org", "github": "epatters", "name": "Evan Patterson", "orcid": "0000-0002-8600-949X" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Data Science Ontology is a research project of IBM Research AI and Stanford University Statistics. Its long-term objective is to improve the efficiency and transparency of collaborative, data-driven science.", "example": "classification-model", "homepage": "https://www.datascienceontology.org/", "keywords": [ "data science", "ontology" ], "name": "Data Science Ontology", "preferred_prefix": "dso", "repository": "https://github.com/IBM/datascienceontology", "uri_format": "https://www.datascienceontology.org/concept/$1" }, "dsw": { "contact": { "email": "steve.baskauf@vanderbilt.edu", "name": "Steve Baskauf" }, "description": "Version 0.4 to 1.0 fixed reversed dsw:locates and dsw:locatedAt. Added labels. Changed comments and descriptions to conform to DC and DwC precedent. Added subClassOf relations to RO hasEvidence and isEvidenceFor. Specified preferred direction for inverse object property pairs., Changes from version 0.2.1 to version 0.3: removal of all functional and inverse function properties of object property terms, use of dwctype classes, deprecation of terms replaced by dwciri: terms, removal of references to TDWG Ontology., Changes from version 0.3 to 0.4 change DwC class namespace from dwctype: to dwc: to follow class proposal, removed references to TDWG TaxonConcept ontology; deprecated terms that now have equivalent terms in Darwin Core., Change from version 1.0 to 1.0.1 Add CC0 license.", "example": "DriedSpecimen", "homepage": "https://github.com/darwin-sw/dsw", "keywords": [ "earth sciences", "ess", "fair data spaces", "life sciences, biology" ], "mappings": { "agroportal": "DSW", "ecoportal": "DSW", "tib": "dsw" }, "name": "Darwin-SW", "preferred_prefix": "dsw", "repository": "https://github.com/darwin-sw/dsw", "uri_format": "http://purl.org/dsw/$1" }, "dto": { "appears_in": [ "pr" ], "contact": { "email": "sschurer@med.miami.edu", "name": "Stephan Schurer" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.", "download_owl": "http://aber-owl.net/media/ontologies/DTO/4/dto.owl", "example": "90000018", "homepage": "https://github.com/DrugTargetOntology/DTO", "keywords": [ "biomedical science", "disease", "drug discovery", "drug target", "ontology", "protein" ], "mappings": { "aberowl": "DTO", "bioportal": "DTO", "fairsharing": "FAIRsharing.tke3y2" }, "name": "Drug Target Ontology", "pattern": "^\\d+$", "preferred_prefix": "dto", "publications": [ { "doi": "10.1186/s13326-017-0161-x", "pmc": "PMC5679337", "pubmed": "29122012", "title": "Drug target ontology to classify and integrate drug discovery data", "year": 2017 } ], "repository": "https://github.com/DrugTargetOntology/DTO", "uri_format": "http://www.drugtargetontology.org/dto/DTO_$1" }, "duo": { "appears_in": [ "scdo" ], "contact": { "email": "mcourtot@gmail.com", "github": "mcourtot", "name": "Melanie Courtot", "orcid": "0000-0002-9551-6370" }, "depends_on": [ "bfo", "iao" ], "description": "DUO is an ontology which represent data use conditions.", "download_owl": "http://purl.obolibrary.org/obo/duo.owl", "example": "0000046", "homepage": "https://github.com/EBISPOT/DUO", "keywords": [ "biomedical science", "computer science", "ess", "metadata standardization", "nfdi4chem", "nfdi4ing", "obo", "ontology", "subject agnostic" ], "license": "CC-BY-4.0", "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdmdCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--9a42083efa91d79ee5c7ed8e7868db0f7faf0b76/DUO_logo_white_background.png?disposition=inline", "mappings": { "aberowl": "DUO", "biocontext": "DUO", "bioportal": "DUO", "fairsharing": "FAIRsharing.5dnjs2", "obofoundry": "duo", "ols": "duo", "ontobee": "DUO", "tib": "duo", "wikidata.entity": "Q113009193" }, "name": "Data Use Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "DUO", "publications": [ { "doi": "10.1016/j.xgen.2021.100028", "pmc": "PMC8591903", "pubmed": "34820659", "title": "The Data Use Ontology to streamline responsible access to human biomedical datasets", "year": 2021 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/DUO_$1", "repository": "https://github.com/EBISPOT/DUO", "uri_format": "http://purl.obolibrary.org/obo/DUO_$1", "version": "2021-02-23" }, "dwc": { "contact": { "email": "gtuco.btuco@gmail.com", "github": "tucotuco", "name": "John Wieczorek", "orcid": "0000-0003-1144-0290" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Darwin Core is a vocabulary standard for transmitting information about biodiversity. This document lists all terms in namespaces currently used in the vocabulary.", "example": "Dataset", "github_request_issue": 1316, "homepage": "https://dwc.tdwg.org/list/", "keywords": [ "biodiversity", "geographic location", "life science", "sample annotation", "taxonomic classification" ], "mappings": { "fairsharing": "FAIRsharing.xvf5y3" }, "name": "Darwin Core Terms", "preferred_prefix": "dwc", "publications": [ { "doi": "10.1371/journal.pone.0102623", "pubmed": "25099149", "title": "The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet", "year": 2014 }, { "doi": "10.3897/bdj.2.e1039", "pubmed": "24723785", "title": "Linking multiple biodiversity informatics platforms with Darwin Core Archives", "year": 2014 }, { "doi": "10.1371/journal.pone.0029715", "pubmed": "22238640", "title": "Darwin Core: an evolving community-developed biodiversity data standard", "year": 2012 } ], "repository": "https://github.com/tdwg/dwc", "uri_format": "http://rs.tdwg.org/dwc/terms/$1" }, "dwc.doe": { "contact": { "email": "steve.baskauf@vanderbilt.edu", "name": "Steve Baskauf" }, "description": "The Darwin Core term degreeOfEstablishment provides information about degree to which an Organism survives, reproduces, and expands its range at the given place and time. The Degree of Establishment Controlled Vocabulary provides term that should be used as values for dwc:degreeOfEstablishment and dwciri:degreeOfEstablishment", "example": "d001", "homepage": "https://dwc.tdwg.org/doe/", "keywords": [ "fair data spaces", "life sciences, biology" ], "mappings": { "ecoportal": "DWCDOE", "tib": "dwcdoe" }, "name": "Degree of Establishment Controlled Vocabulary", "preferred_prefix": "dwc.doe", "uri_format": "http://rs.tdwg.org/dwcdoe/$1" }, "dwc.em": { "contact": { "email": "tuco@berkeley.edu", "name": "John Wieczorek" }, "description": "The Darwin Core term establishmentMeans provides information about whether an organism or organisms have been introduced to a given place and time through the direct or indirect activity of modern humans. The Establishment Means Controlled Vocabulary provides terms that should be used as values for dwc:establishmentMeans and dwciri:establishmentMeans.", "example": "e001", "homepage": "http://rs.tdwg.org/dwc/doc/em/", "keywords": [ "fair data spaces", "life sciences, biology" ], "mappings": { "ecoportal": "DWCEM", "tib": "dwcem" }, "name": "Establishment Means Controlled Vocabulary", "preferred_prefix": "dwc.em", "uri_format": "http://rs.tdwg.org/dwcem/$1" }, "dwc.pw": { "contact": { "email": "tuco@berkeley.edu", "name": "John Wieczorek" }, "description": "The Darwin Core term pathway provides information about the process by which an Organism came to be in a given place at a given time. The Pathway Controlled Vocabulary provides terms that should be used as values for dwc:pathway and dwciri:pathway.", "example": "p001", "homepage": "http://rs.tdwg.org/dwc/doc/pw/", "keywords": [ "fair data spaces", "life sciences, biology" ], "mappings": { "ecoportal": "DWCPW", "tib": "dwcpw" }, "name": "Darwin Core pathway controlled vocabulary", "preferred_prefix": "dwc.pw", "uri_format": "http://rs.tdwg.org/dwcpw/$1" }, "eaglei": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "Discovery tool for biomedical research resources available at institutions throughout the U.S.", "example": "0000012b-5661-2f63-2f73-b43980000000", "homepage": "https://hawaii.eagle-i.net", "mappings": { "cellosaurus": "eagle-i", "re3data": "r3d100011564" }, "name": "eagle-i", "preferred_prefix": "eaglei", "uri_format": "http://hawaii.eagle-i.net/i/$1" }, "earl": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "EARL is a vocabulary, the terms of which are defined across a set of specifications and technical notes, and that is used to describe test results. The primary motivation for developing this vocabulary is to facilitate the exchange of test results between Web accessibility evaluation tools in a vendor-neutral and platform-independent format. It also provides reusable terms for generic quality assurance and validation purposes. [from homepage]", "example": "Assertion", "homepage": "https://www.w3.org/TR/EARL10/", "keywords": [ "quality" ], "mappings": { "lov": "earl", "zazuko": "earl" }, "name": "Evaluation and Report Language", "preferred_prefix": "earl", "rdf_uri_format": "http://www.w3.org/ns/earl#$1", "uri_format": "http://www.w3.org/ns/earl#$1" }, "earthcube.aut": { "contact": { "email": "ruth.duerr3@gmail.com", "github": "rduerr", "name": "Ruth Duerr", "orcid": "0000-0003-4808-4736" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Audience Types Controlled Vocabulary was created for NSF's EarthCube program's Resource Registry. The vocabulary defines the types of audience each resource in the program is targeted to. At this point the vocabulary is very bare - no term definitions even; however, the intention is to extend the vocabulary over time. If you would like to assist with this or in extending any of the other controlled vocabularies/ontologies developed as part of the Resource Registry project, please see https://github.com/earthcubearchitecture-ecresourcereg.", "download_rdf": "https://github.com/earthcubearchitecture-ecresourcereg/AUT/raw/refs/heads/master/aut.ttl", "example": "0000001", "github_request_issue": 1627, "homepage": "http://cor.esipfed.org/ont/earthcube/AUT", "keywords": [ "audience type", "person", "role" ], "name": "Audience Types Controlled Vocabulary", "pattern": "^\\d{7}$", "preferred_prefix": "earthcube.aut", "repository": "https://github.com/earthcubearchitecture-ecresourcereg/AUT", "uri_format": "http://cor.esipfed.org/ont/earthcube/AUT_$1" }, "earthcube.mola": { "contact": { "email": "ruth.duerr3@gmail.com", "github": "rduerr", "name": "Ruth Duerr", "orcid": "0000-0003-4808-4736" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Data Model Language Controlled Vocabulary was created for NSF's EarthCube Program's Resource Registry. At this point it merely lists a few of the languages used by data model resources in the registry.", "download_rdf": "https://github.com/earthcubearchitecture-ecresourcereg/mola/raw/refs/heads/master/mola.ttl", "example": "000001", "github_request_issue": 1627, "homepage": "http://cor.esipfed.org/ont/earthcube/mola", "keywords": [ "metamodel" ], "name": "Data Model Language Controlled Vocabulary", "pattern": "^\\d+$", "preferred_prefix": "earthcube.mola", "rdf_uri_format": "http://cor.esipfed.org/ont/earthcube/MOLA_$1", "repository": "https://github.com/earthcubearchitecture-ecresourcereg/mola", "uri_format": "http://cor.esipfed.org/ont/earthcube/MOLA_$1" }, "earthcube.sfo": { "contact": { "email": "ruth.duerr3@gmail.com", "github": "rduerr", "name": "Ruth Duerr", "orcid": "0000-0003-4808-4736" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This ontology defines a taxonomy of software functions based on the work of the NSF-funded EarthCube Resource Registry working group. The functions are generally organized by their role in the research process.", "download_rdf": "https://github.com/earthcubearchitecture-ecresourcereg/sfo/raw/refs/heads/master/sfo.ttl", "example": "0000001", "github_request_issue": 1627, "homepage": "http://cor.esipfed.org/ont/earthcube/sfo", "keywords": [ "software", "software function" ], "name": "Software Functions Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "earthcube.sfo", "repository": "https://github.com/earthcubearchitecture-ecresourcereg/sfo", "uri_format": "http://cor.esipfed.org/ont/earthcube/SFO_$1" }, "earthcube.srt": { "contact": { "email": "ruth.duerr3@gmail.com", "github": "rduerr", "name": "Ruth Duerr", "orcid": "0000-0003-4808-4736" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Semantic Resource Types Vocabulary was created for NSF's EarthCube Program's Resource Repository. Includes entries for things like 'thesaurus', 'ontology', 'controlled vocabulary', 'taxonomy'.", "download_rdf": "https://github.com/earthcubearchitecture-ecresourcereg/srt/raw/refs/heads/master/srt.ttl", "example": "000001", "github_request_issue": 1627, "homepage": "http://cor.esipfed.org/ont/earthcube/srt", "keywords": [ "semantic resource" ], "name": "Semantic Resource Types Vocabulary", "pattern": "^\\d+$", "preferred_prefix": "earthcube.srt", "rdf_uri_format": "http://cor.esipfed.org/ont/earthcube/srt_$1", "repository": "https://github.com/earthcubearchitecture-ecresourcereg/srt", "uri_format": "http://cor.esipfed.org/ont/earthcube/srt_$1" }, "earthcube.swl": { "contact": { "email": "ruth.duerr3@gmail.com", "github": "rduerr", "name": "Ruth Duerr", "orcid": "0000-0003-4808-4736" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "This mini-ontology contains classes and instances for each version of the licenses that are commonly used in software projects, particularly open source software projects. The URI's for each are the canonical URI's for that license (where they exist).", "download_rdf": "https://earthcubearchitecture-ecresourcereg.github.io/swl/ontology.ttl", "example": "0000013", "github_request_issue": 1627, "homepage": "https://earthcubearchitecture-ecresourcereg.github.io/swl/index-en.html", "keywords": [ "license" ], "license": "CC0-1.0", "name": "Software Licenses Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "earthcube.swl", "providers": [ { "code": "earthcube", "description": "It's not clear why some URIs have this earthcube subpath", "homepage": "https://earthcubearchitecture-ecresourcereg.github.io/swl/index-en.html", "name": "Earthcube URI", "uri_format": "http://cor.esipfed.org/ont/earthcube/swl/SWL_$1" } ], "rdf_uri_format": "http://cor.esipfed.org/ont/SWL_$1", "repository": "https://github.com/earthcubearchitecture-ecresourcereg/swl", "uri_format": "http://cor.esipfed.org/ont/SWL_$1" }, "easychair.cfp": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Conferences in EasyChair", "example": "SysBioCancer2022", "homepage": "https://easychair.org/cfp/", "keywords": [ "conferences", "metascience" ], "name": "EasyChair Call for Paper", "preferred_prefix": "easychair.cfp", "uri_format": "https://easychair.org/cfp/$1" }, "easychair.topic": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Call for paper topics in EasyChair", "example": "27106865", "homepage": "https://easychair.org/cfp/", "keywords": [ "metascience", "topics" ], "name": "EasyChair Topic", "pattern": "^\\d+$", "preferred_prefix": "easychair.topic", "uri_format": "https://easychair.org/cfp/topic.cgi?tid=$1" }, "ebisc": { "description": "Cell line collections (Providers)", "example": "ESi007-A", "example_extras": [ "EDi008-B" ], "homepage": "https://www.ebisc.org", "mappings": { "cellosaurus": "EBiSC" }, "name": "European Bank for induced pluripotent Stem Cells", "pattern": "^E(S|D)i\\d+-\\w$", "preferred_prefix": "ebisc", "uri_format": "https://cells.ebisc.org/$1" }, "ec": { "comment": "The Nomenclature Committee website does not yet contain an official policy regarding the use of dashes in the hierarchical categorization of enzymes, so the Bioregistry's regular expression is permissive and accepts both EC identifiers with dashes (e.g. 2.3.-.-) and without dashes (e.g., 2.3). This means you may have to do post-processing of EC identifiers in data integration scenarios.", "contact": { "email": "kristian.axelsen@sib.swiss", "github": "kaxelsen", "name": "Kristian Axelsen", "orcid": "0000-0003-3889-2879" }, "description": "The Enzyme Nomenclature (also known as the Enzyme Commission Code) is a species-agnostic controlled vocabulary for specific enzymes and an associated hierarchical classification into 7 main categories.\n\nThe Enzyme Nomenclature is maintained by the [Nomenclature Committee](https://iubmb.org/about/committees/nomenclature-committee/) of the International Union of Biochemistry and Molecular Biology (IUBMB). A detailed history of the nomenclature since the 1950s can be found [here](https://iubmb.qmul.ac.uk/enzyme/history.html).\n\nThere are few notable resources providing access to the Enzyme Nomenclature:\n\n
WebsiteHomepageNotes
ExplorEnzhttps://www.enzyme-database.orgThis is the resource officially recommended by IUBMB
IUBMB (via by Queen Mary)https://iubmb.qmul.ac.uk/enzymeThis is a web-based version of the 1992 publication.
IntEnzhttps://www.ebi.ac.uk/intenzShutdown in 2024
ExPaSyhttps://enzyme.expasy.org
EnzymePortalhttps://www.ebi.ac.uk/enzymeportal
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The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology).", "download_json": "http://purl.obolibrary.org/obo/ecto.json", "download_obo": "http://purl.obolibrary.org/obo/ecto.obo", "download_owl": "http://purl.obolibrary.org/obo/ecto.owl", "example": "0000001", "homepage": "https://github.com/EnvironmentOntology/environmental-exposure-ontology", "keywords": [ "environmental science", "exposure", "obo", "ontology" ], "license": "CC0-1.0", "logo": "https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/ecto-logos/ecto-logo_black-banner.png", "mappings": { "aberowl": "ECTO", "agroportal": "ECTO", "biolink": "ECTO", "bioportal": "ECTO", "fairsharing": "FAIRsharing.6b77ac", "obofoundry": "ecto", "ols": "ecto", "ontobee": "ECTO", "wikidata.entity": "Q113012651" }, "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_$1", "version": "2023-02-14" }, "ecyano.entity": { "description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities.", "example": "23", "homepage": "http://www.e-cyanobacterium.org/bcs/entity/", "mappings": { "biocontext": "ECYANO.ENTITY", "miriam": "ecyano.entity", "n2t": "ecyano.entity" }, "name": "E-cyanobacterium entity", "pattern": "^\\d+$", "preferred_prefix": "ecyano.entity", "uri_format": "https://www.e-cyanobacterium.org/bcs/entity/$1" }, "ecyano.experiment": { "description": "E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments.", "example": "18", "homepage": "https://www.e-cyanobacterium.org/experiments-repository/", "mappings": { "miriam": "ecyano.experiment" }, "name": "E-cyanobacterium Experimental Data", "pattern": "^\\d+$", "preferred_prefix": "ecyano.experiment", "uri_format": "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1" }, "ecyano.model": { "description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models.", "example": "26", "homepage": "http://e-cyanobacterium.org/models/", "mappings": { "biocontext": "ECYANO.MODEL", "miriam": "ecyano.model", "n2t": "ecyano.model" }, "name": "E-cyanobacterium model", "pattern": "^\\d+$", "preferred_prefix": "ecyano.model", "uri_format": "https://e-cyanobacterium.org/models/model/$1" }, "ecyano.rule": { "description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules.", "example": "56", "homepage": "http://www.e-cyanobacterium.org/bcs/rule/", "mappings": { "biocontext": "ECYANO.RULE", "miriam": "ecyano.rule", "n2t": "ecyano.rule" }, "name": "E-cyanobacterium rule", "pattern": "^\\d+$", "preferred_prefix": "ecyano.rule", "uri_format": "https://e-cyanobacterium.org/bcs/rule/$1" }, "edam": { "contact": { "email": "matus.kalas@uib.no", "github": "matuskalas", "name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981" }, "description": "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "download_owl": "http://edamontology.org/1.25-20251112T1620Z-unstable(1.26)", "example": "data_1664", "homepage": "http://edamontology.org", "keywords": [ "bioinformatics", "computer science", "data acquisition", "data analysis", "data transformation", "dataplant", "earth sciences", "ess", "life science", "life sciences, biology", "nfdi4cat", "nfdi4chem", "nfdi4ing", "obo", "omics", "ontology" ], "license": "CC BY-SA 4.0", "mappings": { "aberowl": "EDAM", "agroportal": "EDAM", "biocontext": "EDAM", "bioportal": "EDAM", "fairsharing": "FAIRsharing.a6r7zs", "miriam": "edam", "n2t": "edam", "ols": "edam", "ontobee": "EDAM", "prefixcommons": "edam", "tib": "edam" }, "name": "EDAM Ontology", "pattern": "^(data|topic|operation|format)\\_\\d{4}$", "preferred_prefix": "edam", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/edam:$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/btt113", "pmc": "PMC3654706", "pubmed": "23479348", "title": "EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats", "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", "repository": "https://github.com/edamontology/edamontology", "twitter": "edamontology", "uri_format": "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1", "version": "1.25-20251112T1620Z-unstable(1.26)" }, "edam.data": { "contact": { "email": "matus.kalas@uib.no", "github": "matuskalas", "name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "example": "1664", "homepage": "http://edamontology.org", "keywords": [ "ontology" ], "mappings": { "biolink": "EDAM-DATA" }, "name": "EDAM Data", "pattern": "^\\d+$", "preferred_prefix": "edam.data", "repository": "https://github.com/edamontology/edamontology", "twitter": "edamontology", "uri_format": "http://edamontology.org/data_$1" }, "edam.format": { "contact": { "email": "matus.kalas@uib.no", "github": "matuskalas", "name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data.", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "example": "1915", "homepage": "http://edamontology.org", "keywords": [ "ontology" ], "mappings": { "biolink": "EDAM-FORMAT" }, "name": "EDAM Format", "pattern": "^\\d+$", "preferred_prefix": "edam.format", "repository": "https://github.com/edamontology/edamontology", "twitter": "edamontology", "uri_format": "http://edamontology.org/format_$1" }, "edam.operation": { "contact": { "email": "matus.kalas@uib.no", "github": "matuskalas", "name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "example": "0004", "homepage": "http://edamontology.org", "keywords": [ "ontology" ], "mappings": { "biolink": "EDAM-OPERATION" }, "name": "EDAM Operation", "pattern": "^\\d+$", "preferred_prefix": "edam.operation", "repository": "https://github.com/edamontology/edamontology", "twitter": "edamontology", "uri_format": "http://edamontology.org/operation_$1" }, "edam.topic": { "contact": { "email": "matus.kalas@uib.no", "github": "matuskalas", "name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "example": "0003", "homepage": "http://edamontology.org", "keywords": [ "ontology" ], "mappings": { "biolink": "EDAM-TOPIC" }, "name": "EDAM Topic", "pattern": "^\\d+$", "preferred_prefix": "edam.topic", "repository": "https://github.com/edamontology/edamontology", "twitter": "edamontology", "uri_format": "http://edamontology.org/topic_$1" }, "edcc": { "description": "EDCC Taxonomy contains the terms that are used to classify citizens' requests to the Europe Direct Contact Centre (EDCC). EDCC Taxonomy is maintained by the Directorate-General for Communication of the European Commission and published by the Publications Office of the European Union on the EU Vocabularies website.", "example": "00098e55", "homepage": "https://op.europa.eu", "keywords": [ "educational resources" ], "mappings": { "tib": "edcc" }, "name": "EDCC Taxonomy", "preferred_prefix": "edcc", "uri_format": "http://data.europa.eu/ett/kos/c_$1" }, "edda": { "contact": { "email": "tanja.bekhuis@tcbinfosci.com", "name": "Tanja Bekhuis", "orcid": "0000-0002-8537-9077" }, "description": "Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries.", "download_owl": "http://aber-owl.net/media/ontologies/EDDA/11/edda.owl", "example": "health_care_quality_assessment", "homepage": "https://bioportal.bioontology.org/ontologies/EDDA", "keywords": [ "medicine", "ontology" ], "mappings": { "aberowl": "EDDA", "bioportal": "EDDA", "fairsharing": "FAIRsharing.2ffmsb" }, "name": "EDDA Study Designs Taxonomy", "preferred_prefix": "edda", "uri_format": "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1" }, "edm": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Europeana Data Model (EDM) is aimed at being an integration medium for collecting, connecting and enriching the descriptions provided by Europeana data providers. The RDF vocabulary for http://www.europeana.eu/schemas/edm/ defines the elements introduced by EDM (as opposed to the ones EDM re-uses from other namespaces).", "download_owl": "https://github.com/europeana/metis-schema/raw/94c73a16320977fac121acfa366072e8e07e9158/src/main/resources/rdf_examples/edm.owl", "example": "Event", "homepage": "http://pro.europeana.eu/edm-documentation", "keywords": [ "catalogs", "ontology" ], "mappings": { "lov": "edm" }, "name": "Europeana Data Model vocabulary", "preferred_prefix": "edm", "repository": "https://github.com/europeana/metis-schema", "uri_format": "http://www.europeana.eu/schemas/edm/$1" }, "edm.fibo": { "comment": "FIBO is contructed as the union of many small ontologies, like sweetrealm, using hierarchical URIs based on the base URI prefix", "description": "FIBO defines the sets of things that are of interest in financial business applications and the ways that those things can relate to one another. In this way, FIBO can give meaning to any data (e.g., spreadsheets, relational databases, XML documents) that describe the business of finance", "example": "BE/MetadataBE/BEDomain", "homepage": "https://github.com/edmcouncil/fibo", "keywords": [ "coypu", "economics" ], "mappings": { "tib": "fibo" }, "name": "Financial Industry Business Ontology", "preferred_prefix": "edm.fibo", "repository": "https://github.com/edmcouncil/fibo", "uri_format": "https://spec.edmcouncil.org/fibo/ontology/$1" }, "educor": { "contact": { "email": "ilkou@l3s.de", "github": "eilkou", "name": "Eleni Ilkou", "orcid": "0000-0002-4847-6177" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An educational ontology for personalised recommendation learning systems that is based on learning path and user profile. It represents the key components for a personalised learning system based on our requirement analysis.", "download_rdf": "https://github.com/tibonto/educor/raw/refs/heads/main/educor.ttl", "example": "stri", "homepage": "http://ontology.tib.eu/educor/", "license": "CC0-1.0", "name": "An Educational and Career-Oriented Recommendation Ontology", "preferred_prefix": "educor", "publications": [ { "doi": "10.1007/978-3-030-88361-4_32", "title": "EduCOR: An Educational and Career-Oriented Recommendation Ontology", "year": 2021 } ], "repository": "https://github.com/tibonto/educor", "uri_format": "https://github.com/tibonto/educor#$1" }, "efo": { "contact": { "email": "plwhetzel@gmail.com", "github": "twhetzel", "name": "Trish Whetzel", "orcid": "0000-0002-3458-4839" }, "description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.", "download_obo": "http://www.ebi.ac.uk/efo/efo.obo", "download_owl": "http://www.ebi.ac.uk/efo/efo.owl", "example": "0005147", "homepage": "http://www.ebi.ac.uk/efo", "keywords": [ "assay", "dataplant", "earth sciences", "ess", "experimental condition", "experimental measurement", "genome-wide association study", "genomics", "life sciences, biology", "medicine", "nfdi4chem", "omics", "ontology", "proteomics", "study design", "study design independent variable" ], "license": "Apache-2.0", "logo": "https://upload.wikimedia.org/wikipedia/en/d/d8/Logo_of_the_Experimental_Factor_Ontlogy.gif", "mappings": { "aberowl": "EFO", "agroportal": "EFO", "biocontext": "EFO", "biolink": "EFO", "bioportal": "EFO", "cellosaurus": "EFO", "fairsharing": "FAIRsharing.1gr4tz", "miriam": "efo", "n2t": "efo", "ols": "efo", "ontobee": "EFO", "tib": "efo", "wikidata": "P11956" }, "name": "Experimental Factor Ontology", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^\\d{7}$", "preferred_prefix": "EFO", "providers": [ { "code": "ebi", "description": "EFO through Functional Genomics Group (EBI)", "homepage": "https://www.ebi.ac.uk/efo/", "name": "EFO through Functional Genomics Group (EBI)", "uri_format": "https://www.ebi.ac.uk/efo/EFO_$1" }, { "code": "ols.curie", "description": "OLS via CURIE", "homepage": "https://www.ebi.ac.uk/ols", "name": "OLS", "uri_format": "http://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/btq099", "pmc": "PMC2853691", "pubmed": "20200009", "title": "Modeling sample variables with an Experimental Factor Ontology", "year": 2010 } ], "repository": "https://github.com/EBISPOT/efo", "uri_format": "http://www.ebi.ac.uk/efo/EFO_$1", "version": "3.86.0" }, "ega": { "description": "The European Genome-phenome Archive (EGA) is a global network for permanent archiving and sharing of personally identifiable genetic, phenotypic, and clinical data generated for the purposes of biomedical research projects or in the context of research-focused healthcare systems. Jointly managed by the European Bioinformatics Institute (EMBL-EBI) in Cambridge (UK) and the Centre for Genomic Regulation (CRG) in Barcelona.", "example": "EGAD00001008392", "homepage": "https://ega-archive.org/", "mappings": { "cellosaurus": "EGA", "edam": "2383", "miriam": "ega" }, "name": "European Genome-phenome Archive", "pattern": "^EGA[SCPNRXZDBF][0-9]{11}$", "preferred_prefix": "ega", "uri_format": "https://ega-archive.org/identifiers/$1" }, "ega.dataset": { "contact": { "email": "tk2@ebi.ac.uk", "github": "tk2", "name": "Thomas Keane", "orcid": "0000-0001-7532-6898" }, "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.", "example": "EGAD00000000001", "homepage": "https://ega-archive.org/", "keywords": [ "biology", "biomedical science", "clinical studies", "genomics", "phenomics" ], "mappings": { "biocontext": "EGA.DATASET", "fairsharing": "FAIRsharing.mya1ff", "miriam": "ega.dataset", "n2t": "ega.dataset", "re3data": "r3d100011242" }, "name": "European Genome-phenome Archive Dataset", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^EGAD\\d{11}$", "preferred_prefix": "ega.dataset", "providers": [ { "code": "omicsdi", "description": "EGA Dataset through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "EGA Dataset through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/ega/$1" } ], "publications": [ { "doi": "10.1093/nar/gkab1059", "pmc": "PMC8728218", "pubmed": "34791407", "title": "The European Genome-phenome Archive in 2021", "year": 2022 }, { "doi": "10.1038/ng.3312", "pmc": "PMC5426533", "pubmed": "26111507", "title": "The European Genome-phenome Archive of human data consented for biomedical research", "year": 2015 } ], "twitter": "EGAarchive", "uri_format": "https://www.ebi.ac.uk/ega/datasets/$1" }, "ega.study": { "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.", "example": "EGAS00000000001", "homepage": "https://www.ebi.ac.uk/ega/studies", "mappings": { "biocontext": "EGA.STUDY", "miriam": "ega.study", "n2t": "ega.study" }, "name": "European Genome-phenome Archive Study", "pattern": "^EGAS\\d{11}$", "preferred_prefix": "ega.study", "uri_format": "https://www.ebi.ac.uk/ega/studies/$1" }, "eggnog": { "contact": { "email": "j.huerta@csic.es", "github": "jhcepas", "name": "Jaime Huerta-Cepas", "orcid": "0000-0003-4195-5025" }, "deprecated": true, "description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. 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This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. 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Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.", "download_obo": "https://github.com/Planteome/plant-experimental-conditions-ontology/raw/refs/heads/master/peco.obo", "download_owl": "https://github.com/Planteome/plant-experimental-conditions-ontology/raw/refs/heads/master/peco.owl", "example": "0007404", "homepage": "http://planteome.org/", "keywords": [ "obo", "ontology", "plant" ], "license": "CC-BY-4.0", "logo": "http://planteome.org/sites/default/files/garland_logo.PNG", "mappings": { "aberowl": "EO", "agroportal": "EO", "biocontext": "EO", "miriam": "eo", "n2t": "eo", "obofoundry": "eo", "prefixcommons": "eo" }, "name": "Plant Environment Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "EO", "providers": [ { "code": "", "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.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/eo:$1" } ], "publications": [ { "doi": "10.3732/ajb.1200222", "pmc": "PMC3492881", "pubmed": "22847540", "title": "Ontologies as integrative tools for plant science", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/EO_$1", "repository": "https://github.com/Planteome/plant-environment-ontology", "uri_format": "http://purl.obolibrary.org/obo/EO_$1" }, "eol": { "contact": { "email": "pylebail@rennes.inra.fr", "name": "Pierre-Yves LeBail", "orcid": "0000-0002-8310-5195" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems.", "download_owl": "http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=eol.owl", "example": "0001927", "homepage": "http://www.atol-ontology.com", "keywords": [ "agriculture", "animal husbandry", "environmental science", "livestock", "ontology", "species-environment interaction" ], "mappings": { "aberowl": "EOL", "agroportal": "EOL", "bioportal": "EOL", "fairsharing": "FAIRsharing.w7bw2y", "ols": "eol", "re3data": "r3d100011663" }, "name": "Environment Ontology for Livestock", "pattern": "^\\d{7}$", "preferred_prefix": "eol", "uri_format": "http://purl.org/obo/owlEOL_$1", "version": "2018-09-13" }, "eol.schema": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Predicates in the Encyclopedia of Life data schema for describing animals, plants, and other organisms", "example": "body_symmetry", "github_request_issue": 1421, "homepage": "https://eol.org/terms/glossary/", "name": "Encyclopedia of Life Schema", "preferred_prefix": "eol.schema", "uri_format": "http://eol.org/schema/terms/$1" }, "eolife": { "contact": { "email": "secretariat@eol.org", "name": "EOL Secretariat", "orcid": "0000-0002-9943-2342" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A collaborative project intended to create an encyclopedia documenting all living species known to science", "example": "1044544", "homepage": "https://eol.org", "keywords": [ "biodiversity", "biology", "ecology", "taxonomy" ], "mappings": { "fairsharing": "FAIRsharing.3J6NYn", "re3data": "r3d100010229", "wikidata": "P830" }, "name": "Encyclopedia of Life", "pattern": "^\\d+$", "preferred_prefix": "eolife", "twitter": "eol", "uri_format": "https://eol.org/pages/$1" }, "epawaste": { "contact": { "email": "brennan.thomas@epa.gov", "name": "Tom Brennan" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "This resource provides identifiers for listed hazardous wastes which are substances explicitly identified due to their potential harm to human health and the environment. These are categorized into four groups (F, K, P, and U) based on specific criteria, such as their source or inherent properties.", "example": "F001", "example_extras": [ "K001", "P001", "U001" ], "github_request_issue": 1246, "homepage": "https://www.ecfr.gov/current/title-40/chapter-I/subchapter-I/part-261", "name": "EPA Hazardous Wastes", "pattern": "^[FKPU]\\d{3}$", "preferred_prefix": "epawaste", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" } }, "epcc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Collection of European paediatric cardiac coding files", "homepage": "https://www.aepc.org/european-paediatric-cardiac-coding", "name": "European Paediatric Cardiac Codes", "preferred_prefix": "epcc", "proprietary": true, "references": [ "https://www.cambridge.org/core/journals/cardiology-in-the-young/article/abs/european-paediatric-cardiac-codes-the-long-list-with-icd9-icd10-crossmapping-and-crossmap-to-epcc-short-list/FCA4DFCCB661298294A3D113FC79D5BE" ] }, "epd": { "contact": { "email": "Philipp.Bucher@sib.swiss", "name": "Philipp Bucher", "orcid": "0000-0002-0816-7775" }, "contributor_extras": [ { "email": "sebastien.moretti@sib.swiss", "github": "smoretti", "name": "Sébastien Moretti", "orcid": "0000-0003-3947-488X" } ], "description": "The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.", "example": "TA_H3", "homepage": "https://epd.expasy.org/epd/", "keywords": [ "bioinformatics", "biology" ], "mappings": { "biocontext": "EPD", "edam": "2386", "fairsharing": "FAIRsharing.yk1krv", "integbio": "nbdc00438", "miriam": "epd", "n2t": "epd", "ncbi": "EPD", "uniprot": "DB-0205" }, "name": "Eukaryotic Promoter Database", "pattern": "^[A-Z-_0-9]+$", "preferred_prefix": "epd", "publications": [ { "doi": "10.1093/nar/27.1.307", "pmc": "PMC148166", "pubmed": "9847211", "title": "The Eukaryotic Promoter Database (EPD): recent developments", "year": 1999 }, { "doi": "10.1093/nar/26.1.353", "pmc": "PMC147208", "pubmed": "9399872", "title": "The Eukaryotic Promoter Database EPD", "year": 1998 }, { "doi": "10.1093/nar/14.24.10009", "pmc": "PMC341352", "pubmed": "3808945", "title": "Compilation and analysis of eukaryotic POL II promoter sequences", "year": 1986 }, { "doi": "10.1093/nar/gkx807", "pmc": "PMC5753345", "pubmed": "28981707", "title": "The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics", "year": 2018 }, { "doi": "10.1093/nar/gkw1069", "pmc": "PMC5210552", "pubmed": "27899657", "title": "The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms", "year": 2016 }, { "doi": "10.1093/nar/gku1111", "pmc": "PMC4383928", "pubmed": "25378343", "title": "The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools", "year": 2014 }, { "doi": "10.1093/nar/gks1233", "pmc": "PMC3531148", "pubmed": "23193273", "title": "EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era", "year": 2012 }, { "doi": "10.1093/nar/gkj146", "pmc": "PMC1347508", "pubmed": "16381980", "title": "EPD in its twentieth year: towards complete promoter coverage of selected model organisms", "year": 2006 }, { "doi": "10.1093/nar/gkh122", "pmc": "PMC308856", "pubmed": "14681364", "title": "The Eukaryotic Promoter Database EPD: the impact of in silico primer extension", "year": 2004 }, { "doi": "10.1093/nar/30.1.322", "pmc": "PMC99099", "pubmed": "11752326", "title": "The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data", "year": 2002 }, { "doi": "10.1093/nar/28.1.302", "pmc": "PMC102462", "pubmed": "10592254", "title": "The eukaryotic promoter database (EPD)", "year": 2000 } ], "uri_format": "https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0=$1" }, "epio": { "contact": { "email": "alpha.tom.kodamullil@scai.fraunhofer.de", "github": "akodamullil", "name": "Alpha Tom Kodamullil", "orcid": "0000-0001-9896-3531" }, "depends_on": [ "bfo" ], "description": "A application driven Epilepsy Ontology with official terms from the ILAE.", "download_owl": "http://purl.obolibrary.org/obo/epio.owl", "example": "0000011", "homepage": "https://github.com/SCAI-BIO/EpilepsyOntology", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "EPIO", "bioportal": "EPIO", "obofoundry": "epio", "ontobee": "EPIO", "wikidata.entity": "Q113012657" }, "name": "Epilepsy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "EPIO", "providers": [ { "code": "legacy", "description": "Legacy internal URL before switching to OBO PURL", "homepage": "https://bio.scai.fraunhofer.de/ontolog", "name": "Legacy", "uri_format": "https://bio.scai.fraunhofer.de/ontology/epilepsy#$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/EPIO_$1", "repository": "https://github.com/SCAI-BIO/EpilepsyOntology", "uri_format": "http://purl.obolibrary.org/obo/EPIO_$1" }, "epo": { "contributor_extras": [ { "github": "djinnome", "name": "Jeremy Zucker", "orcid": "0000-0002-7276-9009" } ], "deprecated": true, "description": "An ontology designed to support the semantic annotation of epidemiology resources", "download_owl": "https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/epidemiology-ontology/epo.owl", "homepage": "https://code.google.com/p/epidemiology-ontology/", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "EPO", "obofoundry": "epo", "ontobee": "EPO" }, "name": "Epidemiology Ontology", "preferred_prefix": "EPO", "rdf_uri_format": "http://purl.obolibrary.org/obo/EPO_$1", "uri_format": "http://purl.obolibrary.org/obo/EPO_$1" }, "epso": { "contact": { "email": "satyasahoo@ieee.org", "name": "Satya S. 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", "download_owl": "http://aber-owl.net/media/ontologies/EPSO/3/epso.owl", "example": "0000400", "homepage": "http://prism.case.edu/prism/index.php/EpilepsyOntology", "keywords": [ "epilepsy", "neurology", "ontology", "patient care" ], "mappings": { "aberowl": "EPSO", "bioportal": "EPSO", "fairsharing": "FAIRsharing.ttprgy", "ontobee": "EPSO" }, "name": "Epilepsy and Seizure Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "epso", "publications": [ { "doi": "10.1136/amiajnl-2013-001696", "pmc": "PMC3912711", "pubmed": "23686934", "title": "Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care", "year": 2013 } ], "uri_format": "http://www.case.edu/EpilepsyOntology.owl#$1" }, "erm": { "contact": { "email": "egon.willighagen@gmail.com", "github": "egonw", "name": "Egon Willighagen", "orcid": "0000-0001-7542-0286" }, "description": "The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project.", "download_rdf": "https://nanocommons.github.io/identifiers/registry", "example": "ERM00000044", "homepage": "https://nanocommons.github.io/identifiers/", "keywords": [ "chemical entity", "materials informatics", "materials science", "nanotechnology" ], "mappings": { "cheminf": "000569", "fairsharing": "FAIRsharing.c26a4e", "miriam": "erm", "n2t": "erm" }, "name": "European Registry of Materials", "pattern": "^ERM[0-9]{8}$", "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", "pmc": "PMC9400299", "pubmed": "36002868", "title": "European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials", "year": 2022 } ], "twitter": "nanocommons", "uri_format": "https://nanocommons.github.io/identifiers/registry#$1" }, "ero": { "contact": { "email": "Marc_Ciriello@hms.harvard.edu", "name": "Marc Ciriello", "orcid": "0000-0002-3734-1859" }, "deprecated": true, "description": "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.", "download_owl": "http://purl.obolibrary.org/obo/ero.owl", "example": "0001655", "homepage": "https://open.med.harvard.edu/wiki/display/eaglei/Ontology", "keywords": [ "biomedical science", "biospecimen", "life science", "obo", "ontology", "reagent", "study design" ], "license": "CC BY 2.0", "mappings": { "aberowl": "ERO", "biocontext": "ERO", "bioportal": "ERO", "fairsharing": "FAIRsharing.nwgynk", "obofoundry": "ero", "ols": "ero", "ontobee": "ERO" }, "name": "eagle-i resource ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ERO", "publications": [ { "doi": "10.1109/jcdl.2017.7991571", "pmc": "PMC5868434", "pubmed": "29599662", "title": "Automating data citation: the eagle-i experience", "year": 2017 }, { "doi": "10.1093/database/bar067", "pmc": "PMC3308157", "pubmed": "22434835", "title": "Research resources: curating the new eagle-i discovery system", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/ERO_$1", "uri_format": "http://purl.obolibrary.org/obo/ERO_$1", "version": "2016-07-27" }, "eropmoscow": { "description": "EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence database which strives to provide a high level of annotations (such as descriptions of the structure of an oligopeptide, its source and function, post-translational modifications, etc.).", "example": "E00002", "homepage": "http://erop.inbi.ras.ru", "keywords": [ "protein" ], "mappings": { "integbio": "nbdc00265", "prefixcommons": "eropmoscow" }, "name": "Endogenous Regulatory OligoPeptide knowledgebase-Moscow", "preferred_prefix": "eropmoscow", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/eropmoscow:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://erop.inbi.ras.ru/result2.php?PepName=$1" }, "erudite": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A metadata stadnard to model data science training materials. Later, was replaced by Bioschemas' [training materials specification](http://bioschemas.org/specifications/TrainingMaterial/specification/).", "example": "enables", "homepage": "https://www.pagestudy.org/erudite-training-resource-standard", "keywords": [ "educational resource", "learning material", "open educational resource", "schema" ], "name": "Educational Resource Discovery Index Schema", "preferred_prefix": "erudite", "uri_format": "http://www.bigdatau.org/schema#$1" }, "erv": { "description": "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features.", "example": "THE1B", "homepage": "https://herv.img.cas.cz/", "mappings": { "biocontext": "ERV", "miriam": "erv", "n2t": "erv" }, "name": "Human Endogenous Retrovirus Database", "pattern": "^[A-Za-z0-9\\-\\_]+$", "preferred_prefix": "erv", "uri_format": "https://herv.img.cas.cz/s/$1" }, "esco.isco": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The European Skills, Competences, Qualifications and Occupations (ESCO) International Standard Classification of Occupations (ISCO).", "example": "C4", "homepage": "https://esco.ec.europa.eu/classification", "name": "ESCO - International Standard Classification of Occupations", "preferred_prefix": "esco.isco", "uri_format": "http://data.europa.eu/esco/isco/$1" }, "esco.model": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The ontology of the taxonomy \"European Skills, Competences, qualifications and Occupations\". The ontology considers three ESCO pillars (or taxonomy) and 2 registers. The three pillars are: 1) Occupation, 2) Skill (and competences), and 3) Qualification", "example": "Occupation", "homepage": "https://ec.europa.eu/esco/lod/static/model.html", "name": "ESCO Ontology", "preferred_prefix": "esco.model", "rdf_uri_format": "http://data.europa.eu/esco/model#$1", "uri_format": "https://ec.europa.eu/esco/lod/static/model.html#$1" }, "esco.occupation": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The ESCO occupations pillar is built on ISCO-08 which serves as its hierarchical structure. ISCO-08 provides the top four levels for the occupations pillar and ESCO occupations are located at level 5 and lower. In ESCO, each occupation is mapped to exactly one ISCO-08 code. [from homepage]", "example": "eea2b5c6-48d1-4612-957e-585783b3c7bb", "homepage": "https://esco.ec.europa.eu/en/classification/occupation_main", "name": "ESCO Occupation", "preferred_prefix": "esco.occupation", "rdf_uri_format": "http://data.europa.eu/esco/occupation/$1", "uri_format": "http://data.europa.eu/esco/occupation/$1" }, "esco.skill": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A vocabulary of knowledge, skills and competences relevant to the European labour market. In ESCO v1.2.0, the skills pillar is structured in a hierarchy which contains the following four sub-classifications: 1) Knowledge, 2) Language skills and knowledge, 3) Skills, and 4) Transversal skills. [adapted from homepage]", "example": "dc06de9f-dd3a-4f28-b58f-b01b5ae72ab8", "homepage": "http://data.europa.eu/esco/skill", "name": "ESCO Skill", "preferred_prefix": "esco.skill", "uri_format": "http://data.europa.eu/esco/skill/$1" }, "esldb": { "description": "eSLDB is a database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.", "example": "HS000015122", "homepage": "http://gpcr.biocomp.unibo.it/esldb", "keywords": [ "protein" ], "mappings": { "prefixcommons": "esldb" }, "name": "eukaryotic Subcellular Localization database", "preferred_prefix": "esldb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/esldb:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice=$1" }, "estdab": { "comment": "Website is dead", "deprecated": true, "description": "Cell line databases/resources", "example": "046", "homepage": "https://www.ebi.ac.uk/ipd/estdab/", "mappings": { "cellosaurus": "ESTDAB" }, "name": "European Searchable Tumour Line Database", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^\\d{3}$", "preferred_prefix": "estdab", "uri_format": "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1" }, "eu.publication": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Datasets published by the Publications Office of the European Union", "example": "euvoc", "homepage": "https://op.europa.eu", "name": "European Union Publications Office dataset", "preferred_prefix": "eu.publication", "uri_format": "http://publications.europa.eu/resource/dataset/$1" }, "eu89h": { "description": "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union.", "example": "jrc-eurl-ecvam-chemagora", "homepage": "http://data.jrc.ec.europa.eu/", "mappings": { "biocontext": "EU89H", "miriam": "eu89h", "n2t": "eu89h" }, "name": "JRC Data Catalogue", "pattern": "^[a-z0-9\\-_]+$", "preferred_prefix": "eu89h", "uri_format": "http://data.europa.eu/89h/$1" }, "eubopen": { "contact": { "email": "tredup@pharmchem.uni-frankfurt.de", "name": "Claudia Tredup", "orcid": "0000-0001-6518-3344" }, "contributor": { "email": "palayoor.n@northeastern.edu", "github": "nalikapalayoor", "name": "Nalika Palayoor", "orcid": "0009-0008-8406-631X" }, "description": "EUbOPEN is a project focusing on organizing chemogenic library collections, advancing chemical probe discovery, profiling bioactive compounds, and making project data more accessible.", "example": "EUB0000221", "github_request_issue": 1378, "homepage": "https://gateway.eubopen.org", "name": "Enabling and Unlocking Biology in the Open", "pattern": "^EUB\\d{7}$", "preferred_prefix": "eubopen", "publications": [ { "doi": "10.1039/d4md00735b", "pmc": "PMC11605244", "pubmed": "39618964", "title": "Toward target 2035: EUbOPEN - a public-private partnership to enable & unlock biology in the open", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://gateway.eubopen.org/compound/$1" }, "euclinicaltrials": { "description": "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.", "example": "2008-005144-16", "homepage": "https://www.clinicaltrialsregister.eu/", "mappings": { "biocontext": "EUCLINICALTRIALS", "miriam": "euclinicaltrials", "n2t": "euclinicaltrials" }, "name": "EU Clinical Trials", "pattern": "^\\d{4}\\-\\d{6}\\-\\d{2}$", "preferred_prefix": "euclinicaltrials", "synonyms": [ "EUCTR" ], "uri_format": "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1" }, "eugenes": { "contact": { "email": "eugenes@iubio.bio.indiana.edu", "name": "Don Gilbert", "orcid": "0000-0002-6646-7274" }, "description": "euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information.", "example": "MGgn0008978", "homepage": "http://eugenes.org/", "keywords": [ "genome", "life science", "ontology" ], "mappings": { "fairsharing": "FAIRsharing.7fc5y6", "prefixcommons": "eugenes" }, "name": "Eukaryotic Genes", "preferred_prefix": "eugenes", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/eugenes:$1" } ], "publications": [ { "doi": "10.1093/nar/30.1.145", "pmc": "PMC99146", "pubmed": "11752277", "title": "euGenes: a eukaryote genome information system", "year": 2002 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://eugenes.org:7072/.bin/fbidq.html?$1" }, "eupath": { "appears_in": [ "scdo" ], "contact": { "email": "jiezhen@med.umich.edu", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "deprecated": true, "description": "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.", "download_owl": "http://purl.obolibrary.org/obo/eupath.owl", "example": "0010316", "homepage": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology", "keywords": [ "biomedical science", "epidemiology", "functional genomics", "microbiome", "obo", "ontology", "population genetics" ], "license": "CC-BY-4.0", "logo": "https://raw.githubusercontent.com/EuPathDB/communitysite/master/assets/images/VEuPathDB-logo-s.png", "mappings": { "aberowl": "EUPATH", "biocontext": "EUPATH", "bioportal": "EUPATH", "fairsharing": "FAIRsharing.9rhr9j", "obofoundry": "eupath", "ols": "eupath", "ontobee": "EUPATH", "wikidata.entity": "Q81661607" }, "name": "VEuPathDB ontology", "pattern": "^\\d{7}$", "preferred_prefix": "EUPATH", "publications": [ { "doi": "10.5281/zenodo.6685957", "title": "Malaria study data integration and information retrieval based on OBO Foundry ontologies", "year": 2016 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/EUPATH_$1", "repository": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology", "uri_format": "http://purl.obolibrary.org/obo/EUPATH_$1", "version": "2023-05-30" }, "eurofir": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries.", "homepage": "https://www.eurofir.org", "name": "European Food Information Resource Network", "preferred_prefix": "eurofir", "proprietary": true }, "europa.dcf": { "description": "The Digital Competence Framework for Citizens standard list identifies the key components of digital competence in 5 broader, and a total of 21 narrower areas, with eight proficiency levels for each concept and a few contextualising examples of use. It is maintained by DG EMPL and published by the Publications Office of the European Union on the EU Vocabularies website.", "example": "00b51s9rc5", "homepage": "https://op.europa.eu/de/home", "keywords": [ "educational resources", "literature", "social sciences" ], "mappings": { "tib": "dcf" }, "name": "Digital Competence Framework", "preferred_prefix": "europa.dcf", "uri_format": "http://data.europa.eu/snb/dcf/$1" }, "europe.pic": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An identifier for an organization", "example": "881104060", "homepage": "https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/how-to-participate/participant-register-search?isExactMatch=true&type=ORGANISATION&order=DESC&pageNumber=1&pageSize=50&sortBy=lastModified", "name": "European Commission Participant Identification Code (PIC)", "pattern": "^\\d{9}$", "preferred_prefix": "europe.pic", "references": [ "https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/how-to-participate/participant-register" ], "uri_format": "https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/how-to-participate/org-details/$1" }, "euroscivoc": { "contact": { "email": "OP-EU-VOCABULARIES@publications.europa.eu", "name": "Publications Office of the European Union" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "European Science Vocabulary (EuroSciVoc) is the taxonomy of fields of science based on OECD's 2015 Frascati Manual taxonomy. It was extended with fields of science categories extracted from CORDIS content through a semi-automatic process developed with Natural Language Processing (NLP) techniques. (from homepage)", "download_rdf": "https://op.europa.eu/o/opportal-service/euvoc-download-handler?cellarURI=http%3A%2F%2Fpublications.europa.eu%2Fresource%2Fdistribution%2Feuroscivoc%2F20250625-0%2Fttl%2Fskos_xl%2FEuroSciVoc.ttl&fileName=EuroSciVoc.ttl", "example": "ceaf4ca0-9b09-4313-85a5-2edf1762e443", "homepage": "https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/euroscivoc", "keywords": [ "computer science", "educational resources" ], "mappings": { "bartoc": "20394", "ecoportal": "EUROSCIVOC", "tib": "euroscivoc" }, "name": "European Science Vocabulary", "preferred_prefix": "euroscivoc", "rdf_uri_format": "http://data.europa.eu/8mn/euroscivoc/$1", "uri_format": "http://data.europa.eu/8mn/euroscivoc/$1" }, "euroscivoc.schema": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Euvoc ontology, published by the Publications Office of the European Union, supports the development of authority tables (Name Authority Lists or NALs), Eurovoc and EU corporate datasets. It contains a set of classes and properties enabling all the information to be expressed in multilingual format. It helps define relationships between terms and concepts across multiple domains, supporting interoperability and standardization across European Union documentation and databases. It also defines a set a commonly use properties (i.e: start date, end dates, status), and supports the reusability on common data (currencies, languages, countries).\n\nThe Euvoc ontology is maintained by the Publications Office of the European Union and disseminated on the EU Vocabularies website.", "download_rdf": "https://op.europa.eu/o/opportal-service/euvoc-download-handler?cellarURI=http%3A%2F%2Fpublications.europa.eu%2Fresource%2Fdistribution%2Feuvoc%2F20241211-0%2Fttl%2Fowl%2Feuvoc.ttl&fileName=euvoc.ttl", "example": "isTextual", "homepage": "https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/euvoc", "name": "European Science Vocabulary Ontology", "preferred_prefix": "euroscivoc.schema" }, "eurovoc": { "contact": { "email": "OP-EU-VOCABULARIES@publications.europa.eu", "name": "Publications Office of the European Union" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "EuroVoc is the EU's multilingual and multidisciplinary thesaurus. It contains keywords, organized in 21 domains and 127 sub-domains, which are used to describe the content of documents in EUR-Lex. [from homepage]", "example": "1837", "homepage": "https://eur-lex.europa.eu/browse/eurovoc.html", "keywords": [ "agriculture", "business administration", "economics", "employment", "energy engineering", "environmental science", "fisheries science", "food", "forest management", "geography", "international relations", "linguistics", "political science", "public finance", "social policy", "social science", "trade", "transport", "transportation planning" ], "mappings": { "bartoc": "15", "ecoportal": "EUROVOC", "fairsharing": "FAIRsharing.d0a681" }, "name": "EuroVoc", "pattern": "^\\d+$", "preferred_prefix": "eurovoc", "rdf_uri_format": "http://eurovoc.europa.eu/$1", "uri_format": "http://eurovoc.europa.eu/$1" }, "ev": { "appears_in": [ "cl" ], "contact": { "email": "evoc@sanbi.ac.za", "name": "eVOC mailing list" }, "deprecated": true, "description": "Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment.", "example": "0100011", "homepage": "http://www.evocontology.org/", "keywords": [ "anatomy", "cell", "development", "experiment", "obo", "ontology" ], "mappings": { "biocontext": "EV", "obofoundry": "ev", "prefixcommons": "evoc", "wikidata.entity": "Q114677886" }, "name": "eVOC (Expressed Sequence Annotation for Humans)", "pattern": "^\\d{7}$", "preferred_prefix": "EV", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/evoc:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/EV_$1", "references": [ "https://twitter.com/Bgeedb/status/1350124337815281664" ], "uri_format": "http://www.evocontology.org/site/Main/BrowseEvoc?x_termid=$1" }, "evm": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "name": "eVOC mouse development stage", "preferred_prefix": "evm", "references": [ "https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r229" ] }, "evorao": { "contact": { "email": "evorao@evora-project.eu", "name": "d3fk" }, "description": "The EVORAO Ontology provides a structured and harmonized vocabulary for describing shareable pathogens as characterized biological materials, along with their derived products and associated services, organized into collections. Developed within the EVORA project, it supports consistent metadata annotation across research infrastructures, promoting findability, accessibility, interoperability, and reusability (FAIR). By aligning with relevant standards and ontologies, EVORAO facilitates cross-domain collaboration, integration, and sharing of pathogenic resources and services to enhance pandemic preparedness and response. While initially focused on virology, EVORAO is designed to be extensible and also supports metadata harmonization for other pathogens. [from repository]", "download_owl": "http://aber-owl.net/media/ontologies/EVORAO/21/evorao.owl", "download_rdf": "https://raw.githubusercontent.com/EVORA-project/evora-ontology/refs/heads/main/models/owl/evora_ontology.owl.ttl", "example": "AlternateName", "homepage": "https://github.com/EVORA-project/evora-ontology", "keywords": [ "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "EVORAO", "bioportal": "EVORAO", "ols": "evorao" }, "name": "EVORA Ontology", "preferred_prefix": "evorao", "rdf_uri_format": "https://w3id.org/evorao/$1", "repository": "https://github.com/EVORA-project/evora-ontology", "uri_format": "https://w3id.org/evorao/$1" }, "evr": { "contact": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An open, community-driven registry of conference and event venues.\n\nEVR assigns persistent identifiers (PIDs) to make referencing venues FAIR. This is similar to how ORCID assigns PIDs to researchers and ROR assigns PIDs to research organizations.\n\nThis benefits researchers assembling information about in-person conferences and events by enabling them to refer in an unambiguous way to the venue where it takes place.\n\nThis repository follows the [Open Data, Open Code, Open Infrastructure (O3) principles](https://www.nature.com/articles/s41597-024-03406-w), meaning that the data and code are all in one repository that anyone can contribute to.", "example": "0000001", "github_request_issue": 1363, "homepage": "https://cthoyt.com/evr", "license": "CC0-1.0", "name": "Event Venue Registry", "pattern": "^\\d{7}$", "preferred_prefix": "evr", "repository": "https://github.com/cthoyt/evr", "uri_format": "https://cthoyt.com/evr/$1" }, "exac.gene": { "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information.", "example": "ENSG00000169174", "homepage": "http://exac.broadinstitute.org/", "mappings": { "biocontext": "EXAC.GENE", "miriam": "exac.gene", "n2t": "exac.gene" }, "name": "ExAC Gene", "pattern": "^ENSG\\d{11}$", "preferred_prefix": "exac.gene", "uri_format": "http://exac.broadinstitute.org/gene/$1" }, "exac.transcript": { "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information.", "example": "ENST00000407236", "homepage": "http://exac.broadinstitute.org/", "mappings": { "biocontext": "EXAC.TRANSCRIPT", "miriam": "exac.transcript", "n2t": "exac.transcript" }, "name": "ExAC Transcript", "pattern": "^ENST\\d{11}$", "preferred_prefix": "exac.transcript", "uri_format": "http://exac.broadinstitute.org/transcript/$1" }, "exac.variant": { "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information.", "example": "22-46615880-T-C", "homepage": "http://exac.broadinstitute.org/", "mappings": { "biocontext": "EXAC.VARIANT", "miriam": "exac.variant", "n2t": "exac.variant" }, "name": "ExAC Variant", "pattern": "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$", "preferred_prefix": "exac.variant", "uri_format": "http://exac.broadinstitute.org/variant/$1" }, "exif": { "description": "Vocabulary to describe an Exif format picture data. All Exif 2.2 tags are defined as RDF properties, as well as several terms to help this schema.", "example": "orientation", "homepage": "http://www.w3.org/2003/12/exif/", "keywords": [ "image" ], "mappings": { "lov": "exif", "zazuko": "exif" }, "name": "Exif data description vocabulary", "preferred_prefix": "exif" }, "exmo": { "contact": { "email": "xyz19940216@163.com", "github": "DarkKnight0-0", "name": "Xingyun Liu", "orcid": "0000-0002-9295-2767" }, "description": "A core reference ontology built upon BFO about exercise medicine. 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It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.", "example": "FB00000917", "homepage": "https://www.facebase.org", "keywords": [ "anatomy", "developmental biology", "epigenetics", "genetics", "medicine" ], "mappings": { "biocontext": "FACEBASE", "fairsharing": "FAIRsharing.mqvqde", "integbio": "nbdc02022", "miriam": "facebase", "n2t": "facebase", "re3data": "r3d100013263" }, "name": "FaceBase Data Repository", "pattern": "^FB\\d{8}$", "preferred_prefix": "facebase", "publications": [ { "doi": "10.1242/dev.191213", "pmc": "PMC7522026", "pubmed": "32958507", "title": "FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research", "year": 2020 } ], "uri_format": "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1" }, "fair": { "description": "This is the formal vocabulary (ontology) describing the FAIR principles.", "example": "FAIR", "homepage": "https://w3id.org/fair/principles/terms/FAIR-Vocabulary", "keywords": [ "computer science", "digital planning and construction", "fid baudigital", "fid move", "nfdi4chem", "nfdi4ing" ], "mappings": { "tib": "fair" }, "name": "FAIR Vocabulary", "preferred_prefix": "fair", "uri_format": "https://w3id.org/fair/principles/terms/$1" }, "fairsharing": { "contact": { "email": "allyson.lister@oerc.ox.ac.uk", "name": "Allyson Lister", "orcid": "0000-0002-7702-4495" }, "description": "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/fao:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/FAO_$1", "repository": "https://github.com/obophenotype/fungal-anatomy-ontology", "uri_format": "http://purl.obolibrary.org/obo/FAO_$1", "version": "2025-07-15" }, "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": { "github": "ddooley", "name": "Damion Dooley", "orcid": "0000-0002-8844-9165" }, "description": "The FAO Statistics Team (NFISS) of Fisheries and Aquaculture Division collates world capture and aquaculture production statistics at either the species, genus, family, or higher taxonomic levels in 3,169 statistical categories (2022 data release) referred to as species items. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/fbcv:$1" } ], "publications": [ { "doi": "10.1186/2041-1480-4-30", "pmc": "PMC3816596", "pubmed": "24138933", "title": "The Drosophila phenotype ontology", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/FBcv_$1", "repository": "https://github.com/FlyBase/flybase-controlled-vocabulary", "synonyms": [ "FBcv" ], "uri_format": "http://purl.obolibrary.org/obo/FBcv_$1", "version": "2026-01-13" }, "fbdv": { "contact": { "email": "cp390@cam.ac.uk", "github": "Clare72", "name": "Clare Pilgrim", "orcid": "0000-0002-1373-1705" }, "description": "A structured controlled vocabulary of the development of Drosophila melanogaster.", "download_json": "http://purl.obolibrary.org/obo/fbdv.json", "download_obo": "http://purl.obolibrary.org/obo/fbdv.obo", "download_owl": "http://purl.obolibrary.org/obo/fbdv.owl", "example": "00000000", "homepage": "http://purl.obolibrary.org/obo/fbdv", "keywords": [ "development", "developmental biology", "fly", "life cycle", "life cycle stage", "life science", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "FBDV", "biocontext": "FBdv", "bioportal": "FB-DV", "fairsharing": "FAIRsharing.p52pzj", "go": "FBdv", "obofoundry": "fbdv", "ols": "fbdv", "ontobee": "FBdv", "prefixcommons": "fbdv", "wikidata.entity": "Q81661623" }, "name": "Drosophila development", "pattern": "^\\d{8}$", "preferred_prefix": "FBdv", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/fbdv:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/FBdv_$1", "repository": "https://github.com/FlyBase/drosophila-developmental-ontology", "synonyms": [ "FBdv" ], "uri_format": "http://purl.obolibrary.org/obo/FBdv_$1", "version": "2026-01-13" }, "fbol": { "comment": "Website down, checked on 2021-10-07", "deprecated": true, "description": "DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms.", "example": "2224", "homepage": "http://www.fungalbarcoding.org/", "mappings": { "biocontext": "FBOL", "miriam": "fbol", "n2t": "fbol", "ncbi": "FBOL" }, "name": "International Fungal Working Group Fungal Barcoding.", "pattern": "^\\d+$", "preferred_prefix": "fbol", "uri_format": "http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T" }, "fbql": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "example": "00005254", "name": "FlyBase Qualifiers", "pattern": "^\\d+$", "preferred_prefix": "fbql" }, "fbrf": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "FlyBase internal citation identifiers", "example": "0187632", "homepage": "https://flybase.org", "name": "FlyBase Reference Report", "pattern": "^\\d{7}$", "preferred_prefix": "fbrf", "uri_format": "https://flybase.org/reports/FBrf$1" }, "fbsp": { "contact": { "email": "cp390@cam.ac.uk", "github": "Clare72", "name": "Clare Pilgrim", "orcid": "0000-0002-1373-1705" }, "deprecated": true, "description": "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.", "download_obo": "http://aber-owl.net/media/ontologies/FB-SP/7/fb-sp.obo", "download_owl": "http://purl.obolibrary.org/obo/fbsp.owl", "example": "00000000", "homepage": "http://www.flybase.org/", "keywords": [ "obo", "ontology" ], "mappings": { "aberowl": "FB-SP", "biocontext": "FBSP", "bioportal": "FB-SP", "obofoundry": "fbsp", "ols": "fbsp", "wikidata.entity": "Q114677887" }, "name": "Fly taxonomy", "pattern": "^\\d{8}$", "preferred_prefix": "FBSP", "rdf_uri_format": "http://purl.obolibrary.org/obo/FBSP_$1", "uri_format": "http://purl.obolibrary.org/obo/FBSP_$1", "version": "2017-11-19" }, "fbtc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The cell line vocabulary inside FlyBase", "example": "0000190", "homepage": "https://flybase.org", "mappings": { "cellosaurus": "FlyBase_Cell_line" }, "name": "Flybase Cell Line", "pattern": "^\\d{7}$", "preferred_prefix": "fbtc", "synonyms": [ "FlyBase_Cell_line" ], "uri_format": "https://flybase.org/reports/FBtc$1" }, "fcb": { "description": "Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR).\n\n", "example": "FCB005", "homepage": "https://w3id.org/faircookbook/", "mappings": { "miriam": "fcb" }, "name": "FAIR Cookbook", "pattern": "^FCB\\d{3}$", "preferred_prefix": "fcb", "repository": "https://github.com/FAIRplus/the-fair-cookbook", "synonyms": [ "faircookbook" ], "uri_format": "https://w3id.org/faircookbook/$1" }, "fcsfree": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Cell line databases/resources", "example": "240-17-488-3-4-12", "homepage": "https://fcs-free.org", "mappings": { "cellosaurus": "FCS-free" }, "name": "Fetal Calf Serum-Free Database", "preferred_prefix": "fcsfree", "uri_format": "https://fcs-free.org/fcs-database?$1" }, "fda.application": { "comment": "The official FDA website doesn't appear to be able to resolve application IDs but these IDs do appear in some PDF documents, e.g., https://www.fda.gov/media/159183/download.", "contributor": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "This prefix is for FDA application identifiers. There are multiple types of FDA applications (https://www.fda.gov/drugs/how-drugs-are-developed-and-approved/types-applications), including New Drug Application (NDA). FDA.report provides access to all FDA databases, including applications, in a single portal, and can resolve FDA application identifiers.", "example": "070886", "github_request_issue": 1146, "homepage": "https://fda.report/applications", "name": "FDA Application", "pattern": "^\\d{6}$", "preferred_prefix": "fda.application", "reviewer": { "email": "tiago.lubiana.alves@usp.br", "github": "lubianat", "name": "Tiago Lubiana", "orcid": "0000-0003-2473-2313" }, "uri_format": "https://fda.report/applications/$1" }, "fema": { "contact": { "email": "staylor@vertosolutions.net", "name": "Sean Taylor", "orcid": "0000-0002-7806-4173" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "FEMA provides identifiers for flavor ingredients deemed safe for food use. These entities include chemical compounds and natural substances used as flavoring agents, each reviewed by the FEMA Expert Panel for GRAS (Generally Recognized As Safe) status. The identifiers link to safety data and regulatory assessments, including evaluations by the U.S. FDA and, where applicable, the Joint FAO/WHO Expert Committee on Food Additives (JECFA).", "example": "4667", "github_request_issue": 1247, "homepage": "https://www.femaflavor.org", "name": "Flavor and Extract Manufacturers Association", "pattern": "^\\d+$", "preferred_prefix": "fema", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" } }, "ferroliganddb": { "contact": { "email": "guqiong@mail.sysu.edu.cn", "name": "Qiong Gu" }, "contributor": { "email": "shah.tanay2@northeastern.edu", "github": "tanayshah2", "name": "Tanay Shah", "orcid": "0009-0001-1912-5132" }, "description": "FerroLigandDB is a meticulously curated, high-quality database of ferroptosis regulators, including inducers and inhibitors.", "example": "486", "github_request_issue": 1145, "homepage": "https://ferr.gulab.org.cn/", "name": "FerroLigandDB", "preferred_prefix": "ferroliganddb", "publications": [ { "doi": "10.1021/acs.jcim.4c00525", "pubmed": "38885636", "title": "FerroLigandDB: A Ferroptosis Ligand Database of Structure-Activity Relations", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://ferr.gulab.org.cn/browse/$1" }, "fhir.implementation": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A set of guides on implementing various processes within hospitals or healthcare systems.", "example": "immds", "homepage": "https://hl7.org/fhir/us/", "name": "FHIR United States Implementation Guides", "preferred_prefix": "fhir.implementation", "uri_format": "https://hl7.org/fhir/us/$1" }, "fidbaudigital.subject": { "description": "This subject heading system has beeen developed for use in FID BAUdigital and its future web services. It covers scientific fields of Civil Engineering, Architecture and Urban Studies with a special section on digitization. This subject classification has been mapped to several other classification systems. The latest version of the subject classification including these mappings is available at https://gitlab.com/fid-bau/terminologie/fid-baudigital-faecherklassifikation/-/raw/main/Subject_Headings_all_mappings.owl.", "example": "004d64e9-a7ab-4a73-b117-0c6fc6c76d81", "homepage": "https://gitlab.com/fid-bau/terminologie/fid-baudigital-faecherklassifikation", "keywords": [ "architecture", "civil engineering", "digital planning and construction", "fid baudigital", "nfdi4ing" ], "mappings": { "tib": "bdsubj" }, "name": "FID BAUdigital Subject Headings", "preferred_prefix": "fidbaudigital.subject", "uri_format": "https://purl.org/fidbaudigital/subjects#$1" }, "fideo": { "contact": { "email": "georgeta.bordea@u-bordeaux.fr", "github": "getbordea", "name": "Georgeta Bordea", "orcid": "0000-0001-9921-8234" }, "description": "Food-Drug interactions automatically extracted from scientific literature", "download_owl": "http://purl.obolibrary.org/obo/fideo.owl", "example": "00000021", "example_extras": [ "000001507" ], "homepage": "https://gitub.u-bordeaux.fr/erias/fideo", "keywords": [ "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "FIDEO", "bioportal": "FIDEO", "obofoundry": "fideo", "ols": "fideo", "ontobee": "FIDEO", "wikidata.entity": "Q111854958" }, "name": "Food Interactions with Drugs Evidence Ontology", "pattern": "^\\d+$", "preferred_prefix": "FIDEO", "rdf_uri_format": "http://purl.obolibrary.org/obo/FIDEO_$1", "repository": "https://gitub.u-bordeaux.fr/erias/fideo", "uri_format": "http://purl.obolibrary.org/obo/FIDEO_$1", "version": "2023-12-18" }, "fiesta.iot": { "description": "The FIESTA-IoT ontology takes inspiration from the well-known Noy et al. methodology for reusing and interconnecting existing ontologies. To build the ontology, we leverage a number of core concepts from various mainstream ontologies and taxonomies, such as Semantic Sensor Network (SSN), M3-lite (a lite version of M3 ontology), WGS84, IoT-lite, Time, and DUL ontology.", "homepage": "https://github.com/fiesta-iot/ontology", "keywords": [ "engineering", "iot", "nfdi4ing" ], "mappings": { "lov": "fiesta-iot", "tib": "fiestaiot" }, "name": "FIESTA-IoT Ontology", "no_own_terms": true, "preferred_prefix": "fiesta.iot", "references": [ "https://zenodo.org/record/1193299" ], "repository": "https://github.com/fiesta-iot/ontology", "uri_format": "http://purl.org/iot/ontology/fiesta-iot#$1" }, "findex.bau": { "description": "SKOS Model of FINDEX Bau by Fraunhofer-Informationszentrum Raum und Bau IRB", "example": "B10000000000_3", "homepage": "https://gitlab.com/fid-bau/terminologie", "keywords": [ "civil engineering", "digital planning and construction", "fid baudigital", "nfdi4ing" ], "mappings": { "tib": "bau" }, "name": "FINDEX Bau as a SKOS Thesaurus - Facetted Indexing System for Civil Engineering", "preferred_prefix": "findex.bau", "repository": "https://gitlab.com/fid-bau/terminologie", "uri_format": "https://terminology.fraunhofer.de/voc/bau#$1" }, "findex.raum": { "description": "SKOS-Modellierung des Thesaurus FINDEX Raum des Fraunhofer-Informationszentrums Raum und Bau IRB", "example": "R00000000000_3", "homepage": "https://terminology.fraunhofer.de/findex-thesauri", "keywords": [ "civil engineering", "digital planning and construction", "earth sciences", "fid baudigital", "nfdi4ing" ], "mappings": { "tib": "raum" }, "name": "FINDEX Raum", "preferred_prefix": "findex.raum", "uri_format": "https://terminology.fraunhofer.de/voc/raum#$1" }, "fishbase.species": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years.", "example": "6472", "homepage": "http://fishbase.org", "mappings": { "integbio": "nbdc00270", "re3data": "r3d100010912", "wikidata": "P938" }, "name": "FishBase", "pattern": "^\\d+$", "preferred_prefix": "fishbase.species", "synonyms": [ "fishbase" ], "uri_format": "https://www.fishbase.ca/summary/$1" }, "fivestars": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata.", "example": "hasOpenAccessRating", "homepage": "http://www.sparontologies.net/ontologies/fivestars", "keywords": [ "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.6dfe9b" }, "name": "Five Stars of Online Research Articles Ontology", "preferred_prefix": "FiveStars", "publications": [ { "doi": "10.1045/january2012-shotton", "title": "The Five Stars of Online Journal Articles - a Framework for Article Evaluation", "year": 2012 } ], "repository": "https://github.com/sparontologies/fivestars", "twitter": "sparontologies" }, "fix": { "contact": { "email": "amalik@ebi.ac.uk", "github": "amalik01", "name": "Adnan Malik", "orcid": "0000-0001-8123-5351" }, "deprecated": true, "description": "An ontology of physico-chemical methods and properties.", "download_obo": "http://purl.obolibrary.org/obo/fix.obo", "download_owl": "http://purl.obolibrary.org/obo/fix.owl", "example": "0000390", "homepage": "https://www.ebi.ac.uk/chebi/", "keywords": [ "chemistry", "experiment", "experimental measurement", "nfdi4chem", "obo", "ontology", "property" ], "mappings": { "aberowl": "FIX", "biocontext": "FIX", "bioportal": "FIX", "fairsharing": "FAIRsharing.wwy1ns", "obofoundry": "fix", "ols": "fix", "ontobee": "FIX", "prefixcommons": "fix", "tib": "fix", "wikidata.entity": "Q114677850" }, "name": "Physico-chemical methods and properties", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^\\d{7}$", "preferred_prefix": "FIX", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/fix:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/FIX_$1", "uri_format": "http://purl.obolibrary.org/obo/FIX_$1" }, "flopo": { "appears_in": [ "gallont" ], "contact": { "email": "robert.hoehndorf@kaust.edu.sa", "github": "leechuck", "name": "Robert Hoehndorf", "orcid": "0000-0001-8149-5890" }, "description": "Traits and phenotypes of flowering plants occurring in digitized Floras", "download_owl": "http://purl.obolibrary.org/obo/flopo.owl", "example": "0005250", "homepage": "https://github.com/flora-phenotype-ontology/flopoontology", "keywords": [ "biodiversity", "botany", "dataplant", "horticulture", "life sciences, biology", "obo", "ontology", "phenomics", "phenotype", "plant anatomy", "plant cell biology", "whole plant development stage" ], "license": "CC0-1.0", "mappings": { "aberowl": "FLOPO", "agroportal": "FLOPO", "biocontext": "FLOPO", "bioportal": "FLOPO", "fairsharing": "FAIRsharing.ny9vnm", "obofoundry": "flopo", "ols": "flopo", "ontobee": "FLOPO", "tib": "flopo", "wikidata.entity": "Q81661625" }, "name": "Flora Phenotype Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "FLOPO", "publications": [ { "doi": "10.1186/s13326-016-0107-8", "pmc": "PMC5109718", "pubmed": "27842607", "title": "The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants", "year": 2016 }, { "doi": "10.3897/bdj.2.e1125", "pmc": "PMC4092319", "pubmed": "25057255", "title": "Enriched biodiversity data as a resource and service", "year": 2014 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/FLOPO_$1", "repository": "https://github.com/flora-phenotype-ontology/flopoontology", "uri_format": "http://purl.obolibrary.org/obo/FLOPO_$1" }, "flowrepository": { "contact": { "email": "rbrinkman@bccrc.ca", "name": "Ryan Brinkman", "orcid": "0000-0002-9765-2990" }, "description": "FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field.", "example": "FR-FCM-ZYGW", "homepage": "http://flowrepository.org/", "keywords": [ "biology", "cell biology", "life science" ], "mappings": { "fairsharing": "FAIRsharing.veg2d6", "integbio": "nbdc01698", "miriam": "flowrepository", "n2t": "flowrepository", "re3data": "r3d100011280" }, "name": "FlowRepository", "pattern": "^FR\\-FCM\\-\\w{4}$", "preferred_prefix": "flowrepository", "publications": [ { "doi": "10.1002/cyto.a.22106", "pubmed": "22887982", "title": "FlowRepository: a resource of annotated flow cytometry datasets associated with peer-reviewed publications", "year": 2012 }, { "doi": "10.1002/0471142956.cy1018s61", "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 } ], "uri_format": "http://flowrepository.org/id/$1" }, "flu": { "contact": { "email": "burkesquires@gmail.com", "name": "R. Burke Squires", "orcid": "0000-0001-9666-6285" }, "deprecated": true, "description": "Starting in the fall of 2007, a collaborative group of influenza researchers have established an influenza ontology. The influenza ontology is an application ontology. Consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS)", "download_owl": "http://purl.obolibrary.org/obo/flu.owl", "example": "0000404", "homepage": "http://purl.obolibrary.org/obo/flu/", "keywords": [ "obo", "ontology" ], "mappings": { "aberowl": "FLU", "biocontext": "FLU", "bioportal": "FLU", "obofoundry": "flu" }, "name": "Influenza Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "FLU", "rdf_uri_format": "http://purl.obolibrary.org/obo/FLU_$1", "uri_format": "http://purl.obolibrary.org/obo/FLU_$1" }, "flybase": { "contact": { "email": "vjenkins@morgan.harvard.edu", "name": "Victoria K. Jenkins", "orcid": "0000-0002-1567-7626" }, "description": "FlyBase is the database of the Drosophila Genome Projects and of associated literature.", "example": "FBgn0011293", "homepage": "https://bioentity.link/", "keywords": [ "allele", "anatomy", "bio.tools", "bioinformatics", "blast", "comparative genomics", "controlled term", "dna", "drosophilidae", "expression", "faseb list", "functional genomics", "gene", "genetics", "genome", "genomics", "genotype", "image", "image collection", "interaction", "life science", "life-cycle", "molecular biology", "molecular genetics", "movie", "mutant", "phenotype", "rna-seq", "sequence", "stock", "video resource" ], "license": "CC-BY-4.0", "logo": "http://flybase.org/images/fly_logo.png", "mappings": { "biocontext": "FlyBase", "cellosaurus": "FlyBase", "edam": "1089", "fairsharing": "FAIRsharing.wrvze3", "go": "FB", "integbio": "nbdc00064", "miriam": "fb", "n2t": "fb", "ncbi": "FLYBASE", "pathguide": "460", "prefixcommons": "flybase", "re3data": "r3d100010591", "rrid": "FlyBase", "uniprot": "DB-0026", "wikidata": "P3852" }, "name": "FlyBase Gene", "pattern": "^FB\\w{2}\\d{7}$", "preferred_prefix": "FlyBase", "providers": [ { "code": "", "description": "The FlyBase Database", "homepage": "http://flybase.org/", "name": "The FlyBase Database", "uri_format": "http://flybase.org/reports/$1.html" }, { "code": "agr", "description": "FlyBase through the Alliance of Genome Resources", "homepage": "https://www.alliancegenome.org", "name": "FlyBase through the Alliance of Genome Resources", "uri_format": "https://www.alliancegenome.org/gene/FB:$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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Gyori", "orcid": "0000-0001-9439-5346" }, "description": "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships.", "example": "GPIb_IX_V", "homepage": "https://sorgerlab.github.io/famplex/", "keywords": [ "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "FPLX", "biocontext": "FPLX", "bioportal": "FPLX", "miriam": "fplx", "n2t": "fplx" }, "name": "FamPlex", "pattern": "^[a-zA-Z0-9][A-Za-z0-9_]+$", "preferred_prefix": "fplx", "publications": [ { "doi": "10.1186/s12859-018-2211-5", "pmc": "PMC6022344", "pubmed": "29954318", "title": "FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining", "year": 2018 } ], "synonyms": [ "famplex" ], "uri_format": "https://sorgerlab.github.io/famplex/$1" }, "fr": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology that enables the description of reviews of scientific articles and other scholarly resources.", "example": "ReviewVersion", "homepage": "http://www.sparontologies.net/ontologies/fr", "keywords": [ "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.e7e609" }, "name": "FAIR* Reviews Ontology", "preferred_prefix": "FR", "repository": "https://github.com/sparontologies/fr", "twitter": "sparontologies" }, "frapo": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc.", "example": "Grant", "homepage": "http://www.sparontologies.net/ontologies/frapo", "keywords": [ "academy", "funding bodies", "grant application", "research project", "subject agnostic" ], "mappings": { "aberowl": "FRAPO", "fairsharing": "FAIRsharing.0a2576", "lov": "frapo" }, "name": "Funding, Research Administration and Projects Ontology", "preferred_prefix": "FRAPO", "repository": "https://github.com/sparontologies/frapo", "twitter": "sparontologies", "uri_format": "http://purl.org/cerif/frapo/$1" }, "frbr": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO.", "example": "Expression", "homepage": "http://www.sparontologies.net/ontologies/frbr", "keywords": [ "frbr", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.b34b43", "lov": "frbr", "zazuko": "frbr" }, "name": "Functional Requirements for Bibliographic Records", "preferred_prefix": "FRBR", "repository": "https://github.com/sparontologies/frbr", "twitter": "sparontologies", "uri_format": "http://purl.org/vocab/frbr/core#$1" }, "frbrer": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This is the element set of native RDF classes and properties described in the current text (Feb 2009) of the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model. (from https://www.iflastandards.info/fr/frbr/frbrer.html)", "download_rdf": "http://iflastandards.info/ns/fr/frbr/frbrer.jsonld", "example": "1001", "homepage": "https://www.iflastandards.info/fr/frbr/frbrer", "keywords": [ "frbr" ], "mappings": { "lov": "frbrer" }, "name": "Functional Requirements for Bibliographic Records Entity-Relationship Model", "preferred_prefix": "frbrer", "uri_format": "http://iflastandards.info/ns/fr/frbr/frbrer/$1" }, "fsnp": { "deprecated": true, "description": "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.", "example": "rs17852708", "homepage": "http://compbio.cs.queensu.ca/F-SNP/", "keywords": [ "dna", "protein" ], "mappings": { "biocontext": "FSNP", "miriam": "fsnp", "n2t": "fsnp", "prefixcommons": "fsnp" }, "name": "F-SNP", "pattern": "^rs\\d+$", "preferred_prefix": "fsnp", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/fsnp:$1" } ], "uri_format": "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1" }, "ftonto": { "comment": "Don't confuse with MASON, which is referenced by FTOnto", "description": "The FTOnto enables reseachers to sematically describe a physical fischertechnik factory simulation environment. This is archieved by aligning concepts from MASON and SOSA with own concepts. Furthermore the FTOnto can capture knowledge about semantic web services which are used to interact between the service-layer and the cyber-physical layer in a cyber-physical production system. This includes precondition which have to be met before a webservice can be performed, postconditions which check if the webservice execution was performed successfully and effects which describe the changed state of the domain after performing a service. [from homepage]", "example": "ADXL345_Pi_1_AccSensor_1_Result_2019-02-26_14_53_54.97", "homepage": "https://wi2.pages.gitlab.rlp.net/iot-lab/ftonto-web-doku/", "keywords": [ "coypu", "engineering", "nfdi4ing" ], "mappings": { "tib": "ftonto" }, "name": "Fischertechnik Ontology", "preferred_prefix": "ftonto", "references": [ "https://ceur-ws.org/Vol-2454/paper_10.pdf" ], "repository": "https://gitlab.rlp.net/iot-lab-uni-trier/ftonto", "uri_format": "http://iot.uni-trier.de/FTOnto#$1" }, "ftt": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific.", "example": "273", "homepage": "https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3", "name": "Feature Type Thesaurus", "pattern": "^\\d+$", "preferred_prefix": "ftt", "references": [ "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200", "https://github.com/EnvironmentOntology/envo/issues/1130" ], "uri_format": "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1" }, "funcbase.fly": { "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data.", "example": "10194", "homepage": "http://func.mshri.on.ca/fly", "mappings": { "biocontext": "FUNCBASE.FLY", "miriam": "funcbase.fly", "n2t": "funcbase.fly" }, "name": "FuncBase Fly", "pattern": "^\\d+$", "preferred_prefix": "funcbase.fly", "uri_format": "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1" }, "funcbase.human": { "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data.", "example": "119514", "homepage": "http://func.mshri.on.ca/human/", "mappings": { "biocontext": "FUNCBASE.HUMAN", "miriam": "funcbase.human", "n2t": "funcbase.human" }, "name": "FuncBase Human", "pattern": "^\\d+$", "preferred_prefix": "funcbase.human", "uri_format": "http://func.mshri.on.ca/human/genes/list_functional_scores/$1" }, "funcbase.mouse": { "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse.", "example": "1351341", "homepage": "http://func.mshri.on.ca/mouse/", "mappings": { "biocontext": "FUNCBASE.MOUSE", "miriam": "funcbase.mouse", "n2t": "funcbase.mouse" }, "name": "FuncBase Mouse", "pattern": "^\\d+$", "preferred_prefix": "funcbase.mouse", "uri_format": "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1" }, "funcbase.yeast": { "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast.", "example": "2701", "homepage": "http://func.mshri.on.ca/yeast", "mappings": { "biocontext": "FUNCBASE.YEAST", "miriam": "funcbase.yeast", "n2t": "funcbase.yeast" }, "name": "FuncBase Yeast", "pattern": "^\\d+$", "preferred_prefix": "funcbase.yeast", "uri_format": "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1" }, "funderregistry": { "description": "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world.", "example": "100000001", "example_extras": [ "501100001230" ], "homepage": "https://www.crossref.org/", "mappings": { "miriam": "funderregistry" }, "name": "FunderRegistry", "pattern": "^\\d+$", "preferred_prefix": "funderregistry", "providers": [ { "code": "crossref.api", "description": "Access funder data through the Crossref API", "homepage": "https://api.crossref.org", "name": "Crossref API", "uri_format": "https://api.crossref.org/funders/$1" }, { "code": "doi", "description": "Access funder data through a DOI for crossref funders.", "homepage": "https://doi.org", "name": "DOI", "uri_format": "https://dx.doi.org/10.13039/$1" } ], "synonyms": [ "FundRef", "crossref.funder" ], "uri_format": "http://data.crossref.org/fundingdata/funder/10.13039/$1" }, "funggrowth": { "contact": { "email": "v.robert@wi.knaw.nl", "name": "Vincent Robert", "orcid": "0000-0002-9370-4677" }, "contributor": { "email": "ji.kang@northeastern.edu", "github": "kanghosaeyo", "name": "Kangho Ji", "orcid": "0009-0009-3402-8013" }, "description": "Identifiers represent experimental growth profiles documenting fungal species' ability to utilize specific carbon sources (plant biomass components, polysaccharides, and monosaccharides) in the FUNG-GROWTH database, which provides phenotypic data to support functional genome annotation and comparative analysis of carbohydrate metabolism across fungal species.", "example": "86", "github_request_issue": 1720, "homepage": "https://www.fung-growth.org", "keywords": [ "fungi", "growth profiles", "monosaccharides", "plant biomass", "polysaccharides" ], "name": "Fungal Growth Database", "pattern": "^\\d+$", "preferred_prefix": "funggrowth", "publications": [ { "doi": "10.1128/mra.00378-25", "pmc": "PMC12424322", "pubmed": "40767478", "title": "The FUNG-GROWTH database: linking fungal phenotype to genome", "year": 2025 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://www.fung-growth.org/page/Display%20page%20FG/$1" }, "fungidb": { "contact": { "email": "jason.stajich@ucr.edu", "name": "Jason E. Stajich", "orcid": "0000-0002-7591-0020" }, "description": "FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina.", "example": "CNBG_0001", "homepage": "https://fungidb.org/fungidb", "keywords": [ "genomics" ], "mappings": { "biocontext": "FUNGIDB", "fairsharing": "FAIRsharing.xf30yc", "miriam": "fungidb", "n2t": "fungidb", "re3data": "r3d100011906" }, "name": "FungiDB", "pattern": "^[A-Za-z_0-9]+$", "preferred_prefix": "fungidb", "publications": [ { "doi": "10.1016/j.fgb.2016.04.002", "pubmed": "27259951", "title": "Database whiplash, crowdsourcing, and FungiDB", "year": 2016 }, { "doi": "10.1128/ec.00083-14", "pmc": "PMC4135733", "pubmed": "24813190", "title": "Literature-based gene curation and proposed genetic nomenclature for cryptococcus", "year": 2014 }, { "doi": "10.1093/nar/gkr918", "pmc": "PMC3245123", "pubmed": "22064857", "title": "FungiDB: an integrated functional genomics database for fungi", "year": 2011 }, { "doi": "10.1128/EC.00083-14", "title": "Literature-based gene curation and proposed genetic nomenclature for cryptococcus." } ], "twitter": "fungidb", "uri_format": "https://fungidb.org/fungidb/app/record/gene/$1" }, "fungorum": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for a fungus taxon in Index Fungorum", "example": "154022", "homepage": "http://www.indexfungorum.org", "mappings": { "ncbi": "Fungorum", "wikidata": "P1391" }, "name": "Index Fungorum", "pattern": "^[1-9]\\d{0,5}$", "preferred_prefix": "fungorum", "uri_format": "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1" }, "fyeco": { "comment": "Rather than admitting FYECO to the OBO foundry, we secure the prefix here at bioregistry. The FYECO namespace shows up in a lot of ingests (basically anywhere you ingest PomBase gene-phenotype data). Future work includes mapping FYECO to other OBO ontologies, but this is way ahead in the future.", "contact": { "email": "vw253@cam.ac.uk", "github": "ValWood", "name": "Valerie Wood", "orcid": "0000-0001-6330-7526" }, "contributor": { "email": "vw253@cam.ac.uk", "github": "ValWood", "name": "Valerie Wood", "orcid": "0000-0001-6330-7526" }, "description": "PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase.", "example": "0000003", "github_request_issue": 268, "homepage": "https://github.com/pombase/fypo", "mappings": { "biolink": "FYECO" }, "name": "Fission Yeast Experimental Conditions Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "FYECO", "repository": "https://github.com/pombase/fypo", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "fyler": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A hierarchical classification of congenital heart disease", "example": "4447", "homepage": "https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906", "name": "Fyler", "pattern": "^\\d+$", "preferred_prefix": "fyler", "references": [ "https://github.com/obophenotype/human-phenotype-ontology/issues/2568", "https://github.com/obophenotype/human-phenotype-ontology/issues/2511" ] }, "fypo": { "contact": { "email": "vw253@cam.ac.uk", "github": "ValWood", "name": "Val Wood", "orcid": "0000-0001-6330-7526" }, "description": "A formal ontology of phenotypes observed in fission yeast.", "download_json": "http://purl.obolibrary.org/obo/fypo.json", "download_obo": "http://purl.obolibrary.org/obo/fypo.obo", "download_owl": "http://purl.obolibrary.org/obo/fypo.owl", "example": "0001707", "homepage": "https://github.com/pombase/fypo", "keywords": [ "genetics", "go-term enrichment data", "life science", "obo", "ontology", "phenotype", "phylogenetics" ], "license": "CC-BY-4.0", "logo": "https://github.com/pombase/website/blob/master/src/assets/FYPO_logo_tiny.png", "mappings": { "aberowl": "FYPO", "biocontext": "FYPO", "biolink": "FYPO", "bioportal": "FYPO", "fairsharing": "FAIRsharing.4vr0ys", "go": "FYPO", "obofoundry": "fypo", "ols": "fypo", "ontobee": "FYPO", "wikidata.entity": "Q55118393" }, "name": "Fission Yeast Phenotype Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "FYPO", "publications": [ { "doi": "10.1093/bioinformatics/btt266", "pmc": "PMC3694669", "pubmed": "23658422", "title": "FYPO: the fission yeast phenotype ontology", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/FYPO_$1", "repository": "https://github.com/pombase/fypo", "uri_format": "http://purl.obolibrary.org/obo/FYPO_$1", "version": "2026-01-16" }, "ga4ghdos": { "description": "Assists in resolving data across cloud resources.", "example": "dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d", "homepage": "http://github.com/ga4gh/data-object-service-schemas", "mappings": { "biocontext": "GA4GHDOS", "miriam": "ga4ghdos", "n2t": "ga4ghdos" }, "name": "Data Object Service", "pattern": "^[a-zA-Z0-9\\-:#/\\.]+$", "preferred_prefix": "ga4ghdos", "uri_format": "https://dataguids.org/ga4gh/dos/v1/dataobjects/$1" }, "gabi": { "contact": { "email": "birgit.kersten@thuenen.de", "name": "Birgit Kersten", "orcid": "0000-0001-9900-9133" }, "deprecated": true, "description": "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'.", "example": "2679240", "homepage": "http://www.gabipd.org/", "keywords": [ "gene", "genome", "plant" ], "mappings": { "biocontext": "GABI", "miriam": "gabi", "n2t": "gabi", "ncbi": "GABI", "prefixcommons": "gabi" }, "name": "Network of Different Plant Genomic Research Projects", "pattern": "^\\w+$", "preferred_prefix": "gabi", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/gabi:$1" } ], "publications": [ { "doi": "10.1093/nar/gkn611", "pmc": "PMC2686513", "pubmed": "18812395", "title": "GabiPD: the GABI primary database--a plant integrative 'omics' database", "year": 2008 } ], "uri_format": "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject" }, "gaidet": { "contact": { "email": "serhii.nazarovets@gmail.com", "github": "panbibliotekar", "name": "Serhii Nazarovets", "orcid": "0000-0002-5067-4498" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Generative Artificial Intelligence Delegation Taxonomy (GAIDeT) assigns identifiers to contributor roles as an extension to the Contributor Roles Taxonomy (CRediT) to support promoting transparency and accountability in academic publishing when AI contribtors are involved in research. It is operationalized in the [GAIDeT Declaration Generator](https://panbibliotekar.github.io/gaidet-declaration/), an interactive tool for researchers to disclose the delegation of tasks to generative AI (GAI) tools in accordance with the GAIDeT taxonomy.", "download_owl": "https://w3id.org/gaidet/gaidet.owl", "example": "0000001", "homepage": "https://github.com/panbibliotekar/gaidet-declaration", "keywords": [ "artificial intelligence", "attribution", "contributor roles", "delegation", "ontology" ], "mappings": { "fairsharing": "FAIRsharing.23b8a3" }, "name": "Generative Artificial Intelligence Delegation Taxonomy", "pattern": "^\\d{7}$", "preferred_prefix": "gaidet", "publications": [ { "doi": "10.59350/psjb9-z1x39", "title": "GAIDeT: a practical taxonomy for declaring AI use in research and publishing", "year": 2025 }, { "doi": "10.1080/08989621.2025.2544331", "title": "A taxonomy for humans to delegate tasks to generative artificial intelligence in scientific research and publishing", "year": 2025 } ], "rdf_uri_format": "https://w3id.org/gaidet/$1", "repository": "https://github.com/panbibliotekar/gaidet-declaration", "uri_format": "https://w3id.org/gaidet/$1" }, "gainesville.core": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Describes typical Computational Chemistry experiments, including Molecular Publications, Molecular Systems, Molecular Calculations", "download_owl": "http://ontologies.makolab.com/gc06/gc.owl", "example": "Aromatic", "homepage": "http://ontologies.makolab.com/gc06/gc.html", "keywords": [ "chemistry", "nfdi4chem", "ontology" ], "license": "CC-BY-3.0", "mappings": { "tib": "gc" }, "name": "Gainesville Core Ontology", "preferred_prefix": "gainesville.core", "references": [ "http://ontologies.makolab.com/gc/" ], "uri_format": "http://purl.org/gc/$1" }, "galen": { "comment": "I really tried, but could not figure out what GALEN stands for", "contact": { "email": "j@deltaflow.com", "name": "Julian Seidenberg" }, "deprecated": true, "description": "A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.", "download_owl": "http://aber-owl.net/media/ontologies/GALEN/1/galen.owl", "example": "MagnitudeValueType", "homepage": "https://www.opengalen.org", "keywords": [ "ontology" ], "mappings": { "aberowl": "GALEN", "bioportal": "GALEN" }, "name": "GALEN", "preferred_prefix": "galen", "uri_format": "http://www.co-ode.org/ontologies/galen#$1" }, "gallont": { "contact": { "email": "adeans@psu.edu", "github": "adeans", "name": "Andy Deans", "orcid": "0000-0002-2119-4663" }, "depends_on": [ "caro", "flopo", "ncbitaxon", "obi", "pato", "po", "poro", "ro" ], "description": "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls.", "download_json": "https://github.com/adeans/gallont/raw/refs/heads/main/gallont.json", "download_obo": "http://purl.obolibrary.org/obo/gallont.obo", "download_owl": "http://purl.obolibrary.org/obo/gallont.owl", "example": "0000001", "homepage": "https://adeans.github.io/gallont/", "keywords": [ "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "GALLONT", "agroportal": "GALLONT", "bioportal": "GALLONT", "obofoundry": "gallont", "ols": "gallont", "ontobee": "GALLONT" }, "name": "Plant Gall Ontology", "pattern": "^\\d{7}$", "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_$1", "version": "2024-04-19" }, "gard": { "contact": { "email": "eric.sid@nih.gov", "github": "ericsid", "name": "Eric Sid", "orcid": "0000-0001-7697-3026" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease.", "example": "6038", "homepage": "https://rarediseases.info.nih.gov/diseases", "keywords": [ "condition", "disease", "symptom" ], "logo": "https://rarediseases.info.nih.gov/assets/GARD_Logo_Mobile.svg", "mappings": { "wikidata": "P4317" }, "name": "Genetic and Rare Diseases Information Center", "pattern": "^\\d+$", "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" ], "uri_format": "https://rarediseases.info.nih.gov/diseases/$1/index" }, "gateway": { "description": "The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access.", "example": "fd8d0743-344a-4758-bb97-f8ad84a37357", "homepage": "https://www.hdruk.ac.uk", "mappings": { "miriam": "gateway" }, "name": "Health Data Research Innovation Gateway", "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "preferred_prefix": "gateway", "uri_format": "https://web.www.healthdatagateway.org/dataset/$1" }, "gaz": { "appears_in": [ "scdo" ], "contact": { "email": "lschriml@som.umaryland.edu", "github": "lschriml", "name": "Lynn Schriml", "orcid": "0000-0001-8910-9851" }, "description": "A gazetteer constructed on ontological principles. The countries are actively maintained.", "download_obo": "http://purl.obolibrary.org/obo/gaz.obo", "download_owl": "http://purl.obolibrary.org/obo/gaz.owl", "example": "00620027", "homepage": "http://environmentontology.github.io/gaz/", "keywords": [ "environmental science", "geographic location", "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "GAZ", "biocontext": "GAZ", "bioportal": "GAZ", "fairsharing": "FAIRsharing.wkdjpb", "obofoundry": "gaz", "ols": "gaz", "ontobee": "GAZ", "wikidata": "P6778", "wikidata.entity": "Q81661634" }, "name": "Gazetteer", "pattern": "^\\d{8}$", "preferred_prefix": "GAZ", "rdf_uri_format": "http://purl.obolibrary.org/obo/GAZ_$1", "repository": "https://github.com/EnvironmentOntology/gaz", "uri_format": "http://purl.obolibrary.org/obo/GAZ_$1" }, "gbif": { "contact": { "email": "timrobertson100@gmail.com", "github": "timrobertson100", "name": "Tim Robertson", "orcid": "0000-0001-6215-3617" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth.", "example": "4238", "homepage": "https://www.gbif.org/species", "keywords": [ "biodiversity", "bioinformatics", "marine biology", "metagenomics", "natural history", "natural science", "taxonomy" ], "mappings": { "fairsharing": "FAIRsharing.zv11j3", "integbio": "nbdc00069", "re3data": "r3d100000039", "wikidata": "P846" }, "name": "Global Biodiversity Information Facility", "pattern": "^\\d+$", "preferred_prefix": "gbif", "publications": [ { "doi": "10.1371/journal.pone.0102623", "pmc": "PMC4123864", "pubmed": "25099149", "title": "The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet", "year": 2014 } ], "repository": "https://github.com/gbif/", "twitter": "GBIF", "uri_format": "https://www.gbif.org/species/$1" }, "gcst": { "description": "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide.", "example": "GCST000035", "homepage": "https://www.ebi.ac.uk", "mappings": { "miriam": "gcst", "n2t": "gcst" }, "name": "GWAS Catalog", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^GCST\\d{6}\\d*$", "preferred_prefix": "gcst", "uri_format": "https://www.ebi.ac.uk/gwas/studies/$1" }, "gdc": { "description": "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis.", "example": "ae8c77fe-e6c8-44d5-8265-4a38c637bbef", "homepage": "https://gdc.cancer.gov", "mappings": { "biocontext": "GDC", "miriam": "gdc", "n2t": "gdc" }, "name": "Genomic Data Commons Data Portal", "pattern": "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$", "preferred_prefix": "gdc", "uri_format": "https://portal.gdc.cancer.gov/cases/$1" }, "gdo": { "contact": { "email": "mclarkson@uky.edu", "name": "Melissa D Clarkson", "orcid": "0000-0001-9979-176X" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Graphic Descriptor Ontology (GDO) is intended for use in describing graphics that represent the form of objects. It uses the language of visual communication, illustration, and technical drawing. The GDO is rooted in the Basic Formal Ontology (BFO) and uses several classes from the Information Entity Ontology of the Common Core Ontologies as a mid-level ontology. [from https://gdo.endlessforms.info/about]", "download_owl": "https://github.com/endlessforms-info/GDO-GDOA/raw/refs/heads/main/gdoa.owl", "example": "0000016", "homepage": "https://gdo.endlessforms.info", "keywords": [ "ontology" ], "name": "Graphic Descriptor Ontology", "preferred_prefix": "gdo", "repository": "https://github.com/endlessforms-info/GDO-GDOA", "uri_format": "https://gdo.endlessforms.info/view/classes?uuid=GDO_$1" }, "gdsc": { "description": "The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies.", "example": "1242", "homepage": "https://www.cancerrxgene.org", "mappings": { "cellosaurus": "GDSC", "miriam": "gdsc", "n2t": "gdsc" }, "name": "Genomics of Drug Sensitivity in Cancer", "pattern": "^[0-9]+$", "preferred_prefix": "gdsc", "uri_format": "https://www.cancerrxgene.org/translation/Drug/$1" }, "gear": { "contact": { "email": "jorvis@gmail.com", "github": "jorvis", "name": "Joshua Orvis", "orcid": "0000-0002-5705-5710" }, "contributor": { "email": "jorvis@gmail.com", "github": "jorvis", "name": "Joshua Orvis", "orcid": "0000-0002-5705-5710" }, "description": "The gEAR portal is a website for visualization and analysis of multi-omic data both in public and private domains.", "example": "d.a59037e8", "example_extras": [ "p.bfd178f5" ], "github_request_issue": 728, "homepage": "https://umgear.org", "license": "AGPL-3.0-only", "name": "Gene Expression Analysis Resource", "pattern": "^[dp]\\.[a-z0-9]{8}$", "preferred_prefix": "gear", "repository": "https://github.com/IGS/gEAR", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://umgear.org/p?id=$1" }, "gecko": { "contact": { "email": "rbca.jackson@gmail.com", "github": "beckyjackson", "name": "Rebecca Jackson", "orcid": "0000-0003-4871-5569" }, "description": "An ontology to represent genomics cohort attributes.", "download_owl": "http://purl.obolibrary.org/obo/gecko.owl", "example": "0000044", "homepage": "https://github.com/IHCC-cohorts/GECKO", "keywords": [ "biospecimen", "experimental measurement", "genomics", "life science", "obo", "ontology", "statistics" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "GECKO", "bioportal": "GECKO", "fairsharing": "FAIRsharing.3da56b", "obofoundry": "gecko", "ols": "gecko", "ontobee": "GECKO", "wikidata.entity": "Q113012662" }, "name": "Genomics Cohorts Knowledge Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "GECKO", "rdf_uri_format": "http://purl.obolibrary.org/obo/GECKO_$1", "repository": "https://github.com/IHCC-cohorts/GECKO", "uri_format": "http://purl.obolibrary.org/obo/GECKO_$1", "version": "2021-01-18" }, "gemet.concept": { "contact": { "email": "helpdesk@eionet.europa.eu", "name": "Eionet Helpdesk" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts.", "example": "627", "homepage": "https://www.eionet.europa.eu/gemet/en/themes/", "keywords": [ "biodiversity", "earth sciences", "ecology", "environmental science", "ess" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "GEMET", "bartoc": "16", "fairsharing": "FAIRsharing.9091d9", "tib": "gemet", "wikidata.entity": "Q1485161" }, "name": "General Multilingual Environmental Thesaurus Concept", "pattern": "^\\d+$", "preferred_prefix": "gemet.concept", "providers": [ { "code": "gemet.multilingual", "description": "An alternate URI that doesn't have the language encoded in it", "homepage": "https://www.eionet.europa.eu/gemet", "name": "GEMET Multilingual", "uri_format": "http://www.eionet.europa.eu/gemet/concept/$1" } ], "rdf_uri_format": " http://www.eionet.europa.eu/gemet/concept/$1", "uri_format": "https://www.eionet.europa.eu/gemet/en/concept/$1" }, "gemet.group": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Groups listed in GEMET", "example": "893", "homepage": "https://www.eionet.europa.eu/gemet/en/groups/", "license": "CC-BY-4.0", "name": "General Multilingual Environmental Thesaurus Group", "pattern": "^\\d+$", "preferred_prefix": "gemet.group", "rdf_uri_format": "http://www.eionet.europa.eu/gemet/group/$1", "uri_format": "https://www.eionet.europa.eu/gemet/en/group/$1" }, "gemet.relation": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Relations in GEMET", "example": "6237", "homepage": "https://www.eionet.europa.eu/gemet/en", "license": "CC-BY-4.0", "name": "General Multilingual Environmental Thesaurus Relation", "pattern": "^\\d+$", "preferred_prefix": "gemet.relation", "uri_format": "https://www.eionet.europa.eu/gemet/en/relations/$1" }, "gemet.theme": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Themes listed in GEMET", "example": "4", "homepage": "https://www.eionet.europa.eu/gemet/en/themes", "license": "CC-BY-4.0", "name": "General Multilingual Environmental Thesaurus Theme", "pattern": "^\\d+$", "preferred_prefix": "gemet.theme", "rdf_uri_format": "http://www.eionet.europa.eu/gemet/theme/$1", "uri_format": "https://www.eionet.europa.eu/gemet/en/theme/$1" }, "genatlas": { "description": "GenAtlas is a database containing information on human genes, markers and phenotypes.", "example": "HBB", "homepage": "http://genatlas.medecine.univ-paris5.fr/", "keywords": [ "disorder", "gene", "human", "life science" ], "mappings": { "biocontext": "GENATLAS", "fairsharing": "FAIRsharing.pmg2vd", "integbio": "nbdc00275", "miriam": "genatlas", "n2t": "genatlas", "prefixcommons": "genatlas", "uniprot": "DB-0027" }, "name": "Genatlas", "pattern": "^\\w+$", "preferred_prefix": "genatlas", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/genatlas:$1" } ], "publications": [ { "doi": "10.1016/s0764-4469(99)80021-3", "pubmed": "9835018", "title": "Genatlas database, genes and development defects", "year": 1998 }, { "doi": "10.1006/mgme.1999.2867", "pubmed": "10444337", "title": "Human genes involved in chromatin remodeling in transcription initiation, and associated diseases: An overview using the GENATLAS database", "year": 1999 } ], "uri_format": "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1" }, "genbank": { "contact": { "email": "nawrocke@ncbi.nlm.nih.gov", "github": "nawrockie", "name": "Eric P. Nawrocki", "orcid": "0000-0002-2497-3427" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42).", "example": "U49845", "homepage": "https://www.ncbi.nlm.nih.gov/genbank/", "keywords": [ "bioinformatics", "data management", "dna", "epidemiology", "functional genomics", "genomics", "metagenomics", "transcriptomics", "virology" ], "mappings": { "biocontext": "GenBank", "cheminf": "000304", "edam": "2292", "fairsharing": "FAIRsharing.9kahy4", "go": "GenBank", "integbio": "nbdc00276", "prefixcommons": "genbank", "re3data": "r3d100010528", "uniprot": "DB-0028" }, "name": "GenBank", "preferred_prefix": "genbank", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/genbank:$1" } ], "publications": [ { "doi": "10.1093/nar/gkae1114", "pubmed": "39558184", "title": "GenBank 2025 update", "year": 2024 }, { "doi": "10.1186/s12859-020-3537-3", "pmc": "PMC7245624", "pubmed": "32448124", "title": "VADR: validation and annotation of virus sequence submissions to GenBank", "year": 2020 }, { "doi": "10.1093/nar/gkz956", "pmc": "PMC7145611", "pubmed": "31665464", "title": "GenBank", "year": 2020 }, { "doi": "10.1093/nar/gky989", "pmc": "PMC6323954", "pubmed": "30365038", "title": "GenBank", "year": 2019 }, { "doi": "10.1093/nar/gkx1094", "pmc": "PMC5753231", "pubmed": "29140468", "title": "GenBank", "year": 2018 }, { "doi": "10.1093/nar/gkw1070", "pmc": "PMC5210553", "pubmed": "27899564", "title": "GenBank", "year": 2016 }, { "doi": "10.1093/nar/gkv1276", "pmc": "PMC4702903", "pubmed": "26590407", "title": "GenBank", "year": 2015 }, { "doi": "10.1093/nar/gku1216", "pmc": "PMC4383990", "pubmed": "25414350", "title": "GenBank", "year": 2014 }, { "doi": "10.1093/nar/gkt1030", "pmc": "PMC3965104", "pubmed": "24217914", "title": "GenBank", "year": 2013 }, { "doi": "10.1093/nar/gks1195", "pmc": "PMC3531190", "pubmed": "23193287", "title": "GenBank", "year": 2012 }, { "doi": "10.1093/nar/gkr1202", "pmc": "PMC3245039", "pubmed": "22144687", "title": "GenBank", "year": 2011 }, { "doi": "10.1093/nar/gkq1079", "pmc": "PMC3013681", "pubmed": "21071399", "title": "GenBank", "year": 2010 }, { "doi": "10.1093/nar/gkn723", "pmc": "PMC2686462", "pubmed": "18940867", "title": "GenBank", "year": 2008 }, { "doi": "10.1093/nar/gkm929", "pmc": "PMC2238942", "pubmed": "18073190", "title": "GenBank", "year": 2007 }, { "doi": "10.1093/nar/gkl1031", "pmc": "PMC1781113", "pubmed": "17170002", "title": "Database resources of the National Center for Biotechnology Information", "year": 2006 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/nucleotide/$1" }, "genbase": { "comment": "CTH: this is a provider of the INSDC resources, not a new prefix.", "contact": { "email": "zhaoxuetong@big.ac.cn", "name": "Xuetong Zhao", "orcid": "0000-0002-3019-8615" }, "contributor": { "email": "shah.tanay2@northeastern.edu", "github": "tanayshah2", "name": "Tanay Shah", "orcid": "0009-0001-1912-5132" }, "description": "GenBase is a genetic sequence database that accepts user submissions (mRNA, genomic DNAs, ncRNA, or small genomes such as organelles, viruses, plasmids, phages from any organism) and integrates data from INSDC.", "example": "C_AA001108.1", "github_request_issue": 1140, "homepage": "https://ngdc.cncb.ac.cn/genbase/?lang=en", "mappings": { "re3data": "r3d100014353" }, "name": "GenBase", "preferred_prefix": "genbase", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://ngdc.cncb.ac.cn/genbase/search/gb/$1" }, "gendis": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases.", "example": "46946", "homepage": "http://caps.ncbs.res.in/gendis/home.html", "keywords": [ "classification", "genome" ], "mappings": { "prefixcommons": "gendis" }, "name": "Genomic Distribution of structural Superfamilies", "preferred_prefix": "gendis", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/gendis:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code=$1" }, "genecards.gene": { "contact": { "email": "marilyn.safran@weizmann.ac.il", "name": "Marilyn Safran", "orcid": "0000-0001-5424-1393" }, "description": "The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/genecards:$1" } ], "publications": [ { "doi": "10.1016/s0168-9525(97)01103-7", "pubmed": "9097728", "title": "GeneCards: integrating information about genes, proteins and diseases", "year": 1997 }, { "doi": "10.1186/s12864-016-2722-2", "pmc": "PMC4928145", "pubmed": "27357693", "title": "VarElect: the phenotype-based variation prioritizer of the GeneCards Suite", "year": 2016 }, { "doi": "10.1002/cpbi.5", "pubmed": "27322403", "title": "The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses", "year": 2016 }, { "doi": "10.1093/database/baw030", "pmc": "PMC4820835", "pubmed": "27048349", "title": "Genic insights from integrated human proteomics in GeneCards", "year": 2016 }, { "doi": "10.1089/omi.2015.0168", "pmc": "PMC4799705", "pubmed": "26983021", "title": "GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data", "year": 2016 }, { "doi": "10.1093/database/bav006", "pmc": "PMC4343183", "pubmed": "25725062", "title": "PathCards: multi-source consolidation of human biological pathways", "year": 2015 }, { "doi": "10.1093/database/baq020", "pmc": "PMC2938269", "pubmed": "20689021", "title": "GeneCards Version 3: the human gene integrator", "year": 2010 }, { "doi": "10.1093/bioinformatics/18.11.1542", "pubmed": "12424129", "title": "GeneCards 2002: towards a complete, object-oriented, human gene compendium", "year": 2002 }, { "doi": "10.1016/S0168-9525(97)01103-7", "title": "GeneCards: integrating information about genes, proteins and diseases." } ], "synonyms": [ "genecards" ], "uri_format": "https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1" }, "genecards.geneannot": { "description": "GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/geneloc:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id=$1" }, "genecards.genenote": { "description": "GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E.", "example": "GC06M052656", "homepage": "http://genecards.weizmann.ac.il/genenote/", "keywords": [ "gene expression" ], "mappings": { "prefixcommons": "genenote" }, "name": "Gene Normal Tissue Expression", "preferred_prefix": "genecards.genenote", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/genenote:$1" } ], "uri_format": "http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl?keyword_type=2_gc_id&keyword=$1&data_type=norm2&results=yes" }, "genedb": { "deprecated": true, "description": "GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the \"Pathogen Genomics\" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed.", "example": "LinJ.20.0070", "homepage": "https://www.genedb.org/", "keywords": [ "genome", "life science", "sequence" ], "logo": "https://www.genedb.org/errors/genedb_logo.png", "mappings": { "biocontext": "GENEDB", "edam": "1035", "fairsharing": "FAIRsharing.j7esqq", "go": "GeneDB", "integbio": "nbdc00469", "miriam": "genedb", "n2t": "genedb", "ncbi": "GeneDB", "prefixcommons": "genedb", "re3data": "r3d100010626", "wikidata": "P3382" }, "name": "GeneDB", "pattern": "^[\\w\\d\\.-]*$", "preferred_prefix": "genedb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/genedb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkh007", "pmc": "PMC308742", "pubmed": "14681429", "title": "GeneDB: a resource for prokaryotic and eukaryotic organisms", "year": 2004 } ], "uri_format": "https://www.genedb.org/gene/$1" }, "genefarm": { "contact": { "email": "sebastien.aubourg@inrae.fr", "name": "sébastien Aubourg", "orcid": "0000-0002-0695-4767" }, "deprecated": true, "description": "GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products.", "example": "4892", "homepage": "http://urgi.versailles.inra.fr/Genefarm/", "keywords": [ "expression", "genome", "life science", "nucleotide", "sequence" ], "mappings": { "biocontext": "GENEFARM", "fairsharing": "FAIRsharing.2mayq0", "miriam": "genefarm", "n2t": "genefarm", "prefixcommons": "genefarm" }, "name": "GeneFarm", "pattern": "^\\d+$", "preferred_prefix": "genefarm", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/genefarm:$1" } ], "publications": [ { "doi": "10.1093/nar/gki115", "pmc": "PMC540069", "pubmed": "15608279", "title": "GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts", "year": 2005 } ], "uri_format": "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1" }, "genepio": { "contact": { "email": "damion_dooley@sfu.ca", "github": "ddooley", "name": "Damion Dooley", "orcid": "0000-0002-8844-9165" }, "depends_on": [ "chebi", "ncbitaxon", "po", "ro", "uberon" ], "description": "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.", "download_owl": "http://purl.obolibrary.org/obo/genepio.owl", "example": "0001885", "homepage": "http://genepio.org/", "keywords": [ "epidemiology", "food", "genome", "genomics", "obo", "ontology", "pathogen" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "GENEPIO", "biocontext": "GENEPIO", "bioportal": "GENEPIO", "fairsharing": "FAIRsharing.y1mmbv", "obofoundry": "genepio", "ols": "genepio", "ontobee": "GENEPIO", "wikidata.entity": "Q55118402" }, "name": "Genomic Epidemiology Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "GENEPIO", "rdf_uri_format": "http://purl.obolibrary.org/obo/GENEPIO_$1", "repository": "https://github.com/GenEpiO/genepio", "uri_format": "http://purl.obolibrary.org/obo/GENEPIO_$1", "version": "2024-12-18" }, "genetree": { "contact": { "email": "flicek@ebi.ac.uk", "name": "Paul Flicek", "orcid": "0000-0002-3897-7955" }, "description": "Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl.", "example": "ENSGT00550000074763", "homepage": "http://www.ensembl.org/", "keywords": [ "classification", "gene", "protein" ], "mappings": { "biocontext": "GENETREE", "miriam": "genetree", "n2t": "genetree", "prefixcommons": "genetree", "uniprot": "DB-0162" }, "name": "GeneTree", "pattern": "^ENSGT\\d+$", "preferred_prefix": "genetree", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/genetree:$1" } ], "publications": [ { "doi": "10.1093/database/bav096", "pmc": "PMC4761110", "pubmed": "26896847", "title": "Ensembl comparative genomics resources", "year": 2016 }, { "doi": "10.1093/nar/gkj133", "pmc": "PMC1347495", "pubmed": "16381931", "title": "Ensembl 2006", "year": 2006 } ], "uri_format": "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1" }, "genewiki": { "contact": { "email": "asu@scripps.edu", "github": "andrewsu", "name": "Andrew I Su", "orcid": "0000-0002-9859-4104" }, "description": "The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI.", "example": "1017", "homepage": "http://en.wikipedia.org/wiki/Gene_Wiki", "keywords": [ "genetics", "life science" ], "mappings": { "biocontext": "GENEWIKI", "fairsharing": "FAIRsharing.t3snf", "integbio": "nbdc00834", "miriam": "genewiki", "n2t": "genewiki" }, "name": "Gene Wiki", "pattern": "^\\d+$", "preferred_prefix": "genewiki", "provides": "ncbigene", "publications": [ { "doi": "10.1093/database/baw015", "pmc": "PMC4795929", "pubmed": "26989148", "title": "Wikidata as a semantic framework for the Gene Wiki initiative", "year": 2016 }, { "doi": "10.1093/nar/gkr925", "pmc": "PMC3245148", "pubmed": "22075991", "title": "The Gene Wiki in 2011: community intelligence applied to human gene annotation", "year": 2011 }, { "doi": "10.1093/nar/gkp760", "pmc": "PMC2808918", "pubmed": "19755503", "title": "The Gene Wiki: community intelligence applied to human gene annotation", "year": 2009 }, { "doi": "10.1371/journal.pbio.0060175", "pmc": "PMC2443188", "pubmed": "18613750", "title": "A gene wiki for community annotation of gene function", "year": 2008 } ], "twitter": "GeneWikiPulse", "uri_format": "http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1" }, "geno": { "contact": { "email": "mhb120@gmail.com", "github": "mbrush", "name": "Matthew Brush", "orcid": "0000-0002-1048-5019" }, "description": "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013", "download_json": "http://purl.obolibrary.org/obo/geno.json", "download_obo": "https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/develop/geno-full.obo", "download_owl": "http://purl.obolibrary.org/obo/geno.owl", "example": "0000632", "homepage": "https://github.com/monarch-initiative/GENO-ontology/", "keywords": [ "disease phenotype", "genomics", "genotype", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "GENO", "biocontext": "GENO", "bioportal": "GENO", "fairsharing": "FAIRsharing.kpbna7", "obofoundry": "geno", "ols": "geno", "ontobee": "GENO", "wikidata.entity": "Q81661639" }, "name": "Genotype Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "GENO", "rdf_uri_format": "http://purl.obolibrary.org/obo/GENO_$1", "repository": "https://github.com/monarch-initiative/GENO-ontology", "uri_format": "http://purl.obolibrary.org/obo/GENO_$1", "version": "2025-07-25" }, "genpept": { "description": "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank.", "example": "CAA71118.1", "homepage": "https://www.ncbi.nlm.nih.gov/protein", "mappings": { "biocontext": "GENPEPT", "miriam": "genpept", "n2t": "genpept" }, "name": "GenPept", "pattern": "^\\w{3}\\d{5}(\\.\\d+)?$", "preferred_prefix": "genpept", "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept" }, "genprop": { "description": "Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome.", "example": "GenProp0699", "homepage": "https://www.ebi.ac.uk/interpro/genomeproperties/", "keywords": [ "classification", "genome" ], "mappings": { "biocontext": "GENPROP", "miriam": "genprop", "n2t": "genprop", "prefixcommons": "jcvi.genprop" }, "name": "Genome Properties", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^GenProp\\d+$", "preferred_prefix": "genprop", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/jcvi.genprop:$1" } ], "uri_format": "https://www.ebi.ac.uk/interpro/genomeproperties/#$1" }, "geo": { "banana_peel": "_", "contact": { "email": "barrett@ncbi.nlm.nih.gov", "name": "Tanya Barrett", "orcid": "0000-0002-9448-8064" }, "description": "The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval.", "example": "GDS1234", "homepage": "https://www.ncbi.nlm.nih.gov/geo/", "keywords": [ "comparative genomics", "epigenomics", "gene expression", "genome", "genomics", "life science", "omics", "phenomics", "transcriptomics" ], "logo": "https://www.ncbi.nlm.nih.gov/geo/img/geo_main.gif", "mappings": { "cellosaurus": "GEO", "edam": "1147", "fairsharing": "FAIRsharing.5hc8vt", "go": "GEO", "integbio": "nbdc00080", "miriam": "geo", "n2t": "geo", "prefixcommons": "geo", "re3data": "r3d100010283" }, "name": "NCBI Gene Expression Omnibus", "pattern": "^G(PL|SM|SE|DS)\\d+$", "preferred_prefix": "geo", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/geo:$1" } ], "publications": [ { "doi": "10.1093/nar/gks1193", "pmc": "PMC3531084", "pubmed": "23193258", "title": "NCBI GEO: archive for functional genomics data sets--update", "year": 2012 }, { "doi": "10.1038/nbt1206-1471", "pmc": "PMC2270403", "pubmed": "17160034", "title": "NCBI GEO standards and services for microarray data", "year": 2006 }, { "doi": "10.1093/nar/30.1.207", "pmc": "PMC99122", "pubmed": "11752295", "title": "Gene Expression Omnibus: NCBI gene expression and hybridization array data repository", "year": 2002 }, { "doi": "10.1038/35001676", "pubmed": "10693778", "title": "One-stop shop for microarray data", "year": 2000 }, { "doi": "10.5281/zenodo.5706412", "title": "MINSEQE: Minimum Information about a high-throughput Nucleotide SeQuencing Experiment - a proposal for standards in functional genomic data reporting", "year": 2012 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1" }, "geogeo": { "banana": "GEO", "banana_peel": "_", "contact": { "email": "hoganwr@gmail.com", "github": "hoganwr", "name": "Bill Hogan", "orcid": "0000-0002-9881-1017" }, "description": "An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in \"The US declared war on Germany\" vs. the US in \"The plane entered US airspace\".", "download_owl": "http://purl.obolibrary.org/obo/geo.owl", "example": "000000021", "homepage": "https://github.com/ufbmi/geographical-entity-ontology/wiki", "keywords": [ "geographic location", "human geography", "obo", "ontology", "physical geography" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "GEO", "biocontext": "GEO", "bioportal": "GEO", "fairsharing": "FAIRsharing.27rndz", "miriam": "geogeo", "obofoundry": "geo", "ols": "geo", "ontobee": "GEO", "wikidata.entity": "Q81661641" }, "name": "Geographical Entity Ontology", "namespace_in_lui": true, "pattern": "^\\d{9}$", "preferred_prefix": "GEOGEO", "rdf_uri_format": "http://purl.obolibrary.org/obo/GEO_$1", "repository": "https://github.com/ufbmi/geographical-entity-ontology", "uri_format": "http://purl.obolibrary.org/obo/GEO_$1", "version": "2016-03-26" }, "geonames": { "contact": { "email": "marc@geonames.org", "name": "Marc Wick" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge.", "example": "3532759", "homepage": "https://www.geonames.org", "keywords": [ "geographic location", "geography", "geoinformatics" ], "license": "CC-BY-4.0", "logo": "https://www.geonames.org/img/globe.gif", "mappings": { "fairsharing": "FAIRsharing.6dba71", "re3data": "r3d100010245" }, "name": "GeoNames", "pattern": "^\\d+$", "preferred_prefix": "geonames", "synonyms": [ "Geomames", "Geonamaes" ], "uri_format": "https://www.geonames.org/$1" }, "geonames.feature": { "contact": { "email": "marc@geonames.org", "name": "Marc Wick" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes.", "example": "ADM1", "homepage": "https://www.geonames.org/export/codes.html", "keywords": [ "geography" ], "license": "CC-BY-4.0", "logo": "https://www.geonames.org/img/globe.gif", "name": "GeoNames Feature Code", "preferred_prefix": "geonames.feature", "uri_format": "https://www.geonames.org/recent-changes/featurecode/$1/" }, "geonames.ontology": { "description": "An ontology used to enable annotating geospatial semantic information to entities in GeoNames", "download_rdf": "https://www.geonames.org/ontology/ontology_v3.3.rdf", "example": "parentFeature", "homepage": "https://www.geonames.org/ontology/documentation.html", "mappings": { "zazuko": "gn" }, "name": "GeoNames Ontology", "preferred_prefix": "geonames.ontology" }, "geosparql": { "contact": { "email": "kdurante@stanford.edu", "name": "Kim Durante" }, "description": "The OGC GeoSPARQL standard supports representing and querying geospatial data on the Semantic Web. GeoSPARQL defines a vocabulary for representing geospatial data in RDF, and it defines an extension to the SPARQL query language for processing geospatial data. In addition, GeoSPARQL is designed to accommodate systems based on qualitative spatial reasoning and systems based on quantitative spatial computations.", "download_owl": "http://aber-owl.net/media/ontologies/GEOSPARQL/1/geosparql.owl", "example": "hasDefaultGeometry", "homepage": "https://opengeospatial.github.io/ogc-geosparql/geosparql11/index.html", "keywords": [ "earth sciences", "ess", "fair data spaces", "nfdi4ing", "ontology" ], "mappings": { "aberowl": "GEOSPARQL", "bioportal": "GEOSPARQL", "tib": "geo", "zazuko": "geo" }, "name": "GeoSPARQL", "preferred_prefix": "geosparql", "uri_format": "http://www.opengis.net/ont/geosparql#$1" }, "geosparql.function": { "description": "Functions for GeoSPARQL", "example": "sfEquals", "homepage": "https://opengeospatial.github.io/ogc-geosparql/geosparql10/servicedescription_all_functions.html", "mappings": { "zazuko": "geof" }, "name": "GeoSPARQL Function", "preferred_prefix": "geosparql.function" }, "geosparql.rule": { "description": "Rules for GeoSPARQL", "example": "rcc", "homepage": "https://opengeospatial.github.io/ogc-geosparql/geosparql11/rules.html", "mappings": { "zazuko": "geor" }, "name": "GeoSPARQL Rule", "preferred_prefix": "geosparql.rule" }, "gesah": { "description": "The GESAH Graphic Arts Ontology is designed for the inventory, classification and structured description of works on paper.", "example": "applies_to", "homepage": "https://sah.tib.eu/", "keywords": [ "architecture", "history", "nfdi4culture" ], "mappings": { "tib": "gesah" }, "name": "GESAH Graphic Arts Ontology", "preferred_prefix": "gesah", "uri_format": "http://ontology.tib.eu/gesah/$1" }, "gesis.kategorienschemawahlstudien": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Category Scheme Election Studies provides the ability to categorize election studies at the question and/or variable level.", "example": "01", "homepage": "https://vocabularies.cessda.eu/vocabulary/KategorienschemaWahlstudien", "license": "CC-BY-4.0", "name": "Category Scheme Election Studies", "owners": [ { "name": "GESIS - Leibniz-Institute for the Social Sciences", "partnered": false, "ror": "018afyw53" } ], "preferred_prefix": "gesis.kategorienschemawahlstudien", "uri_format": "https://vocabularies.cessda.eu/vocabulary/KategorienschemaWahlstudien?lang=en#code_$1", "version": "1.0.1" }, "gesis.rexconcepts": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This CV, developed within the framework of the DP-R|EX joint project, involving the partner institutions DeZIM, Qualiservice and GESIS, maps the central concepts and theoretical approaches in research on racism and right-wing extremism. The compilation is based on a systematic evaluation of the relevant national and international empirical research literature. The CV equally takes into account the different thematic (racism, right-wing extremism, discrimination) as well as methodological (qualitative research, standardised surveys, data from social media and messaging services) research strands.", "example": "33", "homepage": "https://vocabularies.cessda.eu/vocabulary/rexconcepts", "license": "CC-BY-4.0", "name": "Central concepts of R|EX research", "owners": [ { "name": "GESIS - Leibniz-Institute for the Social Sciences", "partnered": false, "ror": "018afyw53" } ], "preferred_prefix": "gesis.rexconcepts", "uri_format": "https://vocabularies.cessda.eu/vocabulary/rexconcepts?lang=en#code_$1", "version": "1.9.0" }, "gesis.rexdatatype": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This CV, developed as part of the DP-R|EX joint project, involving the partner institutions DeZIM, Qualiservice and GESIS, maps the data types relevant to the research field. The CV includes data types that can result from a variety of different collection methods. These include, for example, standardised or unstandardised surveys, individual or repeated observations, as well as process-produced or user-generated types of data generation. The data types can be subject-, event-, space- or time-related and refer to the individual or aggregate level.", "example": "01a", "homepage": "https://vocabularies.cessda.eu/vocabulary/rexdatatype", "license": "CC-BY-4.0", "name": "Data types in R|EX research", "owners": [ { "name": "GESIS - Leibniz-Institute for the Social Sciences", "partnered": false, "ror": "018afyw53" } ], "preferred_prefix": "gesis.rexdatatype", "uri_format": "https://vocabularies.cessda.eu/vocabulary/rexdatatype?lang=en#code_$1", "version": "1.4.1" }, "gesis.rexgroups": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This CV, developed within the framework of the DP-R|EX joint project, involving the partner institutions DeZIM, Qualiservice and GESIS, maps the dimensions of discrimination and racialised characteristics relevant to the research area. The compilation is based on a systematic evaluation of the relevant national and international empirical research literature. These include self-attributed characteristics as well as anticipated attributions by others. The characteristics do not necessarily correspond to the studied units in the data set, but can also be the subject of studied concepts or theories in the surveys, such as on specific prejudices and attitudes.", "example": "v1", "homepage": "https://vocabularies.cessda.eu/vocabulary/rexgroups", "license": "CC-BY-4.0", "name": "Diversification criteria of R|EX research", "owners": [ { "name": "GESIS - Leibniz-Institute for the Social Sciences", "partnered": false, "ror": "018afyw53" } ], "preferred_prefix": "gesis.rexgroups", "uri_format": "https://vocabularies.cessda.eu/vocabulary/rexgroups?lang=en#code_$1", "version": "1.10.0" }, "gesis.variables-relations": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "As the variable is one of the most relevant entities to enhance data reuse in the Social Sciences, we provide a framework design to better semantics the variables' relations descriptions. These explicit relations between variables enable comparability and facilitate harmonization across waves. We provide a brief textual identification of the relation type, supported by a controlled vocabulary (CV) and an extended description of the relationship. These relations within variables include but are not limited to different versions, derived formats in new waves, new labels and name wording, and alternative response schema through questionnaires and surveys. For instance, a given variable label is changed from one wave to another, even though its concept remains the same. Their values also are subject to change, such as new cardinalities settings, their categorization, or response scheme and scale measurement. They change based on different conditions, e.g., values are updated by any constraints or modified to comply with the study evolution requirements or a new sociological approach. In the Social Sciences, Economics, and Behaviour Sciences, which investigate, for instance, the social structure of the population, political attitudes of voters and candidates, opinions on family, work, religion, politics and society or competencies of adults, those topics are highly subject to change to fit the empirical reality in a constantly changing world. Thus, we propose widening relations descriptions for Social Sciences variables within datasets beginning from the BasedOnObjectType DDI as a first approach.", "example": "01", "homepage": "https://vocabularies.cessda.eu/vocabulary/Variables-Relations", "license": "CC-BY-4.0", "name": "Variables relations for Social Sciences research data", "owners": [ { "name": "GESIS - Leibniz-Institute for the Social Sciences", "partnered": false, "ror": "018afyw53" } ], "preferred_prefix": "gesis.variables-relations", "uri_format": "https://vocabularies.cessda.eu/vocabulary/Variables-Relations?lang=en#code_$1", "version": "1.0.0" }, "gesiskg": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Predicates that are used to construct the GESIS Knowledge Graph, a bibliometrics KG.", "example": "linkContext", "github_request_issue": 1632, "homepage": "https://data.gesis.org/gesiskg", "keywords": [ "data schema", "nfdi" ], "name": "GESIS Knowledge Graph Schema", "preferred_prefix": "gesiskg", "uri_format": "https://data.gesis.org/gesiskg/schema/$1" }, "getty.att": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The AAT includes generic terms, and associated dates, relationships, and other rich information about concepts related to or required to catalog, discover, and retrieve information about art, architecture, and other visual cultural heritage, including related disciplines such as archaeology and conservation. Visual works include not only visual cultural works classified as \"art\" according to Western aesthetics, but also utilitarian and ceremonial works. Terminology may be used for work types, roles, materials, styles, cultures, techniques, subject, etc., so long as terms are within the defined scope of AAT. [from https://www.getty.edu/research/tools/vocabularies/aat/aat_faq.html]", "download_rdf": "https://vocab.getty.edu/aat.ttl", "example": "300011154", "homepage": "http://vocab.getty.edu/ontology", "license": "ODC-By-1.0", "name": "Art and Architecture Thesaurus", "preferred_prefix": "getty.att", "providers": [ { "code": "legacy", "uri_format": "http://vocab.getty.edu/resource/aat/$1" } ], "references": [ "https://www.getty.edu/research/tools/vocabularies/lod/aat_semantic_representation.pdf", "https://www.getty.edu/research/tools/vocabularies/lod/index.html" ], "uri_format": "http://vocab.getty.edu/aat/$1" }, "getty.cona": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "CONA compiles titles, attributions, depicted subjects, and other metadata about works of art, architecture, and cultural heritage, both extant and historical, physical and conceptual. Metadata is gathered and linked from museum collections, special collections, archives, libraries, scholarly research, and other sources. CONA is linked to the AAT, TGN, ULAN, and the IA (Iconography Authority). Through rich metadata and links, CONA may provide a powerful conduit for research and discovery for digital art history. [from homepage]", "example": "700054086", "homepage": "https://www.getty.edu/research/tools/vocabularies/cona/", "license": "ODC-By-1.0", "name": "Cultural Objects Names Authority", "preferred_prefix": "getty.cona", "uri_format": "http://vocab.getty.edu/page/cona/$1" }, "getty.gvp": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The GVP Ontology defines classes, properties and values (skos:Concepts) used in GVP LOD. As of version 3.0, it is complete regarding AAT, TGN and ULAN, and will be extended in time with more elements needed for other GVP vocabularies (CONA).", "download_rdf": "http://vocab.getty.edu/ontology.ttl", "example": "prefLabelGVP", "homepage": "http://vocab.getty.edu/ontology", "name": "Getty Vocabulary Program ontology", "preferred_prefix": "getty.gvp", "providers": [ { "code": "legacy", "uri_format": "http://vocab.getty.edu/resource/ontology#$1" } ], "references": [ "https://www.getty.edu/research/tools/vocabularies/lod/aat_semantic_representation.pdf", "https://www.getty.edu/research/tools/vocabularies/lod/index.html" ], "uri_format": "http://vocab.getty.edu/ontology#$1" }, "getty.ia": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Getty Iconography Authority ™ (IA), Cultural Objects Name Authority ® (CONA), the Union List of Artist Names ® (ULAN), the Art & Architecture Thesaurus ® (AAT), the Getty Thesaurus of Geographic Names ® (TGN) are structured resources that can be used to improve access to information about art, architecture, and other material culture. The Vocabularies are not simply 'value vocabularies,' but knowledge bases. Through rich metadata and links, the Getty Vocabularies provide powerful conduits for knowledge creation, complex research, and discovery for digital art history and related disciplines. [from https://www.getty.edu/research/tools/vocabularies/cona/about.html#purpose_ia]", "example": "901001034", "homepage": "https://www.getty.edu/cona/CONAIconographyHierarchy.aspx?iconid=901000000", "name": "Getty Iconography Authority", "preferred_prefix": "getty.ia", "uri_format": "http://vocab.getty.edu/page/ia/$1" }, "getty.tgn": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Thesaurus of Geographic Names (TGN) is a terminology that focuses on places relevant to art, architecture, and related disciplines, recording names, relationships, place types, dates, notes, and coordinates for current and historical cities, nations, empires, archaeological sites, lost settlements, and physical features. The TGN is one of 5 Getty Vocabularies intended to provide terminology and other information about the objects, artists, concepts, and places important to various disciplines that specialize in art, architecture, and other material culture.", "example": "1023371", "homepage": "https://www.getty.edu/research/tools/vocabularies/tgn/", "keywords": [ "ancient cultures", "architecture", "art history", "culture", "fine arts", "geographic location", "geography", "history", "human geography" ], "license": "ODC-By-1.0", "mappings": { "bartoc": "109", "fairsharing": "FAIRsharing.1413b5", "wikidata.entity": "Q1520117" }, "name": "Getty Thesaurus of Geographic Names", "pattern": "^\\d+$", "preferred_prefix": "getty.tgn", "providers": [ { "code": "getty.tgn.page", "uri_format": "http://vocab.getty.edu/page/tgn/$1" } ], "references": [ "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200" ], "synonyms": [ "tgn" ], "uri_format": "http://vocab.getty.edu/tgn/$1" }, "getty.ulan": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Getty Thesaurus of Geographic Names (TGN) is a structured vocabulary, including names, descriptions, and other metadata for extant and historical cities, empires, archaeological sites, and physical features important to research of art and architecture. TGN may be linked to GIS (Geographical Information System), maps, and other geographic resources. [from https://collectionstrust.org.uk/resource/thesaurus-of-geographic-names-tgn-getty/]", "example": "500202846", "homepage": "http://vocab.getty.edu/ulan/", "license": "ODC-By-1.0", "name": "Union List of Artist Names", "preferred_prefix": "getty.ulan", "uri_format": "http://vocab.getty.edu/ulan/$1" }, "gexo": { "contact": { "email": "kuiper@bio.ntnu.no", "github": "makuintnu", "name": "Martin Kuiper", "orcid": "0000-0002-1171-9876" }, "description": "Gene Expression Ontology", "download_obo": "https://www.bio.ntnu.no/ontology/GeXO/gexo.obo", "download_owl": "https://www.bio.ntnu.no/ontology/GeXO/gexo.owl", "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" ], "mappings": { "aberowl": "GEXO", "bioportal": "GEXO", "fairsharing": "FAIRsharing.3e0sn4", "ols": "gexo" }, "name": "Gene Expression Ontology", "no_own_terms": true, "preferred_prefix": "gexo", "publications": [ { "doi": "10.1186/s12859-014-0386-y", "pmc": "PMC4279962", "pubmed": "25490885", "title": "Finding gene regulatory network candidates using the gene expression knowledge base", "year": 2014 } ] }, "gfbio.ets": { "description": "The Ecological Trait-data Standard defines terms for the use in datasets containing quantitative and qualitative functional traits.", "example": "BiodiversityExploratories", "homepage": "https://terminologies.gfbio.org/terms/ets/pages/index.html", "keywords": [ "earth sciences", "ess", "fair data spaces", "life sciences, biology" ], "mappings": { "tib": "ets" }, "name": "Ecological Trait-data Standard", "preferred_prefix": "gfbio.ets", "uri_format": "http://terminologies.gfbio.org/terms/ETS/$1" }, "gfo": { "contact": { "email": "heinrich.herre@imise.uni-leipzig.de", "name": "Heinrich Herre" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The General Formal Ontology is a top-level ontology for conceptual modeling, which is being constantly further developed by Onto-Med. It includes elaborations of categories like objects, processes, time and space, properties, relations, roles, functions, facts, and situations. Moreover, we are working on an integration with the notion of levels of reality in order to more appropriately capture entities in the material, mental, and social areas.", "download_owl": "http://www.onto-med.de/ontologies/gfo.owl", "example": "projects_to", "homepage": "https://www.onto-med.de/ontologies/gfo", "keywords": [ "biomedical science", "engineering", "foundational ontologies", "life science", "ontology" ], "mappings": { "aberowl": "GFO", "bioportal": "GFO", "fairsharing": "FAIRsharing.175hsz", "tib": "gfo" }, "name": "General Formal Ontology", "preferred_prefix": "gfo", "providers": [ { "code": "alt1", "description": "Alternate identifier using gfo-basic.owl instead of gfo.owl", "homepage": "http://www.onto-med.de/ontologies", "name": "Alternate 1", "uri_format": "http://www.onto-med.de/ontologies/gfo-basic.owl#$1" } ], "uri_format": "http://www.onto-med.de/ontologies/gfo.owl#$1" }, "ghr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA).", "example": "saddan", "homepage": "https://medlineplus.gov/genetics/condition", "name": "Genetics Home Reference", "preferred_prefix": "ghr", "uri_format": "https://medlineplus.gov/genetics/condition/$1" }, "giardiadb": { "contact": { "email": "oharb@upenn.edu", "github": "ramobrah", "name": "Omar S. Harb", "orcid": "0000-0003-4446-6200" }, "description": "GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "GL50803_102438", "homepage": "https://giardiadb.org/giardiadb/", "keywords": [ "eukaryotic", "genome", "genomics" ], "mappings": { "biocontext": "GIARDIADB", "fairsharing": "FAIRsharing.e7skwg", "integbio": "nbdc01782", "miriam": "giardiadb", "n2t": "giardiadb", "prefixcommons": "giardiadb", "re3data": "r3d100012458" }, "name": "GiardiaDB", "pattern": "^\\w+$", "preferred_prefix": "giardiadb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/giardiadb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkn631", "pmc": "PMC2686445", "pubmed": "18824479", "title": "GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis", "year": 2008 } ], "twitter": "EuPathDB", "uri_format": "https://giardiadb.org/giardiadb/app/record/gene/$1" }, "gist": { "description": "gist is a minimalist upper ontology created by Semantic Arts.", "example": "Account", "homepage": "https://www.semanticarts.com/gist/", "keywords": [ "engineering", "foundational ontologies", "nfdi4ing" ], "mappings": { "tib": "gist" }, "name": "gist", "preferred_prefix": "gist", "uri_format": "https://w3id.org/semanticarts/ns/ontology/gist/$1" }, "github": { "description": "GitHub is an online host of Git source code repositories.", "example": "biopragmatics/bioregistry", "example_extras": [ "biopragmatics", "cthoyt" ], "homepage": "https://github.com/", "keywords": [ "knowledge and information systems", "software engineering", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.c55d5e", "miriam": "github", "re3data": "r3d100010375", "wikidata": "P2037" }, "name": "GitHub username", "pattern": "^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$", "preferred_prefix": "github", "repository": "https://services.github.com/", "uri_format": "https://github.com/$1" }, "github.issue": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An issue in any public repository on GitHub.", "example": "biopragmatics/bioregistry/424", "homepage": "https://github.com/", "keywords": [ "knowledge and information systems", "project management", "software engineering", "version control" ], "name": "GitHub Issue", "preferred_prefix": "github.issue", "uri_format": "https://bioregistry.io/resolve/github/issue/$1" }, "github.pull": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A pull request in any public repository on GitHub.", "example": "biopragmatics/bioregistry/416", "homepage": "https://github.com/", "keywords": [ "knowledge and information systems", "project management", "software engineering", "version control" ], "name": "GitHub Pull Request", "preferred_prefix": "github.pull", "uri_format": "https://bioregistry.io/resolve/github/pull/$1" }, "gitlab": { "description": "GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance. With GitLab, every team in your organization can collaboratively plan, build, secure, and deploy software to drive business outcomes faster with complete transparency, consistency and traceability.", "example": "morpheus.lab/morpheus", "homepage": "https://gitlab.com/", "keywords": [ "knowledge and information systems", "software engineering", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.530e61", "miriam": "gitlab" }, "name": "GitLab", "pattern": "^.*/.*$", "preferred_prefix": "gitlab", "twitter": "gitlab", "uri_format": "https://gitlab.com/$1" }, "glida.gpcr": { "deprecated": true, "description": "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors.", "example": "ACM1_HUMAN", "homepage": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/", "mappings": { "biocontext": "GLIDA.GPCR", "miriam": "glida.gpcr", "n2t": "glida.gpcr" }, "name": "GLIDA GPCR", "pattern": "^[A-Z-_0-9]+$", "preferred_prefix": "glida.gpcr", "uri_format": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1" }, "glida.ligand": { "deprecated": true, "description": "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands.", "example": "L000001", "homepage": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/", "mappings": { "biocontext": "GLIDA.LIGAND", "miriam": "glida.ligand", "n2t": "glida.ligand" }, "name": "GLIDA Ligand", "pattern": "^L\\d+$", "preferred_prefix": "glida.ligand", "uri_format": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1" }, "glottolog": { "appears_in": [ "gsso" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Comprehensive reference information for the world's languages, especially the lesser known languages. [from homepage]", "example": "nort3314", "github_request_issue": 1310, "homepage": "https://glottolog.org", "license": "CC-BY-4.0", "name": "Glottolog", "preferred_prefix": "glottolog", "uri_format": "https://glottolog.org/resource/languoid/id/$1" }, "glycoepitope": { "description": "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes.", "example": "EP0311", "homepage": "https://www.glycoepitope.jp/epitopes/", "mappings": { "biocontext": "GLYCOEPITOPE", "integbio": "nbdc00087", "miriam": "glycoepitope", "n2t": "glycoepitope" }, "name": "GlycoEpitope", "pattern": "^EP\\d{4}$", "preferred_prefix": "glycoepitope", "uri_format": "https://www.glycoepitope.jp/epitopes/$1" }, "glycomapsdb": { "description": "A database of GlycoMaps containing 2585 conformational maps.", "example": "6819", "homepage": "http://www.glycosciences.de/modeling/glycomapsdb/", "keywords": [ "small molecule" ], "mappings": { "prefixcommons": "glycomapsdb" }, "name": "GlycoMapsDB", "preferred_prefix": "glycomapsdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/glycomapsdb:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=$1" }, "glycomedb": { "contact": { "email": "rr@uga.edu", "github": "ReneRanzinger", "name": "René Ranzinger", "orcid": "0000-0003-3147-448X" }, "description": "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.", "example": "G77500AY", "has_canonical": "glytoucan", "homepage": "https://glytoucan.org/", "keywords": [ "life science", "molecules", "small molecules", "structure" ], "mappings": { "biocontext": "GLYCOMEDB", "edam": "2664", "fairsharing": "FAIRsharing.k5k0yh", "integbio": "nbdc00899", "miriam": "glycomedb", "n2t": "glycomedb", "prefixcommons": "glycomedb", "re3data": "r3d100011527" }, "name": "GlycomeDB", "pattern": "^\\w+$", "preferred_prefix": "glycomedb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/glycomedb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkq1014", "pmc": "PMC3013643", "pubmed": "21045056", "title": "GlycomeDB--a unified database for carbohydrate structures", "year": 2010 }, { "doi": "10.1093/glycob/cwp137", "pubmed": "19759275", "title": "Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences", "year": 2009 }, { "doi": "10.1186/1471-2105-9-384", "pmc": "PMC2567997", "pubmed": "18803830", "title": "GlycomeDB - integration of open-access carbohydrate structure databases", "year": 2008 } ], "uri_format": "https://glytoucan.org/Structures/Glycans/$1" }, "glyconavi": { "contact": { "email": "issaku@noguchi.or.jp", "name": "Issaku Yamada", "orcid": "0000-0001-9504-189X" }, "description": "GlycoNAVI is a website for carbohydrate research. It consists of the \"GlycoNAVI Database\" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the \"GlycoNAVI tools\" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools.", "example": "GN_G03681DA", "example_extras": [ "GN_GlyTouCan_G03681DA" ], "homepage": "https://www.noguchi.or.jp/", "keywords": [ "chemistry", "glycomics", "life science", "organic chemistry" ], "mappings": { "fairsharing": "FAIRsharing.wvp1t7", "integbio": "nbdc01174", "miriam": "glyconavi" }, "name": "GlycoNAVI", "pattern": "^GN_[A-Za-z0-9_:]+$", "preferred_prefix": "glyconavi", "repository": "https://glyconavi.github.io/doc/", "uri_format": "https://glyconavi.org/hub/?id=$1" }, "glycopost": { "description": "GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their \"raw/processed\" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines.", "example": "GPST000024", "homepage": "https://glycopost.glycosmos.org", "keywords": [ "glycomics", "life science" ], "mappings": { "fairsharing": "FAIRsharing.2y1KMt", "miriam": "glycopost" }, "name": "GlycoPOST", "pattern": "^GPST[0-9]{6}$", "preferred_prefix": "glycopost", "uri_format": "https://glycopost.glycosmos.org/entry/$1" }, "glycosciencesdb": { "contact": { "email": "thomas@luetteke-online.de", "github": "glycosciences", "name": "Thomas Lütteke", "orcid": "0000-0002-7140-9933" }, "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "A database to support glycobiology and glycomics research. Its main focus is on 3D structures, including 3D structure models as well as references to PDB entries that feature carbohydrates.", "example": "1", "github_request_issue": 537, "homepage": "http://www.glycosciences.de/database/", "name": "Glycosciences.DB", "pattern": "^\\d+$", "preferred_prefix": "glycosciencesdb", "publications": [ { "doi": "10.1093/nar/gky994", "pmc": "PMC6323918", "pubmed": "30357361", "title": "Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update)", "year": 2019 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "glycosciences.db" ], "uri_format": "http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=$1" }, "glytoucan": { "contact": { "email": "rr@uga.edu", "github": "ReneRanzinger", "name": "René Ranzinger", "orcid": "0000-0003-3147-448X" }, "description": "GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data.", "example": "G00054MO", "homepage": "https://glytoucan.org", "keywords": [ "glycomics", "structural biology" ], "mappings": { "biocontext": "GLYTOUCAN", "fairsharing": "FAIRsharing.5Pze7l", "integbio": "nbdc02434", "miriam": "glytoucan", "n2t": "glytoucan", "re3data": "r3d100012388", "togoid": "Glytoucan", "uniprot": "DB-0254" }, "name": "GlyTouCan", "pattern": "^G[0-9]{5}[A-Z]{2}$", "preferred_prefix": "glytoucan", "providers": [ { "code": "glygen", "description": "GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. ", "homepage": "https://www.glygen.org/", "name": "GlyGen", "uri_format": "https://glygen.org/glycan/$1" } ], "publications": [ { "doi": "10.1093/glycob/cwz080", "pubmed": "31616925" }, { "doi": "10.1093/glycob/cwx066", "pmc": "PMC5881658", "pubmed": "28922742", "title": "GlyTouCan: an accessible glycan structure repository", "year": 2017 }, { "doi": "10.1093/nar/gkv1041", "pmc": "PMC4702779", "pubmed": "26476458", "title": "GlyTouCan 1.0--The international glycan structure repository", "year": 2015 } ], "synonyms": [ "glygen" ], "twitter": "glytoucan", "uri_format": "https://glytoucan.org/Structures/Glycans/$1" }, "gmd": { "contact": { "email": "kopka@mpimp-golm.mpg.de", "name": "Joachim Kopka", "orcid": "0000-0001-9675-4883" }, "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena.", "example": "68513255-fc44-4041-bc4b-4fd2fae7541d", "homepage": "http://gmd.mpimp-golm.mpg.de/", "keywords": [ "life science", "metabolomics" ], "mappings": { "biocontext": "GMD", "fairsharing": "FAIRsharing.jykmkw", "miriam": "gmd", "n2t": "gmd", "re3data": "r3d100011046" }, "name": "Golm Metabolome Database", "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", "preferred_prefix": "gmd", "publications": [ { "doi": "10.1007/s11306-010-0198-7", "pmc": "PMC2874469", "pubmed": "20526350", "title": "Decision tree supported substructure prediction of metabolites from GC-MS profiles", "year": 2010 }, { "doi": "doi:10.1007/s11306-010-0198-7", "title": "Decision tree supported substructure prediction of metabolites from GC-MS profiles" } ], "uri_format": "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx" }, "gmd.analyte": { "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes.", "example": "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80", "homepage": "http://gmd.mpimp-golm.mpg.de/", "mappings": { "biocontext": "GMD.ANALYTE", "miriam": "gmd.analyte", "n2t": "gmd.analyte" }, "name": "Golm Metabolome Database Analyte", "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", "preferred_prefix": "gmd.analyte", "uri_format": "http://gmd.mpimp-golm.mpg.de/Analytes/$1" }, "gmd.gcms": { "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra.", "example": "53d583d8-40c6-40e1-9296-23f821cd77a5", "homepage": "http://gmd.mpimp-golm.mpg.de/", "mappings": { "biocontext": "GMD.GCMS", "miriam": "gmd.gcms", "n2t": "gmd.gcms" }, "name": "Golm Metabolome Database GC-MS spectra", "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", "preferred_prefix": "gmd.gcms", "uri_format": "http://gmd.mpimp-golm.mpg.de/Spectrums/$1" }, "gmd.profile": { "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues.", "example": "10b38aaf-b977-4950-85b8-f4775f66658d", "homepage": "http://gmd.mpimp-golm.mpg.de/", "mappings": { "biocontext": "GMD.PROFILE", "miriam": "gmd.profile", "n2t": "gmd.profile" }, "name": "Golm Metabolome Database Profile", "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", "preferred_prefix": "gmd.profile", "uri_format": "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1" }, "gmd.ref": { "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances.", "example": "8cf84adb-b4db-4807-ac98-0004247c35df", "homepage": "http://gmd.mpimp-golm.mpg.de/", "mappings": { "biocontext": "GMD.REF", "miriam": "gmd.ref", "n2t": "gmd.ref" }, "name": "Golm Metabolome Database Reference Substance", "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", "preferred_prefix": "gmd.ref", "uri_format": "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1" }, "gmelin": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s.", "example": "1466", "example_extras": [ "606", "80" ], "homepage": "https://link.springer.com/bookseries/562", "mappings": { "edam": "1004", "wikidata": "P1578" }, "name": "Gmelin's Handbook of Inorganic Chemistry", "pattern": "^[1-9][0-9]{1,6}$", "preferred_prefix": "gmelin", "proprietary": true, "references": [ "https://en.wikipedia.org/wiki/Gmelin_database" ] }, "gnd": { "description": "The Gemeinsame Normdatei (Integrated Authority File) or GND is an international authority file for person names, subject headings and corporate bodies. It is used mainly for documentation in libraries and increasingly also by archives and museums. The GND is managed by the German National Library in cooperation with various regional library networks in German-speaking Europe and other partners.", "example": "117145750", "homepage": "https://lobid.org/", "keywords": [ "culture", "knowledge and information systems", "social science" ], "mappings": { "bartoc": "430", "fairsharing": "FAIRsharing.8337e2", "miriam": "gnd", "wikidata": "P227", "wikidata.entity": "Q54506313" }, "name": "GND ID", "pattern": "^[0-9X\\-]+$", "preferred_prefix": "gnd", "rdf_uri_format": "https://d-nb.info/gnd/$1", "twitter": "gndnet", "uri_format": "https://lobid.org/gnd/$1" }, "gndo": { "description": "GND stands for \"Gemeinsame Normdatei\" (Integrated Authority File) and offers a broad range of elements to describe authorities. The GND originates from the German library community and aims to solve the name ambiguity problem in the library world.", "example": "AdministrativeUnit", "homepage": "http://d-nb.info/standards/elementset/gnd#", "keywords": [ "catalogs", "computer science", "ess" ], "mappings": { "lov": "gndo", "tib": "gndo" }, "name": "GND-Ontologie", "preferred_prefix": "gndo", "uri_format": "https://d-nb.info/standards/elementset/gnd#$1" }, "gno": { "contact": { "email": "nje5@georgetown.edu", "github": "edwardsnj", "name": "Nathan Edwards", "orcid": "0000-0001-5168-3196" }, "description": "An ontology for glycans based on GlyTouCan, but organized by subsumption.", "download_json": "http://purl.obolibrary.org/obo/gno.json", "download_obo": "http://purl.obolibrary.org/obo/gno.obo", "download_owl": "http://purl.obolibrary.org/obo/gno.owl", "example": "10004892", "example_extras": [ "G99373GG" ], "homepage": "https://gnome.glyomics.org/", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "GNO", "bioportal": "GNO", "obofoundry": "gno", "ols": "gno", "ontobee": "GNO", "wikidata.entity": "Q113012663" }, "name": "Glycan Naming and Subsumption Ontology", "pattern": "^(\\d{8}|(\\w+\\d+\\w+))$", "preferred_prefix": "GNO", "providers": [ { "code": "gno.composition", "description": "GNOme composition browser", "homepage": "https://gnome.glyomics.org/CompositionBrowser.html", "name": "GNOme Composition Browser", "uri_format": "https://gnome.glyomics.org/CompositionBrowser.html?focus=$1" }, { "code": "gno.structure", "description": "GNOme structure browser", "homepage": "https://gnome.glyomics.org/StructureBrowser.html", "name": "GNOme Structure Viewer", "uri_format": "https://gnome.glyomics.org/StructureBrowser.html?focus=$1" } ], "publications": [ { "doi": "10.5281/zenodo.6678278", "title": "GNOme - Glycan Naming and Subsumption Ontology", "year": 2021 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/GNO_$1", "repository": "https://github.com/glygen-glycan-data/GNOme", "synonyms": [ "gnome" ], "uri_format": "http://purl.obolibrary.org/obo/GNO_$1", "version": "2025-10-10" }, "gnomad": { "contact": { "email": "hrehm@mgh.harvard.edu", "github": "heidirehm", "name": "Heidi L. Rehm", "orcid": "0000-0002-6025-0015" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community (from https://gnomad.broadinstitute.org).", "example": "1-55516888-G-GA", "example_extras": [ "DUP_2_5708", "M-8602-T-C" ], "github_request_issue": 695, "homepage": "https://gnomad.broadinstitute.org", "license": "CC0-1.0", "mappings": { "integbio": "nbdc02561" }, "name": "Genome Aggregation Database", "preferred_prefix": "gnomad", "publications": [ { "doi": "10.1038/s41586-020-2308-7", "pmc": "PMC7334197", "pubmed": "32461654", "title": "The mutational constraint spectrum quantified from variation in 141,456 humans", "year": 2020 }, { "doi": "10.1038/s41586-020-2287-8", "pmc": "PMC7334194", "pubmed": "32461652", "title": "A structural variation reference for medical and population genetics", "year": 2020 } ], "uri_format": "https://gnomad.broadinstitute.org/variant/$1" }, "gnpis": { "contact": { "email": "hadi.quesneville@versailles.inra.fr", "name": "Hadi Quesneville", "orcid": "0000-0003-3001-4908" }, "description": "GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest.", "example": "AY109603", "homepage": "https://urgi.versailles.inra.fr/gnpis/", "keywords": [ "life science" ], "mappings": { "biocontext": "GNPIS", "fairsharing": "FAIRsharing.dw22y3", "miriam": "gnpis", "n2t": "gnpis", "re3data": "r3d100012647" }, "name": "GnpIS", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "gnpis", "publications": [ { "doi": "10.1093/database/bat058", "pmc": "PMC3746681", "pubmed": "23959375", "title": "GnpIS: an information system to integrate genetic and genomic data from plants and fungi", "year": 2013 } ], "uri_format": "https://urgi.versailles.inra.fr/gnpis/#result/term=$1" }, "gnps.task": { "contact": { "email": "mingxun.wang@cs.ucr.edu", "github": "mwang87", "name": "Mingxun Wang", "orcid": "0000-0001-7647-6097" }, "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS)", "example": "4b848c342a4f4abc871bdf8a09a60807", "github_request_issue": 833, "homepage": "https://gnps.ucsd.edu/", "name": "Global Natural Products Social Molecular Networking Task", "pattern": "^[a-f0-9]+$", "preferred_prefix": "gnps.task", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=$1" }, "go": { "appears_in": [ "agro", "chiro", "cl", "ecocore", "ecto", "envo", "maxo", "pcl", "pco", "planp", "uberon", "xpo", "zp" ], "banana": "GO", "contact": { "email": "suzia@stanford.edu", "github": "suzialeksander", "name": "Suzi Aleksander", "orcid": "0000-0001-6787-2901" }, "contributor_extras": [ { "email": "jmcl@ebi.ac.uk", "github": "jamesamcl", "name": "James Alastair McLaughlin", "orcid": "0000-0002-8361-2795" } ], "depends_on": [ "cl", "ncbitaxon", "ro", "uberon" ], "description": "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.", "download_json": "http://purl.obolibrary.org/obo/go.json", "download_obo": "http://purl.obolibrary.org/obo/go.obo", "download_owl": "http://purl.obolibrary.org/obo/go.owl", "example": "0032571", "homepage": "http://geneontology.org/", "keywords": [ "annotation", "biocuration", "biological_process", "cellular_component", "dataplant", "expression data", "gene", "gene functional annotation", "go-term enrichment data", "knowledge representation", "life science", "life sciences, biology", "medicine", "molecular_function", "obo", "ontology", "protein", "sequence annotation", "transcript" ], "license": "CC-BY-4.0", "logo": "https://obofoundry.org/images/go_logo.png", "mappings": { "aberowl": "GO", "agroportal": "GO", "bartoc": "572", "biocontext": "GO", "bioportal": "GO", "edam": "1176", "fairsharing": "FAIRsharing.6xq0ee", "go": "GO", "hl7": "2.16.840.1.113883.6.128", "integbio": "nbdc00074", "miriam": "go", "n2t": "go", "ncbi": "GO", "obofoundry": "go", "ols": "go", "ontobee": "GO", "pathguide": "272", "prefixcommons": "go", "re3data": "r3d100014165", "tib": "go", "togoid": "Go", "uniprot": "DB-0037", "wikidata": "P686", "wikidata.entity": "Q135085" }, "mastodon": "go@genomic.social", "name": "Gene Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "GO", "providers": [ { "code": "", "description": "GO Browser", "homepage": "http://www.informatics.jax.org/searches/GO_form.shtml", "name": "GO Browser", "uri_format": "http://www.informatics.jax.org/searches/GO.cgi?id=GO:$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/go:$1" }, { "code": "go_site", "description": "A non-PURL link through the GO site", "homepage": "http://www.geneontology.org", "name": "GO Site Link", "uri_format": "http://www.geneontology.org/GO:$1" }, { "code": "jax", "description": "The JAX endpoint for exploring GO", "homepage": "http://www.informatics.jax.org", "name": "Jackson Laboratories", "uri_format": "http://www.informatics.jax.org/vocab/gene_ontology/GO:$1" }, { "code": "miriam_obo_legacy", "description": "An old URI style for MIRIAM + GO", "homepage": "https://identifiers.org/", "name": "MIRIAM OBO Legacy", "uri_format": "http://identifiers.org/obo.go/GO:$1" }, { "code": "nextprot", "description": "The neXtProt endpoint for exploring GO", "homepage": "https://www.nextprot.org/", "name": "neXtProt GO Browser", "uri_format": "https://www.nextprot.org/term/GO:$1" }, { "code": "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": "purlorg", "name": "PURL.org Legacy", "uri_format": "http://purl.org/obo/owl/GO#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 (Legacy URL)", "uri_format": "https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:$1" } ], "publications": [ { "doi": "10.1093/genetics/iyad031", "pubmed": "36866529" }, { "doi": "10.1093/nar/gkaa1113", "pmc": "PMC7779012", "pubmed": "33290552", "title": "The Gene Ontology resource: enriching a GOld mine", "year": 2021 }, { "doi": "10.1093/nar/gky1055", "pmc": "PMC6323945", "pubmed": "30395331", "title": "The Gene Ontology Resource: 20 years and still GOing strong", "year": 2019 }, { "doi": "10.1093/nar/gku1179", "pmc": "PMC4383973", "pubmed": "25428369", "title": "Gene Ontology Consortium: going forward", "year": 2014 }, { "doi": "10.1186/1471-2164-14-513", "pmc": "PMC3733925", "pubmed": "23895341", "title": "Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology", "year": 2013 }, { "doi": "10.1093/nar/gks1050", "pmc": "PMC3531070", "pubmed": "23161678", "title": "Gene Ontology annotations and resources", "year": 2012 }, { "doi": "10.1093/nar/gkr1028", "pmc": "PMC3245151", "pubmed": "22102568", "title": "The Gene Ontology: enhancements for 2011", "year": 2011 }, { "doi": "10.1093/nar/gkp1018", "pmc": "PMC2808930", "pubmed": "19920128", "title": "The Gene Ontology in 2010: extensions and refinements", "year": 2009 }, { "doi": "10.1093/nar/gkh036", "pmc": "PMC308770", "pubmed": "14681407", "title": "The Gene Ontology (GO) database and informatics resource", "year": 2004 }, { "doi": "10.1038/75556", "pmc": "PMC3037419", "pubmed": "10802651", "title": "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium", "year": 2000 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/GO_$1", "repository": "https://github.com/geneontology/go-ontology", "synonyms": [ "gobp", "gobpid", "gocc", "goccid", "gomf", "gomfid" ], "twitter": "news4go", "uri_format": "http://purl.obolibrary.org/obo/GO_$1", "version": "2025-10-10" }, "go.gpi": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "smoxon@lbl.gov", "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" } ], "description": "This describes the metadata schema for the Gene Product Information (GPI) files in the Gene Ontology, i.e., the local unique identifiers in this identifier space refer to the columns in GPI files.", "example": "db-object-id", "homepage": "http://geneontology.org/docs/gene-product-information-gpi-format/#db-object-id", "mappings": { "biolink": "gpi" }, "name": "Gene Product Information Schema", "preferred_prefix": "go.gpi", "uri_format": "http://geneontology.org/docs/gene-product-information-gpi-format/#$1" }, "go.issue": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An issue on the Gene Ontology GitHub issue tracker", "example": "23000", "github_request_issue": 1553, "homepage": "https://github.com/geneontology/go-ontology/issues", "name": "Gene Ontology Issue Tracker", "pattern": "^\\d+$", "preferred_prefix": "go.issue", "uri_format": "https://github.com/geneontology/go-ontology/issues/$1" }, "go.model": { "description": "GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform.", "example": "5fce9b7300001250", "homepage": "https://geneontology.org/go-cam", "mappings": { "go": "gomodel" }, "name": "Gene Ontology Causal Activity Model", "preferred_prefix": "go.model", "providers": [ { "code": "legacy", "description": "This was the old URI for the GO CAM editor", "homepage": "https://model.geneontology.org", "name": "Legacy", "uri_format": "http://noctua.geneontology.org/editor/graph/gomodel:$1" } ], "uri_format": "https://model.geneontology.org/$1" }, "go.ref": { "banana": "GO_REF", "description": "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made.", "example": "0000041", "homepage": "http://www.geneontology.org", "mappings": { "biocontext": "GO_REF", "go": "GO_REF", "miriam": "go_ref", "n2t": "go.ref" }, "name": "Gene Ontology Database references", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "go.ref", "providers": [ { "code": "legacy", "description": "The README file on GO's github repository has been replaced with a structured YAML file, so this URl is no longer available.", "homepage": "https://github.com/geneontology/go-site/blob/master/metadata/gorefs.yaml", "name": "Legacy", "uri_format": "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md#goref$1" } ], "uri_format": "https://geneontology.org/GO_REF/$1" }, "go.resource": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A database-specific registry supporting curation in the Gene Ontology", "example": "CHEBI", "homepage": "https://raw.githubusercontent.com/geneontology/go-site/master/metadata/db-xrefs.yaml", "name": "Gene Ontology Registry", "preferred_prefix": "go.resource", "uri_format": "https://bioregistry.io/metaregistry/go/$1" }, "go.rule": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "GO Rules are a way of documenting the set of filters and reports that should apply to GAF annotation data. Some rules are expressed as SPARQL on a triplestore, some are code in the GAF parsing software, ontobio.", "example": "0000004", "homepage": "https://github.com/geneontology/go-site/tree/master/metadata/rules", "name": "Gene Ontology Rules", "pattern": "^\\d{7}$", "preferred_prefix": "GORULE", "uri_format": "https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-$1.md" }, "goa": { "contact": { "email": "r.huntley@ucl.ac.uk", "github": "rachhuntley", "name": "Rachael P. Huntley", "orcid": "0000-0001-6718-3559" }, "description": "The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups.", "example": "P12345", "homepage": "https://www.ebi.ac.uk/GOA/", "keywords": [ "biology", "gene", "life science", "ontology", "protein" ], "mappings": { "biocontext": "GOA", "fairsharing": "FAIRsharing.7zffgc", "integbio": "nbdc00468", "miriam": "goa", "n2t": "goa", "ncbi": "GOA", "prefixcommons": "goa" }, "name": "Gene Ontology Annotation Database", "pattern": "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$", "preferred_prefix": "goa", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/goa:$1" } ], "provides": "uniprot", "publications": [ { "doi": "10.1093/nar/gku1113", "pmc": "PMC4383930", "pubmed": "25378336", "title": "The GOA database: gene Ontology annotation updates for 2015", "year": 2014 }, { "doi": "10.1093/nar/gkn803", "pmc": "PMC2686469", "pubmed": "18957448", "title": "The GOA database in 2009--an integrated Gene Ontology Annotation resource", "year": 2008 } ], "uri_format": "https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1" }, "goche": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Represent chemical entities having particular CHEBI roles", "download_owl": "https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl", "example": "25512", "homepage": "https://github.com/geneontology/go-ontology", "keywords": [ "ontology" ], "name": "GO Chemicals", "pattern": "^\\d+$", "preferred_prefix": "GOCHE", "rdf_uri_format": "http://purl.obolibrary.org/obo/GOCHE_$1", "references": [ "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638472847049400", "https://github.com/geneontology/go-ontology/issues/19535" ], "repository": "https://github.com/geneontology/go-ontology", "synonyms": [ "go.chebi", "go.chemical", "go.chemicals" ], "uri_format": "https://biopragmatics.github.io/providers/goche/$1" }, "goeco": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported.", "example": "IPI", "homepage": "http://geneontology.org/docs/guide-go-evidence-codes/", "name": "GO Evidence Code", "preferred_prefix": "goeco" }, "gold": { "contact": { "email": "tbreddy@lbl.gov", "github": "TBKReddy", "name": "TBK Reddy", "orcid": "0000-0002-0871-5567" }, "description": "The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.", "download_owl": "https://raw.githubusercontent.com/cmungall/gold-ontology/refs/heads/main/gold.owl", "example": "Gs0000008", "homepage": "https://gold.jgi.doe.gov/", "keywords": [ "genome", "genomics", "metabolomics", "metagenomics", "ontology", "ontology and terminology", "phylogenetics" ], "mappings": { "fairsharing": "FAIRsharing.5q1p14", "integbio": "nbdc00483", "miriam": "gold", "ols": "gold", "prefixcommons": "gold", "re3data": "r3d100010808" }, "name": "Genomes Online Database", "pattern": "^[A-Z][a-z][0-9]+$", "preferred_prefix": "gold", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/gold:$1" } ], "publications": [ { "doi": "10.1093/nar/gkae1000", "pubmed": "39498478", "title": "Genomes OnLine Database (GOLD) v.10: new features and updates", "year": 2024 }, { "doi": "10.1093/nar/gkaa983", "pmc": "PMC7778979", "pubmed": "33152092", "title": "Genomes OnLine Database (GOLD) v.8: overview and updates", "year": 2021 }, { "doi": "10.1093/nar/gky977", "pmc": "PMC6323969", "pubmed": "30357420", "title": "Genomes OnLine database (GOLD) v.7: updates and new features", "year": 2019 }, { "doi": "10.1093/nar/gkp848", "pmc": "PMC2808860", "pubmed": "19914934", "title": "The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata", "year": 2009 }, { "doi": "10.1093/nar/gkm884", "pmc": "PMC2238992", "pubmed": "17981842", "title": "The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata", "year": 2007 }, { "doi": "10.1093/nar/29.1.126", "pmc": "PMC29859", "pubmed": "11125068", "title": "Genomes OnLine Database (GOLD): a monitor of genome projects world-wide", "year": 2001 }, { "doi": "10.1093/bioinformatics/15.9.773", "pubmed": "10498782", "title": "Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide", "year": 1999 }, { "doi": "11125068", "title": "Genomes OnLine Database (GOLD): a monitor of genome projects world-wide." } ], "uri_format": "https://gold.jgi.doe.gov/resolver?id=$1" }, "gold.genome": { "deprecated": true, "description": "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace.\n\nThe GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes.", "example": "Gi07796", "homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi", "mappings": { "biocontext": "GOLD.GENOME", "miriam": "gold.genome", "n2t": "gold.genome" }, "name": "GOLD genome", "pattern": "^(Gi|Gc)\\d+$", "preferred_prefix": "gold.genome", "provides": "gold", "uri_format": "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1" }, "gold.meta": { "description": "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples.", "example": "Gm00047", "has_canonical": "gold", "homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi", "mappings": { "biocontext": "GOLD.META", "miriam": "gold.meta", "n2t": "gold.meta" }, "name": "GOLD metadata", "pattern": "^Gm\\d+$", "preferred_prefix": "gold.meta", "uri_format": "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1" }, "goldbook": { "contact": { "email": "schalk@unf.edu", "github": "stuchalk", "name": "Stuart Chalk", "orcid": "0000-0002-0703-7776" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Compendium is popularly referred to as the \"Gold Book\", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC \"Colour Books\" on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books.\n\nTerminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC's Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry.\n\nThe API can be accessed [here](https://goldbook.iupac.org/pages/api)", "example": "G02681", "example_extras": [ "08306", "11214", "A00494", "AT07327", "B00737", "BT07002", "C00778", "CT07136" ], "homepage": "https://goldbook.iupac.org", "license": "CC BY 4.0-SA", "mappings": { "bartoc": "1884", "wikidata": "P4732", "wikidata.entity": "Q902163" }, "name": "IUPAC Gold Book Compendium of Chemical Terminology", "pattern": "^(\\wT?)?\\d{5}$", "preferred_prefix": "goldbook", "providers": [ { "code": "goldbook.html", "description": "This appears in REX", "homepage": "http://goldbook.iupac.org", "name": "GoldBook direct", "uri_format": "http://goldbook.iupac.org/$1.html" } ], "rdf_uri_format": "http://dx.doi.org/10.1351/goldbook.$1", "references": [ "https://goldbook.iupac.org/pages/api", "https://github.com/biopragmatics/bioregistry/pull/1689" ], "uri_format": "https://goldbook.iupac.org/terms/view/$1" }, "google.book": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Search the world's most comprehensive index of full-text books.", "example": "qafeQTWIWmcC", "github_request_issue": 511, "homepage": "https://books.google.com", "mappings": { "wikidata": "P675" }, "name": "Google Books", "preferred_prefix": "google.book", "providers": [ { "code": "alt1", "description": "Alternate URL 1", "homepage": "https://books.google.com", "name": "Alternate URL 1", "uri_format": "https://books.google.com/books/?id=$1" } ], "uri_format": "https://books.google.com/books?id=$1" }, "google.patent": { "contributor_extras": [ { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. 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Google Patents can be searched using patent number, inventor, classification, and filing date.", "example": "US4145692", "example_extras": [ "USRE38117E1" ], "homepage": "https://www.google.com/patents/", "mappings": { "biocontext": "GOOGLE.PATENT", "cellosaurus": "Patent", "miriam": "google.patent", "n2t": "google.patent" }, "name": "Google Patents", "pattern": "^[A-Z]{2,4}\\d+([A-Z])?([0-9])?$", "preferred_prefix": "google.patent", "synonyms": [ "Patent", "patent" ], "uri_format": "https://www.google.com/patents/$1" }, "google.scholar": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.", "example": "PjrpzUIAAAAJ", "homepage": "https://scholar.google.com/", "mappings": { "biolink": "GSID", "wikidata": "P1960" }, "name": "Google Scholar Researcher", "pattern": "^[-_0-9A-Za-z]{12}$", "preferred_prefix": "google.scholar", "uri_format": "https://scholar.google.com/citations?user=$1" }, "gorel": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "github": "ArslaanZahid", "name": "Arslaan Zahid", "orcid": "0009-0006-4842-7427" } ], "description": "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.", "download_owl": "ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl", "example": "0002005", "homepage": "http://geneontology.org/docs/ontology-relations/", "keywords": [ "ontology" ], "mappings": { "biolink": "GOREL", "go": "GOREL" }, "name": "GO Relations", "pattern": "^\\d{7}$", "preferred_prefix": "gorel", "providers": [ { "code": "obo.legacy", "description": "Legacy OBO PURLs", "homepage": "http://purl.obolibrary.org/obo/gorel.owl", "name": "Legacy OBO", "status": { "contributor": "0009-0006-4842-7427", "date": "2024-04-14", "notes": "The URL is not working and no alternate link found on homepage", "value": "degraded" }, "uri_format": "http://purl.obolibrary.org/obo/GOREL_$1" } ], "uri_format": "http://purl.obolibrary.org/obo/GOREL_$1" }, "gpcrdb": { "contact": { "email": "david.gloriam@sund.ku.dk", "name": "David Gloriam", "orcid": "0000-0002-4299-7561" }, "description": "The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models.", "example": "RL3R1_HUMAN", "homepage": "http://www.gpcrdb.org/", "keywords": [ "life science", "molecular biology", "protein", "small molecule" ], "mappings": { "biocontext": "GPCRDB", "fairsharing": "FAIRsharing.e4n3an", "integbio": "nbdc00484", "miriam": "gpcrdb", "n2t": "gpcrdb", "prefixcommons": "gpcrdb", "uniprot": "DB-0038" }, "name": "G protein-coupled receptor database", "pattern": "^\\w+$", "preferred_prefix": "gpcrdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/gpcrdb:$1" } ], "publications": [ { "doi": "10.1093/nar/26.1.275", "pmc": "PMC147194", "pubmed": "9399852", "title": "GPCRDB: an information system for G protein-coupled receptors", "year": 1998 }, { "doi": "10.1093/nar/gkae1065", "pubmed": "39558158", "title": "GPCRdb in 2025: adding odorant receptors, data mapper, structure similarity search and models of physiological ligand complexes", "year": 2024 }, { "doi": "10.1093/nar/gkaa1080", "pmc": "PMC7778909", "pubmed": "33270898", "title": "GPCRdb in 2021: integrating GPCR sequence, structure and function", "year": 2021 }, { "doi": "10.1093/nar/gkx1109", "pmc": "PMC5753179", "pubmed": "29155946", "title": "GPCRdb in 2018: adding GPCR structure models and ligands", "year": 2018 }, { "doi": "10.1111/bph.13509", "pmc": "PMC4919580", "pubmed": "27155948", "title": "GPCRdb: the G protein-coupled receptor database - an introduction", "year": 2016 }, { "doi": "10.1093/nar/gkv1178", "pmc": "PMC4702843", "pubmed": "26582914", "title": "GPCRdb: an information system for G protein-coupled receptors", "year": 2015 }, { "doi": "10.1093/nar/gkt1255", "pmc": "PMC3965068", "pubmed": "24304901", "title": "GPCRDB: an information system for G protein-coupled receptors", "year": 2013 }, { "doi": "10.1093/nar/gkq1009", "pmc": "PMC3013641", "pubmed": "21045054", "title": "GPCRDB: information system for G protein-coupled receptors", "year": 2010 }, { "doi": "10.1093/nar/gkg103", "pmc": "PMC165550", "pubmed": "12520006", "title": "GPCRDB information system for G protein-coupled receptors", "year": 2003 }, { "doi": "10.1093/nar/29.1.346", "pmc": "PMC29816", "pubmed": "11125133", "title": "Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems", "year": 2001 } ], "twitter": "gpcrdb", "uri_format": "https://gpcrdb.org/protein/$1" }, "gpcrnava": { "description": "The GPCR NaVa database describes sequence variants within the family of human G Protein-Coupled Receptors (GPCRs). GPCRs regulate many physiological functions and are the targets for most of today's medicines. The acronym NaVa stands for Natural Variant, which means any (non-artificial) variant that occurs in humans.", "example": "1150", "homepage": "http://nava.liacs.nl/", "keywords": [ "pathway", "protein" ], "mappings": { "prefixcommons": "gnd" }, "name": "GPCR Natural Variants database", "preferred_prefix": "gpcrnava", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/gnd:$1" } ], "uri_format": "http://nava.liacs.nl/cgi-bin/nava.py?id=$1" }, "gpmdb": { "contact": { "email": "rbeavis@thegpm.org", "github": "RonBeavis", "name": "Ronald C. Beavis (Ron Beavis)", "orcid": "0000-0001-5782-1000" }, "description": "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns.", "example": "GPM32310002988", "homepage": "http://gpmdb.thegpm.org/", "keywords": [ "bioinformatics", "proteomics" ], "mappings": { "biocontext": "GPMDB", "fairsharing": "FAIRsharing.fhcmwq", "miriam": "gpmdb", "n2t": "gpmdb" }, "name": "Global Proteome Machine Database", "pattern": "^GPM\\d+$", "preferred_prefix": "gpmdb", "providers": [ { "code": "omicsdi", "description": "GPMDB through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "GPMDB through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/gpmdb/$1" } ], "publications": [ { "doi": "10.1021/pr049882h", "pubmed": "15595733", "title": "Open source system for analyzing, validating, and storing protein identification data", "year": 2004 } ], "twitter": "GPMDB", "uri_format": "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1" }, "gpml": { "contact": { "email": "egon.willighagen@gmail.com", "github": "egonw", "name": "Egon Willighagen", "orcid": "0000-0001-7542-0286" }, "contributor": { "email": "javier.millanacosta@maastrichtuniversity.nl", "github": "jmillanacosta", "name": "Javier Millán Acosta", "orcid": "0000-0001-5608-781X" }, "contributor_extras": [ { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene.", "example": "GR:0080039", "homepage": "http://www.gramene.org/", "mappings": { "biocontext": "GRAMENE.GENE", "go": "GR_GENE", "miriam": "gramene.gene", "n2t": "gramene.gene" }, "name": "Gramene Gene", "pattern": "^GR\\:\\d+$", "preferred_prefix": "gramene.gene", "synonyms": [ "GR_GENE" ], "uri_format": "http://www.gramene.org/db/genes/search_gene?acc=$1" }, "gramene.growthstage": { "banana": "GRO", "contact": { "email": "po-discuss@plantontology.org", "name": "Plant Ontology Administrators" }, "deprecated": true, "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.", "example": "0007133", "homepage": "http://www.gramene.org/plant_ontology/", "keywords": [ "anatomy", "obo", "ontology" ], "mappings": { "biocontext": "GRAMENE.GROWTHSTAGE", "bioportal": "GRO-CPGA", "miriam": "gro", "n2t": "gramene.growthstage", "obofoundry": "gro", "prefixcommons": "gramene.po", "wikidata.entity": "Q114677888" }, "name": "Gramene Growth Stage Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "GRO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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This datatype refers to proteins in Gramene.", "example": "78073", "homepage": "http://www.gramene.org/", "mappings": { "biocontext": "GRAMENE.PROTEIN", "go": "GR_PROTEIN", "miriam": "gramene.protein", "n2t": "gramene.protein" }, "name": "Gramene protein", "pattern": "^\\d+$", "preferred_prefix": "gramene.protein", "synonyms": [ "GR_PROTEIN" ], "uri_format": "http://www.gramene.org/db/protein/protein_search?protein_id=$1" }, "gramene.qtl": { "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene.", "example": "CQG5", "homepage": "http://www.gramene.org/", "mappings": { "biocontext": "GRAMENE.QTL", "go": "GR_QTL", "miriam": "gramene.qtl", "n2t": "gramene.qtl" }, "name": "Gramene QTL", "pattern": "^\\w+$", "preferred_prefix": "gramene.qtl", "synonyms": [ "GR_QTL" ], "uri_format": "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1" }, "gramene.reference": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Literature references in Gramene", "example": "6200", "homepage": "http://www.gramene.org", "name": "Gramene Reference", "pattern": "^\\d+$", "preferred_prefix": "gramene.reference", "synonyms": [ "gramene.ref" ], "uri_format": "http://www.gramene.org/db/literature/pub_search?ref_id=$1" }, "gramene.taxonomy": { "banana": "GR_tax", "banana_peel": ":", "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene.", "example": "013681", "homepage": "http://www.gramene.org/", "mappings": { "biocontext": "GRAMENE.TAXONOMY", "miriam": "gramene.taxonomy", "n2t": "gramene.taxonomy" }, "name": "Gramene Taxonomy", "pattern": "^\\d+$", "preferred_prefix": "gramene.taxonomy", "uri_format": "https://archive.gramene.org/db/ontology/search?id=GR_tax:$1" }, "grassbase": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species.", "example": "imp10873", "github_request_issue": 218, "homepage": "https://www.kew.org/data/grasses-syn/index.htm", "mappings": { "wikidata": "P1832" }, "name": "GrassBase", "pattern": "^(imp|gen)\\d{5}$", "preferred_prefix": "grassbase", "uri_format": "https://www.kew.org/data/grasses-db/www/$1" }, "grddl": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "GRDDL is a mechanism for Gleaning Resource Descriptions from Dialects of Languages. It is a technique for obtaining RDF data from XML documents and in particular XHTML pages. Authors may explicitly associate documents with transformation algorithms, typically represented in XSLT, using a link element in the head of the document. Alternatively, the information needed to obtain the transformation may be held in an associated metadata profile document or namespace document. Clients reading the document can follow links across the Web using techniques described in the GRDDL specification to discover the appropriate transformations. This document uses a number of examples from the GRDDL Use Cases document to illustrate, in detail, the techniques GRDDL provides for associating documents with appropriate instructions for extracting any embedded data. (from homepage)", "example": "transformation", "homepage": "https://www.w3.org/TR/grddl-primer/", "keywords": [ "vocabularies" ], "mappings": { "lov": "grddl", "zazuko": "grddl" }, "name": "Gleaning Resource Descriptions from Dialects of Languages", "preferred_prefix": "grddl", "rdf_uri_format": "http://www.w3.org/2003/g/data-view#$1", "uri_format": "http://www.w3.org/2003/g/data-view#$1" }, "greengenes": { "contact": { "email": "GLAndersen@lbl.gov", "name": "Gary L Andersen", "orcid": "0000-0002-1618-9827" }, "deprecated": true, "description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.", "example": "100000", "homepage": "http://greengenes.lbl.gov/", "keywords": [ "genetics", "life science", "rna" ], "mappings": { "biocontext": "GREENGENES", "fairsharing": "FAIRsharing.bpxgb6", "integbio": "nbdc01824", "miriam": "greengenes", "n2t": "greengenes", "ncbi": "Greengenes", "prefixcommons": "greengenes", "re3data": "r3d100010549" }, "name": "16S rRNA gene database", "pattern": "^\\d+$", "preferred_prefix": "greengenes", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/greengenes:$1" } ], "publications": [ { "doi": "10.1128/aem.03006-05", "pmc": "PMC1489311", "pubmed": "16820507", "title": "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB", "year": 2006 }, { "doi": "10.1128/AEM.03006-05", "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=$1" }, "grid": { "description": "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally.", "example": "grid.225360.0", "homepage": "https://www.grid.ac/", "keywords": [ "data management" ], "mappings": { "biocontext": "GRID", "fairsharing": "FAIRsharing.0pUMYW", "miriam": "grid", "n2t": "grid" }, "name": "Global Research Identifier Database", "pattern": "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$", "preferred_prefix": "grid", "twitter": "grid_ac", "uri_format": "https://www.grid.ac/institutes/$1" }, "grin.publication": { "description": "GRIN provides National Genetic Resources Program (NGRP) personnel and germplasm users continuous access to databases for the maintenance of passport, characterization, evaluation, inventory, and distribution data important for the effective management and utilization of national germplasm collections.", "example": "159787", "homepage": "http://www.ars-grin.gov/", "keywords": [ "life science" ], "mappings": { "fairsharing": "FAIRsharing.3axym7", "prefixcommons": "grin" }, "name": "Germplasm Resources Information Network", "preferred_prefix": "grin.publication", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/grin:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "grin" ], "uri_format": "http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=$1" }, "grin.taxonomy": { "description": "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact.", "example": "19333", "homepage": "https://npgsweb.ars-grin.gov/gringlobal/taxon/abouttaxonomy", "mappings": { "biocontext": "GRIN.TAXONOMY", "go": "GRIN", "miriam": "grin.taxonomy", "n2t": "grin.taxonomy", "ncbi": "GRIN", "wikidata": "P1421", "wikidata.entity": "Q19576476" }, "name": "GRIN URL", "pattern": "^\\d+$", "preferred_prefix": "grin.taxonomy", "uri_format": "https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomydetail?id=$1" }, "gro": { "contact": { "email": "vlee@ebi.ac.uk", "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.", "download_owl": "http://aber-owl.net/media/ontologies/GRO/5/gro.owl", "example": "Lipid", "homepage": "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html", "keywords": [ "obo", "ontology" ], "mappings": { "aberowl": "GRO", "biocontext": "BOOTSTREP", "bioportal": "GRO", "obofoundry": "bootstrep" }, "name": "Gene Regulation Ontology", "preferred_prefix": "BOOTSTREP", "rdf_uri_format": "http://purl.obolibrary.org/obo/BOOTSTREP_$1", "synonyms": [ "bootstrep" ], "uri_format": "http://www.bootstrep.eu/ontology/GRO#$1" }, "grsdb": { "deprecated": true, "description": "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.", "example": "10142", "homepage": "http://bioinformatics.ramapo.edu/GRSDB2/", "keywords": [ "dna", "rna" ], "mappings": { "biocontext": "GRSDB", "miriam": "grsdb", "n2t": "grsdb", "prefixcommons": "grsdb" }, "name": "G-Rich Sequences Database", "pattern": "^\\d+$", "preferred_prefix": "grsdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/grsdb:$1" } ], "uri_format": "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1" }, "gs1": { "description": "The initial focus of the GS1 Web Vocabulary is consumer-facing properties for clothing, shoes, food beverage/tobacco and properties common to all products. [from homepage]", "download_rdf": "https://ref.gs1.org/voc/data/gs1Voc.ttl", "example": "AllergenTypeCode-3-AMINOPHENOL", "homepage": "https://ref.gs1.org/voc/", "mappings": { "zazuko": "gs1" }, "name": "GS1 Web Vocabulary", "preferred_prefix": "gs1", "repository": "https://github.com/gs1/WebVoc" }, "gsfa": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The \"Codex General Standard for Food Additives\" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database.", "example": "174", "homepage": "http://www.fao.org/gsfaonline", "name": "General Standard for Food Additives Online Database", "pattern": "^\\d+$", "preferred_prefix": "gsfa", "synonyms": [ "FAO/WHO_standards" ], "uri_format": "http://www.fao.org/gsfaonline/additives/details.html?id=$1" }, "gsso": { "appears_in": [ "ontoavida", "scdo" ], "banana": "GSSO", "contact": { "email": "kronkcj@mail.uc.edu", "github": "Superraptor", "name": "Clair Kronk", "orcid": "0000-0001-8397-8810" }, "description": "The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology.", "download_json": "http://purl.obolibrary.org/obo/gsso.json", "download_obo": "http://purl.obolibrary.org/obo/gsso.obo", "download_owl": "http://purl.obolibrary.org/obo/gsso.owl", "example": "002368", "homepage": "https://gsso.research.cchmc.org/", "keywords": [ "obo", "ontology" ], "license": "Apache 2.0 License", "mappings": { "aberowl": "GSSO", "bartoc": "20833", "bioportal": "GSSO", "miriam": "gsso", "obofoundry": "gsso", "ols": "gsso", "ontobee": "GSSO", "wikidata.entity": "Q97063846" }, "name": "Gender, Sex, and Sexual Orientation Ontology", "namespace_in_lui": true, "pattern": "^\\d{6}$", "preferred_prefix": "GSSO", "rdf_uri_format": "http://purl.obolibrary.org/obo/GSSO_$1", "repository": "https://github.com/Superraptor/GSSO", "uri_format": "http://purl.obolibrary.org/obo/GSSO_$1", "version": "2.0.5" }, "gtdb": { "contact": { "email": "donovan.parks@gmail.com", "github": "donovan-h-parks", "name": "Donovan Parks", "orcid": "0000-0001-6662-9010" }, "contributor": { "email": "aireland@lbl.gov", "github": "ialarmedalien", "name": "AJ Ireland", "orcid": "0000-0003-1982-9065" }, "description": "The Genome Taxonomy Database (GTDB) is an initiative to establish a standardized microbial taxonomy based on genome phylogeny.", "example": "g__Prochlorococcus_A", "github_request_issue": 1242, "homepage": "https://gtdb.ecogenomic.org", "keywords": [ "taxonomy" ], "license": "CC-BY-SA-4.0", "logo": "https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcQqQRuB8VW0FaaLLXHx8O6oKfFEZzY5jtgtRg&s", "mappings": { "pathguide": "190" }, "name": "Genome Taxonomy Database", "pattern": "^[cdfgops]__\\w+\\S+$", "preferred_prefix": "gtdb", "publications": [ { "doi": "10.1093/nar/gkab776", "pmc": "PMC8728215", "pubmed": "34520557", "title": "GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy", "year": 2021 }, { "doi": "10.1038/s41564-021-00918-8", "pubmed": "34155373", "title": "A standardized archaeal taxonomy for the Genome Taxonomy Database", "year": 2021 }, { "doi": "10.1038/s41587-020-0501-8", "pubmed": "32341564", "title": "A complete domain-to-species taxonomy for Bacteria and Archaea", "year": 2020 }, { "doi": "10.1038/nbt.4229", "pubmed": "30148503", "title": "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life", "year": 2018 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://gtdb.ecogenomic.org/tree?r=$1" }, "gtex": { "description": "The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation.", "example": "BRIP1", "homepage": "https://www.gtexportal.org", "mappings": { "biocontext": "GTEX", "biolink": "GTEx", "miriam": "gtex", "n2t": "gtex" }, "name": "Genotype-Tissue Expression", "pattern": "^\\w.+$", "preferred_prefix": "gtex", "uri_format": "https://www.gtexportal.org/home/gene/$1" }, "gtn": { "contact": { "email": "saskia.hiltemann@rz.uni-freiburg.de", "github": "shiltemann", "name": "Saskia Hiltemann", "orcid": "0000-0003-3803-468X" }, "contributor": { "email": "d.djamalova@fz-juelich.de", "github": "ddjamalova", "name": "Dilfuza Djamalova", "orcid": "0009-0004-7782-2894" }, "contributor_extras": [ { "email": "jacobo.miranda@embl.de", "github": "mirandaembl", "name": "Jacobo Miranda", "orcid": "0009-0005-0673-021X" } ], "description": "Identifiers in the GTN correspond to training materials in various formats (markdown, slides, video). The users can apply learned concepts directly within the framework via galaxy workflows.", "example": "T00148", "github_request_issue": 1778, "homepage": "https://training.galaxyproject.org/training-material/", "keywords": [ "galaxy", "learning materials", "learning resources", "training materials" ], "license": "CC-BY-4.0", "name": "Galaxy Training Network", "pattern": "^[A-Z]\\d+$", "preferred_prefix": "gtn", "publications": [ { "doi": "10.1371/journal.pcbi.1010752", "pmc": "PMC9829167", "pubmed": "36622853", "title": "Galaxy Training: A powerful framework for teaching!", "year": 2023 }, { "doi": "10.1371/journal.pcbi.1007854", "pmc": "PMC7241697", "pubmed": "32437350", "title": "Ten simple rules for making training materials FAIR", "year": 2020 }, { "doi": "10.1016/j.cels.2018.05.012", "pmc": "PMC6296361", "pubmed": "29953864", "title": "Community-Driven Data Analysis Training for Biology", "year": 2018 } ], "repository": "https://github.com/galaxyproject/training-material", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://gxy.io/GTN:$1" }, "gtr.condition": { "appears_in": [ "mondo" ], "comment": "Identifiers appearing in MONDO don't match any of the resources apparent endpoints", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease", "example": "AN0097748", "homepage": "https://www.ncbi.nlm.nih.gov/gtr/", "name": "Genetic Testing Registry", "preferred_prefix": "gtr.condition", "synonyms": [ "gtr", "medgen.gtr" ], "uri_format": "https://www.ncbi.nlm.nih.gov/gtr/conditions/$1" }, "gtr.lab": { "description": "The Genetic Testing Registry provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease.", "example": "000320401", "homepage": "https://www.ncbi.nlm.nih.gov/", "mappings": { "miriam": "gtrl" }, "name": "Genetic Testing Registry Labs", "pattern": "^\\d+$", "preferred_prefix": "gtr.lab", "uri_format": "https://www.ncbi.nlm.nih.gov/gtr/labs/$1" }, "gtr.test": { "description": "The Genetic Testing Registry provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease.", "example": "000260236", "homepage": "https://www.ncbi.nlm.nih.gov/", "mappings": { "miriam": "gtr" }, "name": "Genetic Testing Registry Tests", "pattern": "^\\d+$", "preferred_prefix": "gtr.test", "uri_format": "https://www.ncbi.nlm.nih.gov/gtr/tests/$1" }, "gudmap": { "contact": { "email": "simon.harding@ed.ac.uk", "github": "simondharding", "name": "Simon Douglas Harding", "orcid": "0000-0002-9262-8318" }, "description": "The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract.", "example": "Q-2958", "homepage": "http://www.gudmap.org/", "keywords": [ "cell biology", "developmental biology", "genomics", "molecular biology" ], "mappings": { "biocontext": "GUDMAP", "fairsharing": "FAIRsharing.910c39", "miriam": "gudmap", "n2t": "gudmap", "re3data": "r3d100012193" }, "name": "Genitourinary Development Molecular Anatomy Project", "pattern": "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$", "preferred_prefix": "gudmap", "publications": [ { "doi": "10.1242/dev.063594", "pmc": "PMC3188593", "pubmed": "21652655", "title": "The GUDMAP database--an online resource for genitourinary research", "year": 2011 }, { "doi": "10.1681/asn.2007101078", "pubmed": "18287559", "title": "GUDMAP: the genitourinary developmental molecular anatomy project", "year": 2008 }, { "doi": "10.1681/ASN.2007101078", "title": "GUDMAP: the genitourinary developmental molecular anatomy project." } ], "twitter": "GUDMAP", "uri_format": "https://gudmap.org/id/$1" }, "gufo": { "contact": { "github": "jpalmeida", "name": "João Paulo A. Almeida" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An _gentle_ implementation of the Unified Foundational Ontology (UFO), which is an upper level ontology like BFO that is concerned with e.g. expressing temporal relationships between events.", "download_rdf": "https://github.com/nemo-ufes/gufo/raw/refs/heads/master/gufo.ttl", "example": "Person", "github_request_issue": 1704, "homepage": "https://nemo-ufes.github.io/gufo", "keywords": [ "events", "general & upper", "ontology", "upper level" ], "license": "CC-BY-4.0", "mappings": { "lov": "gufo" }, "name": "Unified Foundational Ontology", "preferred_prefix": "gufo", "publications": [ { "doi": "10.3233/ao-150157", "title": "Towards ontological foundations for conceptual modeling: The unified foundational ontology (UFO) story", "year": 2015 }, { "doi": "10.1007/978-3-642-41924-9_27", "title": "Towards Ontological Foundations for the Conceptual Modeling of Events", "year": 2013 }, { "doi": "10.1007/978-3-030-33223-5_4", "title": "Relations in ontology-driven conceptual modeling", "year": 2019 }, { "doi": "10.1007/978-3-030-00847-5_12", "title": "Endurant Types in Ontology-Driven Conceptual Modeling: Towards OntoUML 2.0", "year": 2018 } ], "rdf_uri_format": "http://purl.org/nemo/gufo#$1", "repository": "https://github.com/nemo-ufes/gufo", "uri_format": "http://purl.org/nemo/gufo#$1" }, "gwascentral.marker": { "contact": { "email": "tb143@leicester.ac.uk", "name": "Tim Beck", "orcid": "0000-0002-0292-7972" }, "description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker.", "example": "HGVM15354", "homepage": "https://www.gwascentral.org/markers", "logo": "https://help.gwascentral.org/wp-content/uploads/2017/04/logo.png", "mappings": { "biocontext": "GWASCENTRAL.MARKER", "miriam": "gwascentral.marker", "n2t": "gwascentral.marker" }, "name": "GWAS Central Marker", "pattern": "^HGVM\\d+$", "preferred_prefix": "gwascentral.marker", "publications": [ { "doi": "10.1093/nar/gkac1017", "pmc": "PMC9825503", "pubmed": "36350644", "title": "GWAS Central: an expanding resource for finding and visualising genotype and phenotype data from genome-wide association studies", "year": 2023 }, { "doi": "10.1038/ejhg.2013.274", "pmc": "PMC4060122", "pubmed": "24301061", "title": "GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies", "year": 2014 } ], "uri_format": "https://www.gwascentral.org/marker/$1" }, "gwascentral.phenotype": { "contact": { "email": "tb143@leicester.ac.uk", "name": "Tim Beck", "orcid": "0000-0002-0292-7972" }, "description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype.", "example": "HGVPM623", "homepage": "https://www.gwascentral.org/phenotypes", "keywords": [ "condition", "disease", "phenotype", "symptom" ], "logo": "https://help.gwascentral.org/wp-content/uploads/2017/04/logo.png", "mappings": { "biocontext": "GWASCENTRAL.PHENOTYPE", "miriam": "gwascentral.phenotype", "n2t": "gwascentral.phenotype" }, "name": "GWAS Central Phenotype", "pattern": "^HGVPM\\d+$", "preferred_prefix": "gwascentral.phenotype", "publications": [ { "doi": "10.1093/nar/gkac1017", "pmc": "PMC9825503", "pubmed": "36350644", "title": "GWAS Central: an expanding resource for finding and visualising genotype and phenotype data from genome-wide association studies", "year": 2023 }, { "doi": "10.1038/ejhg.2013.274", "pmc": "PMC4060122", "pubmed": "24301061", "title": "GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies", "year": 2014 } ], "uri_format": "https://www.gwascentral.org/phenotype/$1" }, "gwascentral.study": { "contact": { "email": "tb143@leicester.ac.uk", "name": "Tim Beck", "orcid": "0000-0002-0292-7972" }, "description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study.", "example": "HGVST1828", "homepage": "https://www.gwascentral.org/studies", "keywords": [ "gene", "genome" ], "logo": "https://help.gwascentral.org/wp-content/uploads/2017/04/logo.png", "mappings": { "biocontext": "GWASCENTRAL.STUDY", "miriam": "gwascentral.study", "n2t": "gwascentral.study", "prefixcommons": "hgvbase" }, "name": "GWAS Central Study", "pattern": "^HGVST\\d+$", "preferred_prefix": "gwascentral.study", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hgvbase:$1" } ], "publications": [ { "doi": "10.1093/nar/gkac1017", "pmc": "PMC9825503", "pubmed": "36350644", "title": "GWAS Central: an expanding resource for finding and visualising genotype and phenotype data from genome-wide association studies", "year": 2023 }, { "doi": "10.1038/ejhg.2013.274", "pmc": "PMC4060122", "pubmed": "24301061", "title": "GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies", "year": 2014 } ], "uri_format": "https://www.gwascentral.org/study/$1" }, "gxa.expt": { "description": "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments.", "example": "E-MTAB-2037", "homepage": "https://www.ebi.ac.uk/gxa/", "mappings": { "biocontext": "GXA.EXPT", "miriam": "gxa.expt", "n2t": "gxa.expt" }, "name": "GXA Expt", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^[AEP]-\\w{4}-\\d+$", "preferred_prefix": "gxa.expt", "providers": [ { "code": "omicsdi", "description": "GXA Expt through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "GXA Expt through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/atlas-experiments/$1" } ], "uri_format": "https://www.ebi.ac.uk/gxa/experiments/$1" }, "gxa.gene": { "description": "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes.", "example": "AT4G01080", "homepage": "https://www.ebi.ac.uk/gxa/", "mappings": { "biocontext": "GXA.GENE", "miriam": "gxa.gene", "n2t": "gxa.gene" }, "name": "GXA Gene", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^\\w+$", "preferred_prefix": "gxa.gene", "uri_format": "https://www.ebi.ac.uk/gxa/genes/$1" }, "habronattus": { "contact": { "email": "peteremidford@yahoo.com", "name": "Peter Midford", "orcid": "0000-0001-6512-3296" }, "deprecated": true, "homepage": "http://www.mesquiteproject.org/ontology/Habronattus/index.html", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "HABRONATTUS", "obofoundry": "habronattus", "wikidata.entity": "Q114677889" }, "name": "Habronattus courtship", "preferred_prefix": "HABRONATTUS", "rdf_uri_format": "http://purl.obolibrary.org/obo/HABRONATTUS_$1", "uri_format": "http://purl.obolibrary.org/obo/HABRONATTUS_$1" }, "hagr.genage": { "contact": { "email": "jp@senescence.info", "name": "Joao Pedro de Magalhaes", "orcid": "0000-0002-6363-2465" }, "description": "GenAge is a database of human and model organism genes related to longevity and aging, maintained by the Human Ageing Genomics Resources (HAGR) group.", "example": "0001", "homepage": "http://genomics.senescence.info/genes/", "keywords": [ "aging", "genes", "longevity" ], "mappings": { "prefixcommons": "genage" }, "name": "The Ageing Gene Database", "preferred_prefix": "hagr.genage", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/genage:$1" } ], "publications": [ { "doi": "10.1093/nar/gks1155", "pmc": "PMC3531213", "pubmed": "23193293", "title": "Human Ageing Genomic Resources: integrated databases and tools for the biology and genetics of ageing", "year": 2012 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://genomics.senescence.info/genes/details.php?id=$1" }, "hagr.gendr": { "contact": { "email": "jp@senescence.info", "name": "Joao Pedro de Magalhaes", "orcid": "0000-0002-6363-2465" }, "description": "GenDR is a database of genes associated with dietary restriction (DR). GenDR includes two datasets: 1) genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of DR; 2) genes robustly altered due to DR, derived from a meta-analysis of microarray DR studies in mammals", "example": "2", "homepage": "http://genomics.senescence.info/diet/", "keywords": [ "aging", "dietary restriction", "genes", "longevity" ], "mappings": { "prefixcommons": "gendr" }, "name": "The Dietary Restriction Gene Database", "preferred_prefix": "hagr.gendr", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/gendr:$1" } ], "publications": [ { "doi": "10.1371/journal.pgen.1002834", "pmc": "PMC3415404", "pubmed": "22912585", "title": "Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes", "year": 2012 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://genomics.senescence.info/diet/details.php?id=$1" }, "hamap": { "contact": { "email": "alan.bridge@isb-sib.ch", "name": "Alan Bridge", "orcid": "0000-0003-2148-9135" }, "description": "HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries.", "example": "MF_01400", "homepage": "https://hamap.expasy.org/", "keywords": [ "life science", "protein" ], "mappings": { "biocontext": "HAMAP", "edam": "2766", "fairsharing": "FAIRsharing.63m4ss", "go": "HAMAP", "miriam": "hamap", "n2t": "hamap", "prefixcommons": "hamap", "uniprot": "DB-0041" }, "name": "High-quality Automated and Manual Annotation of microbial Proteomes", "pattern": "^MF_\\d+$", "preferred_prefix": "hamap", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hamap:$1" } ], "publications": [ { "doi": "10.1093/nar/gku1002", "pmc": "PMC4383873", "pubmed": "25348399", "title": "HAMAP in 2015: updates to the protein family classification and annotation system", "year": 2014 }, { "doi": "10.1093/nar/gks1157", "pmc": "PMC3531088", "pubmed": "23193261", "title": "HAMAP in 2013, new developments in the protein family classification and annotation system", "year": 2012 } ], "uri_format": "https://hamap.expasy.org/unirule/$1" }, "hancestro": { "contact": { "email": "dwelter.ontologist@gmail.com", "github": "daniwelter", "name": "Danielle Welter", "orcid": "0000-0003-1058-2668" }, "description": "Human ancestry ontology for the NHGRI GWAS Catalog", "download_owl": "http://purl.obolibrary.org/obo/hancestro.owl", "example": "0290", "homepage": "https://ebispot.github.io/hancestro/", "keywords": [ "demographics", "genome-wide association study", "human genetics", "obo", "ontology", "population genetics" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "HANCESTRO", "biolink": "HANCESTRO", "bioportal": "HANCESTRO", "fairsharing": "FAIRsharing.rja8qp", "obofoundry": "hancestro", "ols": "hancestro", "ontobee": "HANCESTRO", "wikidata.entity": "Q81661647" }, "name": "Human Ancestry Ontology", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^\\d{4}$", "preferred_prefix": "HANCESTRO", "providers": [ { "code": "legacy", "description": "Legacy URI", "homepage": "http://www.ebi.ac.uk/ancestro", "name": "Legacy", "uri_format": "http://www.ebi.ac.uk/ancestro/ancestro_$1" } ], "publications": [ { "doi": "10.1186/s13059-018-1396-2", "pmc": "PMC5815218", "pubmed": "29448949", "title": "A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog", "year": 2018 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/HANCESTRO_$1", "repository": "https://github.com/EBISPOT/ancestro", "uri_format": "http://purl.obolibrary.org/obo/HANCESTRO_$1", "version": "2025-10-14" }, "hao": { "contact": { "email": "diapriid@gmail.com", "github": "mjy", "name": "Matt Yoder", "orcid": "0000-0002-5640-5491" }, "description": "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)", "download_obo": "http://purl.obolibrary.org/obo/hao.obo", "download_owl": "http://purl.obolibrary.org/obo/hao.owl", "example": "0000187", "homepage": "http://hymao.org", "keywords": [ "anatomy", "life science", "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "HAO", "biocontext": "HAO", "bioportal": "HAO", "fairsharing": "FAIRsharing.kj3m5n", "obofoundry": "hao", "ols": "hao", "ontobee": "HAO", "wikidata.entity": "Q81661648" }, "name": "Hymenoptera Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "HAO", "publications": [ { "doi": "10.1371/journal.pone.0015991", "pmc": "PMC3012123", "pubmed": "21209921", "title": "A gross anatomy ontology for hymenoptera", "year": 2010 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/HAO_$1", "repository": "https://github.com/hymao/hao", "uri_format": "http://purl.obolibrary.org/obo/HAO_$1", "version": "2023-06-01" }, "hao.ref": { "contact": { "email": "diapriid@gmail.com", "github": "mjy", "name": "Matt Yoder", "orcid": "0000-0002-5640-5491" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Literature references in the Hymenoptera Anatomy Ontology Portal", "example": "98127", "github_request_issue": 1322, "homepage": "http://hymao.org", "name": "Hymenoptera Anatomy Reference", "pattern": "^\\d+$", "preferred_prefix": "hao.ref", "uri_format": "http://api.hymao.org/api/ref/$1" }, "hathitrust": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world.", "example": "008893080", "github_request_issue": 510, "homepage": "https://www.hathitrust.org", "name": "Hathi Trust Digital Library", "pattern": "^\\d+$", "preferred_prefix": "hathitrust", "uri_format": "https://catalog.hathitrust.org/Record/$1" }, "hba": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A controlled vocabulary to support the study of transcription in the human brain", "download_obo": "https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-hba.obo", "download_owl": "https://purl.brain-bican.org/ontology/hbao/releases/2025-02-10/hbao.owl", "example": "4005", "example_extras": [ "265504410" ], "homepage": "https://human.brain-map.org", "keywords": [ "ontology" ], "mappings": { "ols": "hba" }, "name": "Human Brain Atlas", "pattern": "^\\d+$", "preferred_prefix": "HBA", "providers": [ { "code": "biopragmatics", "description": "A static site generated for the HBA resource", "homepage": "https://biopragmatics.github.io/providers", "name": "Biopragmatics Browser", "uri_format": "https://biopragmatics.github.io/providers/hba/$1" } ], "repository": "https://github.com/brain-bican/human_brain_atlas_ontology", "uri_format": "https://purl.brain-bican.org/ontology/hbao/HBA_$1", "version": "2025-02-10" }, "hbvar": { "description": "This is a relational database of information about hemoglobin variants and mutations that cause thalassemia.", "example": "2526", "homepage": "http://globin.cse.psu.edu/globin/hbvar", "keywords": [ "protein" ], "mappings": { "prefixcommons": "hbvar" }, "name": "A Database of Human Hemoglobin Variants and Thalassemias", "preferred_prefix": "hbvar", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hbvar:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=$1" }, "hc.din": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A Drug Identification Number (DIN) is a computer-generated eight digit number assigned by Health Canada to a drug product prior to being marketed in Canada. It uniquely identifies all drug products sold in a dosage form in Canada and is located on the label of prescription and over-the-counter drug products that have been evaluated and authorized for sale in Canada.", "example": "02069237", "homepage": "https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/fact-sheets/drug-identification-number.html", "mappings": { "hl7": "2.16.840.1.113883.5.1105" }, "name": "Health Canada Drug Identification Number", "pattern": "^\\d{8}$", "preferred_prefix": "hc.din", "references": [ "http://www.hc-sc.gc.ca/dhp-mps/prodpharma/databasdon/index-eng.php" ] }, "hc.npn": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Licensed Natural Health Products Database contains information about natural health products that have been issued a product licence by Health Canada.", "example": "18125", "homepage": "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/search-rechercheReq.do?lang=eng", "mappings": { "hl7": "2.16.840.1.113883.5.1107" }, "name": "Health Canada Natural Product Number", "pattern": "^\\d+$", "preferred_prefix": "hc.npn", "references": [ "https://www.canada.ca/en/health-canada/services/drugs-health-products/natural-non-prescription/applications-submissions/product-licensing/licensed-natural-health-products-database.html" ], "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=$1" }, "hcao": { "description": "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas.", "download_owl": "http://ontology.data.humancellatlas.org/ontologies/hcao/releases/2023-05-16/hcao.owl", "homepage": "https://www.humancellatlas.org", "keywords": [ "ontology" ], "mappings": { "ols": "hcao" }, "name": "Human Cell Atlas Ontology", "no_own_terms": true, "preferred_prefix": "hcao" }, "hco": { "description": "The Human Chromosome Ontology (HCO) provides simple and stable URIs for human reference genome versions to semantically identify human chromosomes.", "example": "MT", "homepage": "https://dbcls.rois.ac.jp/", "mappings": { "miriam": "hco" }, "name": "Human Chromosome Ontology", "pattern": "^.+$", "preferred_prefix": "hco", "uri_format": "http://biohackathon.org/resource/hco#$1" }, "hcpcs": { "contact": { "email": "Cynthia.Hake@cms.hhs.gov", "name": "Cynthia Hake" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers.", "example": "G8944", "homepage": "https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo", "keywords": [ "biomedical science", "business administration", "ontology" ], "mappings": { "aberowl": "HCPCS", "biolink": "HCPCS", "bioportal": "HCPCS", "fairsharing": "FAIRsharing.x81wz8" }, "name": "Healthcare Common Procedure Coding System", "preferred_prefix": "hcpcs", "uri_format": "http://purl.bioontology.org/ontology/HCPCS/$1" }, "hcvdb": { "description": "the European Hepatitis C Virus Database (euHCVdb, euhcvdb.lyon.inserm.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses.", "example": "M58335", "homepage": "https://euhcvdb.lyon.inserm.fr/euHCVdb", "keywords": [ "gene" ], "mappings": { "biocontext": "HCVDB", "miriam": "hcvdb", "n2t": "hcvdb", "prefixcommons": "hcv" }, "name": "Hepatitis C Virus Database Project", "pattern": "^M\\d{5}$", "preferred_prefix": "hcvdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hcv:$1" } ], "uri_format": "https://euhcvdb.lyon.inserm.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1" }, "hdl": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Welcome to the web site of the Handle.Net Registry (HNR), run by Corporation for National Research Initiatives (CNRI). CNRI is a Multi-Primary Administrator (MPA) of the Global Handle Registry (GHR), authorized by the DONA Foundation to allot prefixes to users of the Handle System. The DONA Foundation is a non-profit organization based in Geneva that has taken over responsibility for the evolution of CNRI's Digital Object (DO) Architecture including outreach around the world. One of the Foundation's responsibilities is to administer and maintain the overall operation of the GHR, a task that was previously performed by CNRI. (from website)", "example": "2381/12775", "example_extras": [ "391/00-0000-0000-0009-3C7E-F" ], "homepage": "https://www.handle.net/", "keywords": [ "centrally registered identifier", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.0b7e54" }, "name": "Handle", "pattern": "^\\d+/.+$", "preferred_prefix": "hdl", "synonyms": [ "handle" ], "uri_format": "http://hdl.handle.net/$1" }, "hdr": { "deprecated": true, "description": "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders.", "example": "63", "homepage": "http://research.nhgri.nih.gov/apps/homeodomain/web/", "keywords": [ "genome" ], "mappings": { "biocontext": "HDR", "miriam": "hdr", "n2t": "hdr", "pathguide": "307", "prefixcommons": "hdr" }, "name": "Homeodomain Research", "pattern": "^\\d+$", "preferred_prefix": "hdr", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hdr:$1" } ], "uri_format": "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1" }, "hemonc": { "comment": "It is unclear if identifiers can be resolved on the website but a spreadsheet of the terminology is available via the NCI at https://evs.nci.nih.gov/ftp1/HemOnc/HemOnc_Terminology.xls", "contributor": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "HemOnc.org is the largest freely available medical wiki of interventions, regimens, and general information relevant to the fields of hematology and oncology.", "example": "15543", "github_request_issue": 1149, "homepage": "https://hemonc.org/", "name": "HemOnc Terminology", "pattern": "^\\d+$", "preferred_prefix": "hemonc", "publications": [ { "doi": "10.1016/j.jbi.2019.103239", "pmc": "PMC6697579", "pubmed": "31238109", "title": "HemOnc: A new standard vocabulary for chemotherapy regimen representation in the OMOP common data model", "year": 2019 } ], "reviewer": { "github": "callahantiff", "name": "Tiffany J. Callahan", "orcid": "0000-0002-8169-9049" } }, "hepro": { "contact": { "email": "paul.fabry@usherbrooke.ca", "github": "pfabry", "name": "Paul Fabry", "orcid": "0000-0002-3336-2476" }, "contributor": { "email": "paul.fabry@usherbrooke.ca", "github": "pfabry", "name": "Paul Fabry", "orcid": "0000-0002-3336-2476" }, "description": "HEPRO is an ontology of informational entities and processes related to health procedures and health activities.", "download_owl": "https://github.com/OpenLHS/HEPRO/raw/main/HEPRO.owl", "example": "0000001", "github_request_issue": 810, "homepage": "https://openlhs.github.io/HEPRO/", "keywords": [ "ontology" ], "license": "CC-BY-4.0", "name": "Health Procedure Ontology", "owners": [ { "name": "Université de Sherbrooke", "partnered": false, "ror": "00kybxq39" } ], "pattern": "^\\d{7}$", "preferred_prefix": "HEPRO", "repository": "https://github.com/OpenLHS/HEPRO", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://purl.obolibrary.org/obo/HEPRO_$1" }, "hesa": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An identifier for institutions in the United Kingdom, used in GRID and ROR.", "example": "0154", "homepage": "https://www.hesa.ac.uk", "keywords": [ "bibliometrics", "institution" ], "name": "UK Higher Education Statistics Agency", "pattern": "^\\d+$", "preferred_prefix": "hesa" }, "hgmd": { "description": "The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases.", "example": "CALM1", "homepage": "http://www.hgmd.cf.ac.uk/ac/index.php", "mappings": { "biocontext": "HGMD", "edam": "3265", "integbio": "nbdc00097", "miriam": "hgmd", "n2t": "hgmd" }, "name": "Human Gene Mutation Database", "pattern": "^[A-Z_0-9]+$", "preferred_prefix": "hgmd", "uri_format": "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1" }, "hgnc": { "contact": { "email": "elspeth@genenames.org", "name": "Elspeth Bruford", "orcid": "0000-0002-8380-5247" }, "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database.", "download_owl": "https://w3id.org/biopragmatics/resources/hgnc/2026-01-06/hgnc.ofn", "example": "16793", "homepage": "http://www.genenames.org", "keywords": [ "classification", "gene", "gene name", "life science", "ncrna", "ontology", "protein", "pseudogene" ], "license": "CC0-1.0", "logo": "https://www.genenames.org/img/hgnc/logo/hgnc-logo-dark-bckgrnd-large.svg", "mappings": { "aberowl": "HGNC", "bartoc": "20688", "biocontext": "HGNC", "bioportal": "HGNC", "cellosaurus": "HGNC", "edam": "2298", "fairsharing": "FAIRsharing.amcv1e", "go": "HGNC", "hl7": "2.16.840.1.113883.6.281", "miriam": "hgnc", "n2t": "hgnc", "ncbi": "HGNC", "ols": "hgnc", "prefixcommons": "hgnc", "togoid": "Hgnc", "uniprot": "DB-0042", "wikidata": "P354" }, "name": "HUGO Gene Nomenclature Committee", "pattern": "^\\d{1,5}$", "preferred_prefix": "hgnc", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hgnc:$1" }, { "code": "gencc", "description": "The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases. Curated gene-disease relationships are submitted by GenCC member organizations. The GenCC comprises organizations that currently provide online resources (e.g. ClinGen, DECIPHER, Genomics England PanelApp, OMIM, Orphanet, PanelApp Australia, TGMI’s G2P), as well as diagnostic laboratories that have committed to sharing their internal curated gene-level knowledge (e.g. Ambry, Illumina, Invitae, Myriad Women’s Health, Mass General Brigham Laboratory for Molecular Medicine).", "homepage": "https://thegencc.org", "name": "The Gene Curation Coalition", "uri_format": "https://search.thegencc.org/genes/HGNC:$1" }, { "code": "indra", "description": "A large scale database of biomedical statements.", "homepage": "https://db.indra.bio", "name": "INDRA Database", "publications": [ { "doi": "10.15252/msb.202211325", "pmc": "PMC10167483", "pubmed": "36938926", "title": "Automated assembly of molecular mechanisms at scale from text mining and curated databases", "year": 2023 }, { "doi": "10.15252/msb.20177651", "pmc": "PMC5731347", "pubmed": "29175850", "title": "From word models to executable models of signaling networks using automated assembly", "year": 2017 } ], "uri_format": "https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@HGNC" } ], "publications": [ { "doi": "10.15252/msb.202211325", "pmc": "PMC10167483", "pubmed": "36938926", "title": "Automated assembly of molecular mechanisms at scale from text mining and curated databases", "year": 2023 }, { "doi": "10.1093/nar/gkaa980", "pmc": "PMC7779007", "pubmed": "33152070", "title": "Genenames.org: the HGNC and VGNC resources in 2021", "year": 2021 }, { "doi": "10.1093/nar/gky930", "pmc": "PMC6324057", "pubmed": "30304474", "title": "Genenames.org: the HGNC and VGNC resources in 2019", "year": 2019 }, { "doi": "10.1159/000131404", "pubmed": "295268", "title": "International system for human gene nomenclature (1979) ISGN (1979)", "year": 1979 }, { "doi": "10.15252/msb.20177651", "pmc": "PMC5731347", "pubmed": "29175850", "title": "From word models to executable models of signaling networks using automated assembly", "year": 2017 } ], "uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1" }, "hgnc.genefamily": { "contact": { "email": "elspeth@genenames.org", "name": "Elspeth Bruford", "orcid": "0000-0002-8380-5247" }, "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.", "example": "2029", "has_canonical": "hgnc.genegroup", "homepage": "http://www.genenames.org", "keywords": [ "gene", "gene family", "gene group" ], "license": "CC0-1.0", "logo": "https://www.genenames.org/img/hgnc/logo/hgnc-logo-dark-bckgrnd-large.svg", "mappings": { "biocontext": "HGNC.GENEFAMILY", "miriam": "hgnc.genefamily", "n2t": "hgnc.genefamily" }, "name": "HGNC gene family", "pattern": "^\\d+$", "preferred_prefix": "hgnc.genefamily", "synonyms": [ "GFAM", "HGNC_GROUP", "hgnc.family" ], "uri_format": "https://www.genenames.org/cgi-bin/genefamilies/set/$1" }, "hgnc.genegroup": { "contact": { "email": "elspeth@genenames.org", "name": "Elspeth Bruford", "orcid": "0000-0002-8380-5247" }, "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.", "download_owl": "https://w3id.org/biopragmatics/resources/hgnc.genegroup/2025-10-07/hgnc.genegroup.ofn", "example": "141", "homepage": "https://www.genenames.org", "keywords": [ "gene", "gene family", "gene group", "ontology" ], "license": "CC0-1.0", "logo": "https://www.genenames.org/img/hgnc/logo/hgnc-logo-dark-bckgrnd-large.svg", "mappings": { "miriam": "hgnc.genegroup", "ols": "hgnc.genegroup" }, "name": "HGNC Gene Group", "pattern": "^\\d+$", "preferred_prefix": "hgnc.genegroup", "uri_format": "https://www.genenames.org/data/genegroup/#!/group/$1" }, "hgnc.symbol": { "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol.", "example": "DAPK1", "homepage": "https://www.genenames.org/", "license": "CC0-1.0", "logo": "https://www.genenames.org/img/hgnc/logo/hgnc-logo-dark-bckgrnd-large.svg", "mappings": { "biocontext": "HGNC.SYMBOL", "miriam": "hgnc.symbol", "n2t": "hgnc.symbol", "togoid": "HgncSymbol", "wikidata": "P353" }, "name": "HGNC gene symbol", "pattern": "^[A-Za-z-0-9_]+(\\@)?$", "preferred_prefix": "hgnc.symbol", "providers": [ { "code": "cbgda", "description": "A database of key host genes involved in the pathogenesis of different diseases identified through genome-wide CRISPR screens", "homepage": "http://cbgda.zhounan.org/main", "name": "CRISPR Based Gene-Disease Associations", "publications": [ { "doi": "10.1093/database/baae077", "pmc": "PMC11363955", "pubmed": "39213392", "title": "CBGDA: a manually curated resource for gene-disease associations based on genome-wide CRISPR", "year": 2024 } ], "uri_format": "http://cbgda.zhounan.org/geneinfo?gene=$1" }, { "code": "depmap", "description": "DepMap summary of the given gene", "homepage": "https://depmap.org", "name": "DepMap Gene Summary", "uri_format": "https://depmap.org/portal/gene/$1" }, { "code": "g2p", "description": "A resource for linking genetic screening outputs to protein sequences and structures", "homepage": "https://g2p.broadinstitute.org/", "name": "Genomics 2 Proteins Portal", "publications": [ { "doi": "10.1038/s41592-024-02409-0", "pmc": "PMC11466821", "pubmed": "39294369", "title": "Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures", "year": 2024 } ], "uri_format": "https://g2p.broadinstitute.org/gene/$1" }, { "code": "hubmap.biomarker", "description": "The Biomarkers subsection of HuBMAP allows you to look up specific information about a gene.", "homepage": "https://portal.hubmapconsortium.org/biomarkers", "name": "Human BioMolecular Atlas Program Biomarkers", "uri_format": "https://portal.hubmapconsortium.org/genes/$1" }, { "code": "oncomx", "description": "Mutation profiles for a gene", "homepage": "https://oncomx.org", "name": "OncoMX", "uri_format": "https://oncomx.org/searchview/?gene=$1" }, { "code": "pathwaycommons", "description": "Interactions between a given gene and other molecular entities", "homepage": "https://www.pathwaycommons.org/", "name": "Pathway Commons Gene Interations", "uri_format": "https://apps.pathwaycommons.org/interactions?source=$1" }, { "code": "resolute", "description": "RESOLUTE is a knowledge base on human SLCs (Solute carrier transporters).", "homepage": "https://re-solute.eu", "name": "RESOLUTE", "publications": [ { "doi": "10.1038/s44320-025-00108-2", "pmc": "PMC12130315", "pubmed": "40355757", "title": "Data- and knowledge-derived functional landscape of human solute carriers", "year": 2025 } ], "uri_format": "https://re-solute.eu/knowledgebase/gene/$1" } ], "publications": [ { "doi": "10.1038/s44320-025-00108-2", "pmc": "PMC12130315", "pubmed": "40355757", "title": "Data- and knowledge-derived functional landscape of human solute carriers", "year": 2025 }, { "doi": "10.1038/s41592-024-02409-0", "pmc": "PMC11466821", "pubmed": "39294369", "title": "Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures", "year": 2024 }, { "doi": "10.1093/database/baae077", "pmc": "PMC11363955", "pubmed": "39213392", "title": "CBGDA: a manually curated resource for gene-disease associations based on genome-wide CRISPR", "year": 2024 } ], "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": [ "GRCh38(chr11):g.112088970del", "NC_000011.10(NM_001276503.2):c.169+998del", "NC_000011.10:g.112088970del", "NG_012337.3(NM_003002.4):c.274G>T", "NG_012337.3(NM_003002.4):r.(274g>u)" ], "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=$1" }, "hinv.locus": { "deprecated": true, "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view.", "example": "HIX0004394", "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", "mappings": { "biocontext": "HINV.LOCUS", "miriam": "hinv.locus", "n2t": "hinv.locus" }, "name": "H-InvDb Locus", "pattern": "^HIX\\d{7}(\\.\\d+)?$", "preferred_prefix": "hinv.locus", "uri_format": "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1" }, "hinv.protein": { "deprecated": true, "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view.", "example": "HIP000030660", "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", "mappings": { "biocontext": "HINV.PROTEIN", "miriam": "hinv.protein", "n2t": "hinv.protein" }, "name": "H-InvDb Protein", "pattern": "^HIP\\d{9}(\\.\\d+)?$", "preferred_prefix": "hinv.protein", "uri_format": "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1" }, "hinv.transcript": { "deprecated": true, "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view.", "example": "HIT000195363", "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", "mappings": { "biocontext": "HINV.TRANSCRIPT", "miriam": "hinv.transcript", "n2t": "hinv.transcript" }, "name": "H-InvDb Transcript", "pattern": "^HIT\\d{9}(\\.\\d+)?$", "preferred_prefix": "hinv.transcript", "uri_format": "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1" }, "hipsci": { "contributor_extras": [ { "email": "mjj@ebi.ac.uk", "github": "mattjeffryes", "name": "Matt Jeffryes", "orcid": "0000-0001-9868-6271" } ], "description": "Cell line databases/resources", "example": "HPSI0114i-bezi_1", "homepage": "https://www.hipsci.org", "mappings": { "cellosaurus": "HipSci" }, "name": "Human Induced Pluripotent Stem Cells Initiative", "preferred_prefix": "hipsci", "uri_format": "https://www.hipsci.org/#/lines/$1" }, "hivreagentprogram": { "description": "Cell line collections (Providers)", "example": "ARP-1513", "homepage": "https://www.hivreagentprogram.org/", "mappings": { "cellosaurus": "HIVReagentProgram" }, "name": "NIH HIV Reagent Program", "preferred_prefix": "hivreagentprogram", "uri_format": "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx" }, "hl7.v2codesystem": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR.", "example": "0778", "homepage": "https://terminology.hl7.org/codesystems-v2.html", "name": "HL7 V2 Code System", "pattern": "^\\d+$", "preferred_prefix": "hl7.v2codesystem", "uri_format": "http://terminology.hl7.org/CodeSystem/v2-$1" }, "hl7.v3codesystem": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR.", "example": "AcknowledgementCondition", "homepage": "https://terminology.hl7.org/codesystems-v2.html", "name": "HL7 V3 Code System", "pattern": "^\\w+$", "preferred_prefix": "hl7.v3codesystem", "uri_format": "https://terminology.hl7.org/CodeSystem-v3-$1" }, "hmdb": { "contact": { "email": "david.wishart@ualberta.ca", "github": "DavidWishartLab", "name": "David S. Wishart", "orcid": "0000-0002-3207-2434" }, "description": "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.", "example": "HMDB00001", "homepage": "http://www.hmdb.ca/", "keywords": [ "biochemistry", "bioinformatics", "chemical", "human", "life science", "metabolite", "metabolomics", "molecular biology", "omics", "phenomics", "proteomics" ], "logo": "https://www.hmdb.ca/assets/hmdb_logo-f7bd764aa882bbbb2cfb8930f5f784e60576755c3de62a23a6d99c845cbff7e3.png", "mappings": { "biocontext": "HMDB", "cheminf": "000408", "edam": "2622", "fairsharing": "FAIRsharing.sye5js", "integbio": "nbdc00909", "miriam": "hmdb", "n2t": "hmdb", "pathguide": "244", "prefixcommons": "hmdb", "re3data": "r3d100011285", "togoid": "Hmdb", "wikidata": "P2057" }, "name": "Human Metabolome Database", "pattern": "^HMDB\\d+$", "preferred_prefix": "hmdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hmdb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkab1062", "pmc": "PMC8728138", "pubmed": "34986597", "title": "HMDB 5.0: the Human Metabolome Database for 2022", "year": 2022 }, { "doi": "10.1093/nar/gkx1089", "pmc": "PMC5753273", "pubmed": "29140435", "title": "HMDB 4.0: the human metabolome database for 2018", "year": 2018 }, { "doi": "10.1093/nar/gks1065", "pmc": "PMC3531200", "pubmed": "23161693", "title": "HMDB 3.0--The Human Metabolome Database in 2013", "year": 2012 }, { "doi": "10.1093/nar/gkl923", "pmc": "PMC1899095", "pubmed": "17202168", "title": "HMDB: the Human Metabolome Database", "year": 2007 }, { "doi": "10.1093/nar/gkn810", "title": "HMDB: a knowledgebase for the human metabolome" } ], "synonyms": [ "HMDB" ], "twitter": "WishartLab", "uri_format": "http://www.hmdb.ca/metabolites/$1" }, "hms.lincs.antibody": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.", "example": "80001", "homepage": "https://lincs.hms.harvard.edu/db/antibodies/", "name": "HMS Library of Integrated Network-based Cellular Signatures Antibodies", "pattern": "^8\\d{4}$", "preferred_prefix": "hms.lincs.antibody", "uri_format": "https://lincs.hms.harvard.edu/db/antibodies/$1" }, "hms.lincs.cell": { "comment": "this is NOT the same as lincs.cell. On https://lincs.hms.harvard.edu/db/cells/?search=MCF-10A&extra_form_shown=&dataset_types=, you can see there's a mapping to the other resource.", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.", "example": "50583", "homepage": "https://lincs.hms.harvard.edu/db/cell/", "name": "HMS LINCS Cell", "pattern": "^5\\d{4}$", "preferred_prefix": "hms.lincs.cell", "references": [ "https://github.com/identifiers-org/identifiers-org.github.io/issues/223" ], "uri_format": "https://lincs.hms.harvard.edu/db/cells/$1" }, "hms.lincs.compound": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.", "example": "10001-101", "example_extras": [ "11996-999" ], "homepage": "https://lincs.hms.harvard.edu/db/sm/", "name": "HMS LINCS Compound", "pattern": "^1\\d{4}-\\d{3}$", "preferred_prefix": "hms.lincs.compound", "synonyms": [ "HMS-LINCS", "hmsl_id" ], "uri_format": "https://lincs.hms.harvard.edu/db/sm/$1" }, "hms.lincs.dataset": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.", "example": "20003", "homepage": "https://lincs.hms.harvard.edu/db/datasets/", "name": "HMS Library of Integrated Network-based Cellular Signatures Datasets", "pattern": "^2\\d{4}$", "preferred_prefix": "hms.lincs.dataset", "uri_format": "https://lincs.hms.harvard.edu/db/datasets/$1" }, "hoelzel": { "contact": { "email": "info@hoelzel.de", "name": "Carsten Linder", "orcid": "0009-0009-3816-8777" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Hölzel is a life science reagent vendor based in Cologne, Germany. As a distributor, they offer products suitable for many kinds of research areas such as oncology, neuroscience, immunology, and more. Their portfolio consists of antibodies, recombinant proteins, inhibitors, ELISA-kits as well as other assays, arrays and kits. Their inhibitor portfolio can be easily accessed via the CAS-register catalog.", "example": "40592-R001-100", "homepage": "https://www.hoelzel-biotech.com", "keywords": [ "antibodies", "assays", "biologics", "elisa-kits", "inhibitors", "life sciences", "proteins", "vendor" ], "logo": "https://www.hoelzel-biotech.com/skin/frontend/ultimo/custom/images/logo.png", "name": "Hölzel Diagnostika", "preferred_prefix": "hoelzel", "synonyms": [ "hölzel" ], "uri_format": "https://www.hoelzel-biotech.com/de/catalogsearch/result/?q=$1" }, "hog": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc.", "download_obo": "ftp://ftp.bgee.org/general/ontologies/HOG.obo", "example": "0000255", "homepage": "https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships", "keywords": [ "ontology" ], "name": "Homologous Organ Groups", "pattern": "^\\d{7}$", "preferred_prefix": "hog", "uri_format": "https://biopragmatics.github.io/providers/hog/$1" }, "hogenom": { "contact": { "email": "perriere@biomserv.univ-lyon1.fr", "name": "Guy Perrière", "orcid": "0000-0002-6850-6265" }, "description": "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.", "example": "HOMO_3.PE998", "example_extras": [ "AEDAE_SUPERCONT1_288.PE16", "ATTCE_SCAFFOLD00004.PE150" ], "homepage": "http://hogenom.univ-lyon1.fr/", "keywords": [ "classification", "life science", "phylogenetics", "phylogeny", "sequence" ], "mappings": { "biocontext": "HOGENOM", "fairsharing": "FAIRsharing.qe8tz8", "integbio": "nbdc01858", "miriam": "hogenom", "n2t": "hogenom", "prefixcommons": "hogenom", "uniprot": "DB-0044" }, "name": "Database of Complete Genome Homologous Genes Families", "pattern": "^[A-Z][A-Z0-9_]+\\.PE\\d+$", "preferred_prefix": "hogenom", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hogenom:$1" } ], "publications": [ { "doi": "10.1186/1471-2105-10-s6-s3", "pmc": "PMC2697650", "pubmed": "19534752", "title": "Databases of homologous gene families for comparative genomics", "year": 2009 }, { "doi": "10.1101/gr.10.3.379", "pmc": "PMC311423", "pubmed": "10720578", "title": "HOBACGEN: database system for comparative genomics in bacteria", "year": 2000 }, { "doi": "10.1186/1471-2105-10-S6-S3", "title": "Databases of homologous gene families for comparative genomics." } ], "uri_format": "http://hogenom.univ-lyon1.fr/query_sequence?Go=Submit+Query&seq=$1" }, "hoip": { "comment": "The ontology file was deleted in https://github.com/yuki-yamagata/hoip/commit/73fcfa114d71a76a984a9ce1166e50d7ebafe158, making it impossible to link to the ontology afterwards.", "contact": { "email": "yuki.yamagata@riken.jp", "github": "yuki-yamagata", "name": "Yuki Yamagata", "orcid": "0000-0002-9673-1283" }, "contributor": { "email": "j.harry.caufield@gmail.com", "github": "caufieldjh", "name": "Harry Caufield", "orcid": "0000-0001-5705-7831" }, "description": "An ontology of processes triggered by homeostatic imbalance, with a focus on COVID-19 infectious processes.", "download_owl": "https://github.com/yuki-yamagata/hoip/blob/c70ae6d4868ca951d075cec409e863fa4abe19b2/hoip_0308.owl", "example": "0040379", "github_request_issue": 668, "homepage": "https://knowledge.brc.riken.jp/bioresource/ontology/HOIP", "keywords": [ "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "HOIP", "bioportal": "HOIP" }, "name": "Homeostasis imbalance process ontology", "pattern": "^\\d{7}$", "preferred_prefix": "hoip", "repository": "https://github.com/yuki-yamagata/hoip", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://purl.bioontology.org/ontology/HOIP/HOIP_$1" }, "holofood.animal": { "contact": { "email": "tgilbert@sund.ku.dk", "name": "Tom Gilbert", "orcid": "0000-0002-5805-7195" }, "contributor": { "email": "palayoor.n@northeastern.edu", "github": "nalikapalayoor", "name": "Nalika Palayoor", "orcid": "0009-0008-8406-631X" }, "description": "The HoloFood Data Portal centralizes access to datasets from the HoloFood project, which explores host microbiota interactions in salmon and chicken production. It links phenotypic data with microbiome samples and derived genomic resources and therefore simplifies data integration, supporting researchers in multiomics and microbiome studies. The identifiers in the animal semantic space correspond to animals that samples in the database are obtained from.", "example": "SAMEA112904733", "github_request_issue": 1400, "homepage": "https://www.holofooddata.org", "name": "HoloFood animal", "pattern": "^SAMEA\\d{9}$", "preferred_prefix": "holofood.animal", "publications": [ { "doi": "10.1093/database/baae112", "pmc": "PMC11724189", "pubmed": "39797569", "title": "HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production", "year": 2025 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://www.holofooddata.org/animal/$1" }, "holofood.sample": { "contact": { "email": "tgilbert@sund.ku.dk", "name": "Tom Gilbert", "orcid": "0000-0002-5805-7195" }, "contributor": { "email": "palayoor.n@northeastern.edu", "github": "nalikapalayoor", "name": "Nalika Palayoor", "orcid": "0009-0008-8406-631X" }, "description": "The HoloFood Data Portal centralizes access to datasets from the HoloFood project, which explores host microbiota interactions in salmon and chicken production. It links phenotypic data with microbiome samples and derived genomic resources and therefore simplifies data integration, supporting researchers in multiomics and microbiome studies. The identifiers in the samples semantic space represent samples derived from animals in HoloFood trials.", "example": "SAMEA10104908", "github_request_issue": 1400, "homepage": "https://www.holofooddata.org", "name": "HoloFood sample", "pattern": "^SAMEA\\d{8}$", "preferred_prefix": "holofood.sample", "publications": [ { "doi": "10.1093/database/baae112", "pmc": "PMC11724189", "pubmed": "39797569", "title": "HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production", "year": 2025 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://www.holofooddata.org/sample/$1" }, "hom": { "contact": { "email": "bgee@sib.swiss", "github": "fbastian", "name": "Frederic Bastian", "orcid": "0000-0002-9415-5104" }, "description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.", "download_owl": "http://purl.obolibrary.org/obo/hom.owl", "example": "0000049", "homepage": "https://github.com/BgeeDB/homology-ontology", "keywords": [ "anatomy", "homologous", "life cycle stage", "life science", "molecular entity", "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "HOM", "biocontext": "HOM", "bioportal": "HOM", "fairsharing": "FAIRsharing.efv7gw", "obofoundry": "hom", "ols": "hom", "ontobee": "HOM", "wikidata.entity": "Q81661651" }, "name": "Homology Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "HOM", "publications": [ { "doi": "10.1016/j.tig.2009.12.012", "pubmed": "20116127", "title": "An ontology to clarify homology-related concepts", "year": 2010 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/HOM_$1", "repository": "https://github.com/BgeeDB/homology-ontology", "uri_format": "http://purl.obolibrary.org/obo/HOM_$1" }, "homd.seq": { "contact": { "email": "tchen@forsyth.org", "github": "tsute", "name": "Tsute Chen", "orcid": "0000-0001-6689-317X" }, "description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.", "example": "SEQF1003.1", "homepage": "https://www.homd.org/", "keywords": [ "genome", "microbial" ], "mappings": { "biocontext": "HOMD.SEQ", "miriam": "homd.seq", "n2t": "homd.seq", "prefixcommons": "homd.seq" }, "name": "HOMD Sequence Metainformation", "pattern": "^SEQF\\d+(?:\\.\\d+)?$", "preferred_prefix": "homd.seq", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/homd.seq:$1" } ], "publications": [ { "doi": "10.1093/database/baq013", "pmc": "PMC2911848", "pubmed": "20624719", "title": "The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information", "year": 2010 } ], "uri_format": "https://v31.homd.org/genome/genome_description?gid=$1" }, "homd.taxon": { "contact": { "email": "tchen@forsyth.org", "github": "tsute", "name": "Tsute Chen", "orcid": "0000-0001-6689-317X" }, "description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.", "example": "811", "homepage": "http://www.homd.org/", "keywords": [ "microbial", "taxonomy" ], "mappings": { "biocontext": "HOMD.TAXON", "miriam": "homd.taxon", "n2t": "homd.taxon", "ncbi": "HOMD", "prefixcommons": "homd.taxon" }, "name": "Human Oral Microbiome Database", "pattern": "^\\d+$", "preferred_prefix": "homd.taxon", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/homd.taxon:$1" } ], "publications": [ { "doi": "10.1093/database/baq013", "pmc": "PMC2911848", "pubmed": "20624719", "title": "The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information", "year": 2010 } ], "uri_format": "http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1" }, "homologene": { "contact": { "email": "sayers@ncbi.nlm.nih.gov", "name": "Eric W. Sayers", "orcid": "0000-0001-8394-3802" }, "description": "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.", "example": "1000", "homepage": "https://www.ncbi.nlm.nih.gov/homologene/", "keywords": [ "gene", "genome", "life science" ], "mappings": { "biocontext": "HOMOLOGENE", "fairsharing": "FAIRsharing.mzc066", "integbio": "nbdc00101", "miriam": "homologene", "n2t": "homologene", "prefixcommons": "homologene", "togoid": "Homologene", "wikidata": "P593" }, "name": "HomoloGene", "pattern": "^\\d+$", "preferred_prefix": "homologene", "providers": [ { "code": "", "description": "Bio2RDF", "homepage": "http://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/describe/?url=http://bio2rdf.org/homologene:$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/homologene:$1" } ], "publications": [ { "doi": "10.1093/nar/gkq1172", "pmc": "PMC3013733", "pubmed": "21097890", "title": "Database resources of the National Center for Biotechnology Information", "year": 2010 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/homologene/$1" }, "homosaurus": { "appears_in": [ "gsso" ], "contact": { "email": "adolphok@vcu.edu", "name": "Keahi Kaʻiwalani Adolpho", "orcid": "0000-0003-1769-112X" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An international LGBTQ+ linked data vocabulary", "example": "queerNewspapers", "github_request_issue": 1310, "homepage": "http://homosaurus.org", "license": "CC BY NC-ND 4.0", "name": "Homosaurus", "preferred_prefix": "homosaurus", "providers": [ { "code": "homosaurus.v2", "description": "Homosaurus API v2", "homepage": "https://homosaurus.org", "name": "Homosaurus API v2", "uri_format": "http://homosaurus.org/v2/$1" }, { "code": "homosaurus.v3", "description": "Homosaurus API v3", "homepage": "https://homosaurus.org", "name": "Homosaurus API v3", "uri_format": "http://homosaurus.org/v3/$1" } ], "repository": "https://github.com/DigitalTransgenderArchive/homosaurus_site", "uri_format": "http://homosaurus.org/terms/$1" }, "horizon_discovery": { "description": "Cell line collections (Providers)", "example": "HD+118-001", "homepage": "https://horizondiscovery.com/", "mappings": { "cellosaurus": "Horizon_Discovery" }, "name": "Horizon Discovery cell line collection", "preferred_prefix": "horizon_discovery", "uri_format": "https://horizondiscovery.com/en/search?searchterm=$1" }, "hoso": { "contact": { "email": "paul.fabry@usherbrooke.ca", "github": "pfabry", "name": "Paul Fabry", "orcid": "0000-0002-3336-2476" }, "contributor": { "email": "paul.fabry@usherbrooke.ca", "github": "pfabry", "name": "Paul Fabry", "orcid": "0000-0002-3336-2476" }, "description": "HOSO is an ontology of informational entities and processes related to healthcare organizations and services.", "example": "0000001", "github_request_issue": 813, "homepage": "https://openlhs.github.io/HOSO/", "license": "CC-BY-4.0", "name": "Healthcare Organizations and Services Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "hoso", "repository": "https://github.com/OpenLHS/HOSO", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "hovergen": { "contact": { "email": "duret@biomserv.univ-lyon1.fr", "name": "Laurent Duret", "orcid": "0000-0003-2836-3463" }, "deprecated": true, "description": "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.", "example": "HBG004341", "homepage": "https://pbil.univ-lyon1.fr/databases/hovergen.php", "keywords": [ "dna", "gene", "life science", "protein" ], "mappings": { "biocontext": "HOVERGEN", "fairsharing": "FAIRsharing.dg1f0e", "integbio": "nbdc00284", "miriam": "hovergen", "n2t": "hovergen", "prefixcommons": "hovergen" }, "name": "Homologous Vertebrate Genes Database", "pattern": "^HBG\\d+$", "preferred_prefix": "hovergen", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hovergen:$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/bti325", "pubmed": "15713731", "title": "Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases", "year": 2005 } ], "uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN" }, "hp": { "appears_in": [ "chiro", "maxo", "scdo" ], "banana": "HP", "contact": { "email": "dr.sebastian.koehler@gmail.com", "github": "drseb", "name": "Sebastian Koehler", "orcid": "0000-0002-5316-1399" }, "description": "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.", "download_json": "http://purl.obolibrary.org/obo/hp.json", "download_obo": "http://purl.obolibrary.org/obo/hp.obo", "download_owl": "http://purl.obolibrary.org/obo/hp.owl", "example": "0011140", "homepage": "http://www.human-phenotype-ontology.org/", "keywords": [ "biomedical science", "disease phenotype", "disorder", "fair data spaces", "genetics", "life sciences, biology", "medicine", "obo", "omics", "ontology", "pathology", "phenomics", "preclinical studies" ], "license": "hpo", "logo": "https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/logo/HPO-logo-black_small.png", "mappings": { "aberowl": "HPO", "bartoc": "1937", "biocontext": "HPO", "bioportal": "HPO", "fairsharing": "FAIRsharing.kbtt7f", "hl7": "2.16.840.1.113883.6.339", "integbio": "nbdc02559", "miriam": "hp", "n2t": "hp", "obofoundry": "hp", "ols": "hp", "ontobee": "HP", "tib": "hp", "wikidata": "P3841", "wikidata.entity": "Q17027854" }, "mastodon": "hpo@masto.ai", "name": "Human Phenotype Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "HP", "publications": [ { "doi": "10.1186/s13059-025-03616-4", "pmc": "PMC12131445", "pubmed": "40462185", "title": "A resource for whole-body gene expression map of human tissues based on integration of single cell and bulk transcriptomics", "year": 2025 }, { "doi": "10.1093/nar/gkad1005", "pubmed": "37953324", "title": "The Human Phenotype Ontology in 2024: phenotypes around the world", "year": 2024 }, { "doi": "10.1093/nar/gky1105", "pmc": "PMC6324074", "pubmed": "30476213", "title": "Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources", "year": 2019 }, { "doi": "10.1093/nar/gkw1039", "pmc": "PMC5210535", "pubmed": "27899602", "title": "The Human Phenotype Ontology in 2017", "year": 2016 }, { "doi": "10.1016/j.ajhg.2015.05.020", "pmc": "PMC4572507", "pubmed": "26119816", "title": "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease", "year": 2015 }, { "doi": "10.1093/nar/gkt1026", "pmc": "PMC3965098", "pubmed": "24217912", "title": "The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data", "year": 2013 }, { "doi": "10.1111/j.1399-0004.2010.01436.x", "pubmed": "20412080", "title": "The human phenotype ontology", "year": 2010 }, { "doi": "10.1016/j.ajhg.2008.09.017", "pmc": "PMC2668030", "pubmed": "18950739", "title": "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease", "year": 2008 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/HP_$1", "repository": "https://github.com/obophenotype/human-phenotype-ontology", "synonyms": [ "hpo" ], "twitter": "hp_ontology", "uri_format": "http://purl.obolibrary.org/obo/HP_$1", "version": "2026-01-08" }, "hpa": { "contact": { "email": "mathias.uhlen@scilifelab.se", "name": "Mathias Uhlen", "orcid": "0000-0002-4858-8056" }, "description": "The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers.", "example": "ENSG00000026508", "homepage": "http://www.proteinatlas.org/", "keywords": [ "biomedical science", "protein", "proteomics", "structure", "systems biology", "transcriptomics" ], "mappings": { "biocontext": "HPA", "fairsharing": "FAIRsharing.j0t0pe", "go": "HPA", "miriam": "hpa", "n2t": "hpa", "prefixcommons": "hpa", "re3data": "r3d100010931", "uniprot": "DB-0046" }, "name": "Human Protein Atlas tissue profile information", "pattern": "^ENSG\\d{11}$", "preferred_prefix": "hpa", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hpa:$1" } ], "publications": [ { "doi": "10.1126/science.aan2507", "pubmed": "28818916", "title": "A pathology atlas of the human cancer transcriptome", "year": 2017 }, { "doi": "10.1126/science.aal3321", "pubmed": "28495876", "title": "A subcellular map of the human proteome", "year": 2017 }, { "doi": "10.15252/msb.20155865", "pmc": "PMC4848759", "pubmed": "27044256", "title": "Transcriptomics resources of human tissues and organs", "year": 2016 }, { "doi": "10.1126/science.1260419", "pubmed": "25613900", "title": "Proteomics. Tissue-based map of the human proteome", "year": 2015 }, { "doi": "10.1038/nbt1210-1248", "pubmed": "21139605", "title": "Towards a knowledge-based Human Protein Atlas", "year": 2010 }, { "doi": "10.1002/path.2440", "pubmed": "18853439", "title": "The Human Protein Atlas--a tool for pathology", "year": 2008 }, { "doi": "10.1074/mcp.r800013-mcp200", "pubmed": "18669619", "title": "A genecentric Human Protein Atlas for expression profiles based on antibodies", "year": 2008 }, { "doi": "10.1074/mcp.m500279-mcp200", "pubmed": "16127175", "title": "A human protein atlas for normal and cancer tissues based on antibody proteomics", "year": 2005 }, { "doi": "eaal3321", "title": "A subcellular map of the human proteome." }, { "doi": "10.1074/mcp.R800013-MCP200", "title": "A genecentric Human Protein Atlas for expression profiles based on antibodies." }, { "doi": "10.1074/mcp.M500279-MCP200", "title": "A human protein atlas for normal and cancer tissues based on antibody proteomics." } ], "twitter": "ProteinAtlas", "uri_format": "http://www.proteinatlas.org/$1" }, "hpath": { "comment": "This ontology used to be available in OLS3, but is no longer available in OLS4.\n\nThe URI format string in this resource takes the form of an OBO PURL, but it is not itself registered with the OBO Foundry, and terms therefore redirect into http://ontologies.berkeleybop.org. This happens because the data is curated natively in the OBO Flat File Format from which CURIEs are automatically assumed to expand to OBO PURLs", "contact": { "email": "carlo.ravagli@novartis.com", "github": "carloravagli", "name": "Carlo Ravagli", "orcid": "0000-0001-8372-8387" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species.\n\nThe original structure of the histopathology ontology was designed ab initio when the [INHAND](http://www.goreni.org/) manuscripts were not available. However, the ontology has been repetitively reviewed and updated to align with the subsequently published INHAND manuscripts. During this process cross references to INHAND lesion identifiers were added to the ontology. [from GitHub]", "download_obo": "https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo", "example": "2000191", "homepage": "https://github.com/Novartis/hpath", "keywords": [ "ontology" ], "name": "Histopathology Ontology", "pattern": "^\\d+$", "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_$1" }, "hpm.peptide": { "description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra.", "example": "9606117", "homepage": "http://www.humanproteomemap.org/index.php", "mappings": { "biocontext": "HPM.PEPTIDE", "miriam": "hpm.peptide", "n2t": "hpm.peptide" }, "name": "Human Proteome Map Peptide", "pattern": "^\\d+$", "preferred_prefix": "hpm.peptide", "uri_format": "http://www.humanproteomemap.org/spectrum.php?pep_id=$1" }, "hpm.protein": { "deprecated": true, "description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.", "example": "1968", "homepage": "http://www.humanproteomemap.org/index.php", "mappings": { "biocontext": "HPM.PROTEIN", "miriam": "hpm.protein", "n2t": "hpm.protein", "ncbi": "HPM" }, "name": "Human Proteome Map", "pattern": "^\\d+$", "preferred_prefix": "hpm.protein", "uri_format": "http://www.humanproteomemap.org/protein.php?hpm_id=$1" }, "hprd": { "contact": { "email": "pandey@jhmi.edu", "name": "Akhilesh Pandey", "orcid": "0000-0001-9943-6127" }, "deprecated": true, "description": "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.", "example": "00001", "homepage": "http://www.hprd.org/", "keywords": [ "protein", "structure" ], "mappings": { "biocontext": "HPRD", "fairsharing": "FAIRsharing.y2qws7", "integbio": "nbdc00103", "miriam": "hprd", "n2t": "hprd", "pathguide": "14", "prefixcommons": "hprd", "re3data": "r3d100010978" }, "name": "Human Protein Reference Database", "pattern": "^\\d+$", "preferred_prefix": "hprd", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hprd:$1" } ], "publications": [ { "doi": "10.1093/nar/gkn892", "pmc": "PMC2686490", "pubmed": "18988627", "title": "Human Protein Reference Database--2009 update", "year": 2008 } ], "uri_format": "http://www.hprd.org/protein/$1" }, "hpscreg": { "contact": { "email": "stefanie.seltmann@ibmt.fraunhofer.de", "name": "Stefanie Seltmann", "orcid": "0000-0002-8411-3226" }, "description": "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines).", "example": "BCRTi001-A", "homepage": "https://hpscreg.eu/", "keywords": [ "biomedical science", "life science" ], "mappings": { "cellosaurus": "hPSCreg", "fairsharing": "FAIRsharing.7C0aVE", "miriam": "hpscreg", "n2t": "hpscreg", "re3data": "r3d100012863" }, "name": "Human Pluripotent Stem Cell Registry", "pattern": "^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$", "preferred_prefix": "hpscreg", "publications": [ { "doi": "10.1016/j.scr.2020.101887", "pubmed": "32707486", "title": "Access to stem cell data and registration of pluripotent cell lines: The Human Pluripotent Stem Cell Registry (hPSCreg)", "year": 2020 }, { "doi": "10.1016/j.stemcr.2020.06.014", "pmc": "PMC7419703", "pubmed": "32679065", "title": "A Manually Curated Database on Clinical Studies Involving Cell Products Derived from Human Pluripotent Stem Cells", "year": 2020 }, { "doi": "10.1016/j.scr.2019.101539", "pubmed": "31450190", "title": "A pathway for attesting ethical provenance of cell lines: Lessons from the European human pluripotent stem cell registry (hPSC", "year": 2019 }, { "doi": "10.1016/j.stemcr.2017.12.002", "pmc": "PMC5768986", "pubmed": "29320760", "title": "A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells", "year": 2018 }, { "doi": "10.1093/nar/gkv963", "pmc": "PMC4702942", "pubmed": "26400179", "title": "hPSCreg--the human pluripotent stem cell registry", "year": 2015 }, { "doi": "S2213-6711(20)30235-6", "title": "A Manually Curated Database on Clinical Studies Involving Cell Products Derived from Human Pluripotent Stem Cells." }, { "doi": "S2213-6711(17)30531-3", "title": "A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells." }, { "doi": "S1873-5061(20)30188-4", "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", "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/$1" }, "hsapdv": { "appears_in": [ "scdo" ], "contact": { "email": "frederic.bastian@unil.ch", "github": "fbastian", "name": "Frédéric Bastian", "orcid": "0000-0002-9415-5104" }, "description": "Life cycle stages for Human", "download_obo": "http://purl.obolibrary.org/obo/hsapdv.obo", "download_owl": "http://purl.obolibrary.org/obo/hsapdv.owl", "example": "0000194", "homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv", "keywords": [ "anatomy", "developmental biology", "life cycle stage", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "HSAPDV", "biocontext": "HSAPDV", "biolink": "HsapDv", "bioportal": "HSAPDV", "fairsharing": "FAIRsharing.c6vhm3", "obofoundry": "hsapdv", "ols": "hsapdv", "ontobee": "HsapDv", "wikidata.entity": "Q81661653" }, "name": "Human Developmental Stages", "pattern": "^\\d{7}$", "preferred_prefix": "HsapDv", "rdf_uri_format": "http://purl.obolibrary.org/obo/HsapDv_$1", "repository": "https://github.com/obophenotype/developmental-stage-ontologies", "synonyms": [ "HsapDv" ], "uri_format": "http://purl.obolibrary.org/obo/HsapDv_$1", "version": "2025-01-23" }, "hsdb": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas.", "example": "5621", "homepage": "https://pubchem.ncbi.nlm.nih.gov/source/hsdb", "mappings": { "integbio": "nbdc00930", "wikidata": "P2062" }, "name": "Hazardous Substances Data Bank", "pattern": "^\\d+$", "preferred_prefix": "hsdb", "uri_format": "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1" }, "hso": { "contact": { "email": "fernanda.dorea@sva.se", "github": "nandadorea", "name": "Fernanda Dorea", "orcid": "0000-0001-8638-8525" }, "depends_on": [ "bfo", "ncbitaxon", "obi", "ro", "uberon" ], "description": "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance.", "download_owl": "http://purl.obolibrary.org/obo/hso.owl", "example": "0000062", "homepage": "https://w3id.org/hso", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "HSO", "bioportal": "HSO", "obofoundry": "hso", "ols": "hso", "ontobee": "HSO", "wikidata.entity": "Q113012664" }, "name": "Health Surveillance Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "HSO", "providers": [ { "code": "hso.legacy", "description": "An incorrect encoding of OBO purls", "homepage": "http://purl.obolibrary.org/obo/hso", "name": "HSO Hash", "uri_format": "http://purl.obolibrary.org/obo/hso.owl#HSO_$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/HSO_$1", "repository": "https://github.com/SVA-SE/HSO", "uri_format": "http://purl.obolibrary.org/obo/HSO_$1", "version": "2021-12-13" }, "hssp": { "contact": { "email": "chris@sanderlab.org", "github": "sanderlab", "name": "Chris Sander", "orcid": "0000-0001-6059-6270" }, "description": "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.", "example": "102l", "homepage": "http://swift.cmbi.kun.nl/swift/hssp/", "keywords": [ "clustering", "protein", "sequence" ], "mappings": { "biocontext": "HSSP", "miriam": "hssp", "n2t": "hssp", "ncbi": "HSSP", "prefixcommons": "hssp" }, "name": "Database of homology-derived secondary structure of proteins", "pattern": "^\\w{4}$", "preferred_prefix": "hssp", "providers": [ { "code": "", "description": "HSSP at CMBI", "homepage": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/", "name": "HSSP at CMBI", "uri_format": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$1.hssp.bz2" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hssp:$1" } ], "publications": [ { "doi": "10.1093/nar/24.1.201", "pmc": "PMC145595", "pubmed": "8594579", "title": "The HSSP database of protein structure-sequence alignments", "year": 1996 }, { "pmc": "PMC308328", "pubmed": "7937066", "title": "The HSSP database of protein structure-sequence alignments", "year": 1994 } ], "uri_format": "ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2" }, "htn": { "contact": { "email": "aellenhicks@gmail.com", "github": "aellenhicks", "name": "Amanda Hicks", "orcid": "0000-0002-1795-5570" }, "description": "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines", "download_owl": "http://purl.obolibrary.org/obo/htn.owl", "example": "00000014", "homepage": "https://github.com/aellenhicks/htn_owl", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "HTN", "bioportal": "HTN", "obofoundry": "htn", "ols": "htn", "ontobee": "HTN", "wikidata.entity": "Q81661655" }, "name": "Hypertension Ontology", "pattern": "^\\d{8}$", "preferred_prefix": "HTN", "rdf_uri_format": "http://purl.obolibrary.org/obo/HTN_$1", "repository": "https://github.com/aellenhicks/htn_owl", "uri_format": "http://purl.obolibrary.org/obo/HTN_$1" }, "hubmap.collection": { "contact": { "email": "katy@indiana.edu", "github": "katyb", "name": "Katy Börner", "orcid": "0000-0002-3321-6137" }, "contributor": { "email": "palayoor.n@northeastern.edu", "github": "nalikapalayoor", "name": "Nalika Palayoor", "orcid": "0009-0008-8406-631X" }, "description": "The collections section of HuBMAP groups related datasets, samples, and metadata into organized categories. Each collection has a unique identifier that links it to its constituent datasets.", "example": "3ae4ddfc175d768af5526a010bfe95aa", "github_request_issue": 1548, "homepage": "https://portal.hubmapconsortium.org/collections", "name": "Human BioMolecular Atlas Program Collection", "pattern": "^[a-f0-9]{32}$", "preferred_prefix": "hubmap.collection", "publications": [ { "doi": "10.1038/s41592-024-02563-5", "pmc": "PMC11978508", "pubmed": "40082611", "title": "Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage", "year": 2025 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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Each donor has a unique identifier used to link them to their associated tissue samples and derived experimental data.", "example": "a3bc9e6193c47998758ac9d9bf9ddbb6", "github_request_issue": 1548, "homepage": "https://portal.hubmapconsortium.org/search/donors", "name": "Human BioMolecular Atlas Program Donor", "pattern": "^[a-f0-9]{32}$", "preferred_prefix": "hubmap.donor", "publications": [ { "doi": "10.1038/s41592-024-02563-5", "pmc": "PMC11978508", "pubmed": "40082611", "title": "Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage", "year": 2025 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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Each sample has a unique identifier that links it to donor information, anatomical source, and related datasets.", "example": "a3bc9e6193c47998758ac9d9bf9ddbb6", "github_request_issue": 1548, "homepage": "https://portal.hubmapconsortium.org/search/samples", "name": "Human BioMolecular Atlas Program Sample", "pattern": "^[a-f0-9]{32}$", "preferred_prefix": "hubmap.sample", "publications": [ { "doi": "10.1038/s41592-024-02563-5", "pmc": "PMC11978508", "pubmed": "40082611", "title": "Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage", "year": 2025 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/huge:$1" } ], "publications": [ { "doi": "10.1093/nar/gkh035", "pmc": "PMC308769", "pubmed": "14681467", "title": "HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE", "year": 2004 } ], "uri_format": "https://www.kazusa.or.jp/huge/gfpage/$1" }, "humap": { "contact": { "email": "ksdrew@uic.edu", "github": "ksdrew", "name": "Kevin Drew", "orcid": "0000-0002-1260-4413" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The hu.MAP integrates several large scale protein interaction datasets to obtain a comprehensive view of protein complexes.", "example": "huMAP3_04143.1", "github_request_issue": 1249, "homepage": "https://humap3.proteincomplexes.org", "license": "CC0-1.0", "name": "Human Protein Complex Map", "preferred_prefix": "humap", "publications": [ { "doi": "10.15252/msb.202010016", "pmc": "PMC8111494", "pubmed": "33973408", "title": "hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies", "year": 2021 }, { "doi": "10.15252/msb.20167490", "pmc": "PMC5488662", "pubmed": "28596423", "title": "Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes", "year": 2017 } ], "synonyms": [ "humap3" ], "uri_format": "https://humap3.proteincomplexes.org/displayComplexes?complex_key=$1" }, "hydra": { "description": "A lightweight vocabulary for hypermedia-driven Web APIs", "example": "TemplatedLink", "homepage": "http://www.w3.org/ns/hydra/spec/latest/core/", "keywords": [ "rdf" ], "mappings": { "lov": "hydra", "re3data": "r3d100011525", "zazuko": "hydra" }, "name": "The Hydra Core Vocabulary", "preferred_prefix": "hydra" }, "iana.mediatype": { "contact": { "email": "alexey.melnikov@isode.com", "name": "Alexey Melnikov" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The official list of MIME types, now renamed to media types", "example": "application/cdmi-queue", "example_extras": [ "application", "application/3gpp-ims+xml", "audio", "audio/1d-interleaved-parityfec", "font", "font/woff", "haptics", "haptics/hmpg", "image", "image/heif-sequence", "message", "message/disposition-notification", "model", "model/3mf", "multipart", "multipart/parallel", "text", "text/directory", "video", "video/vnd.blockfact.factv" ], "homepage": "https://www.iana.org/assignments/media-types/media-types.xhtml", "keywords": [ "data classification" ], "logo": "https://www.iana.org/_img/2022/iana-logo-header.svg", "name": "Media Types", "pattern": 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artifacts", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/IAO_$1", "repository": "https://github.com/information-artifact-ontology/IAO", "uri_format": "http://purl.obolibrary.org/obo/IAO_$1", "version": "2022-11-07" }, "iao.issue": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An issue on the Information Artifact Ontology GitHub issue tracker", "example": "206", "github_request_issue": 1553, "homepage": "https://github.com/information-artifact-ontology/IAO/issues", "name": "Information Artifact Ontology Issue Tracker", "pattern": "^\\d+$", "preferred_prefix": "iao.issue", "uri_format": "https://github.com/information-artifact-ontology/IAO/issues/$1" }, "ical": { "description": "A vocabulary for calendar events and related objects", "example": "Vevent", "homepage": "https://www.w3.org/2002/12/cal/", "mappings": { "zazuko": "ical" }, "name": "iCalendar in RDF", "preferred_prefix": "ical" }, "icd10": { "contact": { "email": "info@who.int", "name": "World Health Organization" }, "contributor_extras": [ { "github": "joeflack4", "name": "Joe Flack", "orcid": "0000-0002-2906-7319" }, { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } ], "description": "The 10th revision of the International Classification of Diseases (ICD) issued by the World Health Organization (WHO). 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/icd:$1" }, { "code": "icd10_2008", "description": "The 2008 revision of ICD-10", "homepage": "https://icd.who.int/browse10/2008/en#", "name": "ICD-10 Version 2008", "uri_format": "https://icd.who.int/browse10/2008/en#/$1" }, { "code": "icd10_2010", "description": "The 2010 revision of ICD-10", "homepage": "https://icd.who.int/browse10/2010/en#", "name": "ICD-10 Version 2010", "uri_format": "https://icd.who.int/browse10/2010/en#/$1" }, { "code": "icd10_2014", "description": "The 2014 revision of ICD-10", "homepage": "https://icd.who.int/browse10/2014/en#", "name": "ICD-10 Version 2014", "uri_format": "https://icd.who.int/browse10/2014/en#/$1" }, { "code": "icd10_2015", "description": "The 2015 revision of ICD-10", "homepage": "https://icd.who.int/browse10/2015/en#", "name": "ICD-10 Version 2015", "uri_format": "https://icd.who.int/browse10/2015/en#/$1" }, { "code": "icd10_2016", "description": "The 2016 revision of ICD-10", "homepage": "https://icd.who.int/browse10/2016/en#", "name": "ICD-10 Version 2016", "uri_format": "https://icd.who.int/browse10/2016/en#/$1" }, { "code": "icdcodelookup", "description": "This site is dedicated exclusively to helping you look up ICD-10 codes, quickly access the codes you use most, and become more comfortable with the new code set in general.", "homepage": "https://icdcodelookup.com/icd-10/codes", "name": "ICD Code Lookup", "status": { "contributor": "0000-0003-4423-4370", "date": "2025-10-25", "value": "hijacked" }, "uri_format": "https://icdcodelookup.com/icd-10/codes/$1" } ], "references": [ "https://www.who.int/about/policies/publishing/copyright" ], "synonyms": [ "ICD", "ICD-10", "ICD10", "ICD10WHO" ], "uri_format": "https://icd.who.int/browse10/2019/en#/$1" }, "icd10cm": { "contact": { "email": "pbrooks@hcfa.gov", "name": "Patricia Brooks" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States issued by the National Center for Health Statistics (NCHS) and Centers for Medicare & Medicaid Services (CMS).", "example": "F45.21", "example_decoys": [ "C000", "c00", "C00-D499", "C00-99", "C34.90000" ], "example_extras": [ "C00-D49", "C34", "C34.90", "C4A.8", "C91.Z", "C91.Z0", "T37.0X1A", "U49" ], "homepage": "https://www.icd10data.com/ICD10CM", "keywords": [ "biomedical science", "diagnosis", "disease", "electronic health record", "health science", "medicine", "morbidity", "ontology" ], "license": "CC BY-ND 3.0 IGO", "mappings": { "aberowl": "ICD10CM", "bioportal": "ICD10CM", "fairsharing": "FAIRsharing.hpvbxb", "hl7": "2.16.840.1.113883.6.90", "wikidata": "P4229" }, "name": "International Classification of Diseases, 10th Revision, Clinical Modification", "pattern": "^([A-Z][0-9][0-9AB]((-[A-Z][0-9][0-9AB])|(\\.[0-9A-KXZ]([0-9A-EXYZ]([0-9A-HX][0-59A-HJKMNP-S]?)?)?)?))$", "preferred_prefix": "icd10cm", "providers": [ { "code": "bioportal.purl", "description": "PURL from BioPortal", "homepage": "http://purl.bioontology.org/ontology/ICD10CM", "name": "BioPortal PURL", "uri_format": "http://purl.bioontology.org/ontology/ICD10CM/$1" }, { "code": "icd.codes", "description": "ICD Codes provider", "homepage": "https://icd.codes", "name": "ICD Codes provider", "status": { "contributor": "0000-0001-9439-5346", "date": "2025-07-28", "value": "gone" }, "uri_format": "https://icd.codes/icd10cm/$1" } ], "references": [ "https://www.who.int/about/policies/publishing/copyright" ], "synonyms": [ "ICD10CM" ], "uri_format": "https://www.icd10data.com/search?s=$1" }, "icd10pcs": { "contact": { "email": "patricia.brooks2@cms.hhs.gov", "name": "Pat Brooks" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis.\n\nICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records.", "example": "01N50ZZ", "homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10PCS", "keywords": [ "biomedical science", "classification", "diagnosis", "disease", "electronic health record", "epidemiology", "health science", "hospital", "morbidity", "ontology" ], "mappings": { "aberowl": "ICD10PCS", "bioportal": "ICD10PCS", "fairsharing": "FAIRsharing.85k1jm", "hl7": "2.16.840.1.113883.6.4", "wikidata": "P1690" }, "name": "International Classification of Diseases, 10th Revision, Procedure Coding System", "preferred_prefix": "icd10pcs", "uri_format": "https://www.findacode.com/code.php?set=ICD10PCS&c=$1" }, "icd11": { "comment": "Clinical codes from an ICD-11 linearization (a structured subset of the ICD-11 Foundation tailored for specific use cases, such as morbidity or mortality coding), such as RA00.0, have their own namespace (icd11.code).", "contact": { "email": "icd@who.int", "name": "ICD Helpdesk" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" } ], "description": "The ICD-11 Foundation is the comprehensive base layer of the International Classification of Diseases, encompassing all diagnostic concepts, definitions, and semantic relationships, designed for flexibility and adaptability across various use cases, including research, ontology development, and detailed health data analysis.", "example": "402558626", "homepage": "https://icd.who.int/", "keywords": [ "biomedical science", "diagnosis", "disease", "electronic health record", "epidemiology", "global health", "health science", "morbidity" ], "license": "CC-BY-ND-3.0-IGO", "logo": "https://upload.wikimedia.org/wikipedia/commons/2/23/ICD-11_Logo.jpg", "mappings": { "biolink": "icd11.foundation", "fairsharing": "FAIRsharing.97805c", "hl7": "2.16.840.1.113883.6.347", "integbio": "nbdc02556", "wikidata": "P7807" }, "name": "International Classification of Diseases, 11th Revision (Foundation Component)", "pattern": "^[1-9]\\d*$", "preferred_prefix": "icd11", "providers": [ { "code": "api", "description": "This goes to an API endpoint. For more information, see https://icd.who.int/icdapi", "homepage": "https://icd.who.int", "name": "ICD 11 API Endpoint", "uri_format": "http://id.who.int/icd/entity/$1" }, { "code": "foundation", "description": "This goes to the Foundation interface to ICD11", "homepage": "https://icd.who.int/browse/2024-01/foundation", "name": "ICD 11 Foundation", "uri_format": "https://icd.who.int/browse/2024-01/foundation/en#$1" }, { "code": "mms", "description": "This goes to the Mortality and Morbidity Statistics interface to ICD11", "homepage": "https://icd.who.int/browse/2024-01/mms", "name": "ICD 11 Mortality and Morbidity Statistics", "uri_format": "https://icd.who.int/browse/2024-01/mms/en#$1" } ], "publications": [ { "doi": "10.1016/s0140-6736(19)31205-x", "pubmed": "31180012", "title": "ICD-11", "year": 2019 } ], "rdf_uri_format": "http://id.who.int/icd/entity/$1", "references": [ "https://icd.who.int/docs/icd-api/license/" ], "synonyms": [ "ICD-11", "ICD11", "icd11.foundation" ], "uri_format": "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1" }, "icd11.code": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ICD-11 code is a standardized alphanumeric identifier used to classify and document diseases, conditions, and health-related issues for global healthcare and statistical purposes.", "example": "NA06.8D", "example_extras": [ "CA71.2", "FB82.00", "XM34M9" ], "github_request_issue": 1349, "homepage": "https://icd.who.int/en", "license": "http://www.who.int/about/licensing/copyright_form/en", "name": "ICD 11 Codes", "pattern": "^[0-9A-Z]+(\\.[0-9A-Z]+)?$", "preferred_prefix": "icd11.code", "references": [ "https://github.com/biopragmatics/bioregistry/issues/1344" ] }, "icd9": { "comment": "Note that ICD9 codes representing mid-hierarchy relations, such as those in the form of XXX-YYY are not possible to resolve, but are useful and appear in many places that make xrefs to ICD9", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics.", "example": "277.9", "example_extras": [ "401", "401-405", "995.81", "E950", "V15.01" ], "homepage": "https://www.cdc.gov/nchs/icd/icd9.htm", "license": "CC BY-ND 3.0 IGO", "mappings": { "bartoc": "447", "biolink": "ICD9", "hl7": "2.16.840.1.113883.6.42", "wikidata": "P493", "wikidata.entity": "Q50018" }, "name": "International Classification of Diseases, 9th Revision", "pattern": "^((\\d\\d\\d|V\\d\\d|E[8-9]\\d\\d)(\\.\\d{1,2})?)|(\\d{1,3}-\\d{1,3})$", "preferred_prefix": "icd9", "references": [ "https://www.who.int/about/policies/publishing/copyright" ], "synonyms": [ "ICD9", "ICD9_2005", "MTHICD9_2006" ], "uri_format": "http://www.icd9data.com/getICD9Code.ashx?icd9=$1" }, "icd9cm": { "contact": { "email": "pbrooks@hcfa.gov", "name": "Patricia Brooks" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States.", "example": "784", "homepage": "https://www.cdc.gov/nchs/icd/icd9cm.htm", "keywords": [ "biomedical science", "diagnosis", "disease", "epidemiology", "health science", "medicine", "morbidity", "ontology", "preclinical studies" ], "license": "CC BY-ND 3.0 IGO", "mappings": { "aberowl": "ICD9CM", "bioportal": "ICD9CM", "fairsharing": "FAIRsharing.10zsxb", "hl7": "2.16.840.1.113883.6.2", "wikidata": "P1692", "wikidata.entity": "Q5737131" }, "name": "International Classification of Diseases, 9th Revision, Clinical Modification", "pattern": "^([\\dA-Z]\\d{2}(\\.\\d{1,3}|))|(\\d{2}(\\.\\d{1,2}|))$", "preferred_prefix": "icd9cm", "references": [ "https://www.who.int/about/policies/publishing/copyright" ], "synonyms": [ "IC9CM", "ICD9CM", "ICD9CM_2005", "ICD9CM_2006", "ICDCM_2005" ], "uri_format": "http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1" }, "icdc": { "contact": { "email": "annika.jahnke-bornemann@uni-hamburg.de", "name": "Annika Jahnke-Bornemann", "orcid": "0000-0001-7815-151X" }, "description": "The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer.", "example": "000009", "homepage": "https://caninecommons.cancer.gov/#/", "keywords": [ "atmospheric science", "earth science", "meteorology", "oceanography", "remote sensing", "social science" ], "mappings": { "fairsharing": "FAIRsharing.d95034", "miriam": "icdc", "re3data": "r3d100010405" }, "name": "Integrated Canine Data Commons", "pattern": "^\\d{6}$", "preferred_prefix": "icdc", "twitter": "ICDC_Hamburg", "uri_format": "https://caninecommons.cancer.gov/#/study/$1" }, "icdo": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases", "example": "9861/3", "homepage": "https://www.who.int/classifications/icd/adaptations/oncology/en/", "license": "CC BY-ND 3.0 IGO", "mappings": { "bartoc": "445", "hl7": "2.16.840.1.113883.6.43", "prefixcommons": "icdo", "wikidata": "P563", "wikidata.entity": "Q1430635" }, "name": "International Classification of Diseases for Oncology", "pattern": "^[8-9]\\d{3}(/[0-3])?$", "preferred_prefix": "icdo", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/icdo:$1" } ], "references": [ "https://www.who.int/about/policies/publishing/copyright" ], "synonyms": [ "ICD-O", "ICDO" ], "uri_format": "http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1" }, "iceberg.cime": { "contact": { "email": "hyou@sjtu.edu.cn", "name": "Hong-Yu Ou", "orcid": "0000-0001-9439-1660" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements.", "example": "6", "homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_CIME.php?type=alpha&alpha=100", "keywords": [ "biology", "genomics" ], "name": "ICEberg cis-integrative and mobilizable element", "pattern": "^\\d+$", "preferred_prefix": "iceberg.cime", "publications": [ { "doi": "10.1093/nar/gky1123", "pmc": "PMC6323972", "pubmed": "30407568", "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements", "year": 2019 }, { "doi": "10.1093/nar/gkr846", "pmc": "PMC3244999", "pubmed": "22009673", "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria", "year": 2011 } ], "uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php?cime_id=$1_CIME" }, "iceberg.element": { "description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements.", "example": "100", "homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=alpha&alpha=100", "mappings": { "biocontext": "ICEBERG.ELEMENT", "miriam": "iceberg.element", "n2t": "iceberg.element" }, "name": "ICEberg integrative and conjugative element", "pattern": "^\\d+$", "preferred_prefix": "iceberg.element", "publications": [ { "doi": "10.1093/nar/gky1123", "pmc": "PMC6323972", "pubmed": "30407568", "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements", "year": 2019 }, { "doi": "10.1093/nar/gkr846", "pmc": "PMC3244999", "pubmed": "22009673", "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria", "year": 2011 } ], "synonyms": [ "iceberg.ice" ], "uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=$1" }, "iceberg.family": { "contact": { "email": "hyou@sjtu.edu.cn", "name": "Hong-Yu Ou", "orcid": "0000-0001-9439-1660" }, "description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families.", "example": "1", "homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_fam.php", "mappings": { "biocontext": "ICEBERG.FAMILY", "miriam": "iceberg.family", "n2t": "iceberg.family" }, "name": "ICEberg family", "pattern": "^\\d+$", "preferred_prefix": "iceberg.family", "publications": [ { "doi": "10.1093/nar/gky1123", "pmc": "PMC6323972", "pubmed": "30407568", "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements", "year": 2019 }, { "doi": "10.1093/nar/gkr846", "pmc": "PMC3244999", "pubmed": "22009673", "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria", "year": 2011 } ], "uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id=$1" }, "iceberg.ime": { "contact": { "email": "hyou@sjtu.edu.cn", "name": "Hong-Yu Ou", "orcid": "0000-0001-9439-1660" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements.", "example": "1", "homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_IME.php?type=alpha&alpha=100", "keywords": [ "biology", "genomics" ], "name": "ICEberg integrative and mobilizable element", "pattern": "^\\d+$", "preferred_prefix": "iceberg.ime", "publications": [ { "doi": "10.1093/nar/gky1123", "pmc": "PMC6323972", "pubmed": "30407568", "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements", "year": 2019 }, { "doi": "10.1093/nar/gkr846", "pmc": "PMC3244999", "pubmed": "22009673", "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria", "year": 2011 } ], "uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.php?ime_id=$1_IME" }, "icechem": { "description": "The Integrated Chemical Environment (ICE) provides high-quality curated data and appropriate tools to support development and evaluation of new, revised, and alternative methods. ICE provides free online access to curated in vivo and in vitro test data, in silico toxicity predictions and chemical property data, reference chemical lists, and computational tools for chemical characterization and predicting toxicity.\nICE supports the following: (i) Data integration: brings together available data, including data on formulations; (ii) Results exploration: enables dynamic, graphical exploration with publication-quality graphics; (iii) Data analysis: allows characterization of data using online workflows, and (iv) FAIR data access: data are findable, accessible, interoperable, and reusable.", "example": "DTXSID7032004", "homepage": "https://ice.ntp.niehs.nih.gov", "mappings": { "miriam": "ice.chem" }, "name": "Integrated Chemical Environment - Chemical data", "pattern": "^\\d{2,7}-\\d{2}-\\d|DTXSID\\d{7,9}|[A-Z]{14}-[A-Z]{8}[SN][A-Z]-[A-Z]$", "preferred_prefix": "icechem", "uri_format": "https://ice.ntp.niehs.nih.gov/api/v1/search?chemid=$1" }, "iceo": { "comment": "ICEO is not consistent about its identfiers like ICEO:0000595:1 and ICEO:0000595_1", "contact": { "email": "liumeng94@sjtu.edu.cn", "github": "Lemon-Liu", "name": "Meng LIU", "orcid": "0000-0003-3781-6962" }, "description": "A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning.", "download_owl": "http://purl.obolibrary.org/obo/iceo.owl", "example": "0000712_1", "example_extras": [ "0000712" ], "homepage": "https://github.com/ontoice/ICEO", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "ICEO", "bioportal": "ICEO", "obofoundry": "iceo", "ols": "iceo", "ontobee": "ICEO", "wikidata.entity": "Q81661661" }, "name": "Integrative and Conjugative Element Ontology", "pattern": "^\\d{7}(_\\d)?$", "preferred_prefix": "ICEO", "publications": [ { "doi": "10.1038/s41597-021-01112-5", "pmc": "PMC8776819", "pubmed": "35058462", "title": "ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements", "year": 2022 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/ICEO_$1", "repository": "https://github.com/ontoice/ICEO", "uri_format": "http://purl.obolibrary.org/obo/ICEO_$1", "version": "2.1" }, "icepo": { "contact": { "email": "pascale.gaudet@isb-sib.ch", "github": "pgaudet", "name": "Pascale Gaudet", "orcid": "0000-0003-1813-6857" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools.", "download_obo": "https://download.nextprot.org/pub/current_release/controlled_vocabularies/icepo.obo", "example": "0000002", "homepage": "https://download.nextprot.org/pub/current_release/controlled_vocabularies/", "keywords": [ "ontology" ], "name": "Ion Channel Electrophysiology Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "icepo", "publications": [ { "pmc": "PMC4823818", "title": "ICEPO: the ion channel electrophysiology ontology" } ], "twitter": "neXtProt_news", "uri_format": "https://biopragmatics.github.io/providers/icepo/$1" }, "icf": { "comment": "This might be possible to roll directly into ICD11", "contact": { "email": "info@who.int", "name": "The World Health Organization" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. As the functioning and disability of an individual occurs in a context, ICF also includes a list of environmental factors. ICF is the WHO framework for measuring health and disability at both individual and population levels.", "download_owl": "http://aber-owl.net/media/ontologies/ICF/3/icf.owl", "example": "326705068", "homepage": "https://icd.who.int/dev11/l-icf/en", "keywords": [ "biomedical science", "electronic health record", "health science", "medicine", "ontology", "primary health care" ], "mappings": { "aberowl": "ICF", "bioportal": "ICF", "fairsharing": "FAIRsharing.7rngj0", "hl7": "2.16.840.1.113883.6.254" }, "name": "International Classification of Functioning, Disability and Health", "pattern": "^\\d+$", "preferred_prefix": "icf", "uri_format": "https://icd.who.int/dev11/l-icf/en#/http://id.who.int/icd/entity/$1" }, "iclc": { "description": "Cell line collections (Providers)", "example": "ATL98012", "homepage": "http://www.iclc.it", "mappings": { "cellosaurus": "ICLC" }, "name": "Interlab Cell Line Collection", "pattern": "^\\w{3}\\d+$", "preferred_prefix": "iclc", "uri_format": "http://www.iclc.it/details/det_list.php?line_id=$1" }, "icldb": { "contact": { "email": "surjeet.arya@uky.edu", "name": "Surjeet Kumar Arya", "orcid": "0000-0002-2212-4771" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "We have developed an online database describing the known cell lines from Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera that originated from crop pest insects. Cell line information has been primarily obtained from previous compilations of insect cell lines. (from homepage)", "example": "64ba", "homepage": "https://entomology.ca.uky.edu/aginsectcellsdatabase", "mappings": { "cellosaurus": "ICLDB" }, "name": "Insect Cell Line Database", "preferred_prefix": "icldb", "uri_format": "https://entomology.ca.uky.edu/content/$1" }, "ico": { "appears_in": [ "scdo" ], "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "description": "The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field.", "download_owl": "http://purl.obolibrary.org/obo/ico.owl", "example": "0000066", "homepage": "https://github.com/ICO-ontology/ICO", "keywords": [ "biomedical science", "clinical studies", "health science", "medicine", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "ICO", "biocontext": "ICO", "bioportal": "ICO", "fairsharing": "FAIRsharing.b9znd5", "obofoundry": "ico", "ols": "ico", "ontobee": "ICO", "wikidata.entity": "Q55118417" }, "name": "Informed Consent Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ICO", "rdf_uri_format": "http://purl.obolibrary.org/obo/ICO_$1", "repository": "https://github.com/ICO-ontology/ICO", "uri_format": "http://purl.obolibrary.org/obo/ICO_$1", "version": "2025-03-15" }, "iconclass": { "contact": { "email": "ep@epoz.org", "github": "epoz", "name": "Etienne Posthumus", "orcid": "0000-0002-0006-7542" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A classification system for the subject matter of works of art, originating from work from Henri van de Waal in the 1940.", "example": "3", "example_extras": [ "11HH(ELISABETH)35", "49E3932", "98C", "98C(...)(%2B1)", "98C(ZENOBIA%20SEPTIMIA)2" ], "homepage": "https://iconclass.org", "mappings": { "bartoc": "459", "wikidata.entity": "Q1502787" }, "name": "Iconclass Classification", "preferred_prefix": "iconclass", "uri_format": "https://iconclass.org/$1" }, "icpd.project": { "contact": { "email": "sonia.balyan@ibdc.rcb.res.in", "github": "soniabalyan24", "name": "Sonia Balyan", "orcid": "0000-0003-2136-4519" }, "contributor": { "email": "sonia.balyan@ibdc.rcb.res.in", "github": "soniabalyan24", "name": "Sonia Balyan", "orcid": "0000-0003-2136-4519" }, "description": "This resource is about projects in the Indian Crop Phenome Database (ICPD). The ICPD is a domain of the Indian Biological Data Center (IBDC), Regional Centre for Biotechnology, Faridabad, developed for the digitization of crop phenome data. Being the global agricultural powerhouse, the bulk of biological data generated in India is associated with agricultural trials. Ironically most of the trial data has been inaccessible to other researchers, and remains unpublished, and is lost as time passes. Therefore, ICPD would act as single-stop user-friendly platform for freely archiving, organizing, analyzing, and sharing the multi-crop phenome data following FAIR (Findable, Accessible, Interoperable and Re-usable) data principles. [from homepage]", "example": "PPJ_100024", "github_request_issue": 1570, "homepage": "https://ibdc.dbtindia.gov.in/icpd", "license": "CC BY-NC-SA 4.0", "logo": "https://ibdc.dbtindia.gov.in/icpd/static/image/ICPD-log.jpg", "name": "Indian Crop Phenome Database Project", "pattern": "^PPJ_\\d+$", "preferred_prefix": "icpd.project", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "icpd.study": { "contact": { "email": "sonia.balyan@ibdc.rcb.res.in", "github": "soniabalyan24", "name": "Sonia Balyan", "orcid": "0000-0003-2136-4519" }, "contributor": { "email": "sonia.balyan@ibdc.rcb.res.in", "github": "soniabalyan24", "name": "Sonia Balyan", "orcid": "0000-0003-2136-4519" }, "description": "This resource is about studies in the Indian Crop Phenome Database (ICPD). The ICPD is a domain of the Indian Biological Data Center (IBDC), Regional Centre for Biotechnology, Faridabad, developed for the digitization of crop phenome data. Being the global agricultural powerhouse, the bulk of biological data generated in India is associated with agricultural trials. Ironically most of the trial data has been inaccessible to other researchers, and remains unpublished, and is lost as time passes. Therefore, ICPD would act as single-stop user-friendly platform for freely archiving, organizing, analyzing, and sharing the multi-crop phenome data following FAIR (Findable, Accessible, Interoperable and Re-usable) data principles. [from homepage]", "example": "PST_100013", "github_request_issue": 1570, "homepage": "https://ibdc.dbtindia.gov.in/icpd", "license": "CC BY-NC-SA 4.0", "logo": "https://ibdc.dbtindia.gov.in/icpd/static/image/ICPD-log.jpg", "name": "Indian Crop Phenome Database Study", "pattern": "^PST_\\d+$", "preferred_prefix": "icpd.study", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://ibdc.dbtindia.gov.in/icpd/study-view-home/$1" }, "ictv": { "description": "Ontology representation of the [International Committee on Taxonomy of Viruses (ICTV)](https://ictv.global/) for the [EVORA project](https://evora-project.eu/)", "example": "ICTV19990991", "homepage": "https://github.com/EVORA-project/ictv-ontology", "mappings": { "bartoc": "507", "ols": "ictv" }, "name": "International Committee on Taxonomy of Viruses Ontology", "preferred_prefix": "ictv", "repository": "https://github.com/EVORA-project/ictv-ontology", "uri_format": "http://ictv.global/id/MSL40/$1", "version": "MSL40" }, "ideal": { "contact": { "email": "sfukuchi@maebashi-it.ac.jp", "github": "sfukuchi", "name": "Satoshi Fukuchi", "orcid": "0000-0002-5705-3061" }, "description": "IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments.", "example": "IID00001", "homepage": "https://www.ideal-db.org", "keywords": [ "biology" ], "mappings": { "biocontext": "IDEAL", "fairsharing": "FAIRsharing.h3y42f", "integbio": "nbdc01456", "miriam": "ideal", "n2t": "ideal", "pathguide": "701", "uniprot": "DB-0251" }, "name": "Intrinsically Disordered proteins with Extensive Annotations and Literature", "pattern": "^IID\\d+$", "preferred_prefix": "ideal", "publications": [ { "doi": "10.1093/nar/gkt1010", "pmc": "PMC3965115", "pubmed": "24178034", "title": "IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners", "year": 2013 } ], "uri_format": "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1" }, "ido": { "appears_in": [ "scdo" ], "contact": { "email": "Lindsay.Cowell@utsouthwestern.edu", "github": "lgcowell", "name": "Lindsay Cowell", "orcid": "0000-0003-1617-8244" }, "contributor_extras": [ { "email": "github@yohannparis.com", "github": "YohannParis", "name": "Yohann Paris", "orcid": "0009-0006-6049-1392" } ], "description": "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases.", "download_owl": "http://purl.obolibrary.org/obo/ido.owl", "example": "0000504", "homepage": "http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology", "keywords": [ "biomedical science", "classification", "disease", "disease course", "molecular infection biology", "obo", "ontology", "preclinical studies" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "IDO", "biocontext": "IDO", "bioportal": "IDO", "fairsharing": "FAIRsharing.aae3v6", "miriam": "ido", "n2t": "ido", "obofoundry": "ido", "ols": "ido", "ontobee": "IDO" }, "name": "Infectious Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "IDO", "providers": [ { "code": "obo.1", "description": "This incorrect encoding was found inside IDO-COVID-19", "homepage": "http://purl.obolibrary.org", "name": "Nonstandard OBO PURL", "uri_format": "http://purl.obolibrary.org/obo/ido.owl/IDO_$1" } ], "publications": [ { "doi": "10.1186/s13326-021-00245-1", "pmc": "PMC8286442", "pubmed": "34275487", "title": "The Infectious Disease Ontology in the age of COVID-19", "year": 2021 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/IDO_$1", "repository": "https://github.com/infectious-disease-ontology/infectious-disease-ontology", "uri_format": "http://purl.obolibrary.org/obo/IDO_$1", "version": "2017-11-03" }, "idocovid19": { "contact": { "email": "johnbeverley2021@u.northwestern.edu", "github": "johnbeve", "name": "John Beverly", "orcid": "0000-0002-1118-1738" }, "description": "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease.", "download_owl": "https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19", "example": "0001191", "homepage": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19", "keywords": [ "ontology" ], "mappings": { "aberowl": "IDO-COVID-19", "bioportal": "IDO-COVID-19", "ols": "idocovid19" }, "name": "The COVID-19 Infectious Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "idocovid19", "providers": [ { "code": "obo1", "description": "This variation uses incorrect usage of dashes instead of underscores", "homepage": "http://purl.obolibrary.org", "name": "Incorrect OBO PURL variation 1", "uri_format": "http://purl.obolibrary.org/obo/IDO-COVID-19_$1" } ], "repository": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19", "uri_format": "http://purl.obolibrary.org/obo/COVIDO_$1", "version": "2020-21-07" }, "idoden": { "contact": { "email": "elvira@imbb.forth.gr", "name": "Elvira Mitraka", "orcid": "0000-0003-0719-3485" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology for dengue fever.", "download_owl": "http://aber-owl.net/media/ontologies/IDODEN/6/idoden.owl", "example": "0003463", "homepage": "https://bioportal.bioontology.org/ontologies/IDODEN", "keywords": [ "medicine", "ontology" ], "mappings": { "aberowl": "IDODEN", "bioportal": "IDODEN", "fairsharing": "FAIRsharing.askzq4" }, "name": "Dengue Fever Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "idoden", "references": [ "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003479" ], "uri_format": "http://purl.bioontology.org/ontology/IDODEN_$1" }, "idog": { "contact": { "email": "baoym@big.ac.cn", "name": "Yiming Bao", "orcid": "0000-0002-9922-9723" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Provides the worldwide dog research community a variety of data services including access to genes, genomes, SNPs, breed/disease Traits, gene expression experiments, dog-guman homology, and literatur. In addition, iDog provides online tools for performing genomic data visualization and analyses.", "example": "4", "homepage": "https://ngdc.cncb.ac.cn/idog/", "license": "CC-BY-4.0", "mappings": { "integbio": "nbdc02480", "re3data": "r3d100012176" }, "name": "Integrated Resource for Domestic Dog", "pattern": "^\\d+$", "preferred_prefix": "idog", "publications": [ { "doi": "10.1093/nar/gky1041", "pmc": "PMC6323916", "pubmed": "30371881", "title": "iDog: an integrated resource for domestic dogs and wild canids", "year": 2019 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/725" ], "uri_format": "https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=$1" }, "idomal": { "appears_in": [ "scdo" ], "contact": { "email": "topalis@imbb.forth.gr", "name": "Pantelis Topalis", "orcid": "0000-0002-1635-4810" }, "deprecated": true, "description": "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.", "download_obo": "http://purl.obolibrary.org/obo/idomal.obo", "download_owl": "http://purl.obolibrary.org/obo/idomal.owl", "example": "0002350", "example_extras": [ "50000015" ], "homepage": "https://www.vectorbase.org/ontology-browser", "keywords": [ "biomedical science", "disease", "intervention design", "life science", "malaria", "molecular infection biology", "obo", "ontology", "pathogen" ], "license": "CC0-1.0", "mappings": { "aberowl": "IDOMAL", "biocontext": "IDOMAL", "bioportal": "IDOMAL", "fairsharing": "FAIRsharing.2q8c28", "obofoundry": "idomal", "ols": "idomal", "ontobee": "IDOMAL" }, "name": "Malaria Ontology", "pattern": "^(5?)\\d{7}$", "preferred_prefix": "IDOMAL", "publications": [ { "doi": "10.1186/2041-1480-4-16", "pmc": "PMC3848731", "pubmed": "24034841", "title": "IDOMAL: the malaria ontology revisited", "year": 2013 }, { "doi": "10.1186/1475-2875-9-230", "pmc": "PMC2925367", "pubmed": "20698959", "title": "IDOMAL: an ontology for malaria", "year": 2010 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/IDOMAL_$1", "repository": "https://github.com/VEuPathDB-ontology/IDOMAL", "twitter": "VectorBase", "uri_format": "http://purl.obolibrary.org/obo/IDOMAL_$1", "version": "2015-03-16" }, "idoo": { "description": "Identifiers.org Ontology", "example": "DataCollection", "homepage": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology", "mappings": { "miriam": "idoo", "n2t": "idoo" }, "name": "Identifiers.org Ontology", "pattern": "^[0-9a-zA-Z]+$", "preferred_prefix": "idoo", "uri_format": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1" }, "idot": { "description": "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.", "example": "Namespace", "homepage": "http://biomodels.net/vocab/idot.rdf", "mappings": { "biocontext": "idot", "miriam": "idot", "n2t": "idot" }, "name": "Identifiers.org Terms", "pattern": "^[A-Za-z]+$", "preferred_prefix": "idot", "uri_format": "https://biomodels.net/vocab/idot.rdf#$1" }, "idpo": { "contact": { "email": "f.quaglia@ibiom.cnr.it", "github": "federicaquaglia", "name": "Federica Quaglia", "orcid": "0000-0002-0341-4888" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. 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IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project.", "example": "NA06985", "homepage": "https://www.internationalgenome.org/", "keywords": [ "comparative genomics", "genomics" ], "mappings": { "cellosaurus": "IGSR", "fairsharing": "FAIRsharing.4Vs9VM", "re3data": "r3d100010180" }, "name": "International Genome Sample Resource", "preferred_prefix": "igsr", "publications": [ { "doi": "10.1093/nar/gkz836", "pmc": "PMC6943028", "pubmed": "31584097", "title": "The International Genome Sample Resource (IGSR) collection of open human genomic variation resources", "year": 2020 }, { "doi": "10.1038/nature15393", "pmc": "PMC4750478", "pubmed": "26432245", "title": "A global reference for human genetic variation", "year": 2015 } ], "twitter": "1000genomes", "uri_format": "https://www.internationalgenome.org/data-portal/sample/$1" }, "ihw": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics.", "example": "IHW09326", "homepage": "https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html", "mappings": { "cellosaurus": "IHW" }, "name": "International Histocompatibility Workshop cell lines", "pattern": "^IHW\\d+$", "preferred_prefix": "ihw" }, "iirds.core": { "description": "An ontology encoding the core metadata based on the Intelligent Information Request and Delivery (iiRDS) standard", "example": "Action", "homepage": "https://github.com/iirds-consortium/models", "keywords": [ "computer science", "nfdi4ing" ], "mappings": { "tib": "iirds" }, "name": "International Standard for Intelligent Information Request and Delivery Core Ontology", "preferred_prefix": "iirds.core", "repository": 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"International Standard for Intelligent Information Request and Delivery Software Ontology", "preferred_prefix": "iirds.sft", "repository": "https://github.com/iirds-consortium/models", "uri_format": "http://iirds.tekom.de/iirds/domain/software#$1" }, "illumina.probe": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip.", "example": "ILMN_129894", "homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6790/A-GEOD-6790.adf.txt", "keywords": [ "transcriptomics" ], "name": "Illumina Probe Identifier", "pattern": "^ILMN_\\d+$", "preferred_prefix": "illumina.probe", "references": [ "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-9184/A-GEOD-9184_comments.txt" ] }, "imanis": { "description": "Cell line collections (Providers)", "example": "CL070", "homepage": 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IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. 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It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data.", "example": "0000001", "homepage": "http://www.inoh.org", "keywords": [ "obo", "ontology", "protein", "small molecule" ], "mappings": { "biocontext": "IMR", "obofoundry": "imr", "prefixcommons": "imr" }, "name": "Molecule role (INOH Protein name/family name ontology)", "pattern": "^\\d{7}$", "preferred_prefix": "IMR", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/imr:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/IMR_$1", "uri_format": "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id=$1" }, "imsr.apb": { "description": "The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. [from RRID]", "example": "7345", "homepage": "https://pb.apf.edu.au/phenbank/homePage.html", "keywords": [ "allele", "alteration", "chromosome", "database", "embryo", "gene", "live mouse", "murine", "mutation", "phenotype", "sperm", "strain", "transgene", "transgenic" ], "mappings": { "rrid": "IMSR_APB" }, "name": "NHMRC Australian PhenomeBank", "pattern": "^\\d+$", "preferred_prefix": "imsr.apb", "uri_format": "https://pb.apf.edu.au/phenbank/strain.html?id=$1" }, "imsr_em": { "contact": { "email": "d.smedley@qmul.ac.uk", "name": "Damian Smedley", "orcid": "0000-0002-5836-9850" }, "description": "Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.With more than 8400 mutant mouse strains and asmall but increasing number of rat mutant strains available, EMMA is the primary mouse repository in Europe and the third largest non-profit repository worldwide. [from RRID]", "example": "11478", "homepage": "https://www.infrafrontier.eu/emma/", "keywords": [ "mouse", "mutant mouse repository", "mutant mouse strain", "mutant strain" ], "mappings": { "rrid": "IMSR_EM" }, "name": "European Mouse Mutant Archive", "pattern": "^\\d+$", "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_$1" }, "inaturalist.observation": { "contributor": { "github": "oolonek", "name": "Pierre-Marie Allard", "orcid": "0000-0003-3389-2191" }, "description": "The identifier for an observation in iNaturalist", "example": "36010371", "github_request_issue": 517, "homepage": "https://www.inaturalist.org/observations", "mappings": { "wikidata": "P5683" }, "name": "iNaturalist Observation", "pattern": "^[1-9]\\d*$", "preferred_prefix": "inaturalist.observation", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.inaturalist.org/observations/$1" }, "inaturalist.place": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Identifier for a place in iNaturalist", "example": "7207", "homepage": "https://www.inaturalist.org/places", "mappings": { "wikidata": "P7471" }, "name": "iNaturalist Place", "pattern": "^[1-9]\\d*$", "preferred_prefix": "inaturalist.place", "uri_format": "https://www.inaturalist.org/places/$1" }, "inaturalist.taxon": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Identifier for a species in iNaturalist", "example": "21723", "homepage": "https://www.inaturalist.org/taxa", "mappings": { "wikidata": "P3151" }, "name": "iNaturalist Taxonomy", "pattern": "^[1-9]\\d{0,6}$", "preferred_prefix": "inaturalist.taxon", "uri_format": "https://www.inaturalist.org/taxa/$1" }, "inaturalist.user": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Identifier for a user in iNaturalist", "example": "1426686", "homepage": "https://www.inaturalist.org/users", "keywords": [ "person" ], "name": "iNaturalist User", "pattern": "^[1-9]\\d*$", "preferred_prefix": "inaturalist.user", "uri_format": "https://www.inaturalist.org/users/$1" }, "inchi": { "contact": { "email": "jmg11@cam.ac.uk", "name": "Stephen R. Heller", "orcid": "0000-0002-5538-8482" }, "description": "The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier.", "example": "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3", "homepage": "https://www.ebi.ac.uk/chebi/", "keywords": [ "centrally registered identifier", "chemical entity", "chemical structure image", "cheminformatics", "chemistry", "molecular entity", "structure" ], "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBcUVFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--250afbf70b1e3f9c188231ff2fb50477040a71f5/inchi-wheel.png?disposition=inline", "mappings": { "biocontext": "INCHI", "fairsharing": "FAIRsharing.ddk9t9", "miriam": "inchi", "n2t": "inchi", "wikidata": "P234", "wikidata.entity": "Q203250" }, "name": "InChI", "pattern": "^InChI\\=1S?\\/[A-Za-z0-9\\.]+(\\+[0-9]+)?(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,\\/\\?\\;\\.]+)*$", "preferred_prefix": "inchi", "providers": [ { "code": "", "description": "InChI through NIST", "homepage": "http://webbook.nist.gov/chemistry", "name": "InChI through NIST", "uri_format": "http://webbook.nist.gov/cgi/cbook.cgi?$1" }, { "code": "um", "description": "InChI through RDF Open Molecules", "homepage": "http://rdf.openmolecules.net/", "name": "InChI through RDF Open Molecules", "uri_format": "http://rdf.openmolecules.net/?$1" } ], "publications": [ { "doi": "10.1186/s13321-021-00517-z", "pmc": "PMC8147039", "pubmed": "34030732", "title": "InChI version 1.06: now more than 99.99% reliable", "year": 2021 }, { "doi": "10.1186/s13321-015-0068-4", "pmc": "PMC4486400", "pubmed": "26136848", "title": "InChI, the IUPAC International Chemical Identifier", "year": 2015 }, { "doi": "10.1007/s10822-015-9854-3", "pubmed": "26081259", "title": "Many InChIs and quite some feat", "year": 2015 }, { "doi": "10.1186/s13321-024-00847-8", "title": "InChI isotopologue and isotopomer specifications", "year": 2024 } ], "repository": "https://github.com/IUPAC-InChI/InChI", "twitter": "inchi_trust", "uri_format": "https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=$1" }, "inchikey": { "description": "The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI.", "example": "RYYVLZVUVIJVGH-UHFFFAOYSA-N", "homepage": "http://www.chemspider.com/", "mappings": { "biocontext": "INCHIKEY", "miriam": "inchikey", "n2t": "inchikey", "togoid": "InchiKey", "wikidata": "P235", "wikidata.entity": "Q21445422" }, "name": "InChIKey", "pattern": "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-Z])?$", "preferred_prefix": "inchikey", "providers": [ { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/inchikey/$1" } ], "uri_format": "https://www.chemspider.com/search?params=$1" }, "infores": { "contact": { "email": "smoxon@lbl.gov", "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" }, "contributor": { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, "description": "The information resource registry is a listing of data sources present in the NCATS Data Translator system. Each information resource has an identifier, a short description, and a URL to more information about that resource.", "example": "agrkb", "github_request_issue": 1601, "homepage": "https://biolink.github.io/information-resource-registry/", "license": "Apache-2.0", "name": "Information Resource Registry", "pattern": "^[a-z0-9-_.]+$", "preferred_prefix": "infores", "repository": "https://github.com/biolink/information-resource-registry", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://w3id.org/information-resource-registry/$1" }, "informall": { "appears_in": [ "doid" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The InformAll database was developed to provide a credible source of information on allergenic food materials of both plant and animal origin.", "example": "410", "github_request_issue": 1311, "homepage": "http://research.bmh.manchester.ac.uk/informAll/", "name": "InformAll Allergenic Food Database", "pattern": "^\\d+$", "preferred_prefix": "informall", "uri_format": "http://research.bmh.manchester.ac.uk/informall/allergenic-food/?FoodId=$1" }, "infosecsos": { "description": "InfoSecSoS - Ontology for Information Security Management in Systems-of-Systems", "example": "Accept", "homepage": "https://zenodo.org/record/6621882", "keywords": [ "engineering", "nfdi4ing" ], "mappings": { "tib": "infosecsos" }, "name": "InfoSecSoS Ontology", "preferred_prefix": "infosecsos", "uri_format": "http://www.labesc.unirio.br/InfoSecSoS#$1" }, "inhand": { "comment": "This nomenclature is available via email. Truly a disgrace.", "contact": { "email": "harkemaj@msu.edu", "name": "Jack R Harkema", "orcid": "0000-0003-4682-0824" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology.", "homepage": "https://www.goreni.org/gr3_nomenclature.php", "keywords": [ "biomedical science", "disease", "toxicity" ], "mappings": { "fairsharing": "FAIRsharing.9gqfpm" }, "name": "The International Harmonization of Nomenclature and Diagnostic criteria", "preferred_prefix": "inhand", "proprietary": true, "publications": [ { "doi": "10.1177/0192623309353423", "pubmed": "20032296", "title": "Proliferative and nonproliferative lesions of the rat and mouse respiratory tract", "year": 2009 } ] }, "inn": { "comment": "can not find a place to resolve to", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.", "example": "fluticasone", "homepage": "https://www.who.int/teams/health-product-and-policy-standards/inn", "mappings": { "wikidata": "P2275", "wikidata.entity": "Q824258" }, "name": "International Nonproprietary Names", "preferred_prefix": "inn", "providers": [ { "code": "dotad", "description": "Database Of Therapeutic Antibody Developability (DOTAD) provides comprehensive developability assessments and annotations for therapeutic antibodies referenced by their INN names.", "homepage": "https://i.uestc.edu.cn/DOTAD/", "name": "Database Of Therapeutic Antibody Developability", "publications": [ { "doi": "10.1007/s12539-024-00613-2", "pubmed": "38530613", "title": "DOTAD: A Database of Therapeutic Antibody Developability", "year": 2025 } ], "uri_format": "https://i.uestc.edu.cn/DOTAD/detail.html?INN=$1" } ], "publications": [ { "doi": "10.1007/s12539-024-00613-2", "pubmed": "38530613", "title": "DOTAD: A Database of Therapeutic Antibody Developability", "year": 2025 } ], "synonyms": [ "INN_ID" ], "uri_format": "https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1" }, "innatedb": { "contact": { "email": "david.lynn@flinders.edu.au", "name": "David Lynn", "orcid": "0000-0003-4664-1404" }, "description": "InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactions and signaling responses involved in mammalian innate immunity. InnateDB incorporates information of the whole human, mouse and bovine interactomes by integrating interaction and pathway information from several of the major publicly available databases but aims to capture an improved coverage of the innate immunity interactome through manual curation.", "example": "20021", "homepage": "http://www.innatedb.ca/", "keywords": [ "gene", "immunology", "interaction", "life science", "pathway", "protein" ], "mappings": { "fairsharing": "FAIRsharing.rb2drw", "integbio": "nbdc01870", "pathguide": "264", "prefixcommons": "innatedb", "re3data": "r3d100010676" }, "name": "A Knowledge Resource for Innate Immunity Interactions and Pathways", "preferred_prefix": "innatedb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/innatedb:$1" } ], "publications": [ { "doi": "10.1093/nar/gks1147", "pmc": "PMC3531080", "pubmed": "23180781", "title": "InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation", "year": 2012 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "twitter": "innatedb", "uri_format": "http://www.innatedb.ca/getGeneCard.do?id=$1" }, "ino": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "description": "he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles.", "download_owl": "http://purl.obolibrary.org/obo/ino.owl", "example": "0000003", "homepage": "https://github.com/INO-ontology/ino", "keywords": [ "life science", "molecular interaction", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "INO", "biolink": "INO", "bioportal": "INO", "fairsharing": "FAIRsharing.mm72as", "obofoundry": "ino", "ols": "ino", "ontobee": "INO", "wikidata.entity": "Q55118418" }, "name": "Interaction Network Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "INO", "publications": [ { "doi": "10.1186/s13040-016-0118-0", "pmc": "PMC5168857", "pubmed": "28031747", "title": "The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature", "year": 2016 }, { "doi": "10.1186/2041-1480-6-2", "pmc": "PMC4362819", "pubmed": "25785184", "title": "Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions", "year": 2015 }, { "doi": "10.1186/2041-1480-2-s2-s8", "pmc": "PMC3102897", "pubmed": "21624163", "title": "Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology", "year": 2011 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/INO_$1", "repository": "https://github.com/INO-ontology/ino", "uri_format": "http://purl.obolibrary.org/obo/INO_$1", "version": "1.1.13" }, "insdc": { "description": "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences.", "example": "X58356", "homepage": "https://www.ebi.ac.uk/ena/", "keywords": [ "dna" ], "mappings": { "biocontext": "INSDC", "integbio": "nbdc02567", "miriam": "insdc", "n2t": "insdc", "prefixcommons": "insdc", "togoid": "Insdc" }, "name": "Nucleotide Sequence Database", "pattern": "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4,6}\\d{8,10}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$", "preferred_prefix": "insdc", "providers": [ { "code": "", "description": "INSDC through GenBank", "homepage": "https://www.ncbi.nlm.nih.gov/Genbank/", "name": "INSDC through GenBank", "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" }, { "code": "", "description": "INSDC through DDBJ", "homepage": "http://www.ddbj.nig.ac.jp/", "name": "INSDC through DDBJ", "uri_format": "https://getentry.ddbj.nig.ac.jp/getentry?database=ddbj&accession_number=$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/insdc:$1" }, { "code": "ncbi", "description": "INSDC through Nucleotide database at NCBI", "homepage": "https://www.ncbi.nlm.nih.gov/nuccore/", "name": "INSDC through Nucleotide database at NCBI", "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" } ], "publications": [ { "doi": "10.1093/nar/gkae1058", "pubmed": "39535044", "title": "The international nucleotide sequence database collaboration (INSDC): enhancing global participation", "year": 2024 }, { "doi": "10.1093/nar/18.6.1517", "pmc": "PMC330520", "pubmed": "2326192", "title": "Recent changes in the GenBank On-line Service", "year": 1990 }, { "doi": "10.1093/nar/gkl986", "pmc": "PMC1781245", "pubmed": "17202161", "title": "GenBank", "year": 2007 }, { "doi": "10.1093/nar/gkl913", "pmc": "PMC1897316", "pubmed": "17148479", "title": "EMBL Nucleotide Sequence Database in 2006", "year": 2006 }, { "doi": "10.1126/science.298.5597.1333b", "pubmed": "12436968", "title": "Nucleotide sequence database policies", "year": 2002 } ], "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" }, "insdc.cds": { "description": "The coding sequence or protein identifiers as maintained in INSDC.", "example": "AAA35559", "has_canonical": "ncbiprotein", "homepage": "http://getentry.ddbj.nig.ac.jp", "mappings": { "biocontext": "INSDC.CDS", "miriam": "insdc.cds", "n2t": "insdc.cds" }, "name": "INSDC CDS", "pattern": "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$", "preferred_prefix": "insdc.cds", "providers": [ { "code": "", "description": "INSDC CDS through ENA", "homepage": "https://www.ebi.ac.uk/ena", "name": "INSDC CDS through ENA", "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" }, { "code": "", "description": "INSDC CDS through NCBI", "homepage": "https://www.ncbi.nlm.nih.gov/protein/", "name": "INSDC CDS through NCBI", "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1" } ], "uri_format": "http://getentry.ddbj.nig.ac.jp/getentry/dad/$1" }, "insdc.gca": { "description": "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage.", "example": "GCA_000155495.1", "has_canonical": "ncbi.assembly", "homepage": "https://www.ncbi.nlm.nih.gov/datasets/genome/", "mappings": { "biocontext": "INSDC.GCA", "miriam": "insdc.gca", "n2t": "insdc.gca" }, "name": "Genome assembly database - INSDC accessions", "pattern": "^GCA_[0-9]{9}(\\.[0-9]+)?$", "preferred_prefix": "insdc.gca", "providers": [ { "code": "", "description": "Genome assembly database through ENA", "homepage": "https://www.ebi.ac.uk/ena/browse/genome-assembly-database", "name": "Genome assembly database through ENA", "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" } ], "uri_format": "https://www.ncbi.nlm.nih.gov/datasets/genome/$1" }, "insdc.gcf": { "description": "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database RefSeq accessions does not extend to viroids and bacteriophage.", "example": "GCF_000001405", "has_canonical": "ncbi.assembly", "homepage": "https://www.ncbi.nlm.nih.gov/", "mappings": { "miriam": "refseq.gcf" }, "name": "Genome assembly database - RefSeq accessions", "pattern": "^GCF_[0-9]{9}(\\.[0-9]+)?$", "preferred_prefix": "insdc.gcf", "synonyms": [ "insdc.gcf" ], "uri_format": "https://www.ncbi.nlm.nih.gov/datasets/genome/$1" }, "insdc.run": { "comment": "https://www.insdc.org/ is the authoritative source for INSDC. However, confusingly, they don't mention runs in this table. I think we should ask them to include. ENA is a partner and they have documentation [here](https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html). Runs | (E\\|D\\|S)RR[0-9]{6,} | ERR123456 -- | -- | --", "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "An experimental run, served thrugh the ENA", "example": "ERR436051", "github_request_issue": 131, "homepage": "https://www.insdc.org/", "name": "International Nucleotide Sequence Database Collaboration (INSDC) Run", "pattern": "^(E|D|S)RR[0-9]{6,}$", "preferred_prefix": "insdc.run", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.ebi.ac.uk/ena/browser/view/$1" }, "insdc.sra": { "contact": { "email": "Hugh.Shanahan@rhul.ac.uk", "github": "hughshanahan", "name": "Hugh P Shanahan", "orcid": "0000-0003-1374-6015" }, "description": "The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.", "example": "SRX000007", "homepage": "https://www.ncbi.nlm.nih.gov/sra", "keywords": [ "biology", "epidemiology", "genomics", "virology" ], "mappings": { "biocontext": "INSDC.SRA", "fairsharing": "FAIRsharing.g7t2hv", "miriam": "insdc.sra", "n2t": "insdc.sra", "re3data": "r3d100010775" }, "name": "Sequence Read Archive", "pattern": "^[SED]R[APRSXZ]\\d+$", "preferred_prefix": "insdc.sra", "providers": [ { "code": "ddbj", "description": "DDBJ Sequence Read Archive (DRA)", "homepage": "https://www.ddbj.nig.ac.jp/dra/index-e.html", "name": "DDBJ Sequence Read Archive (DRA)", "uri_format": "https://ddbj.nig.ac.jp/resource/sra-experiment/$1" }, { "code": "ebi", "description": "European Nucleotide Archive (ENA)", "homepage": "https://www.ebi.ac.uk/ena", "name": "European Nucleotide Archive (ENA)", "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" } ], "publications": [ { "doi": "10.1186/s13742-015-0064-7", "pmc": "PMC4425880", "pubmed": "25960871", "title": "Investigation into the annotation of protocol sequencing steps in the sequence read archive", "year": 2015 }, { "doi": "10.1093/nar/gkr854", "pmc": "PMC3245110", "pubmed": "22009675", "title": "The Sequence Read Archive: explosive growth of sequencing data", "year": 2011 }, { "doi": "10.1093/nar/gkm1000", "pmc": "PMC2238880", "pubmed": "18045790", "title": "Database resources of the National Center for Biotechnology Information", "year": 2007 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/sra/$1" }, "inspire.theme": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The INSPIRE theme register contains all spatial data themes, as defined in the Annexes of the INSPIRE Directive ( Directive 2007/2/EC of the European Parliament and of the Council of 14 March 2007 establishing an Infrastructure for Spatial Information in the European Community (INSPIRE)). The descriptions of the themes are based on version 3.0 of the \"Definition of Annex Themes and Scope (D 2.3)\" by the data specifications drafting team and subsequent updates by the INSPIRE Thematic Working Groups (TWGs). (from homepage)", "download_rdf": "http://inspire.ec.europa.eu/theme/theme.en.rdf", "example": "mr", "homepage": "https://inspire.ec.europa.eu/theme", "name": "INSPIRE theme register", "preferred_prefix": "inspire.theme", "uri_format": "https://inspire.ec.europa.eu/theme/$1" }, "intact": { "contact": { "email": "kalpanap@ebi.ac.uk", "github": "Kalpanapanneerselvam", "name": "Kalpana Panneerselvam", "orcid": "0000-0003-2534-198X" }, "contributor_extras": [ { "email": "sbalu@ebi.ac.uk", "github": "CP-SB", "name": "Sucharitha Balu", "orcid": "0000-0001-7456-0594" } ], "description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data.", "example": "EBI-2307691", "homepage": "https://www.ebi.ac.uk/intact/", "keywords": [ "biology", "interaction", "protein" ], "license": "CC-BY-4.0", "logo": "https://raw.githubusercontent.com/intact-portal/intact-portal-documentation/master/assets/logo_gradient_250x82_transparentbg_300dpi.png", "mappings": { "biocontext": "INTACT", "fairsharing": "FAIRsharing.d05nwx", "go": "IntAct", "integbio": "nbdc00507", "miriam": "intact", "n2t": "intact", "pathguide": "111", "prefixcommons": "intact", "re3data": "r3d100010671", "togoid": "Intact", "uniprot": "DB-0051" }, "name": "IntAct protein interaction", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^EBI\\-[0-9]+$", "preferred_prefix": "intact", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/intact:$1" } ], "publications": [ { "doi": "10.1002/cpz1.70018", "pubmed": "39401100", "title": "IntAct Database for Accessing IMEx's Contextual Metadata of Molecular Interactions", "year": 2024 }, { "doi": "10.1093/nar/gkt1115", "pmc": "PMC3965093", "pubmed": "24234451", "title": "The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases", "year": 2013 }, { "doi": "10.1038/nmeth.1637", "pmc": "PMC3246345", "pubmed": "21716279", "title": "PSICQUIC and PSISCORE: accessing and scoring molecular interactions", "year": 2011 }, { "doi": "10.1093/nar/gkp878", "pmc": "PMC2808934", "pubmed": "19850723", "title": "The IntAct molecular interaction database in 2010", "year": 2009 }, { "doi": "10.1186/1741-7007-5-44", "pmc": "PMC2189715", "pubmed": "17925023", "title": "Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions", "year": 2007 }, { "doi": "10.1093/nar/gkh052", "pmc": "PMC308786", "pubmed": "14681455", "title": "IntAct: an open source molecular interaction database", "year": 2004 } ], "twitter": "intact_project", "uri_format": "https://www.ebi.ac.uk/intact/interaction/$1" }, "intact.molecule": { "description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules.", "example": "EBI-366083", "homepage": "https://www.ebi.ac.uk/intact/", "mappings": { "biocontext": "INTACT.MOLECULE", "miriam": "intact.molecule", "n2t": "intact.molecule" }, "name": "IntAct Molecule", "pattern": "^EBI\\-[0-9]+$", "preferred_prefix": "intact.molecule", "publications": [ { "doi": "10.1002/cpz1.70018", "pubmed": "39401100", "title": "IntAct Database for Accessing IMEx's Contextual Metadata of Molecular Interactions", "year": 2024 } ], "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://catalog.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", "homepage": "http://www.interfil.org", "keywords": [ "genome" ], "mappings": { "prefixcommons": "interfil" }, "name": "Human Intermediate Filament Database", "preferred_prefix": "interfil", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/interfil:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.interfil.org/details.php?id=$1" }, "interlex": { "contact": { "email": "mmartone@ucsd.edu", "github": "memartone", "name": "Maryann Elizabeth Martone", "orcid": "0000-0002-8406-3871" }, "description": "InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. ", "example": "0101963", "homepage": "https://www.fdilab.org", "keywords": [ "anatomy", "biomedical science", "brain", "imaging", "neurobiology" ], "mappings": { "fairsharing": "FAIRsharing.67sssf", "miriam": "ilx", "wikidata": "P696" }, "name": "InterLex", "pattern": "^[0-9]+$", "preferred_prefix": "interlex", "publications": [ { "doi": "10.3389/fninf.2013.00018", "pmc": "PMC3757470", "pubmed": "24009581", "title": "NeuroLex.org: an online framework for neuroscience knowledge", "year": 2013 } ], "references": [ "https://github.com/AllenInstitute/nomenclature" ], "synonyms": [ "ILX" ], "uri_format": "https://scicrunch.org/scicrunch/interlex/view/ilx_$1" }, "interpro": { "contact": { "email": "agb@ebi.ac.uk", "github": "bateman-research", "name": "Alex Bateman", "orcid": "0000-0002-6982-4660" }, "description": "InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.", "example": "IPR016380", "homepage": "http://www.ebi.ac.uk/interpro/index.html", "keywords": [ "bioinformatics", "biology", "domain", "obo", "ontology", "protein" ], "license": "CC0-1.0", "logo": "https://content.embl.org/sites/default/files/03-2025/interpro_newlogo-2-scaled-1.jpg", "mappings": { "biocontext": "IPR", "biolink": "interpro", "edam": "1133", "fairsharing": "FAIRsharing.pda11d", "go": "InterPro", "integbio": "nbdc00108", "miriam": "interpro", "n2t": "interpro", "ncbi": "InterPro", "obofoundry": "ipr", "prefixcommons": "interpro", "re3data": "r3d100010798", "togoid": "Interpro", "uniprot": "DB-0052", "wikidata": "P2926", "wikidata.entity": "Q114677890" }, "name": "InterPro", "pattern": "^IPR\\d{6}$", "preferred_prefix": "interpro", "providers": [ { "code": "", "description": "Bio2RDF", "homepage": "http://bio2rdf.org/", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/interpro:$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/interpro:$1" } ], "publications": [ { "doi": "10.1093/nar/gkae1082", "pubmed": "39565202", "title": "InterPro: the protein sequence classification resource in 2025", "year": 2024 }, { "doi": "10.1093/nar/gkac993", "pmc": "PMC9825450", "pubmed": "36350672", "title": "InterPro in 2022", "year": 2023 }, { "doi": "10.1093/nar/gkaa977", "pmc": "PMC7778928", "pubmed": "33156333", "title": "The InterPro protein families and domains database: 20 years on", "year": 2021 }, { "doi": "10.1093/nar/gky1100", "pmc": "PMC6323941", "pubmed": "30398656", "title": "InterPro in 2019: improving coverage, classification and access to protein sequence annotations", "year": 2019 }, { "doi": "10.1093/nar/gki106", "pmc": "PMC540060", "pubmed": "15608177", "title": "InterPro, progress and status in 2005", "year": 2005 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/IPR_$1", "repository": "https://proteinswebteam.github.io/interpro-blog/", "synonyms": [ "IP", "IPR", "InterPro" ], "twitter": "InterProDB", "uri_format": "https://www.ebi.ac.uk/interpro/entry/InterPro/$1" }, "iobc": { "contact": { "email": "kushida@biosciencedbc.jp", "github": "kushidatatsuya", "name": "Tatsuya Kushida", "orcid": "0000-0002-0784-4113" }, "description": "Interlinking Ontology for Biological Concepts (IOBC) contains approximately 80,000 biological concepts such as biological phenomena, diseases, molecular functions, gene products, chemicals, and medical cares, and approximately 20,000 related concepts such as earth science and environmental science. The concepts are structured by thirty-five relations such as has function, has role, has quality, and precedes. Each concept has both of English and Japanese labels. For further information including the developmental method, see papers in the PUBLICATIONS PAGE. The license for this ontology is specified in the Creative Commons Attribution-NonCommercial 4.0 International. If you use data from this ontology, please be sure attribute this ontology as follows: \"Interlinking Ontology for Biological Concepts © National Bioscience Database Center licensed under CC Attribution-NonCommercial 4.0 International\".", "download_owl": "http://aber-owl.net/media/ontologies/IOBC/25/iobc.owl", "example": "200906038218908385", "example_extras": [ "AC21", "AC21_cat", "OWLClass_00000000000000000321" ], "homepage": "https://github.com/kushidat/IOBC", "keywords": [ "ontology" ], "license": "CC-BY-NC-4.0", "mappings": { "aberowl": "IOBC", "bioportal": "IOBC" }, "name": "Interlinking Ontology for Biological Concepts", "preferred_prefix": "iobc", "publications": [ { "doi": "10.1007/s00354-019-00074-y", "title": "Interconnection of Biological Knowledge Using NikkajiRDF and Interlinking Ontology for Biological Concepts", "year": 2019 } ], "repository": "https://github.com/kushidat/IOBC", "uri_format": "http://purl.jp/bio/4/id/$1" }, "iofcore": { "description": "The IOF Core Ontology contains notions found to be common across multiple manufacturing domains. This file is an RDF implementation of these notions. The ontology utilizes the Basic Formal Ontology or BFO as a top-level ontology but also borrows terms from various domain-independent or mid-level ontologies. The purpose of the ontology is to serve as a foundation for ensuring consistency and interoperability across various domain-specific reference ontologies the IOF publishes.", "download_owl": "https://github.com/iofoundry/ontology/raw/refs/heads/master/core/Core.rdf", "example": "hasSpecifiedOutput", "homepage": "https://oagi.org/pages/Released-Ontologies", "keywords": [ "engineering", "nfdi4ing", "ontology" ], "mappings": { "tib": "iofcore" }, "name": "Industrial Ontology Foundry (IOF) Core Ontology", "preferred_prefix": "iofcore", "repository": "https://github.com/iofoundry/ontology", "uri_format": "https://spec.industrialontologies.org/ontology/core/Core/$1" }, "ioio": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology of information entities about an individual", "download_owl": "https://github.com/OpenLHS/IOIO/raw/refs/heads/main/IOIO.owl", "example": "0000001", "homepage": "https://openlhs.github.io/IOIO/", "keywords": [ "ontology" ], "name": "Individual Organism Information Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ioio", "repository": "https://github.com/OpenLHS/IOIO", "uri_format": "http://purl.obolibrary.org/obo/IOIO_$1" }, "ipi": { "deprecated": true, "description": "IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI maintaisn a database of cross references between the primary data sources, it provides minimally redundant but complete sets of proteins for featured species, and it maintains stable and unique identifiers.", "example": "IPI00000001", "homepage": "http://www.ebi.ac.uk/IPI", "keywords": [ "protein" ], "mappings": { "biocontext": "IPI", "integbio": "nbdc00911", "prefixcommons": "ipi" }, "name": "International Protein Index", "preferred_prefix": "ipi", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/ipi:$1" } ], "publications": [ { "doi": "10.1002/pmic.200300721", "pubmed": "15221759", "title": "The International Protein Index: an integrated database for proteomics experiments", "year": 2004 } ], "uri_format": "http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$1&format=default" }, "irct": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Iranian Registry of Clinical Trials. This is a Primary Registry in the WHO Registry Network set up with the help from the Ministry of Health and Medical Education (MOHME) and hosted by Iran University of Medical Sciences (IUMS). (from homepage)\nNote that the website uses a different identifier then the one reported in this semantic space.", "example": "IRCT20080904001199N7", "homepage": "https://en.irct.ir/", "name": "Iranian Registry of Clinical Trials", "pattern": "^IRCT\\d+N\\d+$", "preferred_prefix": "irct", "references": [ "https://en.irct.ir/trial/65035" ] }, "ird.segment": { "contact": { "email": "richard.scheuermann@nih.gov", "github": "scheuerm", "name": "Richard H. Scheuermann", "orcid": "0000-0003-1355-892X" }, "description": "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s).", "example": "CY077097", "homepage": "http://www.fludb.org/", "keywords": [ "gene", "protein" ], "mappings": { "biocontext": "IRD.SEGMENT", "miriam": "ird.segment", "n2t": "ird.segment", "prefixcommons": "ird.segment" }, "name": "IRD Segment Sequence", "pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$", "preferred_prefix": "ird.segment", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/ird.segment:$1" } ], "publications": [ { "doi": "10.1093/nar/gkm905", "pmc": "PMC2238987", "pubmed": "17965094", "title": "BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence", "year": 2007 } ], "uri_format": "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1" }, "irefweb": { "contact": { "email": "shoshana@sickkids.ca", "name": "Shoshana J. Wodak", "orcid": "0000-0002-0701-6545" }, "deprecated": true, "description": "iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.", "example": "617102", "homepage": "http://wodaklab.org/iRefWeb/", "keywords": [ "interaction", "life science", "protein" ], "mappings": { "biocontext": "IREFWEB", "fairsharing": "FAIRsharing.t31wcb", "miriam": "irefweb", "n2t": "irefweb", "pathguide": "300", "prefixcommons": "irefweb", "re3data": "r3d100012725" }, "name": "iRefWeb", "pattern": "^\\d+$", "preferred_prefix": "irefweb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/irefweb:$1" } ], "publications": [ { "doi": "10.1093/database/baq023", "pmc": "PMC2963317", "pubmed": "20940177", "title": "iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence", "year": 2010 } ], "twitter": "wodaklab", "uri_format": "http://wodaklab.org/iRefWeb/interaction/show/$1" }, "iresite": { "contact": { "email": "martin.pospisek@natur.cuni.cz", "name": "Martin Pospíšek", "orcid": "0000-0002-9490-8911" }, "description": "The IRESite database presents information about experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract the eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure.", "example": "322", "homepage": "http://www.iresite.org", "keywords": [ "life science", "regulation", "rna" ], "mappings": { "fairsharing": "FAIRsharing.kd39j4", "integbio": "nbdc01752", "prefixcommons": "iresite" }, "name": "Database of experimentally verified IRES structures", "preferred_prefix": "iresite", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/iresite:$1" } ], "publications": [ { "doi": "10.1093/nar/gkp981", "pmc": "PMC2808886", "pubmed": "19917642", "title": "IRESite--a tool for the examination of viral and cellular internal ribosome entry sites", "year": 2009 }, { "doi": "10.1093/nar/gkj081", "pmc": "PMC1347444", "pubmed": "16381829", "title": "IRESite: the database of experimentally verified IRES structures (www.iresite.org)", "year": 2006 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.iresite.org/IRESite_web.php?page=view&entry_id=$1" }, "iro": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "example": "0000008", "name": "Insect Resistance Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "iro", "uri_format": "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1" }, "isbn": { "description": "The International Standard Book Number (ISBN) is for identifying printed books.", "example": "9789211613865", "example_extras": [ "978-92-1-161386-5" ], "homepage": "http://www.worldcat.org/", "keywords": [ "bibliography" ], "mappings": { "biocontext": "ISBN-13", "biolink": "isbn", "edam": "2634", "go": "ISBN", "miriam": "isbn", "n2t": "isbn", "prefixcommons": "isbn" }, "name": "International Standard Book Number", "pattern": "^(ISBN)?(-13|-10)?[:]?[ ]?(\\d{2,3}[ -]?)?\\d{1,5}[ -]?\\d{1,7}[ -]?\\d{1,6}[ -]?(\\d|X)$", "preferred_prefix": "isbn", "providers": [ { "code": "", "description": "ISBNDB - ISBN Database", "homepage": "http://isbndb.com/", "name": "ISBNDB - ISBN Database", "uri_format": "http://isbndb.com/search-all.html?kw=$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/isbn:$1" }, { "code": "google.isbn", "description": "Google Books provider for ISBN numbers", "homepage": "https://books.google.com", "name": "Google Books", "uri_format": "https://books.google.com/books?isbn=$1" }, { "code": "isbnsearch", "description": "ISBN Search is an unofficial search engine for ISBNs.", "homepage": "https://isbnsearch.org", "name": "ISBN Search", "uri_format": "https://isbnsearch.org/isbn/$1" } ], "synonyms": [ "ISBN-10", "ISBN-13" ], "uri_format": "https://www.worldcat.org/isbn/$1" }, "isced1997": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ISCED is designed to serve as a framework to classify educational activities as defined in programmes and the resulting qualifications into internationally agreed categories. 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The basic concepts and definitions of ISCED are therefore intended to be internationally valid and comprehensive of the full range of education systems.", "download_rdf": "https://github.com/dini-ag-kim/vocabs-edu/raw/refs/heads/master/isced-2011.ttl", "example": "1", "github_request_issue": 1625, "homepage": "https://ec.europa.eu/eurostat/statistics-explained/index.php?title=International_Standard_Classification_of_Education_(ISCED)", "keywords": [ "education level", "open educational resources" ], "name": "International Standard Classification of Education, 2011 Edition", "preferred_prefix": "isced2011", "references": [ "https://uis.unesco.org/sites/default/files/documents/international-standard-classification-of-education-isced-2011-en.pdf" ], "uri_format": "https://w3id.org/kim/isced-2011/level$1" }, "isced2013": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ISCED is designed to serve as a framework to classify educational activities as defined in programmes and the resulting qualifications into internationally agreed categories. The basic concepts and definitions of ISCED are therefore intended to be internationally valid and comprehensive of the full range of education systems.", "download_rdf": "https://github.com/dini-ag-kim/vocabs-edu/raw/refs/heads/master/isced-2013.ttl", "example": "n0021", "github_request_issue": 1625, "homepage": "https://ec.europa.eu/eurostat/statistics-explained/index.php?title=International_Standard_Classification_of_Education_(ISCED)", "keywords": [ "education level", "educational resources", "open educational resources" ], "mappings": { "tib": "isced" }, "name": "International Standard Classification of Education, 2013 Edition", "preferred_prefix": "isced2013", "references": [ "http://www.uis.unesco.org/Education/Documents/isced-fields-of-education-training-2013.pdf" ], "uri_format": "https://w3id.org/kim/isced-2013/$1" }, "ised": { "description": "ISED catalogues the influenza sequence and epitope information obtained in countries worldwide and currently hosts a total of 49368 influenza A and 4761 influenza B virus sequence data including pandemic A/H1N1 2009 virus sequences collected in 42 countries, and a total of 545 amantadine-resistant influenza virus sequences collected in Korea.", "example": "AY209920", "homepage": "http://influenza.korea.ac.kr", "keywords": [ "protein" ], "mappings": { "prefixcommons": "ised" }, "name": "Influenza Sequence and Epitope Database", "preferred_prefix": "ised", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/ised:$1" } ] }, "isfinder": { "contact": { "email": "patricia.siguier@univ-tlse3.fr", "name": "Patricia Siguier", "orcid": "0000-0003-1620-6495" }, "deprecated": true, "description": "ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available.", "example": "ISA1083-2", "homepage": "http://www-is.biotoul.fr/i", "keywords": [ "gene", "life science", "sequence" ], "mappings": { "biocontext": "ISFINDER", "fairsharing": "FAIRsharing.xhpc3h", "integbio": "nbdc00510", "miriam": "isfinder", "n2t": "isfinder", "ncbi": "ISFinder", "prefixcommons": "isfinder" }, "name": "Insertion sequence elements database", "pattern": "^IS\\w+(\\-\\d)?$", "preferred_prefix": "isfinder", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/isfinder:$1" } ], "publications": [ { "doi": "10.1093/nar/gkj014", "pmc": "PMC1347377", "pubmed": "16381877", "title": "ISfinder: the reference centre for bacterial insertion sequences", "year": 2006 } ], "uri_format": "https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1" }, "isni": { "description": "ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC.\n\nThe mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described.", "example": "000000012281955X", "homepage": "http://www.isni.org", "mappings": { "bartoc": "20464", "biolink": "isni", "miriam": "isni", "n2t": "isni", "wikidata": "P213", "wikidata.entity": "Q423048" }, "name": "International Standard Name Identifier", "pattern": "^[0-9]{15}[0-9X]{1}$", "preferred_prefix": "isni", "providers": [ { "code": "isni.short", "description": "Unqualified ISNI URI", "homepage": "http://www.isni.org", "name": "ISNI short", "uri_format": "http://www.isni.org/$1" } ], "uri_format": "http://www.isni.org/isni/$1" }, "iso.3166": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An identifier for a country in numeric format per ISO 3166-1", "example": "554", "homepage": "https://www.iso.org/iso-3166-country-codes.html", "mappings": { "wikidata": "P299" }, "name": "ISO 3166-1 Country Code", "pattern": "^\\d+$", "preferred_prefix": "iso.3166", "uri_format": "https://data.who.int/countries/$1" }, "iso.639-3": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Since the introduction of ISO 639-3 in 2007, access to language information has increased tremendously. The code set initially adopted as ISO639-3:2007 was based on a harmonization of ISO 639-2 with the code set of SIL’s Ethnologue 15th edition and languages from Linguist List to form a comprehensive set of code elements for world languages. SIL International, the Language Coding Agency for 639-3, relies on the contributions of linguists, language coding experts, and language users around the world to maintain and improve the code set through the change request process defined in the ISO 639 standard. [from homepage]", "example": "spa", "github_request_issue": 1614, "homepage": "https://iso639-3.sil.org/", "keywords": [ "computer science", "informatics", "language", "linguistics" ], "mappings": { "fairsharing": "FAIRsharing.33aa85", "hl7": "1.0.639.3" }, "name": "ISO 639 3-Letter Language Code", "preferred_prefix": "iso.639-3", "providers": [ { "code": "loc", "description": "ISO 639-2 is part of the ISO 639 language code family, which provides also a two-character code set (ISO 639-1) for the representation of names of languages. ISO 639-2 contains codes for all languages contained in ISO 639-1 and several hundred additional languages. The ISO 639-2 (Bibliographic) codes were devised for use in bibliographic metadata, e.g., for libraries, information services, and publishers, and ISO 639-2 (Terminology) targets terminology, lexicography, and linguistic applications. The lists are the same except for 20 languages that have different Bibliographic and Terminology codes. The list contains over 500 discrete codes. The ISO 639-2 (Bibliographic) codes are equivalent to the MARC Language Codes. The ISO 639-2 codes are linked to two-character codes for the same language in ISO 639-1, to the MARC Language Codes, and to equivalent codes for language groups in ISO 639-5. [from homepage]", "homepage": "http://id.loc.gov/vocabulary/iso639-2", "name": "ISO 639-2: Codes for the Representation of Names of Languages - Part 2: Alpha-3 Code for the Names of Languages", "uri_format": "http://id.loc.gov/vocabulary/iso639-2/$1" } ], "uri_format": "https://iso639-3.sil.org/code/$1" }, "iso15926": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The primary purpose of ISO 15926 is to provide a foundation ontology to support the integration and sharing of data related to the lifecycle of a process plant in such a way that it is consistent, unambiguous, and minimizing the number of ways something could be expressed. Further purpose of ISO 15926-14 is to meet needs for OWL 2 ontologies that are based on ISO 15926-2, that enable efficient reasoning and that capture lifecycle information. A specific purpose is to demonstrate lifecycle modelling through a representation of the lifecycle model of ISO/IEC 81346-1. Another specific purpose is to exemplify how this standard can be used to develop industrial ontologies through various real-world use cases from industry. (from https://nfdi4cat.org/services/ontologie-sammlung/)", "download_rdf": "https://github.com/uwasystemhealth/modular_ontologies/raw/master/LIS-14.ttl", "example": "activityBoundOf", "homepage": "https://15926.org/home/", "name": "ISO 15926-14", "preferred_prefix": "iso15926", "uri_format": "http://standards.iso.org/iso/15926/part14/$1" }, "isrctn": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The International Clinical Trials Registry Platform, originally called International Standard Randomised Controlled Trial Number (ISRCTN) registry, is a primary clinical study registry recognised by the World Health Organisation (WHO) and the International Committee of Medical Journal Editors (ICMJE) that accepts all clinical research studies (whether proposed, ongoing or completed), providing content validation and curation and the unique identification number necessary for publication. All study records in the database are freely accessible and searchable. (from homepage)", "example": "ISRCTN10175490", "homepage": "https://www.isrctn.com", "name": "International Clinical Trials Registry Platform", "pattern": "^ISRCTN\\d+$", "preferred_prefix": "isrctn", "providers": [ { "code": "doi", "description": "DOI resolution of ISRCTN", "homepage": "https://doi.org/10.1186", "name": "DOI", "uri_format": "https://doi.org/10.1186/$1" }, { "code": "who", "description": "WHO Clinical Trials Search", "homepage": "https://trialsearch.who.int", "name": "WHO Clinical Trials Search", "uri_format": "https://trialsearch.who.int/Trial2.aspx?TrialID=$1" } ], "uri_format": "https://www.isrctn.com/$1" }, "issn": { "description": "The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books.", "example": "0745-4570", "homepage": "https://portal.issn.org", "mappings": { "biocontext": "ISSN", "biolink": "issn", "go": "ISSN", "miriam": "issn", "n2t": "issn" }, "name": "International Standard Serial Number", "pattern": "^\\d{4}-\\d{3}[\\dX]$", "preferred_prefix": "issn", "providers": [ { "code": "", "description": "ISSN at Library of Congress", "homepage": "http://catalog.loc.gov", "name": "ISSN at Library of Congress", "uri_format": "https://search.catalog.loc.gov/search?option=keyword&query=$1" } ], "uri_format": "https://portal.issn.org/resource/ISSN/$1" }, "istransbase": { "contact": { "email": "oriental-cds@163.com", "name": "Dongsheng Cao" }, "contributor": { "email": "shah.tanay2@northeastern.edu", "github": "tanayshah2", "name": "Tanay Shah", "orcid": "0009-0001-1912-5132" }, "description": "ISTransbase is a highly reliable and accessible database that focuses on inhibitors and substrates of drug transporters, offering a wealth of vital information encompassing experimental methods, transport parameters, and references.", "example": "IST028", "github_request_issue": 1145, "homepage": "https://istransbase.scbdd.com/", "name": "ISTransbase", "preferred_prefix": "istransbase", "publications": [ { "doi": "10.1093/database/baae053", "pmc": "PMC11214160", "pubmed": "38943608", "title": "ISTransbase: an online database for inhibitor and substrate of drug transporters", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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It isoperated by the China Academy of Chinese Medical Sciences and The China Center For Evidence Based Traditional Chinese Medicine. It is recognized as a Primary Registry of WHO, and contributes data to the WHO ICTRP. (from website)", "example": "ITMCTR2023000002", "homepage": "http://itmctr.ccebtcm.org.cn", "logo": "http://itmctr.ccebtcm.org.cn/Content/images/ny_logo.png", "name": "International Traditional Medicine Clinical Trial Registry", "pattern": "^ITMCTR\\d+$", "preferred_prefix": "itmctr" }, "ito": { "banana": "ITO", "banana_peel": "_", "contact": { "email": "matthias.samwald@meduniwien.ac.at", "name": "Matthias Samwald", "orcid": "0000-0002-4855-2571" }, "description": "The Intelligence Task Ontology (ITO) provides a comprehensive map of machine intelligence tasks, as well as broader human intelligence or hybrid human/machine intelligence tasks.", "download_owl": "http://aber-owl.net/media/ontologies/ITO/17/ito.owl", "example": "01625", "homepage": "https://openbiolink.github.io/ITOExplorer/", "keywords": [ "artificial intelligence", "machine learning", "natural language processing", "ontology" ], "mappings": { "aberowl": "ITO", "bioportal": "ITO", "fairsharing": "FAIRsharing.89e853", "miriam": "ito" }, "name": "Intelligence Task Ontology", "pattern": "^\\d+$", "preferred_prefix": "ito", "publications": [ { "doi": "10.1038/s41597-022-01435-x", "pmc": "PMC9205953", "pubmed": "35715466", "title": "A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks", "year": 2022 }, { "doi": "10.5281/zenodo.5561989", "title": "Intelligence Task Ontology and Knowledge Graph (ITO)", "year": 2022 }, { "doi": "10.48550/arxiv.2110.01434", "title": "A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks", "year": 2021 } ], "repository": "https://github.com/OpenBioLink/ITO", "uri_format": "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:ITO_$1" }, "iuphar.family": { "description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits.", "example": "78", "homepage": "http://www.guidetopharmacology.org/", "keywords": [ "protein" ], "license": "CC-BY-SA-4.0", "mappings": { "biocontext": "IUPHAR.FAMILY", "miriam": "iuphar.family", "n2t": "iuphar.family", "prefixcommons": "iuphar.family" }, "name": "IUPHAR family", "pattern": "^\\d+$", "preferred_prefix": "iuphar.family", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/iuphar.family:$1" } ], "synonyms": [ "IUPHARfam" ], "uri_format": "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1" }, "iuphar.ligand": { "description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands.", "example": "1755", "homepage": "http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all", "license": "CC-BY-SA-4.0", "mappings": { "biocontext": "IUPHAR.LIGAND", "biolink": "GTOPDB", "miriam": "iuphar.ligand", "n2t": "iuphar.ligand", "togoid": "IupharLigand", "wikidata": "P595" }, "name": "Guide to Pharmacology Ligand", "pattern": "^\\d+$", "preferred_prefix": "iuphar.ligand", "synonyms": [ "IUPHAR_LIGAND", "IUPHAR_LIGAND_ID" ], "uri_format": "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1" }, "iuphar.receptor": { "contact": { "email": "simon.harding@igmm.ed.ac.uk", "github": "simondharding", "name": "Simon Douglas Harding", "orcid": "0000-0002-9262-8318" }, "description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits.", "example": "101", "homepage": "http://www.guidetopharmacology.org/targets.jsp", "license": "CC-BY-SA-4.0", "mappings": { "biocontext": "IUPHAR.RECEPTOR", "go": "IUPHAR_RECEPTOR", "miriam": "iuphar.receptor", "n2t": "iuphar.receptor", "uniprot": "DB-0182", "wikidata": "P5458" }, "name": "Guide to Pharmacology Target", "pattern": "^\\d+$", "preferred_prefix": "iuphar.receptor", "publications": [ { "doi": "10.1093/nar/gkab1010", "pmc": "PMC8689838", "pubmed": "34718737", "title": "The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials", "year": 2022 }, { "doi": "10.1111/j.1476-5381.2012.02141.x", "pmc": "PMC3575771", "pubmed": "23003568", "title": "GuideToPharmacology.org--an update", "year": 2012 } ], "synonyms": [ "IUPHAR_GPCR", "IUPHARobj" ], "uri_format": "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1" }, "ivdb": { "description": "IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively.", "example": "E13035", "homepage": "http://influenza.psych.ac.cn/", "keywords": [ "dna", "gene", "genome" ], "mappings": { "prefixcommons": "ivdb" }, "name": "Influenza Virus Database", "preferred_prefix": "ivdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/ivdb:$1" } ], "uri_format": "http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id=$1" }, "jaxmice": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A catalogue of mouse strains supplied by The Jackson Laboratory. Each identifier corresponds to a mouse strain.", "example": "004435", "homepage": "https://mice.jax.org", "keywords": [ "gene", "genetic engineering", "knockout", "life science", "mice", "model", "mouse", "repository", "research", "strain", "subject", "supply" ], "mappings": { "biocontext": "JAXMICE", "fairsharing": "FAIRsharing.5701h1", "miriam": "jaxmice", "n2t": "jaxmice", "rrid": "IMSR_JAX" }, "name": "Jackson Laboratories Mouse Strain", "pattern": "^\\d{6}$", "preferred_prefix": "jaxmice", "synonyms": [ "jax", "jaxMiceUID" ], "uri_format": "https://www.jax.org/strain/$1" }, "jcggdb": { "deprecated": true, "description": "JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc.", "example": "JCGG-STR008690", "homepage": "http://jcggdb.jp/index_en.html", "mappings": { "biocontext": "JCGGDB", "integbio": "nbdc01164", "miriam": "jcggdb", "n2t": "jcggdb" }, "name": "Japan Consortium for Glycobiology and Glycotechnology Database", "pattern": "^JCGG-STR\\d{6}$", "preferred_prefix": "jcggdb", "uri_format": "http://jcggdb.jp/idb/jcggdb/$1" }, "jcm": { "description": "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2.", "example": "17254", "homepage": "http://www.jcm.riken.go.jp/", "keywords": [ "life science", "microbial", "taxonomy" ], "mappings": { "biocontext": "JCM", "fairsharing": "FAIRsharing.h2wrt2", "miriam": "jcm", "n2t": "jcm", "ncbi": "JCM", "prefixcommons": "jcm" }, "name": "Japan Collection of Microorganisms", "pattern": "^\\d+$", "preferred_prefix": "jcm", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/jcm:$1" } ], "uri_format": "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1" }, "jcrb": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Cell line collections (Providers)", "example": "JCRB1355", "homepage": "https://cellbank.nibiohn.go.jp", "mappings": { "cellosaurus": "JCRB" }, "name": "JRBC Cell Bank", "pattern": "^JCRB\\d+$", "preferred_prefix": "jcrb", "uri_format": "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1" }, "jcsd": { "contributor_extras": [ { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" } ], "description": "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST).", "example": "J55.713G", "homepage": "http://jglobal.jst.go.jp/en/", "keywords": [ "drug" ], "mappings": { "biocontext": "JCSD", "miriam": "jcsd", "n2t": "jcsd", "prefixcommons": "nikkaji" }, "name": "Japan Chemical Substance Dictionary", "pattern": "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$", "preferred_prefix": "jcsd", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/nikkaji:$1" }, { "code": "stirdf", "description": "Appears in iobc", "homepage": "http://stirdf.jst.go.jp", "name": "Unknown", "uri_format": "http://stirdf.jst.go.jp/cde/nikkaji/$1" } ], "synonyms": [ "Nikkaji number", "nikkaji" ], "uri_format": "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1" }, "jecfa": { "contact": { "email": "kpetersen@who.int", "name": "Kim Petersen" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "JECFA provides identifiers for flavors, food additives, contaminants, toxicants, and veterinary drugs. Each entry includes chemical details, acceptable or tolerable intake limits, and links to related reports and monographs.", "example": "2116", "github_request_issue": 1247, "homepage": "https://apps.who.int/food-additives-contaminants-jecfa-database", "mappings": { "wikidata": "P9557" }, "name": "Joint FAO/WHO Expert Committee on Food Additives", "pattern": "^\\d+$", "preferred_prefix": "jecfa", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" } }, "jgi.proposal": { "contact": { "email": "sewilson@lbl.gov", "name": "Steven E. Wilson", "orcid": "0000-0002-8489-208X" }, "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor_extras": [ { "email": "aclum@lbl.gov", "github": "aclum", "name": "Alicia Clum", "orcid": "0000-0002-5004-3362" } ], "description": "Identifiers for proposals/projects at the Joint Genome Institute", "example": "502930", "github_request_issue": 853, "homepage": "https://genome.jgi.doe.gov/portal/", "name": "Joint Genome Institute Proposals", "pattern": "^\\d+$", "preferred_prefix": "jgi.proposal", "publications": [ { "doi": "10.1128/msystems.00804-20", "pmc": "PMC8269246", "pubmed": "34006627", "title": "DOE JGI Metagenome Workflow", "year": 2021 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue=$1" }, "jrct": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This system submits an implementation plan to the Minister of Health, Labor and Welfare for clinical research conducted at medical institutions, etc. based on the provisions of the 'Clinical Research Act' and the 'Act on Ensuring Safety of Regenerative Medicine, etc.' It is a system for performing notification procedures such as In addition, based on the clinical research practice standards stipulated in the same law, we disclose information that the World Health Organization (WHO) requires to be disclosed, information that ensures the transparency of the research process, and information that contributes to the selection of participation in clinical research by the public. (translated from website)", "example": "jRCTs041220087", "homepage": "https://jrct.niph.go.jp", "name": "Japan Registry of Clinical Trials", "pattern": "^jRCT\\w?\\d+$", "preferred_prefix": "jrct", "providers": [ { "code": "detail", "description": "Japan Registry of Clinical Trials (Details)", "homepage": "https://jrct.niph.go.jp", "name": "Japan Registry of Clinical Trials (Details)", "uri_format": "https://jrct.niph.go.jp/latest-detail/$1" } ], "uri_format": "https://jrct.niph.go.jp/en-latest-detail/$1" }, "jstor": { "description": "JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration.", "example": "3075966", "homepage": "http://www.jstor.org/", "mappings": { "biocontext": "JSTOR", "go": "JSTOR", "miriam": "jstor", "n2t": "jstor" }, "name": "Digital archive of scholarly articles", "pattern": "^\\d+$", "preferred_prefix": "jstor", "uri_format": "http://www.jstor.org/stable/$1" }, "jws": { "contact": { "email": "brettolivier@gmail.com", "github": "bgoli", "name": "Brett G. Olivier", "orcid": "0000-0002-5293-5321" }, "description": "JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser.", "example": "achcar11", "homepage": "http://jjj.bio.vu.nl/models/", "keywords": [ "model", "pathway" ], "mappings": { "biocontext": "JWS", "miriam": "jws", "n2t": "jws", "prefixcommons": "jws" }, "name": "JWS Online", "pattern": "^\\w+$", "preferred_prefix": "jws", "providers": [ { "code": "", "description": "JWS Online Model Repository at Stellenbosch", "homepage": "http://jjj.biochem.sun.ac.za/models/", "name": "JWS Online Model Repository at Stellenbosch", "uri_format": "http://jjj.biochem.sun.ac.za/models/$1/" }, { "code": "", "description": "JWS Online Model Repository at Manchester", "homepage": "http://jjj.mib.ac.uk/models", "name": "JWS Online Model Repository at Manchester", "uri_format": "http://jjj.mib.ac.uk/models/$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/jws:$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/bth200", "pubmed": "15072998", "title": "Web-based kinetic modelling using JWS Online", "year": 2004 } ], "uri_format": "https://jjj.bio.vu.nl/models/$1" }, "kaggle": { "description": "Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions.", "example": "nasa/kepler-exoplanet-search-results", "homepage": "https://kaggle.com", "mappings": { "miriam": "kaggle", "n2t": "kaggle", "re3data": "r3d100012705" }, "name": "Kaggle", "pattern": "^[0-9a-zA-Z\\-]+\\/[0-9a-zA-Z\\-]+$", "preferred_prefix": "kaggle", "uri_format": "https://www.kaggle.com/$1" }, "kaken": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for researchers in Japan used in government-based research funding (from 1980s)", "example": "00011461", "homepage": "https://nrid.nii.ac.jp/ja/search/?kw=", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P9776" }, "name": "e-Rad researcher number", "pattern": "^\\d{8}$", "preferred_prefix": "kaken", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://nrid.nii.ac.jp/ja/nrid/10000$1" }, "kclb": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Cell line collections (Providers)", "example": "10020.2", "homepage": "https://cellbank.snu.ac.kr/english", "mappings": { "cellosaurus": "KCLB" }, "name": "Korean Cell Line Bank", "preferred_prefix": "kclb", "uri_format": "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1" }, "kcris": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Clinical Research Information Service (CRIS) is a non-profit online registration system for clinical trials (researches) to be conducted in Korea. It has been established at the Korea Disease Control and Prevention Agency (KDCA) with support from the Ministry of Health and Welfare (MOHW). It joined the WHO International Clinical Trials Registry Platform (ICTRP) as 11th member of Primary Registry. (from about page)\nNote that the web page that resolves this trial does not correspond to the semantic space", "example": "KCT0008394", "homepage": "https://cris.nih.go.kr", "name": "Korean Clinical Research Information Service", "pattern": "^KCT\\d+$", "preferred_prefix": "kcris", "references": [ "https://cris.nih.go.kr/cris/search/detailSearchEn.do?seq=23973" ] }, "kdbirp": { "contact": { "email": "zengxian@fudan.edu.cn", "name": "Xian Zeng", "orcid": "0000-0002-1397-554X" }, "contributor": { "email": "ji.kang@northeastern.edu", "github": "kanghosaeyo", "name": "Kangho Ji", "orcid": "0009-0009-3402-8013" }, "description": "Identifiers represent RNA-protein interaction entries with quantitative kinetic data in the Kinetic Data of Biomolecular Interactions for RNA-Protein database (KDBI-RP), which is an open-access database cataloging association rates, dissociation rates, and equilibrium dissociation constants for RNA-protein interactions.", "example": "183", "github_request_issue": 1717, "homepage": "http://www.kdbirp.aiddlab.com", "keywords": [ "binding affinity", "kinetics", "rna-protein interactions" ], "logo": "http://www.kdbirp.aiddlab.com/static/images/logo2.png", "name": "Kinetic Data of RNA-Protein Interactions Database", "pattern": "^\\d+$", "preferred_prefix": "kdbirp", "publications": [ { "doi": "10.1016/j.jmb.2025.169357", "pubmed": "40716733", "title": "KDBI-RP: Kinetic Data of RNA-Protein Interactions Database", "year": 2025 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.kdbirp.aiddlab.com/detail/$1" }, "kdsf.ffk": { "description": "Klassifikation für interdisziplinäre Forschungsfelder im Rahmen des Kerndatensatz Forschung", "example": "ErdeUndKosmos", "example_extras": [ "111" ], "homepage": "https://github.com/KDSF-FFK/kdsf-ffk", "keywords": [ "computer science", "digital planning and construction", "fid baudigital", "fid move", "nfdi4ing" ], "mappings": { "bartoc": "20288", "tib": "kdsfffk" }, "name": "Interdisziplinäre Forschungsfeldklassifikation", "preferred_prefix": "kdsf.ffk", "repository": "https://github.com/KDSF-FFK/kdsf-ffk", "uri_format": "https://w3id.org/kdsf-ffk/$1" }, "kegg": { "comment": "KEGG prefix has been split into several others", "deprecated": true, "description": "Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.", "example": "hsa00190", "homepage": "http://www.kegg.jp/", "logo": "https://www.kegg.jp/Fig/kegg128.gif", "mappings": { "biocontext": "KEGG", "biolink": "KEGG", "cheminf": "000409", "go": "KEGG", "integbio": "nbdc00530", "miriam": "kegg", "n2t": "kegg", "pathguide": "16", "uniprot": "DB-0053" }, "name": "Kyoto Encyclopedia of Genes and Genomes", "pattern": "^([CHDEGTMKR]\\d+)|(\\w+:[\\w\\d\\.-]*)|([a-z]{3,5})|(\\w{2,4}\\d{5})$", "preferred_prefix": "kegg", "publications": [ { "doi": "10.1093/nar/gkae909", "pubmed": "39417505" }, { "doi": "10.1093/nar/gkw1092", "pmc": "PMC5210567", "pubmed": "27899662", "title": "KEGG: new perspectives on genomes, pathways, diseases and drugs", "year": 2016 } ], "synonyms": [ "KEGG" ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.brite": { "description": "KEGG BRITE is a collection of hierarchical classifications (see new hierarchies and last updates) representing our knowledge on various aspects of biological systems. In contrast to KEGG PATHWAY, which is limited to molecular interactions and reactions, KEGG BRITE incorporates many different types of relationships.", "example": "ko00002", "homepage": "https://www.genome.jp/kegg/brite.html", "keywords": [ "classification", "ontology", "pathway" ], "logo": "https://www.genome.jp/Fig/kegg128.gif", "mappings": { "biolink": "KEGG.BRITE", "integbio": "nbdc00115", "prefixcommons": "kegg.brite" }, "name": "KEGG BRITE", "preferred_prefix": "kegg.brite", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/kegg.brite:$1" } ], "uri_format": "https://www.kegg.jp/brite/$1" }, "kegg.compound": { "contact": { "email": "kanehisa@kuicr.kyoto-u.ac.jp", "name": "Minoru Kanehisa", "orcid": "0000-0001-6123-540X" }, "description": "KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life.", "example": "C12345", "homepage": "https://www.genome.jp/kegg/ligand.html", "keywords": [ "small molecule" ], "logo": "https://www.genome.jp/Fig/kegg128.gif", "mappings": { "biocontext": "KEGG.COMPOUND", "edam": "2605", "integbio": "nbdc00814", "miriam": "kegg.compound", "n2t": "kegg.compound", "prefixcommons": "kegg.compound", "wikidata": "P665" }, "name": "KEGG Compound", "part_of": "kegg", "pattern": "^C\\d+$", "preferred_prefix": "kegg.compound", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/kegg.compound:$1" } ], "publications": [ { "doi": "10.1002/0471250953.bi0112s38", "pubmed": "22700311", "title": "Using the KEGG database resource", "year": 2012 } ], "synonyms": [ "KEGG COMPOUND", "KEGG.COMPOUND" ], "uri_format": "https://www.kegg.jp/entry/$1" }, "kegg.dgroup": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. There are five types of drug groups.\n\n Chemical - grouped as identical chemical structures with minor variations of salts, hydration states, etc.\n Structure - grouped as similar chemical structures having the same skeleton, etc.\n Target - grouped by drug targets\n Class - drug classes often representing similar mechanisms of action\n Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters\n\nChemical groups are often used for identifying essentially the same active ingredients of drugs in different countries.", "example": "DG00301", "homepage": "http://www.genome.jp/kegg/reaction/", "logo": "https://www.genome.jp/Fig/kegg128.gif", "mappings": { "biolink": "KEGG.DGROUP" }, "name": "KEGG Drug Group", "part_of": "kegg", "pattern": "^DG\\d+$", "preferred_prefix": "kegg.dgroup", "references": [ "https://github.com/prefixcommons/prefixes/pull/4" ], "synonyms": [ "KEGG_DGROUP", "KEGG_DRUG_GROUP" ] }, "kegg.disease": { "description": "The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system.", "example": "H00076", "homepage": "http://www.genome.jp/kegg/disease/", "keywords": [ "classification" ], "logo": "https://www.genome.jp/Fig/kegg128.gif", "mappings": { "biocontext": "KEGG.DISEASE", "integbio": "nbdc00813", "miriam": "kegg.disease", "n2t": "kegg.disease", "prefixcommons": "kegg.disease" }, "name": "KEGG Disease", "part_of": "kegg", "pattern": "^H\\d+$", "preferred_prefix": "kegg.disease", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/kegg.disease:$1" } ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.drug": { "contact": { "email": "kanehisa@kuicr.kyoto-u.ac.jp", "name": "Minoru Kanehisa", "orcid": "0000-0001-6123-540X" }, "description": "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules.", "example": "D00123", "homepage": "https://www.genome.jp/kegg/drug/", "keywords": [ "small molecule" ], "logo": "https://www.genome.jp/Fig/kegg128.gif", "mappings": { "biocontext": "KEGG.DRUG", "edam": "2609", "integbio": "nbdc00812", "miriam": "kegg.drug", "n2t": "kegg.drug", "prefixcommons": "kegg.drug", "wikidata": "P665" }, "name": "KEGG Drug", "part_of": "kegg", "pattern": "^D\\d+$", "preferred_prefix": "kegg.drug", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/kegg.drug:$1" } ], "publications": [ { "doi": "10.1093/nar/gkj102", "pmc": "PMC1347464", "pubmed": "16381885", "title": "From genomics to chemical genomics: new developments in KEGG", "year": 2006 } ], "synonyms": [ "KEGG DRUG", "KEGG.DRUG" ], "uri_format": "https://www.kegg.jp/entry/$1" }, "kegg.environ": { "deprecated": true, "description": "KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable.", "example": "ev:E00032", "homepage": "http://www.genome.jp/kegg/drug/environ.html", "logo": "https://www.genome.jp/Fig/kegg128.gif", "mappings": { "biocontext": "KEGG.ENVIRON", "integbio": "nbdc01059", "miriam": "kegg.environ", "n2t": "kegg.environ" }, "name": "KEGG Environ", "part_of": "kegg", "pattern": "^(ev\\:)?E\\d+$", "preferred_prefix": "kegg.environ", "synonyms": [ "KEGG.EDRUG" ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.enzyme": { "description": "KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links.", "homepage": "http://www.genome.jp/dbget-bin/www_bfind?enzyme", "logo": "https://www.genome.jp/Fig/kegg128.gif", "mappings": { "biolink": "KEGG.ENZYME", "go": "KEGG_ENZYME" }, "name": "KEGG Enzyme", "part_of": "kegg", "preferred_prefix": "kegg.enzyme", "provides": "ec", "uri_format": "http://www.genome.jp/dbget-bin/www_bget?ec:$1" }, "kegg.genes": { "contact": { "email": "kanehisa@kuicr.kyoto-u.ac.jp", "name": "Minoru Kanehisa", "orcid": "0000-0001-6123-540X" }, "description": "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources.", "example": "bsu:BSU01340", "homepage": "http://www.genome.jp/kegg/genes.html", "keywords": [ "dna", "gene", "protein" ], "logo": "https://www.genome.jp/Fig/kegg128.gif", "mappings": { "biocontext": "KEGG.GENES", "biolink": "KEGG.GENES", "miriam": "kegg.genes", "n2t": "kegg.genes", "prefixcommons": "kegg.gene", "wikidata": "P665" }, "name": "KEGG gene", "part_of": "kegg", "pattern": "^\\w+:[\\w\\d\\.-]*$", "preferred_prefix": "kegg.genes", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/kegg.gene:$1" } ], "publications": [ { "doi": "10.1093/nar/gkj102", "pmc": "PMC1347464", "pubmed": "16381885", "title": "From genomics to chemical genomics: new developments in KEGG", "year": 2006 } ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.genome": { "contact": { "email": "kanehisa@kuicr.kyoto-u.ac.jp", "name": "Minoru Kanehisa", "orcid": "0000-0001-6123-540X" }, "description": "KEGG Genome is a collection of organisms whose genomes have been completely sequenced.", "example": "T06648", "homepage": "http://www.genome.jp/kegg/catalog/org_list.html", "keywords": [ "genome" ], "license": "https://www.kegg.jp/kegg/legal.html", "logo": "https://www.genome.jp/Fig/kegg128.gif", "mappings": { "biocontext": "KEGG.GENOME", "integbio": "nbdc00816", "miriam": "kegg.genome", "n2t": "kegg.genome", "prefixcommons": "kegg.genome", "wikidata": "P665" }, "name": "KEGG genome", "part_of": "kegg", "pattern": "^(T0\\d+|\\w{3,5})$", "preferred_prefix": "kegg.genome", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/kegg.genome:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr988", "pmc": "PMC3245020", "pubmed": "22080510", "title": "KEGG for integration and interpretation of large-scale molecular data sets", "year": 2011 } ], "synonyms": [ "kegg_genome", "kegg_genomes" ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.glycan": { "contact": { "email": "kanehisa@kuicr.kyoto-u.ac.jp", "name": "Minoru Kanehisa", "orcid": "0000-0001-6123-540X" }, "description": "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways.", "example": "G00123", "homepage": "https://www.genome.jp/kegg/glycan/", "keywords": [ "small molecule" ], "logo": "https://www.genome.jp/Fig/kegg128.gif", "mappings": { "biocontext": "KEGG.GLYCAN", "edam": "2613", "integbio": "nbdc00533", "miriam": "kegg.glycan", "n2t": "kegg.glycan", "prefixcommons": "kegg.glycan" }, "name": "KEGG Glycan", "part_of": "kegg", "pattern": "^G\\d+$", "preferred_prefix": "kegg.glycan", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/kegg.glycan:$1" } ], "publications": [ { "doi": "10.1093/glycob/cwj010", "pubmed": "16014746", "title": "KEGG as a glycome informatics resource", "year": 2005 } ], "uri_format": "https://www.kegg.jp/entry/$1" }, "kegg.ligand": { "comment": "This database has been discontinued by KEGG. It now lives inside the compound database", "deprecated": true, "homepage": "http://www.genome.ad.jp/kegg/docs/upd_ligand.html", "logo": "https://www.genome.jp/Fig/kegg128.gif", "mappings": { "go": "KEGG_LIGAND" }, "name": "KEGG LIGAND", "part_of": "kegg", "preferred_prefix": "kegg.ligand", "uri_format": "http://www.genome.jp/dbget-bin/www_bget?cpd:$1" }, "kegg.metagenome": { "contact": { "email": "kanehisa@kuicr.kyoto-u.ac.jp", "name": "Minoru Kanehisa", "orcid": "0000-0001-6123-540X" }, "description": "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species.", "example": "T30002", "homepage": "http://www.genome.jp/kegg/catalog/org_list3.html", "keywords": [ "genome" ], "logo": "https://www.genome.jp/Fig/kegg128.gif", "mappings": { "biocontext": "KEGG.METAGENOME", "miriam": "kegg.metagenome", "n2t": "kegg.metagenome", "prefixcommons": "kegg.metagenome" }, "name": "KEGG Metagenome", "part_of": "kegg", "pattern": "^T3\\d+$", "preferred_prefix": "kegg.metagenome", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/kegg.metagenome:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr988", "pmc": "PMC3245020", "pubmed": "22080510", "title": "KEGG for integration and interpretation of large-scale molecular data sets", "year": 2011 } ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.module": { "description": "KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules.", "example": "M00002", "homepage": "http://www.kegg.jp/kegg/module.html", "logo": "https://www.genome.jp/Fig/kegg128.gif", "mappings": { "biocontext": "KEGG.MODULE", "integbio": "nbdc01428", "miriam": "kegg.module", "n2t": "kegg.module" }, "name": "KEGG Module", "part_of": "kegg", "pattern": "^([a-z]{3,5}_)?M\\d{5}$", "preferred_prefix": "kegg.module", "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.orthology": { "description": "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms.", "example": "K00001", "homepage": "http://www.genome.jp/kegg/ko.html", "keywords": [ "classification", "pathway" ], "logo": "https://www.genome.jp/Fig/kegg128.gif", "mappings": { "biocontext": "KEGG.ORTHOLOGY", "miriam": "kegg.orthology", "n2t": "kegg.orthology", "prefixcommons": "kegg.orthology" }, "name": "KEGG Orthology", "part_of": "kegg", "pattern": "^K\\d+$", "preferred_prefix": "kegg.orthology", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/kegg.orthology:$1" } ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.pathway": { "contact": { "email": "kanehisa@kuicr.kyoto-u.ac.jp", "name": "Minoru Kanehisa", "orcid": "0000-0001-6123-540X" }, "description": "KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.", "example": "rsk00410", "homepage": "https://www.genome.jp/kegg/pathway.html", "keywords": [ "pathway" ], "logo": "https://www.genome.jp/Fig/kegg128.gif", "mappings": { "biocontext": "KEGG.PATHWAY", "biolink": "KEGG.PATHWAY", "edam": "2343", "go": "KEGG_PATHWAY", "miriam": "kegg.pathway", "n2t": "kegg.pathway", "prefixcommons": "kegg.pathway", "wikidata": "P665" }, "name": "KEGG pathway", "pattern": "^\\w{2,4}\\d{5}$", "preferred_prefix": "kegg.pathway", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/kegg.pathway:$1" } ], "publications": [ { "doi": "10.1002/0471250953.bi0112s38", "pubmed": "22700311", "title": "Using the KEGG database resource", "year": 2012 } ], "synonyms": [ "KEGG-path", "KEGG_PATHWAY" ], "uri_format": "https://www.kegg.jp/pathway/$1" }, "kegg.rclass": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns.", "example": "RC00001", "homepage": "http://www.genome.jp/kegg/reaction/", "logo": "https://www.genome.jp/Fig/kegg128.gif", "mappings": { "biolink": "KEGG.RCLASS", "integbio": "nbdc00860" }, "name": "KEGG Reaction Class", "part_of": "kegg", "pattern": "^RC\\d+$", "preferred_prefix": "kegg.rclass", "references": [ "https://github.com/prefixcommons/prefixes/pull/2" ], "synonyms": [ "KEGG_RCLASS", "KEGG_REACTION_CLASS" ] }, "kegg.reaction": { "contact": { "email": "kanehisa@kuicr.kyoto-u.ac.jp", "name": "Minoru Kanehisa", "orcid": "0000-0001-6123-540X" }, "description": "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life.", "example": "R00100", "homepage": "https://www.genome.jp/kegg/reaction/", "keywords": [ "enzyme", "pathway" ], "logo": "https://www.genome.jp/Fig/kegg128.gif", "mappings": { "biocontext": "KEGG.REACTION", "edam": "2608", "go": "KEGG_REACTION", "integbio": "nbdc00818", "miriam": "kegg.reaction", "n2t": "kegg.reaction", "prefixcommons": "kegg.reaction", "wikidata": "P665" }, "name": "KEGG Reaction", "part_of": "kegg", "pattern": "^R\\d+$", "preferred_prefix": "kegg.reaction", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/kegg.reaction:$1" } ], "publications": [ { "doi": "10.1002/0471250953.bi0112s38", "pubmed": "22700311", "title": "Using the KEGG database resource", "year": 2012 } ], "rdf_uri_format": "http://www.kegg.jp/entry/$1", "synonyms": [ "KEGG_REACTION" ], "uri_format": "https://www.kegg.jp/entry/$1" }, "kerafast": { "description": "Cell line collections (Providers)", "example": "EJH014", "homepage": "https://www.kerafast.com/", "mappings": { "cellosaurus": "Kerafast" }, "name": "Kerafast cell lines", "preferred_prefix": "kerafast", "uri_format": "https://www.kerafast.com/Search?SearchTerm="$1"" }, "kestrelo": { "contact": { "email": "lindsey.anderson@pnnl.gov", "github": "lnanderson", "name": "Lindsey N. Anderson", "orcid": "0000-0002-8741-7823" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology for harmonizing and extending severeral existing resources in the vaccine and immunology domains", "example": "0000001", "homepage": "https://gitlab.pnnl.gov/kestrel/kestrel_ontology", "name": "KESTREL Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "kestrelo", "uri_format": "http://purl.obolibrary.org/obo/kestrelo_$1" }, "kim.amb": { "contact": { "github": "acka47", "name": "Adrian Pohl", "orcid": "0000-0001-9083-7442" }, "contributor": { "email": "m.voigt@hzdr.de", "github": "eilmiv", "name": "Martin Voigt", "orcid": "0000-0001-5556-838X" }, "description": "A cross-sectoral metadata profile for describing teaching and learning resources, primarily based on [schema.org](https://schema.org) and the Learning Resource Metadata Initiative LRMI, and additionally utilizing elements of the Simple Knowledge Organization System SKOS. A JSON-LD11-compliant data structure is defined in the form of this HTML specification, including a JSON schema against which data can be automatically checked for conformity with the profile.", "example": "conditionsofaccess", "github_request_issue": 1780, "homepage": "https://dini-ag-kim.github.io/amb/20231019/", "keywords": [ "learning material", "learning materials", "open educational resource", "open educational resources", "schema" ], "license": "CC0-1.0", "name": "Allgemeines Metadatenprofil für Bildungsressourcen", "pattern": "^[a-z]\\w+$", "preferred_prefix": "kim.amb", "repository": "https://gitub.com/dini-ag-kim/amb", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://dini-ag-kim.github.io/amb/20231019/#$1" }, "kim.conditionsofaccess": { "contributor": { "github": "eilmiv", "name": "Martin Voigt", "orcid": "0000-0001-5556-838X" }, "description": "Identifiers describing conditions of access to an object (login) as defined by the [OER metadata group](https://oerworldmap.org/resource/urn:uuid:fd06253e-fe67-4910-b923-51db9d27e59f).", "example": "no_login", "example_decoys": [ "nope" ], "example_extras": [ "login" ], "github_request_issue": 1782, "homepage": "https://skohub.io/dini-ag-kim/value-lists/heads/main/w3id.org/kim/conditionsOfAccess/index.html", "keywords": [ "learning material", "learning materials", "open educational resource", "open educational resources" ], "license": "CC0-1.0", "name": "Conditions of Access", "pattern": "^login|no_login$", "preferred_prefix": "kim.conditionsofaccess", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://skohub.io/dini-ag-kim/value-lists/heads/main/w3id.org/kim/conditionsOfAccess/$1.html" }, "kim.educationlevel": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A controlled vocabulary for education levels, such as primary eduation, secondary education, and post-secondary education", "download_rdf": "https://github.com/dini-ag-kim/educationalLevel/raw/refs/heads/main/educationalLevel.ttl", "example": "6", "example_extras": [ "B" ], "homepage": "https://w3id.org/kim/educationalLevel/", "keywords": [ "education level", "educational resources", "educational science", "open educational resources" ], "mappings": { "tib": "educationallevel" }, "name": "KIM Education Level", "preferred_prefix": "kim.educationlevel", "repository": "https://github.com/dini-ag-kim/educationalLevel", "uri_format": "https://w3id.org/kim/educationalLevel/level_$1" }, "kim.esv": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This is a vocabulary for educational sectors as used in the OER World Map (https://oerworldmap.org)", "download_rdf": "https://github.com/dini-ag-kim/vocabs-edu/raw/refs/heads/master/sectors.ttl", "example": "earlyChildhood", "homepage": "https://w3id.org/kim/educationalLevel/", "name": "Educational Sectors Vocabulary", "preferred_prefix": "kim.esv", "repository": "https://github.com/dini-ag-kim/vocabs-edu", "uri_format": "https://w3id.org/class/sectors/$1" }, "kim.hcrt": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A controlled vocbualry of higher education resource types", "example": "simulation", "homepage": "https://w3id.org/kim/hcrt/scheme.html", "keywords": [ "educational resources", "educational science" ], "mappings": { "tib": "hcrt" }, "name": "Higher Education Resource Types", "preferred_prefix": "kim.hcrt", "rdf_uri_format": "https://w3id.org/kim/hcrt/$1", "repository": "https://github.com/dini-ag-kim/hcrt", "uri_format": "https://w3id.org/kim/hcrt/$1" }, "kim.hochschulfaechersystematik": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A classification of subjects in Hochschule (universities of applied sciences)", "download_rdf": "https://github.com/dini-ag-kim/hochschulfaechersystematik/raw/refs/heads/master/hochschulfaechersystematik.ttl", "example": "n2", "homepage": "https://w3id.org/kim/hochschulfaechersystematik/scheme", "keywords": [ "educational resources", "educational science" ], "mappings": { "tib": "hfs" }, "name": "German University Subject Classification System", "preferred_prefix": "kim.hochschulfaechersystematik", "rdf_uri_format": "https://w3id.org/kim/hochschulfaechersystematik/$1", "repository": "https://github.com/dini-ag-kim/hochschulfaechersystematik", "uri_format": "https://w3id.org/kim/hochschulfaechersystematik/$1" }, "kim.license": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A vocabulary describing licenses for data and code", "download_rdf": "https://github.com/dini-ag-kim/license/raw/refs/heads/main/license.ttl", "example": "nonCommercial", "homepage": "https://w3id.org/kim/license/", "keywords": [ "license" ], "name": "KIM License", "preferred_prefix": "kim.license", "rdf_uri_format": "https://w3id.org/kim/license/$1", "repository": "https://github.com/dini-ag-kim/license", "uri_format": "https://w3id.org/kim/license/$1" }, "kim.lp": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This ontology is a formal representation that captures the fundamental concepts and their relationships to one another in the field of curriculum design and implementation of the German school system.", "download_owl": "https://github.com/dini-ag-kim/school-curriculum-pg/raw/refs/heads/main/lp.owl", "example": "0000141", "homepage": "https://github.com/dini-ag-kim/school-curriculum-pg", "keywords": [ "ontology" ], "name": "Lehrplan Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "kim.lp", "repository": "https://github.com/dini-ag-kim/school-curriculum-pg", "uri_format": "https://w3id.org/lehrplan/ontology/LP_$1" }, "kim.schularten": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This SKOS vocabulary describes types of primary and secondary schools in Germany, such as Grundschule, Gymnasium, and Realschule. This does not include post-secondary education such as universities or hochschulen.", "download_rdf": "https://github.com/dini-ag-kim/schularten/raw/refs/heads/main/schularten.ttl", "example": "s02", "github_request_issue": 1626, "homepage": "https://github.com/dini-ag-kim/schularten", "keywords": [ "primary school type", "school type", "seconary school type" ], "license": "CC0-1.0", "name": "KIM German School Types", "preferred_prefix": "kim.schularten", "rdf_uri_format": "https://w3id.org/kim/schularten/$1", "repository": "https://github.com/dini-ag-kim/schularten", "uri_format": "https://w3id.org/kim/schularten/$1" }, "kim.schulfaecher": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A vocabulary describing subjects taught in German primary and secondary school (not university/hochschulen), such as German, math, and art.", "download_rdf": "https://github.com/dini-ag-kim/schulfaecher/raw/refs/heads/main/schulfaecher.ttl", "example": "s1000", "github_request_issue": 1626, "homepage": "https://github.com/dini-ag-kim/schulfaecher", "keywords": [ "discipline", "school subject", "subject" ], "name": "KIM School Subjects", "preferred_prefix": "kim.schulfaecher", "rdf_uri_format": "http://w3id.org/kim/schulfaecher/$1", "repository": "https://github.com/dini-ag-kim/schulfaecher", "uri_format": "http://w3id.org/kim/schulfaecher/$1" }, "kit.mtxx": { "description": "Objects of this class contain a self-bound collection of mass bearing particles.", "example": "002_xxx_xxx-a228d7e065dc45b4b5ab48876aab7228-vp", "homepage": "https://gitlab.com/linked-tribological-data/vocabulary-materials-tribology-lab-at-kit", "keywords": [ "material science", "nfdi4ing" ], "mappings": { "tib": "kitmtxx" }, "name": "Vocabulary of Materials Tribology Lab at KIT", "preferred_prefix": "kit.mtxx", "uri_format": "https://purls.helmholtz-metadaten.de/vp/kitmtxx-41732562-vp/$1" }, "knapsack": { "description": "KNApSAcK provides information on metabolites and the\ntaxonomic class with which they are associated.", "example": "C00000001", "homepage": "http://www.knapsackfamily.com/KNApSAcK/", "mappings": { "biocontext": "KNAPSACK", "integbio": "nbdc00545", "miriam": "knapsack", "n2t": "knapsack", "wikidata": "P2064" }, "name": "KNApSAcK", "pattern": "^C\\d{8}$", "preferred_prefix": "knapsack", "synonyms": [ "KNApSAcK" ], "uri_format": "http://www.knapsackfamily.com/knapsack_core/information.php?word=$1" }, "kpio": { "description": "The Key Performance Indicator module aims to model the metrics defined at the beginning of building renovation activities to monitor the conformance with typical requirements related to energy efficient buildings.", "example": "Goal", "homepage": "http://bimerr.iot.linkeddata.es/def/key-performance-indicator", "keywords": [ "civil engineering", "computer science", "digital planning and construction", "fid baudigital", "nfdi4ing" ], "mappings": { "tib": "kpi" }, "name": "Key Performance Indicator ontology", "preferred_prefix": "kpio", "uri_format": "http://bimerr.iot.linkeddata.es/def/key-performance-indicator#$1" }, "kupo": { "appears_in": [ "cl" ], "comment": "Website is down, now it redirects to something else that is not related", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "example": "0001009", "homepage": "http://www.kupkb.org/", "name": "Kidney and Urinary Pathway Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "kupo", "references": [ "https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-2-S2-S7" ] }, "kyinno": { "description": "Cell line collections (Providers)", "example": "KC-0979", "homepage": "https://www.kyinno.com/", "mappings": { "cellosaurus": "KYinno" }, "name": "KYinno cell lines", "preferred_prefix": "kyinno", "uri_format": "https://www.kyinno.com/?s=$1" }, "labo": { "contact": { "email": "paul.fabry@usherbrooke.ca", "github": "pfabry", "name": "Paul Fabry", "orcid": "0000-0002-3336-2476" }, "depends_on": [ "iao", "obi", "ogms", "omiabis", "omrse", "opmi" ], "description": "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents.", "download_owl": "http://purl.obolibrary.org/obo/labo.owl", "example": "0000124", "homepage": "https://github.com/OpenLHS/LABO", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "LABO", "bioportal": "LABO", "obofoundry": "labo", "ols": "labo", "ontobee": "LABO", "wikidata.entity": "Q81661673" }, "name": "clinical LABoratory Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "LABO", "publications": [ { "doi": "10.5281/zenodo.6522019", "title": "LABO: An ontology for laboratory test prescription and reporting", "year": 2019 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/LABO_$1", "repository": "https://github.com/OpenLHS/LABO", "uri_format": "http://purl.obolibrary.org/obo/LABO_$1", "version": "2021-06-08" }, "langual": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Langual stands for \"langua alimentaria\" or \"language of food\". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases", "example": "B2067", "github_request_issue": 507, "homepage": "https://www.langual.org", "name": "Langua aLimentaria Thesaurus", "pattern": "^B\\d+$", "preferred_prefix": "langual", "uri_format": "https://www.langual.org/langual_thesaurus.asp?termid=$1" }, "lattes": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "number for the Lattes Platform entry on the person or group. Relationship between entry and subject must be supported by a source.", "example": "0061106995455595", "homepage": "https://lattes.cnpq.br", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P1007" }, "name": "Lattes Platform number", "pattern": "^\\d{16}$", "preferred_prefix": "lattes", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://lattes.cnpq.br/$1" }, "lbctr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Lebanese Clinical Trials Registry is an online register of clinical trials being undertaken in Lebanon. It includes trials that target humans from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. (from homepage)", "example": "LBCTR2023015204", "homepage": "https://lbctr.moph.gov.lb/", "name": "Lebanon Clinical Trials Registry", "pattern": "^LBCTR\\d+$", "preferred_prefix": "lbctr", "references": [ "https://lbctr.moph.gov.lb/Trials/Details/5204" ] }, "lbo": { "contact": { "email": "caripark@iastate.edu", "github": "caripark", "name": "Carissa Park", "orcid": "0000-0002-2346-5201" }, "description": "A vocabulary for cattle, chicken, horse, pig, and sheep breeds.", "download_obo": "https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.obo", "download_owl": "https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.owl", "example": "0000487", "homepage": "http://bioportal.bioontology.org/ontologies/LBO", "keywords": [ "animal breeding", "animal husbandry", "genetics", "genomics", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "LBO", "agroportal": "LBO", "bioportal": "LBO", "fairsharing": "FAIRsharing.309v57", "ols": "lbo" }, "name": "Livestock Breed Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "lbo", "rdf_uri_format": "http://purl.obolibrary.org/obo/LBO_$1", "repository": "https://github.com/AnimalGenome/livestock-breed-ontology", "uri_format": "https://bioportal.bioontology.org/ontologies/LBO/?p=classes&conceptid=http://purl.obolibrary.org/obo/LBO_$1" }, "lccn": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "LCCN Permalinks are persistent URLs for bibliographic records in the LC Catalog and authority records in LC Authorities. These links are constructed using the record's LCCN (or Library of Congress Control Number), an identifier assigned by the Library of Congress to bibliographic and authority records. LCCN Permalinks are also available for citation records in the Handbook for Latin American Studies (HLAS). [from homepage]", "example": "2011488555", "github_request_issue": 1310, "homepage": "https://lccn.loc.gov", "name": "Library of Congress Control Number", "pattern": "^\\d+$", "preferred_prefix": "lccn", "uri_format": "https://lccn.loc.gov/$1" }, "lcsh": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Library of Congress Subject Headings (LCSH) has been actively maintained since 1898 to catalog materials held at the Library of Congress. (from homepage)", "example": "nb2018006591", "homepage": "https://id.loc.gov/authorities", "keywords": [ "subject agnostic" ], "mappings": { "bartoc": "454", "fairsharing": "FAIRsharing.d31795", "wikidata": "P244", "wikidata.entity": "Q17109002" }, "name": "Library of Congress Subject Headings", "pattern": "^\\w{1,2}\\d{8,10}$", "preferred_prefix": "lcsh", "providers": [ { "code": "subject", "description": "a subspace", "homepage": "https://id.loc.gov/authorities/subjects.html", "name": "LOC Subject", "uri_format": "http://id.loc.gov/authorities/subjects/$1" } ], "rdf_uri_format": "http://id.loc.gov/authorities/names/$1", "synonyms": [ "lcnaf", "lcnafid" ], "uri_format": "https://id.loc.gov/authorities/$1" }, "lcsh.genreforms": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A subset of Library of Congress (LOC) subject headings", "example": "gf2018026088", "homepage": "https://id.loc.gov/authorities", "name": "Library of Congress Subject Headings - Genre Forms", "part_of": "lcsh", "preferred_prefix": "lcsh.genreforms", "uri_format": "http://id.loc.gov/authorities/genreForms/$1" }, "ldp": { "description": "A set of best practices and simple approach for a read-write Linked Data architecture, based on HTTP access to web resources that describe their state using the RDF data model.", "example": "Resource", "homepage": "http://www.w3.org/TR/ldp/", "keywords": [ "api" ], "mappings": { "lov": "ldp", "zazuko": "ldp" }, "name": "Linked Data Platform Vocabulary", "preferred_prefix": "ldp" }, "leafsnap": { "description": "identifier for a tree species of the United States and Canada on the Leafsnap electronic field guide", "example": "Amelanchier laevis", "homepage": "http://leafsnap.com/", "mappings": { "wikidata": "P10538" }, "name": "Leafsnap", "preferred_prefix": "leafsnap", "uri_format": "http://leafsnap.com/species/$1/" }, "lei": { "description": "Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland.", "example": "HWUPKR0MPOU8FGXBT394", "homepage": "https://www.gleif.org/", "mappings": { "miriam": "lei", "n2t": "lei" }, "name": "Global LEI Index", "pattern": "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$", "preferred_prefix": "lei", "uri_format": "https://www.gleif.org/lei/$1" }, "lepao": { "contact": { "email": "lagonzalezmo@unal.edu.co", "github": "luis-gonzalez-m", "name": "Luis A. Gonzalez-Montana", "orcid": "0000-0002-9136-9932" }, "depends_on": [ "aism", "bfo", "bspo", "caro", "pato", "ro", "uberon" ], "description": "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research.", "download_obo": "http://purl.obolibrary.org/obo/lepao.obo", "download_owl": "http://purl.obolibrary.org/obo/lepao.owl", "example": "0000005", "homepage": "https://github.com/insect-morphology/lepao", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "LEPAO", "bioportal": "LEPAO", "obofoundry": "lepao", "ols": "lepao", "ontobee": "LEPAO", "wikidata.entity": "Q113012667" }, "name": "Lepidoptera Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "LEPAO", "rdf_uri_format": "http://purl.obolibrary.org/obo/LEPAO_$1", "repository": "https://github.com/insect-morphology/lepao", "uri_format": "http://purl.obolibrary.org/obo/LEPAO_$1", "version": "2023-02-18" }, "lexvo.ontology": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The data model underlying lexvo", "download_owl": "http://lexvo.org/ontology", "example": "Language", "homepage": "http://lexvo.org", "keywords": [ "ontology", "vocabularies" ], "mappings": { "lov": "lvont", "zazuko": "lvont" }, "name": "Lexvo Ontology", "preferred_prefix": "lexvo.ontology", "synonyms": [ "lvont" ], "uri_format": "http://lexvo.org/ontology#$1" }, "lgai.cede": { "description": "LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR).", "example": "LGCEDe-S-000002244", "homepage": "https://www.lgresearch.ai", "mappings": { "miriam": "lgai.cede" }, "name": "LG Chemical Entity Detection Dataset (LGCEDe)", "pattern": "^LGCEDe-S-\\d{9}$", "preferred_prefix": "lgai.cede", "uri_format": "https://s3.us-east-2.amazonaws.com/lg.cede/$1" }, "lgic": { "comment": "Website is gone", "deprecated": true, "description": "The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available.", "example": "5HT3Arano", "homepage": "https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php", "keywords": [ "gene", "protein", "sequence" ], "mappings": { "biocontext": "LGIC", "miriam": "lgic", "n2t": "lgic", "prefixcommons": "lgicdb" }, "name": "Ligand-Gated Ion Channel database", "pattern": "^\\w+$", "preferred_prefix": "lgic", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/lgicdb:$1" } ], "publications": [ { "doi": "10.1093/nar/27.1.340", "pmc": "PMC148177", "pubmed": "9847222", "title": "The Ligand Gated Ion Channel Database", "year": 1999 } ], "uri_format": "https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php" }, "licebase": { "contact": { "email": "Inge.Jonassen@uib.no", "name": "Inge Jonassen", "orcid": "0000-0003-4110-0748" }, "description": "Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects.", "example": "EMLSAT00000003403", "homepage": "https://licebase.org", "keywords": [ "life science" ], "mappings": { "biocontext": "LICEBASE", "fairsharing": "FAIRsharing.c7w81a", "integbio": "nbdc02217", "miriam": "licebase", "n2t": "licebase", "re3data": "r3d100013547" }, "name": "LiceBase", "pattern": "^[A-Za-z0-9\\-\\/]+$", "preferred_prefix": "licebase", "uri_format": "https://licebase.org/?q=$1" }, "lifestylefactors": { "contact": { "email": "lars.juhl.jensen@cpr.ku.dk", "name": "Lars Juhl Jensen" }, "description": "In this ontology, we defined nine distinct categories that encompass various aspects of lifestyle factors (LSFs), creating a unified Lifestyle Factors Ontology (LSFO) across these categories. Within the context of lifestyle, we have identified nine categories that can collectively describe all LSFs, namely: 1-Nutrition, a category that covers different branches such as dietary habits, food groups, food processing and preparation, macronutrients, and micronutrients, among others. 2-Socioeconomic factors, which includes social and economic conditions such as income, wealth, education and socioeconomic status. 3-Environmental exposures, includes exposure to various environmental factors, such as air pollution, water quality, and workplace hazards, that can impact an individual’s health. 4-Substance use, covers concepts such as smoking, as well as illicit drug use. 5-Physical activities, includes regular exercise and physically demanding activities like leisure time, occupational, and household physical activities. 6-Non-physical leisure time activities, describes any activity an individual might engage in during their free time that is not a physical activity. 7-Personal care products and cosmetic procedures, covers activities related to hygiene, use of cosmetic and cleaning products as well as invasive procedures that people undergo to improve their appearance, such as cosmetic surgery. 8-Sleep, covers sleep quality, stages, and habits. 9-Mental health practices, includes the behaviors and habits related to maintaining good mental health and emotional well-being such as meditation, and psychotherapy.", "download_owl": "https://raw.githubusercontent.com/EsmaeilNourani/Lifestyle-factors-ontology/main/LSFO/owl/LSFO.owl", "example": "0000015", "homepage": "https://bioportal.bioontology.org/ontologies/LSFO", "keywords": [ "ontology" ], "mappings": { "bioportal": "LSFO", "ols": "lifestylefactors" }, "name": "Lifestyle Factors Ontology", "preferred_prefix": "lifestylefactors", "uri_format": "http://purl.obolibrary.org/obo/LFID_$1" }, "ligandbook": { "description": "Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community.", "example": "785", "homepage": "https://ligandbook.org/", "mappings": { "miriam": "ligandbook", "n2t": "ligandbook" }, "name": "LigandBook", "pattern": "^[0-9]+$", "preferred_prefix": "ligandbook", "uri_format": "https://ligandbook.org/package/$1" }, "ligandbox": { "description": "LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds.", "example": "D00001", "homepage": "http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en", "mappings": { "biocontext": "LIGANDBOX", "integbio": "nbdc00551", "miriam": "ligandbox", "n2t": "ligandbox" }, "name": "LigandBox", "pattern": "^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$", "preferred_prefix": "ligandbox", "uri_format": "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1" }, "ligandexpo": { "contact": { "email": "jwest@rcsb.rutgers.edu", "name": "John Westbrook", "orcid": "0000-0002-6686-5475" }, "description": "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.", "example": "ABC", "homepage": "http://ligand-depot.rutgers.edu/index.html", "keywords": [ "chemical", "interaction", "life science", "nucleic acid", "protein", "structure" ], "mappings": { "biocontext": "LIGANDEXPO", "fairsharing": "FAIRsharing.2ma4gq", "integbio": "nbdc01864", "miriam": "ligandexpo", "n2t": "ligandexpo", "pathguide": "154", "prefixcommons": "ligandexpo" }, "name": "Ligand Expo", "pattern": "^(\\w){3}$", "preferred_prefix": "ligandexpo", "providers": [ { "code": "", "description": "Ligand Expo at Rutgers", "homepage": "http://ligand-expo.rcsb.org/", "name": "Ligand Expo at Rutgers", "uri_format": "http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/ligandexpo:$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/bth214", "pubmed": "15059838", "title": "Ligand Depot: a data warehouse for ligands bound to macromolecules", "year": 2004 } ], "uri_format": "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid" }, "ligea": { "comment": "This might just be a provider for CCLE", "description": "Polymorphism and mutation databases", "example": "CCLE_867", "homepage": "http://hpc-bioinformatics.cineca.it/fusion/main", "mappings": { "cellosaurus": "LiGeA" }, "name": "Cancer cell LInes GEne fusions portAl", "preferred_prefix": "ligea", "uri_format": "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1" }, "limore": { "description": "Cell line databases/resources", "example": "Li7", "homepage": "https://www.picb.ac.cn/limore/home", "mappings": { "cellosaurus": "LIMORE" }, "name": "Liver Cancer Model Repository", "preferred_prefix": "limore", "uri_format": "https://www.picb.ac.cn/limore/cellLines/single?para=$1" }, "lincs.cell": { "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.", "example": "LCL-2085", "homepage": "http://lincsportal.ccs.miami.edu/cells/", "mappings": { "biocontext": "LINCS.CELL", "cellosaurus": "LINCS_LDP", "miriam": "lincs.cell", "n2t": "lincs.cell" }, "name": "LINCS Cell", "pattern": "^(LCL|LDC|ES|LSC|LPC)-\\d+$", "preferred_prefix": "lincs.cell", "synonyms": [ "LINCS_LDP" ], "uri_format": "http://lincsportal.ccs.miami.edu/cells/#/view/$1" }, "lincs.data": { "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level).", "example": "LDS-1110", "homepage": "http://lincsportal.ccs.miami.edu/datasets/", "mappings": { "biocontext": "LINCS.DATA", "miriam": "lincs.data", "n2t": "lincs.data" }, "name": "LINCS Data", "pattern": "^[EL]D[SG]-\\d+$", "preferred_prefix": "lincs.data", "providers": [ { "code": "omicsdi", "description": "Lincs through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "Lincs through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/lincs/$1" } ], "uri_format": "http://lincsportal.ccs.miami.edu/datasets/#/view/$1" }, "lincs.protein": { "description": "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins.", "example": "200282", "homepage": "http://lincs.hms.harvard.edu/db/proteins/", "mappings": { "biocontext": "LINCS.PROTEIN", "miriam": "lincs.protein", "n2t": "lincs.protein" }, "name": "LINCS Protein", "pattern": "^\\d+$", "preferred_prefix": "lincs.protein", "uri_format": "https://lincs.hms.harvard.edu/db/proteins/$1" }, "lincs.smallmolecule": { "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC).", "example": "LSM-6306", "homepage": "http://lincsportal.ccs.miami.edu/SmallMolecules/", "mappings": { "biocontext": "LINCS.SMALLMOLECULE", "miriam": "lincs.smallmolecule", "n2t": "lincs.smallmolecule" }, "name": "LINCS Small Molecule", "pattern": "^LSM-\\d+$", "preferred_prefix": "lincs.smallmolecule", "synonyms": [ "lincs" ], "uri_format": "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1" }, "linguist": { "description": "Registry of programming languages for the Linguist program for detecting and highlighting programming languages.", "example": "Python", "homepage": "https://github.com/github/linguist", "mappings": { "miriam": "linguist" }, "name": "Linguist", "pattern": "^[a-zA-Z0-9 +#'*]+$", "preferred_prefix": "linguist", "repository": "https://github.com/github/linguist", "uri_format": "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1" }, "linguist.gold": { "comment": "This resource has been deprecated and was last released in 2010. The homepage links to a zip folder that includes an OWL artifact, but it doesn't follow any typical standards. The ontology browser is not perfect, it only works for classes.", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "example": "Term", "github_request_issue": 1310, "homepage": "https://linguistlist.org/gold/", "name": "Genderal Ontology for Linguistic Description", "preferred_prefix": "linguist.gold", "rdf_uri_format": "http://purl.org/linguistics/gold/$1", "uri_format": "https://lambdamusic.github.io/ontospy-examples/gold-2010owl/class-gold$1.html" }, "linkedin": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for a person, on the LinkedIn website", "example": "deborahlehr", "homepage": "https://www.linkedin.com", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P6634" }, "name": "LinkedIn personal profile ID", "pattern": "^[\\w0-9\\-&_'’\\.]+$", "preferred_prefix": "linkedin", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://www.linkedin.com/in/$1" }, "linkml": { "comment": "Closes #508", "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks.", "example": "SchemaDefinition", "github_request_issue": 512, "homepage": "https://linkml.io/linkml-model/docs/SchemaDefinition/", "keywords": [ "data integration", "ontology and terminology" ], "mappings": { "biolink": "linkml", "fairsharing": "FAIRsharing.cb7086" }, "name": "LinkML", "preferred_prefix": "linkml", "publications": [ { "doi": "10.5281/zenodo.5598314", "title": "linkml/linkml-model: v1.5.2", "year": 2023 } ], "repository": "https://github.com/linkml/", "twitter": "linkml_data", "uri_format": "https://w3id.org/linkml/$1" }, "lipidbank": { "contact": { "email": "e-yasugi@umin.ac.jp", "name": "Etsuko Yasugi", "orcid": "0000-0003-1898-4426" }, "deprecated": true, "description": "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.", "example": "BBA0001", "homepage": "http://lipidbank.jp/index.html", "keywords": [ "life science", "lipid", "molecule", "structure" ], "mappings": { "biocontext": "LIPIDBANK", "edam": "2665", "fairsharing": "FAIRsharing.bdn9br", "integbio": "nbdc00126", "miriam": "lipidbank", "n2t": "lipidbank", "prefixcommons": "lipidbank" }, "name": "LipidBank", "pattern": "^\\w+\\d+$", "preferred_prefix": "lipidbank", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/lipidbank:$1" } ], "publications": [ { "pubmed": "12058481", "title": "[LIPIDBANK for Web, the newly developed lipid database]", "year": 2002 } ], "uri_format": "https://lipidbank.jp/data/$1.cdx" }, "lipidmaps": { "contact": { "email": "edennis@ucsd.edu", "name": "Edward A Dennis", "orcid": "0000-0003-3738-3140" }, "description": "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.", "example": "LMPR0102010012", "homepage": "https://lipidmaps.org", "keywords": [ "biomedical science", "endocrinology", "life science", "lipid", "structure", "systems biology", "taxonomy" ], "logo": "https://www.lipidmaps.org/assets/images/logos/lipid_maps_transparent_sm.png", "mappings": { "biocontext": "LIPIDMAPS", "cheminf": "000564", "edam": "2625", "fairsharing": "FAIRsharing.cpneh8", "integbio": "nbdc02669", "miriam": "lipidmaps", "n2t": "lipidmaps", "ols": "lipidmaps", "pathguide": "503", "prefixcommons": "lipidmaps", "re3data": "r3d100012315", "togoid": "Lipidmaps", "wikidata": "P2063" }, "name": "LIPID MAPS", "pattern": "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$", "preferred_prefix": "lipidmaps", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/lipidmaps:$1" }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/lipidmaps/$1" } ], "publications": [ { "doi": "10.1194/jlr.r800095-jlr200", "pmc": "PMC2674711", "pubmed": "19098281", "title": "Update of the LIPID MAPS comprehensive classification system for lipids", "year": 2008 }, { "doi": "10.1093/nar/gkm324", "pmc": "PMC1933166", "pubmed": "17584797", "title": "LIPID MAPS online tools for lipid research", "year": 2007 }, { "doi": "10.1093/nar/gkl838", "pmc": "PMC1669719", "pubmed": "17098933", "title": "LMSD: LIPID MAPS structure database", "year": 2006 }, { "doi": "10.1194/jlr.e400004-jlr200", "pubmed": "15722563", "title": "A comprehensive classification system for lipids", "year": 2005 }, { "doi": "10.1194/jlr.R800095-JLR200", "title": "Update of the LIPID MAPS comprehensive classification system for lipids." } ], "synonyms": [ "LIPID MAPS", "LIPID_MAPS_class", "LIPID_MAPS_instance" ], "twitter": "lipidmaps", "uri_format": "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1" }, "lipro": { "contact": { "email": "bakerc@unb.ca", "name": "Christopher Baker", "orcid": "0000-0003-4004-6479" }, "deprecated": true, "description": "An ontology representation of the LIPIDMAPS nomenclature classification.", "download_owl": "http://aber-owl.net/media/ontologies/LIPRO/4/lipro.owl", "keywords": [ "obo", "ontology" ], "mappings": { "aberowl": "LIPRO", "biocontext": "LIPRO", "bioportal": "LIPRO", "obofoundry": "lipro", "wikidata.entity": "Q114677891" }, "name": "Lipid Ontology", "preferred_prefix": "LIPRO", "rdf_uri_format": "http://purl.obolibrary.org/obo/LIPRO_$1", "uri_format": "http://purl.obolibrary.org/obo/LIPRO_$1" }, "listdb.onto": { "description": "This is an ontology draft for the description of metadata of traffic observations, in particular video recordings of road traffic. The traffic observations are e.g. used to design test scenarios for the effectiveness assessment of automated driving systems. \n\nThe ontology draft resulted from an exchange of the Chair of Automobile Engineering at TU Dresden (https://tu-dresden.de/bu/verkehr/iad/kft?set_language=en) with representatives of NFDI4Ing (Community Cluster 4.4, Archetype Golo, Base Services S3) and FID move in NFDI4Ing's Special Interest Group \"Metadata and Ontologies\". An essential part of that meeting was the presentation of the reseaerch data management approach at the Chair of Automobile Engineering, in particular its tooling, its metadata approach and its workflow.\n\nTraffic observations are managed with ListDB, a solution combined of a SharePoint instance and a virtual machine for data servicing . An accompanying Codebook defines relevant metadata that should be provided for each road traffic observation. ListDB is currently used internally within TU Dresden, but is intentended to be hosted publicly until spring 2023. \n\nThe ontology draft is, in fact, based on the Codebook (v. 1.0.0.) and an attempt to make a machine-readable document out of it, applying standards from the Semantic Web Stack (RDF(S) and OWL). The draft is constantly being developed further in this context.", "example": "C0000000001", "homepage": "https://w3id.org/listdb/onto", "keywords": [ "fid move", "nfdi4ing", "traffic engineering" ], "mappings": { "tib": "listdb" }, "name": "ListDB Ontology", "preferred_prefix": "listdb.onto", "repository": "https://gitlab.com/listdb", "uri_format": "https://w3id.org/listdb/onto#$1" }, "lncbook": { "description": "LncBook accommodates a high-quality collection of human lncRNA genes and transcripts, and incorporates their abundant annotations at different omics levels, thereby enabling users to decipher functional signatures of lncRNAs in human diseases and different biological contexts.\n\n", "example": "HSALNG0006197", "homepage": "https://ngdc.cncb.ac.cn/?lang=en", "mappings": { "integbio": "nbdc02541", "miriam": "lncbook" }, "name": "LncBook", "pattern": "^HSALNG\\d{7}$", "preferred_prefix": "lncbook", "uri_format": "https://ngdc.cncb.ac.cn/lncbook/gene?geneid=$1" }, "lncipedia": { "contact": { "email": "pieter.mestdagh@ugent.be", "github": "OncoRNALab", "name": "Pieter Mestdagh", "orcid": "0000-0001-7821-9684" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A comprehensive compendium of human long non-coding RNAs", "example": "SNHG3", "homepage": "https://lncipedia.org", "keywords": [ "life science" ], "mappings": { "fairsharing": "FAIRsharing.84c1a7" }, "name": "LNCipedia", "preferred_prefix": "lncipedia", "publications": [ { "doi": "10.1093/nar/gkv295", "pmc": "PMC4417186", "pubmed": "25829178", "title": "An update on LNCipedia: a database for annotated human lncRNA sequences", "year": 2015 }, { "doi": "10.1093/nar/gku1060", "pmc": "PMC4383901", "pubmed": "25378313", "title": "An update on LNCipedia: a database for annotated human lncRNA sequences", "year": 2014 }, { "doi": "10.1093/nar/gks915", "pmc": "PMC3531107", "pubmed": "23042674", "title": "LNCipedia: a database for annotated human lncRNA transcript sequences and structures", "year": 2012 } ] }, "loc.fdd": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The digital content format descriptions accessible here provide specific information about individual formats and their characteristics. Each description provides moderately detailed information and citations. Planned for inclusion are a wide variety of formats: file formats, file-format classes, bitstream structures and encodings, and the mechanisms used to compress files or bitstreams. Inclusion of a description for a format does not imply that the format is preferred or acceptable for Library of Congress collections. [from homepage]", "example": "fdd000613", "github_request_issue": 1725, "homepage": "https://www.loc.gov/preservation/digital/formats/fdd/", "keywords": [ "file format", "media type" ], "name": "Library of Congress Format Description Document", "pattern": "^fdd\\d+$", "preferred_prefix": "loc.fdd", "providers": [ { "code": "xml", "description": "LOC FDD XML", "homepage": "https://www.loc.gov/preservation/digital/formats/fddXML/fddXMLreadme.txt", "name": "LOC FDD XML", "uri_format": "https://www.loc.gov/preservation/digital/formats/fddXML/$1" } ], "references": [ "https://www.loc.gov/preservation/digital/formats/fddXML/fddXMLreadme.txt" ], "uri_format": "https://www.loc.gov/preservation/digital/formats/fdd/$1" }, "loc.relator": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Relator terms and their associated codes designate the relationship between an agent and a bibliographic resource.", "download_rdf": "https://id.loc.gov/download/vocabulary/relators.skosrdf.ttl.gz", "example": "arc", "homepage": "http://id.loc.gov/vocabulary/relators", "name": "Library of Congress Relator", "preferred_prefix": "loc.relator", "rdf_uri_format": "http://id.loc.gov/vocabulary/relators/$1", "uri_format": "https://id.loc.gov/vocabulary/relators/$1" }, "loc.resourcetype": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "github": "petrasteiner", "name": "Petra C. Steiner", "orcid": "0000-0001-8997-2620" } ], "description": "A controlled vocabulary of media resources, such as audio, cartographic, manuscript, multimedia, etc.", "download_rdf": "http://id.loc.gov/vocabulary/resourceTypes.skos.rdf", "example": "dig", "homepage": "https://id.loc.gov/vocabulary/resourceTypes.html", "keywords": [ "data classification" ], "name": "Library of Congress Resource Types Scheme", "preferred_prefix": "loc.resourcetype", "uri_format": "http://id.loc.gov/vocabulary/resourceTypes/$1" }, "locn": { "description": "The ISA Programme Location Core Vocabulary provides a minimum set of classes and properties for describing any place in terms of its name, address or geometry. The vocabulary is specifically designed to aid the publication of data that is interoperable with EU INSPIRE Directive.", "example": "Address", "homepage": "http://www.w3.org/ns/locn", "keywords": [ "geography", "geometry" ], "mappings": { "lov": "locn", "zazuko": "locn" }, "name": "ISA Programme Location Core Vocabulary", "preferred_prefix": "locn" }, "log": { "description": "Une ontologie \"historique\" utilisée par l'outil en ligne de commande cwm, au temps des balbutiements du web sémantique (~ 2000 - 2003 ?)", "example": "dtlit", "homepage": "http://www.w3.org/2000/10/swap/doc/CwmBuiltins", "keywords": [ "rdf" ], "mappings": { "lov": "log", "zazuko": "log" }, "name": "SWAP Logic Ontology", "preferred_prefix": "log" }, "loggerhead": { "contact": { "email": "peteremidford@yahoo.com", "name": "Peter Midford", "orcid": "0000-0001-6512-3296" }, "deprecated": true, "homepage": "http://www.mesquiteproject.org/ontology/Loggerhead/index.html", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "LOGGERHEAD", "obofoundry": "loggerhead", "wikidata.entity": "Q114677892" }, "name": "Loggerhead nesting", "preferred_prefix": "LOGGERHEAD", "rdf_uri_format": "http://purl.obolibrary.org/obo/LOGGERHEAD_$1", "uri_format": "http://purl.obolibrary.org/obo/LOGGERHEAD_$1" }, "loinc": { "contact": { "email": "loinc@regenstrief.org", "name": "LOINC Support" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The international standard for identifying health measurements, observations, and documents.", "example": "LL379-9", "homepage": "https://loinc.org/", "keywords": [ "assay", "biomedical science", "diagnosis", "genetic disorder", "genetic polymorphism", "life science", "ontology", "phenotype", "preclinical studies" ], "license": "https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf", "mappings": { "aberowl": "LOINC", "bartoc": "1897", "biolink": "LOINC", "bioportal": "LOINC", "fairsharing": "FAIRsharing.2mk2zb", "hl7": "2.16.840.1.113883.6.1", "wikidata": "P4338", "wikidata.entity": "Q502480" }, "name": "Logical Observation Identifiers Names and Codes", "pattern": "^(\\d|\\w)+-\\d$", "preferred_prefix": "loinc", "publications": [ { "doi": "10.1016/s1386-5056(98)00089-6", "pubmed": "9749897", "title": "Combining laboratory data sets from multiple institutions using the logical observation identifier names and codes (LOINC)", "year": 1998 }, { "doi": "10.1093/jamia/ocu012", "pmc": "PMC5566197", "pubmed": "25656513", "title": "Supporting interoperability of genetic data with LOINC", "year": 2015 }, { "doi": "10.1016/j.jbi.2012.01.005", "pmc": "PMC3376691", "pubmed": "22285984", "title": "Enabling international adoption of LOINC through translation", "year": 2012 } ], "rdf_uri_format": "http://loinc.org/rdf/$1", "synonyms": [ "LNC" ], "twitter": "LOINC", "uri_format": "https://loinc.org/$1" }, "lonza": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Contains information about cells and data sheets related to transfection.", "example": "968", "homepage": "https://knowledge.lonza.com", "mappings": { "cellosaurus": "Lonza" }, "name": "Lonza", "pattern": "^\\d+$", "preferred_prefix": "lonza", "uri_format": "https://knowledge.lonza.com/cell?id=$1" }, "loop": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for a person, in the Loop database of researcher impact", "example": "1859", "homepage": "https://loop.frontiersin.org/", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P2798" }, "name": "Loop ID", "pattern": "^[1-9]\\d*$", "preferred_prefix": "loop", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://loop.frontiersin.org/people/$1/overview" }, "loqate": { "contact": { "email": "maya.schuldiner@weizmann.ac.il", "github": "Maya-Schuldiner-lab", "name": "Maya Schuldiner", "orcid": "0000-0001-9947-115X" }, "description": "The data presented here is a result of systematically tracking the localization and abundance of 5330 yeast proteins at single-cell resolution under three different stress conditions (DTT, H2O2 and nitrogen starvation) using the GFP-tagged yeast library", "example": "1001", "homepage": "http://www.weizmann.ac.il/molgen/loqate/", "mappings": { "prefixcommons": "loqate" }, "name": "The localization and quantitation atlas of the yeast proteome", "preferred_prefix": "loqate", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/loqate:$1" } ], "publications": [ { "doi": "10.1093/nar/gkt933", "pmc": "PMC3965041", "pubmed": "24150937", "title": "LoQAtE--Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast", "year": 2013 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.weizmann.ac.il/molgen/loqate/gene/view/$1" }, "lotus": { "comment": "IDs are actually leading to the structural part of LOTUS only, which might change in the future. Will adapt the regexp in case.", "contact": { "email": "adriano.rutz@ik.me", "github": "adafede", "name": "Adriano Rutz", "orcid": "0000-0003-0443-9902" }, "contributor": { "email": "adriano.rutz@ik.me", "github": "adafede", "name": "Adriano Rutz", "orcid": "0000-0003-0443-9902" }, "description": "LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry.", "example": "LTS0004651", "github_request_issue": 222, "homepage": "https://lotus.naturalproducts.net", "keywords": [ "chemistry", "drugs", "metabolites" ], "logo": "https://upload.wikimedia.org/wikipedia/commons/6/64/Lotus_initiative_logo.svg", "mappings": { "wikidata.entity": "Q104225190" }, "name": "LOTUS Initiative for Open Natural Products Research", "pattern": "^LTS\\d{7}$", "preferred_prefix": "lotus", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://lotus.naturalproducts.net/compound/lotus_id/$1" }, "lpt": { "contact": { "email": "caripark@iastate.edu", "github": "caripark", "name": "Carissa Park", "orcid": "0000-0002-2346-5201" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.", "download_obo": "https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.obo", "download_owl": "https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.owl", "example": "0000156", "homepage": "https://github.com/AnimalGenome/livestock-product-trait-ontology", "keywords": [ "animal husbandry", "ontology", "phenotype" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "LPT", "agroportal": "LPT", "biocontext": "LPT", "bioportal": "LPT", "fairsharing": "FAIRsharing.g78mbm" }, "name": "Livestock Product Trait Ontology", "pattern": "^\\d+$", "preferred_prefix": "lpt", "repository": "https://github.com/AnimalGenome/livestock-product-trait-ontology", "uri_format": "http://purl.obolibrary.org/obo/LPT_$1" }, "lrg": { "banana": "LRG", "banana_peel": "_", "description": "A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI.", "example": "1", "homepage": "http://www.lrg-sequence.org/", "mappings": { "biocontext": "LRG", "hl7": "2.16.840.1.113883.6.283", "integbio": "nbdc02566", "miriam": "lrg", "n2t": "lrg", "togoid": "Lrg" }, "name": "Locus Reference Genomic", "pattern": "^\\d+$", "preferred_prefix": "lrg", "providers": [ { "code": "", "description": "Locus Reference Genomic through Ensembl", "homepage": "http://www.ensembl.org/", "name": "Locus Reference Genomic through Ensembl", "uri_format": "http://www.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1" }, { "code": "", "description": "Locus Reference Genomic through Ensembl mirror (asia)", "homepage": "http://asia.ensembl.org/", "name": "Locus Reference Genomic through Ensembl mirror (asia)", "uri_format": "http://asia.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1" }, { "code": "", "description": "Locus Reference Genomic through Ensembl mirror (US east)", "homepage": "http://useast.ensembl.org/", "name": "Locus Reference Genomic through Ensembl mirror (US east)", "uri_format": "http://useast.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1" } ], "uri_format": "http://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml" }, "lrmi": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Learning Resource Metadata Innovation (LRMI) specification is a collection of classes and properties for markup and description of educational resources. The specification builds on the extensive vocabulary provided by Schema.org and other standards. LRMI terms not included in schema.org may nevertheless be used to augment and enrich Schema.org markup. (from homepage)", "download_rdf": "https://www.dublincore.org/specifications/lrmi/lrmi_terms/2022-06-14/lrmi-terms.ttl", "example": "AlignmentObject", "github_request_issue": 1677, "homepage": "https://www.dublincore.org/specifications/lrmi/lrmi_terms/2022-06-14/", "keywords": [ "education", "educational resource", "open educational resources" ], "license": "CC-BY-4.0", "name": "Learning Resource Metadata Innovation Terms", "preferred_prefix": "lrmi", "rdf_uri_format": "http://purl.org/dcx/lrmi-terms/$1", "uri_format": "http://purl.org/dcx/lrmi-terms/$1" }, "lrmi.alignmenttype": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A concept scheme that defines the types of relationships between a learning resource and a node in an educational framework.", "example": "assesses", "github_request_issue": 1750, "homepage": "https://www.dublincore.org/specifications/lrmi/concept_schemes/alignmentType/", "keywords": [ "learning resource", "open educational resource" ], "license": "CC-BY-4.0", "name": "LRMI Alignment Type Vocabulary", "preferred_prefix": "lrmi.alignmenttype", "repository": "https://github.com/dcmi/lrmi", "uri_format": "http://purl.org/dcx/lrmi-vocabs/alignmentType/$1" }, "lrmi.educationalaudiencerole": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A concept scheme that defines the primary or intended roles of the audience (beneficiary) of the resource being described.", "example": "mentor", "github_request_issue": 1750, "homepage": "https://www.dublincore.org/specifications/lrmi/concept_schemes/alignmentType/", "keywords": [ "learning resource", "open educational resource" ], "license": "CC-BY-4.0", "name": "LRMI Educational Audience Role Vocabulary", "preferred_prefix": "lrmi.educationalaudiencerole", "repository": "https://github.com/dcmi/lrmi", "uri_format": "http://purl.org/dcx/lrmi-vocabs/educationalAudienceRole/$1" }, "lrmi.eduse": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A concept scheme that enumerates the educational uses of a learning resource.", "example": "instruction", "github_request_issue": 1750, "homepage": "https://www.dublincore.org/specifications/lrmi/concept_schemes/educationalUse/", "keywords": [ "learning resource", "open educational resource" ], "license": "CC-BY-4.0", "name": "LRMI Educational Use Vocabulary", "preferred_prefix": "lrmi.eduse", "repository": "https://github.com/dcmi/lrmi", "uri_format": "http://purl.org/dcx/lrmi-vocabs/educationalUse/$1" }, "lrmi.interact": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A concept scheme that defines the predominate interact mode of the learning resource being described.", "example": "active", "github_request_issue": 1750, "homepage": "https://www.dublincore.org/specifications/lrmi/concept_schemes/interactivityType/", "keywords": [ "learning resource", "open educational resource" ], "license": "CC-BY-4.0", "name": "LRMI Interact Type Vocabulary", "preferred_prefix": "lrmi.interact", "repository": "https://github.com/dcmi/lrmi", "uri_format": "http://purl.org/dcx/lrmi-vocabs/interactivityType/$1" }, "lrmi.resourcetype": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A top-level concept scheme that enumerates different types of Learning Resource, designed to supplement existing more generic resource type schemes and which can support local extensions.", "example": "activityPlan", "github_request_issue": 1750, "homepage": "https://www.dublincore.org/specifications/lrmi/concept_schemes/learningResourceType/", "keywords": [ "learning resource", "open educational resource" ], "license": "CC-BY-4.0", "name": "LRMI Learning Resource Type Concept Scheme", "preferred_prefix": "lrmi.resourcetype", "repository": "https://github.com/dcmi/lrmi", "uri_format": "http://purl.org/dcx/lrmi-vocabs/learningResourceType/$1" }, "lspci": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)", "example": "1", "homepage": "https://labsyspharm.github.io/lspci/", "keywords": [ "chemistry", "drugs", "metabolites" ], "name": "Laboratory of Systems Pharmacology Compound", "pattern": "^\\d+$", "preferred_prefix": "lspci", "uri_format": "https://labsyspharm.github.io/lspci/$1" }, "lter": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Ecological terms", "example": "182", "homepage": "https://vocab.lternet.edu/vocab/vocab/index.php", "name": "Long Term Ecological Research Controlled Vocabulary", "pattern": "^\\d+$", "preferred_prefix": "lter", "uri_format": "https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1" }, "lw": { "description": "The LifeWatch Metadata Catalogues plays a crucial role in managing metadata for digital objects, including Datasets, Services, Workflows and Virtual Research Environments. This catalogue serves as the central repository, ensuring that resources are accessible and reusable by stakeholders.", "example": "6e3b1371-59d7-481a-9db4-cd0d0de98436", "homepage": "https://metadatacatalogue.lifewatch.eu/", "mappings": { "miriam": "lw" }, "name": "LifeWatch Metadata Catalogue", "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "preferred_prefix": "lw", "uri_format": "https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/$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_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", "digital planning and construction", "engineering", "engineering science", "fid baudigital", "metadata", "nfdi4cat", "nfdi4ing" ], "license": "CC-BY-4.0", "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaWNHIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--6435da59153a976c6b09d30ac0ee96286c50a32c/Logo.png?disposition=inline", "mappings": { "bartoc": "20402", "fairsharing": "FAIRsharing.f8b3ec", "lov": "m4i", "miriam": "m4i", "tib": "m4i", "wikidata.entity": "Q111516803", "zazuko": "m4i" }, "mastodon": "nfdi4ing@nfdi.social", "name": "Metadata4Ing", "owners": [ { "name": "Nationale Forschungsdateninfrastruktur", "partnered": false, "ror": "05qj6w324" } ], "pattern": "^[A-Za-z_0-9]*$", "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#$1" }, "ma": { "banana": "MA", "contact": { "email": "Terry.Hayamizu@jax.org", "github": "tfhayamizu", "name": "Terry Hayamizu", "orcid": "0000-0002-0956-8634" }, "description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)", "download_obo": "http://purl.obolibrary.org/obo/ma.obo", "download_owl": "http://purl.obolibrary.org/obo/ma.owl", "example": "0002502", "homepage": "https://github.com/obophenotype/adult-mouse-anatomy-ontology", "keywords": [ "anatomy", "mouse", "obo", "ontology", "organ", "tissue" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "MA", "bartoc": "1143", "biocontext": "MA", "bioportal": "MA", "fairsharing": "FAIRsharing.pdwqcr", "go": "MA", "miriam": "ma", "n2t": "ma", "obofoundry": "ma", "ols": "ma", "ontobee": "MA", "prefixcommons": "ma", "wikidata.entity": "Q81661674" }, "name": "Mouse adult gross anatomy", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "MA", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/ma:$1" } ], "publications": [ { "doi": "10.1186/gb-2005-6-3-r29", "pmc": "PMC1088948", "pubmed": "15774030", "title": "The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data", "year": 2005 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MA_$1", "repository": "https://github.com/obophenotype/adult-mouse-anatomy-ontology", "uri_format": "http://purl.obolibrary.org/obo/MA_$1", "version": "2026-01-09" }, "macie": { "contact": { "email": "gemma.l.holliday@gmail.com", "github": "GLHolliday79", "name": "Gemma L. Holliday", "orcid": "0000-0002-6731-6398" }, "description": "MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved.", "example": "M0001", "homepage": "https://www.ebi.ac.uk/thornton-srv/m-csa/about/", "keywords": [ "enzyme", "life science", "pathway" ], "mappings": { "biocontext": "MACIE", "edam": "2641", "fairsharing": "FAIRsharing.7xkx69", "miriam": "macie", "n2t": "macie", "prefixcommons": "macie" }, "name": "Mechanism, Annotation and Classification in Enzymes", "pattern": "^M\\d{4}$", "preferred_prefix": "macie", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/macie:$1" } ], "publications": [ { "doi": "10.1093/nar/gkl774", "pmc": "PMC1634735", "pubmed": "17082206", "title": "MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms", "year": 2006 }, { "doi": "10.1093/bioinformatics/bti693", "pmc": "PMC2748267", "pubmed": "16188925", "title": "MACiE: a database of enzyme reaction mechanisms", "year": 2005 } ], "uri_format": "https://www.ebi.ac.uk/thornton-srv/m-csa/search/?s=$1" }, "maggot": { "description": "Sharing descriptive Metadata is the first essential step towards Open Scientific Data. With this in mind, Maggot was specifically designed to annotate datasets by creating a metadata file to attach to the storage space. Indeed, it allows users to easily add descriptive metadata to datasets produced within a collective of people (research unit, platform, multi-partner project, etc.). This approach fits perfectly into a data management plan as it addresses the issues of data organization and documentation, data storage and frictionless metadata sharing within this same collective and beyond.", "example": "frim1", "homepage": "https://eng-bfp.bordeaux-aquitaine.hub.inrae.fr/resources/metabolome-platform", "mappings": { "miriam": "maggot" }, "name": "Maggot", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "maggot", "uri_format": "https://pmb-bordeaux.fr/maggot/metadata/$1" }, "maizegdb.locus": { "contact": { "email": "margaret.woodhouse@usda.gov", "github": "margaretwoodhouse", "name": "Margaret R. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/maizegdb:$1" } ], "publications": [ { "doi": "10.1186/s12870-021-03173-5", "pubmed": "34416864" }, { "doi": "10.3389/fpls.2019.01050", "pmc": "PMC6724615", "pubmed": "31555312", "title": "MaizeDIG: Maize Database of Images and Genomes", "year": 2019 }, { "doi": "10.1093/nar/gky1046", "pmc": "PMC6323944", "pubmed": "30407532", "title": "MaizeGDB 2018: the maize multi-genome genetics and genomics database", "year": 2019 }, { "doi": "10.1007/978-1-4939-3167-5_9", "pubmed": "26519406", "title": "MaizeGDB: The Maize Genetics and Genomics Database", "year": 2016 }, { "doi": "10.1093/nar/gkv1007", "pmc": "PMC4702771", "pubmed": "26432828", "title": "MaizeGDB update: new tools, data and interface for the maize model organism database", "year": 2015 }, { "doi": "10.1155/2008/496957", "pmc": "PMC2518694", "pubmed": "18769488", "title": "MaizeGDB: The maize model organism database for basic, translational, and applied research", "year": 2008 }, { "doi": "10.1093/nar/gkl1048", "pmc": "PMC1899092", "pubmed": "17202174", "title": "MaizeGDB's new data types, resources and activities", "year": 2007 } ], "synonyms": [ "MaizeGDB" ], "uri_format": "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1" }, "mamo": { "banana": "MAMO", "banana_peel": "_", "contact": { "email": "n.lenovere@gmail.com", "name": "Nicolas Le Novere", "orcid": "0000-0002-6309-7327" }, "deprecated": true, "description": "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.", "download_owl": "http://purl.obolibrary.org/obo/mamo.owl", "download_rdf": "https://raw.githubusercontent.com/EBISPOT/mamo/main/mamo.rdf", "example": "0000026", "homepage": "http://sourceforge.net/p/mamo-ontology/wiki/Home/", "keywords": [ "computational biology", "mathematics", "obo", "ontology", "systems biology" ], "license": "Artistic License 2.0", "mappings": { "aberowl": "MAMO", "biocontext": "MAMO", "bioportal": "MAMO", "fairsharing": "FAIRsharing.kbz5jh", "miriam": "mamo", "n2t": "mamo", "obofoundry": "mamo", "ols": "mamo", "ontobee": "MAMO", "wikidata.entity": "Q113014441" }, "name": "Mathematical modeling ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MAMO", "rdf_uri_format": "http://purl.obolibrary.org/obo/MAMO_$1", "repository": "http://sourceforge.net/p/mamo-ontology", "uri_format": "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1", "version": "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).", "example": "MAMpol005339", "homepage": "http://mampol.uab.es", "keywords": [ "dna" ], "mappings": { "prefixcommons": "mampol" }, "name": "Mammalia Polymorphism Database", "preferred_prefix": "mampol", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/mampol:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://mampol.uab.es/cgi-bin/MamPol_s2.pl?Accession=$1" }, "mao": { "contact": { "email": "julie@igbmc.u-strasbg.fr", "name": "Julie Thompson" }, "deprecated": true, "description": "An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment.", "example": "0000061", "homepage": "http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html", "keywords": [ "alignment", "obo", "ontology", "sequence" ], "mappings": { "biocontext": "MAO", "obofoundry": "mao", "prefixcommons": "mao", "wikidata.entity": "Q114677893" }, "name": "Multiple alignment", "pattern": "^\\d{7}$", "preferred_prefix": "MAO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/mao:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MAO_$1", "uri_format": "http://purl.obolibrary.org/obo/MAO_$1" }, "marc21": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "MARC List for Languages provides three-character lowercase alphabetic strings that serve as the identifiers of languages and language groups. The codes are usually based on the first three letters of the English form or, in some cases, vernacular form of the corresponding language name. The codes are varied where necessary to resolve conflicts and are not intended to be abbreviations of a language name. When the name of a language is changed in the list, the original code is generally retained. The codes in this list are equivalent to those of ISO 639-2 (Bibliographic) codes and some codes from ISO 639-5, although the language name labels may differ. They are linked to the equivalent codes in ISO 639-2 and ISO 639-5 and the corresponding two-character codes in ISO 639-1. The list contains over 480 discrete codes. It is also searchable at: MARC Code List for Languages.", "download_rdf": "https://id.loc.gov/vocabulary/languages.skos.rdf", "example": "amh", "homepage": "https://id.loc.gov/vocabulary/languages.html", "name": "Machine-readable Cataloging (MARC) List for Languages", "preferred_prefix": "marc21", "rdf_uri_format": "http://id.loc.gov/vocabulary/languages/$1", "uri_format": "https://id.loc.gov/vocabulary/languages/$1" }, "markerdb": { "contact": { "email": "dwishart@ualberta.ca", "github": "DavidWishartLab", "name": "David S. Wishart", "orcid": "0000-0002-3207-2434" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "MarkerDB is a freely available electronic database that attempts to consolidate information on all known clinical and pre-clinical biomarkers into a single resource. It provides identifiers for known clinical and pre-clinical biomarkers. Each entry provides detailed annotations, including biomarker descriptions, associated conditions, specificity, sensitivity, molecular structures, chromosomal locations, and clinical approval status.", "example": "MDB00000001", "github_request_issue": 1330, "homepage": "https://markerdb.ca", "name": "MarkerDB", "pattern": "^MDB\\d{8}$", "preferred_prefix": "markerdb", "publications": [ { "doi": "10.1093/nar/gkae1056", "pubmed": "39535054", "title": "MarkerDB 2.0: a comprehensive molecular biomarker database for 2025", "year": 2024 }, { "doi": "10.1093/nar/gkaa1067", "pmc": "PMC7778954", "pubmed": "33245771", "title": "MarkerDB: an online database of molecular biomarkers", "year": 2021 } ], "reviewer": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" } }, "massbank": { "contact": { "email": "tobias.schulze@ufz.de", "github": "tsufz", "name": "Tobias Schulze", "orcid": "0000-0002-9744-8914" }, "description": "MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da).", "example": "MSBNK-IPB_Halle-PB000166", "homepage": "http://www.massbank.jp", "keywords": [ "chemistry", "life science", "physics" ], "mappings": { "biocontext": "MASSBANK", "fairsharing": "FAIRsharing.dk451a", "integbio": "nbdc00298", "miriam": "massbank", "n2t": "massbank", "wikidata": "P6689" }, "name": "MassBank", "pattern": "^MSBNK-[0-9a-zA-Z_]+-[A-Z0-9_]+$", "preferred_prefix": "massbank", "providers": [ { "code": "massbankeu", "description": "MassBank in Europe", "homepage": "https://massbank.eu/", "name": "MassBank in Europe", "uri_format": "https://massbank.eu/MassBank/RecordDisplay?id=$1" } ], "publications": [ { "doi": "10.1002/jms.1777", "pubmed": "20623627", "title": "MassBank: a public repository for sharing mass spectral data for life sciences", "year": 2010 } ], "repository": "https://github.com/MassBank", "uri_format": "https://massbank.jp/MassBank/RecordDisplay?id=$1" }, "massive": { "contact": { "email": "miw023@ucsd.edu", "name": "Mingxun Wang", "orcid": "0000-0001-7647-6097" }, "description": "MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data.", "example": "MSV000082131", "homepage": "https://www.omicsdi.org/", "keywords": [ "functional genomics", "metabolomics", "metaproteomics", "omics", "phenomics", "proteomics" ], "mappings": { "biocontext": "MASSIVE", "fairsharing": "FAIRsharing.LYsiMd", "miriam": "massive", "n2t": "massive", "uniprot": "DB-0241" }, "name": "MassIVE", "pattern": "^MSV\\d+$", "preferred_prefix": "massive", "providers": [ { "code": "", "description": "MassIVE", "homepage": "https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp", "name": "MassIVE", "uri_format": "https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1" } ], "publications": [ { "doi": "10.1038/s41592-020-0955-0", "pmc": "PMC7541731", "pubmed": "32929271", "title": "MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets", "year": 2020 }, { "doi": "10.1093/nar/gkz984", "pmc": "PMC7145525", "pubmed": "31686107", "title": "The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics", "year": 2020 }, { "doi": "10.1016/j.cels.2018.08.004", "pmc": "PMC6279426", "pubmed": "30172843", "title": "Assembling the Community-Scale Discoverable Human Proteome", "year": 2018 }, { "doi": "10.1093/nar/gkw936", "pmc": "PMC5210636", "pubmed": "27924013", "title": "The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition", "year": 2016 }, { "doi": "10.1038/nbt.3597", "pmc": "PMC5321674", "pubmed": "27504778", "title": "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking", "year": 2016 } ], "repository": "https://ccms-ucsd.github.io/MassIVEDocumentation", "uri_format": "https://www.omicsdi.org/dataset/massive/$1" }, "mastodon": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "address on the Mastodon decentralized social network (the form is 'user@server.domain' without a leading '@')", "example": "jz@mamot.fr", "homepage": "https://mastodon.social", "mappings": { "wikidata": "P4033" }, "name": "Mastodon", "pattern": "^[A-Za-z0-9_]+([A-Za-z0-9_\\.]+[A-Za-z0-9_]+)?@[\\d\\w\\.\\-]+[0-9a-z]+$", "preferred_prefix": "mastodon", "uri_format": "https://fedirect.toolforge.org/?id=$1" }, "mat": { "contact": { "email": "j.bard@ed.ac.uk", "name": "Jonathan Bard" }, "deprecated": true, "description": "Minimal set of terms for anatomy", "download_obo": "http://aber-owl.net/media/ontologies/MAT/3/mat.obo", "example": "0000000", "keywords": [ "obo", "ontology" ], "mappings": { "aberowl": "MAT", "biocontext": "MAT", "bioportal": "MAT", "obofoundry": "mat", "wikidata.entity": "Q114677894" }, "name": "Minimal Anatomical Terminology", "pattern": "^\\d{7}$", "preferred_prefix": "MAT", "rdf_uri_format": "http://purl.obolibrary.org/obo/MAT_$1", "uri_format": "http://purl.obolibrary.org/obo/MAT_$1" }, "mathmoddb": { "description": "This is the MathModDB Ontology for documenting mathematical models.", "example": "ComputationalTask", "homepage": "https://github.com/mardi4nfdi/MathModDB", "keywords": [ "computer science", "engineering", "mathematics", "nfdi4ing" ], "mappings": { "tib": "mathmoddb" }, "name": "MathModDB Ontology", "preferred_prefix": "mathmoddb", "repository": "https://github.com/mardi4nfdi/MathModDB", "uri_format": "https://mardi4nfdi.de/mathmoddb#$1" }, "matrixdb": { "appears_in": [ "complexportal" ], "contact": { "email": "sylvie.ricard-blum@univ-lyon1.fr", "github": "ricardblum", "name": "Sylvie Ricard-Blum", "orcid": "0000-0001-9263-1851" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "sbalu@ebi.ac.uk", "github": "CP-SB", "name": "Sucharitha Balu", "orcid": "0000-0001-7456-0594" } ], "description": "MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides", "example": "MULT_4_VAR1_bovine", "homepage": "http://matrixdb.univ-lyon1.fr/", "keywords": [ "biology", "interaction", "protein", "small molecule" ], "mappings": { "fairsharing": "FAIRsharing.91yrz6", "integbio": "nbdc01222", "pathguide": "298", "prefixcommons": "matrixdb", "re3data": "r3d100010672" }, "name": "MatrixDB", "preferred_prefix": "matrixdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/matrixdb:$1" } ], "publications": [ { "doi": "10.1093/nar/gky1035", "pmc": "PMC6324007", "pubmed": "30371822", "title": "MatrixDB: integration of new data with a focus on glycosaminoglycan interactions", "year": 2019 }, { "doi": "10.1093/nar/gku1091", "pmc": "PMC4383919", "pubmed": "25378329", "title": "MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities", "year": 2014 }, { "doi": "10.1093/nar/gkq830", "pmc": "PMC3013758", "pubmed": "20852260", "title": "MatrixDB, the extracellular matrix interaction database", "year": 2010 }, { "doi": "10.1093/bioinformatics/btp025", "pmc": "PMC2647840", "pubmed": "19147664", "title": "MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions", "year": 2009 } ], "uri_format": "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1" }, "matrixdb.association": { "description": "MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations.", "example": "P00747__P07355", "homepage": "https://matrixdb.univ-lyon1.fr/", "mappings": { "biocontext": "MATRIXDB.ASSOCIATION", "miriam": "matrixdb.association", "n2t": "matrixdb.association" }, "name": "MatrixDB Association", "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$", "preferred_prefix": "matrixdb.association", "uri_format": "https://matrixdb.univ-lyon1.fr/association/$1" }, "mavedb": { "comment": "This is an interesting one as the full IDs as they appear on the page are of the form `urn:mavedb:00000011-a` suggesting this is the preferred URI expansion for identification purposes. However, mavedb hasn't been registered with IANA https://www.iana.org/assignments/urn-namespaces/urn-namespaces.xhtml", "contact": { "email": "alan.rubin@wehi.edu.au", "github": "afrubin", "name": "Alan Rubin", "orcid": "0000-0003-1474-605X" }, "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "Some IDs may represent experiment sets, e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011 Others represent genomic regions (specifically deep mutational scans thereof) e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011-a", "example": "00000011-a", "example_extras": [ "00000011" ], "github_request_issue": 1045, "homepage": "https://www.mavedb.org", "name": "Multiplexed Assays of Variant Effect Database", "pattern": "^\\S+$", "preferred_prefix": "mavedb", "publications": [ { "doi": "10.1186/s13059-025-03476-y", "pmc": "PMC11753097", "pubmed": "39838450", "title": "MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays", "year": 2025 }, { "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:$1" }, "maxo": { "appears_in": [ "ecto" ], "contact": { "email": "Leigh.Carmody@jax.org", "github": "LCCarmody", "name": "Leigh Carmody", "orcid": "0000-0001-7941-2961" }, "depends_on": [ "chebi", "foodon", "go", "hp", "iao", "nbo", "obi", "ro", "uberon" ], "description": "An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations.", "download_json": "http://purl.obolibrary.org/obo/maxo.json", "download_obo": "http://purl.obolibrary.org/obo/maxo.obo", "download_owl": "http://purl.obolibrary.org/obo/maxo.owl", "example": "0000008", "homepage": "https://github.com/monarch-initiative/MAxO", "keywords": [ "medicine", "obo", "ontology", "rare disorder" ], "license": "CC-BY-4.0", "logo": "https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/maxo-logos/maxo_logo_black-banner.png", "mappings": { "aberowl": "MAXO", "biolink": "MAXO", "bioportal": "MAXO", "fairsharing": "FAIRsharing.945c78", "miriam": "maxo", "obofoundry": "maxo", "ols": "maxo", "ontobee": "MAXO", "wikidata.entity": "Q113012668" }, "name": "Medical Action Ontology", "pattern": "^\\d{7}$", "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_$1", "version": "2026-01-15" }, "mba": { "contact": { "email": "cellsemantics@gmail.com", "name": "Allen Institute for Brain Science" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A controlled vocabulary to support the study of transcription in the mouse brain", "download_obo": "https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-mba.obo", "download_owl": "https://purl.brain-bican.org/ontology/mbao/releases/2025-10-29/mbao.owl", "example": "688", "homepage": "https://mouse.brain-map.org", "keywords": [ "ontology" ], "mappings": { "bioportal": "ABA-AMB", "ols": "mba" }, "name": "Mouse Brain Atlas", "pattern": "^\\d+$", "preferred_prefix": "MBA", "providers": [ { "code": "biopragmatics", "description": "Biopragmatics provider for MBA", "homepage": "https://biopragmatics.github.io/providers/mba", "name": "MBA from Biopragmatics", "uri_format": "https://biopragmatics.github.io/providers/mba/$1" } ], "repository": "https://github.com/brain-bican/mouse_brain_atlas_ontology", "uri_format": "https://purl.brain-bican.org/ontology/mbao/MBA_$1", "version": "2025-10-29" }, "mcc": { "contact": { "email": "usha@molecularconnections.com", "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.", "example": "ThoracicArtery", "homepage": "http://www.molecularconnections.com", "keywords": [ "ontology" ], "mappings": { "bioportal": "MCCL" }, "name": "Cell Line Ontology [derivative]", "preferred_prefix": "mcc", "uri_format": "http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#$1" }, "mco": { "contact": { "email": "citlalli.mejiaalmonte@gmail.com", "github": "citmejia", "name": "Citlalli Mejía-Almonte", "orcid": "0000-0002-0142-5591" }, "depends_on": [ "bfo", "chebi", "cl", "clo", "micro", "ncbitaxon", "ncit", "obi", "omit", "omp", "pato", "peco", "uberon", "zeco" ], "description": "Microbial Conditions Ontology is an ontology...", "download_obo": "http://purl.obolibrary.org/obo/mco.obo", "download_owl": "http://purl.obolibrary.org/obo/mco.owl", "example": "0000858", "homepage": "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "MCO", "bioportal": "MCO", "obofoundry": "mco", "ols": "mco", "ontobee": "MCO", "wikidata.entity": "Q81661676" }, "name": "Microbial Conditions Ontology", "pattern": "^\\d+$", "preferred_prefix": "MCO", "rdf_uri_format": "http://purl.obolibrary.org/obo/MCO_$1", "repository": "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology", "uri_format": "http://purl.obolibrary.org/obo/MCO_$1", "version": "2019-05-15" }, "mcro": { "banana": "MCRO", "contact": { "email": "muamith@utmb.edu", "github": "ProfTuan", "name": "Tuan Amith", "orcid": "0000-0003-4333-1857" }, "depends_on": [ "iao", "swo" ], "description": "An ontology representing the model card structure, he aim of this work is to describe machine learning models to communicate information about specific details about the model (trade offs, intended users, licensing, etc.). ", "download_owl": "http://purl.obolibrary.org/obo/mcro.owl", "example": "0000001", "homepage": "https://github.com/UTHealth-Ontology/MCRO", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "MCRO", "bioportal": "MCRO", "miriam": "mcro", "obofoundry": "mcro", "ols": "mcro", "ontobee": "MCRO" }, "name": "Model Card Report Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "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:$1", "version": "2023-03-07" }, "mdl": { "appears_in": [ "xlmod" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The MDL number contains a unique identification number for each reaction and variation. The format is RXXXnnnnnnnn. R indicates a reaction, XXX indicates which database contains the reaction record. The numeric portion, nnnnnnnn, is an 8-digit number. [wikipedia]", "example": "MFCD00011659", "github_request_issue": 1311, "homepage": "https://en.wikipedia.org/wiki/Chemical_file_format#MDL_number", "name": "Molecular Design Limited Hash", "pattern": "^\\w{4}\\d{8}$", "preferred_prefix": "mdl", "references": [ "https://en.wikipedia.org/wiki/Chemical_file_format#MDL_number" ] }, "mdm": { "contact": { "email": "bernd.mueller@zbmed.de", "name": "Bernd Müller", "orcid": "0000-0003-3062-8192" }, "description": "The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems.", "download_owl": "http://aber-owl.net/media/ontologies/MDM/4/mdm.owl", "example": "4776", "homepage": "https://medical-data-models.org/", "keywords": [ "biomedical science", "medicine", "ontology", "translational medicine" ], "mappings": { "aberowl": "MDM", "biocontext": "MDM", "bioportal": "MDM", "fairsharing": "FAIRsharing.wnk2eq", "miriam": "mdm", "n2t": "mdm", "re3data": "r3d100013816" }, "name": "Medical Data Models", "pattern": "^\\d+$", "preferred_prefix": "mdm", "publications": [ { "doi": "10.1093/database/bav121", "pmc": "PMC4750548", "pubmed": "26868052", "title": "Portal of medical data models: information infrastructure for medical research and healthcare", "year": 2016 } ], "uri_format": "https://medical-data-models.org/forms/$1" }, "meddra": { "contact": { "email": "mssohelp@meddra.org", "name": "MedDRA MSSO" }, "description": "The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT).", "example": "10015919", "homepage": "http://bioportal.bioontology.org/ontologies/MEDDRA", "keywords": [ "biomedical science", "disease", "medicine", "ontology", "preclinical studies" ], "mappings": { "aberowl": "MEDDRA", "bartoc": "1237", "biocontext": "MEDDRA", "bioportal": "MEDDRA", "fairsharing": "FAIRsharing.ad3137", "hl7": "2.16.840.1.113883.6.163", "integbio": "nbdc02564", "miriam": "meddra", "n2t": "meddra", "togoid": "Meddra", "wikidata": "P3201", "wikidata.entity": "Q1539689" }, "name": "Medical Dictionary for Regulatory Activities Terminology", "pattern": "^\\d+$", "preferred_prefix": "meddra", "publications": [ { "doi": "10.1016/s1386-5056(00)00062-9", "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", "pubmed": "10082069", "title": "The medical dictionary for regulatory activities (MedDRA)", "year": 1999 } ], "rdf_uri_format": "http://purl.bioontology.org/ontology/MDRFRE/$1", "synonyms": [ "MEDRA", "MeDRA", "MedDRA", "Medical Dictionary for Regulatory Activities" ], "uri_format": "https://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid=$1" }, "medgen": { "contact": { "email": "megan.kane@nih.gov", "github": "kanems", "name": "Megan S. Kane", "orcid": "0000-0001-5493-2602" }, "contributor_extras": [ { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" } ], "description": "MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder.", "example": "760050", "example_decoys": [ "N1849341", "C1849341" ], "example_extras": [ "610", "CN970821" ], "homepage": "https://www.ncbi.nlm.nih.gov/medgen/", "mappings": { "biocontext": "MedGen", "biolink": "medgen", "integbio": "nbdc02560", "miriam": "medgen", "n2t": "medgen", "ncbi": "MedGen", "togoid": "Medgen" }, "name": "Human Medical Genetics", "pattern": "^(CN)?\\d{2,7}$", "preferred_prefix": "medgen", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1567" ], "synonyms": [ "medgen.uid" ], "uri_format": "https://www.ncbi.nlm.nih.gov/medgen/$1" }, "medgen.cid": { "contact": { "email": "megan.kane@nih.gov", "github": "kanems", "name": "Megan S. Kane", "orcid": "0000-0001-5493-2602" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This vocabulary is used internally inside MedGen to assign temporary identifiers to terms that will later get put in UMLS. Mappings between MedGen, MedGen CIDs, and UMLS can be found [here](https://ftp.ncbi.nlm.nih.gov/pub/medgen/MedGenIDMappings.txt.gz).", "example": "CN970821", "github_request_issue": 1576, "homepage": "https://www.ncbi.nlm.nih.gov/medgen", "name": "MedGen Concept Unique ID", "pattern": "^CN\\d+$", "preferred_prefix": "medgen.cid", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1567" ] }, "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/$1" }, "mediadive.medium": { "contact": { "email": "joerg.overmann@dsmz.de", "name": "Jörg Overmann", "orcid": "0000-0003-3909-7201" }, "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]", "example": "77", "example_extras": [ "54b" ], "github_request_issue": 941, "homepage": "https://mediadive.dsmz.de/media", "license": "CC-BY-4.0", "mappings": { "miriam": "mediadive.medium" }, "name": "MediaDive Medium", "pattern": "^\\d+\\w?$", "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/$1" }, "medlineplus": { "contact": { "email": "custserv@nlm.nih.gov", "name": "NLM Customer Service" }, "description": "MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language.", "example": "002804", "homepage": "http://www.nlm.nih.gov/medlineplus/", "keywords": [ "biomedical science", "disease", "health science", "medicine", "ontology" ], "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaEFGIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--611e307f6ed5ae6a6f06017953d913cdcacc490b/Screenshot%20from%202024-10-04%2017-49-50.png?disposition=inline", "mappings": { "aberowl": "MEDLINEPLUS", "biocontext": "MEDLINEPLUS", "bioportal": "MEDLINEPLUS", "fairsharing": "FAIRsharing.bf8dsb", "hl7": "2.16.840.1.113883.6.173", "integbio": "nbdc00836", "miriam": "medlineplus", "n2t": "medlineplus" }, "name": "MedlinePlus Health Topics", "pattern": "^\\d+$", "preferred_prefix": "medlineplus", "providers": [ { "code": "medlineplus.fp", "description": "First-party version of medline plus.", "homepage": "https://medlineplus.gov", "name": "MedLine Plus home page", "uri_format": "https://medlineplus.gov/ency/article/$1.htm" } ], "uri_format": "http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm" }, "meno": { "contact": { "email": "mirjam.stappel@uni-osnabrueck.de", "github": "stap-m", "name": "Mirjam Stappel", "orcid": "0000-0003-3722-5564" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The midlevel energy ontology (MENO) is a BFO-based midlevel ontology. It comprises the concepts for energy qualities, energy-based dispositions and energy-driven transformation and transfer processes and their interrelations. It has the goal to provide an upper level structure for these concepts for energy-related domain ontologies.", "download_owl": "https://github.com/stap-m/midlevel-energy-ontology/raw/refs/heads/dev/ontology/src/midlevel-energy.owl", "example": "01013", "homepage": "https://github.com/stap-m/midlevel-energy-ontology", "keywords": [ "ontology" ], "license": "CC-BY-4.0", "name": "Mid-level Energy Ontology", "pattern": "^\\d+$", "preferred_prefix": "meno", "references": [ "https://www.utwente.nl/en/eemcs/fois2024/resources/papers/stappel-neuhaus-representing-energy-in-the-midlevel-energy-ontology-meno.pdf" ], "repository": "https://github.com/stap-m/midlevel-energy-ontology" }, "merckindex.monograph": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A semantic space of small molecules", "example": "M2871", "github_request_issue": 1554, "homepage": "https://merckindex.rsc.org", "name": "Merck Index Monograph", "preferred_prefix": "merckindex.monograph", "uri_format": "https://merckindex.rsc.org/monographs/$1" }, "merckindex.reaction": { "appears_in": [ "rxno" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "Chemical reactions in the Merck Index. This website doesn't exist anymore", "example": "r376", "github_request_issue": 1554, "homepage": "https://merckindex.rsc.org", "name": "Merck Index Reaction", "pattern": "^r\\d+$", "preferred_prefix": "merckindex.reaction", "uri_format": "https://www.rsc.org/Merck-Index/reaction/$1" }, "merops.clan": { "contact": { "email": "ndr@ebi.ac.uk", "name": "Neil D Rawlings", "orcid": "0000-0001-5557-7665" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.", "example": "IA", "homepage": "https://www.ebi.ac.uk/merops", "name": "MEROPS Clan", "preferred_prefix": "merops.clan", "publications": [ { "doi": "10.1093/nar/gkx1134", "pmc": "PMC5753285", "pubmed": "29145643", "title": "The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database", "year": 2018 } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/439" ], "uri_format": "https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=$1" }, "merops.entry": { "contact": { "email": "ndr@ebi.ac.uk", "name": "Neil D Rawlings", "orcid": "0000-0001-5557-7665" }, "description": "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors.", "example": "I31.952", "example_extras": [ "S01.001", "XM02.001" ], "homepage": "https://www.ebi.ac.uk/merops", "keywords": [ "biomedical science", "enzyme", "life science", "protein", "structure" ], "mappings": { "biocontext": "MEROPS.INHIBITOR", "edam": "2629", "fairsharing": "FAIRsharing.2s4n8r", "go": "MEROPS", "miriam": "merops.inhibitor", "n2t": "merops.inhibitor", "prefixcommons": "merops" }, "name": "MEROPS Entry", "pattern": "^[SCTAGMNUIX]{1,2}\\d{2}\\.([AB]\\d{2}|\\d{3})$", "preferred_prefix": "merops.entry", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/merops:$1" } ], "publications": [ { "doi": "10.1093/nar/27.1.325", "pmc": "PMC148173", "pubmed": "9847218", "title": "MEROPS: the peptidase database", "year": 1999 }, { "doi": "10.1042/bj2900205", "pmc": "PMC1132403", "pubmed": "8439290", "title": "Evolutionary families of peptidases", "year": 1993 }, { "doi": "10.1093/nar/gkx1134", "pmc": "PMC5753285", "pubmed": "29145643", "title": "The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database", "year": 2018 }, { "doi": "10.1093/nar/gkv1118", "pmc": "PMC4702814", "pubmed": "26527717", "title": "Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors", "year": 2015 }, { "doi": "10.1016/j.biochi.2015.10.003", "pmc": "PMC4756867", "pubmed": "26455268", "title": "Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation", "year": 2015 }, { "doi": "10.1093/nar/gkr987", "pmc": "PMC3245014", "pubmed": "22086950", "title": "MEROPS: the database of proteolytic enzymes, their substrates and inhibitors", "year": 2011 }, { "doi": "10.1093/nar/gkm954", "pmc": "PMC2238837", "pubmed": "17991683", "title": "MEROPS: the peptidase database", "year": 2007 } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/439" ], "synonyms": [ "merops.inhibitor" ], "uri_format": "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1" }, "merops.family": { "contact": { "email": "ndr@ebi.ac.uk", "name": "Neil D Rawlings", "orcid": "0000-0001-5557-7665" }, "description": "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families.", "example": "S1", "homepage": "https://www.ebi.ac.uk/merops/", "mappings": { "biocontext": "MEROPS.FAMILY", "miriam": "merops.family", "n2t": "merops.family" }, "name": "MEROPS Family", "pattern": "^[SCTAGMNU]\\d+$", "preferred_prefix": "merops.family", "publications": [ { "doi": "10.1093/nar/gkx1134", "pmc": "PMC5753285", "pubmed": "29145643", "title": "The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database", "year": 2018 } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/439" ], "uri_format": "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1" }, "merriamwebster": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Online Dictionary", "example": "buccal_gland", "github_request_issue": 1310, "homepage": "https://www.merriam-webster.com", "name": "Merriam Webster Dictionary", "preferred_prefix": "merriamwebster", "synonyms": [ "merriam_webster" ], "uri_format": "https://www.merriam-webster.com/dictionary/$1" }, "mesh": { "contact": { "email": "custserv@nlm.nih.gov", "name": "NLM Customer Service" }, "contributor_extras": [ { "email": "baum@zbmed.de", "github": "rombaum", "name": "Roman Baum", "orcid": "0000-0001-5246-9351" } ], "description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc.", "download_owl": "https://w3id.org/biopragmatics/resources/mesh/2025/mesh.ofn", "example": "C063233", "example_extras": [ "D000001", "Q000473" ], "homepage": "https://www.nlm.nih.gov/", "keywords": [ "bioinformatics", "biomedical science", "classification", "data retrieval", "life science", "literature curation", "metascience", "ontology", "topics" ], "license": "CC0-1.0", "logo": "https://meshb.nlm.nih.gov/public/img/meshLogo.jpg", "mappings": { "aberowl": "MESH", "bartoc": "391", "biocontext": "MESH", "biolink": "MESH", "bioportal": "MESH", "cellosaurus": "MeSH", "edam": "1177", "fairsharing": "FAIRsharing.qnkw45", "go": "MeSH", "hl7": "2.16.840.1.113883.6.177", "integbio": "nbdc00132", "miriam": "mesh", "n2t": "mesh", "ols": "mesh", "prefixcommons": "mesh", "togoid": "Mesh", "wikidata": "P486", "wikidata.entity": "Q199897" }, "name": "Medical Subject Headings", "pattern": "^(C|D|Q)\\d+$", "preferred_prefix": "mesh", "providers": [ { "code": "", "description": "MeSH Linked Data at National Library of Medicine", "homepage": "http://id.nlm.nih.gov/mesh/", "name": "MeSH Linked Data at National Library of Medicine", "uri_format": "http://id.nlm.nih.gov/mesh/$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/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.2008", "description": "Appears in birnlex", "homepage": "http://id.nlm.nih.gov/mesh/", "name": "Legacy 2008 MeSH URL", "uri_format": "http://www.nlm.nih.gov/cgi/mesh/2008/MB_cgi?field=uid&term=$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": [ { "pmc": "PMC197951", "pubmed": "13982385", "title": "Medical subject headings", "year": 1963 } ], "rdf_uri_format": "http://id.nlm.nih.gov/mesh/$1", "synonyms": [ "MESH", "MESHA", "MESHC", "MESHCS", "MESHD", "MESHPP", "MESH_DESCRIPTOR_UI", "MESH_SUPPLEMENTAL_RECORD_UI", "MSH", "MSH2010_2010_02_22", "MeSH", "meshUID" ], "uri_format": "https://meshb.nlm.nih.gov/record/ui?ui=$1" }, "mesh.2012": { "description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012.", "example": "17186", "homepage": "http://www.nlm.nih.gov/mesh/", "mappings": { "biocontext": "MESH.2012", "miriam": "mesh.2012", "n2t": "mesh.2012" }, "name": "MeSH 2012", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "mesh.2012", "provides": "mesh", "uri_format": "http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded" }, "mesh.2013": { "description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013.", "example": "17165", "homepage": "http://www.nlm.nih.gov/mesh/", "mappings": { "biocontext": "MESH.2013", "miriam": "mesh.2013", "n2t": "mesh.2013" }, "name": "MeSH 2013", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "mesh.2013", "provides": "mesh", "uri_format": "http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded" }, "mesh.vocab": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump", "example": "term", "homepage": "https://hhs.github.io/meshrdf/", "name": "Medical Subject Headings Vocabulary", "preferred_prefix": "mesh.vocab", "references": [ "https://id.nlm.nih.gov/mesh/query" ], "repository": "https://github.com/HHS/meshrdf", "uri_format": "http://id.nlm.nih.gov/mesh/vocab#$1" }, "metabolights": { "description": "MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies.", "example": "MTBLS1", "homepage": "https://www.ebi.ac.uk/metabolights/", "mappings": { "biocontext": "METABOLIGHTS", "cellosaurus": "MetaboLights", "integbio": "nbdc02124", "miriam": "metabolights", "n2t": "metabolights", "re3data": "r3d100011556", "wikidata": "P3890" }, "name": "MetaboLights Compound", "pattern": "^MTBL[CS]\\d+$", "preferred_prefix": "metabolights", "providers": [ { "code": "omicsdi", "description": "MataboLights through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "MataboLights through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/metabolights_dataset/$1" } ], "uri_format": "https://www.ebi.ac.uk/metabolights/$1" }, "metacyc.compound": { "contact": { "email": "pkarp@ai.sri.com", "github": "pkarp111", "name": "Peter D. Karp", "orcid": "0000-0002-5876-6418" }, "description": "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.", "example": "CPD-10330", "homepage": "https://metacyc.org", "keywords": [ "life science", "metabolomics", "systems biology" ], "logo": "https://metacyc.org/graphics2021/MetaCyc-logo-color.svg", "mappings": { "biocontext": "METACYC.COMPOUND", "biolink": "MetaCyc", "fairsharing": "FAIRsharing.yytevr", "go": "MetaCyc", "integbio": "nbdc00907", "miriam": "metacyc.compound", "n2t": "metacyc.compound", "pathguide": "10", "re3data": "r3d100011294" }, "name": "Metabolic Encyclopedia of metabolic and other pathways", "pattern": "^[A-Za-z0-9+_.%-:]+$", "preferred_prefix": "metacyc.compound", "publications": [ { "doi": "10.1093/nar/gkv1164", "pmc": "PMC4702838", "pubmed": "26527732", "title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases", "year": 2015 }, { "doi": "10.1093/nar/gkt1103", "pmc": "PMC3964957", "pubmed": "24225315", "title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases", "year": 2013 }, { "doi": "10.1093/nar/gkr1014", "pmc": "PMC3245006", "pubmed": "22102576", "title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases", "year": 2011 } ], "synonyms": [ "MetaCyc" ], "twitter": "BioCyc", "uri_format": "https://metacyc.org/compound?orgid=META&id=$1" }, "metacyc.pathway": { "contact": { "email": "pkarp@ai.sri.com", "github": "pkarp111", "name": "Peter D. 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=$1" }, "metacyc.reaction": { "contact": { "email": "pkarp@ai.sri.com", "github": "pkarp111", "name": "Peter D. Karp", "orcid": "0000-0002-5876-6418" }, "description": "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.", "example": "RXN-14904", "homepage": "https://metacyc.org", "mappings": { "biocontext": "METACYC.REACTION", "biolink": "metacyc.reaction", "miriam": "metacyc.reaction", "n2t": "metacyc.reaction" }, "name": "MetaCyc Reaction", "pattern": "^[A-Za-z0-9+_.%-:]+$", "preferred_prefix": "metacyc.reaction", "uri_format": "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1" }, "metanetx.chemical": { "description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components.", "example": "MNXM1723", "homepage": "https://www.metanetx.org/", "mappings": { "biocontext": "METANETX.CHEMICAL", "miriam": "metanetx.chemical", "n2t": "metanetx.chemical" }, "name": "MetaNetX chemical", "pattern": "^(MNXM\\d+|BIOMASS|WATER)$", "preferred_prefix": "metanetx.chemical", "uri_format": "https://www.metanetx.org/chem_info/$1" }, "metanetx.compartment": { "description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments.", "example": "MNXC15", "homepage": "https://www.metanetx.org/", "mappings": { "biocontext": "METANETX.COMPARTMENT", "miriam": "metanetx.compartment", "n2t": "metanetx.compartment" }, "name": "MetaNetX compartment", "pattern": "^(MNX[CD]\\d+|BOUNDARY|IN|OUT)$", "preferred_prefix": "metanetx.compartment", "uri_format": "https://www.metanetx.org/comp_info/$1" }, "metanetx.reaction": { "description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions.", "example": "MNXR101574", "homepage": "https://www.metanetx.org/", "mappings": { "biocontext": "METANETX.REACTION", "biolink": "METANETX.REACTION", "miriam": "metanetx.reaction", "n2t": "metanetx.reaction" }, "name": "MetaNetX reaction", "pattern": "^(MNXR\\d+|EMPTY)$", "preferred_prefix": "metanetx.reaction", "uri_format": "https://www.metanetx.org/equa_info/$1" }, "metatlas": { "contact": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "contributor": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "description": "A resource for exploring metabolism, starting with a set of of community-curated genome-scale metabolic models of human and model organisms, enriched with pathway maps and other tools for easy browsing and analysis.", "example": "MAM01234c", "example_decoys": [ "MAR11851c" ], "example_extras": [ "MAR11851" ], "github_request_issue": 495, "homepage": "https://metabolicatlas.org", "keywords": [ "chemistry", "metabolites", "reactions" ], "mappings": { "miriam": "metatlas" }, "name": "Metabolic Atlas", "pattern": "^(MAM\\d{5}\\w)|(MAR\\d{5})$", "preferred_prefix": "metatlas", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://metabolicatlas.org/identifier/MetabolicAtlas/$1" }, "metatlas.metabolite": { "contact": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "contributor": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "description": "A subspace of Metabolic Atlas for compartment-specific records for metabolites.", "example": "MAM01234c", "github_request_issue": 495, "homepage": "https://metabolicatlas.org", "keywords": [ "chemistry", "metabolites" ], "name": "Metabolic Atlas Metabolite", "part_of": "metatlas", "pattern": "^MAM\\d{5}\\w$", "preferred_prefix": "metatlas.metabolite", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://metabolicatlas.org/identifier/MetabolicAtlas/$1" }, "metatlas.reaction": { "contact": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "contributor": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "description": "A subspace of Metabolic Atlas for reactions.", "example": "MAR11851", "github_request_issue": 495, "homepage": "https://metabolicatlas.org", "keywords": [ "chemistry", "reactions" ], "name": "Metabolic Atlas Reaction", "part_of": "metatlas", "pattern": "^MAR\\d{5}$", "preferred_prefix": "metatlas.reaction", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://metabolicatlas.org/identifier/MetabolicAtlas/$1" }, "metlin": { "deprecated": true, "description": "The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry.", "example": "1455", "homepage": "http://masspec.scripps.edu/", "mappings": { "biocontext": "METLIN", "miriam": "metlin", "n2t": "metlin", "re3data": "r3d100012311" }, "name": "Metabolite and Tandem Mass Spectrometry Database", "pattern": "^\\d{4}$", "preferred_prefix": "metlin", "uri_format": "http://metlin.scripps.edu/metabo_info.php?molid=$1" }, "metnetdb": { "description": "The MetNet database (MetNetDB) contains information on networks of metabolic and regulatory and interactions in Arabidopsis. 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"https://github.com/RDruzinsky/feedontology", "uri_format": "http://purl.obolibrary.org/obo/MFMO_$1", "version": "2013-11-16" }, "mfo": { "contact": { "email": "henrich@embl.de", "github": "ThorstenHen", "name": "Thorsten Henrich", "orcid": "0000-0002-1548-3290" }, "deprecated": true, "description": "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.", "download_obo": "http://aber-owl.net/media/ontologies/MFO/14/mfo.obo", "download_owl": "http://purl.obolibrary.org/obo/mfo.owl", "example": "0000001", "homepage": "http://ani.embl.de:8080/mepd/", "keywords": [ "anatomy", "development", "fish", "obo", "ontology" ], "mappings": { "aberowl": "MFO", "biocontext": "MFO", "bioportal": "MFO", "obofoundry": "mfo", "prefixcommons": "mfo", "wikidata.entity": "Q114677896" }, "name": "Medaka fish anatomy and development", "pattern": "^\\d{7}$", "preferred_prefix": "MFO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/mfo:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MFO_$1", "uri_format": "http://purl.obolibrary.org/obo/MFO_$1" }, "mfoem": { "contact": { "email": "janna.hastings@gmail.com", "github": "jannahastings", "name": "Janna Hastings", "orcid": "0000-0002-3469-4923" }, "description": "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings.", "download_owl": "http://purl.obolibrary.org/obo/mfoem.owl", "example": "000204", "homepage": "https://github.com/jannahastings/emotion-ontology", "keywords": [ "biomedical science", "emotion process", "mental health", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "MFOEM", "biocontext": "MFOEM", "bioportal": "MFOEM", "fairsharing": "FAIRsharing.dx30m8", "obofoundry": "mfoem", "ols": "mfoem", "ontobee": "MFOEM", "wikidata.entity": "Q55118370" }, "name": "Emotion Ontology", "pattern": "^\\d{6}$", "preferred_prefix": "MFOEM", "publications": [ { "doi": "10.1186/2041-1480-5-38", "pmc": "PMC4417517", "pubmed": "25937879", "title": "Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference", "year": 2014 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MFOEM_$1", "repository": "https://github.com/jannahastings/emotion-ontology", "uri_format": "http://purl.obolibrary.org/obo/MFOEM_$1", "version": "2025-07-31" }, "mfomd": { "contact": { "email": "janna.hastings@gmail.com", "github": "jannahastings", "name": "Janna Hastings", "orcid": "0000-0002-3469-4923" }, "description": "The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF).", "download_owl": "http://purl.obolibrary.org/obo/mfomd.owl", "example": "0000046", "homepage": "https://github.com/jannahastings/mental-functioning-ontology", "keywords": [ "disease", "obo", "ontology", "psychiatry" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "MFOMD", "biocontext": "MFOMD", "bioportal": "MFOMD", "fairsharing": "FAIRsharing.q053vb", "obofoundry": "mfomd", "ols": "mfomd", "ontobee": "MFOMD", "wikidata.entity": "Q55118439" }, "name": "Mental Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MFOMD", "rdf_uri_format": "http://purl.obolibrary.org/obo/MFOMD_$1", "repository": "https://github.com/jannahastings/mental-functioning-ontology", "uri_format": "http://purl.obolibrary.org/obo/MFOMD_$1", "version": "2020-04-26" }, "mge": { "banana": "mge", "deprecated": true, "description": "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.", "example": "2", "homepage": "http://aclame.ulb.ac.be/", "keywords": [ "gene", "genome", "life science" ], "mappings": { "biocontext": "ACLAME", "edam": "2631", "fairsharing": "FAIRsharing.5tfcy8", "integbio": "nbdc00355", "miriam": "mge", "n2t": "mge", "prefixcommons": "aclame" }, "name": "Aclame", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "mge", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.", "example": "ERP004492", "homepage": "https://www.ebi.ac.uk/metagenomics", "mappings": { "miriam": "mgnify.proj", "n2t": "mgnify.proj" }, "name": "MGnify Project", "pattern": "^[A-Z]+[0-9]+$", "preferred_prefix": "mgnify.proj", "uri_format": "https://www.ebi.ac.uk/metagenomics/projects/$1" }, "mgnify.samp": { "description": "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.", "example": "SRS086444", "homepage": "https://www.ebi.ac.uk/metagenomics", "mappings": { "miriam": "mgnify.samp", "n2t": "mgnify.samp" }, "name": "MGnify Sample", "pattern": "^[A-Z]+[0-9]+$", "preferred_prefix": "mgnify.samp", "uri_format": "https://www.ebi.ac.uk/metagenomics/samples/$1" }, "mgnifygenome": { "description": "The free-to-use MGnify platform provides assembly, analysis and archiving of microbiome-derived nucleic acid sequence data from a wide range of biomes, with analysis results providing taxonomic and functional\nprofiles. The platform also includes MGnify Proteins, a database of protein sequences derived from the analysis of metagenomic assemblies, and MGnify Genomes, a resource of biome-specific catalogues of microbial genomes, including extensive functional annotations.", "example": "MGYG000004903", "homepage": "https://www.ebi.ac.uk/metagenomics", "mappings": { "miriam": "mgnify.genome" }, "name": "MGnify Genome", "pattern": "^MGYG\\d{9}(\\.\\d+)?$", "preferred_prefix": "mgnifygenome", "uri_format": "https://www.ebi.ac.uk/metagenomics/genomes/$1" }, "mgnifyprotein": { "description": "The free-to-use MGnify platform provides assembly, analysis and archiving of microbiome-derived nucleic acid sequence data from a wide range of biomes, with analysis results providing taxonomic and functional\nprofiles. The platform also includes MGnify Proteins, a database of protein sequences derived from the analysis of metagenomic assemblies, and MGnify Genomes, a resource of biome-specific catalogues of microbial genomes, including extensive functional annotations.", "example": "MGYP000261684433", "homepage": "https://www.ebi.ac.uk/metagenomics", "mappings": { "miriam": "mgnify.protein" }, "name": "MGnify Protein", "pattern": "^MGYP\\d{12}$", "preferred_prefix": "mgnifyprotein", "uri_format": "https://www.ebi.ac.uk/metagenomics/proteins/$1" }, "mgnifystudy": { "description": "The free-to-use MGnify platform provides assembly, analysis and archiving of microbiome-derived nucleic acid sequence data from a wide range of biomes, with analysis results providing taxonomic and functional\nprofiles. The platform also includes MGnify Proteins, a database of protein sequences derived from the analysis of metagenomic assemblies, and MGnify Genomes, a resource of biome-specific catalogues of microbial genomes, including extensive functional annotations.", "example": "MGYS00006794", "homepage": "https://www.ebi.ac.uk/metagenomics", "mappings": { "miriam": "mgnify.study" }, "name": "MGnify Study", "pattern": "^MGYS\\d{8}$", "preferred_prefix": "mgnifystudy", "uri_format": "https://www.ebi.ac.uk/metagenomics/studies/$1" }, "mi": { "banana": "MI", "contact": { "email": "luana.licata@gmail.com", "github": "luanalicata", "name": "Luana Licata", "orcid": "0000-0001-5084-9000" }, "description": "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.", "download_obo": "http://purl.obolibrary.org/obo/mi.obo", "download_owl": "http://purl.obolibrary.org/obo/mi.owl", "example": "0058", "homepage": "https://github.com/HUPO-PSI/psi-mi-CV", "keywords": [ "interaction", "life science", "life sciences, biology", "molecular interaction", "molecule", "obo", "ontology", "protein", "protein interactions", "tib" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "MI", "biocontext": "PSIMI", "biolink": "MI", "bioportal": "MI", "fairsharing": "FAIRsharing.8qzmtr", "go": "PSI-MI", "miriam": "mi", "n2t": "psimi", "obofoundry": "mi", "ols": "mi", "ontobee": "MI", "prefixcommons": "psi.mi", "tib": "mi", "wikidata.entity": "Q81661689" }, "name": "Molecular Interactions Controlled Vocabulary", "namespace_in_lui": true, "pattern": "^\\d{4}$", "preferred_prefix": "MI", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/psi.mi:$1" } ], "publications": [ { "doi": "10.1038/nbt926", "pubmed": "14755292", "title": "The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data", "year": 2004 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MI_$1", "repository": "https://github.com/HUPO-PSI/psi-mi-CV", "synonyms": [ "PSI-MI" ], "uri_format": "http://purl.obolibrary.org/obo/MI_$1" }, "miaa": { "comment": "same as MAT", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "name": "Minimal Information About Anatomy ontology", "preferred_prefix": "miaa", "references": [ "https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/rols/inst/doc/rols.pdf" ] }, "miapa": { "contact": { "email": "hilmar.lapp@duke.edu", "github": "hlapp", "name": "Hilmar Lapp", "orcid": "0000-0001-9107-0714" }, "description": "The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies.\n\nThis ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA.", "download_owl": "http://purl.obolibrary.org/obo/miapa.owl", "example": "0000010", "homepage": "http://www.evoio.org/wiki/MIAPA", "keywords": [ "life science", "obo", "ontology", "phylogenetics", "phylogeny" ], "license": "CC0-1.0", "mappings": { "aberowl": "MIAPA", "biocontext": "MIAPA", "bioportal": "MIAPA", "fairsharing": "FAIRsharing.ca48xs", "obofoundry": "miapa", "ols": "miapa", "ontobee": "MIAPA", "wikidata.entity": "Q81661690" }, "name": "Minimum Anformation About a Phylogenetic Analysis Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MIAPA", "publications": [ { "doi": "10.1089/omi.2006.10.231", "pmc": "PMC3167193", "pubmed": "16901231", "title": "Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)", "year": 2006 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MIAPA_$1", "repository": "https://github.com/evoinfo/miapa", "uri_format": "http://purl.obolibrary.org/obo/MIAPA_$1" }, "mibig": { "contact": { "email": "kblin@biosustain.dtu.dk", "github": "kblin", "name": "Kai Blin", "orcid": "0000-0003-3764-6051" }, "contributor": { "email": "zdoucmm@gmail.com", "github": "mmzdouc", "name": "Mitja M. Zdouc", "orcid": "0000-0001-6534-6609" }, "description": "MIBiG (Minimum Information about a Biosynthetic Gene Cluster) is a data repository and associated data standard designed to describe biosynthetic gene clusters involved in the production of specialized metabolites. It also stores data on measured biological activities and links to other resources such as NCBI, NPAtlas, and ChEBI. MIBiG is used as a reference database, knowledgebase, and training dataset for machine learning.", "example": "BGC0000001", "github_request_issue": 1407, "homepage": "https://mibig.secondarymetabolites.org", "license": "CC-BY-4.0", "name": "Minimum Information about a Biosynthetic Gene Cluster data repository", "pattern": "^BGC\\d{7}$", "preferred_prefix": "mibig", "publications": [ { "doi": "10.1093/nar/gkae1115", "pmc": "PMC11701617", "pubmed": "39657789", "title": "MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration", "year": 2024 } ], "repository": "https://github.com/mibig-secmet/mibig-json", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://mibig.secondarymetabolites.org/go/$1" }, "micro": { "appears_in": [ "mco" ], "contact": { "email": "carrine.blank@umontana.edu", "github": "carrineblank", "name": "Carrine Blank", "orcid": "0000-0002-2100-6351" }, "deprecated": true, "description": "An ontology of prokaryotic phenotypic and metabolic characters", "download_owl": "http://purl.obolibrary.org/obo/micro.owl", "example": "0002999", "homepage": "https://github.com/carrineblank/MicrO", "keywords": [ "assay", "bioinformatics", "cell culture", "microbiology", "obo", "ontology", "phenotype" ], "license": "CC BY 2.0", "mappings": { "aberowl": "MICRO", "biocontext": "MICRO", "fairsharing": "FAIRsharing.brhpb0", "obofoundry": "micro", "ols": "micro", "ontobee": "MICRO", "wikidata.entity": "Q81661692" }, "name": "Ontology of Prokaryotic Phenotypic and Metabolic Characters", "pattern": "^\\d{7}$", "preferred_prefix": "MICRO", "publications": [ { "doi": "10.1186/s13326-016-0060-6", "pmc": "PMC4830071", "pubmed": "27076900", "title": "MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions", "year": 2016 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MICRO_$1", "repository": "https://github.com/carrineblank/MicrO", "uri_format": "http://purl.obolibrary.org/obo/MICRO_$1", "version": "1.5.1" }, "microscope": { "contact": { "email": "cmedigue@genoscope.cns.fr", "name": "MEDIGUE Claudine", "orcid": "0000-0002-3905-1054" }, "description": "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis.", "example": "5601141", "homepage": "http://www.genoscope.cns.fr/agc/microscope", "keywords": [ "comparative genomics", "life science" ], "mappings": { "biocontext": "MICROSCOPE", "fairsharing": "FAIRsharing.3t5qc3", "miriam": "microscope", "n2t": "microscope", "re3data": "r3d100012928" }, "name": "MicroScope", "pattern": "^\\d+$", "preferred_prefix": "microscope", "publications": [ { "doi": "10.1093/nar/gks1194", "pmc": "PMC3531135", "pubmed": "23193269", "title": "MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data", "year": 2012 } ], "uri_format": "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1" }, "microsporidia": { "contact": { "email": "oharb@upenn.edu", "github": "ramobrah", "name": "Omar S. Harb", "orcid": "0000-0003-4446-6200" }, "description": "MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "ECU03_0820i", "homepage": "http://microsporidiadb.org/micro/", "keywords": [ "eukaryotic", "genome" ], "mappings": { "biocontext": "MICROSPORIDIA", "miriam": "microsporidia", "n2t": "microsporidia", "prefixcommons": "microsporidia" }, "name": "MicrosporidiaDB", "pattern": "^\\w+$", "preferred_prefix": "microsporidia", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/microsporidia:$1" } ], "publications": [ { "doi": "10.1093/nar/gkp941", "pmc": "PMC2808945", "pubmed": "19914931", "title": "EuPathDB: a portal to eukaryotic pathogen databases", "year": 2009 } ], "uri_format": "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" }, "millipore": { "description": "Cell line collections (Providers)", "example": "SCC111", "homepage": "https://www.merckmillipore.com/", "mappings": { "cellosaurus": "Millipore" }, "name": "Merck Millipore (EMD Millipore)", "preferred_prefix": "millipore", "uri_format": "https://www.merckmillipore.com/catalogue/item/$1" }, "mimodb": { "contact": { "email": "hj@uestc.edu.cn", "name": "Jian Huang", "orcid": "0000-0003-2314-7104" }, "description": "MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank.", "example": "1", "homepage": "http://immunet.cn/bdb/", "keywords": [ "interaction", "life science", "protein" ], "mappings": { "biocontext": "MIMODB", "fairsharing": "FAIRsharing.bv0zjz", "miriam": "mimodb", "n2t": "mimodb", "prefixcommons": "mimodb" }, "name": "MimoDB", "pattern": "^\\d+$", "preferred_prefix": "mimodb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/mimodb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkv1100", "pmc": "PMC4702802", "pubmed": "26503249", "title": "BDB: biopanning data bank", "year": 2015 }, { "doi": "10.1093/nar/gkr922", "pmc": "PMC3245166", "pubmed": "22053087", "title": "MimoDB 2.0: a mimotope database and beyond", "year": 2011 }, { "doi": "10.3390/molecules15118279", "pmc": "PMC6259156", "pubmed": "21079566", "title": "MimoDB: a new repository for mimotope data derived from phage display technology", "year": 2010 } ], "uri_format": "http://immunet.cn/bdb/index.php/mimoset/$1" }, "minid": { "contact": { "email": "foster@uchicago.edu", "name": "Ian Foster", "orcid": "0000-0003-2129-5269" }, "description": "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation.", "example": "b97957", "homepage": "https://fair-research.org", "keywords": [ "data retrieval", "subject agnostic" ], "mappings": { "biocontext": "MINID", "fairsharing": "FAIRsharing.d099fb", "miriam": "minid", "n2t": "minid" }, "name": "Minimal Viable Identifier", "pattern": "^[A-Za-z0-9]+$", "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/$1" }, "minid.test": { "description": "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. ", "example": "3SBPLMKKVEVR", "homepage": "https://fair-research.org", "mappings": { "miriam": "minid.test" }, "name": "MINID Test", "part_of": "minid", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "minid.test", "uri_format": "https://hdl.handle.net/hdl:20.500.12633/$1" }, "mint": { "banana": "MINT", "banana_peel": "-", "contact": { "email": "luana.licata@gmail.com", "name": "Luana Licata", "orcid": "0000-0001-5084-9000" }, "description": "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals.", "example": "6978836", "homepage": "https://mint.bio.uniroma2.it", "keywords": [ "interaction", "life science", "protein", "proteomics" ], "logo": "https://mint.bio.uniroma2.it/wp-content/uploads/2017/11/cropped-mint-1-e1509905882312.png", "mappings": { "biocontext": "MINT", "edam": "2615", "fairsharing": "FAIRsharing.2bdvmk", "miriam": "mint", "n2t": "mint", "pathguide": "17", "prefixcommons": "mint", "re3data": "r3d100010414", "uniprot": "DB-0158" }, "name": "Molecular Interaction Database", "pattern": "^\\d{1,7}$", "preferred_prefix": "mint", "providers": [ { "code": "", "description": "The Molecular INTeraction database (MINT)", "homepage": "http://mint.bio.uniroma2.it/mint/", "name": "The Molecular INTeraction database (MINT)", "uri_format": "https://mint.bio.uniroma2.it/index.php/results-interactions/?id=$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/mint:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr930", "pmc": "PMC3244991", "pubmed": "22096227", "title": "MINT, the molecular interaction database: 2012 update", "year": 2011 }, { "doi": "10.1093/nar/gkp983", "pmc": "PMC2808973", "pubmed": "19897547", "title": "MINT, the molecular interaction database: 2009 update", "year": 2009 }, { "doi": "10.1093/nar/gkl950", "pmc": "PMC1751541", "pubmed": "17135203", "title": "MINT: the Molecular INTeraction database", "year": 2006 }, { "doi": "10.1016/s0014-5793(01)03293-8", "pubmed": "11911893", "title": "MINT: a Molecular INTeraction database", "year": 2002 } ], "twitter": "MINT_database", "uri_format": "https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-$1" }, "mipmod": { "contact": { "email": "rsankar@iitk.ac.in", "name": "Ramasubbu Sankararamakrishnan", "orcid": "0000-0002-8527-5614" }, "description": "MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures.", "example": "HOSAPI0399", "homepage": "http://bioinfo.iitk.ac.in/MIPModDB", "keywords": [ "protein", "structure" ], "mappings": { "biocontext": "MIPMOD", "miriam": "mipmod", "n2t": "mipmod", "prefixcommons": "mipmod" }, "name": "MIPModDB", "pattern": "^\\w+$", "preferred_prefix": "mipmod", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/mipmod:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr914", "pmc": "PMC3245135", "pubmed": "22080560", "title": "MIPModDB: a central resource for the superfamily of major intrinsic proteins", "year": 2011 } ], "uri_format": "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1" }, "mir": { "banana": "MIR", "description": "The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or \"PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources.", "example": "00100037", "homepage": "https://registry.identifiers.org/registry", "mappings": { "biocontext": "MIR", "miriam": "mir", "n2t": "mir" }, "name": "Identifiers.org Registry", "namespace_in_lui": true, "pattern": "^\\d{8}$", "preferred_prefix": "mir", "uri_format": "https://registry.identifiers.org/registry?query=MIR:$1" }, "mirbase": { "contact": { "email": "sam.griffiths-jones@manchester.ac.uk", "github": "samgriffithsjones", "name": "Sam Griffiths-Jones", "orcid": "0000-0001-6043-807X" }, "description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR).", "example": "MI0026471", "homepage": "http://www.mirbase.org/", "keywords": [ "biology", "gene", "rna" ], "license": "public domain", "logo": "https://www.mirbase.org/static/images/mirbase-logo_new.png", "mappings": { "biocontext": "MIRBASE", "biolink": "mirbase", "edam": "2642", "fairsharing": "FAIRsharing.hmgte8", "integbio": "nbdc00136", "miriam": "mirbase", "n2t": "mirbase", "ncbi": "miRBase", "pathguide": "210", "prefixcommons": "mirbase", "re3data": "r3d100010566", "togoid": "Mirbase", "wikidata": "P2870" }, "name": "miRBase pre-miRNA", "pattern": "^MI\\d{7}$", "preferred_prefix": "mirbase", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/mirbase:$1" } ], "publications": [ { "doi": "10.1093/nar/gky1141", "pmc": "PMC6323917", "pubmed": "30423142", "title": "miRBase: from microRNA sequences to function", "year": 2019 }, { "doi": "10.1093/nar/gkt1181", "pmc": "PMC3965103", "pubmed": "24275495", "title": "miRBase: annotating high confidence microRNAs using deep sequencing data", "year": 2013 }, { "doi": "10.1093/nar/gkq1027", "pmc": "PMC3013655", "pubmed": "21037258", "title": "miRBase: integrating microRNA annotation and deep-sequencing data", "year": 2010 }, { "doi": "10.1093/nar/gkm952", "pmc": "PMC2238936", "pubmed": "17991681", "title": "miRBase: tools for microRNA genomics", "year": 2007 }, { "doi": "10.1093/nar/gkj112", "pmc": "PMC1347474", "pubmed": "16381832", "title": "miRBase: microRNA sequences, targets and gene nomenclature", "year": 2006 }, { "doi": "10.1093/nar/gkh023", "pmc": "PMC308757", "pubmed": "14681370", "title": "The microRNA Registry", "year": 2004 } ], "uri_format": "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1" }, "mirbase.family": { "contact": { "email": "sam.griffiths-jones@manchester.ac.uk", "github": "samgriffithsjones", "name": "Sam Griffiths-Jones", "orcid": "0000-0001-6043-807X" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download.", "example": "MIPF0000002", "homepage": "http://www.mirbase.org/", "keywords": [ "gene", "mirna" ], "license": "public domain", "logo": "https://www.mirbase.org/static/images/mirbase-logo_new.png", "mappings": { "wikidata.entity": "Q6826947" }, "name": "miRBase Families", "preferred_prefix": "mirbase.family", "synonyms": [ "MIRBASE_FAMILY" ], "uri_format": "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1" }, "mirbase.mature": { "contact": { "email": "sam.griffiths-jones@manchester.ac.uk", "github": "samgriffithsjones", "name": "Sam Griffiths-Jones", "orcid": "0000-0001-6043-807X" }, "description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence.", "example": "MIMAT0046872", "homepage": "http://www.mirbase.org/", "keywords": [ "nucleotide", "sequence" ], "license": "public domain", "logo": "https://www.mirbase.org/static/images/mirbase-logo_new.png", "mappings": { "biocontext": "MIRBASE.MATURE", "miriam": "mirbase.mature", "n2t": "mirbase.mature", "prefixcommons": "mirbase.mature", "wikidata": "P2871" }, "name": "miRBase mature miRNA", "pattern": "^MIMAT\\d{7}$", "preferred_prefix": "mirbase.mature", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/mirbase.mature:$1" } ], "synonyms": [ "MIRBASEM" ], "uri_format": "http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1" }, "mirex": { "contact": { "email": "wmk@amu.edu.pl", "name": "Wojciech M. Karlowski", "orcid": "0000-0002-8086-5404" }, "description": "mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages.", "example": "165a", "homepage": "http://comgen.pl/mirex/?page=home", "keywords": [ "life science" ], "mappings": { "biocontext": "MIREX", "fairsharing": "FAIRsharing.q3b39v", "integbio": "nbdc02064", "miriam": "mirex", "n2t": "mirex" }, "name": "mirEX", "pattern": "^\\d+(\\w+)?$", "preferred_prefix": "mirex", "publications": [ { "doi": "10.1186/s12870-015-0533-2", "pmc": "PMC4490709", "pubmed": "26141515", "title": "mirEX 2.0 - an integrated environment for expression profiling of plant microRNAs", "year": 2015 }, { "doi": "10.1093/nar/gkr878", "pmc": "PMC3245179", "pubmed": "22013167", "title": "mirEX: a platform for comparative exploration of plant pri-miRNA expression data", "year": 2011 } ], "uri_format": "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes" }, "mirgenedb": { "contact": { "email": "BastianFromm@gmail.com", "name": "Bastian Fromm", "orcid": "0000-0003-0352-3037" }, "contributor": { "email": "palayoor.n@northeastern.edu", "github": "nalikapalayoor", "name": "Nalika Palayoor", "orcid": "0009-0008-8406-631X" }, "description": "mircoRNA Gene Database is a collection of animal microRNA genes. This database allows researchers to analyze mircoRNA properties like secondary structure and features in a phylogenetic context.", "example": "Hsa-Let-7-P2a3", "github_request_issue": 1393, "homepage": "https://mirgenedb.org/", "name": "microRNA Gene Database", "pattern": "^[a-zA-Z0-9]+(-[a-zA-Z0-9]+)+$", "preferred_prefix": "mirgenedb", "publications": [ { "doi": "10.1093/nar/gkae1094", "pmc": "PMC11701709", "pubmed": "39673268", "title": "MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models", "year": 2025 }, { "doi": "10.1093/nar/gkab1101", "pmc": "PMC8728216", "pubmed": "34850127", "title": "MirGeneDB 2.1: toward a complete sampling of all major animal phyla", "year": 2022 }, { "doi": "10.1093/nar/gkz885", "pmc": "PMC6943042", "pubmed": "31598695", "title": "MirGeneDB 2.0: the metazoan microRNA complement", "year": 2020 }, { "doi": "10.1146/annurev-genet-120213-092023", "pmc": "PMC4743252", "pubmed": "26473382", "title": "A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome", "year": 2015 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://mirgenedb.org/browse?qtype=mgid&org=ALL&query=$1" }, "miriam": { "contact": { "email": "n.lenovere@gmail.com", "name": "Nicolas Le Novère", "orcid": "0000-0002-6309-7327" }, "description": "Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain.", "example": "pubmed", "homepage": "https://www.ebi.ac.uk", "keywords": [ "biochemistry", "biomedical science", "life science" ], "mappings": { "edam": "1162", "fairsharing": "FAIRsharing.ap169a", "miriam": "identifiers.namespace" }, "name": "Identifiers.org namespace", "pattern": "^[0-9a-z_:\\.-]+$", "preferred_prefix": "miriam", "publications": [ { "doi": "10.1093/nar/gkr1097", "pmc": "PMC3245029", "pubmed": "22140103", "title": "Identifiers.org and MIRIAM Registry: community resources to provide persistent identification", "year": 2011 }, { "doi": "10.1186/1752-0509-1-58", "pmc": "PMC2259379", "pubmed": "18078503", "title": "MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology", "year": 2007 }, { "doi": "10.1038/nbt1156", "pubmed": "16333295", "title": "Minimum information requested in the annotation of biochemical models (MIRIAM)", "year": 2005 } ], "synonyms": [ "identifiers.namespace" ], "uri_format": "https://registry.identifiers.org/registry/$1" }, "miriam.collection": { "banana": "MIR", "deprecated": true, "description": "MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections.", "example": "00000008", "homepage": "https://www.ebi.ac.uk/miriam/", "mappings": { "biocontext": "MIRIAM.COLLECTION", "miriam": "miriam.collection", "n2t": "miriam.collection" }, "name": "MIRIAM Registry collection", "pattern": "^000\\d{5}$", "preferred_prefix": "miriam.collection", "uri_format": "https://www.ebi.ac.uk/miriam/main/$1" }, "miriam.resource": { "banana": "MIR", "deprecated": true, "description": "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases.", "example": "00100005", "homepage": "https://www.ebi.ac.uk/miriam/", "keywords": [ "registry" ], "mappings": { "biocontext": "MIRIAM.RESOURCE", "miriam": "miriam.resource", "n2t": "miriam.resource", "prefixcommons": "miriam.resource" }, "name": "MIRIAM Legacy Registry Identifier", "pattern": "^001\\d{5}$", "preferred_prefix": "miriam.resource", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/miriam.resource:$1" } ], "publications": [ { "doi": "10.1186/1752-0509-1-58", "pmc": "PMC2259379", "pubmed": "18078503", "title": "MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology", "year": 2007 } ], "uri_format": "https://resolver.api.identifiers.org/resolveMirId/$1" }, "mirnao": { "contact": { "email": "topalis@imbb.forth.gr", "name": "Pantelis Topalis", "orcid": "0000-0002-1635-4810" }, "deprecated": true, "description": "An application ontology for use with miRNA databases.", "download_owl": "http://aber-owl.net/media/ontologies/MIRNAO/11/mirnao.owl", "homepage": "http://code.google.com/p/mirna-ontology/", "keywords": [ "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "MIRNAO", "biocontext": "MIRNAO", "bioportal": "MIRNAO", "obofoundry": "mirnao", "ontobee": "miRNAO" }, "name": "microRNA Ontology", "preferred_prefix": "MIRNAO", "rdf_uri_format": "http://purl.obolibrary.org/obo/MIRNAO_$1", "uri_format": "http://purl.obolibrary.org/obo/MIRNAO_$1" }, "mirnest": { "contact": { "email": "miszcz@amu.edu.pl", "name": "Michael Szcześniak", "orcid": "0000-0002-6050-9525" }, "description": "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species.", "example": "MNEST029358", "homepage": "http://rhesus.amu.edu.pl/mirnest/copy/", "keywords": [ "expression", "genomics", "life science", "prediction" ], "mappings": { "biocontext": "MIRNEST", "fairsharing": "FAIRsharing.5pfx4r", "integbio": "nbdc01703", "miriam": "mirnest", "n2t": "mirnest", "prefixcommons": "mirnest" }, "name": "miRNEST", "pattern": "^MNEST\\d+$", "preferred_prefix": "mirnest", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/mirnest:$1" } ], "publications": [ { "doi": "10.1093/nar/gkt1156", "pmc": "PMC3965105", "pubmed": "24243848", "title": "miRNEST 2.0: a database of plant and animal microRNAs", "year": 2013 }, { "doi": "10.1093/nar/gkr1159", "pmc": "PMC3245016", "pubmed": "22135287", "title": "miRNEST database: an integrative approach in microRNA search and annotation", "year": 2011 } ], "uri_format": "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1" }, "miro": { "contact": { "email": "louis@imbb.forth.gr", "name": "Christos Louis", "orcid": "0000-0003-2497-2210" }, "deprecated": true, "description": "Application ontology for entities related to insecticide resistance in mosquitos", "download_obo": "http://purl.obolibrary.org/obo/miro.obo", "download_owl": "http://purl.obolibrary.org/obo/miro.owl", "example": "40000617", "homepage": "https://github.com/VEuPathDB-ontology/MIRO", "keywords": [ "life science", "mutation", "obo", "ontology", "phenotype" ], "mappings": { "aberowl": "MIRO", "biocontext": "MIRO", "bioportal": "MIRO", "fairsharing": "FAIRsharing.sjf113", "obofoundry": "miro", "ols": "miro", "ontobee": "MIRO" }, "name": "Mosquito insecticide resistance", "pattern": "^\\d{8}$", "preferred_prefix": "MIRO", "publications": [ { "doi": "10.1371/journal.pntd.0000465", "pmc": "PMC2694272", "pubmed": "19547750", "title": "MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide resistance in mosquito disease vectors", "year": 2009 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MIRO_$1", "repository": "https://github.com/VEuPathDB-ontology/MIRO", "uri_format": "http://purl.obolibrary.org/obo/MIRO_$1", "version": "2014-05-14" }, "mirtarbase": { "contact": { "email": "ken.sd.hsu@gmail.com", "name": "Sheng-Da Hsu", "orcid": "0000-0002-8214-1696" }, "contributor_extras": [ { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } ], "deprecated": true, "description": "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments.", "example": "MIRT000002", "homepage": "https://mirtarbase.cuhk.edu.cn/", "keywords": [ "life science" ], "mappings": { "biocontext": "MIRTARBASE", "fairsharing": "FAIRsharing.f0bxfg", "integbio": "nbdc01217", "miriam": "mirtarbase", "n2t": "mirtarbase", "pathguide": "715", "wikidata": "P2646" }, "name": "mirTarBase", "pattern": "^MIRT\\d{6}$", "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", "pubmed": "21071411", "title": "miRTarBase: a database curates experimentally validated microRNA-target interactions", "year": 2010 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/940" ], "uri_format": "https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid=$1" }, "mirte": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs", "example": "miR-1", "homepage": "http://www.russelllab.org/miRNAs/", "name": "miRNA Target Prediction at EMBL", "preferred_prefix": "mirte" }, "mite": { "contact": { "email": "zdoucmm@gmail.com", "github": "mmzdouc", "name": "Mitja M. Zdouc", "orcid": "0000-0001-6534-6609" }, "contributor": { "email": "zdoucmm@gmail.com", "github": "mmzdouc", "name": "Mitja M. Zdouc", "orcid": "0000-0001-6534-6609" }, "description": "MITE (Minimum Information about a Tailoring Enzyme) is a data repository and associated data standard designed to capture the reaction- and substrate-specificities of tailoring enzymes. Community-driven and fully expert-reviewed, it represents enzymatic reactions using reaction SMARTS and links to established resources such as UniProt, NCBI GenPept, Rhea, and MIBiG. MITE serves as a knowledgebase for enzyme and pathway annotation, in silico biosynthesis, and machine learning applications.", "example": "MITE0000001", "github_request_issue": 1405, "homepage": "https://mite.bioinformatics.nl", "license": "CC0-1.0", "name": "Minimum Information about a Tailoring Enzyme data repository", "pattern": "^MITE\\d{7}$", "preferred_prefix": "mite", "publications": [ { "doi": "10.26434/chemrxiv-2024-78mtl", "title": "The Minimum Information about a Tailoring Enzyme/Maturase data standard for capturing natural product biosynthesis", "year": 2024 } ], "repository": "https://github.com/mite-standard/mite_data", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://mite.bioinformatics.nl/repository/$1" }, "mito": { "contact": { "github": "matteo-guenci", "name": "Matteo Guenci", "orcid": "0009-0006-3139-1667" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology with predicates to formalization of the concept of mentions. The mentions may be either explicit (e.g. as when well stated into an article \"Dr. Johnson's groundbreaking research on climate change\") or implicit (e.g. such as discussing \"seminal studies in the field\"). MiTO contains the object property mito:mentions and its inverse mito:isMentionedBy.", "example": "MentionType", "github_request_issue": 1663, "homepage": "http://purl.org/spar/mito", "keywords": [ "mentions", "natural language processing", "ner", "nlp", "ontology", "text mining" ], "name": "Mention Typing Ontology", "preferred_prefix": "mito", "repository": "https://github.com/SPAROntologies/mito", "uri_format": "http://purl.org/spar/mito/$1" }, "mixs": { "comment": "Some things to be decided before granting - [ ] should the prefix be mixs, gsc.mixs, MIxS, MIXS, ...? - [ ] MIxS terms are most commonly identified by a short computable stable label, e.g ph_regm. The GSC CIG team are creating numeric identifiers, e.g. MIXS:0001056 - Should we support both schemes? - If we do, should these be different prefixes? I would strongly recommend this. E.g. mixs.term:ph_regm, mixs:0001056. We can then have different regex patterns for both Additional notes: - It currently redirects to the tdwg wiki but this is I assume temporary", "contact": { "email": "mam@lbl.gov", "github": "turbomam", "name": "Mark Andrew Miller", "orcid": "0000-0001-9076-6066" }, "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor_extras": [ { "email": "chris@gigasciencejournal.com", "github": "only1chunts", "name": "Chris Hunter", "orcid": "0000-0002-1335-0881" }, { "email": "lindsey.anderson@pnnl.gov", "github": "lnanderson", "name": "Lindsey N. Anderson", "orcid": "0000-0002-8741-7823" }, { "email": "mam@lbl.gov", "github": "turbomam", "name": "Mark Andrew Miller", "orcid": "0000-0001-9076-6066" } ], "description": "The GSC family of minimum information standards (checklists) – Minimum Information about any (x) Sequence (MIxS). MIxS identifiers are for terms describing an aspect of an environmental sample.", "download_owl": "https://w3id.org/mixs/mixs.owl.ttl", "download_rdf": "https://w3id.org/mixs/mixs.owl.ttl", "example": "0001056", "github_request_issue": 151, "homepage": "https://w3id.org/mixs", "keywords": [ "ontology" ], "mappings": { "aberowl": "MIXS", "bioportal": "MIXS", "fairsharing": "FAIRsharing.9aa0zp", "ols": "gscmixs" }, "name": "Minimum Information about any (x) Sequence", "pattern": "^\\d{7}$", "preferred_prefix": "MIXS", "providers": [ { "code": "github", "description": "MIxS LinkML schema", "homepage": "https://genomicsstandardsconsortium.github.io/mixs", "name": "MIxS LinkML schema", "uri_format": "https://genomicsstandardsconsortium.github.io/mixs/$1" } ], "publications": [ { "doi": "10.1038/nbt.1823", "pmc": "PMC3367316", "pubmed": "21552244", "title": "Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications", "year": 2011 } ], "rdf_uri_format": "https://w3id.org/mixs/$1", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1738" ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://w3id.org/mixs/$1" }, "mlc": { "description": "MLCommons Association artifacts, including benchmark results, datasets, and saved models.", "example": "0.7-123", "homepage": "https://mlcommons.org/en/", "mappings": { "miriam": "mlc" }, "name": "MLCommons Association", "pattern": "^[0-9a-zA-Z\\.\\-\\_]+$", "preferred_prefix": "mlc", "uri_format": "https://www.mlcommons.org/mlc-id/$1" }, "mmdb": { "contact": { "email": "siqian.he@nih.gov", "name": "Siqian He", "orcid": "0000-0002-1707-4167" }, "description": "The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites.", "example": "50885", "homepage": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure", "keywords": [ "dna", "interaction", "protein", "small molecule", "structure" ], "mappings": { "biocontext": "MMDB", "edam": "2667", "miriam": "mmdb", "n2t": "mmdb", "pathguide": "508", "prefixcommons": "mmdb" }, "name": "Molecular Modeling Database", "pattern": "^\\d{1,5}$", "preferred_prefix": "mmdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/mmdb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkl952", "pmc": "PMC1751549", "pubmed": "17135201", "title": "MMDB: annotating protein sequences with Entrez's 3D-structure database", "year": 2006 } ], "uri_format": "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1" }, "mmmp.biomaps": { "description": "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.", "example": "37", "homepage": "http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp", "keywords": [ "interaction", "molecule", "pathway" ], "mappings": { "biocontext": "MMMP:BIOMAPS", "biolink": "mmmp.biomaps", "miriam": "mmmp.biomaps", "n2t": "biomaps", "prefixcommons": "mmmp" }, "name": "Melanoma Molecular Map Project Biomaps", "pattern": "^\\d+$", "preferred_prefix": "mmmp.biomaps", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/psi.mod:$1" } ], "publications": [ { "doi": "10.1038/nbt0808-864", "pubmed": "18688235", "title": "The PSI-MOD community standard for representation of protein modification data", "year": 2008 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MOD_$1", "repository": "https://github.com/HUPO-PSI/psi-mod-CV", "synonyms": [ "PSI-MOD" ], "uri_format": "http://purl.obolibrary.org/obo/MOD_$1", "version": "1.032.4" }, "modalia": { "contact": { "email": "abdelmoneim.desouki@tu-darmstadt.de", "github": "abdoudesouki", "name": "Abdelmoneim Amer Desouki", "orcid": "0000-0003-2083-1277" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The aim of DALIA project is to build a platform for learning material for Research Data Management (RDM) and Data Science. The platform is based on a knowledge graph. We introduce MoDalia, the base ontology of DALIA knowledge graph. Modalia inherits some modules from EduCOR. It includes also modelling of micro -credentials and certificates", "download_obo": "https://git.rwth-aachen.de/dalia/dalia-ontology/-/raw/main/modalia.obo", "download_rdf": "https://git.rwth-aachen.de/dalia/dalia-ontology/-/raw/main/MoDalia.ttl", "example": "belongsToCluster", "homepage": "https://dalia.pages.rwth-aachen.de/dalia-ontology/", "keywords": [ "educational science", "ontology", "tib" ], "license": "CC-BY-4.0", "mappings": { "bartoc": "20825", "tib": "modalia" }, "name": "MoDALIA Ontology", "preferred_prefix": "modalia", "rdf_uri_format": "https://purl.org/ontology/modalia#$1", "repository": "https://git.rwth-aachen.de/dalia/dalia-ontology", "uri_format": "https://purl.org/ontology/modalia#$1" }, "modeldb": { "contact": { "email": "perry.miller@yale.edu", "name": "Perry Miller", "orcid": "0000-0002-5176-943X" }, "description": "ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment.", "example": "45539", "homepage": "https://modeldb.science", "keywords": [ "computational biology", "life science", "neurobiology" ], "mappings": { "biocontext": "MODELDB", "edam": "2669", "fairsharing": "FAIRsharing.5rb3fk", "integbio": "nbdc02085", "miriam": "modeldb", "n2t": "modeldb", "prefixcommons": "modeldb", "re3data": "r3d100011330" }, "name": "ModelDB", "pattern": "^\\d+$", "preferred_prefix": "modeldb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/modeldb:$1" } ], "publications": [ { "doi": "10.1136/jamia.1996.97084512", "pmc": "PMC116323", "pubmed": "8930855", "title": "ModelDB: an environment for running and storing computational models and their results applied to neuroscience", "year": 1996 }, { "doi": "10.1007/s10827-016-0623-7", "pmc": "PMC5279891", "pubmed": "27629590", "title": "Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience", "year": 2016 }, { "doi": "10.1023/b:jcns.0000023869.22017.2e", "pmc": "PMC3732827", "pubmed": "15218350", "title": "ModelDB: A Database to Support Computational Neuroscience", "year": 2004 }, { "doi": "10.1385/ni:1:1:135", "pmc": "PMC3728921", "pubmed": "15055399", "title": "ModelDB: making models publicly accessible to support computational neuroscience", "year": 2003 }, { "doi": "10.1385/NI:1:1:135", "title": "ModelDB: making models publicly accessible to support computational neuroscience." }, { "doi": "10.1023/B:JCNS.0000023869.22017.2e", "title": "ModelDB: A Database to Support Computational Neuroscience." } ], "twitter": "SenseLabProject", "uri_format": "https://modeldb.science/$1" }, "modeldb.concept": { "description": "Concept used by ModelDB, an accessible location for storing and efficiently retrieving computational neuroscience models.", "example": "3639", "homepage": "https://www.yale.edu", "mappings": { "miriam": "modeldb.concept" }, "name": "ModelDB concept", "pattern": "^\\d+$", "preferred_prefix": "modeldb.concept", "uri_format": "https://modeldb.science/modellist/$1" }, "modsci": { "contact": { "email": "sm_fathalla@yahoo.com", "name": "SaidFathalla" }, "description": "Modern Science Ontology (ModSci), for modeling relationships between modern science branches and related entities, such as scientific discoveries, phenomena, renowned scientists, instruments, etc. ModSci is an upper ontology that provides a unifying framework for the various domain ontologies that make up the Science Knowledge Graph Ontology Suite. The Systematic Approach for Building Ontologies (SABiO) has been followed in the development of ModSci. ModSci is a poly-hierarchical ontology that can be utilized in semantic web applications. ModSci powers two projects for semantically representing scholarly information: Open Research Knowledge Graph (for the categorization of research papers) and OpenResearch.org (for the categorization of the information about scientific events, research projects, scientific papers, publishers, and journals).", "download_owl": "http://aber-owl.net/media/ontologies/ModSci/2/modsci.owl", "example": "AcidbaseChemistry", "homepage": "https://saidfathalla.github.io/Science-knowledge-graph-ontologies/doc/ModSci_doc/index-en.html", "keywords": [ "academy", "nfdi4ing", "ontology", "society" ], "mappings": { "aberowl": "ModSci", "bioportal": "MODSCI", "lov": "modsci", "tib": "modsci" }, "name": "Modern Science Ontology", "preferred_prefix": "modsci", "uri_format": "https://w3id.org/skgo/modsci#$1" }, "moid": { "description": "M3G stands for “Metadata Management and distribution system for Multiple GNSS Networks”. M3G allows to upload, validate, and distribute GNSS station metadata such as IGS-style site logs, information about local networks, DOIs, nominal data provision, data licenses attached to the daily RINEX data, etc...", "example": "station.6051b2f8b9142a5b8c676342", "homepage": "https://www.astro.oma.be/en/", "mappings": { "miriam": "moid" }, "name": "Metadata Management and distribution system for Multiple GNSS Networks", "pattern": "^[a-zA-Z0-9]+\\.[a-f0-9]{24}$", "preferred_prefix": "moid", "uri_format": "https://gnss-metadata.eu/MOID/$1" }, "molbase": { "description": "Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier.", "example": "128796-39-4", "homepage": "http://www.molbase.com/", "mappings": { "biocontext": "MOLBASE", "miriam": "molbase", "n2t": "molbase" }, "name": "Molbase", "pattern": "^(\\d{1,7}\\-\\d{2}\\-\\d)|([A-Za-z0-9\\+\\-\\_]+)$", "preferred_prefix": "molbase", "uri_format": "http://www.molbase.com/en/index.php?app=search&search_keyword=$1" }, "molbase.sheffield": { "comment": "Do not confuse with molbase, which is a provider. These resources are unrelated.", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students.", "example": "1868", "homepage": "https://winter.group.shef.ac.uk/molbase/", "name": "MolBase", "pattern": "^\\d+$", "preferred_prefix": "molbase.sheffield" }, "molbic.cellline": { "contact": { "email": "zhufeng@zju.edu.cn", "name": "Feng Zhu", "orcid": "0000-0001-8069-0053" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "MolBiC provides information about cell-based molecular bioactivities along with associated compounds, proteins and cell lines. 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The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance.", "download_obo": "http://purl.obolibrary.org/obo/ms.obo", "download_owl": "http://purl.obolibrary.org/obo/ms.owl", "example": "1000560", "homepage": "http://www.psidev.info/groups/controlled-vocabularies", "keywords": [ "chemistry", "dataplant", "nfdi4cat", "nfdi4chem", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "MS", "biocontext": "MS", "bioportal": "MS", "miriam": "ms", "n2t": "ms", "obofoundry": "ms", "ols": "ms", "ontobee": "MS", "tib": "ms", "wikidata.entity": "Q81661714" }, "name": "Mass spectrometry ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "MS", "publications": [ { "doi": "10.1093/database/bat009", "pmc": "PMC3594986", "pubmed": "23482073", "title": "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary", "year": 2013 } ], "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_$1", "version": "4.1.231" }, "msigdb": { "contact": { "email": "jmesirov@ucsd.edu", "name": "Jill P. Mesirov", "orcid": "0000-0002-9755-2818" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can", "example": "M1", "homepage": "https://www.gsea-msigdb.org", "keywords": [ "gene family", "gene group", "gene set", "pathway", "reaction" ], "license": "CC-BY-4.0", "logo": "https://www.gsea-msigdb.org/gsea/images/GSEA-logo.gif", "mappings": { "biolink": "MSigDB", "integbio": "nbdc02550" }, "name": "Molecular Signatures Database", "pattern": "^M\\d+$", "preferred_prefix": "msigdb", "providers": [ { "code": "biopragmatics", "description": "An OBO to Website of MMSigDB", "homepage": "https://biopragmatics.github.io/providers/msigdb/", "name": "MMSigDB from Biopragmatics", "uri_format": "https://biopragmatics.github.io/providers/msigdb/$1" } ], "synonyms": [ "msig" ], "uri_format": "https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/$1" }, "msio": { "contact": { "email": "philippe.rocca-serra@oerc.ox.ac.uk", "name": "Philippe Rocca-Serra", "orcid": "0000-0001-9853-5668" }, "description": "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.", "download_owl": "https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl", "example": "0000111", "homepage": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO", "keywords": [ "annotation", "data analysis", "dataplant", "experimental measurement", "functional magnetic resonance imaging", "life sciences, biology", "mass spectrum", "metabolomics", "nmr", "nuclear magnetic resonance spectroscopy", "omics", "ontology" ], "mappings": { "fairsharing": "FAIRsharing.4c7f91", "ols": "msio", "tib": "msio" }, "name": "Metabolomics Standards Initiative Ontology", "pattern": "^\\d{7}$", "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" }, "mtbd": { "description": "The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, and information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors.", "example": "1374", "homepage": "http://tumor.informatics.jax.org", "keywords": [ "dna", "gene expression" ], "mappings": { "prefixcommons": "mtbd" }, "name": "Mouse Tumor Biology Database", "preferred_prefix": "mtbd", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/mtbd:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key=$1" }, "mth": { "appears_in": [ "mondo", "umls" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Unified Medical Language System® (UMLS®) Metathesaurus (MTH) was developed and is maintained by the U.S. National Library of Medicine (NLM). MTH contains concept names, attributes, relationships, and other data that were created by NLM to facilitate construction of the UMLS Metathesaurus.", "example": "U001388", "github_request_issue": 1573, "homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MTH/index.html", "mappings": { "hl7": "2.16.840.1.113883.6.189" }, "name": "Metathesaurus Names", "pattern": "^U\\d+$", "preferred_prefix": "mth", "synonyms": [ "umls.mth" ], "uri_format": "https://uts.nlm.nih.gov/uts/umls/vocabulary/MTH/$1" }, "multicellds": { "contact": { "email": "samuel.friedman@cammlab.org", "name": "Samuel Friedman", "orcid": "0000-0001-8003-6860" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.", "example": "MCDS_S_0000000001", "homepage": "http://multicellds.org/MultiCellDB.php", "keywords": [ "life science" ], "mappings": { "fairsharing": "FAIRsharing.pqzyd5" }, "name": "MultiCellDS", "preferred_prefix": "multicellds", "uri_format": "http://multicellds.org/MultiCellDB/$1" }, "multicellds.cell_line": { "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.", "example": "MCDS_L_0000000001", "homepage": "http://multicellds.org/MultiCellDB.php", "mappings": { "biocontext": "MULTICELLDS.CELL_LINE", "miriam": "multicellds.cell_line", "n2t": "multicellds.cell_line" }, "name": "MultiCellDS Digital Cell Line", "part_of": "multicellds", "pattern": "^MCDS_L_[a-zA-Z0-9]{1,10}$", "preferred_prefix": "multicellds.cell_line", "uri_format": "http://multicellds.org/MultiCellDB/$1" }, "multicellds.collection": { "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections).", "example": "MCDS_C_0000000001", "homepage": "http://multicellds.org/MultiCellDB.php", "mappings": { "biocontext": "MULTICELLDS.COLLECTION", "miriam": "multicellds.collection", "n2t": "multicellds.collection" }, "name": "MultiCellDS collection", "part_of": "multicellds", "pattern": "^MCDS_C_[a-zA-Z0-9]{1,10}$", "preferred_prefix": "multicellds.collection", "uri_format": "http://multicellds.org/MultiCellDB/$1" }, "multicellds.snapshot": { "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data.", "example": "MCDS_S_0000000001", "homepage": "http://multicellds.org/MultiCellDB.php", "mappings": { "biocontext": "MULTICELLDS.SNAPSHOT", "miriam": "multicellds.snapshot", "n2t": "multicellds.snapshot" }, "name": "MultiCellDS Digital snapshot", "part_of": "multicellds", "pattern": "^MCDS_S_[a-zA-Z0-9]{1,10}$", "preferred_prefix": "multicellds.snapshot", "uri_format": "http://multicellds.org/MultiCellDB/$1" }, "mvx": { "contributor": { "email": "lindsey.anderson@pnnl.gov", "github": "lnanderson", "name": "Lindsey N. Anderson", "orcid": "0000-0002-8741-7823" }, "description": "The CDC's National Center for Immunization and Respiratory Diseases ([NCIRD](https://www.cdc.gov/ncird/)) developed and maintains HL7 Table 0227, Manufacturers of Vaccines (MVX). It includes both active and inactive manufacturers of vaccines in the US. Inactive MVX codes allow transmission of historical immunization records. When [MVX code is paired with a CVX code](https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=tradename) (vaccine administered code), the specific trade named vaccine may be indicated.", "example": "ASZ", "github_request_issue": 986, "homepage": "https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=mvx", "mappings": { "hl7": "2.16.840.1.113883.6.60" }, "name": "Manufacturers of Vaccines", "pattern": "^\\w+$", "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=$1" }, "mw.project": { "description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).", "example": "PR000001", "homepage": "http://www.metabolomicsworkbench.org/", "mappings": { "biocontext": "MW.PROJECT", "miriam": "mw.project", "n2t": "mw.project" }, "name": "Metabolomics Workbench Project", "pattern": "^PR[0-9]{6}$", "preferred_prefix": "mw.project", "uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1" }, "mw.study": { "description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).", "example": "ST000900", "homepage": "http://www.metabolomicsworkbench.org/", "mappings": { "biocontext": "MW.STUDY", "miriam": "mw.study", "n2t": "mw.study" }, "name": "Metabolomics Workbench Study", "pattern": "^ST[0-9]{6}$", "preferred_prefix": "mw.study", "providers": [ { "code": "omicsdi", "description": "Metabolomics Workbench Study through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "Metabolomics Workbench Study through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/metabolomics_workbench/$1" } ], "uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1" }, "mwo": { "contact": { "email": "ho_beygi@yahoo.com", "name": "Hossein Beygi Nasrabadi" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "NFDI-MatWerk aims to establish a digital infrastructure for Materials Science and Engineering (MSE), fostering improved data sharing and collaboration. This repository provides comprehensive documentation for NFDI MatWerk Ontology (MWO) v3.0.0, a foundational framework designed to structure research data and enhance interoperability within the MSE community. To ensure compliance with top-level ontology standards, MWO v3.0.0 is aligned with the Basic Formal Ontology (BFO) and incorporates the modular approach of the NFDIcore mid-level ontology, enriching metadata through standardized classes and properties. The mwo addresses key aspects of MSE research data, including the NFDI-MatWerk community structure, covering task areas, infrastructure use cases, projects, researchers, and organizations. It also describes essential NFDI resources, such as software, workflows, ontologies, publications, datasets, metadata schemas, instruments, facilities, and educational materials. Additionally, mwo represents NFDI-MatWerk services, academic events, courses, and international collaborations. As the foundation for the MSE Knowledge Graph, mwo facilitates efficient data integration and retrieval, promoting collaboration and knowledge representation across MSE domains. This digital transformation enhances data discoverability, reusability, and accelerates scientific exchange, innovation, and discoveries by optimizing research data management and accessibility. (from repository)", "download_owl": "https://github.com/ISE-FIZKarlsruhe/mwo/raw/refs/heads/main/mwo.owl", "example": "0001109", "homepage": "https://github.com/ISE-FIZKarlsruhe/mwo", "keywords": [ "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "MWO", "bioportal": "MWO" }, "name": "NFDI MatWerk Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "mwo", "repository": "https://github.com/ISE-FIZKarlsruhe/mwo", "uri_format": "http://purls.helmholtz-metadaten.de/mwo/mwo_$1" }, "myco": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.", "example": "ML0224", "example_extras": [ "MMAR_2462", "MSMEG_3769", "Rv1908c" ], "homepage": "https://mycobrowser.epfl.ch", "name": "MycoBrowser", "preferred_prefix": "myco", "uri_format": "https://mycobrowser.epfl.ch/genes/$1" }, "myco.lepra": { "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.", "example": "ML0224", "homepage": "https://mycobrowser.epfl.ch/", "keywords": [ "genome", "sequence" ], "mappings": { "biocontext": "MYCO.LEPRA", "miriam": "myco.lepra", "n2t": "myco.lepra", "prefixcommons": "myco.lepra" }, "name": "MycoBrowser leprae", "part_of": "myco", "pattern": "^ML\\w+$", "preferred_prefix": "myco.lepra", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/myco.lepra:$1" } ], "uri_format": "https://mycobrowser.epfl.ch/genes/$1" }, "myco.marinum": { "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information.", "example": "MMAR_2462", "homepage": "https://mycobrowser.epfl.ch", "keywords": [ "genome", "sequence" ], "mappings": { "biocontext": "MYCO.MARINUM", "miriam": "myco.marinum", "n2t": "myco.marinum", "prefixcommons": "myco.marinum" }, "name": "MycoBrowser marinum", "part_of": "myco", "pattern": "^MMAR\\_\\d+$", "preferred_prefix": "myco.marinum", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/myco.marinum:$1" } ], "uri_format": "https://mycobrowser.epfl.ch/genes/$1" }, "myco.smeg": { "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.", "example": "MSMEG_3769", "homepage": "https://mycobrowser.epfl.ch", "keywords": [ "genome", "sequence" ], "mappings": { "biocontext": "MYCO.SMEG", "miriam": "myco.smeg", "n2t": "myco.smeg", "prefixcommons": "myco.smeg" }, "name": "MycoBrowser smegmatis", "part_of": "myco", "pattern": "^MSMEG\\w+$", "preferred_prefix": "myco.smeg", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/myco.smeg:$1" } ], "uri_format": "https://mycobrowser.epfl.ch/genes/$1" }, "myco.tuber": { "contact": { "email": "stewart.cole@epfl.ch", "name": "Stewart Thomas Cole", "orcid": "0000-0003-1400-5585" }, "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information.", "example": "Rv1908c", "homepage": "http://tuberculist.epfl.ch/", "keywords": [ "dna", "genome", "protein" ], "mappings": { "biocontext": "MYCO.TUBER", "miriam": "myco.tuber", "n2t": "myco.tuber", "ncbi": "TubercuList", "prefixcommons": "tuberculist", "uniprot": "DB-0106" }, "name": "TubercuList knowledge base", "part_of": "myco", "pattern": "^Rv\\d{4}(A|B|c)?$", "preferred_prefix": "myco.tuber", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/tuberculist:$1" } ], "publications": [ { "doi": "10.1016/j.tube.2010.09.006", "pubmed": "20980200", "title": "The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes", "year": 2010 } ], "synonyms": [ "TubercuList" ], "uri_format": "https://mycobrowser.epfl.ch/genes/$1" }, "mycobank": { "contact": { "email": "vrobert@unistra.fr", "name": "Vincent Robert", "orcid": "0000-0002-9370-4677" }, "contributor_extras": [ { "email": "carlosm@ebi.ac.uk", "github": "CarMoreno", "name": "Carlos Moreno", "orcid": "0000-0003-0066-1717" } ], "description": "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.", "example": "349124", "homepage": "http://www.mycobank.org/", "keywords": [ "biology", "classification", "taxonomy" ], "mappings": { "biocontext": "MYCOBANK", "fairsharing": "FAIRsharing.v8se8r", "integbio": "nbdc01815", "miriam": "mycobank", "n2t": "mycobank", "ncbi": "MycoBank", "prefixcommons": "mycobank", "re3data": "r3d100011222" }, "name": "Fungal Nomenclature and Species Bank", "pattern": "^\\d+$", "preferred_prefix": "mycobank", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/mycobank:$1" } ], "publications": [ { "doi": "10.5598/imafungus.2013.04.02.16", "pmc": "PMC3905949", "pubmed": "24563843", "title": "MycoBank gearing up for new horizons", "year": 2013 } ], "uri_format": "https://www.mycobank.org/page/Name%20details%20page/$1" }, "mzspec": { "banana": "mzspec", "contact": { "email": "gerhard.mayer@rub.de", "github": "germa", "name": "Gerhard Mayer", "orcid": "0000-0002-1767-2343" }, "contributor_extras": [ { "email": "lindsey.anderson@pnnl.gov", "github": "lnanderson", "name": "Lindsey N. Anderson", "orcid": "0000-0002-8741-7823" } ], "description": "The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it.", "example": "PXD002255:ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2", "homepage": "http://www.psidev.info/usi", "keywords": [ "data analysis", "data identity and mapping", "data retrieval", "lipidomics", "mass spectrum", "metabolomics", "proteomics" ], "mappings": { "biocontext": "MZSPEC", "fairsharing": "FAIRsharing.b549b8", "miriam": "mzspec", "n2t": "mzspec" }, "name": "Universal Spectrum Identifier", "namespace_in_lui": true, "pattern": "^.+$", "preferred_prefix": "mzspec", "providers": [ { "code": "", "description": "Universal Spectrum Identifier through Peptide Atlas", "homepage": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum", "name": "Universal Spectrum Identifier through Peptide Atlas", "uri_format": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum?usi=mzspec:$1" }, { "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": [ { "doi": "10.1038/s41592-021-01184-6", "pmc": "PMC8405201", "pubmed": "34183830", "title": "Universal Spectrum Identifier for mass spectra", "year": 2021 } ], "repository": "https://github.com/HUPO-PSI/usi", "uri_format": "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1" }, "n2t": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org", "example": "chebi", "homepage": "https://n2t.net", "name": "Name-to-Thing", "preferred_prefix": "n2t", "uri_format": "https://n2t.net/$1:" }, "n4e": { "description": "The ontology and metadata schema for the NFDI4Earth Knowledge Hub. See serializations of this schema as an OWL ontology here:\n - [RDF/XML](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.xml)\n - [RDF/Turtle](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.ttl)\n - [RDF/JSON-LD](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.jsonld)\n - [RDF/N-Triples](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.nt)", "example": "API", "homepage": "https://nfdi4earth.de/ontology/", "keywords": [ "earth sciences", "ess" ], "mappings": { "tib": "n4e" }, "name": "NFDI4Earth Ontology", "preferred_prefix": "n4e", "uri_format": "http://nfdi4earth.de/ontology/$1" }, "namerxn": { "contact": { "email": "gregory.landrum@phys.chem.ethz.ch", "github": "greglandrum", "name": "Gregory Landrum", "orcid": "0000-0001-6279-4481" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO).", "example": "4.2.78", "homepage": "https://www.nextmovesoftware.com/namerxn.html", "keywords": [ "chemistry", "reactions", "text mining" ], "name": "NameRXN", "preferred_prefix": "namerxn", "proprietary": true, "publications": [ { "doi": "10.1021/acs.jmedchem.6b00153", "pubmed": "27028220", "title": "Big Data from Pharmaceutical Patents: A Computational Analysis of Medicinal Chemists' Bread and Butter", "year": 2016 }, { "doi": "10.1038/s42256-020-00284-w", "title": "Mapping the space of chemical reactions using attention-based neural networks", "year": 2021 } ], "references": [ "https://www.nextmovesoftware.com/products/HazELNutPoster.pdf", "https://twitter.com/cthoyt/status/1443929184745758723" ] }, "nando": { "banana": "NANDO", "contact": { "email": "takatter@dbcls.rois.ac.jp", "name": "Terue Takatsuki" }, "description": "Nanbyo Disease Ontology (NANDO) is the ontology creating a comprehensive hierarchical controlled vocabulary for intractable and rare disease (i.e., nanbyo) representation in Japan.", "download_owl": "http://aber-owl.net/media/ontologies/NANDO/19/nando.owl", "example": "1200031", "homepage": "https://nanbyodata.jp/", "keywords": [ "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "NANDO", "bioportal": "NANDO", "miriam": "nando", "togoid": "Nando" }, "name": "Nanbyo Disease Ontology", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "nando", "uri_format": "https://nanbyodata.jp/disease/NANDO:$1" }, "napdi": { "contact": { "email": "rdb20@pitt.edu", "name": "Richard Boyce", "orcid": "0000-0002-2993-2085" }, "description": "The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs).", "example": "28", "homepage": "https://repo.napdi.org/", "keywords": [ "biomedical science", "pharmacology" ], "mappings": { "biocontext": "NAPDI", "fairsharing": "FAIRsharing.y9x8wk", "miriam": "napdi", "n2t": "napdi" }, "name": "Natural Product-Drug Interaction Research Data Repository", "pattern": "^[0-9]+$", "preferred_prefix": "napdi", "publications": [ { "doi": "10.1186/s13326-018-0183-z", "pmc": "PMC5944177", "pubmed": "29743102", "title": "Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse", "year": 2018 } ], "uri_format": "https://repo.napdi.org/study/$1" }, "napp": { "contact": { "email": "daniel.gautheret@u-psud.fr", "name": "Daniel Gautheret", "orcid": "0000-0002-1508-8469" }, "description": "NAPP (Nucleic Acids Phylogenetic Profiling) is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters.", "example": "351", "homepage": "http://rssf.i2bc.paris-saclay.fr/NAPP/index.php", "keywords": [ "clustering", "genomics", "nucleotide" ], "mappings": { "biocontext": "NAPP", "fairsharing": "FAIRsharing.vr52p3", "miriam": "napp", "n2t": "napp", "prefixcommons": "napp" }, "name": "Nucleic Acids Phylogenetic Profiling", "pattern": "^\\d+$", "preferred_prefix": "napp", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/napp:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr807", "pmc": "PMC3245103", "pubmed": "21984475", "title": "NAPP: the Nucleic Acid Phylogenetic Profile Database", "year": 2011 }, { "doi": "10.1101/gr.089714.108", "pmc": "PMC2694484", "pubmed": "19237465", "title": "Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles", "year": 2009 } ], "uri_format": "http://rssf.i2bc.paris-saclay.fr/NAPP/Niveau2.php?specie=$1" }, "narcis": { "description": "NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases.", "example": "oai:cwi.nl:4725", "homepage": "http://www.narcis.nl", "keywords": [ "subject agnostic" ], "mappings": { "biocontext": "NARCIS", "fairsharing": "FAIRsharing.f63h4k", "integbio": "nbdc01862", "miriam": "narcis", "n2t": "narcis" }, "name": "National Academic Research and Collaborations Information System", "pattern": "^oai\\:cwi\\.nl\\:\\d+$", "preferred_prefix": "narcis", "uri_format": "http://www.narcis.nl/publication/RecordID/$1" }, "nasaosdr.biospecimen": { "contact": { "email": "sylvain.v.costes@nasa.gov", "name": "Sylvain V Costes", "orcid": "0000-0002-8542-2389" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "Identifiers for biospecimens used in experiments that investigate biological and health responses of terrestrial life to spaceflight", "example": "7943", "github_request_issue": 1298, "homepage": "https://www.nasa.gov/osdr", "name": "NASA Open Science Data Repository Biospecimen", "pattern": "^\\d+$", "preferred_prefix": "nasaosdr.biospecimen", "publications": [ { "doi": "10.1093/nar/gkae1116", "pubmed": "39558178", "title": "NASA open science data repository: open science for life in space", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://osdr.nasa.gov/bio/repo/data/biospecimens/$1" }, "nasaosdr.experiment": { "contact": { "email": "sylvain.v.costes@nasa.gov", "name": "Sylvain V Costes", "orcid": "0000-0002-8542-2389" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "Identifiers for space-related data from experiments that investigate biological and health responses of terrestrial life to spaceflight", "example": "OS-27", "github_request_issue": 1298, "homepage": "https://www.nasa.gov/osdr", "name": "NASA Open Science Data Repository Experiment", "pattern": "^OS-\\d+$", "preferred_prefix": "nasaosdr.experiment", "publications": [ { "doi": "10.1093/nar/gkae1116", "pubmed": "39558178", "title": "NASA open science data repository: open science for life in space", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://osdr.nasa.gov/bio/repo/data/experiments/$1" }, "nasaosdr.hardware": { "contact": { "email": "sylvain.v.costes@nasa.gov", "name": "Sylvain V Costes", "orcid": "0000-0002-8542-2389" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "Identifiers for hardware used in experiments that investigate biological and health responses of terrestrial life to spaceflight", "example": "2011", "github_request_issue": 1298, "homepage": "https://www.nasa.gov/osdr", "name": "NASA Open Science Data Repository Hardware", "pattern": "^\\d+$", "preferred_prefix": "nasaosdr.hardware", "publications": [ { "doi": "10.1093/nar/gkae1116", "pubmed": "39558178", "title": "NASA open science data repository: open science for life in space", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://osdr.nasa.gov/bio/repo/data/hardware/$1" }, "nasaosdr.mission": { "contact": { "email": "sylvain.v.costes@nasa.gov", "name": "Sylvain V Costes", "orcid": "0000-0002-8542-2389" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "Identifiers for missions associated with experiments that investigate biological and health responses of terrestrial life to spaceflight", "example": "ARCBedrest", "example_extras": [ "Bion 11", "STS-46" ], "github_request_issue": 1298, "homepage": "https://www.nasa.gov/osdr", "name": "NASA Open Science Data Repository Mission", "pattern": "^.+$", "preferred_prefix": "nasaosdr.mission", "publications": [ { "doi": "10.1093/nar/gkae1116", "pubmed": "39558178", "title": "NASA open science data repository: open science for life in space", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://osdr.nasa.gov/bio/repo/data/missions/$1" }, "nasaosdr.payload": { "contact": { "email": "sylvain.v.costes@nasa.gov", "name": "Sylvain V Costes", "orcid": "0000-0002-8542-2389" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "Identifiers for payloads associated with experiments that investigate biological and health responses of terrestrial life to spaceflight", "example": "VEG-03D", "example_extras": [ "HyperG2-SIMBA2", "NanoRacks-UF-Squids-1", "PSE.02" ], "github_request_issue": 1298, "homepage": "https://www.nasa.gov/osdr", "name": "NASA Open Science Data Repository Payload", "pattern": "^.+$", "preferred_prefix": "nasaosdr.payload", "publications": [ { "doi": "10.1093/nar/gkae1116", "pubmed": "39558178", "title": "NASA open science data repository: open science for life in space", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://osdr.nasa.gov/bio/repo/data/payloads/$1" }, "nasaosdr.study": { "comment": "NASA OSDR is NASA's new integrated life sciences data archive which encompasses NASA GeneLAB (ngl), their old database for omics data. The studies from ngl are relabelled with new identifier formats, thus this is curated as a new prefix", "contact": { "email": "sylvain.v.costes@nasa.gov", "name": "Sylvain V Costes", "orcid": "0000-0002-8542-2389" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "Identifiers for space-related data from studies that investigate biological and health responses of terrestrial life to spaceflight", "example": "OSD-678", "github_request_issue": 1298, "homepage": "https://www.nasa.gov/osdr", "name": "NASA Open Science Data Repository Study", "pattern": "^OSD-\\d+$", "preferred_prefix": "nasaosdr.study", "publications": [ { "doi": "10.1093/nar/gkae1116", "pubmed": "39558178", "title": "NASA open science data repository: open science for life in space", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://osdr.nasa.gov/bio/repo/data/studies/$1" }, "nasaosdr.subject": { "contact": { "email": "sylvain.v.costes@nasa.gov", "name": "Sylvain V Costes", "orcid": "0000-0002-8542-2389" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "Identifiers for subjects of experiments that investigate biological and health responses of terrestrial life to spaceflight", "example": "58", "github_request_issue": 1298, "homepage": "https://www.nasa.gov/osdr", "name": "NASA Open Science Data Repository Subject", "pattern": "^\\d+$", "preferred_prefix": "nasaosdr.subject", "publications": [ { "doi": "10.1093/nar/gkae1116", "pubmed": "39558178", "title": "NASA open science data repository: open science for life in space", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://osdr.nasa.gov/bio/repo/data/subjects/$1" }, "nasc": { "contact": { "email": "sean@arabidopsis.org.uk", "name": "Sean May", "orcid": "0000-0001-5282-3250" }, "description": "The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.", "example": "N1899", "homepage": "http://arabidopsis.info/", "keywords": [ "genome", "life science" ], "mappings": { "biocontext": "NASC", "fairsharing": "FAIRsharing.2sqcxs", "miriam": "nasc", "n2t": "nasc", "prefixcommons": "nasc", "re3data": "r3d100010906" }, "name": "NASC code", "pattern": "^(\\w+)?\\d+$", "preferred_prefix": "nasc", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/nasc:$1" } ], "publications": [ { "doi": "10.1093/nar/gkh133", "pmc": "PMC308867", "pubmed": "14681484", "title": "NASCArrays: a repository for microarray data generated by NASC's transcriptomics service", "year": 2004 } ], "twitter": "NascArabidopsis", "uri_format": "http://arabidopsis.info/StockInfo?NASC_id=$1" }, "nbn": { "description": "The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier.", "example": "urn:nbn:fi:tkk-004781", "homepage": "http://nbn-resolving.org/resolve_urn.htm", "mappings": { "biocontext": "NBN", "miriam": "nbn", "n2t": "nbn" }, "name": "National Bibliography Number", "pattern": "^(urn|URN):(nbn|NBN)(:[A-Za-z_0-9]+)*.+$", "preferred_prefix": "nbn", "uri_format": "http://nbn-resolving.org/$1" }, "nbo": { "appears_in": [ "ecto", "maxo", "pcl", "scdo", "uberon" ], "contact": { "email": "g.gkoutos@bham.ac.uk", "github": "gkoutos", "name": "George Gkoutos", "orcid": "0000-0002-2061-091X" }, "description": "An ontology of human and animal behaviours and behavioural phenotypes", "download_obo": "https://github.com/obo-behavior/behavior-ontology/raw/master/nbo.obo", "download_owl": "http://purl.obolibrary.org/obo/nbo.owl", "example": "0000564", "homepage": "https://github.com/obo-behavior/behavior-ontology/", "keywords": [ "behavior", "obo", "ontology", "phenotype", "social and behavioural science", "systemic neuroscience" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "NBO", "biocontext": "NBO", "bioportal": "NBO", "fairsharing": "FAIRsharing.pktgc6", "obofoundry": "nbo", "ols": "nbo", "ontobee": "NBO", "wikidata.entity": "Q81661716" }, "name": "Neuro Behavior Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "NBO", "publications": [ { "doi": "10.1007/s00335-013-9481-z", "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", "pubmed": "23195121", "title": "The neurobehavior ontology: an ontology for annotation and integration of behavior and behavioral phenotypes", "year": 2012 } ], "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_$1", "version": "2023-07-04" }, "nbrc": { "description": "NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information.", "example": "00001234", "homepage": "http://www.nbrc.nite.go.jp/e/index.html", "keywords": [ "microbial", "microbiology", "taxonomy" ], "mappings": { "biocontext": "NBRC", "fairsharing": "FAIRsharing.ftamrc", "miriam": "nbrc", "n2t": "nbrc", "ncbi": "NBRC", "prefixcommons": "nbrc" }, "name": "NITE Biological Resource Center", "pattern": "^\\d+$", "preferred_prefix": "nbrc", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/nbrc:$1" } ], "uri_format": "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1" }, "ncats.bioplanet": { "contact": { "email": "ruili.huang@nih.gov", "name": "Ruili Huang", "orcid": "0000-0001-8886-8311" }, "contributor": { "email": "smoxon@lbl.gov", "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" }, "description": "The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays.", "example": "3", "github_request_issue": 445, "homepage": "https://tripod.nih.gov/bioplanet/", "mappings": { "biolink": "ncats.bioplanet" }, "name": "National Center for Advancing Translation Sciences BioPlanet", "pattern": "^\\d+$", "preferred_prefix": "ncats.bioplanet", "publications": [ { "doi": "10.3389/fphar.2019.00445", "pmc": "PMC6524730", "pubmed": "31133849", "title": "The NCATS BioPlanet - An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics", "year": 2019 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "twitter": "ncats_nih_gov", "uri_format": "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1" }, "ncats.drug": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, { "github": "vdancik", "name": "Vlado Dancik", "orcid": "0000-0002-5970-6660" }, { "email": "smoxon@lbl.gov", "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" } ], "description": "The National Center for Advancing Translational Sciences](http://www.ncats.nih.gov/) (NCATS) has developed Inxight Drugs as a comprehensive portal for drug development information. NCATS Inxight Drugs contains information on ingredients in medicinal products, including:\n\n- US Approved Drugs\n- Marketed Drugs\n- Investigational Drugs\n- Other Substances", "example": "44259", "example_extras": [ "1IJV77EI07" ], "homepage": "https://drugs.ncats.io/", "mappings": { "biolink": "ncats.drug" }, "name": "NCATS Drugs", "preferred_prefix": "ncats.drug", "synonyms": [ "inxight", "inxight-drugs" ], "uri_format": "https://drugs.ncats.io/drug/$1" }, "ncbi.assembly": { "description": "A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data.", "example": "GCF_000005845.2", "homepage": "https://www.ncbi.nlm.nih.gov/", "mappings": { "biocontext": "NCBIAssembly", "miriam": "assembly", "re3data": "r3d100012688" }, "name": "Assembly", "pattern": "^[a-zA-Z0-9_\\.]+$", "preferred_prefix": "ncbi.assembly", "uri_format": "https://www.ncbi.nlm.nih.gov/datasets/genome/$1" }, "ncbi.gc": { "comment": "see comment here: https://github.com/obophenotype/ncbitaxon/issues/47", "contact": { "email": "elzanowski@biol.uni.wroc.pl", "name": "Andrzej Elzanowski" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries.", "example": "11", "homepage": "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes", "keywords": [ "genetic code", "genome" ], "license": "public domain", "logo": "https://www.ncbi.nlm.nih.gov/corehtml/logo256.gif", "name": "NCBI Genetic Code", "pattern": "^\\d+$", "preferred_prefix": "ncbi.gc", "references": [ "https://github.com/obophenotype/ncbitaxon/issues/47", "https://www.ncbi.nlm.nih.gov/home/about/policies" ], "synonyms": [ "gc", "gc_id" ], "uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1" }, "ncbi.genome": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations.", "example": "51", "homepage": "https://www.ncbi.nlm.nih.gov/genome", "mappings": { "biocontext": "NCBIGenome", "edam": "2787", "re3data": "r3d100010785" }, "name": "NCBI Genome", "pattern": "^\\d+$", "preferred_prefix": "ncbi.genome", "uri_format": "https://www.ncbi.nlm.nih.gov/genome/$1" }, "ncbi.resource": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources", "example": "ECOCYC", "homepage": "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/", "name": "NCBI Registry", "preferred_prefix": "ncbi.resource", "uri_format": "https://bioregistry.io/metaregistry/ncbi/$1" }, "ncbibook": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover.", "example": "NBK331", "homepage": "https://www.ncbi.nlm.nih.gov/books", "name": "NCBI Bookshelf", "pattern": "^NBK\\d+$", "preferred_prefix": "ncbibook", "uri_format": "https://www.ncbi.nlm.nih.gov/books/$1" }, "ncbidrs": { "description": "This is the namespace for the archive of sequence and other files provided by NCBI e.g. in SRA and dbGaP. These files are related to objects in the sequencing data model managed under the insdc.sra namespace. ", "example": "72ff6ff882ec447f12df018e6183de59", "homepage": "https://www.ncbi.nlm.nih.gov/", "mappings": { "miriam": "ncbidrs" }, "name": "NCBI Data Repository Service", "pattern": "^[0-9a-fA-F]{32}$", "preferred_prefix": "ncbidrs", "uri_format": "https://locate.be-md.ncbi.nlm.nih.gov/ga4gh/drs/v1/objects/$1" }, "ncbigene": { "contact": { "email": "murphyte@ncbi.nlm.nih.gov", "github": "murphyte", "name": "Terence D. Murphy", "orcid": "0000-0001-9311-9745" }, "contributor_extras": [ { "email": "rcameron@sfu.com", "github": "cmrn-rhi", "name": "Rhiannon Cameron", "orcid": "0000-0002-9578-0788" } ], "description": "Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis.", "example": "100010", "homepage": "https://www.ncbi.nlm.nih.gov/gene", "keywords": [ "dna", "gene", "genetics", "genome", "genomics" ], "logo": "https://www.ncbi.nlm.nih.gov/corehtml/logo256.gif", "mappings": { "biocontext": "NCBIGene", "biolink": "NCBIGene", "edam": "1027", "fairsharing": "FAIRsharing.5h3maw", "go": "NCBIGene", "hl7": "2.16.840.1.113883.6.340", "integbio": "nbdc00073", "miriam": "ncbigene", "n2t": "ncbigene", "ncbi": "GeneID", "prefixcommons": "ncbigene", "re3data": "r3d100010650", "togoid": "Ncbigene", "uniprot": "DB-0118", "wikidata": "P351" }, "name": "NCBI Gene", "owners": [ { "name": "National Center for Biotechnology Information", "partnered": false, "ror": "02meqm098" } ], "pattern": "^\\d+$", "preferred_prefix": "NCBIGene", "providers": [ { "code": "", "description": "Bio2RDF", "homepage": "http://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/ncbigene:$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/ncbigene:$1" }, { "code": "marrvel", "description": "Helps browse potential orthologs in model organisms for a given gene", "homepage": "http://marrvel.org", "name": "Model organism Aggregated Resources for Rare Variant ExpLoration", "uri_format": "http://marrvel.org/model/gene/$1" }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/ncbi-gene/$1" } ], "publications": [ { "doi": "10.1093/nar/gku1055", "pubmed": "25355515" }, { "doi": "10.1093/nar/gkq1237", "pmc": "PMC3013746", "pubmed": "21115458", "title": "Entrez Gene: gene-centered information at NCBI", "year": 2010 }, { "doi": "10.1093/nar/gki031", "pmc": "PMC539985", "pubmed": "15608257", "title": "Entrez Gene: gene-centered information at NCBI", "year": 2005 } ], "rdf_uri_format": "http://purl.uniprot.org/geneid/$1", "references": [ "https://github.com/biopragmatics/bioregistry/issues/983" ], "synonyms": [ "EGID", "EntrezGene", "GeneID", "NCBIGene", "NCBI_GeneID", "entrez", "entrez gene/locuslink", "nihgeneid" ], "uri_format": "https://www.ncbi.nlm.nih.gov/gene/$1" }, "ncbigi": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A GI number (for GenInfo Identifier, sometimes written in lower case, _gi_) is a simple series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Version number of the sequence record. Each time a sequence record is changed, it is assigned a new GI number.", "example": "568815597", "has_canonical": "genbank", "homepage": "https://www.ncbi.nlm.nih.gov/genbank/sequenceids/", "mappings": { "biocontext": "NCBIGI", "edam": "2314", "go": "NCBI_gi", "ncbi": "GI" }, "name": "GenInfo Identifier", "owners": [ { "name": "National Center for Biotechnology Information", "partnered": false, "ror": "02meqm098" } ], "pattern": "^\\d+$", "preferred_prefix": "ncbigi", "references": [ "https://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html", "https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/Format/exercises/qa_accession_vs_gi.html" ], "synonyms": [ "NCBI_gi", "ncbi.gi" ], "uri_format": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$1" }, "ncbiortholog": { "comment": "We do not currently have the source code for our ortholog resource available publicly, although we are looking at how to split it off and make it available in the next year. We are now in the process of adding this tag to the INSDC list for use in annotations, so I'd like to mirror that tag in bioregistry.", "contact": { "email": "murphyte@ncbi.nlm.nih.gov", "github": "murphyte", "name": "Terence D. Murphy", "orcid": "0000-0001-9311-9745" }, "contributor": { "email": "murphyte@ncbi.nlm.nih.gov", "github": "murphyte", "name": "Terence D. Murphy", "orcid": "0000-0001-9311-9745" }, "description": "Database of one-to-one ortholog information provided by the NCBI as a subset of their Gene resource. Used for users to access ortholog information for over 1000 species of vertebrates and arthropods.", "example": "2", "github_request_issue": 1181, "homepage": "https://www.ncbi.nlm.nih.gov/gene/", "license": "US gov't public domain", "name": "NCBI Orthologs", "pattern": "^\\d+$", "preferred_prefix": "ncbiortholog", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://www.ncbi.nlm.nih.gov/gene/$1/ortholog" }, "ncbiprotein": { "description": "The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.", "example": "CAA71118.1", "homepage": "https://www.ncbi.nlm.nih.gov/protein", "keywords": [ "protein" ], "logo": "https://www.ncbi.nlm.nih.gov/corehtml/logo256.gif", "mappings": { "biocontext": "NCBIProtein", "go": "NCBI_NP", "integbio": "nbdc00636", "miriam": "ncbiprotein", "n2t": "ncbiprotein", "prefixcommons": "ncbi.protein", "re3data": "r3d100010776" }, "name": "NCBI Protein", "owners": [ { "name": "National Center for Biotechnology Information", "partnered": false, "ror": "02meqm098" } ], "pattern": "^\\w+_?\\d+(.\\d+)?$", "preferred_prefix": "NCBIProtein", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/ncbi.protein:$1" } ], "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1" }, "ncbitaxon": { "appears_in": [ "agro", "chiro", "cl", "clo", "ecto", "envo", "foodon", "gallont", "genepio", "go", "hso", "mco", "ons", "pcl", "pco", "uberon", "vbo" ], "contact": { "email": "schoch2@ncbi.nlm.nih.gov", "github": "fbastian", "name": "Conrad L Schoch", "orcid": "0000-0003-1839-5322" }, "description": "The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.", "download_json": "http://purl.obolibrary.org/obo/ncbitaxon.json", "download_obo": "http://purl.obolibrary.org/obo/ncbitaxon.obo.gz", "download_owl": "http://purl.obolibrary.org/obo/ncbitaxon.owl", "example": "2170610", "example_extras": [ "subclass" ], "homepage": "https://github.com/obophenotype/ncbitaxon", "keywords": [ "biology", "classification", "dna", "evolutionary biology", "genomics", "knowledge and information systems", "life science", "obo", "omics", "ontology", "phylogenetics", "protein", "proteomics", "structure", "taxonomic classification", "taxonomy" ], "license": "CC0-1.0", "mappings": { "aberowl": "NCBITAXON", "agroportal": "TAX", "bartoc": "509", "biocontext": "TAXONOMY", "bioportal": "NCBITAXON", "cellosaurus": "NCBI_TaxID", "edam": "1179", "fairsharing": "FAIRsharing.fj07xj", "go": "NCBITaxon", "hl7": "2.16.840.1.113883.6.205", "lov": "tax", "miriam": "taxonomy", "n2t": "taxonomy", "ncbi": "taxon", "obofoundry": "ncbitaxon", "ols": "ncbitaxon", "ontobee": "NCBITaxon", "prefixcommons": "taxonomy", "re3data": "r3d100010415", "togoid": "Taxonomy", "wikidata": "P685", "wikidata.entity": "Q81661717" }, "name": "NCBI Taxonomy", "owners": [ { "name": "National Center for Biotechnology Information", "partnered": false, "ror": "02meqm098" } ], "pattern": "^(\\d+)|([a-zA-Z_]+)$", "preferred_prefix": "NCBITaxon", "providers": [ { "code": "", "description": "Bio2RDF", "homepage": "https://bio2rdf.org/", "name": "Bio2RDF", "uri_format": "https://bio2rdf.org/taxonomy:$1" }, { "code": "", "description": "Taxonomy through UniProt PURL", "homepage": "https://www.uniprot.org/taxonomy/", "name": "Taxonomy through UniProt PURL", "uri_format": "https://purl.uniprot.org/taxonomy/$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/taxonomy:$1" }, { "code": "bioportal.purl", "description": "BioPortal assigns their own PURLs to entities in NCBI taxonomy database.", "homepage": "https://purl.bioontology.org/ontology/NCBITAXON", "name": "BioPortal", "uri_format": "http://purl.bioontology.org/ontology/NCBITAXON/$1" }, { "code": "ebi", "description": "European Nucleotide Archive (ENA)", "homepage": "https://www.ebi.ac.uk/ena/", "name": "European Nucleotide Archive (ENA)", "uri_format": "https://www.ebi.ac.uk/ena/data/view/Taxon:$1" }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/ncbi-taxon/$1" } ], "publications": [ { "doi": "10.1093/database/baaa062", "pmc": "PMC7408187", "pubmed": "32761142", "title": "NCBI Taxonomy: a comprehensive update on curation, resources and tools", "year": 2020 }, { "doi": "10.1093/nar/gkx1094", "pmc": "PMC5753231", "pubmed": "29140468", "title": "GenBank", "year": 2018 }, { "doi": "10.1093/nar/gkr1178", "pmc": "PMC3245000", "pubmed": "22139910", "title": "The NCBI Taxonomy database", "year": 2011 }, { "doi": "10.5281/zenodo.8065005", "title": "obophenotype/ncbitaxon: 2023-06-20 Release (v2023-06-20)", "year": 2023 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/NCBITaxon_$1", "repository": "https://github.com/obophenotype/ncbitaxon", "synonyms": [ "NCBI Taxonomy", "NCBITaxon", "NCBITaxonomyID", "NCBI_Taxon_ID", "NCBI_taxid", "TAX", "TaxonomyID", "ncbiTaxUID", "taxid", "taxon", "taxonomy", "uniprot.taxonomy" ], "uri_format": "http://purl.obolibrary.org/obo/NCBITaxon_$1", "version": "2025-12-03" }, "nci.drug": { "description": "identifier of an entry in the NCI Drug Dictionary", "example": "beta-carotene", "homepage": "https://www.cancer.gov/publications/dictionaries/cancer-drug", "mappings": { "wikidata": "P11623" }, "name": "NCI Drug Dictionary ID", "preferred_prefix": "nci.drug", "uri_format": "https://www.cancer.gov/publications/dictionaries/cancer-drug/def/$1" }, "ncim": { "description": "NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical.", "example": "C0026339", "homepage": "http://ncim.nci.nih.gov/", "mappings": { "biocontext": "NCIM", "miriam": "ncim", "n2t": "ncim" }, "name": "NCI Metathesaurus", "owners": [ { "name": "National Cancer Institute", "partnered": false, "ror": "040gcmg81" } ], "pattern": "^C\\d+$", "preferred_prefix": "ncim", "uri_format": "http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1" }, "ncit": { "appears_in": [ "ecto", "mco", "ontoavida", "scdo" ], "contact": { "email": "ncithesaurus@mail.nih.gov", "name": "NCI Thesaurus Mailbox" }, "description": "NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code.", "download_obo": "http://purl.obolibrary.org/obo/ncit.obo", "download_owl": "http://purl.obolibrary.org/obo/ncit.owl", "example": "C138986", "example_extras": [ "A14", "P320", "R123" ], "homepage": "https://github.com/ncit-obo-org/ncit-obo-edition", "keywords": [ "biomedical science", "cancer", "dataplant", "disease", "life sciences, biology", "nfdi4chem", "obo", "ontology", "preclinical studies", "thesaurus", "translational medicine" ], "license": "CC-BY-4.0", "logo": "https://evsexplore.semantics.cancer.gov/evsexplore/assets/images/NCItTile.png", "mappings": { "aberowl": "NCIT", "biocontext": "NCIT", "bioportal": "NCIT", "cellosaurus": "NCIt", "fairsharing": "FAIRsharing.4cvwxa", "hl7": "2.16.840.1.113883.6.206", "integbio": "nbdc02651", "miriam": "ncit", "n2t": "ncit", "obofoundry": "ncit", "ols": "ncit", "ontobee": "NCIT", "prefixcommons": "ncit", "tib": "ncit", "wikidata": "P1748", "wikidata.entity": "Q113012671" }, "name": "NCI Thesaurus", "owners": [ { "name": "National Cancer Institute", "partnered": false, "ror": "040gcmg81" } ], "pattern": "^[CRPA]\\d+$", "preferred_prefix": "NCIT", "providers": [ { "code": "", "description": "NCIt at National Cancer Institute", "homepage": "http://ncit.nci.nih.gov/", "name": "NCIt at National Cancer Institute", "uri_format": "http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones.", "example": "6b1", "homepage": "http://nematode.lab.nig.ac.jp/", "keywords": [ "dna", "gene expression", "genome", "life science" ], "mappings": { "biocontext": "NEXTDB", "fairsharing": "FAIRsharing.xz5m1a", "integbio": "nbdc00594", "miriam": "nextdb", "n2t": "nextdb", "ncbi": "NextDB", "prefixcommons": "nextdb" }, "name": "Nematode Expression Pattern DataBase", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "nextdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/nextdb:$1" } ], "uri_format": "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1" }, "nextprot": { "contact": { "email": "monique.zahn@sib.swiss", "name": "Monique Zahn", "orcid": "0000-0001-7961-6091" }, "description": "neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases.", "example": "NX_O00165", "homepage": "https://www.nextprot.org/", "keywords": [ "life science", "proteomics" ], "mappings": { "biocontext": "NEXTPROT", "fairsharing": "FAIRsharing.62evqh", "integbio": "nbdc02107", "miriam": "nextprot", "n2t": "nextprot", "uniprot": "DB-0161", "wikidata.entity": "Q6983890" }, "name": "nextProt", "pattern": "^NX_\\w+$", "preferred_prefix": "nextprot", "publications": [ { "doi": "10.1093/nar/gkz995", "pmc": "PMC7145669", "pubmed": "31724716", "title": "The neXtProt knowledgebase in 2020: data, tools and usability improvements", "year": 2020 }, { "doi": "10.1093/nar/gkw1062", "pmc": "PMC5210547", "pubmed": "27899619", "title": "The neXtProt knowledgebase on human proteins: 2017 update", "year": 2016 }, { "doi": "10.1093/nar/gku1178", "pmc": "PMC4383972", "pubmed": "25593349", "title": "The neXtProt knowledgebase on human proteins: current status", "year": 2015 }, { "doi": "10.1021/pr300830v", "pubmed": "23205526", "title": "neXtProt: organizing protein knowledge in the context of human proteome projects", "year": 2012 }, { "doi": "10.1093/nar/gkr1179", "pmc": "PMC3245017", "pubmed": "22139911", "title": "neXtProt: a knowledge platform for human proteins", "year": 2011 }, { "doi": "10.1093/nar/gkw1062.", "title": "The neXtProt knowledgebase on human proteins: 2017 update." }, { "doi": "10.1093/nar/gku1178.", "title": "The neXtProt knowledgebase on human proteins: current status." }, { "doi": "10.1021/pr300830v.", "title": "neXtProt: organizing protein knowledge in the context of human proteome projects." } ], "synonyms": [ "NXP" ], "twitter": "neXtProt_news", "uri_format": "https://www.nextprot.org/db/entry/$1" }, "nextprot.family": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "NeXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data. \n(Developed by the SIB Swiss Institute of Bioinformatics)", "example": "01406", "homepage": "https://www.nextprot.org/", "name": "neXtProt family", "pattern": "^\\d+$", "preferred_prefix": "nextprot.family", "synonyms": [ "NXPFA" ], "twitter": "neXtProt_news", "uri_format": "https://www.nextprot.org/term/FA-$1" }, "nexus": { "description": "NeXusOntology: Machine-readable ontology of the NeXus definitions", "example": "version", "homepage": "https://github.com/nexusformat/NeXusOntology", "keywords": [ "fairmat", "physics", "tib" ], "mappings": { "tib": "nexus" }, "name": "NeXusOntology", "preferred_prefix": "nexus", "uri_format": "http://purl.org/nexusformat/definitions/NeXusOntology#$1" }, "nfdi.core": { "contact": { "email": "joerg.waitelonis@fiz-karlsruhe.de", "github": "joergwa", "name": "Jörg Waitelonis", "orcid": "0000-0001-7192-7143" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A mid-level ontology for representing metadata related to NFDI resources, including individuals, organizations, projects, data portals, and more", "download_owl": "https://github.com/ISE-FIZKarlsruhe/nfdicore/raw/refs/heads/main/nfdicore.owl", "download_rdf": "https://github.com/ISE-FIZKarlsruhe/nfdicore/raw/refs/heads/main/nfdicore.ttl", "example": "0000106", "github_request_issue": 1448, "homepage": "https://ise-fizkarlsruhe.github.io/nfdicore/", "keywords": [ "ontology" ], "license": "CC0-1.0", "name": "NFDI Core Ontology", "pattern": "^\\d+$", "preferred_prefix": "nfdi.core", "repository": "https://github.com/ISE-FIZKarlsruhe/nfdicore", "uri_format": "https://nfdi.fiz-karlsruhe.de/ontology/NFDI_$1" }, "nfdi.kgi": { "contact": { "email": "lozana.rossenova@tib.eu", "github": "lozanaross", "name": "Lozana Rossenova", "orcid": "0000-0002-5190-1867" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Assigns identifiers to knowledge graphs (KGs) that are used and/or maintained within any NFDI consortium.", "example": "KGR1", "github_request_issue": 1665, "homepage": "https://kgi.services.base4nfdi.de", "keywords": [ "knowledge graph" ], "license": "CC-BY-SA-4.0", "name": "NFDI Knowledge Graph Registry", "pattern": "^KGR\\d+$", "preferred_prefix": "nfdi.kgi", "repository": "https://github.com/KGI4NFDI/kgi4nfdi_registry_data", "uri_format": "http://kgi.services.base4nfdi.de/entity/$1" }, "nfdi4chem.ontocape": { "comment": "This ontology ecosystem is near unusable", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "OntoCAPE is a large-scale ontology for the domain of Computer Aided Process Engineering (CAPE). Represented in a formal, machine-interpretable ontology language, OntoCAPE captures consensual knowledge of the process engineering domain in a generic way such that it can be reused and shared by groups of people and across software systems. On the basis of OntoCAPE, novel software support for various engineering activities can be developed; possible applications include the systematic management and retrieval of simulation models and design documents, electronic procurement of plant equipment, mathematical modeling, as well as the integration of design data from distributed sources.", "homepage": "https://www.avt.rwth-aachen.de/cms/AVT/Forschung/Software/~ipts/OntoCape/", "license": "GPL-2.0", "name": "Ontology for computer aided process engineering", "preferred_prefix": "nfdi4chem.ontocape" }, "nfdi4chem.osmo": { "comment": "locked behind a private GitLab instance", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "OSMO is an ontologization and extension of MODA, a workflow metadata standard that constitutes a mandatory requirement within a number of European calls and projects in the context of materials modelling. OSMO was developed within the Horizon 2020 project VIMMP (Virtual Materials Marketplace) and is part of a larger effort in ontology engineering driven by the European Materials Modelling Council, with the European Materials and Modelling Ontology (EMMO) as its core. (from https://nfdi4cat.org/services/ontologie-sammlung/)", "example": "application_case", "homepage": "https://zenodo.org/record/5237774#.YXq72hxCRGo", "keywords": [ "computer science", "material science", "nfdi4cat" ], "mappings": { "bartoc": "20710", "tib": "osmo" }, "name": "Ontology for simulation, modelling, and optimization", "preferred_prefix": "nfdi4chem.osmo", "uri_format": "https://purl.org/vimmp/osmo#$1" }, "nfdi4culture.cto": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NFDI4Culture Ontology (CTO) is a domain-specific ontology module developed within the Task Area 5 of the NFDI4Culture initiative. (from homepage)", "download_owl": "https://github.com/ISE-FIZKarlsruhe/nfdi4culture/raw/refs/heads/main/cto.owl", "example": "0001003", "homepage": "https://nfdi4culture.de/ontology/", "keywords": [ "architecture", "nfdi4culture", "ontology", "other subjects" ], "license": "CC0-1.0", "mappings": { "tib": "cto" }, "name": "NFDI4Culture Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "nfdi4culture.cto", "repository": "https://github.com/ISE-FIZKarlsruhe/nfdi4culture", "uri_format": "https://nfdi4culture.de/ontology/CTO_$1" }, "nfdi4culture.id": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NFDI4Culture portal offers all content as Linked Open Data over this RESTful API. The API implements the Hydra-Specification of the W3C Hydra Community Group. The semantic description of this API can be retrieved by clients via the Hydra documentation file (JSON). Each metadata record offered via this API can also be retrieved in one of following machine-readable LOD serializations. The API is the basis for the Culture Research Information Graph, which together with the Culture Research Data Graph forms the [Culture Knowledge Graph](https://nfdi4culture.de/services/details/culture-knowledge-graph.html) (for more details see [this presentation](https://doi.org/10.5281/zenodo.7748740)) (from homepage).", "example": "E4330", "github_request_issue": 1627, "homepage": "https://nfdi4culture.de/id", "keywords": [ "digital humanities", "generic", "organization" ], "name": "NFDI4Culture Metadata API", "preferred_prefix": "nfdi4culture.id", "rdf_uri_format": "https://nfdi4culture.de/id/$1", "uri_format": "https://nfdi4culture.de/id/$1" }, "nfdi4dso": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NFDI4DS ontology (nfdi4dso) is an ontology describing various resources all resources (datasets, data providers, persons, projects and other entities) within the domain of NFDI4DataScience. nfdi4dso is a module that builds upon the NFDIcore Ontology (https://ise-fizkarlsruhe.github.io/nfdicore/2.0.0/) and maintains alignment with the Basic Formal Ontology (BFO). [from homepage]", "download_rdf": "https://ise-fizkarlsruhe.github.io/NFDI4DS-Ontology/ontology.ttl", "example": "City", "homepage": "https://nfdi.fiz-karlsruhe.de/nfdi4dso/", "name": "NFDI4DS Ontology", "preferred_prefix": "nfdi4dso", "rdf_uri_format": "https://nfdi.fiz-karlsruhe.de/nfdi4dso/$1", "uri_format": "https://nfdi.fiz-karlsruhe.de/nfdi4dso/$1" }, "nfportal.tool": { "contact": { "email": "robert.j.allaway@gmail.com", "github": "allaway", "name": "Robert Allaway", "orcid": "0000-0003-3573-3565" }, "contributor": { "email": "ji.kang@northeastern.edu", "github": "kanghosaeyo", "name": "Kangho Ji", "orcid": "0009-0009-3402-8013" }, "description": "Identifiers represent experimental tools and resources for neurofibromatosis (NF) research in the NF Data Portal Tools catalog.", "example": "02dacc42-ea46-48fb-a4df-7a875d801086", "github_request_issue": 1724, "homepage": "https://nf.synapse.org", "keywords": [ "experimental tools", "neurofibromatosis", "research resources" ], "name": "Neurofibromatosis Data Portal Tools", "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$", "preferred_prefix": "nfportal.tool", "publications": [ { "doi": "10.1038/s41597-019-0317-x", "pmc": "PMC6910996", "pubmed": "31836719", "title": "Engaging a community to enable disease-centric data sharing with the NF Data Portal", "year": 2019 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://nf.synapse.org/Explore/Tools/DetailsPage?resourceId=$1" }, "ngbo": { "contact": { "email": "dal.alghamdi92@gmail.com", "github": "dalalghamdi", "name": "Dalia Alghamdi", "orcid": "0000-0002-2801-0767" }, "description": "Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.", "download_owl": "http://purl.obolibrary.org/obo/ngbo.owl", "example": "6000122", "homepage": "https://github.com/Dalalghamdi/NGBO", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "NGBO", "bioportal": "NGBO", "obofoundry": "ngbo", "ols": "ngbo", "ontobee": "NGBO" }, "name": "Next Generation Biobanking Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "NGBO", "rdf_uri_format": "http://purl.obolibrary.org/obo/NGBO_$1", "repository": "https://github.com/Dalalghamdi/NGBO", "uri_format": "http://purl.obolibrary.org/obo/NGBO_$1", "version": "2024-08-27" }, "ngl": { "description": "NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA.", "example": "GLDS-141", "homepage": "https://genelab-data.ndc.nasa.gov/genelab/", "mappings": { "biocontext": "NGL", "miriam": "ngl", "n2t": "ngl" }, "name": "NASA GeneLab", "pattern": "^GLDS-\\d+$", "preferred_prefix": "ngl", "uri_format": "https://genelab-data.ndc.nasa.gov/genelab/accession/$1" }, "nhcdr": { "description": "Cell line collections (Providers)", "example": "ND50028", "homepage": "https://stemcells.nindsgenetics.org", "mappings": { "cellosaurus": "NHCDR" }, "name": "NINDS Human Cell and Data Repository", "preferred_prefix": "nhcdr", "uri_format": "https://stemcells.nindsgenetics.org?line=$1" }, "niaest": { "contact": { "email": "dawood@helix.nih.gov", "name": "Dawood B. Dudekula", "orcid": "0000-0002-4054-1827" }, "deprecated": true, "description": "A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones.", "example": "J0705A10", "homepage": "http://lgsun.grc.nia.nih.gov/cDNA/", "keywords": [ "dna", "life science" ], "mappings": { "biocontext": "NIAEST", "fairsharing": "FAIRsharing.xwqg9h", "miriam": "niaest", "n2t": "niaest", "ncbi": "niaEST", "prefixcommons": "niaest" }, "name": "NIA Mouse cDNA Project", "pattern": "^\\w\\d{4}\\w\\d{2}(\\-[35])?$", "preferred_prefix": "niaest", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/niaest:$1" } ], "publications": [ { "doi": "10.1016/j.crvi.2003.09.008", "pubmed": "14744099", "title": "The NIA cDNA project in mouse stem cells and early embryos", "year": 2003 } ], "uri_format": "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1" }, "niaid.chemdb": { "description": "ID in NIAID ChemDB", "example": "059486", "homepage": "http://chemdb.niaid.nih.gov", "mappings": { "wikidata": "P2065" }, "name": "NIAID ChemDB ID", "preferred_prefix": "niaid.chemdb", "uri_format": "http://chemdb.niaid.nih.gov/CompoundDetails.aspx?AIDSNO=$1" }, "nif.cell": { "contact": { "email": "smtifahim@gmail.com", "name": "Fahim Imam", "orcid": "0000-0003-4752-543X" }, "deprecated": true, "description": "Neuronal cell types", "download_owl": "http://aber-owl.net/media/ontologies/NIFCELL/15/nifcell.owl", "homepage": "http://neuinfo.org/", "keywords": [ "obo", "ontology" ], "mappings": { "aberowl": "NIFCELL", "biocontext": "NIF_CELL", "bioportal": "NIFCELL", "obofoundry": "nif_cell" }, "name": "NIF Cell", "preferred_prefix": "NIF_CELL", "rdf_uri_format": "http://purl.obolibrary.org/obo/NIF_CELL_$1", "uri_format": "http://purl.obolibrary.org/obo/NIF_CELL_$1" }, "nif.dysfunction": { "contact": { "email": "smtifahim@gmail.com", "name": "Fahim Imam", "orcid": "0000-0003-4752-543X" }, "deprecated": true, "homepage": "http://neuinfo.org/", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "NIF_DYSFUNCTION", "obofoundry": "nif_dysfunction" }, "name": "NIF Dysfunction", "preferred_prefix": "NIF_DYSFUNCTION", "rdf_uri_format": "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1", "uri_format": "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1" }, "nif.ext": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NIFEXT covers IRIs that were \"external\" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed.", "example": "7123", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "license": "CC BY-4.0", "name": "NIF Standard Ontology: External", "pattern": "^\\d+$", "preferred_prefix": "nif.ext", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NIFEXT" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nifext_$1" }, "nif.grossanatomy": { "contact": { "email": "smtifahim@gmail.com", "name": "Fahim Imam", "orcid": "0000-0003-4752-543X" }, "deprecated": true, "homepage": "http://neuinfo.org/", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "NIF_GROSSANATOMY", "obofoundry": "nif_grossanatomy" }, "name": "NIF Gross Anatomy", "preferred_prefix": "NIF_GROSSANATOMY", "rdf_uri_format": "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1", "uri_format": "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1" }, "nif.std": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing.", "download_owl": "http://aber-owl.net/media/ontologies/NIFSTD/23/nifstd.owl", "example": "BAMSC981", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "brain", "disease", "neuroscience", "ontology" ], "license": "CC BY-4.0", "mappings": { "aberowl": "NIFSTD", "bioportal": "NIFSTD", "fairsharing": "FAIRsharing.vgw1m6" }, "name": "NIF Standard Ontology", "pattern": "^BAMSC\\d+$", "preferred_prefix": "nif.std", "publications": [ { "doi": "10.1007/s12021-008-9032-z", "pmc": "PMC2743139", "pubmed": "18975148", "title": "The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience", "year": 2008 } ], "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NIFSTD" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/$1" }, "nihhesc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NIH registration number should be used on all NIH competing applications and annual progress reports to identify the stem cell line proposed for use. Identify the specific line(s) from the Registry using the NIH Registration Number (e.g., 0001), in the specified location in the application (from homepage)", "example": "NIHhESC-10-0083", "homepage": "https://grants.nih.gov/stem_cells/registry/current.htm", "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=$1" }, "nihreporter.project": { "contact": { "email": "report@mail.nih.gov", "name": "NIH Reporter Helpdesk" }, "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding.", "example": "10343835", "github_request_issue": 400, "homepage": "https://reporter.nih.gov/", "keywords": [ "bibliometrics", "project" ], "logo": "https://files.nccih.nih.gov/nccih-nih-reporter-twitter-card-01.jpg", "name": "NIH RePORTER", "pattern": "^\\d+$", "preferred_prefix": "nihreporter.project", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://reporter.nih.gov/project-details/$1" }, "nist": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species.", "homepage": "https://webbook.nist.gov/chemistry/", "name": "NIST Chemistry WebBook", "no_own_terms": true, "preferred_prefix": "nist", "synonyms": [ "NIST", "NIST Chemistry WebBook" ] }, "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": "https://physics.nist.gov/cgi-bin/cuu/Value?$1" }, "nkos": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "NKOS is devoted to the discussion of the functional and data model for enabling knowledge organization systems/services (KOS), such as classification systems, thesauri, gazetteers, and ontologies, as networked interactive information services to support the description and retrieval of diverse information resources through the Internet.\n\nKnowledge Organization Systems/Services (KOS) model the underlying semantic structure of a domain. Embodied as Web-based services, they can facilitate resource discovery and retrieval. They act as semantic road maps and make possible a common orientation by indexers and future users (whether human or machine). -- Douglas Tudhope, Traugott Koch (2004).", "download_rdf": "https://nkos.dublincore.org/nkos.rdf", "example": "alignedWith", "homepage": "http://w3id.org/nkos", "name": "Networked Knowledge Organization Systems/Services/Structures", "preferred_prefix": "nkos", "uri_format": "http://w3id.org/nkos/$1" }, "nlcd": { "appears_in": [ "envo" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A vocabulary for describing the usage of land cover (e.g., pasture, wetlands, barren, forest, water) extended from the original 16 land cover classes proposed by the [Anderson Level II classification system](https://doi.org/10.3133/pp964) in 1976", "example": "12", "homepage": "https://www.mrlc.gov/data/type/land-cover", "keywords": [ "environment", "forestry" ], "name": "United States Geological Survey - National Land Cover Database", "pattern": "^\\d+$", "preferred_prefix": "nlcd", "references": [ "https://www.mrlc.gov/data/legends/national-land-cover-database-class-legend-and-description", "https://www.usgs.gov/centers/eros/science/national-land-cover-database" ] }, "nlfff": { "description": "Nonlinear Force-Free Field Three-Dimensional Magnetic Fields Data of Solar Active Regions Database", "example": "345201101230312003", "homepage": "https://nlfff.dataset.deepsolar.space/en/", "mappings": { "miriam": "nlfff" }, "name": "NLFFF Database", "pattern": "^[0-9]+$", "preferred_prefix": "nlfff", "uri_format": "http://database.deepsolar.space:18080/dbs/nlfff/$1" }, "nlm": { "contact": { "email": "custserv@nlm.nih.gov", "name": "NLM Customer Service" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NLM Catalog provides access to NLM bibliographic data for journals, books, audiovisuals, computer software, electronic resources and other materials. Links to the library's holdings in LocatorPlus, NLM's online public access catalog, are also provided. [from homepage]", "example": "101775319", "homepage": "https://www.ncbi.nlm.nih.gov/nlmcatalog", "keywords": [ "journal" ], "license": "public domain", "logo": "https://upload.wikimedia.org/wikipedia/commons/5/52/Logo_of_U.S._National_Library_of_Medicine.png", "mappings": { "bartoc": "528", "biolink": "NLMID", "wikidata.entity": "Q986957" }, "name": "National Library of Medicine Catalog", "pattern": "^\\d+$", "preferred_prefix": "nlm", "uri_format": "https://www.ncbi.nlm.nih.gov/nlmcatalog/$1" }, "nlm.publisher": { "appears_in": [ "nlm" ], "contact": { "email": "custserv@nlm.nih.gov", "name": "NLM Customer Service" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Publisher short codes appearin in the NLM Catalog.", "example": "wiley", "github_request_issue": 1318, "homepage": "https://ftp.ncbi.nlm.nih.gov/pubmed/xmlprovidernames.txt", "keywords": [ "bibliometrics", "publisher" ], "license": "public domain", "logo": "https://upload.wikimedia.org/wikipedia/commons/5/52/Logo_of_U.S._National_Library_of_Medicine.png", "name": "NLM Publisher Codes", "preferred_prefix": "nlm.publisher" }, "nlx.anat": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "NLXANAT covers anatomy terms. Almost all terms are also in Uberon.", "example": "090201", "homepage": "https://scicrunch.org/scicrunch/interlex/dashboard", "keywords": [ "anatomy" ], "name": "NeuroLex Anatomy", "pattern": "^\\d+$", "preferred_prefix": "nlx.anat", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1" }, "nlx.br": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999).", "example": "145", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "anatomy", "brain regions", "neuroscience" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Brain Regions", "pattern": "^\\d+$", "preferred_prefix": "nlx.br", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXBR" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_br_$1" }, "nlx.cell": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXCELL conatins cell types with a focus on neuron types.", "example": "091005", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "cell lines", "cell types", "cells", "neuroscience" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Cell Types", "pattern": "^\\d+$", "preferred_prefix": "nlx.cell", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXCELL" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1" }, "nlx.chem": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXCHEM covers chemicals. Most classes are also in ChEBI.", "example": "090801", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "chemistry" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Chemical", "pattern": "^\\d+$", "preferred_prefix": "nlx.chem", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXCHEM" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1" }, "nlx.dys": { "appears_in": [ "mondo" ], "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc.", "example": "20090602", "homepage": "https://scicrunch.org/scicrunch/interlex/dashboard", "keywords": [ "disease", "disorders", "phenotypes" ], "name": "NeuroLex Dysfunction", "pattern": "^\\d+$", "preferred_prefix": "nlx.dys", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1" }, "nlx.func": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXFUNC covers terms for cognitive function.", "example": "90801", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "neuroscience" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Cognitive Function", "pattern": "^\\d+$", "preferred_prefix": "nlx.func", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXFUNC" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_func_$1" }, "nlx.inv": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis.", "example": "90901", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "data analysis", "funding agencies" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Investigations", "pattern": "^\\d+$", "preferred_prefix": "nlx.inv", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXINV" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1" }, "nlx.mol": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system.", "example": "90806", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "biology", "chemistry", "neuroscience", "proteins" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Molecules", "pattern": "^\\d+$", "preferred_prefix": "nlx.mol", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXMOL" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1" }, "nlx.oen": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results).", "example": "0001000", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "neuroscience" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: OEN Terms in Neurolex", "pattern": "^\\d+$", "preferred_prefix": "nlx.oen", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXOEN" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/oen_$1" }, "nlx.org": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXORG covers organisms.", "example": "090701", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "taxonomy" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Organisms", "pattern": "^\\d+$", "preferred_prefix": "nlx.org", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXORG" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1" }, "nlx.qual": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO).", "example": "100810", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "dispositions", "qualities" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Qualities", "pattern": "^\\d+$", "preferred_prefix": "nlx.qual", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXQUAL" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1" }, "nlx.res": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites", "example": "090924", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "software and information systems" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Digital Resources", "pattern": "^\\d+$", "preferred_prefix": "nlx.res", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXRES" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_res_$1" }, "nlx.sub": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO).", "example": "090803", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "cellular components" ], "license": "CC BY-4.0", "mappings": { "go": "NIF_Subcellular" }, "name": "NIF Standard Ontology: Subcellular Entities", "part_of": "neurolex", "pattern": "^\\d+$", "preferred_prefix": "nlx.sub", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXSUB", "nif_subcellular" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1" }, "nmdc": { "contact": { "email": "donny@polyneme.xyz", "github": "dwinston", "name": "Donny Winston", "orcid": "0000-0002-8424-0604" }, "contributor": { "email": "donny@polyneme.xyz", "github": "dwinston", "name": "Donny Winston", "orcid": "0000-0002-8424-0604" }, "contributor_extras": [ { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } ], "description": "An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem.", "example": "y3ax-8bq3-60", "github_request_issue": 130, "homepage": "https://microbiomedata.org/", "keywords": [ "microbiome" ], "mappings": { "miriam": "nmdc", "wikidata.entity": "Q107698738" }, "name": "National Microbiome Data Collaborative", "pattern": "^.{2,}$", "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://w3id.org/nmdc/$1" }, "nmpdr": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "The NMPDR provided curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma.", "example": "fig|306254.1.peg.183", "homepage": "http://www.nmpdr.org", "keywords": [ "genome" ], "mappings": { "ncbi": "NMPDR", "prefixcommons": "nmpdr" }, "name": "National Microbial Pathogen Data Resource", "preferred_prefix": "nmpdr", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/nmpdr:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature=$1" }, "nmr": { "banana": "NMR", "contact": { "email": "schober@imbi.uni-freiburg.de", "github": "DSchober", "name": "Daniel Schober", "orcid": "0000-0001-8014-6648" }, "deprecated": true, "description": "nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi.", "download_owl": "https://nmrml.org/cv/stable/nmrCV.owl", "example": "1000003", "homepage": "http://msi-ontology.sourceforge.net/", "keywords": [ "chemical and environmental engineering", "chemistry", "nfdi4chem", "nmr", "obo", "ontology", "owl" ], "mappings": { "aberowl": "NMR", "biocontext": "NMR", "bioportal": "NMR", "miriam": "nmr", "n2t": "nmr", "obofoundry": "nmr", "ols": "nmrcv", "prefixcommons": "nmr", "tib": "nmrcv", "wikidata.entity": "Q114677901" }, "name": "NMR-instrument specific component of metabolomics investigations", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "NMR", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/nmr:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/NMR_$1", "repository": "https://github.com/nmrML/nmrCV", "synonyms": [ "nmrcv" ], "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/nmrcv/terms?curie=NMR:$1", "version": "1.1.0" }, "nmrshiftdb2": { "contact": { "email": "stefan.kuhn@dmu.ac.uk", "name": "Stefan Kuhn", "orcid": "0000-0002-5990-4157" }, "contributor_extras": [ { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" } ], "description": "NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties.", "example": "234", "homepage": "https://nmrshiftdb.nmr.uni-koeln.de", "keywords": [ "analytical chemistry" ], "mappings": { "fairsharing": "FAIRsharing.nYaZ1N", "miriam": "nmrshiftdb2", "re3data": "r3d100010316", "wikidata": "P9405" }, "name": "NMRShiftDB structure", "pattern": "^[0-9]+$", "preferred_prefix": "nmrshiftdb2", "publications": [ { "doi": "10.1002/mrc.4263", "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", "pubmed": "15464159", "title": "NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database", "year": 2004 }, { "doi": "10.1021/ci0341363", "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" }, "nmrxiv.compound": { "contact": { "github": "vcnainala", "name": "Chandu Nainala", "orcid": "0000-0002-2564-3243" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "compounds appearing in nmrXiv that have associated spectra.", "example": "188", "github_request_issue": 1708, "homepage": "https://nmrxiv.org/compounds", "keywords": [ "chemical", "compound" ], "name": "nmrXiv compound", "preferred_prefix": "nmrxiv.compound", "uri_format": "https://nmrxiv.org/spectra?compound=$1" }, "nmrxiv.project": { "contact": { "github": "vcnainala", "name": "Chandu Nainala", "orcid": "0000-0002-2564-3243" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A project in the nmrXiv", "example": "P136", "github_request_issue": 1708, "homepage": "https://nmrxiv.org/projects", "keywords": [ "datasets", "project" ], "name": "nmrXiv project", "pattern": "^P\\d+$", "preferred_prefix": "nmrxiv.project", "uri_format": "https://nmrxiv.org/project/$1" }, "nmrxiv.sample": { "contact": { "github": "vcnainala", "name": "Chandu Nainala", "orcid": "0000-0002-2564-3243" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "spectra (samples) in the nmrXiv database", "example": "S1295", "github_request_issue": 1708, "homepage": "https://nmrxiv.org/spectra", "keywords": [ "nmr", "sample", "spectra", "spectrum" ], "name": "nmrXiv sample", "pattern": "^S\\d+$", "preferred_prefix": "nmrxiv.sample", "uri_format": "https://nmrxiv.org/sample/$1" }, "noaa.cameo": { "description": "CAMEO Chemicals is a database of hazardous chemical datasheets that emergency responders and planners can use to get response recommendations and predict hazards—such as explosions or toxic fumes.", "example": "19757", "homepage": "https://cameochemicals.noaa.gov", "mappings": { "wikidata": "P11931", "wikidata.entity": "Q125807660" }, "name": "CAMEO Chemicals ID", "pattern": "^\\d*$", "preferred_prefix": "noaa.cameo", "uri_format": "https://cameochemicals.noaa.gov/chemical/$1" }, "noaa.species": { "contributor": { "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" }, "description": "Identifier for a species on the noaa fisheries website", "example": "long-finned-pilot-whale", "github_request_issue": 456, "homepage": "https://www.fisheries.noaa.gov/species-directory", "mappings": { "wikidata": "P6049" }, "name": "NOAA Fisheries Species Directory", "pattern": "^[a-z]+(\\-[a-z]+)*$", "preferred_prefix": "noaa.species", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "noaa" ], "uri_format": "https://www.fisheries.noaa.gov/species/$1" }, "nomen": { "contact": { "email": "diapriid@gmail.com", "github": "mjy", "name": "Matt Yoder", "orcid": "0000-0002-5640-5491" }, "description": "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature.", "download_owl": "http://purl.obolibrary.org/obo/nomen.owl", "example": "0000295", "homepage": "https://github.com/SpeciesFileGroup/nomen", "keywords": [ "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "NOMEN", "bioportal": "NOMEN", "obofoundry": "nomen", "ols": "nomen", "ontobee": "NOMEN", "wikidata.entity": "Q81661723" }, "name": "A nomenclatural ontology for biological names", "pattern": "^\\d{7}$", "preferred_prefix": "NOMEN", "rdf_uri_format": "http://purl.obolibrary.org/obo/NOMEN_$1", "repository": "https://github.com/SpeciesFileGroup/nomen", "uri_format": "http://purl.obolibrary.org/obo/NOMEN_$1" }, "noncodev3": { "contact": { "email": "biozy@ict.ac.cn", "name": "Yi Zhao", "orcid": "0000-0001-6049-8347" }, "deprecated": true, "description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4.", "example": "377550", "homepage": "http://www.noncode.org/", "keywords": [ "expression", "nucleotide" ], "mappings": { "biocontext": "NONCODEV3", "miriam": "noncodev3", "n2t": "noncodev3", "prefixcommons": "noncode" }, "name": "NONCODE v3", "pattern": "^\\d+$", "preferred_prefix": "noncodev3", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/noncode:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr1175", "pmc": "PMC3245065", "pubmed": "22135294", "title": "NONCODE v3.0: integrative annotation of long noncoding RNAs", "year": 2011 } ], "uri_format": "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1" }, "noncodev4.gene": { "deprecated": true, "description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions.", "example": "NONHSAG00001", "homepage": "http://www.bioinfo.org/NONCODEv4/", "mappings": { "biocontext": "NONCODEV4.GENE", "miriam": "noncodev4.gene", "n2t": "noncodev4.gene" }, "name": "NONCODE v4 Gene", "pattern": "^NONHSAG\\d{5}$", "preferred_prefix": "noncodev4.gene", "uri_format": "http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1" }, "noncodev4.rna": { "deprecated": true, "description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts.", "example": "NONHSAT000001", "homepage": "http://www.bioinfo.org/NONCODEv4/", "mappings": { "biocontext": "NONCODEV4.RNA", "miriam": "noncodev4.rna", "n2t": "noncodev4.rna" }, "name": "NONCODE v4 Transcript", "pattern": "^NONHSAT\\d{6}$", "preferred_prefix": "noncodev4.rna", "uri_format": "http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1" }, "nord": { "appears_in": [ "mondo" ], "contact": { "email": "sean@skm.digital", "github": "skm16", "name": "Sean Roberts" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A website containing information about rare diseases, powered by Wordpress.", "example": "1693", "github_request_issue": 1375, "homepage": "https://rarediseases.org", "name": "National Organization for Rare Disorders", "pattern": "^\\d+$", "preferred_prefix": "nord", "references": [ "https://github.com/monarch-initiative/mondo/issues/8588" ], "uri_format": "https://rarediseases.org/?p=$1" }, "norine": { "contact": { "email": "maude.pupin@univ-lille.fr", "name": "Maude Pupin", "orcid": "0000-0003-3197-0715" }, "description": "Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings.", "example": "NOR00681", "homepage": "https://bioinfo.cristal.univ-lille.fr/norine/", "keywords": [ "life science", "protein" ], "mappings": { "biocontext": "NORINE", "fairsharing": "FAIRsharing.gf8yhy", "miriam": "norine", "n2t": "norine", "prefixcommons": "norine" }, "name": "Nonribosomal Peptides Database", "pattern": "^NOR\\d+$", "preferred_prefix": "norine", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/norine:$1" } ], "publications": [ { "doi": "10.1093/nar/gkz1000", "pmc": "PMC7145658", "pubmed": "31691799", "title": "Norine: update of the nonribosomal peptide resource", "year": 2020 }, { "doi": "10.1093/nar/gkm792", "pmc": "PMC2238963", "pubmed": "17913739", "title": "NORINE: a database of nonribosomal peptides", "year": 2007 } ], "uri_format": "https://bioinfo.cristal.univ-lille.fr/norine/result.jsp?ID=$1" }, "novus": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A vendor of antibodies and other biologics", "example": "nb100-56351", "homepage": "https://www.novusbio.com", "name": "Novus Biologicals", "preferred_prefix": "novus", "uri_format": "https://www.novusbio.com/products/$1" }, "npass": { "comment": "This resource does not have an explicit license. The [lotus database](https://github.com/lotusnprod/lotus-processor/blob/main/docs/licenses/npass.md) inferred that the CC-BY-NC license from the paper might be good enough for applying to the data itself.", "contact": { "email": "chenyuzong@sz.tsinghua.edu.cn", "name": "Yu Zong Chen", "orcid": "0000-0002-5473-8022" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data.", "example": "NPC139585", "homepage": "http://bidd.group/NPASS/", "keywords": [ "chemical", "compound", "natural product", "small molecule" ], "license": "CC-BY-NC", "logo": "https://bidd.group/NPASS/images/logo.png", "name": "Natural Product Activity and Species Source Database", "pattern": "^NPC\\d+$", "preferred_prefix": "npass", "publications": [ { "doi": "10.1093/nar/gkac1069", "pmc": "PMC9825494", "pubmed": "36624664", "title": "NPASS database update 2023: quantitative natural product activity and species source database for biomedical research", "year": 2023 }, { "doi": "10.1093/nar/gkx1026", "pmc": "PMC5753227", "pubmed": "29106619", "title": "NPASS: natural product activity and species source database for natural product research, discovery and tool development", "year": 2018 } ], "uri_format": "https://bidd.group/NPASS/compound.php?compoundID=$1" }, "npatlas": { "contact": { "email": "rliningt@sfu.ca", "name": "Roger Linington", "orcid": "0000-0003-1818-4971" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "Identifiers for microbially derived natural products that contains compound structures, producing organism taxonomy, biosynthetic and chemical properties.", "example": "NPA000001", "github_request_issue": 1295, "homepage": "https://www.npatlas.org", "name": "The Natural Products Atlas", "pattern": "^NPA\\d{6}$", "preferred_prefix": "npatlas", "publications": [ { "doi": "10.1093/nar/gkae1093", "pubmed": "39588755", "title": "The Natural Products Atlas 3.0: extending the database of microbially derived natural products", "year": 2024 }, { "doi": "10.1093/nar/gkab941", "pmc": "PMC8728154", "pubmed": "34718710", "title": "The Natural Products Atlas 2.0: a database of microbially-derived natural products", "year": 2021 }, { "doi": "10.1021/acscentsci.9b00806", "pmc": "PMC6891855", "pubmed": "31807684", "title": "The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery", "year": 2019 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://www.npatlas.org/explore/compounds/$1" }, "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/$1" }, "npo": { "contact": { "email": "nathan.baker@pnnl.gov", "github": "sobolevnrm", "name": "Nathan Baker", "orcid": "0000-0002-5892-6506" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.", "download_owl": "http://aber-owl.net/media/ontologies/NPO/31/npo.owl", "example": "1731", "homepage": "https://bioportal.bioontology.org/ontologies/NPO", "keywords": [ "life science", "molecular entity", "nanoparticle", "ontology", "structure" ], "mappings": { "aberowl": "NPO", "bioportal": "NPO", "fairsharing": "FAIRsharing.vy0p71" }, "name": "NanoParticle Ontology", "pattern": "^\\d+$", "preferred_prefix": "npo", "publications": [ { "doi": "10.1016/j.jbi.2010.03.001", "pmc": "PMC3042056", "pubmed": "20211274", "title": "NanoParticle Ontology for cancer nanotechnology research", "year": 2010 } ], "repository": "https://github.com/sobolevnrm/npo", "uri_format": "http://purl.bioontology.org/ontology/npo#NPO_$1" }, "nrfc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NRFC was established at ICAR-National Bureau of Fish Genetic Resources, Lucknow in the form of a research project entitled ‘Establishment of a National Repository at NBFGR, Lucknow for conservation and characterization of fish cell lines’ during 09 November, 2010 to 08 November, 2014 with the financial support from Department of Biotechnology, Govt. of India, New Delhi. NRFC aims to receive, authenticate, store and supply the fish cell lines to the researchers and academicians for Research & Development works and to serve as a National Referral Centre for fish cell lines in the country. NRFC also aims to provide need-based support for training and education to stakeholders. (from homepage)", "example": "NRFC051", "homepage": "https://mail.nbfgr.res.in/nrfc/index.php", "mappings": { "cellosaurus": "NRFC" }, "name": "National Repository of Fish Cell Lines", "pattern": "^NRFC\\d+$", "preferred_prefix": "nrfc" }, "nsc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Identifier used by the Cancer Chemotherapy National Service Center.", "example": "27223", "homepage": "https://wiki.nci.nih.gov/display/NCIDTPdata/Chemical+Data", "mappings": { "cheminf": "000565" }, "name": "USA National Service Center Number", "pattern": "^\\d+$", "preferred_prefix": "nsc", "references": [ "https://pubchem.ncbi.nlm.nih.gov/source/DTP/NCI" ], "uri_format": "https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist=$1" }, "nsf.award": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Information about research projects that NSF has funded since 1989 can be found by searching the Award Abstracts database. The information includes abstracts that describe the research, and names of principal investigators and their institutions. The database includes both completed and in-process research.", "example": "1458400", "homepage": "https://www.nsf.gov/awards/about.jsp", "name": "National Science Foundation Award", "pattern": "^\\d+$", "preferred_prefix": "nsf.award", "uri_format": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=$1" }, "nsrrc": { "description": "Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research. [from RRID]", "example": "0005", "homepage": "http://www.nsrrc.missouri.edu/", "keywords": [ "biomaterial manufacture", "breeding", "consulting", "cryopreservation", "fetal fibroblast", "fetus", "fibroblast", "genetically modified pig", "genetics", "genome", "genotyping", "health monitoring", "live animal", "phenotyping", "pig", "reproduction", "tissue" ], "mappings": { "rrid": "NSRRC" }, "name": "National Swine Resource and Research Center", "pattern": "^\\d+$", "preferred_prefix": "nsrrc", "uri_format": "https://nsrrc.missouri.edu/nsrrc$1info/" }, "nucc.characteristic": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Provider Characteristics code set is for use with health care provider information for enrollment and credentialing transactions and their corresponding responses. It is intended to provide codified responses to questions presented to a health care provider applying to or registering with an entity and to report the outcome of such application or registration. It may also be used for responses to inquiries regarding provider participation or registration in a program or plan.", "example": "2A", "example_extras": [ "10", "11" ], "homepage": "https://nucc.org/index.php/code-sets-mainmenu-41/provider-characteristics-mainmenu-39", "name": "National Uniform Claim Committee Characteristic", "pattern": "^\\d(\\d|\\w)$", "preferred_prefix": "nucc.characteristic" }, "nucc.taxonomy": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Health Care Provider Taxonomy code set is an external, nonmedical data code set designed for use in an electronic environment, specifically within the ASC X12N Health Care transactions. This includes the transactions mandated under HIPAA.\n\nThe taxonomy code is a unique alphanumeric code, ten characters in length. The code set is structured into three distinct \"Levels\" including Provider Grouping, Classification, and Area of Specialization.\n\n - **Level I, Provider Grouping** A major grouping of service(s) or occupation(s) of health care providers. For example: Allopathic & Osteopathic Physicians, Dental Providers, Hospitals, etc.\n - **Level II, Classification** A more specific service or occupation related to the Provider Grouping. For example, the Classification for Allopathic & Osteopathic Physicians is based upon the General Specialty Certificates as issued by the appropriate national boards. The following boards will however, have their general certificates appear as Level III areas of specialization strictly due to display limitations of the code set for Boards that have multiple general certificates: Medical Genetics, Preventive Medicine, Psychiatry & Neurology, Radiology, Surgery, Otolaryngology, Pathology.\n - **Level III, Area of Specialization** A more specialized area of the Classification in which a provider chooses to practice or make services available. For example, the Area of Specialization for provider grouping Allopathic & Osteopathic Physicians is based upon the Subspecialty Certificates as issued by the appropriate national boards.", "example": "207LH0002X", "homepage": "https://taxonomy.nucc.org", "name": "National Uniform Claim Committee Taxonomy", "pattern": "^\\d{3}\\w(\\w|\\d_)\\d{4}X$", "preferred_prefix": "nucc.taxonomy", "references": [ "https://www.nucc.org/images/stories/CSV/nucc_taxonomy_221.csv", "https://www.nucc.org" ] }, "nucleardb": { "comment": "Note that the typo from MIRIAM has spread to several other sources", "contact": { "email": "vriend@cmbi.ru.nl", "name": "Gert Vriend", "orcid": "0000-0002-1067-7053" }, "description": "NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs.", "example": "prgr_human", "homepage": "http://www.receptors.org/nucleardb/", "keywords": [ "classification" ], "mappings": { "biocontext": "NUCLEARBD", "integbio": "nbdc00599", "miriam": "nuclearbd", "n2t": "nuclearbd", "prefixcommons": "nucleardb" }, "name": "NucleaRDB", "pattern": "^\\w+\\_\\w+$", "preferred_prefix": "nucleardb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/nucleardb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr960", "pmc": "PMC3245090", "pubmed": "22064856", "title": "NucleaRDB: information system for nuclear receptors", "year": 2011 } ], "synonyms": [ "nuclearbd" ], "uri_format": "http://www.receptors.org/nucleardb/proteins/$1" }, "nucleotide": { "description": "The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.", "example": "880798137", "has_canonical": "insdc", "homepage": "https://www.ncbi.nlm.nih.gov/", "mappings": { "integbio": "nbdc00600", "miriam": "nucleotide" }, "name": "Nucleotide", "pattern": "^[a-zA-Z0-9_\\.]+$", "preferred_prefix": "nucleotide", "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" }, "nvs": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "SKOS concept collections held in the NERC Vocabulary Server. A concept collection is useful where a group of concepts shares something in common, and it is convenient to group them under a common label. In the NVS, concept collections are synonymous with controlled vocabularies or code lists. Each collection is associated with its governance body. An external website link is displayed when applicable.", "example": "P06", "homepage": "https://vocab.nerc.ac.uk/collection/", "name": "NERC Vocabulary Server", "preferred_prefix": "nvs", "uri_format": "https://vocab.nerc.ac.uk/collection/$1" }, "nxr": { "description": "National stock center for X. laevis and X. tropicalis and training center for advanced technologies (e.g. husbandry, cell biology, imaging, genetics, transgenesis, genomics). [from RRID]", "example": "0024", "homepage": "http://www.mbl.edu/xenopus/", "keywords": [ "laevis", "tropicalis", "xenopus" ], "mappings": { "rrid": "NXR" }, "name": "National Xenopus Resource", "pattern": "^\\d+$", "preferred_prefix": "nxr", "uri_format": "https://scicrunch.org/resolver/RRID:NXR_$1" }, "nztcs": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "SumirHPandit", "name": "Sumir Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "identifier for species classified under the New Zealand Threat Classification System", "example": "11061", "homepage": "https://nztcs.org.nz/", "keywords": [ "taxon", "taxonomy" ], "license": "CC-BY-4.0", "mappings": { "wikidata": "P9889" }, "name": "New Zealand Threat Classification System", "pattern": "^[1-9]\\d{2,6}$", "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", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture.", "download_owl": "http://aber-owl.net/media/ontologies/OA/4/oa.owl", "example": "sourceDateStart", "homepage": "http://www.w3.org/ns/oa", "keywords": [ "ontology", "quality" ], "mappings": { "aberowl": "OA", "biocontext": "oa", "bioportal": "OA", "lov": "oa", "zazuko": "oa" }, "name": "Web Annotation Ontology", "preferred_prefix": "oa", "uri_format": "http://www.w3.org/ns/oa#$1" }, "oae": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqunh He", "orcid": "0000-0001-9189-9661" }, "description": "The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc.", "download_owl": "http://purl.obolibrary.org/obo/oae.owl", "example": "0002959", "homepage": "https://github.com/OAE-ontology/OAE/", "keywords": [ "adverse reaction", "biomedical science", "drug", "obo", "ontology", "vaccine" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OAE", "biocontext": "OAE", "bioportal": "OAE", "fairsharing": "FAIRsharing.tw4q8x", "obofoundry": "oae", "ols": "oae", "ontobee": "OAE", "wikidata.entity": "Q81661725" }, "name": "Ontology of Adverse Events", "pattern": "^\\d{7}$", "preferred_prefix": "OAE", "publications": [ { "doi": "10.1186/2041-1480-5-29", "pmc": "PMC4120740", "pubmed": "25093068", "title": "OAE: The Ontology of Adverse Events", "year": 2014 }, { "doi": "10.1371/journal.pone.0049941", "title": "Ontology-Based Combinatorial Comparative Analysis of Adverse Events Associated with Killed and Live Influenza Vaccines", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OAE_$1", "repository": "https://github.com/OAE-ontology/OAE", "uri_format": "http://purl.obolibrary.org/obo/OAE_$1", "version": "1.2.47" }, "oarcs": { "contact": { "email": "mjyoder@illinois.edu", "github": "mjy", "name": "Matt Yoder", "orcid": "0000-0002-5640-5491" }, "description": "OArCS is an ontology describing the Arthropod ciruclatory system.", "download_owl": "http://purl.obolibrary.org/obo/oarcs.owl", "example": "0000029", "homepage": "https://github.com/aszool/oarcs", "keywords": [ "anatomy", "angiology", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OARCS", "biocontext": "OARCS", "bioportal": "OARCS", "fairsharing": "FAIRsharing.yqn857", "obofoundry": "oarcs", "ols": "oarcs", "ontobee": "OARCS", "wikidata.entity": "Q81661727" }, "name": "Ontology of Arthropod Circulatory Systems", "pattern": "^\\d{7}$", "preferred_prefix": "OARCS", "publications": [ { "doi": "10.1093/sysbio/syw108", "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 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OARCS_$1", "repository": "https://github.com/aszool/oarcs", "uri_format": "http://purl.obolibrary.org/obo/OARCS_$1", "version": "2019-04-18" }, "oba": { "appears_in": [ "fovt" ], "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO.", "download_json": "http://purl.obolibrary.org/obo/oba.json", "download_obo": "http://purl.obolibrary.org/obo/oba.obo", "download_owl": "http://purl.obolibrary.org/obo/oba.owl", "example": "0000001", "example_extras": [ "VT0003769" ], "homepage": "https://github.com/obophenotype/bio-attribute-ontology", "keywords": [ "biology", "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "OBA", "agroportal": "OBA", "biocontext": "OBA", "bioportal": "OBA", "fairsharing": "FAIRsharing.mp0rwf", "obofoundry": "oba", "ols": "oba", "ontobee": "OBA", "wikidata.entity": "Q81661730" }, "name": "Ontology of Biological Attributes", "pattern": "^(VT)?\\d{7}$", "preferred_prefix": "OBA", "publications": [ { "doi": "10.1007/s00335-023-09992-1", "pubmed": "37076585", "title": "The Ontology of Biological Attributes (OBA)-computational traits for the life sciences", "year": 2023 }, { "doi": "10.1101/2023.01.26.525742", "pmc": "PMC9900877", "pubmed": "36747660", "title": "The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences", "year": 2023 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OBA_$1", "repository": "https://github.com/obophenotype/bio-attribute-ontology", "uri_format": "http://purl.obolibrary.org/obo/OBA_$1", "version": "2025-10-29" }, "oban": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "It is an ontology model used to describe associations between biomedical entities in triple format based on W3C specification. OBAN is a generic association representation model that loosely couples a subject and object (e.g. disease and its associated phenotypes supported by the source of evidence for that association) via a construction of class OBAN:association. [from GitHub]", "download_owl": "https://raw.githubusercontent.com/EBISPOT/OBAN/master/ontology/oban_core.owl", "download_rdf": "https://raw.githubusercontent.com/EBISPOT/OBAN/master/ontology/oban_core.ttl", "example": "provenance", "homepage": "https://github.com/EBISPOT/OBAN", "keywords": [ "ontology" ], "mappings": { "biocontext": "OBAN", "biolink": "OBAN" }, "name": "Open Biomedical Annotations", "pattern": "^\\w+$", "preferred_prefix": "oban", "repository": "https://github.com/EBISPOT/OBAN", "uri_format": "http://purl.org/oban/$1" }, "obci": { "contact": { "email": "dan5@georgetown.edu", "github": "nataled", "name": "Darren A. 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It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI)", "download_owl": "http://purl.obolibrary.org/obo/obcs.owl", "example": "0000121", "homepage": "https://github.com/obcs/obcs", "keywords": [ "biology", "biomedical science", "medical informatics", "medicine", "obo", "ontology", "statistics", "vaccine" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OBCS", "biocontext": "OBCS", "bioportal": "OBCS", "fairsharing": "FAIRsharing.5p12xh", "miriam": "obcs", "obofoundry": "obcs", "ols": "obcs", "ontobee": "OBCS", "wikidata.entity": "Q55118544" }, "name": "Ontology of Biological and Clinical Statistics", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "OBCS", "publications": [ { "doi": "10.1186/s13326-016-0100-2", "pmc": "PMC5024438", "pubmed": "27627881", "title": "The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis", "year": 2016 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OBCS_$1", "repository": "https://github.com/obcs/obcs", "uri_format": "http://purl.obolibrary.org/obo/OBCS_$1", "version": "2023-12-08" }, "obi": { "appears_in": [ "agro", "foodon", "gallont", "hso", "labo", "maxo", "mco", "one", "ons", "proco", "rbo", "scdo" ], "banana": "OBI", "banana_peel": "_", "contact": { "email": "bpeters@lji.org", "github": "bpeters42", "name": "Bjoern Peters", "orcid": "0000-0002-8457-6693" }, "description": "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).", "download_obo": "https://github.com/obi-ontology/obi/raw/master/views/obi.obo", "download_owl": "http://purl.obolibrary.org/obo/obi.owl", "example": "0400109", "homepage": "http://obi-ontology.org", "keywords": [ "assay", "biomedical science", "data transformation", "dataplant", "device", "functional genomics", "life science", "life sciences, biology", "nfdi4cat", "nfdi4chem", "obo", "ontology", "reagent", "study design" ], "license": "CC-BY-4.0", "logo": "https://svn.code.sf.net/p/obi/code/trunk/web/htdocs/images/obi-lotext.png", "mappings": { "aberowl": "OBI", "biocontext": "OBI", "bioportal": "OBI", "fairsharing": "FAIRsharing.284e1z", "go": "OBI", "miriam": "obi", "n2t": "obi", "obofoundry": "obi", "ols": "obi", "ontobee": "OBI", "prefixcommons": "obi", "tib": "obi", "wikidata.entity": "Q7095051" }, "name": "Ontology for Biomedical Investigations", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "OBI", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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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" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OBIB", "biocontext": "OBIB", "bioportal": "OBIB", "fairsharing": "FAIRsharing.bxc508", "obofoundry": "obib", "ols": "obib", "ontobee": "OBIB", "wikidata.entity": "Q55118499" }, "name": "Ontology for Biobanking", "pattern": "^\\d{7}$", "preferred_prefix": "OBIB", "publications": [ { "doi": "10.1186/s13326-016-0068-y", "pmc": "PMC4855778", "pubmed": "27148435", "title": "OBIB-a novel ontology for biobanking", "year": 2016 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OBIB_$1", "repository": "https://github.com/biobanking/biobanking", "uri_format": "http://purl.obolibrary.org/obo/OBIB_$1", "version": "2023-04-05" }, "obo": { "contact": { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, "description": "The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies.", "download_owl": "http://aber-owl.net/media/ontologies/OBO/2/obo.owl", "example": "uberon", "example_extras": [ "go", "uberon.owl" ], "homepage": "http://www.obofoundry.org/", "keywords": [ "biology", "health", "ontology", "ontology and terminology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OBO", "biocontext": "OBO", "bioportal": "OBO", "fairsharing": "FAIRsharing.847069", "integbio": "nbdc00305", "lov": "obo" }, "name": "Open Biological and Biomedical Ontologies", "preferred_prefix": "obo", "publications": [ { "doi": "10.1038/nbt1346", "pmc": "PMC2814061", "pubmed": "17989687", "title": "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration", "year": 2007 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/$1", "references": [ "https://github.com/biopragmatics/bioregistry/pull/913", "https://github.com/biopragmatics/bioregistry/issues/910" ], "repository": "https://github.com/OBOFoundry/OBOFoundry.github.io", "twitter": "OBOFoundry", "uri_format": "http://purl.obolibrary.org/obo/$1" }, "oboe": { "contact": { "email": "brycemecum@gmail.com", "github": "amoeba", "name": "Bryce Mecum", "orcid": "0000-0002-0381-3766" }, "contributor": { "email": "philip.stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "description": "The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations.", "download_owl": "https://raw.githubusercontent.com/NCEAS/oboe/refs/heads/master/oboe.owl", "example": "Characteristic", "github_request_issue": 1276, "homepage": "https://github.com/NCEAS/oboe", "keywords": [ "biodiversity", "ecology", "environmental science", "ess", "fair data spaces", "nfdi4chem", "observations", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OBOE", "agroportal": "OBOE", "bioportal": "OBOE", "ecoportal": "OBOE", "fairsharing": "FAIRsharing.5970hq", "tib": "oboe-core" }, "name": "The Extensible Observation Ontology", "preferred_prefix": "oboe", "publications": [ { "doi": "10.1016/j.ecoinf.2007.05.004", "pmc": "PMC8612252", "pubmed": "34817235", "title": "An ontology for describing and synthesizing ecological observation data", "year": 2007 } ], "repository": "https://github.com/NCEAS/oboe", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#$1" }, "oboe.standard": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Units in OBOE", "example": "Acre", "github_request_issue": 1643, "homepage": "https://github.com/NCEAS/oboe", "keywords": [ "ontology", "unit", "units" ], "name": "OBOE Standard", "preferred_prefix": "oboe.standard", "uri_format": "http://ecoinformatics.org/oboe/oboe.1.2/oboe-standards.owl$1" }, "oboinowl": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties", "download_obo": "http://www.geneontology.org/formats/oboInOwl.obo", "download_owl": "http://www.geneontology.org/formats/oboInOwl.owl", "example": "hasDbXref", "example_extras": [ "auto_generated_by", "hasBroadSynonym", "hasExactSynonym", "hasNarrowSynonym" ], "homepage": "https://github.com/geneontology/go-ontology/tree/master/contrib", "keywords": [ "life science", "ontology" ], "mappings": { "biocontext": "oboInOwl", "biolink": "oboformat", "fairsharing": "FAIRsharing.aa0eat", "ols": "oio" }, "name": "OBO in OWL", "pattern": "^[\\w-]+$", "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", "oio" ], "uri_format": "http://www.geneontology.org/formats/oboInOwl#$1" }, "obv": { "description": "The Austrian Library Network (OBV) is the largest network of scientific and administrative libraries in Austria with 70 participants, representing more than 90 individual institutions - including the Austrian National Library, university libraries, the colleges of education, individual ministries, numerous technical colleges and other important collections.", "example": "AC00963334", "homepage": "https://www.obvsg.at/", "mappings": { "bartoc": "20430", "miriam": "obv" }, "name": "Austrian Library Network", "pattern": "^AC[0-9]{8}$", "preferred_prefix": "obv", "uri_format": "https://permalink.obvsg.at/$1" }, "occ": { "description": "The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law.", "example": "br/1", "homepage": "https://w3id.org/oc/corpus", "mappings": { "miriam": "occ", "n2t": "occ" }, "name": "OpenCitations Corpus", "pattern": "^[a-z][a-z]/[0-9]+$", "preferred_prefix": "occ", "uri_format": "https://w3id.org/oc/corpus/$1" }, "occo": { "contact": { "email": "zhengj2007@gmail.com", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "description": "This Occupaton Ontology (OccO) is an ontology in the domain of human occupaitons. Current OccO version is developed based on the US Bureau of Labor Statistics Standard Occupation Classification (SOC) and the related O*Net System. The OccO development follows the principles of the Open Biological and Biomedical (OBO) Foundry.", "download_owl": "http://purl.obolibrary.org/obo/occo.owl", "example": "00000001", "homepage": "https://github.com/Occupation-Ontology/OccO", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OCCO", "bioportal": "OCCO", "obofoundry": "occo", "ols": "occo", "ontobee": "OCCO" }, "name": "Occupation Ontology", "pattern": "^\\d+$", "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", "version": "2025-10-06" }, "ocdo": { "contact": { "email": "a.azocar.guzman@fz-juelich.de", "github": "aazocar", "name": "Abril Azocar Guzman", "orcid": "0000-0001-7564-7990" }, "contributor": { "email": "philip.stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "description": "The Crystallographic Defect Core Ontology (CDCO) defines the common terminology shared across all types of crystallographic defects, providing a unified framework for data integration in materials science.", "download_owl": "https://github.com/OCDO/cdco/raw/refs/heads/main/cdco.owl", "example": "hasDefectComplex", "github_request_issue": 1742, "homepage": "https://github.com/OCDO/cdco", "keywords": [ "ontology" ], "license": "CC-BY-4.0", "logo": "https://raw.githubusercontent.com/OCDO/.github/refs/heads/main/profile/ocdo_logo.png", "name": "Crystallographic Defect Core Ontology", "preferred_prefix": "ocdo", "repository": "https://github.com/OCDO/cdco", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://purls.helmholtz-metadaten.de/cdos/cdco/$1" }, "oci": { "description": "Each OCI (Open Citation Identifier) has a simple structure: oci:-, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entity - see https://doi.org/10.6084/m9.figshare.7127816.v2 for additional information. In each OCI, the first is the identifier for the citing bibliographic resource, while the second is the identifier for the cited bibliographic resource.", "example": "01027931310-01022252312", "homepage": "http://opencitations.net", "mappings": { "biocontext": "OCI", "miriam": "oci", "n2t": "oci" }, "name": "Open Citation Identifier", "pattern": "^0[1-9]+0[0-9]+-0[1-9]+0[0-9]+$", "preferred_prefix": "oci", "uri_format": "https://opencitations.net/index/ci/$1" }, "ocid": { "banana": "ocid", "description": "'ocid' stands for \"Ontology Concept Identifiers\" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology.", "example": "190000021540", "homepage": "https://ontochem.com/", "mappings": { "miriam": "ocid" }, "name": "Ontology Concept Identifiers", "namespace_in_lui": true, "pattern": "^[0-9]{12}$", "preferred_prefix": "ocid", "uri_format": "https://ocid.ontochem.com/prefname?ocid=$1" }, "oclc": { "description": "The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information.", "example": "634515043", "homepage": "https://www.oclc.org/en/about.html", "mappings": { "biocontext": "OCLC", "miriam": "oclc", "n2t": "oclc" }, "name": "Online Computer Library Center WorldCat", "pattern": "^[0-9]+$", "preferred_prefix": "oclc", "uri_format": "https://www.worldcat.org/oclc/$1" }, "odam": { "description": "Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed.", "example": "frim1", "homepage": "https://metabolome.cgfb.u-bordeaux.fr/", "mappings": { "miriam": "odam" }, "name": "Open Data for Access and Mining", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "odam", "uri_format": "http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1" }, "odamexplorer": { "description": "ODAM (Open Data for Access and Mining) is an Experimental data table management software (EDTMS) to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines.\n\nODAM allows datasets to be explored and then extracted in whole or in part as needed.\n\nFor more information/explanation, see ODAM User's Guide : https://inrae.github.io/ODAM/", "example": "frim1", "homepage": "https://eng-bfp.bordeaux-aquitaine.hub.inrae.fr/", "mappings": { "miriam": "odam.explorer" }, "name": "ODAM Data explorer", "pattern": "^[A-Za-z][A-Za-z0-9]+$", "preferred_prefix": "odamexplorer", "uri_format": "https://pmb-bordeaux.fr/dataexplorer/?ds=$1" }, "odc.sci": { "contact": { "email": "jgrethe@ucsd.edu", "name": "Jeffrey Grethe", "orcid": "0000-0001-5212-7052" }, "description": "The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data.", "example": "602", "homepage": "https://odc-sci.org", "keywords": [ "biomedical science", "neurobiology", "neurology", "neuroscience" ], "mappings": { "fairsharing": "FAIRsharing.M6Ruz3", "miriam": "odc.sci", "re3data": "r3d100014071" }, "name": "Open Data Commons for Spinal Cord Injury", "pattern": "^[0-9]*$", "preferred_prefix": "odc.sci", "publications": [ { "doi": "10.1089/neu.2019.6674", "pmc": "PMC7071068", "pubmed": "31608767", "title": "FAIR SCI Ahead: The Evolution of the Open Data Commons for Pre-Clinical Spinal Cord Injury Research", "year": 2019 }, { "doi": "10.1016/j.expneurol.2017.05.012", "pmc": "PMC6448396", "pubmed": "28576567", "title": "Developing a data sharing community for spinal cord injury research", "year": 2017 }, { "doi": "10.1038/ncomms9581", "pmc": "PMC4634208", "pubmed": "26466022", "title": "Topological data analysis for discovery in preclinical spinal cord injury and traumatic brain injury", "year": 2015 }, { "doi": "10.1038/nn.3838", "pmc": "PMC4728080", "pubmed": "25349910", "title": "Big data from small data: data-sharing in the 'long tail' of neuroscience", "year": 2014 }, { "doi": "10.1089/neu.2014.3399", "pmc": "PMC4186058", "pubmed": "25077610", "title": "Development of a database for translational spinal cord injury research", "year": 2014 }, { "doi": "10.1371/journal.pone.0059712", "pmc": "PMC3609747", "pubmed": "23544088", "title": "Derivation of multivariate syndromic outcome metrics for consistent testing across multiple models of cervical spinal cord injury in rats", "year": 2013 }, { "doi": "10.1007/s12975-011-0121-1", "pmc": "PMC3236294", "pubmed": "22207883", "title": "Syndromics: a bioinformatics approach for neurotrauma research", "year": 2011 }, { "doi": "S0014-4886(17)30137-1", "title": "Developing a data sharing community for spinal cord injury research." } ], "uri_format": "https://odc-sci.org/data/$1" }, "odc.tbi": { "description": "The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data.", "example": "408", "homepage": "https://odc-tbi.org", "mappings": { "miriam": "odc.tbi" }, "name": "Open Data Commons for Traumatic Brain Injury", "pattern": "^[0-9]*$", "preferred_prefix": "odc.tbi", "uri_format": "https://odc-tbi.org/data/$1" }, "odor": { "description": "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors", "example": "74", "homepage": "https://ordb.biotech.ttu.edu/OdorDB", "mappings": { "biocontext": "ODOR", "miriam": "odor", "n2t": "odor" }, "name": "Odor Molecules DataBase", "pattern": "^\\d+$", "preferred_prefix": "odor", "uri_format": "https://ordb.biotech.ttu.edu/OdorDB/Data/$1" }, "odrl": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The ODRL Vocabulary and Expression defines a set of concepts and terms (the vocabulary) and encoding mechanism (the expression) for permissions and obligations statements describing digital content usage based on the ODRL Information Model.", "download_rdf": "https://www.w3.org/ns/odrl/2/ODRL22.rdf", "example": "assetConcepts", "homepage": "http://www.w3.org/ns/odrl/2", "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" } }, "oefos": { "description": "The Austrian Fields of Science and Technology Classification (ÖFOS 2012) is the Austrian version of the revised international Fields of Science and Technology Classification of the OECD (FOS) published in the Frascati Manual 2015 as Fields of Research and Development (FORD). These fields are adjusted to national needs, whose application for international comparisons is binding, particularly within the European Statistical System. The six major Fields of Science: Natural Sciences; Technical Sciences; Human Medicine, Health Sciences; Agricultural Sciences, Veterinary Medicine; Social Sciences and Humanities remained unchanged in comparison to ÖFOS 2002. In order to ensure international comparability, the previous 2-digit levels from 2002, which are no longer applicable, were replaced by new 3-digit levels (groups) according to the international FOS respectively FORD. These 3-digit levels were provided with further sub-groups (4-digits) taking into account the comments of the international classification. It is therefore feasible that the new Austrian Fields of Science adapt to national peculiarities of the Austrian research activities. The research area with the corresponding 6-digits in alphabetical order serves as a description of the fields of activities and research projects and/or for the coverage of the main scientific activities of a statistical unit in the research and development surveys. (Current revision status: August 2017)", "example": "509015", "homepage": "https://vocabs.dariah.eu/oefos/en/", "keywords": [ "educational resources", "educational science" ], "mappings": { "tib": "oefos" }, "name": "Austrian Fields of Science and Technology Classification", "preferred_prefix": "oefos", "uri_format": "https://vocabs.acdh.oeaw.ac.at/oefosdisciplines/$1" }, "oeh.educationlevel": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A list of values for class levels. Created in the context of the OpenEduHub", "download_rdf": "https://github.com/openeduhub/oeh-metadata-vocabs/raw/refs/heads/master/educationalLevel.ttl", "example": "1", "github_request_issue": 1626, "homepage": "https://github.com/openeduhub/oeh-metadata-vocabs", "keywords": [ "education level", "open educational resources" ], "name": "OpenEduHub Education Level", "preferred_prefix": "oeh.educationlevel", "rdf_uri_format": "http://w3id.org/openeduhub/vocabs/educationalLevel/$1", "repository": "https://github.com/openeduhub/oeh-metadata-vocabs", "uri_format": "http://w3id.org/openeduhub/vocabs/educationalLevel/$1" }, "oeo": { "contact": { "email": "mirjam.stappel@uni-osnabrueck.de", "github": "stap-m", "name": "Mirjam Stappel", "orcid": "0000-0003-3722-5564" }, "contributor": { "email": "mirjam.stappel@uni-osnabrueck.de", "github": "stap-m", "name": "Mirjam Stappel", "orcid": "0000-0003-3722-5564" }, "description": "OEO is a domain reference ontology for energy system modeling.", "download_owl": "https://openenergyplatform.org/ontology/oeo/dev/oeo-full.owl", "example": "00030015", "github_request_issue": 1757, "homepage": "https://openenergyplatform.org/ontology/", "keywords": [ "energy", "energy engineering", "engineering", "mechanical engineering, energy technology", "nfdi4energy", "nfdi4ing", "ontology" ], "license": "CC0-1.0", "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBallIIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--7d85634a28722b48af9b2ccf2398db652d0b9753/OpenEnergyFamily_Logo_OpenEnergyOntology_OEO.png?disposition=inline", "mappings": { "bartoc": "20826", "fairsharing": "FAIRsharing.b91873", "tib": "oeo" }, "name": "Open Energy Ontology", "pattern": "^\\d+$", "preferred_prefix": "OEO", "publications": [ { "doi": "10.1016/j.egyai.2021.100074", "title": "Introducing the Open Energy Ontology: Enhancing data interpretation and interfacing in energy systems analysis", "year": 2021 } ], "rdf_uri_format": "https://openenergyplatform.org/ontology/oeo/OEO_$1", "repository": "https://github.com/OpenEnergyPlatform/ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://openenergyplatform.org/ontology/oeo/OEO_$1" }, "oerschema": { "contact": { "github": "michael-collins", "name": "Michael Collins" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A RDF vocabulary for OER content on the web.", "example": "InstructionalPattern", "github_request_issue": 1661, "homepage": "https://oerschema.org", "keywords": [ "curricula", "curriculum", "education", "oer", "oers", "open educational resources" ], "license": "MIT", "name": "OER Schema", "preferred_prefix": "oerschema", "repository": "https://github.com/open-curriculum/oerschema", "uri_format": "https://oerschema.org/$1" }, "og": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A vocabulary for embedding provenance metadata into webpages via RDFa", "example": "title", "github_request_issue": 1632, "homepage": "https://ogp.me", "keywords": [ "api", "data schema", "linked open data", "semantic web" ], "mappings": { "lov": "og", "zazuko": "og" }, "name": "Open Graph protocol", "preferred_prefix": "og", "rdf_uri_format": "https://ogp.me/ns#$1", "uri_format": "https://ogp.me/ns#$1" }, "ogc.sf": { "description": "An RDF/OWL vocabulary for defining SimpleFeature geometry types", "download_rdf": "https://opengeospatial.github.io/ogc-geosparql/geosparql11/sf_geometries.ttl", "example": "Triangle", "homepage": "https://opengeospatial.github.io/ogc-geosparql/geosparql11/sf_geometries.html", "mappings": { "zazuko": "sf" }, "name": "Open Geospatial Consortium Simple Features Vocabulary", "preferred_prefix": "ogc.sf", "uri_format": "http://www.opengis.net/ont/sf#$1" }, "ogg": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "description": "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets.", "download_owl": "http://purl.obolibrary.org/obo/ogg.owl", "example": "3000887619", "homepage": "https://bitbucket.org/hegroup/ogg", "keywords": [ "biology", "gene", "gene name", "genome", "life science", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OGG", "biocontext": "OGG", "bioportal": "OGG", "fairsharing": "FAIRsharing.zmx7nn", "obofoundry": "ogg", "ols": "ogg", "ontobee": "OGG", "wikidata.entity": "Q81661736" }, "name": "The Ontology of Genes and Genomes", "pattern": "^\\d+$", "preferred_prefix": "OGG", "rdf_uri_format": "http://purl.obolibrary.org/obo/OGG_$1", "repository": "https://bitbucket.org/hegroup/ogg", "uri_format": "http://purl.obolibrary.org/obo/OGG_$1", "version": "1.0.59" }, "ogi": { "contact": { "email": "linikujp@gmail.com", "github": "linikujp", "name": "Asiyah Yu Lin", "orcid": "0000-0002-5379-5359" }, "deprecated": true, "description": "OGI formalized the genomic element by defining an upper class 'genetic interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\nYu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI) to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n", "download_owl": "http://purl.obolibrary.org/obo/ogi.owl", "example": "0000019", "homepage": "https://code.google.com/archive/p/ontology-for-genetic-interval/", "keywords": [ "obo", "ontology" ], "mappings": { "aberowl": "OGI", "biocontext": "OGI", "bioportal": "OGI", "obofoundry": "ogi", "ols": "ogi", "ontobee": "OGI", "wikidata.entity": "Q55118520" }, "name": "Ontology for genetic interval", "pattern": "^\\d{7}$", "preferred_prefix": "OGI", "rdf_uri_format": "http://purl.obolibrary.org/obo/OGI_$1", "synonyms": [ "OGI.owl" ], "uri_format": "http://purl.obolibrary.org/obo/OGI_$1", "version": "2.0" }, "ogms": { "appears_in": [ "labo", "scdo" ], "contact": { "email": "baeverma@jcvi.org", "github": "BAevermann", "name": "Brian Aevermann", "orcid": "0000-0003-1346-1327" }, "description": "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats.\n\nOGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.", "download_obo": "http://purl.obolibrary.org/obo/ogms.obo", "download_owl": "http://purl.obolibrary.org/obo/ogms.owl", "example": "0000031", "homepage": "https://github.com/OGMS/ogms", "keywords": [ "biomedical science", "cancer", "diagnosis", "disease", "disease phenotype", "medicine", "obo", "ontology" ], "license": "CC-BY-4.0", "logo": "https://avatars2.githubusercontent.com/u/12973154?s=200&v=4", "mappings": { "aberowl": "OGMS", "bartoc": "216", "biocontext": "OGMS", "bioportal": "OGMS", "fairsharing": "FAIRsharing.rvz0m9", "obofoundry": "ogms", "ols": "ogms", "ontobee": "OGMS", "wikidata.entity": "Q55118512" }, "name": "Ontology for General Medical Science", "pattern": "^\\d{7}$", "preferred_prefix": "OGMS", "providers": [ { "code": "omre", "uri_format": "http://purl.obolibrary.org/obo/ogms/OMRE_$1" } ], "publications": [ { "pubmed": "25991121", "title": "Biomarkers in the ontology for general medical science", "year": 2015 }, { "doi": "10.1186/2041-1480-4-42", "pmc": "PMC4028878", "pubmed": "24314207", "title": "The neurological disease ontology", "year": 2013 }, { "pmc": "PMC3041577", "pubmed": "21347182", "title": "Toward an ontological treatment of disease and diagnosis", "year": 2009 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OGMS_$1", "repository": "https://github.com/OGMS/ogms", "synonyms": [ "ogms/OMRE" ], "uri_format": "http://purl.obolibrary.org/obo/OGMS_$1", "version": "2021-08-19" }, "ogsf": { "contact": { "email": "linikujp@gmail.com", "github": "linikujp", "name": "Asiyah Yu Lin", "orcid": "0000-0002-5379-5359" }, "deprecated": true, "description": "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.", "download_owl": "http://purl.obolibrary.org/obo/ogsf.owl", "example": "0000025", "homepage": "https://github.com/linikujp/OGSF", "keywords": [ "adverse reaction", "biomedical science", "disease", "epidemiology", "genetic disorder", "genetics", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OGSF", "biocontext": "OGSF", "bioportal": "OGSF", "fairsharing": "FAIRsharing.egv2cz", "obofoundry": "ogsf", "ols": "ogsf", "ontobee": "OGSF", "wikidata.entity": "Q113012672" }, "name": "Ontology of Genetic Susceptibility Factor", "pattern": "^\\d{7}$", "preferred_prefix": "OGSF", "publications": [ { "doi": "10.1186/2041-1480-5-19", "pmc": "PMC4068904", "pubmed": "24963371", "title": "The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events", "year": 2014 }, { "pubmed": "20847592", "title": "Ontology driven modeling for the knowledge of genetic susceptibility to disease", "year": 2009 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OGSF_$1", "repository": "https://github.com/linikujp/OGSF", "uri_format": "http://purl.obolibrary.org/obo/OGSF_$1", "version": "2.0" }, "ohd": { "contact": { "email": "wdduncan@gmail.com", "github": "wdduncan", "name": "Bill Duncan", "orcid": "0000-0001-9625-1899" }, "description": "The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies.", "download_owl": "http://purl.obolibrary.org/obo/ohd.owl", "example": "0000006", "homepage": "https://purl.obolibrary.org/obo/ohd/home", "keywords": [ "dentistry", "medicine", "obo", "ontology", "oral surgery" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OHD", "biocontext": "OHD", "bioportal": "OHD", "fairsharing": "FAIRsharing.bg7bb6", "obofoundry": "ohd", "ols": "ohd", "ontobee": "OHD", "wikidata.entity": "Q55118561" }, "name": "Oral Health and Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "OHD", "publications": [ { "doi": "10.1186/s13326-020-00222-0", "pmc": "PMC7439527", "pubmed": "32819435", "title": "Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology", "year": 2020 } ], "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_$1", "version": "2025-06-28" }, "ohmi": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "description": "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.", "download_owl": "http://purl.obolibrary.org/obo/ohmi.owl", "example": "0000460", "homepage": "https://github.com/ohmi-ontology/ohmi", "keywords": [ "host", "life science", "microbiome", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OHMI", "biocontext": "OHMI", "bioportal": "OHMI", "fairsharing": "FAIRsharing.cz9cnp", "obofoundry": "ohmi", "ols": "ohmi", "ontobee": "OHMI", "wikidata.entity": "Q113012673" }, "name": "Ontology of Host-Microbiome Interactions", "pattern": "^\\d{7}$", "preferred_prefix": "OHMI", "publications": [ { "doi": "10.1186/s13326-019-0217-1", "title": "OHMI: the ontology of host-microbiome interactions", "year": 2019 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OHMI_$1", "repository": "https://github.com/ohmi-ontology/ohmi", "uri_format": "http://purl.obolibrary.org/obo/OHMI_$1", "version": "2025-12-28" }, "ohpi": { "contact": { "email": "edong@umich.edu", "github": "e4ong1031", "name": "Edison Ong", "orcid": "0000-0002-5159-414X" }, "description": "OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration).", "download_owl": "http://purl.obolibrary.org/obo/ohpi.owl", "example": "9001411", "homepage": "https://github.com/OHPI/ohpi", "keywords": [ "bioinformatics", "biomedical science", "host", "infection process", "obo", "ontology", "pathogen" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OHPI", "bioportal": "OHPI", "fairsharing": "FAIRsharing.vxpUJ6", "obofoundry": "ohpi", "ols": "ohpi", "ontobee": "OHPI", "wikidata.entity": "Q113012674" }, "name": "Ontology of Host Pathogen Interactions", "pattern": "^\\d+$", "preferred_prefix": "OHPI", "publications": [ { "doi": "10.1093/nar/gky999", "pmc": "PMC6324020", "pubmed": "30365026", "title": "Victors: a web-based knowledge base of virulence factors in human and animal pathogens", "year": 2019 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OHPI_$1", "repository": "https://github.com/OHPI/ohpi", "uri_format": "http://purl.obolibrary.org/obo/OHPI_$1", "version": "2019-09-30" }, "oid": { "contact": { "email": "info@daniel-marschall.de", "github": "danielmarschall", "name": "Daniel Marschall", "orcid": "0009-0001-5055-9262" }, "contributor_extras": [ { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, { "email": "info@daniel-marschall.de", "github": "danielmarschall", "name": "Daniel Marschall", "orcid": "0009-0001-5055-9262" } ], "description": "OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes.", "example": "2.16.840", "example_extras": [ "2", "2.16", "2.16.840.1", "2.16.840.1.113883", "2.16.840.1.113883.6", "2.16.840.1.113883.6.88" ], "homepage": "https://oid-base.com", "mappings": { "miriam": "oid", "n2t": "oid" }, "name": "ISO Object Identifier", "pattern": "^[\\d.]+$", "preferred_prefix": "oid", "providers": [ { "code": "oid_www", "description": "OID w/ WWW", "homepage": "http://www.oid-info.com", "name": "OID w/ WWW", "status": { "contributor": "0000-0003-4423-4370", "date": "2025-07-02", "value": "gone" }, "uri_format": "http://www.oid-info.com/get/$1" }, { "code": "orange", "description": "Mirror of OID site from Orange", "homepage": "https://oid-rep.orange-labs.fr", "name": "Mirror of OID site from Orange", "status": { "contributor": "0000-0003-4423-4370", "date": "2025-07-02", "value": "gone" }, "uri_format": "https://oid-rep.orange-labs.fr/get/$1" } ], "references": [ "https://en.wikipedia.org/wiki/Object_identifier" ], "uri_format": "https://oid-base.com/get/$1" }, "oidc": { "description": "The OpenID Connect vocabulary used by the Solid-OIDC authentication specification", "download_rdf": "http://www.w3.org/ns/solid/oidc", "example": "client_name", "homepage": "https://solidproject.org/TR/oidc", "mappings": { "zazuko": "oidc" }, "name": "Solid OpenID Connect vocabulary", "preferred_prefix": "oidc" }, "okn.sd": { "description": "An ontology for describing software components, including their metadata (attribution, licensing, usage instructions, how to get support) and their inputs, outputs and variables. The ontology extends schema.org and codemeta vocabularies and is based on OntoSoft, which proposed a vocabulary for describing software by asking scientists questions.", "example": "CatalogIdentifier", "homepage": "https://knowledgecaptureanddiscovery.github.io/SoftwareDescriptionOntology/release/1.9.0/index-en.html", "keywords": [ "computer science", "nfdi4ing" ], "mappings": { "tib": "sd" }, "name": "The Software Description Ontology", "preferred_prefix": "okn.sd", "uri_format": "https://w3id.org/okn/o/sd#$1" }, "olatdv": { "contact": { "email": "frederic.bastian@unil.ch", "github": "fbastian", "name": "Frédéric Bastian", "orcid": "0000-0002-9415-5104" }, "deprecated": true, "description": "Life cycle stages for Medaka", "download_obo": "http://purl.obolibrary.org/obo/olatdv.obo", "download_owl": "http://purl.obolibrary.org/obo/olatdv.owl", "example": "0000210", "homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv", "keywords": [ "aquaculture", "developmental biology", "life cycle stage", "life science", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OLATDV", "biocontext": "OLATDV", "bioportal": "OLATDV", "fairsharing": "FAIRsharing.c86z66", "obofoundry": "olatdv", "ols": "olatdv", "ontobee": "OlatDv", "wikidata.entity": "Q81661748" }, "name": "Medaka Developmental Stages", "pattern": "^\\d{7}$", "preferred_prefix": "OlatDv", "rdf_uri_format": "http://purl.obolibrary.org/obo/OlatDv_$1", "repository": "https://github.com/obophenotype/developmental-stage-ontologies", "uri_format": "http://purl.obolibrary.org/obo/OlatDv_$1" }, "om": { "contact": { "email": "hajo.rijgersberg@wur.nl", "name": "Hajo Rijgersberg" }, "description": "The Ontology of units of Measure (OM) 2.0 models concepts and relations important to scientific research. It has a strong focus on units, quantities, measures, and dimensions.", "download_owl": "http://aber-owl.net/media/ontologies/OM/33/om.owl", "download_rdf": "https://raw.githubusercontent.com/HajoRijgersberg/OM/master/om-2.0.rdf", "example": "Dimension", "homepage": "https://github.com/HajoRijgersberg/OM", "keywords": [ "earth sciences", "ess", "life sciences, biology", "nfdi4cat", "nfdi4chem", "nfdi4ing", "ontology", "physics", "unit", "units" ], "mappings": { "aberowl": "OM", "agroportal": "OM", "bioportal": "OM", "ols": "om", "ontobee": "OM", "tib": "om" }, "name": "Ontology of units of Measure", "preferred_prefix": "om", "repository": "https://github.com/HajoRijgersberg/OM", "uri_format": "http://www.ontology-of-units-of-measure.org/resource/om-2/$1", "version": "2.0.59" }, "oma.grp": { "description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs.", "example": "LCSCCPN", "homepage": "https://omabrowser.org/cgi-bin/gateway.pl", "mappings": { "biocontext": "OMA.GRP", "miriam": "oma.grp", "n2t": "oma.grp" }, "name": "OMA Group", "pattern": "^[A-Z]+$", "preferred_prefix": "oma.grp", "uri_format": "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1" }, "oma.hog": { "banana": "HOG", "description": "Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. ", "example": "0459895", "homepage": "https://omabrowser.org", "mappings": { "miriam": "oma.hog" }, "name": "OMA HOGs", "pattern": "^[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$", "preferred_prefix": "oma.hog", "uri_format": "https://omabrowser.org/oma/hog/HOG:$1" }, "oma.protein": { "description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records.", "example": "HUMAN16963", "homepage": "https://omabrowser.org/oma/home/", "mappings": { "biocontext": "OMA.PROTEIN", "miriam": "oma.protein", "n2t": "oma.protein", "togoid": "OmaProtein" }, "name": "OMA Protein", "pattern": "^[A-Z0-9]{5}\\d+$", "preferred_prefix": "oma.protein", "uri_format": "https://omabrowser.org/oma/vps/$1" }, "omia": { "contact": { "email": "imke.tammen@sydney.edu.au", "github": "ImkeTammen", "name": "Imke Tammen", "orcid": "0000-0002-5520-6597" }, "contributor_extras": [ { "email": "imke.tammen@sydney.edu.au", "github": "ImkeTammen", "name": "Imke Tammen", "orcid": "0000-0002-5520-6597" } ], "description": "Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources). The 'omia' prefix is used for phenes, either across species (omia:001000) or in a specific species (omia:001000-9615)", "example": "001000", "example_extras": [ "001000-9615" ], "homepage": "https://omia.org", "keywords": [ "classification", "disorders", "gene", "model organism database", "traits" ], "mappings": { "biocontext": "OMIA", "integbio": "nbdc00153", "miriam": "omia", "n2t": "omia", "prefixcommons": "omia" }, "name": "Online Mendelian Inheritance in Animals", "pattern": "^\\d{6}(-\\d+)?$", "preferred_prefix": "omia", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/omia:$1" } ], "publications": [ { "doi": "10.1007/s00335-024-10059-y", "pubmed": "39143381", "title": "Online Mendelian Inheritance in Animals (OMIA): a genetic resource for vertebrate animals", "year": 2024 } ], "synonyms": [ "OMIA" ], "uri_format": "https://omia.org/phene/omia:$1" }, "omia.variant": { "contact": { "email": "imke.tammen@sydney.edu.au", "github": "ImkeTammen", "name": "Imke Tammen", "orcid": "0000-0002-5520-6597" }, "contributor_extras": [ { "email": "imke.tammen@sydney.edu.au", "github": "ImkeTammen", "name": "Imke Tammen", "orcid": "0000-0002-5520-6597" } ], "description": "Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources). The 'omia.variant' prefix is used for genetic variants associated with phenes listed in OMIA", "example": "1710", "example_extras": [ "620" ], "homepage": "https://omia.org", "keywords": [ "disorders", "model organism database", "traits" ], "mappings": { "biocontext": "OMIA", "integbio": "nbdc00153" }, "name": "OMIA variants", "pattern": "^\\d+$", "preferred_prefix": "omia.variant", "publications": [ { "doi": "10.1007/s00335-024-10059-y", "pubmed": "39143381", "title": "Online Mendelian Inheritance in Animals (OMIA): a genetic resource for vertebrate animals", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://omia.org/variant/omia.variant:$1" }, "omiabis": { "appears_in": [ "labo" ], "contact": { "email": "mbrochhausen@gmail.com", "name": "Mathias Brochhausen", "orcid": "0000-0003-1834-3856" }, "deprecated": true, "description": "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)", "download_owl": "http://purl.obolibrary.org/obo/omiabis.owl", "example": "0001079", "homepage": "https://github.com/OMIABIS/omiabis-dev", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OMIABIS", "biocontext": "OMIABIS", "bioportal": "OMIABIS", "obofoundry": "omiabis", "ols": "omiabis", "ontobee": "OMIABIS" }, "name": "Ontologized MIABIS", "pattern": "^\\d{7}$", "preferred_prefix": "OMIABIS", "rdf_uri_format": "http://purl.obolibrary.org/obo/OMIABIS_$1", "repository": "https://github.com/OMIABIS/omiabis-dev", "uri_format": "http://purl.obolibrary.org/obo/OMIABIS_$1", "version": "2014-05-28" }, "omid": { "description": "Every entity in OpenCitations Meta (https://opencitations.net/meta) is assigned persistent internal identifier called OpenCitations Meta Identifier (OMID). The OMID has structure [[entity_type_abbreviation]]/[[supplier_prefix]][[sequential_number]]. For example, the first journal article ever processed has OMID br/0601 (the full URI is https://w3id.org/oc/meta/br/0601), where br is the abbreviation of bibliographic resource, and 060 corresponds to the supplier prefix, helpful in recognising at a glance the index it belongs to (i.e., OpenCitations Meta). Finally, 1 indicates that this is the index's first bibliographic resource ever minted.", "example": "br/0601", "homepage": "http://opencitations.net/", "mappings": { "miriam": "omid" }, "name": "OpenCitations Meta Identifier", "pattern": "^[a-z][a-z]/06[1-9]*0[1-9][0-9]*$", "preferred_prefix": "omid", "uri_format": "https://w3id.org/oc/meta/$1" }, "omim": { "contact": { "email": "ahamosh@jhmi.edu", "github": "ahamosh", "name": "Ada Hamosh", "orcid": "0000-0002-1780-5230" }, "description": "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.", "example": "603903", "homepage": "https://omim.org/", "keywords": [ "biomedical science", "disease", "disease course", "gene", "gene expression", "genetic disorder", "genotype", "ontology", "phenotype" ], "license": "https://www.omim.org/help/agreement", "logo": "https://omim.org/static/omim/icons/OMIM_davinciman.001.png", "mappings": { "aberowl": "OMIM", "biocontext": "OMIM", "bioportal": "OMIM", "edam": "1153", "fairsharing": "FAIRsharing.b084yh", "go": "OMIM", "hl7": "2.16.840.1.113883.6.174", "integbio": "nbdc00154", "miriam": "mim", "n2t": "mim", "ncbi": "MIM", "prefixcommons": "omim", "uniprot": "DB-0062", "wikidata": "P492", "wikidata.entity": "Q7187" }, "name": "Online Mendelian Inheritance in Man", "pattern": "^\\d+$", "preferred_prefix": "omim", "providers": [ { "code": "", "description": "OMIM mirror at John Hopkins", "homepage": "http://mirror.omim.org/", "name": "OMIM mirror at John Hopkins", "uri_format": "http://mirror.omim.org/entry/$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/omim:$1" }, { "code": "legacy", "description": "This is the actual endpoint for OMIM entries", "homepage": "https://www.omim.org", "name": "OMIM", "uri_format": "https://www.omim.org/entry/$1" }, { "code": "miriam_legacy", "description": "Legacy URLs for identifiers.org", "homepage": "http://identifiers.org", "name": "MIRIAM Legacy", "uri_format": "http://identifiers.org/omim/$1" }, { "code": "ncbi.omim", "description": "An NCBI endpoint for OMIM entries", "homepage": "http://www.ncbi.nlm.nih.gov/omim", "name": "NCBI", "uri_format": "http://www.ncbi.nlm.nih.gov/omim/$1" }, { "code": "purl", "description": "An extra purl that was registred, but probably won't be used.", "homepage": "https://www.omim.org", "name": "OMIM PURL (not in use)", "uri_format": "https://purl.org/mim/MIM:$1" }, { "code": "purl2", "description": "An extra purl that was registred, but probably won't be used.", "homepage": "https://www.omim.org", "name": "OMIM PURL (not in use)", "uri_format": "https://omim.org/OMIM:$1" } ], "publications": [ { "doi": "10.1093/nar/gky1151", "pubmed": "30445645" }, { "doi": "10.1093/nar/gku1205", "pmc": "PMC4383985", "pubmed": "25428349", "title": "OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders", "year": 2014 }, { "doi": "10.1093/nar/gki033", "pmc": "PMC539987", "pubmed": "15608251", "title": "Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders", "year": 2005 } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/497" ], "synonyms": [ "OMIM", "mim" ], "uri_format": "https://omim.org/MIM:$1" }, "omim.ps": { "banana": "PS", "contact": { "email": "ahamosh@jhmi.edu", "github": "ahamosh", "name": "Ada Hamosh", "orcid": "0000-0002-1780-5230" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "smoxon@lbl.gov", "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" } ], "description": "A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.", "example": "214100", "homepage": "https://www.omim.org/phenotypicSeriesTitles/all", "keywords": [ "disease", "phenotype" ], "license": "https://www.omim.org/help/agreement", "logo": "https://www.omim.org/static/omim/icons/OMIM_davinciman.001.png", "mappings": { "biolink": "OMIM.PS" }, "name": "OMIM Phenotypic Series", "pattern": "^\\d+$", "preferred_prefix": "omim.ps", "providers": [ { "code": "legacy", "description": "This is the actual endpoint for OMIM phenotypic series entries", "homepage": "https://www.omim.org", "name": "OMIM", "uri_format": "https://omim.org/phenotypicSeries/PS$1" } ], "synonyms": [ "MIMPS", "OMIMPS", "PS", "mim.ps" ], "uri_format": "https://omim.org/MIM:PS$1" }, "omit": { "appears_in": [ "mco" ], "contact": { "email": "huang@southalabama.edu", "github": "Huang-OMIT", "name": "Jingshan Huang", "orcid": "0000-0003-2408-2883" }, "description": "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes).", "download_obo": "https://raw.githubusercontent.com/OmniSearch/omit/master/src/ontology/omit.obo", "download_owl": "http://purl.obolibrary.org/obo/omit.owl", "example": "0000069", "homepage": "http://omit.cis.usouthal.edu/", "keywords": [ "annotation", "biology", "cell", "gene", "gene prediction", "life science", "mirna", "molecular entity", "molecular interaction", "obo", "ontology", "prediction and recognition", "protein", "regulation of gene expression" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OMIT", "biocontext": "OMIT", "bioportal": "OMIT", "fairsharing": "FAIRsharing.mf91p5", "miriam": "omit", "n2t": "omit", "obofoundry": "omit", "ols": "omit", "ontobee": "OMIT", "wikidata.entity": "Q81661752" }, "name": "Ontology for MicroRNA Target", "pattern": "^\\d{7}$", "preferred_prefix": "OMIT", "publications": [ { "doi": "10.1186/s13326-016-0064-2", "pmc": "PMC4863347", "pubmed": "27175225", "title": "OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data", "year": 2016 }, { "doi": "10.1371/journal.pone.0100855", "pmc": "PMC4099014", "pubmed": "25025130", "title": "OMIT: dynamic, semi-automated ontology development for the microRNA domain", "year": 2014 }, { "doi": "10.1007/s11095-011-0573-8", "pubmed": "21879385", "title": "OMIT: a domain-specific knowledge base for microRNA target prediction", "year": 2011 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OMIT_$1", "repository": "https://github.com/OmniSearch/omit", "synonyms": [ "OMIT" ], "uri_format": "http://purl.obolibrary.org/obo/OMIT_$1", "version": "dev" }, "omo": { "appears_in": [ "cl", "pcl", "uberon" ], "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO).", "download_owl": "http://purl.obolibrary.org/obo/omo.owl", "example": "0003003", "homepage": "https://github.com/information-artifact-ontology/ontology-metadata", "keywords": [ "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "OMO", "bioportal": "OMO", "obofoundry": "omo", "ols": "omo", "ontobee": "OMO", "wikidata.entity": "Q113012675" }, "name": "OBO Metadata Ontology", "pattern": "^\\d{7}$", "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_$1", "version": "2025-06-18" }, "omon": { "contributor": { "email": "oga.t@northeastern.edu", "github": "tomo-oga", "name": "Tomohiro Oga", "orcid": "0009-0001-6787-3995" }, "description": "The new national clinical trials registry of the Netherlands", "example": "53367", "github_request_issue": 1157, "homepage": "https://onderzoekmetmensen.nl/en", "logo": "https://onderzoekmetmensen.nl/themes/custom/trialregister/logo.svg", "name": "Overview of Medical Research in the Netherlands", "pattern": "^\\d{5}$", "preferred_prefix": "omon", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://onderzoekmetmensen.nl/en/trial/$1" }, "omop": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" } ], "description": "The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format.", "example": "1", "homepage": "https://www.ohdsi.org/data-standardization/the-common-data-model/", "name": "Observational Medical Outcomes Partnership", "pattern": "^\\d+$", "preferred_prefix": "omop", "providers": [ { "code": "ohdsi.api", "description": "Programmatic access to OMOP terms", "homepage": "http://api.ohdsi.org", "name": "OHDSI API", "uri_format": "http://api.ohdsi.org/WebAPI/vocabulary/concept/$1" }, { "code": "ohdsi.data", "description": " https://faircookbook.elixir-europe.org/content/recipes/applied-examples/ehden-ohdsi.html suggests https://data.ohdsi.org/concept/ as another uri expansion but it does not resolve.", "homepage": "https://data.ohdsi.org/concept", "name": "OHDSI Data Endpoint", "uri_format": "https://data.ohdsi.org/concept/$1" } ], "references": [ "https://github.com/callahantiff/OMOP2OBO", "https://github.com/biopragmatics/bioregistry/issues/599", "https://github.com/biopragmatics/bioregistry/pull/600" ], "synonyms": [ "OMOP" ], "uri_format": "https://athena.ohdsi.org/search-terms/terms/$1" }, "omp": { "appears_in": [ "mco" ], "contact": { "email": "jimhu@tamu.edu", "github": "jimhu-tamu", "name": "James C. Hu", "orcid": "0000-0001-9016-2684" }, "description": "An ontology of phenotypes covering microbes", "download_obo": "http://purl.obolibrary.org/obo/omp.obo", "download_owl": "http://purl.obolibrary.org/obo/omp.owl", "example": "0005067", "homepage": "http://microbialphenotypes.org", "keywords": [ "chemical biology", "data analysis", "dataplant", "life sciences, biology", "microbe-host interaction phenotype", "microbial ecology", "microbiology", "obo", "omics", "ontology", "phenomics", "phenotype" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OMP", "biocontext": "OMP", "bioportal": "OMP", "fairsharing": "FAIRsharing.cc3f2x", "obofoundry": "omp", "ols": "omp", "ontobee": "OMP", "tib": "omp", "wikidata.entity": "Q81661753" }, "name": "Ontology of Microbial Phenotypes", "pattern": "^\\d{7}$", "preferred_prefix": "OMP", "publications": [ { "doi": "10.1186/s12866-014-0294-3", "pmc": "PMC4287307", "pubmed": "25433798", "title": "An ontology for microbial phenotypes", "year": 2014 }, { "doi": "10.1186/s13326-019-0205-5", "title": "Phenotype annotation with the ontology of microbial phenotypes (OMP)", "year": 2019 } ], "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_$1", "version": "2024-03-25" }, "omrse": { "appears_in": [ "labo" ], "contact": { "email": "hoganwr@gmail.com", "github": "hoganwr", "name": "Bill Hogan", "orcid": "0000-0002-9881-1017" }, "description": "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations.", "download_json": "http://purl.obolibrary.org/obo/omrse.json", "download_obo": "https://github.com/ufbmi/OMRSE/raw/master/omrse-full.obo", "download_owl": "http://purl.obolibrary.org/obo/omrse.owl", "example": "00000022", "homepage": "https://github.com/mcwdsi/OMRSE/wiki/OMRSE-Overview", "keywords": [ "biomedical science", "demographics", "health science", "hospital", "obo", "ontology", "patient care", "social science" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OMRSE", "biocontext": "OMRSE", "bioportal": "OMRSE", "fairsharing": "FAIRsharing.z0p37e", "obofoundry": "omrse", "ols": "omrse", "ontobee": "OMRSE", "wikidata.entity": "Q55118551" }, "name": "Ontology for Modeling and Representation of Social Entities", "pattern": "^\\d{8}$", "preferred_prefix": "OMRSE", "publications": [ { "doi": "10.1186/s13326-016-0087-8", "pmc": "PMC4942889", "pubmed": "27406187", "title": "The ontology of medically related social entities: recent developments", "year": 2016 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OMRSE_$1", "repository": "https://github.com/mcwdsi/OMRSE", "uri_format": "http://purl.obolibrary.org/obo/OMRSE_$1", "version": "2026-01-06" }, "omx.dataset": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "OncoMX is a knowledgebase for exploring cancer biomarkers in the context of related cancer and healthy data. This resource is for datasets within OncoMX.", "example": "000059", "homepage": "https://data.oncomx.org", "name": "OncoMX Dataset", "pattern": "^\\d+$", "preferred_prefix": "omx.dataset", "uri_format": "https://data.oncomx.org/OMX_$1" }, "oncotree": { "appears_in": [ "efo" ], "contact": { "email": "SchultzN@mskcc.org", "name": "Nikolaus Schultz", "orcid": "0000-0002-0131-4904" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research.", "example": "BLL", "homepage": "http://oncotree.mskcc.org", "keywords": [ "cancer", "clinical decision support systems", "oncology" ], "name": "OncoTree", "preferred_prefix": "oncotree", "publications": [ { "doi": "10.1200/cci.20.00108", "pmc": "PMC8240791", "pubmed": "33625877", "title": "OncoTree: A Cancer Classification System for Precision Oncology", "year": 2021 } ], "uri_format": "http://oncotree.mskcc.org/api/tumorTypes/search/code/$1" }, "one": { "contact": { "email": "chenyangnutrition@gmail.com", "github": "cyang0128", "name": "Chen Yang", "orcid": "0000-0001-9202-5309" }, "depends_on": [ "foodon", "obi", "ons" ], "description": "An ontology to standardize research output of nutritional epidemiologic studies.", "download_owl": "http://purl.obolibrary.org/obo/one.owl", "example": "0001021", "homepage": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies", "keywords": [ "epidemiology", "metabolomics", "nutritional science", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "ONE", "bioportal": "ONE", "fairsharing": "FAIRsharing.USxx0K", "obofoundry": "one", "ols": "one", "ontobee": "ONE", "wikidata.entity": "Q113014430" }, "name": "Ontology for Nutritional Epidemiology", "pattern": "^\\d{7}$", "preferred_prefix": "ONE", "publications": [ { "doi": "10.3390/nu11061300", "pmc": "PMC6628051", "pubmed": "31181762", "title": "An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content", "year": 2019 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/ONE_$1", "repository": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies", "uri_format": "http://purl.obolibrary.org/obo/ONE_$1" }, "ons": { "appears_in": [ "one" ], "contact": { "email": "francesco.vitali@ibba.cnr.it", "github": "FrancescoVit", "name": "Francesco Vitali", "orcid": "0000-0001-9125-4337" }, "depends_on": [ "bfo", "chebi", "envo", "foodon", "ncbitaxon", "obi", "ro", "uberon" ], "description": "An ontology for description of concepts in the nutritional studies domain.", "download_owl": "http://purl.obolibrary.org/obo/ons.owl", "example": "0000060", "homepage": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies", "keywords": [ "biomedical science", "nutritional science", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "ONS", "agroportal": "ONS", "bioportal": "ONS", "fairsharing": "FAIRsharing.rfec93", "obofoundry": "ons", "ols": "ons", "ontobee": "ONS", "wikidata.entity": "Q113014431" }, "name": "Ontology for Nutritional Studies", "pattern": "^\\d{7}$", "preferred_prefix": "ONS", "publications": [ { "doi": "10.1186/s12263-018-0601-y", "pmc": "PMC5928560", "pubmed": "29736190", "title": "ONS: an ontology for a standardized description of interventions and observational studies in nutrition", "year": 2018 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/ONS_$1", "repository": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies", "uri_format": "http://purl.obolibrary.org/obo/ONS_$1", "version": "2024-07-03" }, "ontie": { "contact": { "email": "bpeters@lji.org", "github": "bpeters42", "name": "Bjoern Peters", "orcid": "0000-0002-8457-6693" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Ontology of Immune Epitopes (ONTIE) is an effort to represent terms in the immunology domain in a formal ontology with the specific goal of representing experiments that identify and characterize immune epitopes.", "download_owl": "https://raw.githubusercontent.com/IEDB/ONTIE/master/ontie.owl", "example": "0000001", "homepage": "https://ontology.iedb.org/", "keywords": [ "immunology", "infection process", "life science", "major histocompatibility complex", "ontology" ], "mappings": { "fairsharing": "FAIRsharing.kx2md1" }, "name": "Ontology for Immune Epitopes", "pattern": "^\\d{7}$", "preferred_prefix": "ontie", "repository": "https://github.com/IEDB/ONTIE", "uri_format": "https://ontology.iedb.org/ontology/ONTIE_$1" }, "ontoavida": { "contact": { "email": "fortuna@ebd.csic.es", "github": "miguelfortuna", "name": "Miguel A. Fortuna", "orcid": "0000-0002-8374-1941" }, "depends_on": [ "fbcv", "gsso", "ncit", "ro", "stato" ], "description": "The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of the most widely used computational approach for performing experimental evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment).\n\nThe lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight.\n\nOntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA).\n\nMore information can be found at https://obofoundry.org/ontology/ontoavida.html", "download_obo": "http://purl.obolibrary.org/obo/ontoavida.obo", "download_owl": "http://purl.obolibrary.org/obo/ontoavida.owl", "example": "00000001", "homepage": "https://gitlab.com/fortunalab/ontoavida", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "ONTOAVIDA", "bioportal": "ONTOAVIDA", "obofoundry": "ontoavida", "ols": "ontoavida", "ontobee": "ONTOAVIDA", "wikidata.entity": "Q113014432" }, "name": "Ontology for Avida digital evolution platform", "pattern": "^\\d{8}$", "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_$1", "version": "2022-03-15" }, "ontodm": { "appears_in": [ "efo" ], "contact": { "email": "pance.panov@ijs.si", "name": "Pance Panov" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "OntoDM-core defines the most essential data mining entities in a three-layered ontological structure comprising of a specification, an implementation and an application layer. It provides a representational framework for the description of mining structured data, and in addition provides taxonomies of datasets, data mining tasks, generalizations, data mining algorithms and constraints, based on the type of data. OntoDM-core is designed to support a wide range of applications/use cases, such as semantic annotation of data mining algorithms, datasets and results; annotation of QSAR studies in the context of drug discovery investigations; and disambiguation of terms in text mining. (from abstract)", "download_owl": "https://raw.githubusercontent.com/panovp/ontodm-core/master/OntoDM.owl", "example": "000072", "homepage": "http://www.ontodm.com/", "keywords": [ "ontology" ], "mappings": { "bioportal": "ONTODM-CORE" }, "name": "Ontology of Core Data Mining Entities", "pattern": "^\\d+$", "preferred_prefix": "ontodm", "providers": [ { "code": "legacy", "description": "legacy URIs", "homepage": "http://kt.ijs.si/panovp", "name": "Legacy URIs", "uri_format": "http://kt.ijs.si/panovp/OntoDM#OntoDM_$1" }, { "code": "legacy2", "description": "legacy URIs", "homepage": "http://kt.ijs.si/panovp", "name": "Legacy URIs", "uri_format": "http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD_$1" } ], "publications": [ { "doi": "10.1007/s10618-014-0363-0", "title": "Ontology of core data mining entities", "year": 2014 } ], "repository": "https://github.com/panovp/ontodm-core", "uri_format": "http://www.ontodm.com/OntoDM-core/OntoDM_$1" }, "ontoneo": { "contact": { "email": "fernanda.farinelli@gmail.com", "github": "FernandaFarinelli", "name": "Fernanda Farinelli", "orcid": "0000-0003-2338-8872" }, "description": "The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby.", "download_owl": "http://purl.obolibrary.org/obo/ontoneo.owl", "example": "00000098", "homepage": "http://ontoneo.com", "keywords": [ "electronic health record", "obo", "obstetrics", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "ONTONEO", "biocontext": "ONTONEO", "bioportal": "ONTONEO", "fairsharing": "FAIRsharing.5a4y1y", "obofoundry": "ontoneo", "ols": "ontoneo", "ontobee": "ONTONEO", "wikidata.entity": "Q113014434" }, "name": "Obstetric and Neonatal Ontology", "pattern": "^\\d{8}$", "preferred_prefix": "ONTONEO", "publications": [ { "doi": "10.5281/zenodo.17508651", "title": "Formal Ontologies in Knowledge Organization within the Obstetric and Neonatal Domain" }, { "doi": "10.5281/zenodo.17429771", "title": "OntONeo: The Obstetric and Neonatal Ontology" }, { "doi": "10.1002/asi.23900", "title": "Ontologies for the representation of electronic medical records: The obstetric and neonatal ontology", "year": 2017 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/ONTONEO_$1", "repository": "https://github.com/ontoneo-project/Ontoneo", "uri_format": "http://purl.obolibrary.org/obo/ONTONEO_$1", "version": "2025-03-14" }, "ontorxn": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "OntoRXN is an ontology for the description of reaction networks as undirected graphs characterized by energies.", "download_owl": "https://gitlab.com/dgarayr/ontorxn/-/raw/prod/OntoRXN.owl", "example": "hasCalculation", "github_request_issue": 1311, "homepage": "https://gitlab.com/dgarayr/ontorxn", "keywords": [ "chemistry", "nfdi4chem", "ontology" ], "license": "CC-BY-4.0", "mappings": { "tib": "ontorxn" }, "name": "OntoRXN", "preferred_prefix": "ontorxn", "publications": [ { "doi": "10.1186/s13321-022-00610-x", "pmc": "PMC9153116", "pubmed": "35637523", "title": "Chemical reaction network knowledge graphs: the OntoRXN ontology", "year": 2022 } ] }, "oostt": { "contact": { "email": "mbrochhausen@gmail.com", "github": "mbrochhausen", "name": "Mathias Brochhausen", "orcid": "0000-0003-1834-3856" }, "description": "The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2).", "download_owl": "http://purl.obolibrary.org/obo/oostt.owl", "example": "00000099", "homepage": "https://github.com/OOSTT/OOSTT", "keywords": [ "obo", "ontology", "traumatology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OOSTT", "biocontext": "OOSTT", "bioportal": "OOSTT", "fairsharing": "FAIRsharing.b4sa0w", "obofoundry": "oostt", "ols": "oostt", "ontobee": "OOSTT", "wikidata.entity": "Q81661760" }, "name": "Ontology of Organizational Structures of Trauma centers and Trauma systems", "pattern": "^\\d{8}$", "preferred_prefix": "OOSTT", "rdf_uri_format": "http://purl.obolibrary.org/obo/OOSTT_$1", "repository": "https://github.com/OOSTT/OOSTT", "uri_format": "http://purl.obolibrary.org/obo/OOSTT_$1", "version": "2025-08-28" }, "opb": { "banana": "OPB", "banana_peel": "_", "contact": { "email": "maxneal@gmail.com", "name": "Maxwell L. Neal", "orcid": "0000-0002-2390-6572" }, "contributor_extras": [ { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" } ], "description": "The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.", "download_owl": "http://aber-owl.net/media/ontologies/OPB/13/opb.owl", "example": "00573", "homepage": "http://bioportal.bioontology.org/ontologies/OPB", "keywords": [ "concentration", "life science", "ontology", "physics", "structure" ], "mappings": { "aberowl": "OPB", "biocontext": "OPB", "bioportal": "OPB", "fairsharing": "FAIRsharing.qcceez", "miriam": "opb", "n2t": "opb", "prefixcommons": "opb" }, "name": "Ontology of Physics for Biology", "pattern": "^\\d+$", "preferred_prefix": "opb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/opb:$1" } ], "publications": [ { "doi": "10.1186/2041-1480-4-41", "pmc": "PMC3904761", "pubmed": "24295137", "title": "Ontology of physics for biology: representing physical dependencies as a basis for biological processes", "year": 2013 }, { "doi": "10.1371/journal.pone.0028708", "pmc": "PMC3246444", "pubmed": "22216106", "title": "Physical properties of biological entities: an introduction to the ontology of physics for biology", "year": 2011 } ], "uri_format": "https://bioportal.bioontology.org/ontologies/OPB/?p=classes&conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1" }, "openadr": { "description": "This ontology describes the openADR protocol based on the documentation provided by the openADR Profile B", "example": "BidEnergySetpointSignal", "homepage": "https://albaizq.github.io/OpenADRontology/OnToology/ontology/openADRontology.owl/documentation/index-en.html", "keywords": [ "engineering", "nfdi4energy" ], "mappings": { "tib": "openadr" }, "name": "OpenADR ontology", "preferred_prefix": "openadr", "uri_format": "https://w3id.org/def/openadr#$1" }, "openalex": { "contact": { "email": "hpiwowar@gmail.com", "github": "hpiwowar", "name": "Heather Piwowar", "orcid": "0000-0003-1613-5981" }, "contributor": { "github": "dhimmel", "name": "Daniel Himmelstein", "orcid": "0000-0002-3012-7446" }, "description": "OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other.", "example": "W2741809807", "github_request_issue": 280, "homepage": "https://openalex.org/", "keywords": [ "knowledge graph", "wikidata" ], "name": "OpenAlex", "pattern": "^[WAICV]\\d{2,}$", "preferred_prefix": "openalex", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://openalex.org/$1" }, "openeduhub.context": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "educational levels", "example": "sekundarstufe_2", "homepage": "http://w3id.org/openeduhub/vocabs/educationalContext/", "keywords": [ "education level", "open educational resources" ], "name": "Educational Context", "preferred_prefix": "openeduhub.context", "rdf_uri_format": "http://w3id.org/openeduhub/vocabs/educationalContext/$1", "uri_format": "http://w3id.org/openeduhub/vocabs/educationalContext/$1" }, "openwemi": { "contact": { "email": "kcoyle@kcoyle.net", "github": "kcoyle", "name": "Karen Coyle", "orcid": "0000-0002-1085-7089" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "openWEMI is a minimally constrained vocabulary for describing created resources using the concepts of Work, Expression, Manifestation, Item.", "example": "Endeavor", "homepage": "https://dcmi.github.io/openwemi/", "license": "CC0-1.0", "name": "openWEMI Vocabulary", "pattern": "^\\w+$", "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#$1" }, "opl": { "banana": "OPL", "contact": { "email": "zhengj2007@gmail.com", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "description": "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc.", "download_owl": "http://purl.obolibrary.org/obo/opl.owl", "example": "0000319", "homepage": "https://github.com/OPL-ontology/OPL", "keywords": [ "anatomy", "developmental biology", "host", "life cycle", "life cycle stage", "life science", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OPL", "biocontext": "OPL", "bioportal": "OPL", "fairsharing": "FAIRsharing.ez2nhb", "miriam": "opl", "obofoundry": "opl", "ols": "opl", "ontobee": "OPL" }, "name": "Ontology for Parasite LifeCycle", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "OPL", "publications": [ { "doi": "10.1186/2041-1480-3-5", "pmc": "PMC3488002", "pubmed": "22621763", "title": "The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms", "year": 2012 } ], "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_$1", "version": "2023-08-28" }, "opm": { "description": "The Orientations of Proteins in Membranes 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It is community-driven and developed by following the OBO Foundry ontology development principles.", "download_owl": "http://purl.obolibrary.org/obo/opmi.owl", "example": "0000101", "homepage": "https://github.com/OPMI/opmi", "keywords": [ "clinical studies", "disease", "obo", "omics", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OPMI", "bioportal": "OPMI", "fairsharing": "FAIRsharing.d2d84f", "obofoundry": "opmi", "ols": "opmi", "ontobee": "OPMI", "wikidata.entity": "Q81661763" }, "name": "Ontology of Precision Medicine and Investigation", "pattern": "^\\d{7}$", "preferred_prefix": "OPMI", "rdf_uri_format": "http://purl.obolibrary.org/obo/OPMI_$1", "repository": "https://github.com/OPMI/opmi", "uri_format": "http://purl.obolibrary.org/obo/OPMI_$1", "version": "1.0.166" }, "oprlm": { "contact": { "email": "wonpil@lehigh.edu", "name": "Wonpil Im", "orcid": "0000-0001-5642-6041" }, "contributor": { "email": "palayoor.n@northeastern.edu", "github": "nalikapalayoor", "name": "Nalika Palayoor", "orcid": "0009-0008-8406-631X" }, "description": "Orientations of Proteins in Realistic Lipid Membranes (OPRLM) is a database for visualizing proteins in realistic lipid membranes. It includes the classification of proteins into types, superfamilies, and families, and also provides information on intracellular localizations of the proteins. Identifiers represent proteins.", "example": "6782", "github_request_issue": 1558, "homepage": "https://oprlm.org", "name": "Orientation of Proteins in Realistic Lipid Membranes", "pattern": "^\\d*$", "preferred_prefix": "oprlm", "publications": [ { "doi": "10.1016/j.jmb.2025.168966", "pubmed": "40133776", "title": "OPRLM: A Web Tool and a Database for Positioning and Simulations of Proteins in Realistic Lipid Membranes", "year": 2025 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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ORCID records hold non-sensitive information such as name, email, organization name, and research activities.", "example": "0000-0003-4423-4370", "homepage": "https://orcid.org", "keywords": [ "person", "subject agnostic" ], "mappings": { "bartoc": "2021", "biocontext": "ORCID", "biolink": "ORCID", "fairsharing": "FAIRsharing.nx58jg", "go": "orcid", "miriam": "orcid", "n2t": "orcid", "wikidata": "P496", "wikidata.entity": "Q51044" }, "mastodon": "ORCID_Org@scicomm.xyz", "name": "Open Researcher and Contributor", "pattern": "^\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$", "preferred_prefix": "orcid", "providers": [ { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/orcid/$1" } ], "publications": [ { "doi": "10.23640/07243.16687207.v1", "title": "From Vision to Value: ORCID's 2022–2025 Strategic Plan", "year": 2021 }, { "doi": "10.23640/07243.12009255.v3", "title": "ORCID's 2025 Vision", "year": 2020 } ], "rdf_uri_format": "https://orcid.org/$1", "repository": "https://github.com/ORCID", "synonyms": [ "ORCID", "ORCiD" ], "twitter": "ORCID_Org", "uri_format": "https://orcid.org/$1" }, "ordb": { "description": "The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs).", "example": "8497", "homepage": "http://senselab.med.yale.edu/OrDB/", "keywords": [ "gene", "life science", "protein" ], "mappings": { "biocontext": "ORDB", "fairsharing": "FAIRsharing.6375zh", "miriam": "ordb", "n2t": "ordb", "pathguide": "65", "prefixcommons": "ordb" }, "name": "Olfactory Receptor Database", "pattern": "^\\d+$", "preferred_prefix": "ordb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/ordb:$1" } ], "publications": [ { "doi": "10.1093/database/baw132", "pmc": "PMC5045865", "pubmed": "27694208", "title": "ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions", "year": 2016 }, { "doi": "10.1093/nar/30.1.354", "pmc": "PMC99065", "pubmed": "11752336", "title": "Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences", "year": 2002 }, { "doi": "10.1093/nar/28.1.341", "pmc": "PMC102443", "pubmed": "10592268", "title": "Olfactory receptor database: a sensory chemoreceptor resource", "year": 2000 } ], "uri_format": "https://ordb.biotech.ttu.edu/ORDB/Data/$1" }, "org": { "description": "Vocabulary for describing organizational structures, specializable to a broad variety of types of organization.", "example": "ChangeEvent", "homepage": "http://www.w3.org/TR/vocab-org/", "keywords": [ "digital planning and construction", "economics", "fid baudigital", "social sciences", "w3c rec" ], "mappings": { "lov": "org", "tib": "org", "zazuko": "org" }, "name": "Core organization ontology", "preferred_prefix": "org", "uri_format": "http://www.w3.org/ns/org#$1" }, "oridb.sacch": { "description": "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae.", "example": "1", "homepage": "http://cerevisiae.oridb.org/index.php", "mappings": { "biocontext": "ORIDB.SACCH", "miriam": "oridb.sacch", "n2t": "oridb.sacch" }, "name": "OriDB Saccharomyces", "pattern": "^\\d+$", "preferred_prefix": "oridb.sacch", "uri_format": "http://cerevisiae.oridb.org/details.php?id=$1" }, "oridb.schizo": { "description": "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe.", "example": "1", "homepage": "http://pombe.oridb.org/index.php", "mappings": { "biocontext": "ORIDB.SCHIZO", "miriam": "oridb.schizo", "n2t": "oridb.schizo" }, "name": "OriDB Schizosaccharomyces", "pattern": "^\\d+$", "preferred_prefix": "oridb.schizo", "uri_format": "http://pombe.oridb.org/details.php?id=$1" }, "ornaseq": { "contact": { "email": "safisher@upenn.edu", "github": "safisher", "name": "Stephen Fisher", "orcid": "0000-0001-8034-7685" }, "description": "An application ontology designed to annotate next-generation sequencing experiments performed on RNA.", "download_obo": "http://purl.obolibrary.org/obo/ornaseq.obo", "download_owl": "http://purl.obolibrary.org/obo/ornaseq.owl", "example": "0000010", "homepage": "http://kim.bio.upenn.edu/software/ornaseq.shtml", "keywords": [ "obo", "ontology", "rna-seq assay", "single cell", "single cell rna-seq", "transcriptomics" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "ORNASEQ", "bioportal": "ORNASEQ", "fairsharing": "FAIRsharing.e6f303", "obofoundry": "ornaseq", "ols": "ornaseq", "ontobee": "ORNASEQ", "wikidata.entity": "Q81661765" }, "name": "Ontology of RNA Sequencing", "pattern": "^\\d{7}$", "preferred_prefix": "ORNASEQ", "rdf_uri_format": "http://purl.obolibrary.org/obo/ORNASEQ_$1", "repository": "https://github.com/safisher/ornaseq", "uri_format": "http://purl.obolibrary.org/obo/ORNASEQ_$1", "version": "2019-07-08" }, "orpha": { "contact": { "email": "marc.hanauer@inserm.fr", "github": "Orphanet", "name": "Marc Hanauer", "orcid": "0000-0002-6758-2506" }, "contributor_extras": [ { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" } ], "description": "Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases.", "download_owl": "http://www.orphadata.org/data/ORDO/ordo_orphanet.owl", "example": "85163", "homepage": "https://www.orpha.net", "keywords": [ "disease", "drug", "human", "life science", "ontology", "ontology and terminology" ], "license": "CC-BY-4.0", "logo": "https://www.orpha.net/build/images/logo-orphanet.png", "mappings": { "biocontext": "Orphanet", "biolink": "orphanet", "fairsharing": "FAIRsharing.6bd5k6", "integbio": "nbdc01422", "miriam": "orphanet", "n2t": "orphanet", "prefixcommons": "orphanet", "uniprot": "DB-0068", "wikidata": "P1550", "wikidata.entity": "Q929833" }, "name": "Orphanet", "pattern": "^C?\\d+$", "preferred_prefix": "ORPHA", "providers": [ { "code": "", "description": "Bio2RDF", "homepage": "http://bio2rdf.org/", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/orphanet:$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/orphanet:$1" } ], "publications": [ { "pubmed": "19058507", "title": "[Orphanet and the Dutch Steering Committee Orphan Drugs. A European and Dutch databank of information on rare diseases]", "year": 2008 } ], "synonyms": [ "Orphanet", "orphanet" ], "twitter": "orphanet", "uri_format": "http://www.orpha.net/ORDO/Orphanet_$1" }, "orphanet.ordo": { "banana": "Orphanet", "banana_peel": "_", "contact": { "email": "marc.hanauer@inserm.fr", "github": "Orphanet", "name": "Marc Hanauer", "orcid": "0000-0002-6758-2506" }, "description": "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.\nIt integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).", "download_owl": "http://www.orphadata.org/data/ORDO/ordo_orphanet.owl", "example": "C023", "example_extras": [ "478" ], "has_canonical": "orpha", "homepage": "https://www.orpha.net", "keywords": [ "biomedical science", "diagnosis", "disease", "gene", "health science", "ontology", "phenotype", "rare disorder" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "ordo", "bartoc": "20698", "biocontext": "ORPHANET.ORDO", "biolink": "ORPHA", "bioportal": "ORDO", "cellosaurus": "ORDO", "fairsharing": "FAIRsharing.pbbnwa", "miriam": "orphanet.ordo", "n2t": "orphanet.ordo", "ols": "ordo" }, "name": "Orphanet Rare Disease Ontology", "pattern": "^C?\\d+$", "preferred_prefix": "orphanet.ordo", "providers": [ { "code": "legacy", "description": "This link is no longer live", "homepage": "https://www.orpha.net", "name": "Legacy Orphanet Expert", "uri_format": "https://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=en&Expert=$1" } ], "publications": [ { "pubmed": "22874158", "title": "Rare diseases knowledge management: the contribution of proximity measurements in OntoOrpha and OMIM", "year": 2012 } ], "synonyms": [ "ordo" ], "uri_format": "http://www.orpha.net/ORDO/Orphanet_$1", "version": "4.7" }, "orth": { "contact": { "email": "jfernand@um.es", "github": "jesualdotomasfernandezbreis", "name": "Jesualdo Tomás Fernández-Breis", "orcid": "0000-0002-7558-2880" }, "description": "The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way.", "download_owl": "https://github.com/qfo/OrthologyOntology/raw/master/orthOntology_RC_v2_A.owl", "example": "HomologyRelation", "homepage": "https://github.com/qfo/OrthologyOntology", "keywords": [ "comparative genomics", "gene", "homologous", "ontology", "orthologous", "paralogous", "protein", "region" ], "mappings": { "aberowl": "ORTH", "bioportal": "ORTH", "fairsharing": "FAIRsharing.4877h0", "ols": "orth" }, "name": "Orthology Ontology", "preferred_prefix": "orth", "publications": [ { "doi": "10.1186/s13326-016-0077-x", "pmc": "PMC4893294", "pubmed": "27259657", "title": "The Orthology Ontology: development and applications", "year": 2016 } ], "repository": "https://github.com/qfo/OrthologyOntology", "uri_format": "http://purl.org/net/orth#$1", "version": "2.0" }, "orthodb": { "contact": { "email": "evgeny.zdobnov@unige.ch", "name": "Evgeny M Zdobnov", "orcid": "0000-0002-5178-1498" }, "description": "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups", "example": "Q9P0K8", "homepage": "https://www.orthodb.org", "keywords": [ "dna", "eukaryotic", "life science", "protein" ], "mappings": { "biocontext": "ORTHODB", "fairsharing": "FAIRsharing.x989d5", "miriam": "orthodb", "n2t": "orthodb", "prefixcommons": "orthodb", "uniprot": "DB-0143" }, "name": "OrthoDB", "pattern": "^\\w+$", "preferred_prefix": "orthodb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/orthodb:$1" } ], "provides": "uniprot", "publications": [ { "doi": "10.1093/nar/gkae987", "pubmed": "39535043" }, { "doi": "10.1093/nar/gky1053", "pmc": "PMC6323947", "pubmed": "30395283", "title": "OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs", "year": 2019 }, { "doi": "10.1093/nar/gku1220", "pmc": "PMC4383991", "pubmed": "25428351", "title": "OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software", "year": 2014 }, { "doi": "10.1093/nar/gkq930", "pmc": "PMC3013786", "pubmed": "20972218", "title": "OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011", "year": 2010 } ], "uri_format": "http://cegg.unige.ch/orthodb/results?searchtext=$1" }, "oryzabase.gene": { "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information.", "example": "117", "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", "mappings": { "biocontext": "ORYZABASE.GENE", "miriam": "oryzabase.gene", "n2t": "oryzabase.gene" }, "name": "Oryzabase Gene", "pattern": "^\\d+$", "preferred_prefix": "oryzabase.gene", "uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1" }, "oryzabase.mutant": { "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information.", "example": "21393", "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", "mappings": { "biocontext": "ORYZABASE.MUTANT", "miriam": "oryzabase.mutant", "n2t": "oryzabase.mutant" }, "name": "Oryzabase Mutant", "pattern": "^\\d+$", "preferred_prefix": "oryzabase.mutant", "uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1" }, "oryzabase.reference": { "description": "The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan.", "example": "42840", "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", "mappings": { "miriam": "oryzabase.reference", "n2t": "oryzabase.reference" }, "name": "Oryzabase Reference", "pattern": "^\\d+$", "preferred_prefix": "oryzabase.reference", "uri_format": "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1" }, "oryzabase.stage": { "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information.", "example": "34", "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", "mappings": { "biocontext": "ORYZABASE.STAGE", "miriam": "oryzabase.stage", "n2t": "oryzabase.stage" }, "name": "Oryzabase Stage", "pattern": "^\\d+$", "preferred_prefix": "oryzabase.stage", "uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1" }, "oryzabase.strain": { "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information.", "example": "1", "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", "mappings": { "biocontext": "ORYZABASE.STRAIN", "miriam": "oryzabase.strain", "n2t": "oryzabase.strain" }, "name": "Oryzabase Strain", "pattern": "^\\d+$", "preferred_prefix": "oryzabase.strain", "uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1" }, "osf": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ID in osf.io", "example": "2u4tf", "homepage": "https://osf.io", "keywords": [ "author", "paper", "person", "researcher", "work" ], "mappings": { "wikidata": "P7238" }, "name": "Open Science Framework ID", "pattern": "^[a-z0-9]{5}$", "preferred_prefix": "osf", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://osf.io/$1" }, "oslc": { "contact": { "email": "jamsden@us.ibm.com", "name": "Jim Amsden" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains.", "example": "Property", "homepage": "http://open-services.net/ns/core", "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 N. 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/$1" }, "otl": { "contact": { "email": "guiderdoni@cirad.fr", "name": "Emmanuel Guiderdoni", "orcid": "0000-0003-2760-2864" }, "description": "Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information.", "example": "AADB12", "homepage": "http://oryzatagline.cirad.fr/", "keywords": [ "dna", "life science" ], "mappings": { "biocontext": "OTL", "fairsharing": "FAIRsharing.61c2x6", "miriam": "otl", "n2t": "otl", "prefixcommons": "otl" }, "name": "Oryza Tag Line", "pattern": "^A[A-Z]+\\d+$", "preferred_prefix": "otl", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/otl:$1" } ], "publications": [ { "doi": "10.1093/nar/gkm762", "pmc": "PMC2238859", "pubmed": "17947330", "title": "Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library", "year": 2007 }, { "doi": "17947330", "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=$1" }, "otol": { "contributor": { "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" }, "description": "Identifier for an entity in open tree of life", "example": "3905431", "github_request_issue": 470, "homepage": "https://tree.opentreeoflife.org", "mappings": { "wikidata": "P9157", "wikidata.entity": "Q22661281" }, "name": "Open Tree of Life", "pattern": "^[1-9]\\d*$", "preferred_prefix": "otol", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://tree.opentreeoflife.org/taxonomy/browse?id=$1" }, "ovae": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqunh He", "orcid": "0000-0001-9189-9661" }, "description": "OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE).", "download_owl": "http://purl.obolibrary.org/obo/ovae.owl", "example": "0000609", "homepage": "http://www.violinet.org/ovae/", "keywords": [ "adverse reaction", "biomedical science", "obo", "ontology", "vaccine" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OVAE", "biocontext": "OVAE", "bioportal": "OVAE", "fairsharing": "FAIRsharing.w4x6n4", "obofoundry": "ovae", "ols": "ovae", "ontobee": "OVAE", "wikidata.entity": "Q55118555" }, "name": "Ontology of Vaccine Adverse Events", "pattern": "^\\d{7}$", "preferred_prefix": "OVAE", "publications": [ { "doi": "10.1186/2041-1480-4-40", "pmc": "PMC4177204", "pubmed": "24279920", "title": "The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OVAE_$1", "repository": "https://github.com/OVAE-Ontology/ovae", "uri_format": "http://purl.obolibrary.org/obo/OVAE_$1", "version": "1.0.34" }, "owl": { "contact": { "email": "rmrich5@gmail.com", "name": "Rafael Richards", "orcid": "0000-0001-5699-0515" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages.", "download_owl": "https://triplydb.com/w3c/owl/download.trig.gz", "example": "Ontology", "homepage": "https://www.w3.org/TR/owl-features/", "keywords": [ "computer science", "informatics", "ontology", "ontology and terminology", "subject agnostic", "w3c rec" ], "mappings": { "biocontext": "owl", "fairsharing": "FAIRsharing.atygwy", "integbio": "nbdc00307", "lov": "owl", "ols": "owl", "zazuko": "owl" }, "name": "Web Ontology Language", "preferred_prefix": "owl", "uri_format": "http://www.w3.org/2002/07/owl#$1", "version": "$Date: 2009/11/15 10:54:12 $" }, "owlstar": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This proposed vocabulary allows edges in Property Graphs (e.g Neo4j, RDF*) to be augmented with edge properties that specify ontological semantics, including (but not limited) to OWL-DL interpretations. [from GitHub]", "download_rdf": "https://github.com/linkml/owlstar/raw/master/owlstar.ttl", "example": "AllSomeInterpretation", "homepage": "https://linkml.io/owlstar/", "license": "CC0-1.0", "mappings": { "biolink": "os" }, "name": "Ontological Interpretations for Web Property Graphs", "pattern": "^\\w+$", "preferred_prefix": "owlstar", "repository": "https://github.com/linkml/owlstar", "uri_format": "http://w3id.org/owlstar/$1" }, "p3db.protein": { "description": "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites.", "example": "70", "homepage": "http://www.p3db.org/", "keywords": [ "protein", "small molecule" ], "mappings": { "biocontext": "P3DB.PROTEIN", "miriam": "p3db.protein", "n2t": "p3db.protein", "prefixcommons": "p3db" }, "name": "P3DB Protein", "pattern": "^\\d+$", "preferred_prefix": "p3db.protein", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/p3db:$1" } ], "uri_format": "http://www.p3db.org/protein.php?id=$1&ref=0" }, "p3db.site": { "description": "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins.", "example": "65", "homepage": "http://www.p3db.org/", "mappings": { "biocontext": "P3DB.SITE", "miriam": "p3db.site", "n2t": "p3db.site" }, "name": "P3DB Site", "pattern": "^\\d+$", "preferred_prefix": "p3db.site", "uri_format": "http://www.p3db.org/phosphosite.php?id=$1&ref=0" }, "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/$1" }, "pactr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Pan African Clinical Trials Registry (PACTR) is a regional register of clinical trials conducted in Africa. The registry is an African initiative serving the needs of Africans. It provides an open-access platform where clinical trials can be registered free of charge. The PACTR aims to increase clinical trial registration in Africa by developing awareness of the need to register trials and supporting trialists during registration. (from homepage)", "example": "PACTR202304525632216", "homepage": "https://pactr.samrc.ac.za/", "logo": "https://pactr.samrc.ac.za/images/Banner_Split.jpg", "name": "Pan African Clinical Trials Registry", "pattern": "^PACTR\\d+$", "preferred_prefix": "pactr", "references": [ "https://pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=25488" ] }, "pahg": { "contact": { "email": "baoym@big.ac.cn", "name": "Yiming Bao", "orcid": "0000-0002-9922-9723" }, "contributor": { "email": "ji.kang@northeastern.edu", "github": "kanghosaeyo", "name": "Kangho Ji", "orcid": "0009-0009-3402-8013" }, "description": "Identifiers correspond to curated multigene families in the human genome from the Phylogenomic Analysis of Human Genome (PAHG) database, focusing on evolutionary relationships and gene duplication events across vertebrates.", "example": "92", "github_request_issue": 1796, "homepage": "https://www.pahgncb.com", "keywords": [ "gene duplication", "human genome", "multigene families", "paralogons", "phylogenomics", "vertebrate evolution" ], "name": "Phylogenomic Analysis of Human Genome", "pattern": "^\\d+$", "preferred_prefix": "pahg", "publications": [ { "doi": "10.1186/s12863-025-01361-y", "pmc": "PMC12522930", "pubmed": "41087926", "title": "PAHG: the database of human multi-gene families", "year": 2025 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.pahgncb.com/genomedb/public/genefamily/$1" }, "paleodb": { "description": "The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data.", "example": "83088", "homepage": "http://paleodb.org/", "keywords": [ "taxonomy" ], "mappings": { "biocontext": "PALEODB", "miriam": "paleodb", "n2t": "paleodb", "prefixcommons": "paleodb" }, "name": "Paleobiology Database", "pattern": "^\\d+$", "preferred_prefix": "paleodb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/paleodb:$1" } ], "uri_format": "http://fossilworks.org/?a=taxonInfo&taxon_no=$1" }, "pandit": { "description": "PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains.", "example": "PF00004", "homepage": "http://www.ebi.ac.uk/goldman-srv/pandit", "keywords": [ "dna", "protein", "structure" ], "mappings": { "integbio": "nbdc00607", "prefixcommons": "pandit", "re3data": "r3d100011232" }, "name": "Protein and Associated NucleotideDomains with Inferred Trees", "preferred_prefix": "pandit", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pandit:$1" } ], "provides": "pfam", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam=$1" }, "panet": { "contact": { "email": "mriyayi@hotmail.com", "name": "Daniel Iyayi" }, "description": "The ExPaNDS Photon and Neutron Experimental Techniques (PaNET) ontology provides a taxonomy and thesaurus of photon and neutron (PaN) experimental techniques. Based mainly on accelerator-based light sources and neutron facilities, the primary use of the ontology is to enhance the FAIRness of PaN data catalogues services. The ontology defines specific techniques in terms of more general technique classes and provides synonyms and references.", "download_owl": "http://aber-owl.net/media/ontologies/PANET/27/panet.owl", "example": "00001", "homepage": "https://github.com/ExPaNDS-eu/ExPaNDS-experimental-techniques-ontology", "keywords": [ "experimental measurement", "imaging", "neutron science", "nfdi4ing", "ontology", "photon science", "physics", "x-ray diffraction" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "PANET", "bioportal": "PANET", "fairsharing": "FAIRsharing.a08d34", "tib": "panet" }, "name": "PaN Experimental technique", "preferred_prefix": "panet", "publications": [ { "doi": "10.5281/zenodo.4806026", "title": "ExPaNDS ontologies v1.0", "year": 2021 } ], "uri_format": "http://purl.org/pan-science/PaNET/PaNET$1" }, "panorama": { "contact": { "email": "brendanx@uw.edu", "name": "Brendan MacLean", "orcid": "0000-0002-9575-0255" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow. It makes links to the Proteomics Exchange when possible.", "example": "FxnI151FMs", "homepage": "https://panoramaweb.org", "keywords": [ "life science", "metabolomics", "proteomics" ], "mappings": { "fairsharing": "FAIRsharing.uBpQ1q" }, "name": "Panorama Public", "preferred_prefix": "panorama", "publications": [ { "doi": "10.1074/mcp.ra117.000543", "pmc": "PMC5986241", "pubmed": "29487113", "title": "Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline", "year": 2018 }, { "doi": "10.1021/pr5006636", "pmc": "PMC4156235", "pubmed": "25102069", "title": "Panorama: a targeted proteomics knowledge base", "year": 2014 }, { "doi": "10.1074/mcp.RA117.000543", "title": "Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline." } ], "uri_format": "https://panoramaweb.org/$1.url" }, "panther.family": { "contact": { "email": "pdthomas@usc.edu", "name": "Paul D Thomas", "orcid": "0000-0002-9074-3507" }, "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families.", "example": "PTHR12345", "homepage": "http://www.pantherdb.org/", "keywords": [ "classification", "gene", "ontology", "pathway", "protein" ], "mappings": { "biocontext": "PANTHER.FAMILY", "biolink": "PANTHER.FAMILY", "go": "PANTHER", "miriam": "panther.family", "n2t": "panther.family", "prefixcommons": "panther", "uniprot": "DB-0069" }, "name": "PANTHER Family", "pattern": "^PTHR\\d{5}(\\:SF\\d{1,3})?$", "preferred_prefix": "panther.family", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/panther:$1" } ], "publications": [ { "doi": "10.1093/nar/gkaa1106", "pubmed": "33290554" }, { "doi": "10.1093/nar/gky1038", "pmc": "PMC6323939", "pubmed": "30407594", "title": "PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools", "year": 2019 }, { "doi": "10.1101/gr.772403", "pmc": "PMC403709", "pubmed": "12952881", "title": "PANTHER: a library of protein families and subfamilies indexed by function", "year": 2003 } ], "uri_format": "http://www.pantherdb.org/panther/family.do?clsAccession=$1" }, "panther.node": { "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes.", "example": "PTN000000026", "homepage": "http://pantree.org/", "mappings": { "biocontext": "PANTHER.NODE", "miriam": "panther.node", "n2t": "panther.node" }, "name": "PANTHER Node", "pattern": "^PTN\\d{9}$", "preferred_prefix": "panther.node", "uri_format": "http://www.pantree.org/node/annotationNode.jsp?id=$1" }, "panther.pathway": { "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components.", "example": "P00024", "homepage": "http://www.pantherdb.org/", "mappings": { "biocontext": "PANTHER.PATHWAY", "edam": "1161", "miriam": "panther.pathway", "n2t": "panther.pathway" }, "name": "PANTHER Pathway", "pattern": "^P\\d{5}$", "preferred_prefix": "panther.pathway", "uri_format": "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1" }, "panther.pthcmp": { "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway\ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation.", "example": "P00266", "homepage": "http://www.pantherdb.org/", "mappings": { "biocontext": "PANTHER.PTHCMP", "miriam": "panther.pthcmp", "n2t": "panther.pthcmp" }, "name": "PANTHER Pathway Component", "pattern": "^(G|P|U|C|S)\\d{5}$", "preferred_prefix": "panther.pthcmp", "uri_format": "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1" }, "pao": { "contact": { "email": "jaiswalp@science.oregonstate.edu", "github": "jaiswalp", "name": "Pankaj Jaiswal", "orcid": "0000-0002-1005-8383" }, "deprecated": true, "homepage": "http://www.plantontology.org", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "PAO", "obofoundry": "pao", "wikidata.entity": "Q114677904" }, "name": "Plant Anatomy Ontology", "preferred_prefix": "PAO", "rdf_uri_format": "http://purl.obolibrary.org/obo/PAO_$1", "uri_format": "http://purl.obolibrary.org/obo/PAO_$1" }, "pass2": { "deprecated": true, "description": "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.", "example": "46977", "homepage": "http://caps.ncbs.res.in/pass2", "keywords": [ "classification", "dna", "genome", "structure" ], "mappings": { "biocontext": "PASS2", "integbio": "nbdc02108", "miriam": "pass2", "n2t": "pass2", "prefixcommons": "pass2" }, "name": "Protein Alignment organised as Structural Superfamily", "pattern": "^\\d+$", "preferred_prefix": "pass2", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pass2:$1" } ], "uri_format": "https://caps.ncbs.res.in/pass2.8/?q=superfamily/$1" }, "pathbank": { "contact": { "email": "david.wishart@ualberta.ca", "github": "DavidWishartLab", "name": "David S. Wishart", "orcid": "0000-0002-3207-2434" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana.", "example": "SMP0000219", "homepage": "https://pathbank.org", "keywords": [ "animal genetics", "bioinformatics", "biology", "cell biology", "cheminformatics", "database management", "drug metabolism", "endocrinology", "genetics", "human genetics", "medical informatics", "metabolomics", "microbiology", "molecular biology", "molecular microbiology", "plant genetics", "proteomics", "systems biology", "transcriptomics" ], "license": "ODbL-1.0", "logo": "https://pathbank.org/assets/pathbank_banner-2f8ec31838b9f453482e0748c0da1b7ebbb77b0f2b1a6e60ff1222ca0984db07.png", "mappings": { "fairsharing": "FAIRsharing.3xwMon", "integbio": "nbdc02670", "togoid": "Pathbank" }, "name": "PathBank", "pattern": "^(SMP|PW)\\d+$", "preferred_prefix": "pathbank", "uri_format": "https://pathbank.org/view/$1" }, "pathguide": { "contact": { "email": "gary.bader@utoronto.ca", "github": "gbader", "name": "Gary Bader", "orcid": "0000-0003-0185-8861" }, "description": "Pathguide contains information about 325 biological related resources and molecular interaction related resources.", "example": "49", "homepage": "http://pathguide.org", "keywords": [ "gene", "interaction", "pathway", "protein", "small molecule" ], "mappings": { "integbio": "nbdc00608", "prefixcommons": "pathguide" }, "name": "Pathguide", "pattern": "^\\d+$", "preferred_prefix": "pathguide", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pathguide:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=$1" }, "pathoplant": { "description": "PathoPlant® is a database on plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. PathoPlant® also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon pathogen infection or elicitor treatment.", "example": "MO000027", "homepage": "http://www.pathoplant.de", "keywords": [ "gene expression", "interaction", "pathway", "protein", "small molecule" ], "mappings": { "pathguide": "333", "prefixcommons": "pathoplant" }, "name": "PathoPlant®", "preferred_prefix": "pathoplant", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pathoplant:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.pathoplant.de/detail.php?accNo=$1" }, "pathwaycommons": { "contact": { "email": "chris@sanderlab.org", "github": "sanderlab", "name": "Chris Sander", "orcid": "0000-0001-6059-6270" }, "description": "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.", "example": "485991", "homepage": "http://www.pathwaycommons.org/pc/", "keywords": [ "pathway" ], "mappings": { "biocontext": "PATHWAYCOMMONS", "miriam": "pathwaycommons", "n2t": "pathwaycommons", "prefixcommons": "pathwaycommons", "re3data": "r3d100012731", "uniprot": "DB-0253" }, "name": "Pathway Commons", "pattern": "^\\d+$", "preferred_prefix": "pathwaycommons", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pathwaycommons:$1" } ], "publications": [ { "doi": "10.1093/nar/gkz946/5606621", "pubmed": "31647099" }, { "doi": "10.1093/nar/gkq1039", "pmc": "PMC3013659", "pubmed": "21071392", "title": "Pathway Commons, a web resource for biological pathway data", "year": 2010 } ], "uri_format": "http://www.pathwaycommons.org/pc/record2.do?id=$1" }, "pato": { "appears_in": [ "agro", "aism", "cdno", "cl", "colao", "ecocore", "ecto", "fovt", "gallont", "lepao", "mco", "ms", "pcl", "pco", "phipo", "planp", "proco", "rbo", "uberon", "xpo", "zp" ], "banana": "PATO", "contact": { "email": "g.gkoutos@gmail.com", "github": "gkoutos", "name": "George Gkoutos", "orcid": "0000-0002-2061-091X" }, "description": "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.", "download_json": "http://purl.obolibrary.org/obo/pato.json", "download_obo": "http://purl.obolibrary.org/obo/pato.obo", "download_owl": "http://purl.obolibrary.org/obo/pato.owl", "example": "0001998", "homepage": "https://github.com/pato-ontology/pato/", "keywords": [ "biodiversity", "biology", "dataplant", "earth sciences", "ess", "life sciences, biology", "nfdi4chem", "obo", "ontology", "phenotype", "quality" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "PATO", "agroportal": "PATO", "biocontext": "PATO", "bioportal": "PATO", "fairsharing": "FAIRsharing.ezwdhz", "go": "PATO", "miriam": "pato", "n2t": "pato", "obofoundry": "pato", "ols": "pato", "ontobee": "PATO", "prefixcommons": "pato", "tib": "pato", "wikidata.entity": "Q81661522" }, "name": "Phenotype And Trait Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "PATO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pato:$1" }, { "code": "purl", "description": "Legacy PURLs found in OAE", "homepage": "http://purl.org/obo/owl/", "name": "Legacy PURL", "uri_format": "http://purl.org/obo/owl/PATO#PATO_$1" } ], "publications": [ { "doi": "10.1093/bib/bbx035", "pmc": "PMC6169674", "pubmed": "28387809", "title": "The anatomy of phenotype ontologies: principles, properties and applications", "year": 2018 }, { "doi": "10.1186/gb-2010-11-1-r2", "pmc": "PMC2847714", "pubmed": "20064205", "title": "Integrating phenotype ontologies across multiple species", "year": 2010 }, { "doi": "10.1186/gb-2004-6-1-r8", "pmc": "PMC549069", "pubmed": "15642100", "title": "Using ontologies to describe mouse phenotypes", "year": 2004 } ], "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_$1", "version": "2025-05-14" }, "pav": { "contact": { "email": "stian@soiland-reyes.com", "name": "Stian Soiland-Reyes", "orcid": "0000-0001-9842-9718" }, "contributor": { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, "contributor_extras": [ { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } ], "description": "PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources.", "download_owl": "http://aber-owl.net/media/ontologies/PAV/3/pav.owl", "example": "authoredBy", "github_request_issue": 186, "homepage": "https://pav-ontology.github.io/pav/", "keywords": [ "data management", "ontology", "quality", "resource metadata", "subject agnostic" ], "mappings": { "aberowl": "PAV", "biocontext": "pav", "biolink": "pav", "bioportal": "PAV", "fairsharing": "FAIRsharing.nbfwwv", "lov": "pav" }, "name": "Provenance, Authoring, and Versioning Vocabulary", "pattern": "^[a-z][a-zA-Z]+$", "preferred_prefix": "pav", "publications": [ { "doi": "10.1186/2041-1480-4-37", "pmc": "PMC4177195", "pubmed": "24267948", "title": "PAV ontology: provenance, authoring and versioning", "year": 2013 } ], "repository": "http://pav-ontology.github.io/pav/", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://purl.org/pav/$1" }, "paxdb.organism": { "description": "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species.", "example": "9606", "homepage": "http://pax-db.org/", "mappings": { "biocontext": "PAXDB.ORGANISM", "miriam": "paxdb.organism", "n2t": "paxdb.organism" }, "name": "PaxDb Organism", "pattern": "^\\d+$", "preferred_prefix": "paxdb.organism", "uri_format": "http://pax-db.org/#!species/$1" }, "paxdb.protein": { "description": "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels.", "example": "977869", "homepage": "http://pax-db.org/", "mappings": { "biocontext": "PAXDB.PROTEIN", "miriam": "paxdb.protein", "n2t": "paxdb.protein" }, "name": "PaxDb Protein", "pattern": "^\\d+$", "preferred_prefix": "paxdb.protein", "uri_format": "http://pax-db.org/#!protein/$1" }, "pazar": { "contact": { "email": "wyeth@cmmt.ubc.ca", "name": "Wyeth W. Wasserman", "orcid": "0000-0001-6098-6412" }, "deprecated": true, "description": "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors.", "example": "TF0001053", "homepage": "http://www.pazar.info/", "keywords": [ "dna", "life science", "regulation", "rna" ], "mappings": { "biocontext": "PAZAR", "fairsharing": "FAIRsharing.33yggg", "integbio": "nbdc00611", "miriam": "pazar", "n2t": "pazar", "pathguide": "521", "prefixcommons": "pazar" }, "name": "Pazar Transcription Factor", "pattern": "^TF\\w+$", "preferred_prefix": "pazar", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pazar:$1" } ], "publications": [ { "doi": "10.1093/nar/gkn783", "pmc": "PMC2686574", "pubmed": "18971253", "title": "The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences", "year": 2008 }, { "doi": "10.1186/gb-2007-8-10-r207", "pmc": "PMC2246282", "pubmed": "17916232", "title": "PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation", "year": 2007 } ], "uri_format": "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1" }, "pba": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A controlled vocabulary to support the study of transcription in the primate brain", "download_obo": "https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-pba.obo", "example": "128011350", "homepage": "https://www.blueprintnhpatlas.org/", "keywords": [ "ontology" ], "name": "Primate Brain Atlas", "pattern": "^\\d+$", "preferred_prefix": "PBA", "repository": "https://github.com/brain-bican/primate_brain_atlas_ontology", "uri_format": "https://biopragmatics.github.io/providers/pba/$1" }, "pcl": { "contact": { "email": "davidos@ebi.ac.uk", "github": "dosumis", "name": "David Osumi-Sutherland", "orcid": "0000-0002-7073-9172" }, "depends_on": [ "bfo", "chebi", "cl", "go", "nbo", "ncbitaxon", "omo", "pato", "pr", "ro", "so", "uberon" ], "description": "Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties.", "download_json": "http://purl.obolibrary.org/obo/pcl.json", "download_obo": "http://purl.obolibrary.org/obo/pcl.obo", "download_owl": "http://purl.obolibrary.org/obo/pcl.owl", "example": "0011124", "homepage": "https://github.com/obophenotype/provisional_cell_ontology", "keywords": [ "anatomy", "annotation", "cell", "cell biology", "life science", "obo", "omics", "ontology", "phenomics", "sequencing assay", "single-cell multimodal omics", "transcriptomics" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "PCL", "bioportal": "PCL", "fairsharing": "FAIRsharing.bfcfd0", "obofoundry": "pcl", "ols": "pcl", "ontobee": "PCL", "wikidata.entity": "Q113014435" }, "name": "Provisional Cell Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "PCL", "publications": [ { "doi": "10.1101/2021.10.10.463703", "title": "Brain Data Standards - A method for building data-driven cell-type ontologies", "year": 2021 }, { "doi": "10.1038/s41597-022-01886-2", "title": "Brain Data Standards - A method for building data-driven cell-type ontologies", "year": 2023 } ], "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_$1", "version": "2025-07-07" }, "pco": { "appears_in": [ "ecocore", "envo" ], "contact": { "email": "rlwalls2008@gmail.com", "github": "ramonawalls", "name": "Ramona Walls", "orcid": "0000-0001-8815-0078" }, "depends_on": [ "bfo", "caro", "envo", "go", "iao", "ncbitaxon", "pato", "ro" ], "description": "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology.", "download_obo": "http://purl.obolibrary.org/obo/pco.obo", "download_owl": "http://purl.obolibrary.org/obo/pco.owl", "example": "0000021", "homepage": "https://github.com/PopulationAndCommunityOntology/pco", "keywords": [ "biodiversity", "community care", "dataplant", "ecology", "evolution", "life sciences, biology", "obo", "ontology", "population genetics", "social and behavioural science", "social sciences" ], "license": "CC0-1.0", "mappings": { "aberowl": "PCO", "agroportal": "PCO", "biocontext": "PCO", "bioportal": "PCO", "ecoportal": "PCO", "fairsharing": "FAIRsharing.vq28qp", "obofoundry": "pco", "ols": "pco", "ontobee": "PCO", "tib": "pco", "wikidata.entity": "Q55118575" }, "name": "Population and Community Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "PCO", "publications": [ { "doi": "10.1371/journal.pone.0089606", "pubmed": "24595056", "title": "Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies", "year": 2014 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/PCO_$1", "repository": "https://github.com/PopulationAndCommunityOntology/pco", "uri_format": "http://purl.obolibrary.org/obo/PCO_$1", "version": "2021-05-03" }, "pd_st": { "contact": { "email": "henrich@embl.de", "github": "ThorstenHen", "name": "Thorsten Henrich", "orcid": "0000-0002-1548-3290" }, "deprecated": true, "homepage": "http://4dx.embl.de/platy", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "PD_ST", "obofoundry": "pd_st" }, "name": "Platynereis stage ontology", "preferred_prefix": "PD_ST", "rdf_uri_format": "http://purl.obolibrary.org/obo/PD_ST_$1", "uri_format": "http://purl.obolibrary.org/obo/PD_ST_$1" }, "pdb": { "contact": { "email": "harukin@protein.osaka-u.ac.jp", "name": "Haruki Nakamura", "orcid": "0000-0001-6690-5863" }, "description": "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.", "example": "2gc4", "example_extras": [ "157d", "9ii2" ], "homepage": "https://www.wwpdb.org/", "keywords": [ "bioinformatics", "epidemiology", "protein", "proteomics", "structural biology", "structure", "virology" ], "logo": "https://cdn.rcsb.org/wwpdb/img/core/wwpdb-logo.png", "mappings": { "biocontext": "PDB", "edam": "1127", "fairsharing": "FAIRsharing.rs2815", "go": "PDB", "integbio": "nbdc00613", "miriam": "pdb", "n2t": "pdb", "ncbi": "PDB", "pathguide": "398", "prefixcommons": "pdbj", "re3data": "r3d100010910", "togoid": "Pdb", "uniprot": "DB-0172", "wikidata": "P638" }, "name": "PDB Structure", "pattern": "^[0-9][A-Za-z0-9]{3}$", "preferred_prefix": "pdb", "providers": [ { "code": "", "description": "Proteopedia", "homepage": "http://www.proteopedia.org/", "name": "Proteopedia", "uri_format": "http://proteopedia.org/wiki/index.php/$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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Each structure is annotated with a number of properties including experimental details, antibody nomenclature (e.g. heavy-light pairings), curated affinity data and sequence annotations.", "example": "9ii2", "homepage": "https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab", "name": "The Structural Antibody Database", "publications": [ { "doi": "10.1093/nar/gkt1043", "pmc": "PMC3965125", "pubmed": "24214988", "title": "SAbDab: the structural antibody database", "year": 2013 } ], "uri_format": "https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab/structureviewer/?pdb=$1" } ], "publications": [ { "doi": "10.1093/nar/gkaf377", "pubmed": "40326518", "title": "ProteinsPlus: a publicly available resource for protein structure mining", "year": 2025 }, { "doi": "10.1016/j.jmb.2025.169012", "pubmed": "40126909", "title": "RNAproDB: A Webserver and Interactive Database for Analyzing Protein-RNA Interactions", "year": 2025 }, { "doi": "10.1093/nar/gkae890", "pubmed": "39436020", "title": "DIONYSUS: a database of protein-carbohydrate interfaces", "year": 2024 }, { "doi": "10.1371/journal.pbio.3002476", "pmc": "PMC11309384", "pubmed": "39074139", "title": "FURNA: A database for functional annotations of RNA structures", "year": 2024 }, { "doi": "10.1002/pro.4211", "pmc": "PMC8740847", "pubmed": "34664328", "title": "Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data", "year": 2021 }, { "doi": "10.1002/pro.3273", "pmc": "PMC5734392", "pubmed": "28815765", "title": "New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)", "year": 2017 }, { "doi": "10.1093/nar/gkw962", "pmc": "PMC5210648", "pubmed": "27789697", "title": "Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures", "year": 2016 }, { "doi": "10.1093/nar/gkt1043", "pmc": "PMC3965125", "pubmed": "24214988", "title": "SAbDab: the structural antibody database", "year": 2013 }, { "doi": "10.1093/nar/gkr811", "pmc": "PMC3245181", "pubmed": "21976737", "title": "Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format", "year": 2011 }, { "doi": "10.1007/s10822-011-9460-y", "pubmed": "21796434", "title": "Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr", "year": 2011 }, { "doi": "10.1093/database/baq021", "pmc": "PMC2997606", "pubmed": "20798081", "title": "PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan", "year": 2010 }, { "pubmed": "12099029", "title": "[Development of PDBj: Advanced database for protein structures]", "year": 2002 } ], "rdf_uri_format": "https://rdf.wwpdb.org/pdb/$1", "synonyms": [ "RCSB_PDB", "pdbe", "pdbj", "wwpdb" ], "twitter": "PDBj_en", "uri_format": "https://www.wwpdb.org/pdb?id=pdb_0000$1" }, "pdb-ccd": { "comment": "might be same as pdb.ligand, not sure though", "contact": { "email": "berman@rcsb.rutgers.edu", "name": "Helen Berman", "orcid": "0000-0002-3337-0660" }, "contributor_extras": [ { "email": "bmeldal@ebi.ac.uk", "github": "bmeldal-eg", "name": "Birgit Meldal", "orcid": "0000-0003-4062-6158" } ], "description": "The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names.", "example": "AB0", "example_extras": [ "A", "PI" ], "has_canonical": "pdb.ligand", "homepage": "https://www.ebi.ac.uk/pdbe-srv/pdbechem/", "keywords": [ "chemical", "classification" ], "mappings": { "biocontext": "PDB-CCD", "miriam": "pdb-ccd", "n2t": "pdb-ccd", "prefixcommons": "ccd", "togoid": "PdbCcd" }, "name": "Chemical Component Dictionary", "pattern": "^\\w{1,3}$", "preferred_prefix": "pdb-ccd", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/ccd:$1" } ], "publications": [ { "doi": "10.1038/nsb1203-980", "pubmed": "14634627", "title": "Announcing the worldwide Protein Data Bank", "year": 2003 } ], "synonyms": [ "PDBeChem", "pdbechem" ], "uri_format": "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1" }, "pdb.ligand": { "description": "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands.", "example": "TRQ", "homepage": "http://www.rcsb.org", "keywords": [ "interaction", "protein", "small molecule", "structure" ], "mappings": { "biocontext": "PDB.LIGAND", "miriam": "pdb.ligand", "n2t": "pdb.ligand", "pathguide": "169", "prefixcommons": "pdbligand", "wikidata": "P3636" }, "name": "PDB ligand", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "pdb.ligand", "providers": [ { "code": "", "description": "PDB Ligand at Protein Databank in Europe (PDBe)", "homepage": "https://www.pdbe.org/", "name": "PDB Ligand at Protein Databank in Europe (PDBe)", "uri_format": "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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"CC-BY-4.0", "mappings": { "aberowl": "PDRO", "biocontext": "PDRO", "bioportal": "PDRO", "fairsharing": "FAIRsharing.9te3ev", "obofoundry": "pdro", "ols": "pdro", "ontobee": "PDRO", "wikidata.entity": "Q81661774" }, "name": "The Prescription of Drugs Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "PDRO", "providers": [ { "code": "pdro.legacy", "description": "An incorrect encoding of OBO purls", "homepage": "http://purl.obolibrary.org/obo/pdro", "name": "PDRO Hash", "uri_format": "http://purl.obolibrary.org/obo/PDRO/PDRO.owl#PDRO_$1" } ], "publications": [ { "doi": "10.3390/ijerph182212025", "pmc": "PMC8619589", "pubmed": "34831777", "title": "The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its Parts", "year": 2021 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/PDRO_$1", "repository": "https://github.com/OpenLHS/PDRO", "uri_format": "http://purl.obolibrary.org/obo/PDRO_$1", "version": "2021-06-08" }, "pdumdv": { "contact": { "email": "frederic.bastian@unil.ch", "github": "fbastian", "name": "Frédéric Bastian", "orcid": "0000-0002-9415-5104" }, "deprecated": true, "description": "Life cycle stages for Platynereis dumerilii", "download_obo": "http://purl.obolibrary.org/obo/pdumdv.obo", "download_owl": "http://purl.obolibrary.org/obo/pdumdv.owl", "example": "0001410", "homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv", "keywords": [ "developmental biology", "life cycle stage", "life science", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "PDUMDV", "biocontext": "PDUMDV", "bioportal": "PDUMDV", "fairsharing": "FAIRsharing.493qns", "obofoundry": "pdumdv", "ols": "pdumdv", "ontobee": "PdumDv", "wikidata.entity": "Q81661775" }, "name": "Platynereis Developmental Stages", "pattern": "^\\d{7}$", "preferred_prefix": "PdumDv", "rdf_uri_format": "http://purl.obolibrary.org/obo/PdumDv_$1", "repository": "https://github.com/obophenotype/developmental-stage-ontologies", "synonyms": [ "PdumDv" ], "uri_format": "http://purl.obolibrary.org/obo/PdumDv_$1" }, "peco": { "appears_in": [ "agro", "mco" ], "contact": { "email": "jaiswalp@science.oregonstate.edu", "github": "jaiswalp", "name": "Pankaj Jaiswal", "orcid": "0000-0002-1005-8383" }, "description": "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.", "download_obo": "https://raw.githubusercontent.com/Planteome/plant-experimental-conditions-ontology/master/peco.obo", "download_owl": "http://purl.obolibrary.org/obo/peco.owl", "example": "0007114", "homepage": "http://planteome.org/", "keywords": [ "botany", "dataplant", "experimental condition", "experimental measurement", "experimentally determined", "life sciences, biology", "obo", "ontology", "study design" ], "license": "CC-BY-4.0", "logo": 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"description": "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins.", "example": "PED00037", "homepage": "https://proteinensemble.org/", "keywords": [ "botany", "plant genetics" ], "mappings": { "fairsharing": "FAIRsharing.4ef690", "integbio": "nbdc02490", "miriam": "ped" }, "name": "Protein Ensemble Database", "pattern": "^PED\\d{5}$", "preferred_prefix": "ped", "publications": [ { "doi": "10.1093/nar/gky1026", "pmc": "PMC6324055", "pubmed": "30364952", "title": "Plant editosome database: a curated database of RNA editosome in plants", "year": 2019 } ], "uri_format": "https://proteinensemble.org/$1" }, "ped.ensemble": { "description": "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins.", "example": "PED00017e001", "homepage": "https://proteinensemble.org/", "mappings": { "miriam": "ped.ensemble" }, "name": "Protein Ensemble Database ensemble", "part_of": "ped", "pattern": "^PED\\d{5}e\\d{3}$", "preferred_prefix": "ped.ensemble", "uri_format": "https://proteinensemble.org/$1" }, "peff": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "download_obo": "https://github.com/HUPO-PSI/PEFF/raw/master/CV/psi-peff-OBSOLETE-DO_NOT_USE.obo", "example": "0001011", "homepage": "https://www.psidev.info/peff", "keywords": [ "ontology" ], "name": "PSI Extended File Format", "pattern": "^\\d{7}$", "preferred_prefix": "peff", "uri_format": "https://biopragmatics.github.io/providers/peff/$1" }, "pennsieve": { "description": "Pennsieve is a publicly accessible Scientific Data Management and publication platform. The platform supports data curation, sharing and publishing complex scientific datasets with a focus on integration between graph-based metadata and file-archival. The platform provides a \"peer\"-reviewed publication mechanism and public datasets are available through its Discover Web Application and APIs. ", "example": "N:package:e3243db3-7986-488e-9a10-c7a0bfdcfe8a", "homepage": "https://discover.pennsieve.io", "mappings": { "miriam": "ps" }, "name": "Pennsieve", "pattern": "^N:package:[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$", "preferred_prefix": "pennsieve", "uri_format": "https://discover.pennsieve.io/package/$1" }, "pepbank": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "PepBank is a database of peptides based on sequence text mining and public peptide data sources. Only peptides that are 20 amino acids or shorter are stored. Only peptides with available sequences are stored.", "example": "21877", "homepage": "http://pepbank.mgh.harvard.edu/", "keywords": [ "protein", "structure" ], "mappings": { "pathguide": "235", "prefixcommons": "pepbank" }, "name": "PepBank Peptide Database", "preferred_prefix": "pepbank", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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PEPhub uses Portable Encapsulated Projects (PEP) biological metadata standard to store, edit, and access PEPs in one place.", "example": "geo", "example_extras": [ "bedbase/gse198944", "databio/encode_batch_1", "geo/gse185244" ], "github_request_issue": 1194, "homepage": "https://pephub.databio.org/", "name": "PEPhub", "pattern": "^[A-Za-z0-9_\\-]+(/[A-Za-z0-9_\\-]+)?$", "preferred_prefix": "pephub", "publications": [ { "doi": "10.1093/gigascience/giae033", "pmc": "PMC11238423", "pubmed": "38991851", "title": "PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://pephub.databio.org/$1" }, "peptideatlas.dataset": { "description": "Experiment details about PeptideAtlas entries. Each PASS entry provides direct access to the data files submitted to PeptideAtlas.", "example": "PASS01237", "homepage": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_Summary", "mappings": { "miriam": "peptideatlas.dataset", "n2t": "peptideatlas.dataset" }, "name": "PeptideAtlas Dataset", "pattern": "^PASS\\d{5}$", "preferred_prefix": "peptideatlas.dataset", "uri_format": "http://www.peptideatlas.org/PASS/$1" }, "peptideatlas.peptide": { "contact": { "email": "edeutsch@systemsbiology.org", "github": "edeutsch", "name": "Eric W. Deutsch", "orcid": "0000-0001-8732-0928" }, "description": "The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools.", "example": "PAp00000009", "homepage": "http://www.peptideatlas.org/", "keywords": [ "mass spectrometry", "protein", "proteomics", "structure" ], "mappings": { "biocontext": "PEPTIDEATLAS", "edam": "2626", "fairsharing": "FAIRsharing.dvyrsz", "integbio": "nbdc01812", "miriam": "peptideatlas", "n2t": "peptideatlas", "prefixcommons": "peptideatlas", "re3data": "r3d100010889", "uniprot": "DB-0071" }, "name": "PeptideAtlas Peptide", "pattern": "^PAp[0-9]{8}$", "preferred_prefix": "peptideatlas.peptide", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/peptideatlas:$1" } ], "publications": [ { "doi": "10.1038/embor.2008.56", "pmc": "PMC2373374", "pubmed": "18451766", "title": "PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows", "year": 2008 }, { "doi": "10.1093/nar/gkj040", "pmc": "PMC1347403", "pubmed": "16381952", "title": "The PeptideAtlas project", "year": 2006 }, { "doi": "10.1038/embor.2008.56.", "title": "PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows." } ], "synonyms": [ "peptideatlas" ], "uri_format": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1" }, "perkinelmer": { "description": "Cell line collections (Providers)", "example": "SCC111", "homepage": "https://www.perkinelmer.com/", "mappings": { "cellosaurus": "PerkinElmer" }, "name": "PerkinElmer cell line collection", "preferred_prefix": "perkinelmer", "uri_format": "https://www.perkinelmer.com/searchresult?searchName=$1" }, "peroxibase": { "contact": { "email": "dunand@lrsv.ups-tlse.fr", "name": "Christophe Dunand", "orcid": "0000-0003-1637-4042" }, "description": "Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences.", "example": "5282", "homepage": "https://peroxibase.toulouse.inra.fr/", "keywords": [ "enzyme", "life science", "protein", "regulation" ], "mappings": { "biocontext": "PEROXIBASE", "fairsharing": "FAIRsharing.z1czxj", "integbio": "nbdc01869", "miriam": "peroxibase", "n2t": "peroxibase", "prefixcommons": "peroxibase", "uniprot": "DB-0072" }, "name": "Peroxibase", "pattern": "^\\d+$", "preferred_prefix": "peroxibase", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/peroxibase:$1" } ], "publications": [ { "doi": "10.1093/nar/gks1083", "pmc": "PMC3531118", "pubmed": "23180785", "title": "PeroxiBase: a database for large-scale evolutionary analysis of peroxidases", "year": 2012 }, { "doi": "10.1093/jxb/ern317", "pubmed": "19112168", "title": "PeroxiBase: a powerful tool to collect and analyse peroxidase sequences from Viridiplantae", "year": 2008 } ], "uri_format": "https://redoxibase.toulouse.inrae.fr/display_perox/view_perox/$1" }, "pesticideinfo": { "description": "chemical in the database supplied by Pesticide Action Network North America", "example": "PRI10", "homepage": "https://www.pesticideinfo.org", "mappings": { "wikidata": "P11949" }, "name": "PesticideInfo chemical ID", "pattern": "^PRI\\d*$", "preferred_prefix": "pesticideinfo", "uri_format": "https://www.pesticideinfo.org/chemical/$1" }, "pesticides": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients.", "example": "derivatives%2Fthiocyclam%20hydrochloride", "homepage": "http://www.alanwood.net/pesticides", "name": "Alan Wood's Pesticides", "preferred_prefix": "pesticides", "uri_format": "http://www.alanwood.net/pesticides/$1.html" }, "pfam": { "contact": { "email": "agb@ebi.ac.uk", "name": "Alex Bateman", "orcid": "0000-0002-6982-4660" }, "description": "The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.", "example": "PF11779", "homepage": "https://www.ebi.ac.uk/interpro/", "keywords": [ "biology", "domain", "protein" ], "license": "CC0-1.0", "logo": "https://upload.wikimedia.org/wikipedia/commons/0/03/Pfam_logo.gif", "mappings": { "biocontext": "PFAM", "edam": "1138", "fairsharing": "FAIRsharing.y3scf6", "go": "Pfam", "integbio": "nbdc00163", "miriam": "pfam", "n2t": "pfam", "ncbi": "PFAM", "prefixcommons": "pfam", "re3data": "r3d100012850", "togoid": "Pfam", "uniprot": "DB-0073", "wikidata": "P3519" }, "name": "Pfam protein family", "pattern": "^PF\\d{5}$", "preferred_prefix": "pfam", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pfam:$1" }, { "code": "sanger", "description": "The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.", "homepage": "http://pfam.sanger.ac.uk/", "name": "Sanger Pfam Mirror", "uri_format": "http://pfam.sanger.ac.uk/family?entry=$1" }, { "code": "xfam", "description": "Pfam's familes in their old home in the xfam.org", "homepage": "https://pfam.xfam.org", "name": "Xfam", "uri_format": "https://pfam.xfam.org/family?acc=$1" } ], "publications": [ { "doi": "10.1093/nar/27.1.260", "pmc": "PMC148151", "pubmed": "9847196", "title": "Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins", "year": 1999 }, { "doi": "10.1093/nar/26.1.320", "pmc": "PMC147209", "pubmed": "9399864", "title": "Pfam: multiple sequence alignments and HMM-profiles of protein domains", "year": 1998 }, { "doi": "10.1002/(sici)1097-0134(199707)28:3<405::aid-prot10>3.0.co;2-l", "pubmed": "9223186", "title": "Pfam: a comprehensive database of protein domain families based on seed alignments", "year": 1997 }, { "doi": "10.1093/nar/gkae997", "pubmed": "39540428", "title": "The Pfam protein families database: embracing AI/ML", "year": 2024 }, { "doi": "10.1093/nar/gkaa913", "pmc": "PMC7779014", "pubmed": "33125078", "title": "Pfam: The protein families database in 2021", "year": 2021 }, { "doi": "10.1093/nar/gky995", "pmc": "PMC6324024", "pubmed": "30357350", "title": "The Pfam protein families database in 2019", "year": 2019 }, { "doi": "10.1093/nar/gkv1344", "pmc": "PMC4702930", "pubmed": "26673716", "title": "The Pfam protein families database: towards a more sustainable future", "year": 2015 }, { "doi": "10.1093/nar/gkt1223", "pmc": "PMC3965110", "pubmed": "24288371", "title": "Pfam: the protein families database", "year": 2013 }, { "doi": "10.1093/nar/gkr1065", "pmc": "PMC3245129", "pubmed": "22127870", "title": "The Pfam protein families database", "year": 2011 }, { "doi": "10.1093/nar/gkp985", "pmc": "PMC2808889", "pubmed": "19920124", "title": "The Pfam protein families database", "year": 2009 }, { "doi": "10.1093/nar/gkm960", "pmc": "PMC2238907", "pubmed": "18039703", "title": "The Pfam protein families database", "year": 2007 }, { "doi": "10.1093/nar/gkj149", "pmc": "PMC1347511", "pubmed": "16381856", "title": "Pfam: clans, web tools and services", "year": 2006 }, { "doi": "10.1093/nar/gkh121", "pmc": "PMC308855", "pubmed": "14681378", "title": "The Pfam protein families database", "year": 2004 }, { "doi": "10.1093/nar/30.1.276", "pmc": "PMC99071", "pubmed": "11752314", "title": "The Pfam protein families database", "year": 2002 }, { "doi": "10.1093/nar/28.1.263", "pmc": "PMC102420", "pubmed": "10592242", "title": "The Pfam protein families database", "year": 2000 } ], "references": [ "https://twitter.com/PfamDB/status/1555149527228813314" ], "synonyms": [ "PF" ], "twitter": "Xfam_EBI", "uri_format": "https://www.ebi.ac.uk/interpro/entry/pfam/$1" }, "pfam.clan": { "contact": { "email": "agb@ebi.ac.uk", "github": "bateman-research", "name": "Alex Bateman", "orcid": "0000-0002-6982-4660" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Higher order grouping of Pfam families", "example": "CL0192", "homepage": "https://pfam.xfam.org", "keywords": [ "protein family" ], "license": "CC0-1.0", "logo": "https://upload.wikimedia.org/wikipedia/commons/0/03/Pfam_logo.gif", "mappings": { "edam": "2758" }, "name": "Pfam protein clan", "pattern": "^CL\\d+$", "preferred_prefix": "pfam.clan", "providers": [ { "code": "xfam", "description": "Pfam's clans in their old home in the xfam.org", "homepage": "https://pfam.xfam.org", "name": "Xfam", "uri_format": "https://pfam.xfam.org/clan/$1" } ], "references": [ "https://twitter.com/PfamDB/status/1555149527228813314" ], "uri_format": "https://www.ebi.ac.uk/interpro/set/pfam/$1" }, "pfr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets.", "example": "1001", "homepage": "http://repository.topdownproteomics.org/proteoforms", "keywords": [ "data management", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.wqsxtg", "re3data": "r3d100012385" }, "name": "Proteoform Atlas", "pattern": "^\\d+$", "preferred_prefix": "pfr", "synonyms": [ "TDR" ], "uri_format": "http://repository.topdownproteomics.org/proteoforms/$1" }, "pgdso": { "contact": { "email": "po-discuss@plantontology.org", "name": "Plant Ontology Administrators" }, "deprecated": true, "homepage": "http://www.plantontology.org", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "PGDSO", "obofoundry": "pgdso", "wikidata.entity": "Q114677907" }, "name": "Plant Growth and Development Stage", "preferred_prefix": "PGDSO", "rdf_uri_format": "http://purl.obolibrary.org/obo/PGDSO_$1", "uri_format": "http://purl.obolibrary.org/obo/PGDSO_$1" }, "pgs": { "description": "The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation.", "example": "PGS000018", "homepage": "http://pgscatalog.org", "mappings": { "miriam": "pgs" }, "name": "Polygenic Score Catalog", "pattern": "^PGS[0-9]{6}$", "preferred_prefix": "pgs", "uri_format": "https://www.pgscatalog.org/pgs/$1" }, "pgx": { "contact": { "email": "mbaudis@me.com", "github": "mbaudis", "name": "Michael Baudis", "orcid": "0000-0002-9903-4248" }, "description": "The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt \"neoplasm\" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs.", "example": "pgxbs-kftva5zv", "homepage": "https://progenetix.org/", "keywords": [ "biomedical science", "genomics" ], "mappings": { "biocontext": "PGX", "cellosaurus": "Progenetix", "fairsharing": "FAIRsharing.65tdnz", "miriam": "pgx", "n2t": "pgx", "re3data": "r3d100012820" }, "name": "Progenetix", "pattern": "^\\w{3,15}[-_]\\w[\\w.-]{3,128}$", "preferred_prefix": "pgx", "publications": [ { "doi": "10.1093/nar/gku1123", "pmc": "PMC4383937", "pubmed": "25428357", "title": "arrayMap 2014: an updated cancer genome resource", "year": 2014 }, { "doi": "10.1186/1471-2164-15-82", "pmc": "PMC3909908", "pubmed": "24476156", "title": "Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens", "year": 2014 }, { "doi": "10.1093/nar/gkt1108", "pmc": "PMC3965091", "pubmed": "24225322", "title": "Progenetix: 12 years of oncogenomic data curation", "year": 2013 }, { "doi": "10.1371/journal.pone.0036944", "pmc": "PMC3356349", "pubmed": "22629346", "title": "arrayMap: a reference resource for genomic copy number imbalances in human malignancies", "year": 2012 }, { "doi": "10.1186/1471-2407-7-226", "pmc": "PMC2225423", "pubmed": "18088415", "title": "Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data", "year": 2007 }, { "doi": "10.2144/000112102", "pubmed": "16568815", "title": "Online database and bioinformatics toolbox to support data mining in cancer cytogenetics", "year": 2006 }, { "doi": "10.1093/bioinformatics/17.12.1228", "pubmed": "11751233", "title": "Progenetix.net: an online repository for molecular cytogenetic aberration data", "year": 2001 } ], "synonyms": [ "Progenetix" ], "twitter": "progenetix", "uri_format": "https://progenetix.org/services/ids/$1" }, "phagedive": { "contact": { "email": "johannes.wittmann@dsmz.de", "name": "Johannes Wittmann", "orcid": "0000-0002-7275-9927" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "PhageDive is a database for bacteriophages and archaeal viruses. It provides information regarding taxonomy, host strain, phage morphology, life cycle, origin and genomic data.", "example": "3", "github_request_issue": 1454, "homepage": "https://phagedive.dsmz.de", "mappings": { "re3data": "r3d100014540" }, "name": "PhageDive", "pattern": "^\\d+$", "preferred_prefix": "phagedive", "publications": [ { "doi": "10.1093/nar/gkae878", "pmc": "PMC11701545", "pubmed": "39373542", "title": "PhageDive: the comprehensive strain database of prokaryotic viral diversity", "year": 2025 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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Query by cell line.", "example": "22RV1_12_2019", "homepage": "https://pharmacodb.ca/cell_lines", "mappings": { "cellosaurus": "PharmacoDB" }, "name": "PharmacoDB Cells", "preferred_prefix": "pharmacodb.cell", "uri_format": "https://pharmacodb.ca/cell_lines/$1" }, "pharmacodb.dataset": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by dataset.", "example": "1", "homepage": "https://pharmacodb.ca/datasets", "name": "PharmacoDB Datasets", "pattern": "^\\d+$", "preferred_prefix": "pharmacodb.dataset", "uri_format": "https://pharmacodb.ca/datasets/$1" }, "pharmacodb.tissue": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by tissue.", "example": "13", "homepage": "https://pharmacodb.ca/tissues", "name": "PharmacoDB Tissues", "pattern": "^\\d+$", "preferred_prefix": "pharmacodb.tissue", "uri_format": "https://pharmacodb.ca/tissues/$1" }, "pharmgkb.disease": { "contact": { "email": "teri.klein@stanford.edu", "github": "TeriKlein", "name": "Teri E Klein", "orcid": "0000-0001-5527-6475" }, "description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.", "example": "PA447218", "homepage": "http://www.pharmgkb.org/", "keywords": [ "pharmacogenomics" ], "license": "CC-BY-SA-4.0", "logo": "https://rxgenomix.com/wp-content/uploads/2019/10/pharmgKB.png", "mappings": { "biocontext": "PHARMGKB.DISEASE", "biolink": "PHARMGKB.DISEASE", "edam": "2651", "miriam": "pharmgkb.disease", "n2t": "pharmgkb.disease", "prefixcommons": "pharmgkb.disease", "wikidata": "P7001" }, "name": "PharmGKB Disease", "pattern": "^PA\\d+$", "preferred_prefix": "pharmgkb.disease", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pharmgkb.disease:$1" } ], "publications": [ { "doi": "10.2217/bmm.11.94", "pmc": "PMC3339046", "pubmed": "22103613", "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource", "year": 2011 }, { "doi": "10.1038/sj.tpj.6500035", "pubmed": "11908751", "title": "Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base", "year": 2001 } ], "uri_format": "http://www.pharmgkb.org/disease/$1" }, "pharmgkb.drug": { "contact": { "email": "teri.klein@stanford.edu", "github": "TeriKlein", "name": "Teri E Klein", "orcid": "0000-0001-5527-6475" }, "description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.", "example": "PA448710", "homepage": "http://www.pharmgkb.org/", "keywords": [ "drug", "pharmacogenomics" ], "license": "CC-BY-SA-4.0", "logo": "https://rxgenomix.com/wp-content/uploads/2019/10/pharmgKB.png", "mappings": { "biocontext": "PHARMGKB.DRUG", "biolink": "PHARMGKB.DRUG", "edam": "2652", "miriam": "pharmgkb.drug", "n2t": "pharmgkb.drug", "prefixcommons": "pharmgkb.drug", "wikidata": "P7001" }, "name": "PharmGKB Drug", "pattern": "^PA\\d+$", "preferred_prefix": "pharmgkb.drug", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pharmgkb.drug:$1" } ], "publications": [ { "doi": "10.2217/bmm.11.94", "pmc": "PMC3339046", "pubmed": "22103613", "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource", "year": 2011 }, { "doi": "10.1038/sj.tpj.6500035", "pubmed": "11908751", "title": "Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base", "year": 2001 } ], "uri_format": "http://www.pharmgkb.org/drug/$1" }, "pharmgkb.gene": { "contact": { "email": "teri.klein@stanford.edu", "github": "TeriKlein", "name": "Teri E Klein", "orcid": "0000-0001-5527-6475" }, "description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.", "example": "PA131", "homepage": "http://www.pharmgkb.org/", "keywords": [ "gene", "ontology", "pharmacogenomics" ], "license": "CC-BY-SA-4.0", "logo": "https://rxgenomix.com/wp-content/uploads/2019/10/pharmgKB.png", "mappings": { "biocontext": "PHARMGKB.GENE", "biolink": "PHARMGKB.GENE", "bioportal": "PHARMGKB", "go": "PharmGKB", "miriam": "pharmgkb.gene", "n2t": "pharmgkb.gene", "prefixcommons": "pharmgkb.gene", "uniprot": "DB-0074", "wikidata": "P7001" }, "name": "PharmGKB Gene", "pattern": "^PA\\w+$", "preferred_prefix": "pharmgkb.gene", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pharmgkb.gene:$1" } ], "publications": [ { "doi": "10.2217/bmm.11.94", "pmc": "PMC3339046", "pubmed": "22103613", "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource", "year": 2011 }, { "doi": "10.1385/1-59259-957-5:179", "pubmed": "16100408", "title": "PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base", "year": 2005 } ], "uri_format": "http://www.pharmgkb.org/gene/$1" }, "pharmgkb.pathways": { "contact": { "email": "teri.klein@stanford.edu", "github": "TeriKlein", "name": "Teri E Klein", "orcid": "0000-0001-5527-6475" }, "description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. \nPharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies.", "example": "PA146123006", "homepage": "http://www.pharmgkb.org/", "keywords": [ "pathway", "pharmacogenomics" ], "license": "CC-BY-SA-4.0", "logo": "https://rxgenomix.com/wp-content/uploads/2019/10/pharmgKB.png", "mappings": { "biocontext": "PHARMGKB.PATHWAYS", "biolink": "PHARMGKB.PATHWAYS", "edam": "2650", "miriam": "pharmgkb.pathways", "n2t": "pharmgkb.pathways", "prefixcommons": "pharmgkb.pathways", "wikidata": "P7001" }, "name": "PharmGKB pathway", "pattern": "^PA\\d+$", "preferred_prefix": "pharmgkb.pathways", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pharmgkb.pathways:$1" } ], "publications": [ { "doi": "10.2217/bmm.11.94", "pmc": "PMC3339046", "pubmed": "22103613", "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource", "year": 2011 }, { "doi": "10.1038/sj.tpj.6500035", "pubmed": "11908751", "title": "Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base", "year": 2001 } ], "uri_format": "http://www.pharmgkb.org/pathway/$1" }, "pharmgkb.variant": { "contact": { "email": "teri.klein@stanford.edu", "github": "TeriKlein", "name": "Teri E Klein", "orcid": "0000-0001-5527-6475" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "SNPs and other variants that can be mapped to dbSNP.", "example": "PA166156302", "github_request_issue": 1368, "homepage": "https://www.pharmgkb.org", "keywords": [ "genetic variant", "genetic variation", "snp" ], "license": "CC-BY-SA-4.0", "logo": "https://rxgenomix.com/wp-content/uploads/2019/10/pharmgKB.png", "mappings": { "biolink": "PHARMGKB.VARIANT" }, "name": "PharmGKB Variant", "pattern": "^PA\\d+$", "preferred_prefix": "pharmgkb.variant", "uri_format": "https://www.pharmgkb.org/variant/$1" }, "pharmvar": { "contact": { "email": "agaedigk@cmh.edu", "name": "Andrea Gaedigk", "orcid": "0000-0001-6968-1893" }, "description": "The Pharmacogene Variation (PharmVar) Consortium is the new home for PGx gene nomenclature serving as a centralized ‘Next-Generation’ Pharmacogene Variation data repository. The major focus of PharmVar is to catalogue allelic variation of genes impacting drug metabolism, disposition and response and provide a unifying designation system (nomenclature) for the global pharmacogenetic/genomic community. Efforts are synchronized between PharmVar, the Pharmacogenomic KnowledgeBase, and the Clinical Pharmacogenetic Implementation Consortium.", "example": "CYP2A6", "homepage": "https://www.pharmvar.org", "keywords": [ "gene", "pharmacogenomics", "variant" ], "mappings": { "prefixcommons": "pharmvar" }, "name": "Pharmacogene Variation Consortium", "preferred_prefix": "pharmvar", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pharmvar:$1" } ], "provides": "hgnc.symbol", "publications": [ { "doi": "10.1002/cpt.910", "pmc": "PMC5836850", "pubmed": "29134625", "title": "The Pharmacogene Variation (PharmVar) Consortium: Incorporation of the Human Cytochrome P450 (CYP) Allele Nomenclature Database", "year": 2017 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.pharmvar.org/gene/$1" }, "phenolexplorer": { "description": "Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis.", "example": "75", "homepage": "http://www.phenol-explorer.eu/foods/", "mappings": { "biocontext": "PHENOLEXPLORER", "miriam": "phenolexplorer", "n2t": "phenolexplorer", "re3data": "r3d100012197" }, "name": "Phenol-Explorer", "pattern": "^\\d+$", "preferred_prefix": "phenolexplorer", "uri_format": "http://phenol-explorer.eu/foods/$1" }, "phenx": { "contact": { "email": "yingqin@rti.org", "name": "PhenX Admin" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants.", "download_owl": "http://aber-owl.net/media/ontologies/PHENX/16/phenx.owl", "example": "130502", "github_request_issue": 503, "homepage": "https://www.phenxtoolkit.org/", "keywords": [ "biomedical science", "disease", "environmental science", "exposure", "life science", "ontology", "phenotype" ], "mappings": { "aberowl": "PHENX", "bioportal": "PHENX", "fairsharing": "FAIRsharing.y5jcwa", "integbio": "nbdc02244" }, "name": "PhenX Toolkit", "pattern": "^\\d+$", "preferred_prefix": "phenx", "publications": [ { "doi": "10.1038/gim.2016.199", "pmc": "PMC5507752", "pubmed": "28079902", "title": "PhenX measures for phenotyping rare genetic conditions", "year": 2017 }, { "doi": "10.1093/aje/kwr193", "pmc": "PMC3141081", "pubmed": "21749974", "title": "The PhenX Toolkit: get the most from your measures", "year": 2011 }, { "doi": "10.1097/mol.0b013e3283377395", "pmc": "PMC8038872", "pubmed": "20154612", "title": "PhenX: a toolkit for interdisciplinary genetics research", "year": 2010 } ], "synonyms": [ "phenxtoolkit" ], "uri_format": "https://www.phenxtoolkit.org/protocols/view/$1" }, "phipo": { "contact": { "email": "alayne.cuzick@rothamsted.ac.uk", "github": "CuzickA", "name": "Alayne Cuzick", "orcid": "0000-0001-8941-3984" }, "depends_on": [ "pato" ], "description": "Ontology of species-neutral phenotypes observed in pathogen-host interactions.", "download_obo": "http://purl.obolibrary.org/obo/phipo.obo", "download_owl": "http://purl.obolibrary.org/obo/phipo.owl", "example": "0000001", "homepage": "https://github.com/PHI-base/phipo", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "PHIPO", "bioportal": "PHIPO", "obofoundry": "phipo", "ols": "phipo", "ontobee": "PHIPO", "wikidata.entity": "Q81661779" }, "name": "Pathogen Host Interaction Phenotype Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "PHIPO", "publications": [ { "doi": "10.1093/nar/gkab1037", "pmc": "PMC8728202", "pubmed": "34788826", "title": "PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions", "year": 2022 } ], "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_$1", "version": "2026-01-26" }, "phosphopoint.kinase": { "description": "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information.", "example": "AURKA", "homepage": "http://kinase.bioinformatics.tw/", "mappings": { "biocontext": "PHOSPHOPOINT.KINASE", "miriam": "phosphopoint.kinase", "n2t": "phosphopoint.kinase" }, "name": "PhosphoPoint Kinase", "pattern": "^\\w+$", "preferred_prefix": "phosphopoint.kinase", "uri_format": "http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1" }, "phosphopoint.protein": { "deprecated": true, "description": "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information.", "example": "AURKA", "homepage": "http://kinase.bioinformatics.tw/", "mappings": { "biocontext": "PHOSPHOPOINT.PROTEIN", "miriam": "phosphopoint.protein", "n2t": "phosphopoint.protein" }, "name": "PhosphoPoint Phosphoprotein", "pattern": "^\\w+$", "preferred_prefix": "phosphopoint.protein", "uri_format": "http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0" }, "phosphosite.curation": { "contributor": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to curation records that collect information extracted from specific publications.", "example": "34665743", "github_request_issue": 1136, "homepage": "https://www.phosphosite.org", "name": "PhosphoSite Curation", "pattern": "^\\d+$", "preferred_prefix": "phosphosite.curation", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.phosphosite.org/curatedInfoAction.action?record=$1" }, "phosphosite.protein": { "description": "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database.", "example": "12300", "homepage": "http://www.phosphosite.org/homeAction.do", "mappings": { "biocontext": "PHOSPHOSITE.PROTEIN", "miriam": "phosphosite.protein", "n2t": "phosphosite.protein" }, "name": "PhosphoSite Protein", "pattern": "^\\d{5}$", "preferred_prefix": "phosphosite.protein", "uri_format": "http://www.phosphosite.org/proteinAction.do?id=$1" }, "phosphosite.residue": { "description": "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence.", "example": "2842", "homepage": "http://www.phosphosite.org/homeAction.do", "mappings": { "biocontext": "PHOSPHOSITE.RESIDUE", "miriam": "phosphosite.residue", "n2t": "phosphosite.residue" }, "name": "PhosphoSite Residue", "pattern": "^\\d+$", "preferred_prefix": "phosphosite.residue", "uri_format": "http://www.phosphosite.org/siteAction.do?id=$1" }, "phosphosite.sitegroup": { "comment": "Potentially could use a URI format like https://www.phosphosite.org/siteGroupAction.action?protOrg=1156&id=$1, but it's not obvious what the protOrg does.", "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur.", "example": "447860", "github_request_issue": 432, "homepage": "https://www.phosphosite.org", "keywords": [ "biochemistry", "grouping", "post-translational modification" ], "name": "PhosphoSite Site Group", "pattern": "^\\d+$", "preferred_prefix": "phosphosite.sitegroup", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "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=$1" }, "phylomedb": { "contact": { "email": "toni.gabaldon@crg.eu", "github": "tgabaldon", "name": "Toni Gabaldón", "orcid": "0000-0003-0019-1735" }, "description": "PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins.", "example": "Phy000CLXM_RAT", "homepage": "http://phylomedb.org/", "keywords": [ "genome", "life science", "phylogenetics", "phylogenomics", "phylogeny", "protein", "taxonomy" ], "mappings": { "biocontext": "PHYLOMEDB", "fairsharing": "FAIRsharing.7hxxc4", "integbio": "nbdc01764", "miriam": "phylomedb", "n2t": "phylomedb", "prefixcommons": "phylomedb", "uniprot": "DB-0144" }, "name": "PhylomeDB", "pattern": "^\\w+$", "preferred_prefix": "phylomedb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/phylomedb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkab966", "pmc": "PMC8728271", "pubmed": "34718760", "title": "PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies", "year": 2022 }, { "doi": "10.1093/nar/gkt1177", "pmc": "PMC3964985", "pubmed": "24275491", "title": "PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome", "year": 2013 }, { "doi": "10.1093/nar/gkq1109", "pmc": "PMC3013701", "pubmed": "21075798", "title": "PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions", "year": 2010 }, { "doi": "10.1093/nar/gkm899", "pmc": "PMC2238872", "pubmed": "17962297", "title": "PhylomeDB: a database for genome-wide collections of gene phylogenies", "year": 2007 } ], "twitter": "phylomedb", "uri_format": "http://phylomedb.org/?seqid=$1" }, "physh": { "description": "PhySH (Physics Subject Headings) is a physics classification scheme developed by the American Physical Society to organize journals, meetings, and other content by topic. The development of PhySH is motivated by the lack of a fully open, high quality classification scheme for physics. It is intended initially to meet the specific goals of the APS for our journal, meeting, and other content. A longer term goal is to make it available for use by the broader community. (...) Right now, the main use of PhySH is to classify manuscripts within the APS peer-review process and, ultimately, published journal articles. The assigned concepts will be used for ensuring articles are routed to the most appropriate handling editor who is knowledgeable in that area. They also help editors in finding similar articles previously submitted and in finding suitable referees.\n\nAs one might expect with something so new, the refinement of PhySH is still very much underway. The facets and disciplines have been identified and almost 3,000 concepts have been added to PhySH through an iterative process that is still ongoing. Many APS journal editors are involved in this process, primarily by lending their expertise in the various subfields in physics. The assignment of concepts to the various facets can be rather subjective. Thus, we expect to make many adjustments to PhySH as we receive feedback from the community (especially authors using PhySH to classify their submissions) and as we incorporate PhySH into the APS journal websites. As we iteratively refine PhySH over the coming months, the rate of new concept additions, concept reassignments within facets, and new relationships among concepts should abate significantly.", "example": "0003fc3f-1522-4fca-bf3f-bcef0dcec405", "homepage": "https://physh.aps.org/", "keywords": [ "nfdi4ing", "physics" ], "mappings": { "bartoc": "1899", "tib": "physh" }, "name": "Physics Subject Headings", "pattern": "^[0-9a-z-]+$", "preferred_prefix": "physh", "uri_format": "https://doi.org/10.29172/$1" }, "phytozome.locus": { "description": "Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information.", "example": "Glyma0021s00410", "homepage": "http://www.phytozome.net/", "mappings": { "biocontext": "PHYTOZOME.LOCUS", "miriam": "phytozome.locus", "n2t": "phytozome.locus", "ncbi": "Phytozome" }, "name": "Plant Genome Network", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "phytozome.locus", "synonyms": [ "JGI Phytozome" ], "uri_format": "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1" }, "pibase": { "description": "PIBASE is a collection of all protein structural interfaces extracted from the Protein Data Bank and PQS structure databases. Both chain-chain and domain-domain (SCOP and CATH definitions) interfaces are detected.", "example": "21692", "homepage": "http://salilab.org/pibase", "keywords": [ "protein", "structure" ], "mappings": { "pathguide": "183", "prefixcommons": "pibase" }, "name": "Database of structurally defined protein interfaces", "preferred_prefix": "pibase", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pibase:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id=$1" }, "pictar": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "example": "hsa-let-7a", "homepage": "https://pictar.mdc-berlin.de/", "name": "PicTar", "preferred_prefix": "pictar", "synonyms": [ "pictar-vert" ] }, "pid.pathway": { "contact": { "email": "schaefec@mail.nih.gov", "name": "Carl F. Schaefer", "orcid": "0000-0002-5941-3390" }, "deprecated": true, "description": "The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information.", "example": "eff796f3-6195-11e5-8ac5-06603eb7f303", "homepage": "https://www.ndexbio.org/index.html#/networkset/8a2d7ee9-1513-11e9-bb6a-0ac135e8bacf", "keywords": [ "gene", "life science", "pathway", "protein", "small molecule" ], "logo": "https://home.ndexbio.org/img/pid-logo-ndex.jpg", "mappings": { "biocontext": "PID.PATHWAY", "edam": "2344", "fairsharing": "FAIRsharing.ncgh1j", "miriam": "pid.pathway", "n2t": "pid.pathway", "pathguide": "119", "prefixcommons": "pid" }, "name": "NCI Pathway Interaction Database: Pathway", "pattern": "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$", "preferred_prefix": "pid.pathway", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pid:$1" } ], "publications": [ { "doi": "10.1093/nar/gkn653", "pmc": "PMC2686461", "pubmed": "18832364", "title": "PID: the Pathway Interaction Database", "year": 2008 } ], "synonyms": [ "pid" ], "uri_format": "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1" }, "pigqtldb": { "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs.", "example": "14", "homepage": "https://www.animalgenome.org/QTLdb", "keywords": [ "dna", "genome" ], "mappings": { "biocontext": "PIGQTLDB", "miriam": "pigqtldb", "n2t": "pigqtldb", "prefixcommons": "pigqtldb" }, "name": "Animal Genome Pig QTL", "part_of": "qtldb", "pattern": "^\\d+$", "preferred_prefix": "pigqtldb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pigqtldb:$1" } ], "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" }, "pii": { "appears_in": [ "pubmed" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A combination of an ISBN and local unique identifier for articles and other published works. Please see the [Wikipedia page](https://en.wikipedia.org/wiki/Publisher_Item_Identifier) for a detailed explanation. Some PIIs are used as the local identifiers in DOIs, such as https://doi.org/10.1136/S0003-4967(24)38620-0.", "example": "S0960-9822(11)01319-4", "example_extras": [ "B0-123-12345-1/12345-1" ], "github_request_issue": 1447, "homepage": "https://en.wikipedia.org/wiki/Publisher_Item_Identifier", "name": "Publisher Item Identifier", "pattern": "^((S\\d{4}-\\d{4}\\(\\d{2}\\)\\d{5})|(B\\d-\\d{3}-\\d{5}-\\d/\\d{5}))-[\\d|X]$", "preferred_prefix": "pii" }, "pina": { "contact": { "email": "wujm@bjmu.edu.cn", "name": "Jianmin Wu", "orcid": "0000-0002-8876-128X" }, "description": "Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms.", "example": "Q13485", "homepage": "https://omics.bjcancer.org/pina/", "keywords": [ "data visualization", "life science" ], "mappings": { "biocontext": "PINA", "fairsharing": "FAIRsharing.7q4gsz", "miriam": "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])$", "preferred_prefix": "pina", "provides": "uniprot", "publications": [ { "doi": "10.1093/nar/gkaa1075", "pmc": "PMC7779002", "pubmed": "33231689", "title": "PINA 3.0: mining cancer interactome", "year": 2021 }, { "doi": "10.1093/nar/gkr967", "pmc": "PMC3244997", "pubmed": "22067443", "title": "PINA v2.0: mining interactome modules", "year": 2011 }, { "doi": "10.1038/nmeth.1282", "pubmed": "19079255", "title": "Integrated network analysis platform for protein-protein interactions", "year": 2008 } ], "uri_format": "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1" }, "piroplasma": { "description": "PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "TA14985", "homepage": "http://piroplasmadb.org/", "mappings": { "biocontext": "PIROPLASMA", "miriam": "piroplasma", "n2t": "piroplasma" }, "name": "PiroplasmaDB", "pattern": "^TA\\d+$", "preferred_prefix": "piroplasma", "uri_format": "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" }, "pirsf": { "contact": { "email": "wuc@udel.edu", "name": "Cathy H. Wu", "orcid": "0000-0001-6379-8601" }, "description": "The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.", "example": "PIRSF000100", "homepage": "https://pir.georgetown.edu/", "keywords": [ "life science", "protein", "proteomics", "structure" ], "mappings": { "biocontext": "PIRSF", "edam": "1136", "fairsharing": "FAIRsharing.vssch2", "go": "PIRSF", "miriam": "pirsf", "n2t": "pirsf", "prefixcommons": "pirsf", "uniprot": "DB-0079" }, "name": "PIR Superfamily Classification System", "pattern": "^PIRSF\\d{6}$", "preferred_prefix": "pirsf", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pirsf:$1" } ], "publications": [ { "doi": "10.1093/nar/gkh097", "pmc": "PMC308831", "pubmed": "14681371", "title": "PIRSF: family classification system at the Protein Information Resource", "year": 2004 } ], "uri_format": "https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1" }, "pkdb": { "contact": { "email": "konigmatt@googlemail.com", "name": "Matthias König", "orcid": "0000-0003-1725-179X" }, "description": "PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. ", "example": "PKDB00198", "homepage": "https://www.hu-berlin.de/?set_language=en&cl=en", "keywords": [ "clinical studies", "clinical veterinary medicine", "life science", "personalized medicine", "pharmacogenomics", "pharmacology", "preclinical studies" ], "mappings": { "fairsharing": "FAIRsharing.AYegqK", "miriam": "pkdb" }, "name": "PK-DB", "pattern": "^PKDB[0-9]{5}$", "preferred_prefix": "pkdb", "publications": [ { "doi": "10.1093/nar/gkaa990", "pmc": "PMC7779054", "pubmed": "33151297", "title": "PK-DB: pharmacokinetics database for individualized and stratified computational modeling", "year": 2021 } ], "repository": "https://github.com/matthiaskoenig/pkdb/issues", "uri_format": "https://pk-db.com/data/$1" }, "plana": { "appears_in": [ "planp" ], "contact": { "email": "smr@stowers.org", "github": "srobb1", "name": "Sofia Robb", "orcid": "0000-0002-3528-5267" }, "depends_on": [ "ro", "uberon" ], "description": "PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea.", "download_obo": "http://purl.obolibrary.org/obo/plana.obo", "download_owl": "http://purl.obolibrary.org/obo/plana.owl", "example": "0000001", "homepage": "https://github.com/obophenotype/planaria-ontology", "keywords": [ "anatomy", "developmental biology", "life science", "obo", "ontology", "organ", "organelle", "tissue" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "PLANA", "biocontext": "PLANA", "bioportal": "PLANA", "fairsharing": "FAIRsharing.g1qrqs", "obofoundry": "plana", "ols": "plana", "ontobee": "PLANA", "wikidata.entity": "Q81661781" }, "name": "Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "PLANA", "publications": [ { "doi": "10.1242/dev.196097", "pmc": "PMC8353266", "pubmed": "34318308", "title": "Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms", "year": 2021 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/PLANA_$1", "repository": "https://github.com/obophenotype/planaria-ontology", "uri_format": "http://purl.obolibrary.org/obo/PLANA_$1", "version": "2023-03-13" }, "planp": { "contact": { "email": "smr@stowers.org", "github": "srobb1", "name": "Sofia Robb", "orcid": "0000-0002-3528-5267" }, "depends_on": [ "go", "pato", "plana", "ro" ], "description": "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea.", "download_obo": "http://purl.obolibrary.org/obo/planp.obo", "download_owl": "http://purl.obolibrary.org/obo/planp.owl", "example": "0000001", "homepage": "https://github.com/obophenotype/planarian-phenotype-ontology", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "PLANP", "bioportal": "PLANP", "obofoundry": "planp", "ols": "planp", "ontobee": "PLANP", "wikidata.entity": "Q81661782" }, "name": "Planarian Phenotype Ontology", "pattern": "^\\d+$", "preferred_prefix": "PLANP", "rdf_uri_format": "http://purl.obolibrary.org/obo/PLANP_$1", "repository": "https://github.com/obophenotype/planarian-phenotype-ontology", "uri_format": "http://purl.obolibrary.org/obo/PLANP_$1", "version": "2020-03-28" }, "plant_reactome": { "description": "PLANT REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. Pathway annotations are authored by expert biologists, in collaboration with the Reactome editorial staff and cross-referenced to many bioinformatics databases. These include project databases like Gramene, Ensembl, UniProt, ChEBI small molecule databases, PubMed, and Gene Ontology.", "example": "R-ACH-1120024", "homepage": "https://www.gramene.org", "mappings": { "miriam": "plant_reactome", "pathguide": "587" }, "name": "Plant Reactome", "pattern": "^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$", "preferred_prefix": "plant_reactome", "uri_format": "https://plantreactome.gramene.org/content/detail/$1" }, "planttfdb": { "contact": { "email": "gaog@mail.cbi.pku.edu.cn", "github": "gao-ge", "name": "Ge Gao", "orcid": "0000-0001-6470-8815" }, "description": "The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors.", "example": "Ath_AT1G01030.1", "homepage": "http://planttfdb.cbi.pku.edu.cn", "keywords": [ "dna", "gene", "life science", "protein", "regulation", "rna", "small molecule" ], "mappings": { "biocontext": "PLANTTFDB", "fairsharing": "FAIRsharing.ex3fqk", "miriam": "planttfdb", "n2t": "planttfdb", "pathguide": "497", "prefixcommons": "planttfdb", "re3data": "r3d100011301" }, "name": "Plant Transcription Factor Database", "pattern": "^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\\._\\-#]*)$", "preferred_prefix": "planttfdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/planttfdb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkw982", "pmc": "PMC5210657", "pubmed": "27924042", "title": "PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants", "year": 2016 }, { "doi": "10.1093/molbev/msv058", "pmc": "PMC4476157", "pubmed": "25750178", "title": "An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors", "year": 2015 }, { "doi": "10.1093/nar/gkt1016", "pmc": "PMC3965000", "pubmed": "24174544", "title": "PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors", "year": 2013 } ], "uri_format": "http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1" }, "plasmodb": { "contact": { "email": "oharb@upenn.edu", "github": "ramobrah", "name": "Omar S. Harb", "orcid": "0000-0003-4446-6200" }, "description": "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "PF11_0344", "homepage": "http://plasmodb.org/plasmo/", "keywords": [ "genome", "genomics", "infectious disease medicine" ], "logo": "https://sites.psu.edu/llinaslab/files/2020/05/plasmodb_logogif-e1590176740521.jpg", "mappings": { "biocontext": "PLASMODB", "fairsharing": "FAIRsharing.g4n8sw", "go": "PlasmoDB", "integbio": "nbdc01783", "miriam": "plasmodb", "n2t": "plasmodb", "ncbi": "ApiDB_PlasmoDB", "pathguide": "514", "prefixcommons": "plasmodb", "re3data": "r3d100011569" }, "name": "PlasmoDB", "pattern": "^\\w+$", "preferred_prefix": "plasmodb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/plasmodb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkn814", "pmc": "PMC2686598", "pubmed": "18957442", "title": "PlasmoDB: a functional genomic database for malaria parasites", "year": 2008 } ], "synonyms": [ "ApiDB_PlasmoDB" ], "twitter": "VEuPathDB", "uri_format": "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" }, "plo": { "contact": { "email": "mb4@sanger.ac.uk", "name": "Matt Berriman" }, "deprecated": true, "homepage": "http://www.sanger.ac.uk/Users/mb4/PLO/", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "PLO", "obofoundry": "plo", "wikidata.entity": "Q114677908" }, "name": "Plasmodium Life Cycle", "preferred_prefix": "PLO", "rdf_uri_format": "http://purl.obolibrary.org/obo/PLO_$1", "uri_format": "http://purl.obolibrary.org/obo/PLO_$1" }, "plos": { "contact": { "email": "subjectareas@plos.org", "name": "PLOS Taxonomy Team" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontologization of Public Library of Science (PLOS) journal keywords and topics. It's not clear how the IDs correspond to the actual pages. Appears in ADCAD.", "example": "1443", "github_request_issue": 1318, "homepage": "http://journals.plos.org", "keywords": [ "ontology", "subject agnostic" ], "mappings": { "aberowl": "PLOSTHES", "bioportal": "PLOSTHES", "fairsharing": "FAIRsharing.2ndf9r" }, "name": "PLOS Thesaurus", "pattern": "^\\d+$", "preferred_prefix": "plos", "synonyms": [ "PLOSTHES" ], "uri_format": "http://localhost/plosthes.2017-1#$1" }, "pmads": { "contact": { "email": "wanglab.tj@outlook.com", "name": "Haiyun Wang", "orcid": "0000-0001-8364-8328" }, "contributor": { "email": "ji.kang@northeastern.edu", "github": "kanghosaeyo", "name": "Kangho Ji", "orcid": "0009-0009-3402-8013" }, "description": "Identifiers correspond to curated and proteomics-inferred associations between protein post-translational modifications (PTM) and drug sensitivity.", "example": "acc0079", "github_request_issue": 1799, "homepage": "https://pmads-db.org", "keywords": [ "drug sensitivity", "modification", "proteomics" ], "name": "PMADS", "pattern": "^acc\\d{4}$", "preferred_prefix": "pmads", "publications": [ { "doi": "10.1093/nar/gkaf1033", "pubmed": "41099621", "title": "PMADS: an integrated database of curated and proteomics-inferred associations between protein post-translational modifications and drug sensitivity.", "year": 2025 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://pmads-db.org/result/?id=$1" }, "pmap.cutdb": { "contact": { "email": "adam@burnham.org", "name": "Adam Godzik", "orcid": "0000-0002-2425-852X" }, "deprecated": true, "description": "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites).", "example": "25782", "homepage": "http://cutdb.burnham.org", "keywords": [ "enzyme", "pathway", "protein" ], "mappings": { "biocontext": "PMAP.CUTDB", "miriam": "pmap.cutdb", "n2t": "pmap.cutdb", "prefixcommons": "pmap.cutdb" }, "name": "CutDB", "pattern": "^\\d+$", "preferred_prefix": "pmap.cutdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pmap.cutdb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkl813", "pmc": "PMC1669773", "pubmed": "17142225", "title": "CutDB: a proteolytic event database", "year": 2006 } ], "uri_format": "http://cutdb.burnham.org/relation/show/$1" }, "pmap.substratedb": { "contact": { "email": "eroshkin@burnham.org", "name": "Alexey M. Eroshkin", "orcid": "0000-0003-2023-4608" }, "description": "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates.", "example": "1915", "homepage": "http://substrate.burnham.org/", "keywords": [ "domain", "protein", "reaction" ], "mappings": { "biocontext": "PMAP.SUBSTRATEDB", "miriam": "pmap.substratedb", "n2t": "pmap.substratedb", "prefixcommons": "pmap.substratedb" }, "name": "SubstrateDB", "pattern": "^\\d+$", "preferred_prefix": "pmap.substratedb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pmap.substratedb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkn683", "pmc": "PMC2686432", "pubmed": "18842634", "title": "PMAP: databases for analyzing proteolytic events and pathways", "year": 2008 } ], "uri_format": "http://substrate.burnham.org/protein/annotation/$1/html" }, "pmc": { "comment": "Note that the Europe PMC instance redirects canonical local unique identifiers from https://europepmc.org/articles/PMC3084216 to https://europepmc.org/article/PMC/3084216. However, this is an implementation detail and does not reflect the official format of a PMC identifier, which indeed does include `PMC` at the beginning of the local unique identifier", "contact": { "email": "beck@ncbi.nlm.nih.gov", "github": "jeffbeckncbi", "name": "Jeff Beck", "orcid": "0000-0002-1798-9797" }, "description": "PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature.", "example": "PMC3084216", "example_extras": [ "PMC7418728", "PMC7418728.1", "PMC7418728.2" ], "homepage": "http://europepmc.org/", "keywords": [ "bibliography", "biomedical science", "centrally registered identifier" ], "mappings": { "biocontext": "PMCID", "biolink": "PMC", "cellosaurus": "PMCID", "fairsharing": "FAIRsharing.2b4316", "go": "PMCID", "miriam": "pmc", "n2t": "pmc", "prefixcommons": "pmc", "togoid": "Pmc", "wikidata": "P932", "wikidata.entity": "Q11801904" }, "name": "PubMed Central", "pattern": "^PMC\\d+(\\.\\d+)?$", "preferred_prefix": "pmc", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pmc:$1" }, { "code": "ncbi.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" } ], "publications": [ { "doi": "10.1093/nar/gkr1184", "pmc": "PMC3245031", "pubmed": "22140104", "title": "Database resources of the National Center for Biotechnology Information", "year": 2011 }, { "doi": "10.1093/nar/gkq1172", "pmc": "PMC3013733", "pubmed": "21097890", "title": "Database resources of the National Center for Biotechnology Information", "year": 2010 } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/965" ], "synonyms": [ "PMC", "PMCID" ], "uri_format": "http://europepmc.org/articles/$1" }, "pmdb": { "description": "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques.", "example": "PM0012345", "homepage": "https://bioinformatics.cineca.it/PMDB/", "keywords": [ "protein", "structural biology", "structure" ], "mappings": { "biocontext": "PMDB", "fairsharing": "FAIRsharing.wkaakq", "miriam": "pmdb", "n2t": "pmdb", "prefixcommons": "pmdb" }, "name": "Protein Model Database", "pattern": "^PM\\d{7}$", "preferred_prefix": "pmdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pmdb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkj105", "pmc": "PMC1347467", "pubmed": "16381873", "title": "The PMDB Protein Model Database", "year": 2006 } ], "uri_format": "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1" }, "pmdco": { "description": "The PMD Core Ontology (PMDco) is a comprehensive framework for representing knowledge that encompasses fundamental concepts from the domains of materials science and engineering (MSE). The PMDco has been designed as a mid-level ontology to establish a connection between specific MSE application ontologies and the domain neutral concepts found in established top-level ontologies. The primary goal of the PMDco is to promote interoperability between diverse domains. PMDco's class structure is both understandable and extensible, making it an efficient tool for organizing MSE knowledge. It serves as a semantic intermediate layer that unifies MSE knowledge representations, enabling data and metadata to be systematically integrated on key terms within the MSE domain. With PMDco, it is possible to seamlessly trace data generation. By building on this foundation, PMDco facilitates the integration of data from various sources and the creation of complex workflows. In summary, PMDco is a valuable tool for researchers and practitioners in the MSE domains. It provides a common language for representing and sharing knowledge, allowing for efficient collaboration and promoting interoperability between diverse domains. Its design allows for the systematic integration of data and metadata, enabling seamless traceability of data generation. Overall, PMDco is a crucial step towards a unified and comprehensive understanding of the MSE domain. PMDco at GitHub: https://github.com/materialdigital/core-ontology Documentation: https://materialdigital.github.io/core-ontology/docs/", "example": "0000000", "homepage": "https://materialdigital.github.io/core-ontology/", "keywords": [ "chemical and environmental engineering", "material science", "mechanical engineering, energy technology", "nfdi4ing" ], "mappings": { "tib": "pmd" }, "name": "Platform Material Digital Core Ontology", "preferred_prefix": "pmdco", "repository": "https://github.com/materialdigital/core-ontology", "uri_format": "https://w3id.org/pmd/co/PMD_$1" }, "pmp": { "contact": { "email": "torsten.schwede@unibas.ch", "name": "Torsten Schwede", "orcid": "0000-0003-2715-335X" }, "deprecated": true, "description": "The number of known protein sequences exceeds those of experimentally solved protein structures. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pmp:$1" } ], "provides": "uniprot", "publications": [ { "doi": "10.1007/s10969-008-9048-5", "pmc": "PMC2704613", "pubmed": "19037750", "title": "The Protein Model Portal", "year": 2008 } ], "uri_format": "http://www.proteinmodelportal.org/query/uniprot/$1" }, "pmr.exposure": { "contact": { "email": "laia.subirats@gmail.com", "name": "Laia Subirats", "orcid": "0000-0001-8646-5463" }, "description": "Resource for the community to store, retrieve, search, reference, and reuse CellML models.", "download_owl": "http://aber-owl.net/media/ontologies/PMR/4/pmr.owl", "example": "ebf69ca24298b28b2361e7d43eb52d6c", "homepage": "https://www.auckland.ac.nz/en.html", "keywords": [ "biomedical science", "life science", "mathematics", "ontology", "physiology", "systems biology" ], "mappings": { "aberowl": "PMR", "bioportal": "PMR", "fairsharing": "FAIRsharing.bcjrnq", "miriam": "pmr" }, "name": "Physical Medicine and Rehabilitation", "pattern": "^[a-z0-9]{32,32}$", "preferred_prefix": "pmr.exposure", "publications": [ { "doi": "10.1098/rsfs.2015.0103", "pmc": "PMC4759754", "pubmed": "27051515", "title": "The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable", "year": 2016 }, { "doi": "10.1186/1471-2105-12-22", "pmc": "PMC3033326", "pubmed": "21235804", "title": "Revision history aware repositories of computational models of biological systems", "year": 2011 }, { "doi": "10.1093/bioinformatics/btq723", "pubmed": "21216774", "title": "The Physiome Model Repository 2", "year": 2011 }, { "doi": "10.1098/rsta.2008.0310", "pmc": "PMC3268215", "pubmed": "19380315", "title": "CellML metadata standards, associated tools and repositories", "year": 2009 }, { "doi": "10.1093/bioinformatics/btn390", "pubmed": "18658182", "title": "The CellML Model Repository", "year": 2008 }, { "doi": "10.1109/iembs.2006.260202", "pubmed": "17947072", "title": "Toward a curated CellML model repository", "year": 2006 }, { "doi": "10.1109/IEMBS.2006.260202", "title": "Toward a curated CellML model repository." } ], "synonyms": [ "pmr" ], "twitter": "physiomeproject", "uri_format": "https://models.physiomeproject.org/exposure/$1" }, "pmr.workspace": { "description": "Workspace (Git repository) for modeling projects managed by the Physiome Model Repository", "example": "modularmassactionprimer", "homepage": "https://www.auckland.ac.nz/en.html", "mappings": { "miriam": "pmr.workspace" }, "name": "Physiome Model Repository workspace", "pattern": "^[a-zA-Z0-9_\\-]+(/.*?)?$", "preferred_prefix": "pmr.workspace", "uri_format": "https://models.physiomeproject.org/workspace/$1" }, "po": { "appears_in": [ "agro", "ecocore", "envo", "gallont", "genepio" ], "banana": "PO", "contact": { "email": "jaiswalp@science.oregonstate.edu", "github": "jaiswalp", "name": "Pankaj Jaiswal", "orcid": "0000-0002-1005-8383" }, "description": "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.", "download_obo": "http://purl.obolibrary.org/obo/po.obo", "download_owl": "http://purl.obolibrary.org/obo/po.owl", "example": "0009089", "homepage": "http://browser.planteome.org/amigo", "keywords": [ "botany", "classification", "dataplant", "earth sciences", "ess", "expression data", "life cycle", "life science", "obo", "ontology", "plant anatomy", "structure", "whole plant development stage" ], "license": "CC-BY-4.0", "logo": "https://raw.githubusercontent.com/Planteome/plant-ontology/refs/heads/master/Planteome_profile.jpg", "mappings": { "aberowl": "PO", "agroportal": "PO", "biocontext": "PO", "bioportal": "PO", "cellosaurus": "PO", "edam": "1180", "fairsharing": "FAIRsharing.3ngg40", "go": "PO", "miriam": "po", "n2t": "po", "obofoundry": "po", "ols": "po", "ontobee": "PO", "prefixcommons": "po", "tib": "po", "wikidata.entity": "Q7201529" }, "name": "Plant Ontology", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "PO", "providers": [ { "code": "amigo", "description": "Plant Ontology through Amigo", "homepage": "http://www.plantontology.org/", "name": "Plant Ontology through Amigo", "uri_format": "https://browser.planteome.org/amigo/term/PO:$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries.", "example": "1433C_TOBAC_1_252", "homepage": "http://www.pocketome.org/sfSearch.cgi?act=browseall", "keywords": [ "life science" ], "mappings": { "biocontext": "POCKETOME", "fairsharing": "FAIRsharing.tc6df8", "miriam": "pocketome", "n2t": "pocketome", "pathguide": "537" }, "name": "Pocketome", "pattern": "^[A-Za-z_0-9]+$", "preferred_prefix": "pocketome", "publications": [ { "doi": "10.1093/nar/gkr825", "pmc": "PMC3245087", "pubmed": "22080553", "title": "Pocketome: an encyclopedia of small-molecule binding sites in 4D", "year": 2011 }, { "doi": "10.1007/978-1-60761-274-2_11", "pmc": "PMC2975493", "pubmed": "19727619", "title": "The flexible pocketome engine for structural chemogenomics", "year": 2009 } ], "uri_format": "http://www.pocketome.org/files/$1.html" }, "polbase": { "contact": { "email": "lreha@ualberta.ca", "name": "Linda Reha-Krantz", "orcid": "0000-0003-4497-423X" }, "description": "Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity.", "example": "19-T4", "homepage": "http://polbase.neb.com/", "keywords": [ "biochemistry", "genetics" ], "mappings": { "biocontext": "POLBASE", "fairsharing": "FAIRsharing.s9ztmd", "integbio": "nbdc02079", "miriam": "polbase", "n2t": "polbase" }, "name": "PolBase", "pattern": "^[A-Za-z-0-9]+$", "preferred_prefix": "polbase", "publications": [ { "doi": "10.1093/nar/gkr847", "pmc": "PMC3245023", "pubmed": "21993301", "title": "Polbase: a repository of biochemical, genetic and structural information about DNA polymerases", "year": 2011 } ], "uri_format": "https://polbase.neb.com/polymerases/$1#sequences" }, "polymat": { "description": "PolyMat is a domain ontology designed for polymer membrane research and tailored for immediate integration within Electronic Laboratory Notebooks (ELNs), facilitating efficient documentation of laboratory experiments and advancing the domain's FAIRification process.", "example": "4PointResistanceSetup", "homepage": "https://gitlab.com/dlr-dw/poly-ontologies/polymat-ontology", "keywords": [ "chemistry", "material science", "nfdi4ing" ], "mappings": { "tib": "pmat" }, "name": "PolyMat Ontology", "preferred_prefix": "polymat", "uri_format": "https://w3id.org/polymat/$1" }, "polytraits.trait": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Reproductive and behavioural traits of both adult and larval stages, as well as information on environmental preferences and a few morphological traits.", "example": "PRED", "github_request_issue": 1422, "homepage": "http://polytraits.lifewatchgreece.eu/terms", "name": "Polytraits Trait Definitions", "preferred_prefix": "polytraits.trait", "rdf_uri_format": "http://polytraits.lifewatchgreece.eu/terms/$1", "uri_format": "http://polytraits.lifewatchgreece.eu/traitspublic_traitdefinitions.php#$1" }, "pombase": { "contact": { "email": "vw253@cam.ac.uk", "github": "ValWood", "name": "Valerie Wood", "orcid": "0000-0001-6330-7526" }, "description": "PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. 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Yamamoto", "orcid": "0000-0002-9667-0572" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties.", "example": "1484", "homepage": "https://sitem.herts.ac.uk/aeru/ppdb/", "keywords": [ "life science" ], "mappings": { "fairsharing": "FAIRsharing.7k8zh0", "integbio": "nbdc01041" }, "name": "Pesticide Properties DataBase", "pattern": "^\\d+$", "preferred_prefix": "ppdb", "publications": [ { "doi": "10.1093/nar/gkt1027", "pmc": "PMC3965062", "pubmed": "24194597", "title": "ppdb: plant promoter database version 3.0", "year": 2013 }, { "doi": "10.1093/nar/gkm785", "pmc": "PMC2238996", "pubmed": "17947329", "title": "ppdb: a plant promoter database", "year": 2007 } ], "uri_format": "https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm" }, "ppeo": { "contact": { "email": "cyril.pommier@inrae.fr", "name": "Cyril Pommier" }, "description": "The Plant Phenotyping Experiment Ontology (PPEO) is an implementation of the Minimal Information About Plant Phenotyping Experiment. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/prosite:$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/btt129", "pmc": "PMC3634184", "pubmed": "23505298", "title": "pfsearchV3: a code acceleration and heuristic to search PROSITE profiles", "year": 2013 }, { "doi": "10.1093/nar/gks1067", "pmc": "PMC3531220", "pubmed": "23161676", "title": "New and continuing developments at PROSITE", "year": 2012 }, { "doi": "10.1093/nar/gkj063", "pmc": "PMC1347426", "pubmed": "16381852", "title": "The PROSITE database", "year": 2006 } ], "uri_format": "https://prosite.expasy.org/$1" }, "protclustdb": { "contact": { "email": "klimke@ncbi.nlm.nih.gov", "name": "William Klimke" }, "description": "ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.", "example": "O80725", "homepage": "https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters", "keywords": [ "genetics", "genomics", "life science", "protein", "structure" ], "mappings": { "biocontext": "PROTCLUSTDB", "fairsharing": "FAIRsharing.da493y", "miriam": "protclustdb", "n2t": "protclustdb", "prefixcommons": "protclustdb" }, "name": "ProtClustDB", "pattern": "^\\w+$", "preferred_prefix": "protclustdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/protclustdb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkn734", "pmc": "PMC2686591", "pubmed": "18940865", "title": "The National Center for Biotechnology Information's Protein Clusters Database", "year": 2008 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1" }, "protcom": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "This database is a collection of protein-protein homo- and hetero-complexes as well as domain-domain structures. This issue of the database contains 17.024 entries (as of October 2007) of which 1350 are two-chain protein hetero-complexes, 7773 homodimers and 1589 are one-chain proteins parsed into two domains (domain structures).", "example": "12e8LH", "homepage": "http://www.ces.clemson.edu/compbio/protcom", "keywords": [ "protein", "structure" ], "mappings": { "pathguide": "242", "prefixcommons": "protcom" }, "name": "Database of protein-protein complexes", "preferred_prefix": "protcom", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/protcom:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.ces.clemson.edu/compbio/protcom/print_file.cgi?pdbid=$1" }, "protege": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology of metadata from protege", "download_rdf": "https://protege.stanford.edu/plugins/owl/protege", "example": "defaultLanguage", "github_request_issue": 1317, "homepage": "http://protege.stanford.edu", "name": "Protege Ontology", "preferred_prefix": "protege", "uri_format": "http://protege.stanford.edu/plugins/owl/protege#$1" }, "proteomicsdb.peptide": { "comment": "The fact that this has .peptide as a subspace is a bit of a misnomer. Its original registration with MIRIAM uses a subview over the protein to point to peptides, but the identifiers in this semantic space seem to be about proteins.", "description": "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein.", "example": "53504", "homepage": "https://www.proteomicsdb.org/#peptideSearch", "mappings": { "biocontext": "PROTEOMICSDB.PEPTIDE", "miriam": "proteomicsdb.peptide", "n2t": "proteomicsdb.peptide" }, "name": "ProteomicsDB Peptide", "pattern": "^\\d+$", "preferred_prefix": "proteomicsdb.peptide", "uri_format": "https://www.proteomicsdb.org/#human/proteinDetails/$1" }, "proteomicsdb.protein": { "description": "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins.", "example": "53504", "homepage": "https://www.proteomicsdb.org/#human", "mappings": { "biocontext": "PROTEOMICSDB.PROTEIN", "miriam": "proteomicsdb.protein", "n2t": "proteomicsdb.protein" }, "name": "ProteomicsDB Protein", "pattern": "^\\d+$", "preferred_prefix": "proteomicsdb.protein", "uri_format": "https://www.proteomicsdb.org/#human/proteinDetails/$1/summary" }, "protonet.cluster": { "contact": { "email": "michall@cc.huji.ac.il", "github": "LinialLab", "name": "Michal Linial", "orcid": "0000-0002-9357-4526" }, "deprecated": true, "description": "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information.", "example": "4349895", "homepage": "http://www.protonet.cs.huji.ac.il/", "keywords": [ "classification", "clustering", "protein" ], "mappings": { "biocontext": "PROTONET.CLUSTER", "miriam": "protonet.cluster", "n2t": "protonet.cluster", "prefixcommons": "protonet.cluster" }, "name": "ProtoNet Cluster", "pattern": "^\\d+$", "preferred_prefix": "protonet.cluster", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/protonet.cluster:$1" } ], "publications": [ { "doi": "10.1110/ps.062185706", "pmc": "PMC2242553", "pubmed": "16672244", "title": "Functional annotation prediction: all for one and one for all", "year": 2006 } ], "uri_format": "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1" }, "protonet.proteincard": { "contact": { "email": "michall@cc.huji.ac.il", "github": "LinialLab", "name": "Michal Linial", "orcid": "0000-0002-9357-4526" }, "deprecated": true, "description": "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information.", "example": "16941567", "homepage": "http://www.protonet.cs.huji.ac.il/", "keywords": [ "protein" ], "mappings": { "biocontext": "PROTONET.PROTEINCARD", "miriam": "protonet.proteincard", "n2t": "protonet.proteincard", "prefixcommons": "protonet.proteincard" }, "name": "ProtoNet ProteinCard", "pattern": "^\\d+$", "preferred_prefix": "protonet.proteincard", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/protonet.proteincard:$1" } ], "publications": [ { "doi": "10.1110/ps.062185706", "pmc": "PMC2242553", "pubmed": "16672244", "title": "Functional annotation prediction: all for one and one for all", "year": 2006 } ], "uri_format": "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1" }, "prov": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web.", "download_owl": "http://aber-owl.net/media/ontologies/PROV/1/prov.owl", "example": "Activity", "homepage": "https://www.w3.org/ns/prov", "keywords": [ "ess", "nfdi4chem", "nfdi4ing", "ontology", "w3c rec" ], "mappings": { "aberowl": "PROV", "biocontext": "prov", "biolink": "prov", "lov": "prov", "ols": "prov", "tib": "prov", "zazuko": "prov" }, "name": "PROV Namespace", "preferred_prefix": "prov", "uri_format": "http://www.w3.org/ns/prov#$1" }, "pscdb": { "contact": { "email": "mota@i.nagoya-u.ac.jp", "name": "Motonori Ota", "orcid": "0000-0001-9090-668X" }, "description": "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion.", "example": "051", "homepage": "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html", "keywords": [ "life science" ], "mappings": { "biocontext": "PSCDB", "fairsharing": "FAIRsharing.3d4jx0", "integbio": "nbdc01636", "miriam": "pscdb", "n2t": "pscdb" }, "name": "Protein Structural Change Database", "pattern": "^\\d+$", "preferred_prefix": "pscdb", "publications": [ { "doi": "10.1093/nar/gkr966", "pmc": "PMC3245091", "pubmed": "22080505", "title": "PSCDB: a database for protein structural change upon ligand binding", "year": 2011 }, { "doi": "10.1016/j.jmb.2011.02.058", "pubmed": "21376729", "title": "Classification and annotation of the relationship between protein structural change and ligand binding", "year": 2011 } ], "uri_format": "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html" }, "psdo": { "contact": { "email": "zachll@umich.edu", "github": "zachll", "name": "Zach Landis-Lewis", "orcid": "0000-0002-9117-9338" }, "depends_on": [ "bfo", "iao", "ro", "stato" ], "description": "Performance Summary Display Ontology (PSDO) is an application ontology about motivating information in performance summaries and the visual and textual entities that are used to communicate about performance. Motivating information includes performance comparisons and changes that motivate improvement or sustainment, such as improvement towards a goal, loss of high performer status, or the presence of a performance gap. Visual and textual entities include charts, tables, and graphs that display performance information. PSDO's domain focus is healthcare organizations that use clinical quality dashboards and feedback interventions for healthcare professionals and teams. Performance information is commonly about the quality of care and health outcomes that have been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is supported by the NIH, National Library of Medicine (1K01LM012528-01, 1R01LM013894-01).\n\nLandis-Lewis Z, Stansbury C, Rincón J, Gross C. Performance Summary Display Ontology: Feedback intervention content, delivery, and interpreted information. International Conference on Biomedical Ontology 2022 (ICBO 2022). https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf", "download_owl": "http://purl.obolibrary.org/obo/psdo.owl", "example": "0000055", "homepage": "https://github.com/Display-Lab/psdo", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "PSDO", "bioportal": "PSDO", "obofoundry": "psdo", "ols": "psdo", "ontobee": "PSDO", "wikidata.entity": "Q81661788" }, "name": "Performance Summary Display Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "PSDO", "rdf_uri_format": "http://purl.obolibrary.org/obo/PSDO_$1", "repository": "https://github.com/Display-Lab/psdo", "uri_format": "http://purl.obolibrary.org/obo/PSDO_$1", "version": "1.0.1" }, "pseudogene": { "contact": { "email": "mark@gersteinlab.org", "name": "Mark Gerstein", "orcid": "0000-0002-9746-3719" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase.", "example": "PGOHUM00000289843", "homepage": "http://www.pseudogene.org", "keywords": [ "gene", "ontology" ], "mappings": { "bioportal": "pseudo", "integbio": "nbdc00178", "prefixcommons": "pseudogene", "wikidata.entity": "Q7254809" }, "name": "PseudoGene", "preferred_prefix": "pseudogene", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pseudogene:$1" } ], "synonyms": [ "pseudogene.org" ], "uri_format": "http://tables.pseudogene.org/[?species_name]/$1" }, "pseudomonas": { "description": "The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.", "example": "PSEEN0001", "homepage": "http://www.pseudomonas.com/", "mappings": { "biocontext": "PSEUDOMONAS", "miriam": "pseudomonas", "n2t": "pseudomonas" }, "name": "Pseudomonas Genome Database", "pattern": "^P\\w+$", "preferred_prefix": "pseudomonas", "uri_format": "http://www.pseudomonas.com/feature/show/?locus_tag=$1" }, "psipar": { "banana": "PAR", "comment": "This resource is no longer loaded on XML and the sourceforge link from the HUPO website to the psi-par.obo artifact is dead.", "deprecated": true, "description": "Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms.", "example": "0116", "homepage": "https://www.psidev.info/psi-par", "mappings": { "biocontext": "PSIPAR", "miriam": "psipar", "n2t": "psipar" }, "name": "Protein Affinity Reagents", "pattern": "^\\d+$", "preferred_prefix": "psipar", "uri_format": "https://www.ebi.ac.uk/ontology-lookup/?termId=PAR:$1" }, "pso": { "contact": { "email": "cooperl@oregonstate.edu", "github": "cooperl09", "name": "Laurel Cooper", "orcid": "0000-0002-6379-8932" }, "depends_on": [ "ro" ], "description": "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter.", "download_obo": "http://purl.obolibrary.org/obo/pso.obo", "download_owl": "http://purl.obolibrary.org/obo/pso.owl", "example": "0000013", "homepage": "https://github.com/Planteome/plant-stress-ontology", "keywords": [ "dataplant", "hospital", "life sciences, biology", "medical informatics", "monitoring", "obo", "occupational medicine", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "PSO", "agroportal": "PSO", "bioportal": "PSO", "fairsharing": "FAIRsharing.dyj433", "obofoundry": "pso", "ols": "pso", "ontobee": "PSO", "tib": "pso", "wikidata.entity": "Q113014437" }, "name": "Plant Stress Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "PSO", "publications": [ { "doi": "10.1093/nar/gkx1152", "pmc": "PMC5753347", "pubmed": "29186578", "title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics", "year": 2018 } ], "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_$1", "version": "2026-01-08" }, "pspub": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Documentation of the Phenoscape Curation Workflow", "homepage": "https://wiki.phenoscape.org/wiki/Curation_workflow", "name": "Phenoscape Publication", "preferred_prefix": "pspub" }, "psskb": { "contact": { "email": "kaysheva1@gmail.com", "name": "Anna L. Kaysheva", "orcid": "0000-0003-4472-2016" }, "contributor": { "email": "palayoor.n@northeastern.edu", "github": "nalikapalayoor", "name": "Nalika Palayoor", "orcid": "0009-0008-8406-631X" }, "description": "PSSKB allows researchers to model post translational modifications and amino acid substitutions in proteins, providing 3D structural representations. Identifiers represent protein motifs on which PSSKB provides data.", "example": "2VM6_A55_A135", "github_request_issue": 1398, "homepage": "https://psskb.org/", "name": "Protein Structure and Stability Knowledge Base", "pattern": "^[A-Za-z0-9_]+$", "preferred_prefix": "psskb", "publications": [ { "doi": "10.1002/jcc.70046", "pubmed": "39876062", "title": "PSSKB: A Web Application to Study Protein Structures", "year": 2025 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://psskb.org/motif/card/$1" }, "pto": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Identifiers for product types (product, price, and company data) based on Wikipedia", "example": "Atlas", "homepage": "http://www.productontology.org/", "license": "CC-BY-SA-3.0", "name": "Product Types Ontology", "preferred_prefix": "pto", "uri_format": "http://www.productontology.org/id/$1" }, "ptr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This specification contains a framework for representing pointers - entities that permit identifying a portion or segment of a piece of content - making use of the Resource Description Framework (RDF). It also describes a number of specific types of pointers that permit portions of a document to be referred to in different ways. When referring to a specific part of, say, a piece of web content, it is useful to be able to have a consistent manner by which to refer to a particular segment of a web document, to have a variety of ways by which to refer to that same segment, and to make the reference robust in the face of changes to that document. This specification is part of the Evaluation And Report Language (EARL) but can be reused in other contexts too. [from homepage]", "download_rdf": "https://www.w3.org/2009/pointers", "example": "Pointer", "homepage": "https://www.w3.org/TR/Pointers-in-RDF/", "name": "Pointer Methods in RDF", "preferred_prefix": "ptr", "rdf_uri_format": "https://www.w3.org/2009/pointers#$1", "references": [ "https://www.w3.org/blog/2009/pointer-methods-in-rdf-first-draft/" ], "uri_format": "https://www.w3.org/2009/pointers#$1", "version": "2009" }, "pubchem.bioassay": { "contact": { "email": "pruitt@ncbi.nlm.nih.gov", "name": "Kim Dixon Pruitt", "orcid": "0000-0001-7950-1374" }, "description": "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results.", "example": "1018", "homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay", "keywords": [ "small molecule" ], "logo": "https://pubchem.ncbi.nlm.nih.gov/pcfe/logo/PubChem_logo_splash.png", "mappings": { "biocontext": "PUBCHEM.BIOASSAY", "edam": "2638", "go": "PubChem_BioAssay", "integbio": "nbdc00640", "miriam": "pubchem.bioassay", "n2t": "pubchem.bioassay", "prefixcommons": "pubchem.bioassay" }, "name": "NCBI PubChem database of bioassay records", "pattern": "^\\d+$", "preferred_prefix": "pubchem.bioassay", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pubchem.bioassay:$1" } ], "publications": [ { "doi": "10.1093/nar/gkl1031", "pmc": "PMC1781113", "pubmed": "17170002", "title": "Database resources of the National Center for Biotechnology Information", "year": 2006 } ], "synonyms": [ "pubchem.aid", "pubchem.assay" ], "twitter": "pubchem", "uri_format": "https://pubchem.ncbi.nlm.nih.gov/bioassay/$1" }, "pubchem.cell": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Cell Lines in PubChem", "example": "31", "homepage": "https://pubchem.ncbi.nlm.nih.gov", "keywords": [ "bioactivities", "cell lines", "chemistry" ], "logo": "https://pubchem.ncbi.nlm.nih.gov/pcfe/logo/PubChem_logo_splash.png", "name": "PubChem Cell Line", "pattern": "^\\d+$", "preferred_prefix": "pubchem.cell", "twitter": "pubchem", "uri_format": "https://pubchem.ncbi.nlm.nih.gov/cell/$1" }, "pubchem.classification": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The PubChem Classification Browser allows you to browse the distribution of PubChem data among nodes in the hierarchy of interest, thereby providing an aggregate view of PubChem data. 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This collection is species-independent.", "example": "4685", "homepage": "https://www.animalgenome.org/QTLdb", "mappings": { "miriam": "qtldb" }, "name": "Animal Genome QTL", "pattern": "^\\d+$", "preferred_prefix": "qtldb", "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" }, "qualo": { "contact": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology of qualifications, distinctions, and certifications that uses the Phenotype And Trait Ontology term quality (PATO:0000001) as a root term.", "example": "0000001", "homepage": "https://github.com/cthoyt/qualo", "license": "CC0-1.0", "name": "Qualification Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "qualo", "rdf_uri_format": "https://w3id.org/qualo/id/$1", "repository": "https://github.com/cthoyt/qualo", "uri_format": "https://w3id.org/qualo/id/$1" }, "qudt": { "contact": { "email": "noreply@bioontology.org", "name": "Unknown" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types.", "download_owl": "http://aber-owl.net/media/ontologies/QUDT/4/qudt.owl", "download_rdf": "http://qudt.org/schema/qudt/", "example": "baseDimensionEnumeration", "homepage": "https://qudt.org", "keywords": [ "experimental measurement", "measurement systems", "methods", "ontology", "quantification", "unit", "units" ], "mappings": { "aberowl": "QUDT", "bartoc": "18206", "biolink": "qud", "bioportal": "QUDT", "fairsharing": "FAIRsharing.d3pqw7", "lov": "qudt", "zazuko": "qudt" }, "name": "Quantities, Units, Dimensions, and Types Ontology", "preferred_prefix": "qudt", "providers": [ { "code": "v11", "description": "Version 1.1 provider", "homepage": "http://qudt.org", "name": "Version 1.1", "uri_format": "http://qudt.org/1.1/schema/qudt#$1" } ], "repository": "https://github.com/qudt/qudt-public-repo", "uri_format": "http://qudt.org/schema/qudt#$1" }, "radiomics": { "contact": { "email": "alberto.traverso@maastro.nl", "name": "Alberto Traverso", "orcid": "0000-0001-6183-4429" }, "description": "The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual. [bioportal]", "example": "LK99", "homepage": "http://www.radiomics.org/RO", "keywords": [ "ontology" ], "mappings": { "bioportal": "RO" }, "name": "Radiomics Ontology", "preferred_prefix": "radiomics", "uri_format": "http://www.radiomics.org/RO/$1" }, "radlex": { "contact": { "email": "radlex-feedback@lists.rsna.org", "name": "Radiological Society of North America" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A comprehensive set of radiology terms for use in radiology reporting, decision support, data mining, data registries, education and research.\n\nRadLex provides the foundation for vital data resources used in radiology:\n\n- The LOINC/RSNA Radiology Playbook\n- RadElement Common Data Elements\n-RadReport Radiology Reporting Templates\n\nThe development of RadLex has been supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the cancer Biomedical Informatics Grid (caBIG) project.", "download_owl": "http://aber-owl.net/media/ontologies/RADLEX/37/radlex.owl", "example": "RID1", "homepage": "https://radlex.org", "keywords": [ "anatomy", "biomedical science", "clinical studies", "diagnosis", "medical imaging", "medical informatics", "ontology", "radiology" ], "license": "http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/RadLex_License_Agreement_and_Terms_of_Use_V2_Final.pdf", "mappings": { "aberowl": "RADLEX", "bartoc": "20689", "bioportal": "RADLEX", "fairsharing": "FAIRsharing.shm2f2", "hl7": "2.16.840.1.113883.6.256" }, "name": "RSNA Informatics RadLex", "pattern": "^RID\\d+$", "preferred_prefix": "radlex", "publications": [ { "doi": "10.1016/j.jvir.2009.04.031", "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", "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", "pubmed": "10789815", "title": "Radiology lexicon", "year": 2000 } ], "uri_format": "https://radlex.org/RID/$1", "version": "4.1" }, "raid": { "description": "RAiD is an identifier and global system, governed by ISO 23527:2022, to uniquely identifiy research projects, collaboratively, collect and publicly share information about them.", "example": "10.26259/0e59e9a5", "homepage": "https://ardc.edu.au/", "keywords": [ "centrally registered identifier", "fair", "knowledge representation", "resource metadata", "subject agnostic" ], "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBZ0VIIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--c5438876bbbcd4c68044b1e22d159b57bc79513f/RAID%20Logo.png?disposition=inline", "mappings": { "fairsharing": "FAIRsharing.dc702a", "miriam": "raid" }, "name": "Research Activity Identifier", "pattern": "^102?\\.\\d+\\/.+$", "preferred_prefix": "raid", "repository": "https://github.com/ResearchDataServices", "uri_format": "https://raid.org/$1" }, "rapdb.locus": { "description": "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB.", "example": "Os01g0883800", "homepage": "https://rapdb.dna.affrc.go.jp/", "mappings": { "miriam": "rapdb.locus" }, "name": "RAP-DB Locus", "pattern": "^Os\\S+g\\d{7}$", "preferred_prefix": "rapdb.locus", "synonyms": [ "irgsp" ], "uri_format": "https://rapdb.dna.affrc.go.jp/locus/?name=$1" }, "rapdb.transcript": { "description": "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB.", "example": "Os01t0883800-02", "homepage": "https://rapdb.dna.affrc.go.jp/", "keywords": [ "dna", "genome" ], "mappings": { "go": "RAP-DB", "miriam": "rapdb.transcript", "ncbi": "RAP-DB", "prefixcommons": "rapdb" }, "name": "Rice annotation Project database", "pattern": "^Os\\S+t\\d{7}-\\d{2}$", "preferred_prefix": "rapdb.transcript", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/rapdb:$1" } ], "uri_format": "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1" }, "ratmap": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "The Rat Genome Database RatMap is focused on presenting rat genes, DNA-markers, QTL:s etc that is localized to chromosome. The database is dedicated to rat gene nomenclature and should be consulted for queries in such matters", "example": "5", "homepage": "http://ratmap.org", "keywords": [ "dna", "gene", "genome" ], "mappings": { "ncbi": "RATMAP", "prefixcommons": "ratmap" }, "name": "Rat Genome Database RatMap", "preferred_prefix": "ratmap", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/ratmap:$1" } ], "provides": "ensembl", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://ratmap.org/Showgene.php?gene_stable_id=$1" }, "rbk": { "contact": { "email": "oxburl@mmc.org", "name": "Leif Oxburgh", "orcid": "0000-0002-2825-7663" }, "description": "(Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function.", "example": "Q-2958", "homepage": "https://www.rebuildingakidney.org/", "keywords": [ "cell biology", "developmental biology", "genomics", "molecular biology" ], "mappings": { "biocontext": "RBK", "fairsharing": "FAIRsharing.78d3ad", "miriam": "rbk", "n2t": "rbk" }, "name": "Rebuilding a Kidney", "pattern": "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$", "preferred_prefix": "rbk", "publications": [ { "doi": "10.1681/asn.2016101077", "pmc": "PMC5407737", "pubmed": "28096308", "title": "(Re)Building a Kidney", "year": 2017 }, { "doi": "10.1681/ASN.2016101077", "title": "(Re)Building a Kidney." } ], "repository": "https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Create-citable-datasets", "uri_format": "https://www.rebuildingakidney.org/id/$1" }, "rbo": { "contact": { "email": "daniel.c.berrios@nasa.gov", "github": "DanBerrios", "name": "Daniel C. Berrios", "orcid": "0000-0003-4312-9552" }, "depends_on": [ "bfo", "chmo", "envo", "obi", "pato", "ro", "uo" ], "description": "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.", "download_json": "http://purl.obolibrary.org/obo/rbo.json", "download_obo": "http://purl.obolibrary.org/obo/rbo.obo", "download_owl": "http://purl.obolibrary.org/obo/rbo.owl", "example": "00000105", "example_extras": [ "010007" ], "homepage": "https://github.com/Radiobiology-Informatics-Consortium/RBO", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "RBO", "bioportal": "RBO", "obofoundry": "rbo", "ols": "rbo", "ontobee": "RBO", "wikidata.entity": "Q113014438" }, "name": "Radiation Biology Ontology", "pattern": "^\\d{6,8}$", "preferred_prefix": "RBO", "rdf_uri_format": "http://purl.obolibrary.org/obo/RBO_$1", "repository": "https://github.com/Radiobiology-Informatics-Consortium/RBO", "uri_format": "http://purl.obolibrary.org/obo/RBO_$1", "version": "2026-01-15" }, "rcb": { "contact": { "email": "atsushi.yoshiki@riken.jp", "name": "Atsushi Yoshiki", "orcid": "0000-0002-9450-5151" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center.", "example": "RCB0002", "homepage": "https://cell.brc.riken.jp/en/rcb", "keywords": [ "animal", "bioresource", "cell", "cell line", "cultured cell", "cultured cell line", "dna", "embryo", "experimental animal", "experimental plant", "faseb list", "gene", "genetic material", "organ", "plant", "recombinant host", "seed", "sperm", "tissue", "virus" ], "mappings": { "cellosaurus": "RCB", "rrid": "IMSR_RBRC" }, "name": "RIKEN Bioresource Center Cell Bank", "pattern": "^RCB\\d+$", "preferred_prefix": "rcb", "publications": [ { "pubmed": "34532769" }, { "pubmed": "19448331" } ], "uri_format": "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1" }, "rdbsb": { "contact": { "email": "gqzhang@sinh.ac.cn", "name": "Guoqing Zhang", "orcid": "0000-0001-8827-7546" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "This database provides identifiers for catalytic bioparts which are fundamental to the design, construction, and optimization of biological systems for specific metabolic pathways. It provides basic information, function information (including catalytic functions, qualitative and quantitative parameters, and biopart expression), and sequence information (nucleotide sequence and amino acid sequence)", "example": "OENC205", "github_request_issue": 1473, "homepage": "https://www.biosino.org/rdbsb", "name": "Registry and database of bioparts for synthetic biology", "pattern": "^OENC\\d+$", "preferred_prefix": "rdbsb", "publications": [ { "doi": "10.1093/nar/gkae844", "pmc": "PMC11701600", "pubmed": "39360609", "title": "RDBSB: a database for catalytic bioparts with experimental evidence", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://www.biosino.org/rdbsb/bioparts_detail/$1" }, "rdf": { "contact": { "email": "rmrich5@gmail.com", "name": "Rafael Richards", "orcid": "0000-0001-5699-0515" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts", "example": "type", "homepage": "http://www.w3.org/1999/02/22-rdf-syntax-ns", "keywords": [ "computer science", "subject agnostic", "w3c rec" ], "mappings": { "biocontext": "rdf", "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", "name": "Dan Brickley", "orcid": "0000-0002-6450-7041" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary.", "download_owl": "https://triplydb.com/w3c/rdfs/download.trig.gz", "example": "label", "homepage": "https://www.w3.org/TR/rdf-schema/", "keywords": [ "bioinformatics", "life science", "linguistics", "ontology", "ontology and terminology", "w3c rec" ], "mappings": { "aberowl": "RDFS", "biocontext": "rdfs", "bioportal": "RDFS", "fairsharing": "FAIRsharing.v9n3gk", "lov": "rdfs", "ols": "rdfs", "zazuko": "rdfs" }, "name": "RDF Schema", "preferred_prefix": "rdfs", "uri_format": "http://www.w3.org/2000/01/rdf-schema#$1" }, "rdo": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms.", "download_obo": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.obo", "download_owl": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.owl", "example": "9002859", "homepage": "https://ratmine.mcw.edu/ontology/disease/", "keywords": [ "ontology" ], "name": "RGD Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "rdo", "uri_format": "http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1" }, "re3data": { "description": "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines.", "example": "r3d100010772", "homepage": "https://datacite.org", "mappings": { "bartoc": "822", "miriam": "re3data" }, "name": "re3data", "pattern": "^r3d\\d{9,9}$", "preferred_prefix": "re3data", "uri_format": "https://www.re3data.org/repository/$1" }, "reactome": { "contact": { "email": "deustp01@med.nyu.edu", "github": "deustp01", "name": "Peter D'Eustachio", "orcid": "0000-0002-5494-626X" }, "contributor_extras": [ { "email": "smoxon@lbl.gov", "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" } ], "description": "The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.", "example": "R-BTA-418592", "homepage": "https://www.reactome.org/", "keywords": [ "human", "pathway", "reaction" ], "license": "CC0-1.0", "logo": "https://reactome.org/templates/favourite/images/logo/logo.png", "mappings": { "biocontext": "REACTOME", "cheminf": "000411", "edam": "1155", "go": "Reactome", "integbio": "nbdc00185", "miriam": "reactome", "n2t": "reactome", "pathguide": "103", "prefixcommons": "reactome", "re3data": "r3d100010861", "togoid": "ReactomePathway", "wikidata": "P3937" }, "name": "Reactome", "pattern": "^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$", "preferred_prefix": "reactome", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/reactome:$1" }, { "code": "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", "homepage": "https://www.pathwaycommons.org", "name": "Pathway Commons", "uri_format": "https://apps.pathwaycommons.org/pathways?uri=http%3A%2F%2Fidentifiers.org%2Freactome%2F$1" } ], "publications": [ { "doi": "10.1093/nar/gki072", "pmc": "PMC540026", "pubmed": "15608231", "title": "Reactome: a knowledgebase of biological pathways", "year": 2005 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/1086" ], "synonyms": [ "RE", "REACT", "Reactome", "reactome.pathway" ], "uri_format": "https://reactome.org/content/detail/$1" }, "reaxys": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier.", "example": "1257009", "homepage": "https://www.reaxys.com", "mappings": { "edam": "1003", "wikidata": "P1579" }, "name": "Reaxys", "pattern": "^\\d+$", "preferred_prefix": "reaxys", "synonyms": [ "Beilstein", "Reaxys" ] }, "rebase": { "contact": { "email": "roberts@neb.com", "name": "Richard John Roberts", "orcid": "0000-0002-4348-0169" }, "description": "REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.", "example": "101", "homepage": "http://rebase.neb.com/rebase/", "keywords": [ "dna", "enzyme", "genome", "life science", "protein", "rna", "small molecule", "structure" ], "logo": "https://rebase.neb.com/rebase/rebase_header_crop3_gray_url_use.png", "mappings": { "biocontext": "REBASE", "edam": "2325", "fairsharing": "FAIRsharing.9sb9qh", "go": "REBASE", "integbio": "nbdc00648", "miriam": "rebase", "n2t": "rebase", "pathguide": "72", "prefixcommons": "rebase", "re3data": "r3d100012171", "uniprot": "DB-0089", "wikidata": "P4866" }, "name": "REBASE Enzyme Number", "pattern": "^\\d+$", "preferred_prefix": "rebase", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/rebase:$1" } ], "publications": [ { "doi": "10.1093/nar/gkac975", "pubmed": "36318248" }, { "doi": "10.1093/nar/gku1046", "pmc": "PMC4383893", "pubmed": "25378308", "title": "REBASE--a database for DNA restriction and modification: enzymes, genes and genomes", "year": 2014 }, { "doi": "10.1093/nar/gkp874", "pmc": "PMC2808884", "pubmed": "19846593", "title": "REBASE--a database for DNA restriction and modification: enzymes, genes and genomes", "year": 2009 } ], "uri_format": "http://rebase.neb.com/rebase/enz/$1.html" }, "rebec": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Presents the new fast tracks for clinical research and observational studies on INDIGENOUS PEOPLE AND TRADITIONAL COMMUNITIES and on NEGLECTED TROPICAL DISEASES (NTDs). Fast-track can reduce the normal approval period for clinical trials to less than 48 hours, if the documentation, information and any mandatory changes requested are provided by the registrant.", "example": "RBR-6qvdftm", "homepage": "https://ensaiosclinicos.gov.br", "name": "Brazilian Registry of Clinical Trials", "pattern": "^RBR-\\w+$", "preferred_prefix": "rebec", "uri_format": "https://ensaiosclinicos.gov.br/rg/$1" }, "rec": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Recommendation Ontology specification provides basic concepts and properties for describing recommendations on/for the Semantic Web.", "download_owl": "https://web.archive.org/web/20250116013621/https://smiy.sourceforge.net/rec/rdf/recommendationontology.owl", "example": "Recommendation", "homepage": "https://web.archive.org/web/20250105164652/https://smiy.sourceforge.net/rec/spec/recommendationontology.html", "keywords": [ "ontology", "rec" ], "license": "CC-BY-3.0", "mappings": { "lov": "rec" }, "name": "Recommendation Ontology", "preferred_prefix": "rec", "rdf_uri_format": "http://purl.org/ontology/rec/core#$1", "uri_format": "http://purl.org/ontology/rec/core#$1" }, "receptome.family": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database.", "example": "5.1", "homepage": "http://www.receptome.org", "keywords": [ "protein" ], "mappings": { "prefixcommons": "hpmr" }, "name": "Human Plasma Membrane Receptome Families", "preferred_prefix": "receptome.family", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hpmr:$1" } ], "uri_format": "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1" }, "redfly": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "REDflyis a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs).", "example": "8", "homepage": "http://redfly.ccr.buffalo.edu", "keywords": [ "regulation" ], "mappings": { "pathguide": "265", "prefixcommons": "redfly" }, "name": "Regulatory Elements Database for Drosophila", "preferred_prefix": "redfly", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/redfly:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id=$1" }, "refseq": { "contact": { "email": "pruitt@ncbi.nlm.nih.gov", "name": "Kim Dixon Pruitt", "orcid": "0000-0001-7950-1374" }, "contributor_extras": [ { "github": "slobentanzer", "name": "Sebastian Lobentanzer", "orcid": "0000-0003-3399-6695" } ], "description": "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.", "example": "NP_012345", "example_extras": [ "WP_029104145.1" ], "has_canonical": "ncbiprotein", "homepage": "https://www.ncbi.nlm.nih.gov/projects/RefSeq/", "keywords": [ "computational biology", "dna", "genetics", "life science", "protein", "rna" ], "mappings": { "biocontext": "RefSeq", "edam": "1098", "fairsharing": "FAIRsharing.4jg0qw", "go": "RefSeq", "hl7": "2.16.840.1.113883.6.280", "integbio": "nbdc00187", "miriam": "refseq", "n2t": "refseq", "prefixcommons": "refseq", "re3data": "r3d100010285", "uniprot": "DB-0117" }, "name": "Reference Sequence Collection", "pattern": "^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\\d+)|(NZ_[A-Z]{2,4}\\d+))(\\.\\d+)?$", "preferred_prefix": "refseq", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/refseq:$1" } ], "publications": [ { "doi": "10.1093/nar/gkae1038", "pubmed": "39526381", "title": "NCBI RefSeq: reference sequence standards through 25 years of curation and annotation", "year": 2024 }, { "doi": "10.1093/nar/gkv1189", "pmc": "PMC4702849", "pubmed": "26553804", "title": "Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation", "year": 2015 }, { "doi": "10.1093/nar/gkl842", "pmc": "PMC1716718", "pubmed": "17130148", "title": "NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins", "year": 2006 } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/545" ], "synonyms": [ "REFSEQ_PROT" ], "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1" }, "reo": { "comment": "From James O.: It was an ontology for \"reagents\" developed by @Matthew Brush. Since OBI was interested in reagents, Matt developed it in coordination with OBI and had plans to submit it to OBO. I believe that REO was once included in Ontobee, and OBI even started using some REO terms. But REO was never submitted to OBO. I believe it was abandoned.", "contact": { "email": "matt@tislab.org", "github": "mbrush", "name": "Matthew Brush", "orcid": "0000-0002-1048-5019" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs.", "download_owl": "https://github.com/tis-lab/reagent-ontology/raw/master/reo/ontology_files/reo_pre-merged_or_reasoned_files/reo_reasoned_9-6-12.owl", "example": "0000079", "homepage": "https://github.com/tis-lab/reagent-ontology", "keywords": [ "ontology" ], "mappings": { "ontobee": "REO" }, "name": "Reagent Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "reo", "references": [ "https://github.com/obi-ontology/obi/issues/1015", "https://code.google.com/archive/p/reagent-ontology/", "https://github.com/obi-ontology/obi/issues/1135" ], "repository": "https://github.com/tis-lab/reagent-ontology", "uri_format": "http://purl.obolibrary.org/obo/REO_$11" }, "repeatsdb.protein": { "description": "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database.", "example": "P29894", "homepage": "https://repeatsdb.org/", "mappings": { "miriam": "repeatsdb.protein" }, "name": "RepeatsDB Protein", "pattern": "^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$", "preferred_prefix": "repeatsdb.protein", "provides": "uniprot", "uri_format": "https://repeatsdb.org/protein/$1" }, "repeatsdb.structure": { "description": "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database.", "example": "2gc4E", "homepage": "https://repeatsdb.org/", "mappings": { "miriam": "repeatsdb.structure" }, "name": "RepeatsDB Structure", "pattern": "^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$", "preferred_prefix": "repeatsdb.structure", "uri_format": "https://repeatsdb.org/structure/$1" }, "repec": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Peruvian Clinical Trials Registry - REPEC is a non-profit online information system developed in 2007 by INS. It is a publicly accessible prospective registry aimed at providing information about clinical trials underway in Peru. REPEC also includes Registries for Trial Sites, Institutional Research Ethics Committees, Sponsors and Contract Research Organizations. REPEC contains records of clinical trials since 1995. Since December 14, 2012, the Peruvian National Institute of Health, by means of the General Office for Research and Technological Transfer (OGITT), has started a process to improve REPEC and to join the WHO International Clinical Trials Registry Platform (ICTRP) and to be acknowledged as a Primary Registry. More information about primary registries is available in ICRTP at http://apps.who.int/trialsearch/. (from website)", "example": "046-19", "homepage": "https://ensayosclinicos-repec.ins.gob.pe/en/", "logo": "https://ensayosclinicos-repec.ins.gob.pe/images/plantilla/img_logo_principal_repec_en.png", "name": "Peruvian Clinical Trial Registry", "pattern": "^\\d+-\\d+(-[A-Z])?$", "preferred_prefix": "repec", "providers": [ { "code": "who", "description": "WHO Clinical Trials Search", "homepage": "https://trialsearch.who.int", "name": "WHO Clinical Trials Search", "uri_format": "https://trialsearch.who.int/Trial2.aspx?TrialID=PER-$1" } ], "uri_format": "https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC=$1" }, "reproduceme": { "contact": { "email": "sheeba.samuel@uni-jena.de", "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": "http://aber-owl.net/media/ontologies/REPRODUCE-ME/7/reproduce-me.owl", "example": "MicrobeamManipulation", "homepage": "https://w3id.org/reproduceme/research", "keywords": [ "nfdi4chem", "ontology" ], "mappings": { "aberowl": "REPRODUCE-ME", "bioportal": "REPRODUCE-ME", "ols": "reproduceme", "tib": "repr" }, "name": "REPRODUCE-ME Ontology", "preferred_prefix": "reproduceme", "uri_format": "https://w3id.org/reproduceme#$1", "version": "1.1" }, "researchgate.profile": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for a person, used by ResearchGate profiles", "example": "Rita-Heuser", "homepage": "https://www.researchgate.net", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P2038" }, "name": "ResearchGate profile ID", "pattern": "^[0-9A-Za-z_-]+$", "preferred_prefix": "researchgate.profile", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://www.researchgate.net/profile/$1" }, "resid": { "contact": { "email": "john.garavelli@ebi.ac.uk", "name": "John Garavelli", "orcid": "0000-0002-4131-735X" }, "deprecated": true, "description": "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.", "example": "AA0001", "homepage": "https://proteininformationresource.org/resid/", "keywords": [ "obo", "ontology", "protein", "small molecule", "structure" ], "mappings": { "biocontext": "RESID", "edam": "2619", "go": "RESID", "miriam": "resid", "n2t": "resid", "obofoundry": "resid", "prefixcommons": "resid", "wikidata.entity": "Q114677910" }, "name": "Protein covalent bond", "pattern": "^AA\\d{4}$", "preferred_prefix": "RESID", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/resid:$1" } ], "publications": [ { "doi": "10.1002/pmic.200300764", "pubmed": "15174124", "title": "Annotation of post-translational modifications in the Swiss-Prot knowledge base", "year": 2004 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/RESID_$1", "uri_format": "https://proteininformationresource.org/cgi-bin/resid?id=$1" }, "reto": { "contact": { "email": "vladimir.n.mironov@gmail.com", "name": "Vladimir Mironov" }, "description": "Regulation of Transcription", "download_obo": "https://www.bio.ntnu.no/ontology/ReTO/reto.obo", "download_owl": "https://www.bio.ntnu.no/ontology/ReTO/reto.owl", "download_rdf": "http://www.bio.ntnu.no/ontology/ReTO/reto.rdf", "homepage": "http://www.semantic-systems-biology.org/apo", "keywords": [ "life science", "ontology", "regulation of gene expression", "transcript", "transcriptomics" ], "mappings": { "aberowl": "RETO", "bioportal": "RETO", "fairsharing": "FAIRsharing.4qyf0f", "ols": "reto" }, "name": "Regulation of Transcription Ontology", "no_own_terms": true, "preferred_prefix": "reto" }, "rex": { "contact": { "email": "amalik@ebi.ac.uk", "github": "amalik01", "name": "Adnan Malik", "orcid": "0000-0001-8123-5351" }, "deprecated": true, "description": "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time.", "download_owl": "http://purl.obolibrary.org/obo/rex.owl", "example": "0000512", "homepage": "https://www.ebi.ac.uk/chebi/", "keywords": [ "biochemistry", "chemistry", "enzymatic reaction", "life science", "nfdi4cat", "nfdi4chem", "obo", "ontology", "reaction data" ], "mappings": { "aberowl": "REX", "biocontext": "REX", "bioportal": "REX", "fairsharing": "FAIRsharing.g0a7s0", "obofoundry": "rex", "ols": "rex", "ontobee": "REX", "prefixcommons": "rex", "tib": "rex" }, "name": "Physico-chemical process", "pattern": "^\\d{7}$", "preferred_prefix": "REX", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/rex:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/REX_$1", "uri_format": "http://purl.obolibrary.org/obo/REX_$1" }, "rexo": { "contact": { "email": "kuiper@bio.ntnu.no", "github": "makuintnu", "name": "Martin Kuiper", "orcid": "0000-0002-1171-9876" }, "description": "Regulation of Gene Expression", "download_obo": "https://www.bio.ntnu.no/ontology/ReXO/rexo.obo", "download_owl": "https://www.bio.ntnu.no/ontology/ReXO/rexo.owl", "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", "orthologous", "regulation of gene expression" ], "mappings": { "aberowl": "REXO", "bioportal": "REXO", "fairsharing": "FAIRsharing.recas1", "ols": "rexo" }, "name": "Regulation of Gene Expression Ontology", "no_own_terms": true, "preferred_prefix": "rexo", "publications": [ { "doi": "10.1186/s12859-014-0386-y", "pmc": "PMC4279962", "pubmed": "25490885", "title": "Finding gene regulatory network candidates using the gene expression knowledge base", "year": 2014 } ] }, "rfam": { "contact": { "email": "apetrov@ebi.ac.uk", "github": "AntonPetrov", "name": "Anton I Petrov", "orcid": "0000-0001-7279-2682" }, "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.org/", "keywords": [ "genetics" ], "mappings": { "biocontext": "RFAM", "edam": "2356", "fairsharing": "FAIRsharing.fex4c8", "go": "Rfam", "integbio": "nbdc00654", "miriam": "rfam", "n2t": "rfam", "ncbi": "RFAM" }, "name": "Rfam database of RNA families", "pattern": "^RF\\d{5}$", "preferred_prefix": "rfam", "publications": [ { "doi": "10.1093/nar/gkae1023", "pubmed": "39526405", "title": "Rfam 15: RNA families database in 2025", "year": 2024 }, { "doi": "10.1093/nar/gkx1038", "pmc": "PMC5753348", "pubmed": "29112718", "title": "Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families", "year": 2018 }, { "doi": "10.1093/nar/gku1063", "pmc": "PMC4383904", "pubmed": "25392425", "title": "Rfam 12.0: updates to the RNA families database", "year": 2014 } ], "twitter": "RfamDB", "uri_format": "https://rfam.org/family/$1" }, "rfc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Legacy site for IETF RFC proposals", "example": "5013", "homepage": "https://www.ietf.org/", "mappings": { "n2t": "rfc" }, "name": "Internet Standard -- IETF Request for Comments", "pattern": "^\\d+$", "preferred_prefix": "rfc", "uri_format": "https://tools.ietf.org/rfc/rfc$1" }, "rgd": { "contact": { "email": "jrsmith@mcw.edu", "name": "Jennifer R Smith", "orcid": "0000-0002-6443-9376" }, "description": "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes.", "example": "7499841", "homepage": "http://rgd.mcw.edu/", "keywords": [ "behavior", "biomedical science", "comparative genomics", "congenic rat", "data analysis service", "disease", "dna", "est", "faseb list", "function", "gene", "genetic", "genome", "genomic", "genomics", "genotype", "gold standard", "human", "immunology", "inbred rat strain", "knockout", "map", "marker", "model organism", "molecular medicine", "mouse", "mutant", "ontology", "organism supplier", "pathway", "phenomics", "phenotype", "physiology", "proteomics", "qtl", "quantitative genetics", "rat", "recombinant inbred rat", "sequence", "strain", "translational medicine", "variation", "veterinary medicine" ], "license": "CC-BY-4.0", "logo": "https://rgd.mcw.edu/rgdweb//common/images/rgd_logo.jpg", "mappings": { "aberowl": "RGD", "biocontext": "RGD", "bioportal": "RGD", "cellosaurus": "RGD", "edam": "2620", "fairsharing": "FAIRsharing.pfg82t", "go": "RGD", "integbio": "nbdc00188", "miriam": "rgd", "n2t": "rgd", "ncbi": "RGD", "pathguide": "267", "prefixcommons": "rgd", "re3data": "r3d100010417", "rrid": "RGD", "togoid": "Rgd", "uniprot": "DB-0091", "wikidata": "P3853" }, "name": "Rat Genome Database", "pattern": "^\\d{4,}$", "preferred_prefix": "rgd", "providers": [ { "code": "agr", "description": "RGD through the Alliance of Genome Resources", "homepage": "https://www.alliancegenome.org", "name": "RGD through the Alliance of Genome Resources", "uri_format": "https://www.alliancegenome.org/gene/RGD:$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/rgd:$1" } ], "publications": [ { "doi": "10.1093/database/baae132", "pmc": "PMC11753291", "pubmed": "39841812", "title": "Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database" }, { "doi": "10.1093/genetics/iyac005", "pmc": "PMC8982048", "pubmed": "35380657", "title": "MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses", "year": 2022 }, { "doi": "10.1007/s00335-021-09932-x", "pmc": "PMC8570235", "pubmed": "34741192", "title": "The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research", "year": 2021 }, { "doi": "10.1093/nar/gkz1041", "pmc": "PMC7145519", "pubmed": "31713623", "title": "The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform", "year": 2020 }, { "doi": "10.1007/978-1-4939-9581-3_3", "pubmed": "31228152", "title": "Rat Genome Databases, Repositories, and Tools", "year": 2019 }, { "doi": "10.1007/978-1-4939-9581-3_2", "pubmed": "31228151", "title": "Rat Genome Assemblies, Annotation, and Variant Repository", "year": 2019 }, { "doi": "10.1007/978-1-4939-9581-3_1", "pubmed": "31228150", "title": "The Rat: A Model Used in Biomedical Research", "year": 2019 }, { "doi": "10.1093/database/baz037", "pmc": "PMC6444380", "pubmed": "30938777", "title": "Quantitative phenotype analysis to identify, validate and compare rat disease models", "year": 2019 }, { "doi": "10.1093/database/baz014", "pmc": "PMC6369425", "pubmed": "30753478", "title": "Integrated curation and data mining for disease and phenotype models at the Rat Genome Database", "year": 2019 }, { "doi": "10.1007/978-1-4939-7737-6_8", "pmc": "PMC6487669", "pubmed": "29761460", "title": "A Primer for the Rat Genome Database (RGD)", "year": 2018 }, { "doi": "10.1093/ilar/ilw041", "pmc": "PMC6057551", "pubmed": "28838068", "title": "Rat Genome and Model Resources", "year": 2017 }, { "doi": "10.1242/dmm.026021", "pmc": "PMC5087824", "pubmed": "27736745", "title": "Exploring human disease using the Rat Genome Database", "year": 2016 }, { "doi": "10.1016/j.csbj.2015.11.006", "pmc": "PMC4700298", "pubmed": "27602200", "title": "Disease, Models, Variants and Altered Pathways-Journeying RGD Through the Magnifying Glass", "year": 2015 }, { "doi": "10.1152/physiolgenomics.00046.2016", "pmc": "PMC5005459", "pubmed": "27287925", "title": "Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database", "year": 2016 }, { "doi": "10.1093/database/baw034", "pmc": "PMC4805243", "pubmed": "27009807", "title": "The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database", "year": 2016 }, { "doi": "10.1093/nar/gku1026", "pmc": "PMC4383884", "pubmed": "25355511", "title": "The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease", "year": 2014 }, { "doi": "10.1186/s40246-014-0017-8", "pmc": "PMC4191248", "pubmed": "25265995", "title": "Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease", "year": 2014 }, { "doi": "10.1093/database/bat015", "pmc": "PMC3630803", "pubmed": "23603846", "title": "PhenoMiner: quantitative phenotype curation at the rat genome database", "year": 2013 }, { "pubmed": "23434633" }, { "doi": "10.1371/journal.pcbi.1000582", "pmc": "PMC2775909", "pubmed": "19956751", "title": "The rat genome database curators: who, what, where, why", "year": 2009 }, { "pubmed": "18996890" }, { "doi": "10.1093/nar/gkl988", "pmc": "PMC1761441", "pubmed": "17151068", "title": "The Rat Genome Database, update 2007--easing the path from disease to data and back again", "year": 2006 }, { "pubmed": "10400928", "title": "A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat", "year": 1999 } ], "synonyms": [ "RGD" ], "twitter": "ratgenome", "uri_format": "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1" }, "rgd.qtl": { "description": "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes.", "example": "1354581", "homepage": "http://rgd.mcw.edu/", "mappings": { "biocontext": "RGD.QTL", "miriam": "rgd.qtl", "n2t": "rgd.qtl" }, "name": "Rat Genome Database qTL", "pattern": "^\\d+$", "preferred_prefix": "rgd.qtl", "twitter": "ratgenome", "uri_format": "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1" }, "rgd.strain": { "description": "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology.", "example": "5688061", "homepage": "http://rgd.mcw.edu/", "mappings": { "biocontext": "RGD.STRAIN", "miriam": "rgd.strain", "n2t": "rgd.strain" }, "name": "Rat Genome Database strain", "pattern": "^\\d+$", "preferred_prefix": "rgd.strain", "twitter": "ratgenome", "uri_format": "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1" }, "rhea": { "contact": { "email": "anne.morgat@sib.swiss", "name": "Anne Morgat", "orcid": "0000-0002-1216-2969" }, "description": " Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants.\n\nRhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB.", "example": "12345", "homepage": "https://www.rhea-db.org/", "keywords": [ "biochemistry", "life science", "reaction", "small molecule" ], "license": "CC-BY-4.0", "logo": "https://www.rhea-db.org/style/images/rhea_logo.png", "mappings": { "biocontext": "RHEA", "edam": "2644", "fairsharing": "FAIRsharing.pn1sr5", "go": "RHEA", "integbio": "nbdc02083", "miriam": "rhea", "n2t": "rhea", "pathguide": "310", "prefixcommons": "rhea", "re3data": "r3d100010891", "togoid": "Rhea", "wikidata.entity": "Q24265951" }, "name": "Rhea reaction", "pattern": "^\\d{5}$", "preferred_prefix": "rhea", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/rhea:$1" } ], "publications": [ { "doi": "10.1093/nar/gkab1016", "pmc": "PMC8728268", "pubmed": "34755880", "title": "Rhea, the reaction knowledgebase in 2022", "year": 2022 }, { "doi": "10.1093/bioinformatics/btz817", "pmc": "PMC7162351", "pubmed": "31688925", "title": "Enzyme annotation in UniProtKB using Rhea", "year": 2020 }, { "doi": "10.1093/nar/gky876", "pmc": "PMC6324061", "pubmed": "30272209", "title": "Updates in Rhea: SPARQLing biochemical reaction data", "year": 2019 }, { "doi": "10.1093/nar/gkw990", "pmc": "PMC5210663", "pubmed": "27789701", "title": "Updates in Rhea - an expert curated resource of biochemical reactions", "year": 2016 }, { "doi": "10.1093/nar/gku961", "pmc": "PMC4384025", "pubmed": "25332395", "title": "Updates in Rhea--a manually curated resource of biochemical reactions", "year": 2014 }, { "doi": "10.1093/nar/gkr1126", "pmc": "PMC3245052", "pubmed": "22135291", "title": "Rhea--a manually curated resource of biochemical reactions", "year": 2011 } ], "synonyms": [ "RHEA" ], "twitter": "rhea_db", "uri_format": "https://www.rhea-db.org/rhea/$1" }, "ribocentre": { "contact": { "email": "huanglin36@mail.sysu.edu.cn", "name": "Lin Huang", "orcid": "0000-0002-2121-365X" }, "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "Ribocentre is designed to contain comprehensive information of all natural ribozymes.", "example": "hammer", "github_request_issue": 611, "homepage": "https://www.ribocentre.org/", "name": "Ribocentre", "pattern": "^[a-zA-Z0-9-]+$", "preferred_prefix": "ribocentre", "publications": [ { "doi": "10.1093/nar/gkac840", "pmc": "PMC9825448", "pubmed": "36177882", "title": "Ribocentre: a database of ribozymes", "year": 2023 } ], "repository": "https://github.com/ribocentre/ribocentre.github.io", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "ribocenter" ], "uri_format": "https://www.ribocentre.org/docs/$1" }, "ribocirc": { "contact": { "email": "xiezhi@gmail.com", "name": "Zhi Xie", "orcid": "0000-0002-7736-5548" }, "contributor": { "email": "ji.kang@northeastern.edu", "github": "kanghosaeyo", "name": "Kangho Ji", "orcid": "0009-0009-3402-8013" }, "description": "Identifiers represent computationally predicted and experimentally verified translatable circular RNAs (circRNAs) across six model species (human, mouse, rat, worm, fly, and zebrafish), including ribosome-associated circRNAs and their encoded peptides with systematic annotation of sequence, structure, and function.", "example": "hsa_ribocircSCD_001", "example_extras": [ "cel_ribocircF54A3.3_001", "dme_ribocirccdi_001", "dre_ribocircim:7151449_001", "mmu_ribocircCoil_001", "rno_ribocircVps13b_003" ], "github_request_issue": 1798, "homepage": "http://www.ribocirc.com", "keywords": [ "circrna", "peptides", "ribosome profiling", "translation" ], "name": "riboCIRC", "pattern": "^(hsa|mmu|rno|cel|dme|dre)_ribocirc[A-Za-z0-9.:]+_\\d{3}$", "preferred_prefix": "ribocirc", "publications": [ { "doi": "10.1093/nar/gkaf1022", "pubmed": "41118507", "title": "riboCIRC v2.0: an expanded resource for translatable CircRNAs", "year": 2025 }, { "doi": "10.1186/s13059-021-02300-7", "pubmed": "33685493", "title": "riboCIRC: a comprehensive database of translatable circRNAs", "year": 2021 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "http://www.ribocirc.com/rna_detail.php?circ_id=$1" }, "ricecyc": { "description": "RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project", "example": "PWY-1042", "homepage": "http://www.gramene.org/pathway/ricecyc.html", "keywords": [ "gene", "pathway" ], "mappings": { "pathguide": "227", "prefixcommons": "ricecyc" }, "name": "Rice Metabolic Pathways", "preferred_prefix": "ricecyc", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/ricecyc:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object=$1" }, "ricegap": { "contact": { "email": "Robin.Buell@uga.edu", "name": "C. Robin Buell", "orcid": "0000-0002-6727-4677" }, "description": "The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines.", "example": "LOC_Os02g13300", "homepage": "https://rice.uga.edu", "keywords": [ "dna", "genome" ], "mappings": { "biocontext": "RICEGAP", "miriam": "ricegap", "n2t": "ricegap", "prefixcommons": "rgap" }, "name": "Rice Genome Annotation Project", "pattern": "^LOC\\_Os\\d{1,2}g\\d{5}$", "preferred_prefix": "ricegap", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/rgap:$1" } ], "publications": [ { "doi": "10.1093/nar/gkae1061", "pubmed": "39558187", "title": "The rice genome annotation project: an updated database for mining the rice genome", "year": 2024 }, { "doi": "10.1093/nar/gkl976", "pmc": "PMC1751532", "pubmed": "17145706", "title": "The TIGR Rice Genome Annotation Resource: improvements and new features", "year": 2006 } ], "synonyms": [ "rgap" ], "uri_format": "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1" }, "ricenetdb.compound": { "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", "example": "OSC1416", "homepage": "http://bis.zju.edu.cn/ricenetdb", "mappings": { "biocontext": "RICENETDB.COMPOUND", "miriam": "ricenetdb.compound", "n2t": "ricenetdb.compound" }, "name": "RiceNetDB Compound", "pattern": "^OSC\\d{4}$", "preferred_prefix": "ricenetdb.compound", "uri_format": "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1" }, "ricenetdb.gene": { "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", "example": "LOC_Os01g49190.1", "homepage": "http://bis.zju.edu.cn/ricenetdb/", "mappings": { "biocontext": "RICENETDB.GENE", "miriam": "ricenetdb.gene", "n2t": "ricenetdb.gene" }, "name": "RiceNetDB Gene", "pattern": "^LOC\\_Os\\d{1,2}g\\d{5}\\.\\d$", "preferred_prefix": "ricenetdb.gene", "uri_format": "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1" }, "ricenetdb.mirna": { "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", "example": "osa-miR446", "homepage": "http://bis.zju.edu.cn/ricenetdb", "mappings": { "biocontext": "RICENETDB.MIRNA", "miriam": "ricenetdb.mirna", "n2t": "ricenetdb.mirna" }, "name": "RiceNetDB miRNA", "pattern": "^osa-miR\\d{3,5}[a-z]{0,1}$", "preferred_prefix": "ricenetdb.mirna", "uri_format": "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1" }, "ricenetdb.protein": { "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", "example": "LOC_Os01g49190", "homepage": "http://bis.zju.edu.cn/ricenetdb/", "mappings": { "biocontext": "RICENETDB.PROTEIN", "miriam": "ricenetdb.protein", "n2t": "ricenetdb.protein" }, "name": "RiceNetDB Protein", "pattern": "^LOC\\_Os\\d{1,2}g\\d{5}$", "preferred_prefix": "ricenetdb.protein", "uri_format": "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1" }, "ricenetdb.reaction": { "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", "example": "OSR0818", "homepage": "http://bis.zju.edu.cn/ricenetdb", "mappings": { "biocontext": "RICENETDB.REACTION", "miriam": "ricenetdb.reaction", "n2t": "ricenetdb.reaction" }, "name": "RiceNetDB Reaction", "pattern": "^OSR\\d{4}$", "preferred_prefix": "ricenetdb.reaction", "uri_format": "http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1" }, "rism": { "description": "RISM Online is a new service that will publish the bibliographic and authority data from the catalogue of the Répertoire International des Sources Musicales project.", "example": "people/11035", "homepage": "https://rism.digital/", "mappings": { "miriam": "rism" }, "name": "RISM Online", "pattern": "^[a-z]+/[0-9]+$", "preferred_prefix": "rism", "uri_format": "https://rism.online/$1" }, "rna_sstrand": { "description": "RNA STRAND contains known RNA secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known RNA secondary structures, and to provide the scientific community with simple yet powerful ways of analysing, searching and updating the proposed database.", "example": "CRW_00469", "homepage": "http://www.rnasoft.ca/sstrand", "keywords": [ "rna", "structure" ], "mappings": { "prefixcommons": "rna_sstrand" }, "name": "RNA SSTRAND", "preferred_prefix": "rna_sstrand", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/rna_sstrand:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID=$1" }, "rnacentral": { "contact": { "email": "bsweeney@ebi.ac.uk", "github": "blakesweeney", "name": "Blake A Sweeney", "orcid": "0000-0002-6497-2883" }, "description": "RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases.", "example": "URS0000759CF4", "homepage": "https://rnacentral.org/", "keywords": [ "bioinformatics", "biology" ], "mappings": { "biocontext": "RNACENTRAL", "edam": "3856", "fairsharing": "FAIRsharing.KcCjL7", "go": "RNAcentral", "integbio": "nbdc02671", "miriam": "rnacentral", "n2t": "rnacentral", "ncbi": "RNAcentral", "wikidata": "P8697" }, "name": "RNACentral", "pattern": "^URS[0-9A-F]{10}(\\_\\d+)?$", "preferred_prefix": "rnacentral", "publications": [ { "doi": "10.1093/nar/gky1034", "pmc": "PMC6324050", "pubmed": "30395267", "title": "RNAcentral: a hub of information for non-coding RNA sequences", "year": 2019 }, { "doi": "10.1093/nar/gkw1008", "pmc": "PMC5210518", "pubmed": "27794554", "title": "RNAcentral: a comprehensive database of non-coding RNA sequences", "year": 2016 } ], "repository": "https://github.com/RNAcentral/", "synonyms": [ "LNCRNADB" ], "twitter": "RNAcentral", "uri_format": "https://rnacentral.org/rna/$1" }, "rnajunction": { "contact": { "email": "ygyingli@ncsu.edu", "name": "Yaroslava G Yingling", "orcid": "0000-0002-8557-9992" }, "description": "RNAJunction is a database of RNA junctions and kissing loop structures. It contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions. It allows searching by PDB code, structural classification, sequence, keyword or inter-helix angles. RNAJunction is designed to aid analysis of RNA structures as well as design of novel RNA structures on a nanoscale. ", "example": "8668", "homepage": "http://rnajunction.abcc.ncifcrf.gov", "keywords": [ "rna", "structural biology", "structure" ], "mappings": { "fairsharing": "FAIRsharing.zzgvrv", "prefixcommons": "rnajunction" }, "name": "Database of RNA Junctions and Kissing loop Structures", "preferred_prefix": "rnajunction", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/rnajunction:$1" } ], "publications": [ { "doi": "10.1093/nar/gkm842", "pmc": "PMC2238914", "pubmed": "17947325", "title": "RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign", "year": 2007 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://rnajunction.ncifcrf.gov/JunctionPage.php?jid=$1" }, "rnaloops": { "contact": { "email": "Maciej.Antczak@cs.put.poznan.pl", "github": "mantczak", "name": "Maciej Antczak", "orcid": "0000-0002-5320-2023" }, "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "Rnaloops stores the information about n-way junctions (where n≥3) found in experimentally determined rna 3d structures deposited in the protein data bank.", "example": "91792", "github_request_issue": 601, "homepage": "https://rnaloops.cs.put.poznan.pl", "keywords": [ "rna", "structural bioinformatcs" ], "name": "RNAloops", "pattern": "^\\d+$", "preferred_prefix": "rnaloops", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://rnaloops.cs.put.poznan.pl/search/details/$1" }, "rnamod": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A comprehensive listing of post-transcriptionally modified nucleosides from RNA -", "example": "051", "homepage": "http://rna.rega.kuleuven.be/rnamods/", "keywords": [ "post-transcriptional modification", "rna", "structural bioinformatcs" ], "name": "The RNA Modification Database", "pattern": "^\\d{3}$", "preferred_prefix": "rnamod", "uri_format": "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1" }, "rnamods": { "description": "The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA.", "example": "101", "homepage": "http://rna.rega.kuleuven.be/rnamods/", "keywords": [ "rna", "structure" ], "mappings": { "biocontext": "RNAMODS", "go": "RNAmods", "miriam": "rnamods", "n2t": "rnamods", "prefixcommons": "rnamods" }, "name": "RNA Modification Database", "pattern": "^\\d{3}$", "preferred_prefix": "rnamods", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/rnamods:$1" } ], "uri_format": "http://rna.rega.kuleuven.be/rnamods/rnashow.pl?$1" }, "rnao": { "contact": { "email": "BatchelorC@rsc.org", "name": "Colin Batchelor", "orcid": "0000-0001-5985-7429" }, "deprecated": true, "description": "Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures.", "download_obo": "http://purl.obolibrary.org/obo/rnao.obo", "download_owl": "http://purl.obolibrary.org/obo/rnao.owl", "example": "0000128", "homepage": "https://github.com/bgsu-rna/rnao", "keywords": [ "biochemistry", "life science", "obo", "ontology", "ribonucleic acid", "rna secondary structure", "sequence motif", "structure" ], "license": "CC0-1.0", "mappings": { "aberowl": "RNAO", "biocontext": "RNAO", "bioportal": "RNAO", "fairsharing": "FAIRsharing.kqt2h2", "obofoundry": "rnao", "ols": "rnao", "ontobee": "RNAO", "prefixcommons": "rnao" }, "name": "RNA ontology", "pattern": "^\\d{7}$", "preferred_prefix": "RNAO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/rnao:$1" } ], "publications": [ { "doi": "10.1261/rna.2343206", "pmc": "PMC1421088", "pubmed": "16484377", "title": "The RNA Ontology Consortium: an open invitation to the RNA community", "year": 2006 }, { "doi": "10.3233/ao-2011-0082", "title": "The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data", "year": 2011 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/RNAO_$1", "repository": "https://github.com/BGSU-RNA/rnao", "uri_format": "http://purl.obolibrary.org/obo/RNAO_$1", "version": "2019-04-15" }, "rnavdb": { "description": "The RNA Virus Database is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments and contains translated genome sequences for all species.", "example": "164750", "homepage": "http://virus.zoo.ox.ac.uk/rnavirusdb/", "keywords": [ "genome", "rna" ], "mappings": { "prefixcommons": "rvd" }, "name": "RNA Virus Database", "preferred_prefix": "rnavdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/rvd:$1" } ], "uri_format": "http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id=$1" }, "ro": { "appears_in": [ "agro", "aism", "cdno", "cl", "clao", "clyh", "colao", "cteno", "ecao", "ecocore", "ecto", "envo", "foodon", "fovt", "gallont", "genepio", "go", "hso", "lepao", "maxo", "ons", "ontoavida", "pcl", "pco", "plana", "planp", "poro", "proco", "psdo", "pso", "rbo", "uberon", "upa", "xpo", "zp" ], "banana": "RO", "banana_peel": "_", "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies.", "download_json": "http://purl.obolibrary.org/obo/ro.json", "download_obo": "http://purl.obolibrary.org/obo/ro.obo", "download_owl": "http://purl.obolibrary.org/obo/ro.owl", "example": "0002533", "example_extras": [ "HOM0000022" ], "homepage": "https://oborel.github.io/", "keywords": [ "dataplant", "foundational ontologies", "life sciences, biology", "nfdi4chem", "obo", "ontology", "relations", "subject agnostic" ], "license": "CC0-1.0", "mappings": { "aberowl": "RO", "agroportal": "RO", "biocontext": "RO", "biolink": "RO", "bioportal": "OBOREL", "fairsharing": "FAIRsharing.9w8ea0", "go": "RO", "miriam": "ro", "n2t": "ro", "obofoundry": "ro", "ols": "ro", "ontobee": "RO", "prefixcommons": "ro", "tib": "ro", "wikidata": "P3590", "wikidata.entity": "Q28729320" }, "name": "Relation Ontology", "namespace_in_lui": true, "pattern": "^(HOM)?\\d{7}$", "preferred_prefix": "RO", "providers": [ { "code": "", "description": "OBO Relation Ontology through OntoBee", "homepage": "http://obofoundry.org/ontology/ro.html", "name": "OBO Relation Ontology through OntoBee", "uri_format": "http://purl.obolibrary.org/obo/$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/ro:$1" } ], "publications": [ { "doi": "10.1186/2041-1480-5-41", "pmc": "PMC4177597", "pubmed": "25276335", "title": "Structuring research methods and data with the research object model: genomics workflows as a case study", "year": 2014 }, { "doi": "10.1186/gb-2005-6-5-r46", "pmc": "PMC1175958", "pubmed": "15892874", "title": "Relations in biomedical ontologies", "year": 2005 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/RO_$1", "repository": "https://github.com/oborel/obo-relations", "synonyms": [ "RO_proposed_relation", "obo_rel", "oborel" ], "uri_format": "http://purl.obolibrary.org/obo/RO_$1", "version": "2025-12-17" }, "roleo": { "banana": "RoleO", "banana_peel": "_", "comment": "This resource doesn't exist on the web anymore", "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "deprecated": true, "description": "The Role Ontology (RoleO) is a ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles.", "download_owl": "http://aber-owl.net/media/ontologies/ROLEO/1/roleo.owl", "example": "0000002", "homepage": "http://sourceforge.net/projects/roleo", "keywords": [ "obo", "ontology" ], "mappings": { "aberowl": "ROLEO", "bioportal": "ROLEO", "prefixcommons": "roleo" }, "name": "Role Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "RoleO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/roleo:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://purl.obolibrary.org/obo/RoleO_$1" }, "ror": { "contact": { "email": "maria.gould@ucop.edu", "github": "mariagould", "name": "Maria Gould", "orcid": "0000-0002-2916-3423" }, "description": "ROR (Research Organization Registry) is a global, community-led registry\nof open persistent identifiers for research organizations. ROR is jointly\noperated by California Digital Library, Crossref, and Datacite.", "download_owl": "https://w3id.org/rorio/rorio.owl", "example": "03yrm5c26", "homepage": "https://ror.org", "keywords": [ "data management", "ontology" ], "license": "CC0-1.0", "logo": "https://ror.org/img/ror-logo.svg", "mappings": { "aberowl": "ROR", "bartoc": "20474", "bioportal": "ROR", "fairsharing": "FAIRsharing.1jKfji", "miriam": "ror", "n2t": "ror", "ols": "ror", "wikidata.entity": "Q110235640" }, "mastodon": "ResearchOrgs@mastodon.social", "name": "Research Organization Registry", "pattern": "^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$", "preferred_prefix": "ror", "repository": "https://github.com/ror-community", "twitter": "ResearchOrgs", "uri_format": "https://ror.org/$1" }, "rosetta": { "description": "The ROSETTA ontology of industrial robotics devices and robotic skills.", "example": "canBePerformedBy", "homepage": "https://github.com/jacekmalec/Rosetta_ontology", "keywords": [ "engineering", "nfdi4ing" ], "mappings": { "tib": "rosetta" }, "name": "The ROSETTA ontology of industrial robotics devices and robotic skills.", "preferred_prefix": "rosetta", "repository": "https://github.com/jacekmalec/Rosetta_ontology", "uri_format": "http://kif.cs.lth.se/ontologies/rosetta.owl#$1" }, "rouge": { "contact": { "email": "ohara@kazusa.or.jp", "name": "Osamu Ohara", "orcid": "0000-0002-3328-9571" }, "description": "The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.", "example": "mKIAA4200", "homepage": "http://www.kazusa.or.jp/rouge/", "keywords": [ "dna", "life science", "protein" ], "mappings": { "biocontext": "ROUGE", "fairsharing": "FAIRsharing.vdbagq", "integbio": "nbdc00672", "miriam": "rouge", "n2t": "rouge", "prefixcommons": "rouge", "uniprot": "DB-0092" }, "name": "Rodent Unidentified Gene-Encoded Large Proteins", "pattern": "^m\\w+$", "preferred_prefix": "rouge", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/rouge:$1" } ], "publications": [ { "doi": "10.1093/nar/gkh035", "pmc": "PMC308769", "pubmed": "14681467", "title": "HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE", "year": 2004 } ], "uri_format": "https://www.kazusa.or.jp/rouge/gfpage/$1" }, "rpcec": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Cuban Public Registry of Clinical Trials (RPCEC) is a website with a database of clinical trials, with national coverage. It was established in 2007 under the leadership of the National Coordinating Center of Clinical Trials (CENCEC) and with INFOMED collaboration. (from homepage)", "example": "RPCEC00000423", "homepage": "https://rpcec.sld.cu/en/home", "name": "Cuban Registry of Clinical Trials", "pattern": "^RPCEC\\d+$", "preferred_prefix": "rpcec", "uri_format": "https://rpcec.sld.cu/en/trials/$1" }, "rrid": { "banana": "RRID", "contact": { "email": "bandrow@gmail.com", "github": "bandrow", "name": "Anita Bandrowski", "orcid": "0000-0002-5497-0243" }, "contributor_extras": [ { "email": "bandrow@gmail.com", "github": "bandrow", "name": "Anita Bandrowski", "orcid": "0000-0002-5497-0243" } ], "description": "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\nThe initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch.", "example": "AB_262044", "homepage": "https://rrid.site", "keywords": [ "annotation", "biochemistry", "biology", "centrally registered identifier", "chemistry", "community resource", "data retrieval", "fair", "life science", "omics", "resource discovery", "resource metadata" ], "mappings": { "biocontext": "RRID", "fairsharing": "FAIRsharing.ATwSZG", "miriam": "rrid", "n2t": "rrid" }, "name": "Research Resource Identification", "namespace_in_lui": true, "pattern": "^[a-zA-Z]+.+$", "preferred_prefix": "rrid", "publications": [ { "doi": "10.1093/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": "PMC10335836", "pubmed": "27595404", "title": "A proposal for validation of antibodies", "year": 2016 }, { "doi": "10.1016/j.neuron.2016.04.030", "pmc": "PMC5854161", "pubmed": "27151636", "title": "RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods", "year": 2016 }, { "doi": "10.1002/cne.23913", "pmc": "PMC4684178", "pubmed": "26599696", "title": "The Resource Identification Initiative: A Cultural Shift in Publishing", "year": 2016 }, { "doi": "10.12688/f1000research.6555.2", "pmc": "PMC4648211", "pubmed": "26594330", "title": "The Resource Identification Initiative: A cultural shift in publishing", "year": 2015 }, { "doi": "10.7717/peerj.148", "pmc": "PMC3771067", "pubmed": "24032093", "title": "On the reproducibility of science: unique identification of research resources in the biomedical literature", "year": 2013 } ], "uri_format": "https://scicrunch.org/resolver/RRID:$1" }, "rrrc": { "description": "Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models. [from RRID]", "example": "961", "homepage": "http://www.rrrc.us/", "keywords": [ "animal", "biomedical", "catalog", "cell line", "cryopreserved", "database", "disease", "drug", "embryo", "embryonic stem cell", "gamete", "genome", "genotyping", "germplasma", "human", "hybrid", "inbred", "infectious", "molecular", "mutant", "nuclear", "ovarian", "pathogen", "protocol", "rat", "rat model", "reagent", "research", "stem cell", "strain", "tissue" ], "mappings": { "rrid": "RRRC" }, "name": "Rat Resource and Research Center", "pattern": "^\\d+$", "preferred_prefix": "rrrc", "uri_format": "https://www.rrrc.us/Strain/?x=$1" }, "rs": { "contact": { "email": "sjwang@mcw.edu", "github": "shurjenw", "name": "Shur-Jen Wang", "orcid": "0000-0001-5256-8683" }, "description": "Ontology of rat strains", "download_obo": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.obo", "download_owl": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.owl", "example": "0001807", "homepage": "http://rgd.mcw.edu/rgdweb/search/strains.html", "keywords": [ "life science", "mutation", "obo", "ontology", "strain" ], "license": "CC-BY-4.0", "logo": "http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif", "mappings": { "aberowl": "RS", "biocontext": "RS", "bioportal": "RS", "cellosaurus": "RS", "fairsharing": "FAIRsharing.vajn3f", "obofoundry": "rs", "ols": "rs", "ontobee": "RS", "prefixcommons": "rs", "wikidata.entity": "Q81661797" }, "name": "Rat Strain Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "RS", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/rs:$1" } ], "publications": [ { "doi": "10.1186/2041-1480-4-36", "pmc": "PMC4177145", "pubmed": "24267899", "title": "Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD", "year": 2013 }, { "doi": "10.1093/database/bat015", "pmc": "PMC3630803", "pubmed": "23603846", "title": "PhenoMiner: quantitative phenotype curation at the rat genome database", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/RS_$1", "repository": "https://github.com/rat-genome-database/RS-Rat-Strain-Ontology", "twitter": "ratgenome", "uri_format": "http://purl.obolibrary.org/obo/RS_$1", "version": "6.266" }, "rtecs": { "contact": { "email": "vep1@cdc.gov", "name": "Vernon Putz-Anderson", "orcid": "0000-0002-3588-3259" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "RTECS is a compendium of data extracted from the open scientific literature. The data are recorded in the format developed by the RTECS staff and arranged in alphabetical order by prime chemical name. Six types of toxicity data are included in the file: (1) primary irritation; (2) mutagenic effects; (3) reproductive effects; (4) tumorigenic effects; (5) acute toxicity; and (6) other multiple dose toxicity. Specific numeric toxicity values such as LD50, LC50, TDLo, and TCLo are noted as well as species studied and route of administration used. For each citation, the bibliographic source is listed thereby enabling the user to access the actual studies cited. No attempt has been made to evaluate the studies cited in RTECS. The user has the responsibility of making such assessments.", "example": "AB1925000", "homepage": "https://www.cdc.gov/niosh/rtecs/", "mappings": { "cheminf": "000566" }, "name": "Registry of Toxic Effects of Chemical Substances", "pattern": "^AB\\d+$", "preferred_prefix": "rtecs", "proprietary": true, "publications": [ { "doi": "10.1016/s1074-9098%2899%2900058-1", "title": "An overview of the Registry of Toxic Effects of Chemical Substances (RTECS): Critical information on chemical hazards", "year": 1999 } ], "references": [ "https://www.cdc.gov/niosh/docs/97-119/pdfs/97-119.pdf", "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/$1" }, "runbiosimulations": { "description": "runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive.", "example": "5fde96bdc5f1aa9ff0cce18a", "homepage": "https://icahn.mssm.edu/", "mappings": { "miriam": "runbiosimulations" }, "name": "runBioSimulations", "pattern": "^[0-9a-z]{24,24}$", "preferred_prefix": "runbiosimulations", "uri_format": "https://run.biosimulations.org/simulations/$1" }, "rxno": { "contact": { "email": "batchelorc@rsc.org", "github": "batchelorc", "name": "Colin Batchelor", "orcid": "0000-0001-5985-7429" }, "description": "RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization.", "download_obo": "https://github.com/rsc-ontologies/rxno/raw/master/rxno.obo", "download_owl": "http://purl.obolibrary.org/obo/rxno.owl", "example": "0000253", "homepage": "https://github.com/rsc-ontologies/rxno", "keywords": [ "chemistry", "molecular chemistry", "nfdi4cat", "nfdi4chem", "obo", "ontology", "reaction data" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "RXNO", "bartoc": "20712", "biocontext": "RXNO", "bioportal": "RXNO", "fairsharing": "FAIRsharing.w4tncg", "obofoundry": "rxno", "ols": "rxno", "ontobee": "RXNO", "tib": "rxno", "wikidata": "P2106" }, "name": "Name Reaction Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "RXNO", "rdf_uri_format": "http://purl.obolibrary.org/obo/RXNO_$1", "repository": "https://github.com/rsc-ontologies/rxno", "uri_format": "http://purl.obolibrary.org/obo/RXNO_$1", "version": "2021-12-16" }, "rxnorm": { "contact": { "email": "rxnorminfo@nlm.nih.gov", "name": "RxNorm Customer Service" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary.", "example": "221058", "homepage": "https://www.nlm.nih.gov/research/umls/rxnorm/", "keywords": [ "biomedical science", "drug", "drug name", "ontology", "preclinical studies" ], "license": "https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf", "mappings": { "aberowl": "RXNORM", "biocontext": "RXCUI", "biolink": "RXNORM", "bioportal": "RXNORM", "fairsharing": "FAIRsharing.36pf8q", "hl7": "2.16.840.1.113883.6.88", "wikidata": "P3345" }, "name": "RxNorm", "pattern": "^[0-9]{1,7}$", "preferred_prefix": "rxnorm", "providers": [ { "code": "bp", "description": "RxNorm in BioPortal", "homepage": "http://purl.bioontology.org/ontology/RXNORM", "name": "BioPortal", "uri_format": "http://purl.bioontology.org/ontology/RXNORM/$1" } ], "publications": [ { "doi": "10.1136/amiajnl-2011-000116", "pmc": "PMC3128404", "pubmed": "21515544", "title": "Normalized names for clinical drugs: RxNorm at 6 years", "year": 2011 }, { "pmc": "PMC2655997", "pubmed": "18998891", "title": "RxTerms - a drug interface terminology derived from RxNorm", "year": 2008 }, { "doi": "10.1109/mitp.2005.122", "title": "RxNorm: prescription for electronic drug information exchange", "year": 2005 } ], "synonyms": [ "RXCUI" ], "uri_format": "https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1" }, "s_mart_db": { "description": "S/MARt DB collects information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix.", "example": "SM0000020", "homepage": "http://smartdb.bioinf.med.uni-goettingen.de/", "keywords": [ "protein" ], "mappings": { "integbio": "nbdc00674", "pathguide": "47", "prefixcommons": "s_mart_db" }, "name": "The S/MAR transaction DataBase", "preferred_prefix": "s_mart_db", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/s_mart_db:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi?$1" }, "sabiork.compound": { "description": "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information.", "example": "75", "homepage": "http://sabiork.h-its.org/", "mappings": { "miriam": "sabiork.compound", "n2t": "sabiork.compound" }, "name": "SABIO-RK Compound", "pattern": "^\\d+$", "preferred_prefix": "sabiork.compound", "uri_format": "http://sabiork.h-its.org/newSearch?q=$1" }, "sabiork.ec": { "contact": { "email": "ulrike.wittig@h-its.org", "name": "Ulrike Wittig", "orcid": "0000-0002-9077-5664" }, "description": "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data.", "example": "2.7.1.1", "homepage": "http://sabiork.h-its.org/", "keywords": [ "reaction" ], "mappings": { "biocontext": "SABIORK.EC", "miriam": "sabiork.ec", "n2t": "sabiork.ec", "prefixcommons": "sabiork.ec" }, "name": "SABIO-RK EC Record", "pattern": "^((\\d+)|(\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$", "preferred_prefix": "sabiork.ec", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/sabiork.ec:$1" } ], "provides": "ec", "publications": [ { "pubmed": "17822389", "title": "Storing and annotating of kinetic data", "year": 2007 } ], "uri_format": "http://sabiork.h-its.org/newSearch?q=ecnumber:$1" }, "sabiork.kineticrecord": { "contact": { "email": "ulrike.wittig@h-its.org", "name": "Ulrike Wittig", "orcid": "0000-0002-9077-5664" }, "description": "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information.", "example": "5046", "homepage": "http://sabiork.h-its.org/", "keywords": [ "classification", "enzyme", "kinetics" ], "mappings": { "biocontext": "SABIORK.KINETICRECORD", "go": "SABIO-RK", "miriam": "sabiork.kineticrecord", "n2t": "sabiork.kineticrecord", "prefixcommons": "sabiork.kinetic" }, "name": "SABIO Reaction Kinetics", "pattern": "^\\d+$", "preferred_prefix": "sabiork.kineticrecord", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/sabiork.kinetic:$1" } ], "publications": [ { "pubmed": "17822389", "title": "Storing and annotating of kinetic data", "year": 2007 } ], "uri_format": "http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1" }, "sabiork.reaction": { "contact": { "email": "ulrike.wittig@h-its.org", "name": "Ulrike Wittig", "orcid": "0000-0002-9077-5664" }, "description": "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information.", "example": "75", "homepage": "http://sabiork.h-its.org/", "keywords": [ "biochemistry", "kinetics", "life science", "pathway", "reaction" ], "mappings": { "biocontext": "SABIORK.REACTION", "edam": "2309", "fairsharing": "FAIRsharing.cwx04e", "miriam": "sabiork.reaction", "n2t": "sabiork.reaction", "pathguide": "226", "prefixcommons": "sabiork.reaction", "re3data": "r3d100011052", "uniprot": "DB-0177" }, "name": "SABIO-RK Reaction", "pattern": "^\\d+$", "preferred_prefix": "sabiork.reaction", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/sabiork.reaction:$1" } ], "publications": [ { "doi": "10.1093/nar/gkx1065", "pubmed": "29092055" }, { "doi": "10.1093/nar/gkr1046", "pmc": "PMC3245076", "pubmed": "22102587", "title": "SABIO-RK--database for biochemical reaction kinetics", "year": 2011 } ], "synonyms": [ "SABIO-RK" ], "uri_format": "http://sabiork.h-its.org/reacdetails.jsp?reactid=$1" }, "sael": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "name": "Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List", "preferred_prefix": "sael", "publications": [ { "doi": "10.1002/cfg.434", "pmc": "PMC2447422", "pubmed": "18629134", "title": "The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data", "year": 2004 } ] }, "sage.socialsciencethesaurus": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The SAGE Social Science Thesaurus is a multidisciplinary vocabulary of the most important concepts in the social sciences. SAGE uses this vocabulary as its principal keyword vocabulary for automated tagging of content on SAGE Knowledge and SAGE Research Methods. You are welcome to browse, download, use and transform the vocabulary for any non-commercial purpose.\n\nThe majority of concepts in the thesaurus have been mined from headwords in SAGE encyclopedias and other reference works. Relationships between concepts have been inferred from implicit structures in those works, for example subject indexes and readers' guides. As such, the thesaurus is a structured representation of what the editors of those reference works consider to be the most important concepts in the social sciences.\n\nAdditional scraping work has extracted and structured concept-specific metadata, such as dates (for events and people) and definitions. In addition to broader-narrower relationships, concepts are grouped by type: concepts, people, organizations, events, methods, theories or laws.", "example": "-LHR8P7WS-K", "homepage": "https://loterre.istex.fr/N9J/en/", "license": "CC BY-NC-SA 4.0", "name": "SAGE Social Science Thesaurus", "preferred_prefix": "sage.socialsciencethesaurus", "uri_format": "http://data.loterre.fr/ark:/67375/N9J$1" }, "salk": { "appears_in": [ "efo" ], "comment": "spider stuff!", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Scientific research institute for neuroscience, genetics, immunology, plant biology and more.", "example": "037727", "homepage": "https://www.salk.edu/", "name": "Salk Institute for Biological Studies", "pattern": "^\\d{6}$", "preferred_prefix": "salk", "uri_format": "https://abrc.osu.edu/stocks/number/SALK_$1" }, "salmon": { "contact": { "email": "brycemecum@gmail.com", "github": "amoeba", "name": "Bryce Mecum", "orcid": "0000-0002-0381-3766" }, "description": "An ontology representing knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. This ontology is considered to be in the early stages of development, though it is based upon considerable previous work. Contributions of all kinds are welcome and encouraged, including alignments, updates to existing terms, and new terms.", "download_owl": "http://aber-owl.net/media/ontologies/SALMON/2/salmon.owl", "example": "00000674", "homepage": "https://github.com/DataONEorg/sem-prov-ontologies/tree/main/salmon", "keywords": [ "ontology" ], "mappings": { "aberowl": "SALMON", "bioportal": "SALMON" }, "name": "Salmon Ontology", "pattern": "^\\d+$", "preferred_prefix": "salmon", "uri_format": "https://purl.dataone.org/odo/SALMON_$1" }, "sao": { "contact": { "email": "slarson@ncmir.ucsd.edu", "name": "Stephen Larson" }, "deprecated": true, "description": "SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules.", "download_owl": "http://aber-owl.net/media/ontologies/SAO/2/sao.owl", "example": "5277619", "homepage": "http://ccdb.ucsd.edu/CCDBWebSite/sao.html", "keywords": [ "biochemistry", "obo", "ontology", "owl" ], "mappings": { "aberowl": "SAO", "biocontext": "SAO", "bioportal": "SAO", "obofoundry": "sao", "prefixcommons": "sao", "wikidata.entity": "Q114677911" }, "name": "Subcellular Anatomy Ontology", "pattern": "^\\d+$", "preferred_prefix": "SAO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/sao:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/SAO_$1", "references": [ "http://www.ontobee.org/ontology/SAO" ], "uri_format": "http://uri.neuinfo.org/nif/nifstd/sao$1" }, "saref": { "contact": { "email": "maxime.lefrancois@emse.fr", "name": "Maxime Lefrançois" }, "description": "The Smart Applications REFerence ontology (SAREF) is intended to enable interoperability between solutions from different providers and among various activity sectors in the Internet of Things (IoT), thus contributing to the development of the global digital market.", "example": "Actuation", "homepage": "https://saref.etsi.org/", "keywords": [ "digital planning and construction", "engineering", "fid baudigital", "industry", "iot", "nfdi4ing", "services" ], "mappings": { "agroportal": "SAREF", "lov": "saref", "tib": "saref" }, "name": "Smart Applications Reference ontology", "preferred_prefix": "saref", "uri_format": "https://saref.etsi.org/core/$1" }, "saref.agri": { "description": "This ontology extends the SAREF ontology for the Agricultural domain. This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx), which was established with the goal to create three SAREF extensions, one of them for the Agricultural domain.", "example": "Animal", "homepage": "https://saref.etsi.org/saref4agri/", "keywords": [ "agriculture", "food", "iot", "tib" ], "mappings": { "lov": "s4agri", "tib": "s4agri" }, "name": "SAREF extension for Agriculture", "preferred_prefix": "saref.agri", "synonyms": [ "s4agri" ], "uri_format": "https://saref.etsi.org/saref4agri/$1" }, "saref.auto": { "description": "This ontology extends the SAREF ontology for the automotive domain. This work has been developed in the context of the STF 566, which was established with the goal to create four SAREF extensions, one of them for the automotive domain.", "example": "AcousticSensor", "homepage": "https://saref.etsi.org/saref4auto/", "keywords": [ "engineering", "fid move", "nfdi4ing", "traffic engineering" ], "mappings": { "tib": "s4auto" }, "name": "SAREF4AUTO: an extension of SAREF for the automotive domain", "preferred_prefix": "saref.auto", "synonyms": [ "s4auto" ], "uri_format": "https://saref.etsi.org/saref4auto/$1" }, "saref.building": { "description": "This ontology extends the SAREF ontology for the building domain by defining building devices and how they are located in a building. This extension is based on the ISO 16739:2013 Industry Foundation Classes (IFC) standard for data sharing in the construction and facility management industries. The descriptions of the classes and properties extracted from IFC have been taken from the IFC documentation.", "example": "Actuator", "homepage": "https://saref.etsi.org/saref4bldg/", "keywords": [ "digital planning and construction", "engineering", "fid baudigital", "iot", "nfdi4ing" ], "mappings": { "lov": "s4bldg", "tib": "s4bldg" }, "name": "SAREF extension for building devices", "preferred_prefix": "saref.building", "synonyms": [ "s4bldg" ], "uri_format": "https://saref.etsi.org/saref4bldg/$1" }, "saref.city": { "description": "This ontology extends the SAREF ontology for the Smart City domain. This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx), which was established with the goal to create three SAREF extensions, one of them for the Smart City domain.", "example": "AccessibilityConcept", "homepage": "https://saref.etsi.org/saref4city/", "keywords": [ "civil engineering", "computer science", "digital planning and construction", "fid move", "government", "iot", "traffic engineering" ], "mappings": { "lov": "s4city", "tib": "s4city" }, "name": "SAREF extension for Smart City", "preferred_prefix": "saref.city", "synonyms": [ "s4city" ], "uri_format": "https://saref.etsi.org/saref4city/$1" }, "saref.ehaw": { "contact": { "email": "mohamed-el-amine.boukerfa@inrae.fr", "name": "LOV Migration" }, "description": "The objective of SAREF4EHAW is to extend SAREF ontology for the eHealth/Ageing-well (EHAW) vertical. Clause 4.1 of the present document shortly introduces a high level view of the envisioned SAREF4EHAW semantic model and modular ontology, with the retained concepts (i.e. classes) and their relations. SAREF4EHAW extension has been specified and formalised by investigating EHAW domain related resources, as reported in ETSI TR 103 509, such as: potential stakeholders, standardization initiatives, alliances/associations, European projects, EC directives, existing ontologies, and data repositories. Therefore, SAREF4EHAW modular ontology shall both: - Allow the implementation of a limited set of typical EHAW related use cases already identified in ETSI TR 103 509, i.e. - Use case 1 ?elderly at home monitoring and support?, - Use case 2 ?monitoring and support of healthy lifestyles for citizens?, - Use case 3 ?Early Warning System (EWS) and Cardiovascular Accidents detection?. - Fulfil the eHealth Ageing Well related requirements provided in ETSI TR 103 509, mainly the ontological ones that were mostly taken as input for the ontology specification. SAREF4EHAW mainly reuses the following existing ontologies: SAREF, ETSI SmartBAN reference model, SAREF 4 Environment extension and W3C SSN System module. The following figure presents the high level view of SAREF4EHAW ontology. ![SAREF4SYST overview](diagrams/SAREF4EHAW_Model.jpg) For semantic interoperability handling purposes, an ontology based solution, combined with sensing-as-a-service and WoT strategies, is retained for SAREF4EHAW. Therefore, an upper level ontology, at service level, shall also behas been fully modelled (Service class and sub-classes depicted in the previous figure). For embedded semantic analytics purposes, SAREF4EHAW shall behas been designed using the modularity principle (see ETSI TR 103 509) and can thus be mainly described by the following self-contained knowledge sub-ontologies (or modules): HealthActor, Ban, HealthDevice, Function (measured data related concepts included) and Service., i.e. - Use case 1 “elderly at home monitoring and support”, - Use case 2 “monitoring and support of healthy lifestyles for citizens”, - Use case 3 “Early Warning System (EWS) and Cardiovascular Accidents detection”. - Fulfil the eHealth Ageing Well related requirements provided in ETSI TR 103 509", "download_owl": "http://aber-owl.net/media/ontologies/S4EHAW/1/s4ehaw.owl", "example": "Activity", "homepage": "https://saref.etsi.org/saref4ehaw/", "keywords": [ "engineering", "iot", "nfdi4ing", "ontology" ], "license": "https://forge.etsi.org/etsi-software-license", "mappings": { "aberowl": "S4EHAW", "bioportal": "S4EHAW", "lov": "s4ehaw", "tib": "s4ehaw" }, "name": "SAREF4EHAW: an extension of SAREF for eHealth Ageing Well domain", "preferred_prefix": "saref.ehaw", "synonyms": [ "s4ehaw" ], "uri_format": "https://saref.etsi.org/saref4ehaw/$1" }, "saref.ener": { "description": "This is the extension of SAREF for the EEBus and Energy@Home project. The documentation of SAREF4EE is available at http://ontology.tno.nl/SAREF4EE_Documentation_v0.1.pdf. SAREF4EE represents 1) The configuration information exchanged in the use case 'Remote Network Management' according to the EEBus Technical Report, Protocol Specification- Remote Network Management, version 1.0.0.2, 2015-09-19; 2) The scheduling information about power sequences exchanged in the use cases Appliance scheduling through CEM and remote start' and 'Automatic cycle rescheduling', according to the message structures described in General Message Structures, version 0.1.1, 2015-10-07; 3) The monitor and control information exchanged in the use case 'Communicate appliance status and info on manually planned cycles', according to the monitoring and control part of the Energy@Home Data Model, version 1.0; and 4) the event-based data exchanged in the use case 'Demand Response', according to General Message Structures, version 0.1.1, 2015-10-07.", "example": "ActuatorLevel", "homepage": "https://saref.etsi.org/saref4ener/", "keywords": [ "digital planning and construction", "engineering", "environment", "fid baudigital", "nfdi4energy", "nfdi4ing", "services" ], "mappings": { "lov": "s4ener", "tib": "s4ener" }, "name": "SAREF4EE: the EEbus/Energy@home extension of SAREF", "preferred_prefix": "saref.ener", "synonyms": [ "s4ener" ], "uri_format": "https://saref.etsi.org/saref4ener/$1" }, "saref.environment": { "description": "This ontology extends the SAREF ontology for the environment domain, specifically for the light pollution domain, including concepts like photometers, light, etc.", "example": "AirEmissionKind", "homepage": "https://saref.etsi.org/saref4envi/", "keywords": [ "engineering", "environment", "iot", "nfdi4ing" ], "mappings": { "lov": "s4envi", "tib": "s4envi" }, "name": "SAREF extension for environment", "preferred_prefix": "saref.environment", "synonyms": [ "s4envi" ], "uri_format": "https://saref.etsi.org/saref4envi/$1" }, "saref.grid": { "description": "This ontology extends the SAREF ontology for the smart grid domain.", "example": "ActionOperation", "homepage": "https://saref.etsi.org/saref4grid/", "keywords": [ "engineering", "nfdi4energy" ], "mappings": { "tib": "s4grid" }, "name": "SAREF4GRID: an extension of SAREF for the Smart Grid domain", "preferred_prefix": "saref.grid", "synonyms": [ "s4grid" ], "uri_format": "https://saref.etsi.org/saref4grid/$1" }, "saref.industry": { "description": "SAREF4INMA is an extension of SAREF for the industry and manufacturing domain. SAREF4INMA focuses on extending SAREF for the industry and manufacturing domain to solve the lack of interoperability between various types of production equipment that produce items in a factory and, once outside the factory, between different organizations in the value chain to uniquely track back the produced items to the corresponding production equipment, batches, material and precise time in which they were manufactured. SAREF4INMA is specified and published by ETSI in the TS 103 410-5 associated to this ontology file. SAREF4INMA was created to be aligned with related initiatives in the smart industry and manufacturing domain in terms of modelling and standardization, such as the Reference Architecture Model for Industry 4.0 (RAMI), which combines several standards used by the various national initiatives in Europe that support digitalization in manufacturing. The full list of use cases, standards and requirements that guided the creation of SAREF4INMA are described in the associated ETSI TR 103 507.", "example": "Area", "homepage": "https://saref.etsi.org/saref4inma/", "keywords": [ "engineering", "industry", "iot", "nfdi4ing" ], "mappings": { "lov": "s4inma", "tib": "s4inma" }, "name": "SAREF4INMA: an extension of SAREF for the industry and manufacturing domain", "preferred_prefix": "saref.industry", "synonyms": [ "s4inma" ], "uri_format": "https://saref.etsi.org/saref4inma/$1" }, "saref.lift": { "description": "This ontology extends the SAREF ontology for the Smart Lifts domain.", "example": "AlarmSignal", "homepage": "https://saref.etsi.org/saref4lift/", "keywords": [ "digital planning and construction", "engineering", "fid baudigital", "nfdi4ing" ], "mappings": { "tib": "s4lift" }, "name": "SAREF4LIFT: an extension of SAREF for the Smart Lifts domain", "preferred_prefix": "saref.lift", "synonyms": [ "s4lift" ], "uri_format": "https://saref.etsi.org/saref4lift/$1" }, "saref.maritime": { "description": "SAREF4MARI is an extension of SAREF for the maritime domain.", "example": "AISDevice", "homepage": "https://saref.etsi.org/saref4mari/", "keywords": [ "fid move", "traffic engineering" ], "mappings": { "tib": "s4mari" }, "name": "SAREF4MARI: an extension of SAREF for the maritime domain", "preferred_prefix": "saref.maritime", "synonyms": [ "s4mari" ], "uri_format": "https://saref.etsi.org/saref4mari/$1" }, "saref.system": { "description": "The present document is the technical specification of SAREF4SYST, a generic extension of [ETSI TS 103 264 SAREF](https://www.etsi.org/deliver/etsi_ts/103200_103299/103264/02.01.01_60/ts_103264v020101p.pdf) that defines an ontology pattern which can be instantiated for different domains. SAREF4SYST defines Systems, Connections between systems, and Connection Points at which systems may be connected. These core concepts can be used generically to define the topology of features of interest, and can be specialized for multiple domains. The topology of features of interest is highly important in many use cases. If a room holds a lighting device, and if it is adjacent with an open window to a room whose luminosity is low, then by turning on the lighting device in the former room one may expect that the luminosity in the latter room will rise.\n\nThe SAREF4SYST ontology pattern can be instantiated for different domains. For example to describe zones inside a building (systems), that share a frontier (connections). Properties of systems are typically state variables (e.g. agent population, temperature), whereas properties of connections are typically flows (e.g. heat flow).\n\nSAREF4SYST has two main aims: on the one hand, to extend SAREF with the capability or representing general topology of systems and how they are connected or interact and, on the other hand, to exemplify how ontology patterns may help to ensure an homogeneous structure of the overall SAREF ontology and speed up the development of extensions.\n\nSAREF4SYST consists both of a core ontology, and guidelines to create ontologies following the SAREF4SYST ontology pattern. The core ontology is a lightweight OWL-DL ontology that defines 3 classes and 9 object properties.\n\nUse cases for ontology patterns are described extensively in [ETSI TR 103 549 Clauses 4.2 and 4.3](https://www.etsi.org/deliver/etsi_tr/103500_103599/103549/01.01.01_60/tr_103549v010101p.pdf).\n\nFor the Smart Energy domain:\n\n- Electric power systems can exchange electricity with other electric power systems. The electric energy can flow both ways in some cases (from the Public Grid to a Prosumer), or in only one way (from the Public Grid to a Load). Electric power systems can be made up of different sub-systems. Generic sub-types of electric power systems include producers, consumers, storage systems, transmission systems. \n- Electric power systems may be connected one to another through electrical connection points. An Electric power system may have multiple connection points (Multiple Winding Transformer generally have one single primary winding with two or more secondary windings). Generic sub-types of electrical connection points include plugs, sockets, direct-current, single-phase, three-phase, connection points. \n- An Electrical connection may exist between two Electric power systems at two of their respective connection points. Generic sub-types of electrical connections include Single-phase Buses, Three-phase Buses. A single-phase electric power system can be connected using different configurations at a three-phase bus (RN, SN, TN types).\n\nFor the Smart Building domain:\n\n- Buildings, Storeys, Spaces, are different sub-types of Zones. Zones can contain sub-zones. Zones can be adjacent or intersect with other zones. \n- Two zones may share one or more connections. For example some fresh air may be created inside a storey if it has two controllable openings to the exterior at different cardinal points. \n\nA graphical overview of the SAREF4SYST ontology is provided in Figure 1. In such figure:\n\n- Rectangles are used to denote Classes. The label of the rectangle is the identifier of the Class.\n- Plain arrows are used to represent Object Properties between Classes. The label of the arrow is the identifier of the Object Property. The origin of the arrow is the domain Class of the property, and the target of the arrow is the range Class of the property.\n- Dashed arrows with identifiers between stereotype signs (i.e. \"`<< >>`\") refer to OWL axioms that are applied to some property. Four pairs of properties are inverse one of the other; the property `s4syst:connectedTo` is symmetric, and properties `s4syst:hasSubSystem` and `s4syst:hasSubSystem` are transitive.\n- A symbol =1 near the target of an arrow denotes that the associated property is functional. A symbol ? denotes a local existential restriction.\n\n\n![SAREF4SYST overview](diagrams/overview.png)", "example": "Connection", "homepage": "https://saref.etsi.org/saref4syst/", "keywords": [ "iot", "nfdi4ing" ], "mappings": { "lov": "s4syst", "tib": "s4syst" }, "name": "SAREF4SYST: an extension of SAREF for typology of systems and their inter-connections", "preferred_prefix": "saref.system", "synonyms": [ "s4syst" ], "uri_format": "https://saref.etsi.org/saref4syst/$1" }, "saref.water": { "description": "This ontology extends the SAREF ontology for the water domain. This work has been developed in the context of the STF 566, which was established with the goal to create three SAREF extensions, one of them for the water domain.", "example": "AcceptabilityProperty", "homepage": "https://saref.etsi.org/saref4watr/", "keywords": [ "engineering", "environment", "iot", "nfdi4ing" ], "mappings": { "lov": "s4watr", "tib": "s4watr" }, "name": "SAREF extension for water", "preferred_prefix": "saref.water", "synonyms": [ "s4watr" ], "uri_format": "https://saref.etsi.org/saref4watr/$1" }, "saref.wearable": { "description": "SAREF4WEAR is an extension of SAREF for Wearables", "example": "BiometricProperty", "homepage": "https://saref.etsi.org/saref4wear/", "keywords": [ "engineering", "iot", "nfdi4ing" ], "mappings": { "lov": "s4wear", "tib": "s4wear" }, "name": "SAREF4WEAR: an extension of SAREF for Wearables", "preferred_prefix": "saref.wearable", "synonyms": [ "s4wear" ], "uri_format": "https://saref.etsi.org/saref4wear/$1" }, "sargon": { "description": "SARGON (SmArt eneRGy dOmain oNtology) is an open-source effort to define semantic descriptions of the smart assets in building automation and smart grid and the relationships between them. SARGON consists of an extensible dictionary of terms and concepts in and around building and smart grid, a set of relationships for linking and composing concepts together, and a flexible data model permitting seamless integration of SARGON with existing tools and databases. Through the use of powerful Semantic Web technology, SARGON can describe the broad set of Devices and custom features, assets and subsystems found across the building stock in a consistent matter.", "example": "AC-DC", "homepage": "https://sargon-n5geh.netlify.app/", "keywords": [ "engineering", "nfdi4energy" ], "mappings": { "tib": "sargon" }, "name": "SARGON (SmArt eneRGy dOmain oNtology)", "preferred_prefix": "sargon", "uri_format": "https://sargon-n5geh.netlify.app/ontology/1.0/object_properties/$1" }, "sasap": { "contact": { "email": "brycemecum@gmail.com", "github": "amoeba", "name": "Bryce Mecum", "orcid": "0000-0002-0381-3766" }, "description": "An ontology which represents information about the State of Alaska's Salmon and People (SASAP) project, as well as knowledge about salmon, features of their habitats, salmon stakeholders, and related entities.", "download_owl": "http://aber-owl.net/media/ontologies/SASAP/2/sasap.owl", "example": "00000101", "homepage": "https://github.com/DataONEorg/sem-prov-ontologies/tree/main/salmon", "keywords": [ "ontology" ], "mappings": { "aberowl": "SASAP", "bioportal": "SASAP" }, "name": "The State of Alaska's Salmon and People Ontology", "pattern": "^\\d+$", "preferred_prefix": "sasap", "uri_format": "https://purl.dataone.org/odo/SASAP_$1" }, "sasbdb": { "contact": { "email": "a.kikhney@embl-hamburg.de", "name": "Al Kikhney", "orcid": "0000-0003-1321-3956" }, "description": "Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data.", "example": "SASDAX8", "homepage": "http://www.sasbdb.org/", "keywords": [ "life science", "molecular biology" ], "mappings": { "biocontext": "SASBDB", "fairsharing": "FAIRsharing.i1F3Hb", "miriam": "sasbdb", "n2t": "sasbdb", "re3data": "r3d100012273", "uniprot": "DB-0258" }, "name": "Small Angle Scattering Biological Data Bank", "pattern": "^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$", "preferred_prefix": "sasbdb", "publications": [ { "doi": "10.1002/pro.3731", "pmc": "PMC6933840", "pubmed": "31576635", "title": "SASBDB: Towards an automatically curated and validated repository for biological scattering data", "year": 2019 }, { "doi": "10.1093/nar/gku1047", "pmc": "PMC4383894", "pubmed": "25352555", "title": "SASBDB, a repository for biological small-angle scattering data", "year": 2014 } ], "uri_format": "http://www.sasbdb.org/data/$1" }, "sbo": { "appears_in": [ "proco", "scdo" ], "banana": "SBO", "contact": { "email": "sheriff@ebi.ac.uk", "github": "rsmsheriff", "name": "Rahuman Sheriff", "orcid": "0000-0003-0705-9809" }, "description": "The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort.", "download_obo": "http://purl.obolibrary.org/obo/sbo.obo", "download_owl": "http://purl.obolibrary.org/obo/sbo.owl", "example": "0000485", "homepage": "http://www.ebi.ac.uk/sbo/", "keywords": [ "earth sciences", "ess", "life sciences, biology", "molecular interaction", "nfdi4cat", "obo", "ontology", "pathway", "systems biology" ], "license": "Artistic License 2.0", "logo": "https://upload.wikimedia.org/wikipedia/commons/f/fd/SBO_logo.png", "mappings": { "aberowl": "SBO", "bartoc": "20713", "biocontext": "SBO", "bioportal": "SBO", "fairsharing": "FAIRsharing.s19src", "miriam": "sbo", "n2t": "sbo", "obofoundry": "sbo", "ols": "sbo", "ontobee": "SBO", "prefixcommons": "sbo", "tib": "sbo", "wikidata.entity": "Q2377160" }, "name": "Systems Biology Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "SBO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/sbo:$1" }, { "code": "biomodels", "description": "Provider for SBO at BioModels", "homepage": "http://biomodels.net", "name": "BioModels", "uri_format": "http://biomodels.net/SBO/SBO_$1" } ], "publications": [ { "doi": "10.1038/msb.2011.77", "pmc": "PMC3261705", "pubmed": "22027554", "title": "Controlled vocabularies and semantics in systems biology", "year": 2011 }, { "doi": "10.1186/1471-2202-7-s1-s11", "pmc": "PMC1775041", "pubmed": "17118155", "title": "Model storage, exchange and integration", "year": 2006 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/SBO_$1", "repository": "https://github.com/EBI-BioModels/SBO", "twitter": "biomodels", "uri_format": "http://purl.obolibrary.org/obo/SBO_$1", "version": "2021-08-28" }, "scancerrna": { "contact": { "email": "zty2009@hit.edu.cn", "name": "Tianyi Zhao", "orcid": "0000-0001-7352-2959" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "SCancerRNA provides identifiers for non-coding RNA biomarkers, including long ncRNA, microRNA, PIWI-interacting RNA, small nucleolar RNA, and circular RNA, with data on their differential expression at the cellular level in cancer.", "example": "9530", "github_request_issue": 1215, "homepage": "http://www.scancerrna.com/", "name": "SCancerRNA", "pattern": "^\\d+$", "preferred_prefix": "scancerrna", "publications": [ { "doi": "10.1093/gpbjnl/qzae023", "pubmed": "39341795", "title": "SCancerRNA: Expression at the Single-cell Level and Interaction Resource of Non-coding RNA Biomarkers for Cancers", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "http://www.scancerrna.com/toDetail?id=$1" }, "scdo": { "contact": { "email": "giant.plankton@gmail.com", "github": "JadeHotchkiss", "name": "Jade Hotchkiss", "orcid": "0000-0002-2193-0704" }, "depends_on": [ "apollosv", "aro", "chebi", "chmo", "cmo", "doid", "dron", "duo", "envo", "eupath", "exo", "gaz", "gsso", "hp", "hsapdv", "ico", "ido", "idomal", "mp", "nbo", "ncit", "obi", "ogms", "opmi", "pr", "sbo", "stato", "symp", "uo", "vo", "vt" ], "description": "An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease.", "download_obo": "http://purl.obolibrary.org/obo/scdo.obo", "download_owl": "http://purl.obolibrary.org/obo/scdo.owl", "example": "0000728", "homepage": "https://scdontology.h3abionet.org/", "keywords": [ "biomedical science", "genetic disorder", "obo", "ontology", "sickle cell disease" ], "license": "GPL-3.0", "logo": 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"name": "Selventa Chemicals", "pattern": "^A\\d{4}$", "preferred_prefix": "schem", "uri_format": "https://biopragmatics.github.io/providers/schem/$1" }, "schema": { "contact": { "email": "johardi@stanford.edu", "name": "Josef Hardi" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond.", "download_owl": "http://aber-owl.net/media/ontologies/SCHEMAORG/2/schemaorg.owl", "download_rdf": "https://schema.org/version/latest/schemaorg-current-https.ttl", "example": "Person", "homepage": "https://schema.org", "keywords": [ "catalogs", "ess", "fair data spaces", "ontology" ], "mappings": { "aberowl": "SCHEMAORG", "biolink": "schema", "bioportal": "SCHEMA", "lov": "sdo", "ols": "schemaorg_http", "tib": "schema", "zazuko": "schema" }, "name": "Schema.org", "preferred_prefix": "schema", "synonyms": [ "schemaorg", "sdo" ], "uri_format": "https://schema.org/$1" }, "scholia.resource": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A frontend to Wikidata", "example": "doi", "homepage": "https://scholia.toolforge.org/", "keywords": [ "registry", "wikidata" ], "name": "Scholia Registry", "preferred_prefix": "scholia.resource", "uri_format": "https://bioregistry.io/metaregistry/scholia/$1" }, "sciflection": { "description": "Sciflection is a public repository for experiments and associated spectra, usually uploaded from Electronic Lab Notebooks, shared under FAIR conditions", "example": "5ede4273-b26c-4ea4-adb7-3ce294ab3397", "homepage": "https://sciformation.com/sciflection.html", "mappings": { "miriam": "sciflection", "re3data": "r3d100013413" }, "name": "Sciflection", "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$", "preferred_prefix": "sciflection", "uri_format": "https://sciflection.com/$1" }, "sciprofiles": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "numerical identifier for an author in SciProfiles by MDPI", "example": "118021", "homepage": "https://sciprofiles.com/", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P8159" }, "name": "SciProfiles ID", "pattern": "^[1-9]\\d*$", "preferred_prefix": "sciprofiles", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://sciprofiles.com/profile/$1" }, "scomp": { "contact": { "github": "ncatlett", "name": "Natalie L Catlett" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Selventa legacy complex namespace used with the Biological Expression Language", "example": "C0001", "homepage": "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-named-complexes.txt", "keywords": [ "bel", "protein complexes", "selventa" ], "license": "Apache-2.0", "logo": "https://biological-expression-language.github.io/img/bel300.png", "name": "Selventa Complexes", "pattern": "^C\\d{4}$", "preferred_prefix": "scomp", "uri_format": "https://biopragmatics.github.io/providers/scomp/$1" }, "scop": { "contact": { "email": "JMChandonia@lbl.gov", "github": "jmchandonia", "name": "John-Marc Chandonia", "orcid": "0000-0002-5153-9079" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "SCOP(e) unique identifier. This is simply a number that may be used to reference any entry in the SCOP(e) hierarchy, from root to leaves (Fold, Superfamily, Family, etc.).", "example": "47419", "homepage": "https://scop.berkeley.edu", "keywords": [ "protein", "structure" ], "mappings": { "biocontext": "SCOP", "edam": "1042", "miriam": "scop", "n2t": "scop", "prefixcommons": "scop" }, "name": "Structural Classification of Proteins - Unique Identifier", "pattern": "^\\d+$", "preferred_prefix": "scop", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/scop:$1" }, { "code": "gendis", "description": "GenDiS is a repository of SCOP-identified homologous sequences of structural superfamily members.", "homepage": "https://caps.ncbs.res.in/gendis3/home", "name": "Genomic Distribution of structural Superfamilies", "publications": [ { "doi": "10.1093/database/baaf035", "pmc": "PMC12063530", "pubmed": "40343712", "title": "GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database", "year": 2025 } ], "uri_format": "https://caps.ncbs.res.in/gendis3/superfamily_display/$1" }, { "code": "mrc", "description": "SCOP at UK Medical Research council (MRC)", "homepage": "https://scop.mrc-lmb.cam.ac.uk", "name": "SCOP at UK Medical Research council (MRC)", "uri_format": "https://scop.mrc-lmb.cam.ac.uk/term/$1" } ], "publications": [ { "doi": "10.1093/nar/27.1.254", "pmc": "PMC148149", "pubmed": "9847194", "title": "SCOP: a Structural Classification of Proteins database", "year": 1999 }, { "doi": "10.1093/nar/25.1.236", "pmc": "PMC146380", "pubmed": "9016544", "title": "SCOP: a structural classification of proteins database", "year": 1997 }, { "doi": "10.1093/database/baaf035", "pmc": "PMC12063530", "pubmed": "40343712", "title": "GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database", "year": 2025 }, { "doi": "10.1093/nar/28.1.257", "pmc": "PMC102479", "pubmed": "10592240", "title": "SCOP: a structural classification of proteins database", "year": 2000 }, { "doi": "10.1107/s0907444998009172", "pubmed": "10089491", "title": "SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data", "year": 1998 } ], "references": [ "https://scop.berkeley.edu/help/#stableidentifiers" ], "synonyms": [ "scop.sun", "scop.sunid" ], "uri_format": "http://scop.berkeley.edu/sunid=$1" }, "scop.sccs": { "contact": { "email": "JMChandonia@lbl.gov", "github": "jmchandonia", "name": "John-Marc Chandonia", "orcid": "0000-0002-5153-9079" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This is a dot notation used to concisely describe a SCOP(e) class, fold, superfamily, and family. For example, a.39.1.1 references the 'Calbindin D9K' family, where 'a' represents the class, '39' represents the fold, '1' represents the superfamily, and the last '1' represents the family.", "example": "a.39.1.1", "example_extras": [ "a", "a.39", "a.39.1" ], "homepage": "https://scop.berkeley.edu", "mappings": { "edam": "1041" }, "name": "SCOP(e) concise classification string", "preferred_prefix": "scop.sccs", "references": [ "https://scop.berkeley.edu/help/#stableidentifiers" ], "uri_format": "http://scop.berkeley.edu/sccs=$1" }, "scop.sid": { "contact": { "email": "JMChandonia@lbl.gov", "github": "jmchandonia", "name": "John-Marc Chandonia", "orcid": "0000-0002-5153-9079" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A 7-character sid consists of \"d\" followed by the 4-character PDB ID of the file of origin, the PDB chain ID ('_' if none, '.' if multiple as is the case in genetic domains), and a single character (usually an integer) if needed to specify the domain uniquely ('_' if not). Sids are currently all lower case, even when the chain letter is upper case. Example sids include d4akea1, d9hvpa_, and d1cph.1.", "example": "d4akea1", "example_extras": [ "d1cph.1", "d9hvpa_" ], "homepage": "https://scop.berkeley.edu", "mappings": { "edam": "1039" }, "name": "Structural Classification of Protein - Stable Domain Identifier", "preferred_prefix": "scop.sid", "references": [ "https://scop.berkeley.edu/help/#stableidentifiers" ], "uri_format": "http://scop.berkeley.edu/sid=$1" }, "scopus": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings. \nDelivering a comprehensive overview of the world's research output in the fields of science, technology, medicine, social sciences, and arts \nand humanities, Scopus features smart tools to track, analyze and visualize research.", "example": "56305849200", "homepage": "https://www.scopus.com", "keywords": [ "subject agnostic" ], "mappings": { "biolink": "ScopusID", "fairsharing": "FAIRsharing.0a674c", "wikidata": "P1153" }, "name": "Scopus Researcher", "pattern": "^\\d+$", "preferred_prefix": "scopus", "synonyms": [ "scopus.author" ], "twitter": "Scopus", "uri_format": "https://www.scopus.com/authid/detail.uri?authorId=$1" }, "scopus.affiliation": { "description": "identifier for an organisation in author affiliations per Scopus", "example": "60025709", "homepage": "http://info.sciencedirect.com/scopus/scopus-in-detail/tools/affiliationidentifier", "mappings": { "wikidata": "P1155" }, "name": "Scopus affiliation ID", "preferred_prefix": "scopus.affiliation", "uri_format": "https://www.scopus.com/affil/profile.uri?afid=$1" }, "scopus.publication": { "description": "identifier for a source/publication venue (journal, conference, etc) in Scopus", "example": "16129", "homepage": "https://www.scopus.com/", "mappings": { "wikidata": "P1156" }, "name": "Scopus Publication", "pattern": "^[1-9]\\d{0,11}$", "preferred_prefix": "scopus.publication", "uri_format": "https://www.scopus.com/sourceid/$1" }, "scopus.work": { "description": "unique academic work identifier assigned in Scopus bibliographic database", "example": "2-s2.0-0030770923", "homepage": "https://www.scopus.com/", "mappings": { "wikidata": "P1154" }, "name": "Scopus Work", "pattern": "^2-s2\\.0-\\d+$", "preferred_prefix": "scopus.work", "synonyms": [ "scopus.eid" ], "uri_format": "http://www.scopus.com/record/display.url?origin=inward&eid=$1" }, "scor": { "description": "The Supply Chain Operation Reference (SCOR) is a cross-industry approach to lay the groundwork for more efficient and effective information exchange in supply networks.", "example": "ActiviateOrArchiveContract", "homepage": "https://github.com/vocol/scor", "keywords": [ "coypu", "economics" ], "mappings": { "tib": "scor" }, "name": "Supply Chain Operation Reference", "preferred_prefix": "scor", "uri_format": "http://purl.org/eis/vocab/scor#$1" }, "scoro": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator).", "example": "IntellectualContribution", "homepage": "http://www.sparontologies.net/ontologies/scoro", "keywords": [ "academy", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.c86b48", "lov": "scoro" }, "name": "Scholarly Contributions and Roles Ontology", "preferred_prefix": "SCoRO", "publications": [ { "doi": "10.3233/sw-150177", "title": "The Document Components Ontology (DoCO)", "year": 2016 } ], "repository": "https://github.com/sparontologies/scoro", "twitter": "sparontologies", "uri_format": "http://purl.org/spar/scoro/$1" }, "scpd": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "Database containing promotor sequences found in Saccharomyces cerevisiae.", "example": "CDC2", "homepage": "http://rulai.cshl.edu/SCPD/", "keywords": [ "dna", "rna" ], "mappings": { "pathguide": "130", "prefixcommons": "scpd" }, "name": "Saccharomyces cerevisiae promoter database", "preferred_prefix": "scpd", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/scpd:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://rulai.cshl.edu/cgi-bin/SCPD/getgene2?$1" }, "scr": { "contact": { "email": "abandrowski@ncmir.ucsd.edu", "github": "bandrow", "name": "Anita Bandrowski", "orcid": "0000-0002-5497-0243" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources.", "example": "022586", "github_request_issue": 421, "homepage": "https://scicrunch.org/browse/resourcedashboard", "keywords": [ "interactive portal", "life science", "neurobiology", "nih initiative", "rrid" ], "mappings": { "fairsharing": "FAIRsharing.kj4pvk", "integbio": "nbdc01937", "rrid": "SCR" }, "name": "SciCrunch Registry", "pattern": "^\\d+$", "preferred_prefix": "scr", "publications": [ { "doi": "10.1002/cne.23913", "pmc": "PMC4684178", "pubmed": "26599696", "title": "The Resource Identification Initiative: A Cultural Shift in Publishing", "year": 2016 }, { "pubmed": "22434839" } ], "synonyms": [ "scicrunch" ], "uri_format": "http://scicrunch.org/resolver/SCR_$1" }, "scretf": { "deprecated": true, "description": "ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor.", "example": "RSC3", "homepage": "http://stormo.wustl.edu/ScerTF/", "mappings": { "biocontext": "SCRETF", "miriam": "scretf", "n2t": "scretf" }, "name": "ScerTF", "pattern": "^\\w+$", "preferred_prefix": "scretf", "uri_format": "http://stormo.wustl.edu/ScerTF/details/$1" }, "sd": { "description": "Un vocabulaire pour décrire des services SPARQL publiés via le protocole SPARQL 1.1 pour RDF. Ces descriptions fournissent un mécanisme par lequel un client ou un utilisateur final peuvent obtenir des informations sur le service SPARQL, telles que les extensions de fonctions supportées ou les détails à propos des jeux de données disponibles.", "example": "endpoint", "homepage": "http://www.w3.org/TR/sparql11-service-description/", "keywords": [ "w3c rec" ], "mappings": { "lov": "sd", "zazuko": "sd" }, "name": "SPARQL 1.1 Service Description", "preferred_prefix": "sd" }, "sdap": { "description": "SDAP is a Web server that integrates a database of allergenic proteins with various bioinformatics tools for performing structural studies related to allergens and characterization of their epitopes.", "example": "610", "homepage": "http://fermi.utmb.edu/SDAP", "keywords": [ "protein", "structure" ], "mappings": { "prefixcommons": "sdap" }, "name": "Structural Database of Allergenic Proteins", "preferred_prefix": "sdap", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/sdap:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid=$1" }, "sdbs": { "description": "The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra.", "example": "4544", "homepage": "https://sdbs.db.aist.go.jp", "mappings": { "biocontext": "SDBS", "integbio": "nbdc01520", "miriam": "sdbs", "n2t": "sdbs" }, "name": "Spectral Database for Organic Compounds", "pattern": "^\\d+$", "preferred_prefix": "sdbs", "uri_format": "https://sdbs.db.aist.go.jp/CompoundView.aspx?sdbsno=$1" }, "sddo": { "contact": { "email": "daniel.c.berrios@nasa.gov", "github": "DanBerrios", "name": "Dan Berrios", "orcid": "0000-0003-4312-9552" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Science Data Discovery Ontology (sddo) is being developed to provide a semantic foundation for the discovery of information managed by NASA's Science Mission Directorate. This information spans many scientific disciplines, fields and subfields, including heliophysics, earth science, planetary science, astrophysics, biology, astrobiology, and physical science. [from repository]", "download_json": "https://github.com/NASA-IMPACT/sddo/raw/refs/heads/master/sddo.json", "download_obo": "https://github.com/NASA-IMPACT/sddo/raw/refs/heads/master/sddo.obo", "download_owl": "https://github.com/NASA-IMPACT/sddo/raw/refs/heads/master/sddo.owl", "example": "3000001", "github_request_issue": 1556, "homepage": "https://github.com/NASA-IMPACT/sddo", "keywords": [ "ontology" ], "license": "CC-BY-3.0", "name": "Science Data Discovery Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "sddo", "repository": "https://github.com/NASA-IMPACT/sddo", "uri_format": "http://purl.obolibrary.org/obo/SDDO_$1" }, "sdgio": { "contact": { "email": "pier.buttigieg@awi.de", "name": "Pier Luigi Buttigieg", "orcid": "0000-0002-4366-3088" }, "description": "An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators.", "download_owl": "https://github.com/SDG-InterfaceOntology/sdgio/raw/master/sdgio.owl", "example": "00020134", "homepage": "https://github.com/SDG-InterfaceOntology/sdgio", "keywords": [ "environmental science", "ontology", "sustainability" ], "mappings": { "agroportal": "SDGIO", "fairsharing": "FAIRsharing.d5ff6e", "ols": "sdgio", "ontobee": "SDGIO" }, "name": "Sustainable Development Goals Interface Ontology", "pattern": "^\\d{8}$", "preferred_prefix": "sdgio", "publications": [ { "doi": "10.1186/s13326-016-0097-6", "pmc": "PMC5035502", "pubmed": "27664130", "title": "The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation", "year": 2016 } ], "references": [ "https://github.com/SDG-InterfaceOntology/sdgio/issues/233" ], "repository": "https://github.com/SDG-InterfaceOntology/sdgio", "uri_format": "http://purl.unep.org/sdg/SDGIO_$1" }, "sdis": { "contact": { "github": "ncatlett", "name": "Natalie L Catlett" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Selventa legacy disease namespace used with the Biological Expression Language", "example": "D0001", "homepage": "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-diseases.txt", "keywords": [ "bel", "diseases", "selventa" ], "license": "Apache-2.0", "logo": "https://biological-expression-language.github.io/img/bel300.png", "name": "Selventa Diseases", "pattern": "^D\\d{4}$", "preferred_prefix": "sdis", "uri_format": "https://biopragmatics.github.io/providers/sdis/$1" }, "sdmx": { "description": "This vocabulary extends the data cube vocabulary to support publication of statistical data in RDF, using an information model based on SDMX", "download_rdf": "http://purl.org/linked-data/sdmx", "example": "EntityRole", "homepage": "https://raw.githubusercontent.com/UKGovLD/publishing-statistical-data/master/specs/src/main/vocab/sdmx.ttl", "keywords": [ "methods" ], "mappings": { "lov": "sdmx", "zazuko": "sdmx" }, "name": "SDMX-RDF vocabulary", "preferred_prefix": "sdmx" }, "sedml.format": { "description": "Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).", "example": "csv", "homepage": "http://sed-ml.org/", "mappings": { "miriam": "sedml.format" }, "name": "SED-ML data format", "pattern": "^[a-z]+(\\..*?)?$", "preferred_prefix": "sedml.format", "uri_format": "https://sed-ml.org/urns.html#format:$1" }, "sedml.language": { "description": "Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).", "example": "sbml.level-3.version-2", "homepage": "http://sed-ml.org/", "mappings": { "miriam": "sedml.language" }, "name": "SED-ML model format", "pattern": "^[a-z]+(\\..*?)?$", "preferred_prefix": "sedml.language", "uri_format": "https://sed-ml.org/urns.html#language:$1" }, "seed.compound": { "description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.", "example": "cpd15380", "homepage": "http://modelseed.org/", "mappings": { "biocontext": "SEED.COMPOUND", "miriam": "seed.compound", "n2t": "seed.compound" }, "name": "SEED Compound", "pattern": "^cpd\\d+$", "preferred_prefix": "seed.compound", "repository": "https://github.com/TheSEED", "uri_format": "http://modelseed.org/biochem/compounds/$1" }, "seed.reaction": { "description": "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions.", "example": "rxn00001", "homepage": "http://modelseed.org/biochem/reactions/", "mappings": { "biolink": "SEED.REACTION", "miriam": "seed.reaction", "n2t": "seed.reaction" }, "name": "SEED Reactions", "pattern": "^rxn\\d+$", "preferred_prefix": "seed.reaction", "uri_format": "http://modelseed.org/biochem/reactions/$1" }, "seed.role": { "contributor": { "email": "seaver@anl.gov", "github": "samseaver", "name": "Sam Seaver", "orcid": "0000-0002-7674-5194" }, "description": "With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [Fellowship for Interpretation of Genomes (FIG)](http://thefig.info/) as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data.\nThis prefix provides identifiers for molecular roles that describe the function of one or more proteins in microbes and plants.", "example": "Histidinol dehydrogenase (EC 1.1.1.23)", "example_extras": [ "Archease", "Xylan oligosaccharide ABC transporter, substrate-binding component" ], "github_request_issue": 1340, "homepage": "https://theseed.org/", "license": "MIT", "name": "The SEED", "preferred_prefix": "seed.role", "publications": [ { "doi": "10.1093/nar/gki866", "pmc": "PMC1251668", "pubmed": "16214803", "title": "The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes", "year": 2005 } ], "repository": "https://github.com/orgs/TheSEED", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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Saccharomyces cerevisiae", "year": 1995 }, { "doi": "10.1093/genetics/iyae185", "pubmed": "39530598" }, { "doi": "10.1101/2024.09.16.613348", "pmc": "PMC11430078", "pubmed": "39345624", "title": "Saccharomyces Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements", "year": 2024 }, { "doi": "10.1093/database/baw020", "pmc": "PMC4795930", "pubmed": "26989152", "title": "From one to many: expanding the Saccharomyces cerevisiae reference genome panel", "year": 2016 }, { "doi": "10.1101/pdb.top083840", "pmc": "PMC5673599", "pubmed": "26631132", "title": "The Saccharomyces Genome Database: A Tool for Discovery", "year": 2015 }, { "doi": "10.1101/pdb.prot088922", "pmc": "PMC5673602", "pubmed": "26631126", "title": "The Saccharomyces Genome Database: Exploring Genome Features and Their Annotations", "year": 2015 }, { "doi": "10.1101/pdb.prot088914", "pmc": "PMC5673600", "pubmed": "26631125", "title": "The Saccharomyces Genome Database: Gene 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/sgd.pathways:$1" } ], "publications": [ { "doi": "10.1101/2024.09.16.613348", "pmc": "PMC11430078", "pubmed": "39345624", "title": "Saccharomyces Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements", "year": 2024 }, { "doi": "10.1093/nar/gkh033", "pmc": "PMC308767", "pubmed": "14681421", "title": "Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms", "year": 2004 } ], "uri_format": "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1" }, "sgn": { "contact": { "email": "lam87@cornell.edu", "github": "lukasmueller", "name": "Lukas A. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/sgn:$1" } ], "publications": [ { "doi": "10.1093/nar/gku1195", "pmc": "PMC4383978", "pubmed": "25428362", "title": "The Sol Genomics Network (SGN)--from genotype to phenotype to breeding", "year": 2014 }, { "doi": "10.1093/nar/gkq866", "pmc": "PMC3013765", "pubmed": "20935049", "title": "The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl", "year": 2010 } ], "twitter": "solgenomics", "uri_format": "http://solgenomics.net/phenome/locus_display.pl?locus_id=$1" }, "sh": { "contact": { "email": "dr.shorthair@pm.me", "github": "dr-shorthair", "name": "Simon Cox", "orcid": "0000-0002-3884-3420" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A language for validating RDF graphs against a set of conditions", "download_owl": "https://triplydb.com/w3c/sh/download.trig.gz", "example": "NodeShape", "homepage": "https://www.w3.org/TR/shacl/", "keywords": [ "computer science", "informatics", "knowledge and information systems", "nfdi4ing", "ontology", "ontology and terminology", "quality", "w3c rec" ], "mappings": { "fairsharing": "FAIRsharing.f1449d", "lov": "sh", "tib": "sh", "zazuko": "sh" }, "name": "Shapes Constraint Language", "preferred_prefix": "sh", "repository": "https://github.com/w3c/data-shapes", "synonyms": [ "shacl" ], "uri_format": "http://www.w3.org/ns/shacl#$1" }, "shareloc": { "description": "ShareLoc defines terms to annotate data sets from single molecule localization microscopy, including but not limited to: imaging technique, biological structures or molecules of interest, cell types, experimental condition, labeling method, fixation protocol, etc.", "download_owl": "https://raw.githubusercontent.com/imodpasteur/ShareLoc.XYZ/ontology/shareloc.owl", "example": "000004", "homepage": "https://shareloc.xyz", "keywords": [ "ontology" ], "mappings": { "ols": "shareloc" }, "name": "ShareLoc", "pattern": "^\\d{6}$", "preferred_prefix": "shareloc", "uri_format": "https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_$1" }, "sharkipedia.species": { "contact": { "email": "creeas@gmail.com", "github": "creeas", "name": "Christopher Mull", "orcid": "0000-0003-1710-8256" }, "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/sheepqtldb:$1" } ], "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" }, "shex": { "contact": { "email": "gregg@greggkellogg.net", "github": "gkellogg", "name": "Gregg Kellogg" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Shape Expressions (ShEx) language describes RDF nodes and graph structures. A node constraint describes an RDF node (IRI, blank node or literal) and a shape describes the triples involving nodes in an RDF graph. These descriptions identify predicates and their associated cardinalities and datatypes. ShEx shapes can be used to communicate data structures associated with some process or interface, generate or validate data, or drive user interfaces.", "download_rdf": "https://www.w3.org/ns/shex.ttl", "example": "TripleExpression", "homepage": "http://www.w3.org/ns/shex#", "keywords": [ "metadata", "rdf", "semantic web" ], "mappings": { "zazuko": "shex" }, "name": "Shape Expression Vocabulary", "pattern": "^\\w+$", "preferred_prefix": "shex", "repository": "https://github.com/shexspec/shexspec.github.io", "uri_format": "http://www.w3.org/ns/shex#$1" }, "shibase": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "The database focuses on the comparative genomics of Shigella and provides a way to summarize large volumes of genomic and comparison data in a visually intuitive format.", "example": "SDY2614", "homepage": "http://www.mgc.ac.cn/ShiBASE/", "keywords": [ "genome" ], "mappings": { "prefixcommons": "shibase" }, "name": "ShiBASE", "preferred_prefix": "shibase", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/shibase:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=$1" }, "shsh": { "description": "This shapes graph can be used to validate SHACL shapes graphs against a subset of the syntax rules.", "download_rdf": "http://www.w3.org/ns/shacl-shacl", "example": "ListShape", "homepage": "http://www.w3.org/ns/shacl-shacl", "mappings": { "zazuko": "shsh" }, "name": "SHACL in SHACL", "preferred_prefix": "shsh" }, "sibo": { "contact": { "email": "cjmungall@lbl.gov", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "deprecated": true, "description": "Social Behavior in insects", "download_obo": "http://purl.obolibrary.org/obo/sibo.obo", "download_owl": "http://purl.obolibrary.org/obo/sibo.owl", "example": "0000509", "homepage": "https://github.com/obophenotype/sibo", "keywords": [ "biology", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "SIBO", "biocontext": "SIBO", "bioportal": "SIBO", "ecoportal": "SIBO", "fairsharing": "FAIRsharing.q09hck", "obofoundry": "sibo", "ols": "sibo", "ontobee": "SIBO", "wikidata.entity": "Q114677952" }, "name": "Social Insect Behavior Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "SIBO", "rdf_uri_format": "http://purl.obolibrary.org/obo/SIBO_$1", "repository": "https://github.com/obophenotype/sibo", "uri_format": "http://purl.obolibrary.org/obo/SIBO_$1" }, "sider.drug": { "description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER.", "example": "2244", "homepage": "http://sideeffects.embl.de/", "mappings": { "biocontext": "SIDER.DRUG", "miriam": "sider.drug", "n2t": "sider.drug" }, "name": "SIDER Drug", "pattern": "^\\d+$", "preferred_prefix": "sider.drug", "uri_format": "http://sideeffects.embl.de/drugs/$1" }, "sider.effect": { "description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER.", "example": "C0017565", "homepage": "http://sideeffects.embl.de/", "mappings": { "biocontext": "SIDER.EFFECT", "miriam": "sider.effect", "n2t": "sider.effect" }, "name": "SIDER Side Effect", "pattern": "^C\\d+$", "preferred_prefix": "sider.effect", "provides": "umls", "uri_format": "http://sideeffects.embl.de/se/$1" }, "sigmaaldrich": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Sigma Aldrich is a life sciences supply vendor.", "example": "HPA000698", "github_request_issue": 216, "homepage": "https://www.sigmaaldrich.com", "keywords": [ "biology", "chemistry", "life sciences", "vendor" ], "mappings": { "cellosaurus": "Sigma-Aldrich", "pathguide": "236" }, "name": "Sigma Aldrich", "preferred_prefix": "sigmaaldrich", "uri_format": "https://www.sigmaaldrich.com/US/en/product/sigma/$1" }, "signaling-gateway": { "contact": { "email": "kenan@ucsd.edu", "name": "Kenan Azam", "orcid": "0000-0001-7016-8624" }, "deprecated": true, "description": "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.", "example": "A001094", "homepage": "http://www.signaling-gateway.org/molecule", "keywords": [ "pathway", "protein", "small molecule" ], "mappings": { "biocontext": "SIGNALING-GATEWAY", "miriam": "signaling-gateway", "n2t": "signaling-gateway", "pathguide": "87", "prefixcommons": "signaling-gateway" }, "name": "Signaling Gateway", "pattern": "^A\\d{6}$", "preferred_prefix": "signaling-gateway", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/signaling-gateway:$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/btr190", "pmc": "PMC3106186", "pubmed": "21505029", "title": "Signaling gateway molecule pages--a data model perspective", "year": 2011 }, { "doi": "10.1093/nar/gkm907", "pmc": "PMC2238911", "pubmed": "17965093", "title": "The Molecule Pages database", "year": 2007 }, { "doi": "10.1038/nature01307", "pubmed": "12478304", "title": "The Molecule Pages database", "year": 2002 } ], "uri_format": "http://www.signaling-gateway.org/molecule/query?afcsid=$1" }, "signor": { "contact": { "email": "gianni.cesareni@torvergata.it", "name": "Gianni Cesareni", "orcid": "0000-0002-9528-6018" }, "description": "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature.", "example": "SIGNOR-C41", "homepage": "https://signor.uniroma2.it/", "keywords": [ "biology" ], "license": "CC-BY-NC-4.0", "logo": "https://signor.uniroma2.it/img/signor_logo_noWhite.png", "mappings": { "fairsharing": "FAIRsharing.ss78t4", "miriam": "signor", "pathguide": "599", "uniprot": "DB-0206" }, "name": "Signaling Network Open Resource", "pattern": "^SIGNOR\\-[A-Z]+\\d+$", "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", "pubmed": "26467481", "title": "SIGNOR: a database of causal relationships between biological entities", "year": 2015 } ], "synonyms": [ "SIGNOR" ], "uri_format": "https://signor.uniroma2.it/relation_result.php?id=$1" }, "signor.relation": { "comment": "Currently, you can put a SIGNOR relation ID into the main page search box and it will resolve, but there is not currently a way to resolve them via a URL pattern", "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "Identifiers for relationships between proteins and complexes, along with their type and provenance", "example": "SIGNOR-252737", "github_request_issue": 604, "homepage": "https://signor.uniroma2.it", "keywords": [ "protein-protein interactions" ], "logo": "https://signor.uniroma2.it/img/signor_logo_noWhite.png", "name": "SIGNOR Relation", "pattern": "^SIGNOR-\\d+$", "preferred_prefix": "signor.relation", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "silva.taxon": { "contact": { "email": "lorenz.reimer@dsmz.de", "name": "Lorenz Reimer", "orcid": "0000-0002-7805-0660" }, "contributor": { "email": "jplfaria@anl.gov", "github": "jplfaria", "name": "Jose P. Faria", "orcid": "0000-0001-9302-7250" }, "description": "SILVA is a resource of aligned ribosomal RNA (rRNA) gene sequences for Bacteria, Archaea, and Eukaryotes.\n\nIt assigns internal, auto-incremented integer identifiers to taxa. However, these identifiers are not persistent nor unique - if the label for a taxon is changed, it assigned a new identifier and the old identifier is removed.", "example": "11084", "github_request_issue": 1306, "homepage": "https://www.arb-silva.de", "license": "CC-BY-SA-4.0", "logo": "https://www.arb-silva.de/fileadmin/graphics_general/main/dissemination/silva-sticker-1_2_ext_33.png", "name": "SILVA Taxon", "pattern": "^\\d+$", "preferred_prefix": "silva.taxon", "publications": [ { "doi": "10.1093/nar/gkt1209", "pmc": "PMC3965112", "pubmed": "24293649", "title": "The SILVA and \"All-species Living Tree Project (LTP)\" taxonomic frameworks", "year": 2014 }, { "doi": "10.1093/nar/gks1219", "pmc": "PMC3531112", "pubmed": "23193283", "title": "The SILVA ribosomal RNA gene database project: improved data processing and web-based tools", "year": 2012 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "sio": { "banana": "SIO", "banana_peel": "_", "contact": { "email": "michel.dumontier@gmail.com", "github": "micheldumontier", "name": "Michel Dumontier", "orcid": "0000-0003-4727-9435" }, "description": "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities.", "download_owl": "http://semanticscience.org/ontology/sio/v1.59/sio-release.owl", "example": "000912", "homepage": "https://github.com/micheldumontier/semanticscience", "keywords": [ "biology", "ess", "knowledge representation", "natural science", "nfdi4chem", "nfdi4ing", "ontology", "subject agnostic" ], "mappings": { "aberowl": "SIO", "agroportal": "SIO", "biocontext": "SIO", "biolink": "SIO", "bioportal": "SIO", "fairsharing": "FAIRsharing.dpkb5f", "lov": "sio", "miriam": "sio", "ols": "sio", "ontobee": "SIO", "tib": "sio" }, "name": "Semanticscience Integrated Ontology", "pattern": "^\\d{6}$", "preferred_prefix": "sio", "publications": [ { "doi": "10.1186/2041-1480-5-14", "pmc": "PMC4015691", "pubmed": "24602174", "title": "The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery", "year": 2014 } ], "repository": "https://github.com/micheldumontier/semanticscience", "uri_format": "https://semanticscience.org/resource/SIO_$1", "version": "1.59" }, "sioc.access": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining basic information on permissions and access rights.", "download_rdf": "http://rdfs.org/sioc/access#", "example": "Permission", "homepage": "http://rdfs.org/sioc/spec/", "license": "CC-BY-1.0", "name": "Semantically-Interlinked Online Communities Access Ontology", "preferred_prefix": "sioc.access", "rdf_uri_format": "http://rdfs.org/sioc/access#$1", "uri_format": "http://rdfs.org/sioc/access#$1" }, "sioc.actions": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology of predicates for actions in SIOC", "download_rdf": "http://rdfs.org/sioc/actions#", "example": "DigitalArtifact", "homepage": "http://rdfs.org/sioc/spec/", "license": "CC-BY-1.0", "name": "Semantically-Interlinked Online Communities Actions Ontology", "preferred_prefix": "sioc.actions", "rdf_uri_format": "http://rdfs.org/sioc/actions#$1", "uri_format": "http://rdfs.org/sioc/actions#$1" }, "sioc.argument": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A vocabulary of argumentation predicates for SIOC", "download_rdf": "http://rdfs.org/sioc/argument#", "example": "decides", "homepage": "http://rdfs.org/sioc/spec/", "license": "CC-BY-1.0", "name": "Semantically-Interlinked Online Communities Argumentation Ontology", "preferred_prefix": "sioc.argument", "rdf_uri_format": "http://rdfs.org/sioc/argument#$1", "uri_format": "http://rdfs.org/sioc/argument#$1" }, "sioc.core": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Semantically-Interlinked Online Communities, or SIOC, is an attempt to link online community sites, to use Semantic Web technologies to describe the information that communities have about their structure and contents, and to find related information and new connections between content items and other community objects. SIOC is based around the use of machine-readable information provided by these sites.", "download_rdf": "http://rdfs.org/sioc/ns#", "example": "Item", "homepage": "http://rdfs.org/sioc/spec/", "keywords": [ "society" ], "license": "CC-BY-1.0", "mappings": { "lov": "sioc", "zazuko": "sioc" }, "name": "Semantically-Interlinked Online Communities Core Ontology", "preferred_prefix": "sioc.core", "rdf_uri_format": "http://rdfs.org/sioc/ns#$1", "synonyms": [ "sioc" ], "uri_format": "http://rdfs.org/sioc/ns#$1" }, "sioc.quote": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining basic information on community-related web services.", "download_rdf": "http://rdfs.org/sioc/services#", "example": "has_service", "homepage": "http://rdfs.org/sioc/spec/", "license": "CC-BY-1.0", "name": "Semantically-Interlinked Online Communities Services Ontology - Quote Ontology", "preferred_prefix": "sioc.quote", "rdf_uri_format": "http://rdfs.org/sioc/services#$1", "uri_format": "http://rdfs.org/sioc/services#$1" }, "sioc.swan": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Mappings from SIOC to SWAN, with a small number of aux terms", "download_rdf": "http://rdfs.org/sioc/swan#", "example": "OnlineJournal", "homepage": "http://rdfs.org/sioc/spec/", "license": "CC-BY-1.0", "name": "Semantically-Interlinked Online Communities Services Ontology - SWAN Mapping", "preferred_prefix": "sioc.swan", "rdf_uri_format": "http://rdfs.org/sioc/swan#$1", "uri_format": "http://rdfs.org/sioc/swan#$1" }, "sioc.types": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining subclasses and subproperties of SIOC terms.", "download_rdf": "http://rdfs.org/sioc/types#", "example": "AddressBook", "homepage": "http://rdfs.org/sioc/spec/", "license": "CC-BY-1.0", "name": "Semantically-Interlinked Online Communities Types Ontology", "preferred_prefix": "sioc.types", "rdf_uri_format": "http://rdfs.org/sioc/types#$1", "uri_format": "http://rdfs.org/sioc/types#$1" }, "siren": { "comment": "appears in FOODON, there is no website other than the spreadsheet referenced below on langual's site", "contact": { "email": "patrice.buche@inrae.fr", "name": "Patrice Buche", "orcid": "0000-0002-9134-5404" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A modern method of records management and an automated cross-referenced subject index for accurate and comprehensive information retrieval developed by the US FDA's Bureau of Foods", "example": "F11903", "homepage": "https://www.langual.org/langual_indexed_datasets.asp", "mappings": { "agroportal": "SIREN" }, "name": "Scientific Information Retrieval and Exchange Network", "pattern": "^F\\d+$", "preferred_prefix": "siren", "publications": [ { "doi": "10.1093/jaoac/65.5.1268", "title": "SIREN: Data Base Approach to Scientific Information Handling in the Bureau of Foods, Food and Drug Administration", "year": 1982 } ], "references": [ "https://github.com/FoodOntology/foodon/issues/267", "https://www.langual.org/download/IndexedDatasets/FDA/SIREN%20(updated).TXT" ], "synonyms": [ "SUBSET_SIREN" ] }, "sisu": { "contact": { "email": "hannele.laivuori@helsinki.fi", "name": "Hannele Laivuori", "orcid": "0000-0003-3212-7826" }, "description": "The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies.", "example": "17:41223048", "homepage": "http://www.sisuproject.fi/", "keywords": [ "biomedical science", "epidemiology", "genomics", "medicine", "preclinical studies" ], "mappings": { "biocontext": "SISU", "fairsharing": "FAIRsharing.t1a232", "miriam": "sisu", "n2t": "sisu" }, "name": "Sequencing Initiative Suomi", "pattern": "^[0-9]+:[0-9]+$", "preferred_prefix": "sisu", "publications": [ { "doi": "10.1371/journal.pone.0128524", "pmc": "PMC4452275", "pubmed": "26030606", "title": "Targeted resequencing of the pericentromere of chromosome 2 linked to constitutional delay of growth and puberty", "year": 2015 }, { "doi": "10.1371/journal.pgen.1004494", "pmc": "PMC4117444", "pubmed": "25078778", "title": "Distribution and medical impact of loss-of-function variants in the Finnish founder population", "year": 2014 } ], "uri_format": "http://search.sisuproject.fi/#/variant/$1" }, "sitex": { "contact": { "email": "imedvedeva@celgene.com", "github": "imedvedeva-celgene", "name": "Irina Medvedeva", "orcid": "0000-0003-2802-8198" }, "deprecated": true, "description": "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.", "example": "1000", "homepage": "http://www-bionet.sscc.ru/sitex/", "keywords": [ "domain", "eukaryotic", "life science", "sequence", "structure" ], "mappings": { "biocontext": "SITEX", "fairsharing": "FAIRsharing.5mr9c5", "miriam": "sitex", "n2t": "sitex", "prefixcommons": "sitex" }, "name": "SitEx", "pattern": "^\\d+$", "preferred_prefix": "sitex", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/sitex:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr1187", "pmc": "PMC3245165", "pubmed": "22139920", "title": "SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes", "year": 2011 } ], "uri_format": "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1" }, "skip": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine.", "example": "SKIP001214", "homepage": "https://skip.stemcellinformatics.org/en/", "mappings": { "cellosaurus": "SKIP" }, "name": "Stemcell Knowledge and Information Portal", "pattern": "^SKIP\\d+$", "preferred_prefix": "skip", "uri_format": "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1" }, "skm": { "description": "Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors. ", "example": "rx00408", "homepage": "http://www.nib.si/eng/", "mappings": { "miriam": "skm" }, "name": "Stress Knowledge Map", "pattern": "^rx[0-9]{5}$", "preferred_prefix": "skm", "uri_format": "https://skm.nib.si/api/pss/reactions?reaction_id=$1&return_field=summary" }, "skos": { "contact": { "email": "alistair.miles@linacre.ox.ac.uk", "github": "alimanfoo", "name": "Alistair Miles", "orcid": "0000-0001-9018-4680" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web", "download_owl": "http://aber-owl.net/media/ontologies/skos/1/skos.owl", "download_rdf": "http://www.w3.org/TR/skos-reference/skos.rdf", "example": "prefLabel", "homepage": "https://www.w3.org/2004/02/skos/", "keywords": [ "computer science", "ontology", "subject agnostic", "tib", "w3c rec" ], "mappings": { "aberowl": "skos", "bartoc": "18274", "biocontext": "skos", "fairsharing": "FAIRsharing.48e326", "lov": "skos", "ols": "skos", "tib": "skos", "zazuko": "skos" }, "name": "Simple Knowledge Organization System", "preferred_prefix": "skos", "uri_format": "http://www.w3.org/2004/02/skos/core#$1" }, "skos.thes": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "SKOS-Thes: An extension to SKOS based on the ISO 25964 data model. The ISO 25964 standard, published in 2011, covers all aspects of developing thesauri and setting up mappings across vocabularies to encourage high quality information retrieval across networked resources. [from https://www.dublincore.org/specifications/skos-thes/]", "download_rdf": "https://www.dublincore.org/specifications/skos-thes/ns/skos-thes.ttl", "example": "CompoundEquivalence", "homepage": "https://www.dublincore.org/specifications/skos-thes/ns/", "name": "SKOS Thesaurus Extension", "preferred_prefix": "skos.thes", "rdf_uri_format": "http://purl.org/iso25964/skos-thes#$1", "synonyms": [ "skos-thes", "skosthes" ], "uri_format": "https://www.dublincore.org/specifications/skos-thes/ns/#$1" }, "skosxl": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Simple Knowledge Organization System (SKOS) is a common data model for sharing and linking knowledge organization systems via the Semantic Web. SKOS-XL defines an extension for the Simple Knowledge Organization System, providing additional support for describing and linking lexical entities.This document provides a brief description of the SKOS-XL vocabulary.", "example": "literalForm", "homepage": "http://www.w3.org/2008/05/skos-xl#", "keywords": [ "computer science", "data model", "metadata", "semantic web", "skos", "tib", "w3c rec" ], "mappings": { "lov": "skosxl", "tib": "skosxl", "zazuko": "skosxl" }, "name": "Simple Knowledge Organization System eXtension for Labels", "preferred_prefix": "skosxl", "synonyms": [ "skos-xl", "skos.xl" ], "uri_format": "http://www.w3.org/2008/05/skos-xl#$1" }, "slctr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Sri Lanka Clinical Trials Registry (SLCTR) is a Registry for clinical trials involving human subjects, conducted in Sri Lanka or overseas. The SLCTR is a Primary Registry linked to the Registry Network of the International Clinical Trials Registry Platform of the WHO (WHO-ICTRP). It is a not-for-profit Registry, with free and open access to researchers, clinicians, and the general public. (from homepage)", "example": "SLCTR/2023/010", "homepage": "https://slctr.lk/", "logo": "https://slctr.lk/images/logo.png", "name": "Sri Lanka Clinical Trials Registry", "pattern": "^SLCTR/\\d{4}/\\d+$", "preferred_prefix": "slctr", "references": [ "https://slctr.lk/trials/slctr-2023-010" ] }, "slkbase": { "description": "Cell line databases/resources", "example": "3618", "homepage": "https://sumlineknowledgebase.com/", "mappings": { "cellosaurus": "SLKBase" }, "name": "SUM Breast Cancer Cell Line Knowledge Base", "pattern": "^\\d+$", "preferred_prefix": "slkbase", "uri_format": "https://sumlineknowledgebase.com/?page_id=$1" }, "slm": { "banana": "SLM", "contact": { "email": "swisslipids@isb-sib.ch", "name": "Alan Bridge", "orcid": "0000-0003-2148-9135" }, "description": "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions.", "example": "000000341", "homepage": "http://www.swisslipids.org/#/", "keywords": [ "life science", "metabolomics" ], "license": "CC-BY-4.0", "logo": "https://www.swisslipids.org/images/SL_title_swiss.png", "mappings": { "biocontext": "SWISSLIPID", "fairsharing": "FAIRsharing.pxr7x2", "integbio": "nbdc02026", "miriam": "slm", "n2t": "swisslipid", "ols": "slm", "pathguide": "687", "re3data": "r3d100012603", "togoid": "Swisslipids", "uniprot": "DB-0197", "wikidata": "P8691" }, "name": "SwissLipid", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "SLM", "publications": [ { "doi": "10.1093/bioinformatics/btv285", "pmc": "PMC4547616", "pubmed": "25943471", "title": "The SwissLipids knowledgebase for lipid biology", "year": 2015 } ], "synonyms": [ "swisslipid", "swisslipids" ], "uri_format": "https://www.swisslipids.org/#/entity/SLM:$1" }, "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": "https://github.com/nasa/LSDAO/raw/refs/heads/master/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", "ols": "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_$1", "version": "2025-12-11" }, "smart": { "contact": { "email": "chris.ponting@ed.ac.uk", "name": "Chris P. Ponting", "orcid": "0000-0003-0202-7816" }, "description": "The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures.", "example": "SM00015", "homepage": "http://smart.embl-heidelberg.de/", "keywords": [ "domain", "life science", "protein", "structure" ], "mappings": { "biocontext": "SMART", "fairsharing": "FAIRsharing.hsbpq3", "go": "SMART", "integbio": "nbdc00682", "miriam": "smart", "n2t": "smart", "prefixcommons": "smart", "togoid": "Smart", "uniprot": "DB-0097" }, "name": "Simple Modular Architecture Research Tool", "pattern": "^SM\\d{5}$", "preferred_prefix": "smart", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/smart:$1" } ], "publications": [ { "doi": "10.1093/nar/27.1.229", "pmc": "PMC148142", "pubmed": "9847187", "title": "SMART: identification and annotation of domains from signalling and extracellular protein sequences", "year": 1999 }, { "doi": "10.1093/nar/gkaf1023", "pubmed": "41062452" }, { "doi": "10.1093/nar/gkx922", "pmc": "PMC5753352", "pubmed": "29040681", "title": "20 years of the SMART protein domain annotation resource", "year": 2018 }, { "doi": "10.1093/nar/gku949", "pmc": "PMC4384020", "pubmed": "25300481", "title": "SMART: recent updates, new developments and status in 2015", "year": 2014 }, { "doi": "10.1093/nar/gkr931", "pmc": "PMC3245027", "pubmed": "22053084", "title": "SMART 7: recent updates to the protein domain annotation resource", "year": 2011 }, { "doi": "10.1093/nar/gkn808", "pmc": "PMC2686533", "pubmed": "18978020", "title": "SMART 6: recent updates and new developments", "year": 2008 }, { "doi": "10.1093/nar/gkj079", "pmc": "PMC1347442", "pubmed": "16381859", "title": "SMART 5: domains in the context of genomes and networks", "year": 2006 }, { "doi": "10.1093/nar/gkh088", "pmc": "PMC308822", "pubmed": "14681379", "title": "SMART 4.0: towards genomic data integration", "year": 2004 }, { "doi": "10.1093/nar/30.1.242", "pmc": "PMC99073", "pubmed": "11752305", "title": "Recent improvements to the SMART domain-based sequence annotation resource", "year": 2002 }, { "doi": "10.1093/nar/28.1.231", "pmc": "PMC102444", "pubmed": "10592234", "title": "SMART: a web-based tool for the study of genetically mobile domains", "year": 2000 }, { "doi": "10.1016/s0959-440x(99)80055-4", "pubmed": "10361098", "title": "Protein families in multicellular organisms", "year": 1999 }, { "doi": "10.1016/S0959-440X(99)80055-4", "title": "Protein families in multicellular organisms." } ], "uri_format": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1" }, "smc.bgc": { "contact": { "email": "dwudwary@lbl.gov", "name": "Daniel W Udwary", "orcid": "0000-0002-3491-0198" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "The secondary metabolism collaboratory is a database for secondary metabolite biosynthetic gene clusters. This prefix represents identifiers for individual biosynthetic gene clusters (BGCs) linked to their corresponding bacterial or archaeal source.", "example": "12039302", "github_request_issue": 1301, "homepage": "https://smc.jgi.doe.gov", "name": "Secondary Metabolism Collaboratory - biosynthetic gene cluster", "pattern": "^\\d+$", "preferred_prefix": "smc.bgc", "publications": [ { "doi": "10.1093/nar/gkae1060", "pubmed": "39540430", "title": "The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://smc.jgi.doe.gov/bgc/$1" }, "smc.source": { "contact": { "email": "dwudwary@lbl.gov", "name": "Daniel W Udwary", "orcid": "0000-0002-3491-0198" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "The secondary metabolism collaboratory is a database for secondary metabolite biosynthetic gene clusters. This prefix represents identifiers for bacteria and archaea sources linked to their associated set of biosynthetic gene clusters (BGCs).", "example": "1", "github_request_issue": 1301, "homepage": "https://smc.jgi.doe.gov", "name": "Secondary Metabolism Collaboratory - taxon", "pattern": "^\\d+$", "preferred_prefix": "smc.source", "publications": [ { "doi": "10.1093/nar/gkae1060", "pubmed": "39540430", "title": "The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://smc.jgi.doe.gov/sources/$1" }, "smid": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C. elegans and other nematodes. SMIDs aim to make life easier for describing biogenic small molecules in metabolomic and genomic applications.", "example": "137", "homepage": "https://smid-db.org/", "name": "C. elegans Small Molecule Identifier Database", "pattern": "^\\d+$", "preferred_prefix": "smid", "synonyms": [ "SMID-DB" ], "uri_format": "https://smid-db.org/smid/$1" }, "smiles": { "contact": { "email": "tim.vandermeersch@gmail.com", "github": "timvdm", "name": "Tim Vandermeersch", "orcid": "0000-0001-7542-0286" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "github": "NishaSharma14", "name": "Nisha Sharma", "orcid": "0009-0006-4755-1039" } ], "description": "Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions.", "example": "CC2(C)C\\1CCC(C)/C=C/12", "homepage": "https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html", "keywords": [ "bioinformatics", "chemistry", "data analysis", "life science", "lipidomics", "metabolomics", "molecular entity", "structure" ], "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBazRFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--047d6c77b3abf77702d511a7e6a66acd8eb554b8/19335777.jpg?disposition=inline", "mappings": { "fairsharing": "FAIRsharing.qv4b3c", "wikidata": "P233", "wikidata.entity": "Q466769" }, "name": "Simplified molecular-input line-entry system", "pattern": "^[A-Za-z0-9+\\-\\*=#$:().>/\\\\\\[\\]%]+$", "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", "pmc": "PMC3551648", "pubmed": "23031664", "title": "mol2chemfig, a tool for rendering chemical structures from molfile or SMILES format to LATE X code", "year": 2012 }, { "doi": "10.1021/ci00067a005", "title": "SMILES. 3. DEPICT. Graphical depiction of chemical structures", "year": 1990 }, { "doi": "10.1021/ci00062a008", "title": "SMILES. 2. Algorithm for generation of unique SMILES notation", "year": 1989 }, { "doi": "10.1021/ci00057a005", "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/opensmiles", "uri_format": "https://www.simolecule.com/cdkdepict/depict/bow/svg?smi=$1&zoom=2.0&annotate=cip" }, "smpdb": { "contact": { "email": "david.wishart@ualberta.ca", "github": "DavidWishartLab", "name": "David S. Wishart", "orcid": "0000-0002-3207-2434" }, "description": "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.", "example": "SMP0000219", "homepage": "https://smpdb.ca/", "keywords": [ "chemical", "human", "life science", "metabolite", "pathway" ], "mappings": { "biocontext": "SMPDB", "biolink": "PathWhiz", "edam": "2659", "fairsharing": "FAIRsharing.y1zyaq", "integbio": "nbdc00908", "miriam": "smpdb", "n2t": "smpdb", "pathguide": "311", "prefixcommons": "smpdb" }, "name": "Small Molecule Pathway Database", "pattern": "^SMP\\d+$", "preferred_prefix": "smpdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/smpdb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkt1067", "pmc": "PMC3965088", "pubmed": "24203708", "title": "SMPDB 2.0: big improvements to the Small Molecule Pathway Database", "year": 2013 }, { "doi": "10.1093/nar/gkp1002", "pmc": "PMC2808928", "pubmed": "19948758", "title": "SMPDB: The Small Molecule Pathway Database", "year": 2009 }, { "doi": "doi:10.1093/nar/gkp1002", "title": "SMPDB: The Small Molecule Pathway Database." } ], "synonyms": [ "SMP" ], "twitter": "WishartLab", "uri_format": "https://smpdb.ca/view/$1" }, "snap": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality.", "example": "Quality", "homepage": "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf", "keywords": [ "gene", "interaction", "pathway", "protein" ], "mappings": { "pathguide": "494", "prefixcommons": "snap" }, "name": "Snapshot", "preferred_prefix": "snap", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/snap:$1" } ], "synonyms": [ "bfo11snap" ], "uri_format": "http://www.ifomis.org/bfo/1.1/snap#$1" }, "snctp": { "comment": "it appears they cede information into WHO", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The SNCTP (Swiss National Clinical Trials Portal) is the portal where clinical trials in Switzerland are published. It contains data from two sources: from BASEC, the national platform for submitting applications for research projects to ethics committees, and from the ICTRP (the WHO International Clinical Trials Registry Platform), which covers the 17 primary registries worldwide. The ICTRP clinical trials shown on the SNCTP are limited to those conducted in Switzerland; there is also an option to display trials conducted in one of Switzerland's neighbouring countries. [from homepage]", "example": "SNCTP000005580", "homepage": "https://kofam.ch/en/snctp-portal", "name": "Swiss National Clinical Trials Portal", "preferred_prefix": "snctp" }, "snodb": { "contact": { "email": "michelle.scott@usherbrooke.ca", "name": "Michelle S Scott", "orcid": "0000-0001-6231-7714" }, "contributor": { "email": "maaya.m466@gmail.com", "github": "maayamanoj466", "name": "Maaya Manoj", "orcid": "0009-0000-6974-6386" }, "description": "Contains identifiers for human small nucleolar RNAs (snoRNAs) from snoDB, an interactive database of human small nucleolar RNAs (snoRNAs) that includes up-to-date information on snoRNA features, genomic location, conservation, host gene, snoRNA–RNA targets and snoRNA abundance and provides links to other resources.", "example": "snoDB0001", "github_request_issue": 1655, "homepage": "https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB", "keywords": [ "human nucleolar rna", "rna", "snorna-protein" ], "mappings": { "integbio": "nbdc02602" }, "name": "snoDB", "pattern": "^snoDB\\d{4}$", "preferred_prefix": "snodb", "publications": [ { "doi": "10.1093/nar/gkac835", "pmc": "PMC9825428", "pubmed": "36165892", "title": "snoDB 2.0: an enhanced interactive database, specializing in human snoRNAs", "year": 2023 }, { "doi": "10.1093/nar/gkz884", "pmc": "PMC6943035", "pubmed": "31598696", "title": "snoDB: an interactive database of human snoRNA sequences, abundance and interactions", "year": 2020 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/detailed_view/$1" }, "snomedct": { "contact": { "email": "custserv@nlm.nih.gov", "name": "NLM Customer Service" }, "contributor_extras": [ { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" } ], "description": "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc.", "download_owl": "http://snomed.info/sct/900000000000207008/version/20251017", "example": "284196006", "homepage": "https://browser.ihtsdotools.org/", "keywords": [ "biomedical science", "health science", "medicine", "ontology", "preclinical studies" ], "license": "https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf", "mappings": { "aberowl": "SNOMEDCT", "bartoc": "20686", "biocontext": "SNOMEDCT", "biolink": "SNOMEDCT", "bioportal": "SNOMEDCT", "fairsharing": "FAIRsharing.d88s6e", "hl7": "2.16.840.1.113883.6.96", "miriam": "snomedct", "n2t": "snomedct", "ols": "snomed", "prefixcommons": "snomedct", "wikidata": "P5806" }, "name": "SNOMED CT (International Edition)", "pattern": "^(\\w+)?\\d+$", "preferred_prefix": "snomedct", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/snomedct:$1" }, { "code": "snomed.info", "description": "Stopped working sometime in 2020's", "uri_format": "http://snomed.info/id/$1" } ], "publications": [ { "doi": "10.1097/00024665-200609000-00011", "pubmed": "16980782", "title": "Standardized nursing language in the systematized nomenclature of medicine clinical terms: A cross-mapping validation method", "year": 2006 } ], "rdf_uri_format": "http://snomed.info/id/$1", "synonyms": [ "SCTID", "SCTID_2010_1_31", "SNOMECT", "SNOMED", "SNOMEDCT", "SNOMEDCTCT", "SNOMEDCTCT_2018_03_01", "SNOMEDCTCT_2019_03_01", "SNOMEDCT_2005_07_31", "SNOMEDCT_2010_1_31", "SNOMEDCT_2020_03_01", "SNOMEDCT_US", "SNOMEDCT_US_2015_03_01", "SNOMEDCT_US_2016_03_01", "SNOMEDCT_US_2018_03_01", "SNOMEDCT_US_2018_09_01", "SNOMEDCT_US_2019_03_01", "SNOMEDCT_US_2019_09_01", "SNOMEDCT_US_2020_03_01", "SNOMEDCT_US_2020_09_01", "SNOMEDCT_US_2021_03_01", "SNOMEDCT_US_2021_07_31", "SNOMEDCT_US_2021_09_01", "SNOMEDCT_US_2022_07_31", "SNOMEDCT_US_2022_09_01", "SNOMEDCT_US_2022_12_31", "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", "SNOMEDCT_US_2024_03_01", "SNOMED_CT", "SNOMED_CT_US_2018_03_01", "SNOWMEDCT", "SNOWMEDCT_US", "SNOWMEDCT_US_2018_03_01" ], "uri_format": "http://purl.bioontology.org/ontology/SNOMEDCT/$1", "version": "20251017" }, "snornabase": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A comprehensive database of\n\nhuman H/ACA and C/D box snoRNAs.", "example": "SR0000178", "homepage": "https://www-snorna.biotoul.fr/", "keywords": [ "rna" ], "mappings": { "integbio": "nbdc00323", "prefixcommons": "snornalbmedb" }, "name": "snoRNABase", "preferred_prefix": "snornabase", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/snornalbmedb:$1" } ], "uri_format": "http://www-snorna.biotoul.fr/plus.php?id=$1" }, "snp2tfbs": { "description": "SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome.", "example": "rs11603840", "homepage": "https://ccg.epfl.ch/snp2tfbs/", "mappings": { "miriam": "snp2tfbs" }, "name": "SNP to Transcription Factor Binding Sites", "pattern": "^rs[0-9]+$", "preferred_prefix": "snp2tfbs", "provides": "dbsnp", "uri_format": "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1" }, "snp500cancer": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer.", "example": "TP53-47", "homepage": "http://snp500cancer.nci.nih.gov", "keywords": [ "dna" ], "mappings": { "prefixcommons": "snp500cancer" }, "name": "SNP500Cancer", "preferred_prefix": "snp500cancer", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/snp500cancer:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id=$1" }, "so": { "appears_in": [ "pcl" ], "banana": "SO", "contact": { "email": "keilbeck@genetics.utah.edu", "github": "keilbeck", "name": "Karen Eilbeck", "orcid": "0000-0002-0831-6427" }, "description": "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data.", "download_obo": "https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/master/Ontology_Files/so.obo", "download_owl": "http://purl.obolibrary.org/obo/so.owl", "example": "0001157", "homepage": "http://www.sequenceontology.org/", "keywords": [ "bioinformatics", "biology", "deoxyribonucleic acid", "dna", "gene", "genome", "genomics", "life science", "obo", "ontology", "region", "ribonucleic acid", "rna", "sequence annotation", "sequence feature", "structure", "transcriptomics" ], "license": "CC-BY-4.0", "logo": "https://obofoundry.org/images/so_logo.png", "mappings": { "aberowl": "SO", "agroportal": "SO", "biocontext": "SO", "bioportal": "SO", "fairsharing": "FAIRsharing.6bc7h9", "go": "SO", "miriam": "so", "n2t": "so", "obofoundry": "so", "ols": "so", "ontobee": "SO", "prefixcommons": "so", "wikidata.entity": "Q81661803" }, "name": "Sequence types and features ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "SO", "providers": [ { "code": "", "description": "Sequence Ontology", "homepage": "http://www.sequenceontology.org/", "name": "Sequence Ontology", "uri_format": "http://www.sequenceontology.org/miso/current_release/term/SO:$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/so:$1" } ], "publications": [ { "doi": "10.1186/gb-2010-11-8-r88", "pmc": "PMC2945790", "pubmed": "20796305", "title": "A standard variation file format for human genome sequences", "year": 2010 }, { "doi": "10.1016/j.jbi.2010.03.002", "pmc": "PMC3052763", "pubmed": "20226267", "title": "Evolution of the Sequence Ontology terms and relationships", "year": 2010 }, { "doi": "10.1186/gb-2005-6-5-r44", "pmc": "PMC1175956", "pubmed": "15892872", "title": "The Sequence Ontology: a tool for the unification of genome annotations", "year": 2005 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/SO_$1", "repository": "https://github.com/The-Sequence-Ontology/SO-Ontologies", "uri_format": "http://purl.obolibrary.org/obo/SO_$1", "version": "2024-11-18" }, "sopharm": { "contact": { "email": "adrien.coulet@loria.fr", "name": "Adrien Coulet", "orcid": "0000-0002-1466-062X" }, "deprecated": true, "description": "SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. SO-Pharm articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables to represent pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables to represent patient and more largely panel included in trials, and populations. SO-Pharm enables the representation of measured items on this patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains.", "download_owl": "http://aber-owl.net/media/ontologies/SOPHARM/18/sopharm.owl", "homepage": "http://www.loria.fr/~coulet/sopharm2.0_description.php", "keywords": [ "obo", "ontology" ], "mappings": { "aberowl": "SOPHARM", "biocontext": "SOPHARM", "bioportal": "SOPHARM", "obofoundry": "sopharm" }, "name": "Suggested Ontology for Pharmacogenomics", "preferred_prefix": "SOPHARM", "rdf_uri_format": "http://purl.obolibrary.org/obo/SOPHARM_$1", "uri_format": "http://purl.obolibrary.org/obo/SOPHARM_$1" }, "sosa": { "contact": { "email": "dr.shorthair@pm.me", "github": "dr-shorthair", "name": "Simon Cox", "orcid": "0000-0002-3884-3420" }, "contributor": { "email": "philip.stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "description": "This ontology is based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group.", "download_rdf": "https://www.w3.org/ns/sosa/", "example": "FeatureOfInterest", "github_request_issue": 1274, "homepage": "https://www.w3.org/TR/vocab-ssn/", "keywords": [ "engineering", "environment", "ess", "iot", "nfdi4chem", "nfdi4ing" ], "license": "http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document", "mappings": { "agroportal": "SOSA", "lov": "sosa", "tib": "sosa", "zazuko": "sosa" }, "name": "Sensor, Observation, Sample, and Actuator Ontology", "preferred_prefix": "sosa", "publications": [ { "doi": "10.1016/j.websem.2018.06.003", "title": "SOSA: A lightweight ontology for sensors, observations, samples, and actuators", "year": 2019 } ], "repository": "https://github.com/w3c/sdw", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.w3.org/ns/sosa/$1" }, "soybase": { "contact": { "email": "Jacqueline.Campbell@usda.gov", "name": "Jacqueline Campbell", "orcid": "0000-0003-2787-3955" }, "description": "SoyBase is a repository for curated genetics, genomics and related data resources for soybean.", "example": "BARC-013845-01256", "homepage": "http://soybase.org/", "keywords": [ "agriculture", "comparative genomics", "development", "life science", "obo", "phenotype", "plant breeding", "spider" ], "mappings": { "biocontext": "SOYBASE", "fairsharing": "FAIRsharing.z4agsr", "integbio": "nbdc01817", "miriam": "soybase", "n2t": "soybase", "ncbi": "SoyBase", "pathguide": "44", "prefixcommons": "soy", "re3data": "r3d100010846" }, "name": "SoyBase", "pattern": "^\\w+(\\-)?\\w+(\\-)?\\w+$", "preferred_prefix": "soybase", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/soy:$1" } ], "publications": [ { "doi": "10.1093/nar/gkp798", "pmc": "PMC2808871", "pubmed": "20008513", "title": "SoyBase, the USDA-ARS soybean genetics and genomics database", "year": 2009 } ], "twitter": "SoyBaseDatabase", "uri_format": "https://legacy.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1" }, "span": { "comment": "see also snap. This ontology only exists in description in the paper and does not have an associated web resource", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality.", "homepage": "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf", "keywords": [ "ontology", "upper-level ontology" ], "name": "Span", "preferred_prefix": "span", "synonyms": [ "bfo11span" ] }, "sparcdrs": { "description": "The SPARC Data Repository Service (DRS) is an implementation of the Global Alliance for Genomics and Health (GA4GH) DRS specification that provides a standardized API that enables researchers and other data consumers to access and retrieve data objects from various data repositories in a consistent and cloud-agnostic way. This implementation provides information for data objects in the SPARC repository (sparc.science).", "example": "package/8ca67504-3167-4cc8-ba74-98137bb7cd0a", "homepage": "https://www.fdilab.org", "mappings": { "miriam": "sparc.drs" }, "name": "SPARC DRS", "pattern": "^(?:[a-zA-Z]+\\/)?[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$", "preferred_prefix": "sparcdrs", "uri_format": "https://services.scicrunch.io/sparc/drs/v1/package/$1" }, "spbase": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "SpBase, is designed to present the results of the genome sequencing project for the purple sea urchin. THe sequences and annotations emerging from this effort are organized in a database that provides the research community access to those data not normally presented through NCBI and other large databases.", "example": "SPU_000001", "homepage": "http://spbase.org", "keywords": [ "dna", "genome", "rna" ], "mappings": { "integbio": "nbdc00686", "prefixcommons": "spbase" }, "name": "SpBase", "preferred_prefix": "spbase", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/spbase:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id=$1" }, "spd": { "contact": { "email": "ramirez@macn.gov.ar", "github": "martinjramirez", "name": "Martin Ramirez", "orcid": "0000-0002-0358-0130" }, "description": "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).", "download_obo": "http://purl.obolibrary.org/obo/spd.obo", "download_owl": "http://purl.obolibrary.org/obo/spd.owl", "example": "0000001", "homepage": "http://research.amnh.org/atol/files/", "keywords": [ "anatomy", "behavior", "life science", "obo", "ontology", "spider" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "SPD", "biocontext": "SPD", "bioportal": "SPD", "fairsharing": "FAIRsharing.yecp83", "obofoundry": "spd", "ols": "spd", "ontobee": "SPD", "prefixcommons": "spdo", "wikidata": "P4537", "wikidata.entity": "Q42404539" }, "name": "Spider Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "SPD", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/spdo:$1" } ], "publications": [ { "doi": "10.3390/d11100202", "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_$1" }, "spdx": { "contact": { "email": "gary@sourceauditor.com", "github": "goneall", "name": "Gary O'Neall" }, "description": "The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception.", "example": "CC-BY-1.0", "example_extras": [ "GPL-1.0+" ], "homepage": "https://spdx.org/licenses", "keywords": [ "license" ], "logo": "https://spdx.dev/wp-content/uploads/sites/31/2023/08/logo-color.svg", "mappings": { "bartoc": "20514", "miriam": "spdx", "n2t": "spdx" }, "name": "Software Package Data Exchange License", "pattern": "^[0-9A-Za-z\\-.\\+]+$", "preferred_prefix": "spdx", "repository": "https://github.com/spdx/license-list-data", "synonyms": [ "spdx.license", "spdx.licenses" ], "uri_format": "https://spdx.org/licenses/$1" }, "spdx.term": { "contact": { "email": "gary@sourceauditor.com", "github": "goneall", "name": "Gary O'Neall" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A dictionary of named properties and classes for Software Package Data Exchange (SPDX) - an open standard for communicating software bill of material information, including components, licenses, copyrights, and security references. SPDX reduces redundant work by providing a common format for companies and communities to share important data, thereby streamlining and improving compliance. [from homepage]", "example": "annotation", "github_request_issue": 1598, "homepage": "https://spdx.org/rdf/terms/", "logo": "https://spdx.dev/wp-content/uploads/sites/31/2023/08/logo-color.svg", "name": "Software Package Data Exchange RDF Vocabulary", "preferred_prefix": "spdx.term", "rdf_uri_format": "http://spdx.org/rdf/terms#$1", "synonyms": [ "spdx.terms" ], "uri_format": "http://spdx.org/rdf/terms#$1" }, "sphn": { "contact": { "email": "Sabine.Oesterle@sib.swiss", "name": "Sabine Oesterle", "orcid": "0000-0003-3248-7899" }, "contributor": { "email": "deepak.unni3@gmail.com", "github": "deepakunni3", "name": "Deepak Unni", "orcid": "0000-0002-3583-7340" }, "description": "The Swiss Personalized Health Network is a national infrastructure initiative with the aim to develop, implement, and validate coordinated data infrastructures in order to make health-relevant data interoperable and shareable for research in Switzerland. The sphn RDF schema builds the foundation for all data exchanges within the sphn by integrating semantic information defined in the [sphn dataset](https://sphn.ch/document/sphn-dataset/).", "download_owl": "https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology/-/raw/master/rdf_schema/sphn_rdf_schema.owl", "download_rdf": "https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology/-/raw/master/rdf_schema/sphn_rdf_schema.ttl", "example": "Allergy", "github_request_issue": 535, "homepage": "https://www.sphn.ch", "keywords": [ "ontology" ], "license": "CC-BY-4.0", "name": "Swiss Personalized Health Network Schema", "pattern": "^\\S+$", "preferred_prefix": "sphn", "repository": "https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://biomedit.ch/rdf/sphn-ontology/sphn#$1" }, "spike.map": { "contact": { "email": "Yossih@tauex.tau.ac.il", "name": "Yosef Shiloh", "orcid": "0000-0002-1538-6060" }, "description": "SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps.", "example": "spike00001", "homepage": "http://www.cs.tau.ac.il/~spike/", "keywords": [ "dna", "gene expression", "pathway" ], "mappings": { "biocontext": "SPIKE.MAP", "miriam": "spike.map", "n2t": "spike.map", "prefixcommons": "spike" }, "name": "SPIKE Map", "pattern": "^spike\\d{5}$", "preferred_prefix": "spike.map", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/spike:$1" } ], "publications": [ { "doi": "10.1093/nar/gkq1167", "pmc": "PMC3014840", "pubmed": "21097778", "title": "SPIKE: a database of highly curated human signaling pathways", "year": 2010 }, { "doi": "10.1186/1471-2105-9-110", "pmc": "PMC2263022", "pubmed": "18289391", "title": "SPIKE--a database, visualization and analysis tool of cellular signaling pathways", "year": 2008 } ], "uri_format": "http://www.cs.tau.ac.il/~spike/maps/$1.html" }, "splash": { "contact": { "email": "ofiehn@ucdavis.edu", "name": "Oliver Fiehn", "orcid": "0000-0002-6261-8928" }, "description": "The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance.", "example": "splash10-0zq2000000-77302b0326a418630a84", "homepage": "http://mona.fiehnlab.ucdavis.edu/", "keywords": [ "lipidomics", "mass spectrum", "metabolomics", "proteomics" ], "mappings": { "biocontext": "SPLASH", "fairsharing": "FAIRsharing.f31b8f", "miriam": "splash", "n2t": "splash" }, "name": "Spectra Hash Code", "pattern": "^splash\\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$", "preferred_prefix": "splash", "publications": [ { "doi": "10.1038/nbt.3689", "pubmed": "27824832", "title": "SPLASH, a hashed identifier for mass spectra", "year": 2016 } ], "repository": "https://github.com/berlinguyinca/spectra-hash", "uri_format": "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1" }, "splicenest": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "SpliceNest [1] is a web based graphical tool to explore gene structure, including alternative splicing, based on a mapping on the EST consensus sequences (contigs) from GeneNest [2] to the complete human genome.", "example": "Hs635", "homepage": "http://splicenest.molgen.mpg.de/", "keywords": [ "dna", "gene", "genome" ], "mappings": { "prefixcommons": "splicenest" }, "name": "SpliceNest", "preferred_prefix": "splicenest", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/splicenest:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster=$1" }, "spp": { "contact": { "email": "nmckenna@bcm.edu", "name": "Neil McKenna", "orcid": "0000-0001-6689-0104" }, "description": "The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways.", "example": "10.1621/vwN2g2HaX3", "homepage": "https://www.signalingpathways.org/index.jsf", "keywords": [ "omics", "transcriptomics" ], "mappings": { "fairsharing": "FAIRsharing.WxI96O", "miriam": "spp", "re3data": "r3d100013650" }, "name": "Signaling Pathways Project", "pattern": "^10.\\w{4}/\\w{10}$", "preferred_prefix": "spp", "publications": [ { "doi": "10.1038/s41597-019-0193-4", "pmc": "PMC6823428", "pubmed": "31672983", "title": "The Signaling Pathways Project, an integrated 'omics knowledgebase for mammalian cellular signaling pathways", "year": 2019 } ], "twitter": "sigpathproject", "uri_format": "https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1" }, "srao": { "contact": { "email": "allyson.lister@oerc.ox.ac.uk", "github": "allysonlister", "name": "Allyson Lister", "orcid": "0000-0002-7702-4495" }, "description": "The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies.", "download_obo": "https://github.com/FAIRsharing/subject-ontology/raw/refs/heads/master/SRAO.obo", "download_owl": "https://github.com/FAIRsharing/subject-ontology/raw/refs/heads/master/SRAO.owl", "example": "0000400", "homepage": "https://github.com/FAIRsharing/subject-ontology", "keywords": [ "agriculture", "biomedical science", "classification", "computer science", "earth science", "environmental science", "fair", "humanities", "life science", "metadata standardization", "metascience", "natural science", "ontology", "resource metadata", "topics" ], "mappings": { "fairsharing": "FAIRsharing.b1xD9f", "ols": "srao" }, "name": "FAIRsharing Subject Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "srao", "repository": "https://github.com/FAIRsharing/subject-ontology", "twitter": "FAIRsharing_org", "uri_format": "http://www.fairsharing.org/ontology/subject/SRAO_$1", "version": "2025-06-01" }, "ssbd.dataset": { "contact": { "email": "sonami@riken.jp", "name": "Shuichi Onami", "orcid": "0000-0002-8255-1724" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations.", "example": "1", "homepage": "https://ssbd.riken.jp", "keywords": [ "cell biology", "developmental biology", "molecular dynamics" ], "mappings": { "fairsharing": "FAIRsharing.we2r5a" }, "name": "System Science of Biological Dynamics dataset", "pattern": "^\\d+$", "preferred_prefix": "ssbd.dataset", "publications": [ { "doi": "10.1093/bioinformatics/btw417", "pmc": "PMC5181557", "pubmed": "27412095", "title": "SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena", "year": 2016 } ], "uri_format": "https://ssbd.riken.jp/database/dataset/$1" }, "ssbd.project": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations.", "example": "1", "homepage": "https://ssbd.riken.jp", "name": "System Science of Biological Dynamics project", "pattern": "^\\d+$", "preferred_prefix": "ssbd.project", "uri_format": "https://ssbd.riken.jp/database/project/$1" }, "ssn": { "contact": { "email": "dr.shorthair@pm.me", "github": "dr-shorthair", "name": "Simon Cox", "orcid": "0000-0002-3884-3420" }, "contributor": { "email": "philip.stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "description": "This ontology describes sensors, actuators and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.", "download_owl": "http://aber-owl.net/media/ontologies/SSN/2/ssn.owl", "download_rdf": "https://www.w3.org/ns/ssn/", "example": "hasProperty", "github_request_issue": 1272, "homepage": "https://www.w3.org/TR/vocab-ssn", "keywords": [ "engineering", "ess", "imaging", "iot", "methods", "monitoring", "nfdi4chem", "nfdi4ing", "ontology", "remote sensing", "resource metadata", "sensor data", "w3c rec", "web of things" ], "license": "http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document", "mappings": { "aberowl": "SSN", "agroportal": "SSN", "bioportal": "SSN", "fairsharing": "FAIRsharing.c0bvcy", "lov": "ssn", "tib": "ssn", "zazuko": "ssn" }, "name": "Semantic Sensor Network Ontology", "preferred_prefix": "ssn", "publications": [ { "doi": "10.3233/sw-180320", "title": "The Modular SSN Ontology: A Joint W3C and OGC Standard Specifying the Semantics of Sensors, Observations, Sampling, and Actuation", "year": 2019 }, { "doi": "10.1016/j.websem.2018.06.003", "title": "SOSA: A lightweight ontology for sensors, observations, samples, and actuators", "year": 2018 }, { "doi": "10.1016/j.websem.2012.05.003", "title": "The SSN ontology of the W3C semantic sensor network incubator group", "year": 2012 } ], "repository": "https://github.com/w3c/sdw-sosa-ssn", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.w3.org/ns/ssn/$1" }, "ssn.system": { "contact": { "email": "dr.shorthair@pm.me", "github": "dr-shorthair", "name": "Simon Cox", "orcid": "0000-0002-3884-3420" }, "contributor": { "email": "philip.stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "description": "This ontology describes system capabilities, operating ranges, and survival ranges. Please report any errors to the W3C Spatial Data on the Web Working Group via the SDW WG Public List public-sdw-wg@w3.org", "download_rdf": "http://www.w3.org/ns/ssn/systems", "example": "qualityOfObservation", "github_request_issue": 1270, "homepage": "https://www.w3.org/TR/vocab-ssn/", "keywords": [ "engineering", "nfdi4chem", "nfdi4ing" ], "license": "http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document", "mappings": { "tib": "ssnsystem" }, "name": "System capabilities, operating ranges, and survival ranges ontology", "preferred_prefix": "ssn.system", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.w3.org/ns/ssn/systems/$1" }, "ssrn.article": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for an article/paper at the SSRN", "example": "1667659", "homepage": "https://ssrn.com", "mappings": { "wikidata": "P893" }, "name": "Social Science Research Network Article", "preferred_prefix": "ssrn.article", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://ssrn.com/abstract=$1" }, "ssrn.author": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for an author at the Social Science Research Network", "example": "112517", "homepage": "https://ssrn.com", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P3747" }, "name": "Social Science Research Network Author", "pattern": "^[1-9]\\d{0,6}$", "preferred_prefix": "ssrn.author", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://ssrn.com/author=$1" }, "sssom": { "contact": { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, "contributor": { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, "description": "SSSOM is a Simple Standard for Sharing Ontological Mappings, providing - a TSV-based representation for ontology term mappings - a comprehensive set of standard metadata elements to describe mappings and - a standard translation between the TSV and the Web Ontology Language (OWL). Most metadata elements, such as \"sssom:mapping_justification\" are defined in the sssom namespace.", "example": "mapping_justification", "example_extras": [ "superClassOf" ], "github_request_issue": 759, "homepage": "https://w3id.org/sssom", "license": "BSD-3-Clause", "name": "Simple Standard for Sharing Ontological Mappings", "pattern": "^[A-Za-z_]+$", "preferred_prefix": "sssom", "repository": "https://github.com/mapping-commons/sssom", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://w3id.org/sssom/$1" }, "sstoss": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "SSToSS is a database which provides sequence-structural templates of single member protein domain superfamilies like PASS2. Sequence-structural templates are recognized by considering the content and overlap of sequence similarity and structural parameters like, solvent inaccessibility, secondary structural content, hydrogen bonding and spatial packing of the residues among the protein of single member superfamilies.", "example": "01.01.005", "homepage": "http://caps.ncbs.res.in/SSTOSS/index.htm", "keywords": [ "protein", "structure" ], "mappings": { "prefixcommons": "sstoss" }, "name": "Sequence-Structural Templates of Single-member Superfamilies", "preferred_prefix": "sstoss", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/sstoss:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code=$1" }, "stap": { "contact": { "email": "bhsung@kribb.re.kr", "name": "Bong Hyun Sung", "orcid": "0000-0002-8992-1118" }, "deprecated": true, "description": "STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB).", "example": "1a24", "homepage": "http://psb.kobic.re.kr/STAP/refinement/", "keywords": [ "life science", "statistics" ], "mappings": { "biocontext": "STAP", "fairsharing": "FAIRsharing.ja9cdq", "miriam": "stap", "n2t": "stap" }, "name": "Statistical Torsional Angles Potentials", "pattern": "^[0-9][A-Za-z0-9]{3}$", "preferred_prefix": "stap", "publications": [ { "doi": "10.1093/bioinformatics/btv595", "pubmed": "26504145", "title": "NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores", "year": 2015 }, { "doi": "10.1371/journal.pone.0108888", "pmc": "PMC4184813", "pubmed": "25279564", "title": "Protein NMR structures refined without NOE data", "year": 2014 }, { "doi": "10.1002/prot.24265", "pubmed": "23408564", "title": "Statistical torsion angle potential energy functions for protein structure modeling: a bicubic interpolation approach", "year": 2013 }, { "doi": "10.1093/nar/gkr1021", "pmc": "PMC3245188", "pubmed": "22102572", "title": "STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures", "year": 2011 } ], "uri_format": "http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1" }, "stato": { "appears_in": [ "ontoavida", "psdo", "scdo" ], "banana": "STATO", "contact": { "email": "proccaserra@gmail.com", "github": "proccaserra", "name": "Philippe Rocca-Serra", "orcid": "0000-0001-9853-5668" }, "description": "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots.", "download_owl": "http://purl.obolibrary.org/obo/stato.owl", "example": "0000288", "homepage": "http://stato-ontology.org/", "keywords": [ "data analysis", "data visualization", "dataplant", "ess", "experimental measurement", "graph", "obo", "omics", "ontology", "statistics", "study design" ], "license": "CC-BY-3.0", "logo": "https://raw.githubusercontent.com/ISA-tools/stato/dev/images/stato-logo-3.png", "mappings": { "aberowl": "STATO", "biocontext": "STATO", "bioportal": "STATO", "fairsharing": "FAIRsharing.na5xp", "miriam": "stato", "obofoundry": "stato", "ols": "stato", "ontobee": "STATO", "tib": "stato", "wikidata.entity": "Q83428681" }, "name": "The Statistical Methods Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "STATO", "publications": [ { "pubmed": "32109232", "title": "Semantic concept schema of the linear mixed model of experimental observations" }, { "pubmed": "31831744", "title": "Experiment design driven FAIRification of omics data matrices, an exemplar" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/STATO_$1", "repository": "https://github.com/ISA-tools/stato", "uri_format": "http://purl.obolibrary.org/obo/STATO_$1", "version": "2025-02-23" }, "stitch": { "contact": { "email": "bork@embl.de", "name": "Peer Bork", "orcid": "0000-0002-2627-833X" }, "description": "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.", "example": "BQJCRHHNABKAKU", "homepage": "http://stitch.embl.de/", "keywords": [ "interaction", "life science", "protein", "small molecule" ], "mappings": { "biocontext": "STITCH", "fairsharing": "FAIRsharing.zhwa8x", "miriam": "stitch", "n2t": "stitch", "pathguide": "313", "prefixcommons": "stitch", "re3data": "r3d100012165" }, "name": "Search Tool for Interactions of Chemicals", "pattern": "^\\w{14}$", "preferred_prefix": "stitch", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/stitch:$1" } ], "publications": [ { "doi": "10.1093/nar/gkt1207", "pmc": "PMC3964996", "pubmed": "24293645", "title": "STITCH 4: integration of protein-chemical interactions with user data", "year": 2013 }, { "doi": "10.1093/nar/gkr1011", "pmc": "PMC3245073", "pubmed": "22075997", "title": "STITCH 3: zooming in on protein-chemical interactions", "year": 2011 }, { "doi": "10.1093/nar/gkp937", "pmc": "PMC2808890", "pubmed": "19897548", "title": "STITCH 2: an interaction network database for small molecules and proteins", "year": 2009 }, { "doi": "10.1093/nar/gkm795", "pmc": "PMC2238848", "pubmed": "18084021", "title": "STITCH: interaction networks of chemicals and proteins", "year": 2007 } ], "uri_format": "http://stitch.embl.de/interactions/$1" }, "stn": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The pre-IND tracking number for submissions to the FDA", "example": "125768", "homepage": "https://www.fda.gov/media/128698/download", "name": "FDA Submission Tracking Number", "preferred_prefix": "stn" }, "storedb": { "banana": "STOREDB", "contact": { "email": "PNS12@cam.ac.uk", "name": "Dr Paul Schofield", "orcid": "0000-0002-5111-7263" }, "description": "STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons.", "example": "STUDY1040", "homepage": "https://www.storedb.org/", "keywords": [ "biomedical science", "ecology", "epidemiology", "life science", "preclinical studies" ], "mappings": { "biocontext": "STOREDB", "fairsharing": "FAIRsharing.6h8d2r", "integbio": "nbdc02191", "miriam": "storedb", "n2t": "storedb", "re3data": "r3d100011049" }, "name": "Store DB", "namespace_in_lui": true, "pattern": "^(STUDY|FILE|DATASET)\\d+$", "preferred_prefix": "storedb", "uri_format": "https://www.storedb.org/?$1" }, "storedb.dataset": { "comment": "Unfortunately, the resolver itself doesn't work since datasets are actually hierarchically assigned within studies.", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "Datasets inside StoreDB at University of Cambridge", "example": "1251", "homepage": "https://www.storedb.org/", "name": "StoreDB Dataset", "pattern": "^\\d+$", "preferred_prefix": "storedb.dataset", "uri_format": "https://www.storedb.org/?STOREDB:DATASET$1" }, "storedb.file": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "File inside StoreDB at University of Cambridge", "example": "12929", "homepage": "https://www.storedb.org/", "name": "StoreDB File", "pattern": "^\\d+$", "preferred_prefix": "storedb.file", "uri_format": "https://www.storedb.org/store_v3/download.jsp?fileId=$1" }, "storedb.study": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Study inside StoreDB at University of Cambridge", "example": "1174", "homepage": "https://www.storedb.org/", "name": "StoreDB Study", "pattern": "^\\d+$", "preferred_prefix": "storedb.study", "providers": [ { "code": "doi", "description": "DOIs for studies", "homepage": "https://www.storedb.org/", "name": "StoreDB DOI", "uri_format": "http://dx.doi.org/doi:10.20348/STOREDB/$1" } ], "uri_format": "https://www.storedb.org/store_v3/study.jsp?studyId=$1" }, "streptomedb": { "contact": { "email": "stefan.guenther@pharmazie.uni-freiburg.de", "name": "Stefan Günther", "orcid": "0000-0003-3744-189X" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "Identifers for natural products isolated or mutasynthesized by bacteria of the genus Streptomyces.", "example": "15753", "github_request_issue": 1287, "homepage": "http://streptomedb.vm.uni-freiburg.de/streptomedb", "name": "StreptomeDB", "pattern": "^\\d+$", "preferred_prefix": "streptomedb", "publications": [ { "doi": "10.1093/nar/gkae1030", "pubmed": "39498494", "title": "StreptomeDB 4.0: a comprehensive database of streptomycetes natural products enriched with protein interactions and interactive spectral visualization", "year": 2024 }, { "doi": "10.1093/nar/gkaa868", "pmc": "PMC7779017", "pubmed": "33051671", "title": "StreptomeDB 3.0: an updated compendium of streptomycetes natural products", "year": 2020 }, { "doi": "10.1093/nar/gkv1319", "pmc": "PMC4702922", "pubmed": "26615197", "title": "StreptomeDB 2.0--an extended resource of natural products produced by streptomycetes", "year": 2015 }, { "doi": "10.1093/nar/gks1253", "pmc": "PMC3531085", "pubmed": "23193280", "title": "StreptomeDB: a resource for natural compounds isolated from Streptomyces species", "year": 2012 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "http://streptomedb.vm.uni-freiburg.de/streptomedb/get_drugcard/$1" }, "string": { "contact": { "email": "bork@embl.de", "name": "Peer Bork", "orcid": "0000-0002-2627-833X" }, "description": "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions.\nThe interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.", "example": "P53350", "homepage": "http://string-db.org/", "keywords": [ "biology", "interaction", "life science", "protein" ], "mappings": { "biocontext": "STRING", "edam": "2302", "fairsharing": "FAIRsharing.9b7wvk", "integbio": "nbdc00690", "miriam": "string", "n2t": "string", "pathguide": "93", "prefixcommons": "string", "re3data": "r3d100010604", "uniprot": "DB-0141" }, "name": "Search Tool for Retrieval of Interacting Genes/Proteins", "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$", "preferred_prefix": "string", "providers": [ { "code": "", "description": "STRING at Heidelberg", "homepage": "http://string.embl.de/", "name": "STRING at Heidelberg", "uri_format": "https://string.embl.de/cgi/network?identifier=$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/string:$1" } ], "provides": "uniprot", "publications": [ { "doi": "10.1093/nar/gkae1113", "pubmed": "39558183", "title": "The STRING database in 2025: protein networks with directionality of regulation", "year": 2024 }, { "doi": "10.1093/nar/gkac1000", "pubmed": "36370105" }, { "doi": "10.1093/nar/gky1131", "pmc": "PMC6323986", "pubmed": "30476243", "title": "STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets", "year": 2019 }, { "doi": "10.1093/nar/gkw937", "pmc": "PMC5210637", "pubmed": "27924014", "title": "The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible", "year": 2016 }, { "doi": "10.1093/bioinformatics/btv696", "pmc": "PMC4896368", "pubmed": "26614125", "title": "SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles", "year": 2015 }, { "doi": "10.1093/nar/gku1003", "pmc": "PMC4383874", "pubmed": "25352553", "title": "STRING v10: protein-protein interaction networks, integrated over the tree of life", "year": 2014 }, { "doi": "10.1093/nar/gks1094", "pmc": "PMC3531103", "pubmed": "23203871", "title": "STRING v9.1: protein-protein interaction networks, with increased coverage and integration", "year": 2012 }, { "doi": "10.1093/nar/gkn760", "pmc": "PMC2686466", "pubmed": "18940858", "title": "STRING 8--a global view on proteins and their functional interactions in 630 organisms", "year": 2008 } ], "uri_format": "https://string-db.org/cgi/network?identifier=$1" }, "sty": { "contact": { "email": "olivier@nlm.nih.gov", "name": "Olivier Bodenreider", "orcid": "0000-0003-4769-4217" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "tiago.lubiana.alves@usp.br", "github": "lubianat", "name": "Tiago Lubiana", "orcid": "0000-0003-2473-2313" } ], "description": "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types.", "example": "T039", "homepage": "https://lhncbc.nlm.nih.gov/semanticnetwork/", "keywords": [ "ontology" ], "license": "https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/license_agreement.html", "logo": "https://www.nlm.nih.gov/research/umls/knowledge_sources/semantic_network/semantic-network.png", "mappings": { "aberowl": "STY", "agroportal": "STY", "biolink": "UMLSSG", "bioportal": "STY", "ecoportal": "STY", "wikidata": "P11955" }, "name": "UMLS Semantic Types Ontology", "pattern": "^T\\d{3}$", "preferred_prefix": "sty", "providers": [ { "code": "bioportal.purl", "description": "BioPortal PURL", "homepage": "http://purl.bioontology.org/ontology/STY", "name": "BioPortal PURL", "uri_format": "http://purl.bioontology.org/ontology/STY/$1" } ], "publications": [ { "doi": "10.1093/nar/gkh061", "pmc": "PMC308795", "pubmed": "14681409", "title": "The Unified Medical Language System (UMLS): integrating biomedical terminology", "year": 2004 } ], "synonyms": [ "UMLSSG", "umls.st", "umls.sty" ], "uri_format": "https://uts.nlm.nih.gov/uts/umls/semantic-network/$1" }, "subtilist": { "contact": { "email": "antoine.danchin@normalesup.org", "name": "Antoine Danchin", "orcid": "0000-0002-6350-5001" }, "deprecated": true, "description": "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\nSubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments.", "example": "BG11523", "homepage": "http://genolist.pasteur.fr/SubtiList/", "keywords": [ "dna", "genome", "protein" ], "mappings": { "biocontext": "SUBTILIST", "fairsharing": "FAIRsharing.40j2vd", "miriam": "subtilist", "n2t": "subtilist", "ncbi": "SubtiList", "prefixcommons": "subtilist" }, "name": "Bacillus subtilis genome sequencing project", "pattern": "^BG\\d+$", "preferred_prefix": "subtilist", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/subtilist:$1" } ], "publications": [ { "doi": "10.1093/nar/30.1.62", "pmc": "PMC99059", "pubmed": "11752255", "title": "SubtiList: the reference database for the Bacillus subtilis genome", "year": 2002 } ], "uri_format": "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1" }, "subtiwiki": { "contact": { "email": "jstuelk@gwdg.de", "name": "Jörg Stülke", "orcid": "0000-0001-5881-5390" }, "description": "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. \nNote: Currently, direct access to RNA products is restricted. 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Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here..", "example": "2.1.1", "homepage": "http://tfclass.bioinf.med.uni-goettingen.de", "keywords": [ "binding", "binding site", "bioinformatics", "expression data", "phylogenetics", "transcription factor", "transcription factor binding site prediction", "transcriptomics" ], "mappings": { "fairsharing": "FAIRsharing.XykycZ", "go": "TFClass", "pathguide": "666" }, "name": "Classification of Transcription Factors in Mammalia", "preferred_prefix": "tfclass", "publications": [ { "doi": "10.1093/nar/gkx987", "pmc": "PMC5753292", "pubmed": "29087517", "title": "TFClass: expanding the classification of human transcription factors to their mammalian orthologs", "year": 2018 } ], "uri_format": "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1" }, "tfsco": { "description": "Domain ontology for thin-film solar cells and related tandem solar cells. Contains relevant terms and concepts from BFO, IAO, UO, PATO, OBI, CHMO.", "example": "00000001", "homepage": "https://github.com/nomad-hzb/autoperosol", "keywords": [ "fairmat", "material science", "mechanical engineering, energy technology", "physics" ], "mappings": { "tib": "tfsco" }, "name": "Thin-film Solar Cells Ontology", "preferred_prefix": "tfsco", "repository": "https://github.com/nomad-hzb/autoperosol", "uri_format": "https://purl.archive.org/tfsco/TFSCO_$1" }, "tgd": { "description": "The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature.", "example": "TTHERM_00648910", "homepage": "http://ciliate.org/index.php/", "keywords": [ "genome" ], "mappings": { "biocontext": "TGD", "go": "TGD", "miriam": "tgd", "n2t": "tgd", "prefixcommons": "tgd" }, "name": "Tetrahymena Genome Database", "pattern": "^TTHERM\\_\\d+$", "preferred_prefix": "tgd", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/tgd:$1" } ], "uri_format": "http://ciliate.org/index.php/feature/details/$1" }, "tgma": { "contact": { "email": "topalis@imbb.forth.gr", "name": "Pantelis Topalis", "orcid": "0000-0002-1635-4810" }, "deprecated": true, "description": "A structured controlled vocabulary of the anatomy of mosquitoes.", "download_obo": "http://purl.obolibrary.org/obo/tgma.obo", "download_owl": "http://purl.obolibrary.org/obo/tgma.owl", "example": "0000984", "homepage": "https://www.vectorbase.org/ontology-browser", "keywords": [ "anatomy", "life science", "mosquito", "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "TGMA", "biocontext": "TGMA", "bioportal": "TGMA", "fairsharing": "FAIRsharing.dqnfkg", "obofoundry": "tgma", "ols": "tgma", "ontobee": "TGMA", "prefixcommons": "tgma" }, "name": "Mosquito gross anatomy ontology", "pattern": "^\\d{7}$", "preferred_prefix": "TGMA", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/tgma:$1" } ], "publications": [ { "doi": "10.1111/j.1365-2583.2008.00781.x", "pubmed": "18237287", "title": "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase", "year": 2008 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/TGMA_$1", "repository": "https://github.com/VEuPathDB-ontology/TGMA", "uri_format": "http://purl.obolibrary.org/obo/TGMA_$1", "version": "2013-06-03" }, "th": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]", "example": "H3.03.00.0.00007", "homepage": "https://ifaa.unifr.ch/", "keywords": [ "biology", "cytology", "histology", "life sciences" ], "mappings": { "wikidata": "P1694" }, "name": "Terminologia Histologica", "pattern": "^H\\d\\.\\d{2}\\.\\d{2}\\.\\d\\.\\d{5}$", "preferred_prefix": "th", "references": [ "https://en.wikipedia.org/wiki/Terminologia_Histologica" ] }, "theiler": { "appears_in": [ "emaps", "mmusdv" ], "contact": { "email": "Terry.Hayamizu@jax.org", "github": "tfhayamizu", "name": "Terry Hayamizu", "orcid": "0000-0002-0956-8634" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Theiler stages (TS) define mouse development by a set of morphological criteria ([Theiler, 1989](https://doi.org/10.1007/978-3-642-88418-4)). This staging scheme is used because embryos at the same gestational age can have developed at different rates and therefore exhibit different morphological characteristics. Theiler stages may in some cases correspond to a single gestation age, but more often cover a range of ages. (from [https://www.informatics.jax.org/glossary/theiler](https://www.informatics.jax.org/glossary/theiler))", "example": "23", "example_decoys": [ "10e" ], "example_extras": [ "10b" ], "github_request_issue": 747, "homepage": "https://embryology.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages", "name": "Theiler Stage", "pattern": "^\\d+[a-d]?$", "preferred_prefix": "theiler", "providers": [ { "code": "legacy", "description": "Legacy URL at UNSW", "homepage": "https://embryology.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages", "name": "Legacy URL at UNSW", "uri_format": "https://embryology.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages#Theiler_Stage_$1" }, { "code": "legacy2", "description": "Legacy URL at UNSW", "homepage": "http://php.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages", "name": "Legacy URL at UNSW", "uri_format": "http://php.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages#Theiler_Stage_$1" } ], "references": [ "https://www.emouseatlas.org/emap/ema/theiler_stages/StageDefinition/stagedefinition.html" ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "thielerstage" ], "uri_format": "https://www.emouseatlas.org/emap/ema/DAOAnatomyJSP/anatomy.html?stage=TS$1" }, "thermofisher": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ThermoFisher is a life sciences supply vendor.", "example": "OSR00185W", "homepage": "https://www.thermofisher.com", "keywords": [ "biology", "chemistry", "life sciences", "vendor" ], "name": "Thermo Fisher Scientific", "pattern": "^\\w+$", "preferred_prefix": "thermofisher", "uri_format": "https://www.thermofisher.com/antibody/product/$1" }, "tib.bk": { "description": "The (Dutch) Basic Classification (nl Nederlandse basisclassificatie), BK or NBC is a hierarchical classification system developed by Dutch libraries specifically for scientific works. The classification system was introduced at the end of the 1980s under the direction of the Royal Library of the Netherlands and has been in use since 1990. Since then it has been continually revised. The BK is mainly used in the Netherlands and in the Common Library Network (GBV).", "example": "0", "homepage": "http://bartoc.org/en/node/18785", "keywords": [ "digital planning and construction", "earth sciences", "ess", "fid baudigital", "fid move", "nfdi4ing" ], "mappings": { "tib": "bk" }, "name": "Basisklassifikation", "preferred_prefix": "tib.bk", "uri_format": "http://uri.gbv.de/terminology/bk/$1" }, "tib.bo": { "description": "This file contains the Base Ontology of oneM2M as specified in TS-0012", "example": "AreaNetwork", "homepage": "https://git.onem2m.org/MAS/BaseOntology", "keywords": [ "engineering", "nfdi4ing" ], "mappings": { "tib": "bo" }, "name": "Base Ontology", "preferred_prefix": "tib.bo", "uri_format": "https://git.onem2m.org/MAS/BaseOntology/raw/master/base_ontology.owl#$1" }, "tib.cgo": { "description": "This ontology describes concepts related to greenhouses. It mainly describes Dutch greenhouses, but can also be applied to greenhouses outside of The Netherlands. The ontology describes multiple aspects of the domain of greenhouses.", "example": "AbioticStressTrait", "homepage": "https://gitlab.com/ddings/common-greenhouse-ontology", "keywords": [ "chemical and environmental engineering", "earth sciences", "horticulture", "tib" ], "mappings": { "tib": "cgo" }, "name": "Common Greenhouse Ontology", "preferred_prefix": "tib.cgo", "uri_format": "https://www.tno.nl/agrifood/ontology/common-greenhouse-ontology#$1" }, "tib.dot": { "description": "The Damage Topology Ontology (DOT) allows the definition of damage representations and their relations with other damages and affected construction components. The ontology supports a generic damage modeling approach and therefore could be applied for any type of degradation as well as for any construction type (e.g. buildings or bridges). Damage representations can be modeled either as damaged areas (dot:DamageArea) or elementary damage elements (dot:DamageElement). Thereby, instances of dot:DamageElement should be aggregated in a dot:DamageArea, however significant damages e.g. large cracks could be modelled as dot:DamageElement without dot:DamageArea. For grouping multiple coherent damages, a damage pattern could be defined by using dot:DamagePattern as third type for damage representation. Besides the topological damage classes, damage can also be categorized acording to a certain damage type using subclasses of dot:ClassifiedDamage as defined in extensions of DOT. A division between structural and non-structural damage is made by using the dot:StructuralDamage or dot:Defect classes. In addition to the topology, damage documentation that is commonly created during inspections and damage assessment can be linked to the damages as well as to the damaged components.", "example": "Causation", "homepage": "https://alhakam.github.io/dot", "keywords": [ "engineering", "nfdi4ing" ], "mappings": { "tib": "dot" }, "name": "Damage Topology Ontology", "preferred_prefix": "tib.dot", "uri_format": "https://w3id.org/dot#$1" }, "tib.dr": { "description": "Holistic Ontology for semiconductor manufacturing and development, products and systems containing semiconductors and connected supply chains.", "example": "Application", "homepage": "https://github.com/tibonto/dr", "keywords": [ "coypu", "economics", "electrical engineering", "nfdi4ing" ], "mappings": { "tib": "dr" }, "name": "Digital Reference", "preferred_prefix": "tib.dr", "uri_format": "http://www.w3id.org/ecsel-dr-SO#$1" }, "tib.fto": { "description": "Modular Ontology Modeling for Food Supply Chains.", "example": "Agent", "homepage": "https://github.com/Data-Semantics-Laboratory/Modular-Ontology-Modeling-for-Food-Supply-Chains", "keywords": [ "coypu", "economics" ], "mappings": { "tib": "fto" }, "name": "Modular Ontology Modeling for Food Supply Chains", "preferred_prefix": "tib.fto", "uri_format": "http://dase.cs.ksu.edu/ontology/food-traceability#$1" }, "tib.gpo": { "description": "Ontology to model processes", "example": "01cd2578_8730_4ac9_a555_9112728ea939", "homepage": "https://github.com/General-Process-Ontology/ontology", "keywords": [ "engineering", "nfdi4ing" ], "license": "CC-BY-4.0", "mappings": { "tib": "gpo" }, "name": "General Process Ontology", "preferred_prefix": "tib.gpo", "repository": "https://github.com/General-Process-Ontology/ontology", "uri_format": "https://gpo.ontology.link/GPO_$1" }, "tib.hpont": { "description": "The Heat Pump Ontology (HPOnt) aims to formalize and represent all the relevant information of Heat Pumps. The HPOnt has been developed as part of the REACT project which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 824395.", "example": "HeatPumpOperatingMode", "homepage": "https://react2020.github.io/REACT-ONTOLOGY/HPOnt/index-en.html", "keywords": [ "engineering", "nfdi4ing" ], "mappings": { "tib": "hpont" }, "name": "Heat Pump Ontology", "preferred_prefix": "tib.hpont", "repository": "https://github.com/react2020/REACT-ONTOLOGY", "uri_format": "https://w3id.org/hpont#$1" }, "tib.ifc": { "description": "OWL ontology for the IFC conceptual data schema and exchange file format for Building Information Model (BIM) data", "download_rdf": "https://standards.buildingsmart.org/IFC/DEV/IFC4/ADD2_TC1/OWL/ontology.ttl", "example": "IfcAbsorbedDoseMeasure", "homepage": "https://standards.buildingsmart.org/IFC/DEV/IFC4/ADD2_TC1/OWL/index.html", "keywords": [ "architecture", "civil engineering", "computer science", "digital planning and construction", "fid baudigital", "nfdi4ing" ], "mappings": { "tib": "ifc" }, "name": "Industrial Foundational Classes", "preferred_prefix": "tib.ifc", "uri_format": "https://standards.buildingsmart.org/IFC/DEV/IFC4/ADD2_TC1/OWL#$1" }, "tib.io": { "description": "An ontology for the description of information objects.", "example": "InformationObject", "homepage": "https://bimerr.iot.linkeddata.es/def/information-objects/", "keywords": [ "computer science", "digital planning and construction", "fid baudigital", "nfdi4ing" ], "mappings": { "tib": "io" }, "name": "Information Objects Ontology", "preferred_prefix": "tib.io", "uri_format": "http://bimerr.iot.linkeddata.es/def/information-objects#$1" }, "tib.ioc": { "description": "The Internet of Construction Ontology (IoC) construction process ontology is intended to represent a comprehensive solution of how processes in the construction industry can be modelled. Due to the iterative nature of creating an ontology, the construction process ontology presented here can at best be considered a working state at the time of publication. Our approach emphasizes the simplest and most comprehensive mapping possible, which is only extended based on insights from practical use when otherwise compelling limitations in usability and applicability arise. Thus, the extension and refinement of the developed construction process ontology strongly depends on the integration of further areas of the construction value chain and the connection of further domain ontologies.", "example": "Actor", "homepage": "https://ip.pages.rwth-aachen.de/ioc/core/", "keywords": [ "civil engineering", "digital planning and construction", "fid baudigital", "nfdi4ing" ], "mappings": { "tib": "ioc" }, "name": "IOC: Internet of Construction Ontology", "preferred_prefix": "tib.ioc", "uri_format": "http://w3id.org/ioc#$1" }, "tib.linsearch": { "description": "Fächer für die LinSearch-Fachzuordnung", "example": "arc", "homepage": "https://github.com/TIBHannover/annif_automated_indexing_at_tib", "keywords": [ "computer science", "tib" ], "mappings": { "tib": "linsearch" }, "name": "Fachsystematik LinSearch", "preferred_prefix": "tib.linsearch", "repository": "https://github.com/TIBHannover/annif_automated_indexing_at_tib", "uri_format": "https://purl.org/linsearch/$1" }, "tib.lis": { "description": "The Industrial Data Ontology is an upper ontology for industrial data, inspired by the ISO 15926-2 data model and Basic Formal Ontology.", "example": "Activity", "homepage": "https://rds.posccaesar.org/ontology/lis14/ont/core/", "keywords": [ "engineering", "nfdi4ing" ], "mappings": { "tib": "lis" }, "name": "Industrial Data Ontology", "preferred_prefix": "tib.lis", "uri_format": "http://rds.posccaesar.org/ontology/lis14/rdl/$1" }, "tib.mat": { "description": "The material properties ontology provides the vocabulary to describe the composition of building elements.", "example": "Accesories", "homepage": "https://bimerr.iot.linkeddata.es/def/material-properties/", "keywords": [ "digital planning and construction", "engineering", "fid baudigital", "nfdi4ing" ], "mappings": { "tib": "mat" }, "name": "Material properties ontology", "preferred_prefix": "tib.mat", "uri_format": "http://bimerr.iot.linkeddata.es/def/material-properties#$1" }, "tib.mdo": { "description": "The Materials Design Ontology is designed to enable semantic query and integrated query over multiple databases. By generating mappings between MDO and the schemas of materials databases, we can create MDO-enabled query interfaces. The querying can occur, for instance, via MDO-based query expansion, MDO-based mediation or through MDO-enabled data warehouses.", "homepage": "https://liusemweb.github.io/mdo/full/1.0/index.html#namespaces", "keywords": [ "material science", "nfdi4ing" ], "mappings": { "tib": "mdo" }, "name": "Materials Design Ontology - Full", "no_own_terms": true, "preferred_prefix": "tib.mdo", "repository": "https://github.com/LiUSemWeb/Materials-Design-Ontology", "uri_format": "https://w3id.org/mdo/$1" }, "tib.mdv": { "description": "A version of the Materials Data Vocabulary structured as Simple Knowledge Organization System (SKOS). The XML was originally created by the TemaTres software. This vocabulary describes the applicability to material science of records in the NIST Materials Resource Registry (NMRR - https://materials.registry.nist.gov/). The NMRR allows for the registration of materials resources, bridging the gap between existing resources and the end users. The NMRR functions as a node in a federated system, making the registered information available for research to the materials community. This is being developed at the National Institute of Standards and Technology and is made available to solicit comments from the Material Science community. (An Excel version of the file is also included in the distributions for ease of use.) Please cite this resource as: Medina-Smith, Andrea; Becker, Chandler (2017), Simple Knowledge Organization System (SKOS) version of Materials Data Vocabulary , National Institute of Standards and Technology, https://doi.org/10.18434/T4/1435037", "example": "953", "homepage": "https://data.nist.gov/od/id/67C783D4BA814C8EE05324570681708A1899", "keywords": [ "material science", "nfdi4ing" ], "mappings": { "tib": "mdv" }, "name": "Simple Knowledge Organization System (SKOS) version of Materials Data Vocabulary", "preferred_prefix": "tib.mdv", "uri_format": "https://data.nist.gov/od/dm/nmrr/vocab/?tema=$1" }, "tib.meth": { "description": "This concept scheme contains skos concepts for analysis methods used to produce observation results with information about the physical properties, chemical or isotopic composition, crystallography, or molecular structure of material samples. Based on spreadsheet compilation of method vocabularies from Geo.X, GEOROC, PetDB and OSIRIS-REx. Definitions added and updated based on web research, and SKOS serialization by S.M. Richard. Note that although there are high-level method categories for 'Physical property measurements' and the 'Bioanalytical method', these are placeholders and only include a few examples that are relevant to analytical methods in geo- or cosmochemistry.", "example": "acceleratormassspectrometry", "homepage": "https://amds-ldeo.github.io/Vocabulary/geochemistry/html/GeochemAnalyticalMethod.html", "keywords": [ "earth sciences", "ess" ], "mappings": { "tib": "meth" }, "name": "Analytical methods for geochemistry", "preferred_prefix": "tib.meth", "uri_format": "https://w3id.org/geochem/1.0/analyticalmethod/$1" }, "tib.mt": { "description": "Controlled vocabulary for the classification of the theme for a mobility dataset.", "example": "accesibility-information-for-vehicles", "homepage": "https://w3id.org/mobilitydcat-ap/mobility-theme", "keywords": [ "fid move", "nfdi4ing", "traffic engineering" ], "mappings": { "tib": "mt" }, "name": "Mobility Theme", "preferred_prefix": "tib.mt", "uri_format": "https://w3id.org/mobilitydcat-ap/mobility-theme/$1" }, "tib.n0": { "description": "The Audio Commons Ontology has been created in the context of the European project [Audio Commons](https://www.audiocommons.org/), which were aimed at favouring sharing and reuse of audio content (both of musical and non-musical nature), specially using [Creative Commons](https://creativecommons.org/) licenses.\n\nIt is designed specifically to integrate access to multiple heterogeneously structured audio content providers. In particular the following ones have been considered in the project:\n- [Freesound](https://freesound.org/), a collaborative database of Creative Commons Licensed sounds;\n- [Jamendo](https://www.jamendo.com/), a music website for independent artists;\n- [Europeana Sounds](https://www.eusounds.eu/), a European project collecting and sharing data from several archives of sounds and sound-related media;\n- [Internet Archive](https://archive.org/), a non-profit library of millions of freely accessible media contents.\n\n### The base model\n
![A diagram showing the entities Work, Expression, Manifestation, Item](./img/FRBR-Group-1-entities-and-basic-relations.svg.png)
\nThe Audio Commons ontology is based on [Functional Requirements for Bibliographic Records (FRBR)](https://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records), a bibliographic model designed for user tasks of retrieval and access in online library catalogues and bibliographic databases. FRBR distinguish the products of intellectual or artistic endeavor in four main classes: work, expression, manifestation, item. It is available as RDF vocabulary at https://vocab.org/frbr/core. For further information on FRBR, check the [standard](https://repository.ifla.org/handle/123456789/811).\n\nAnother important model related to audio is the [Music Ontology](http://musicontology.com/), which is also based on the FRBR model. Our ontology is more generic than the Music Ontology but is interoperable with it to support the specificities of music-related audio content.\n\nThe Audio Commons ontology works also in conjunction with\n- [Dublin Core](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/) for basic metadata,\n- [EBU Core](https://www.ebu.ch/metadata/ontologies/ebucore/) for technical properties of audio files,\n- [SKOS](https://www.w3.org/TR/skos-primer/) to support taxonomic classifications,\n- [Creative Commons Licensing schema](https://creativecommons.org/ns) to represent media licensing,\n- [Event ontology](http://motools.sf.net/event/event.html) for the formalisation of events,\n- [Audio Features Ontology](https://w3id.org/afo/onto/) for the characterisation of audio features.\n\n### Ontology overview\n\n![A diagram showing the main classes of the Audio Commons ontology](./img/AC-Ontology-Skeleton.png)\n\nThe figure above shows the most general classes and properties of the Audio Commons ontology and their relationship with classes of the FRBR and the Music Ontology:\n- **`ac:AudioExpression`**, the specific intellectual or artistic form that a work takes each time it is _realised_, in the audio domain, e.g., the recording or synthesis of music or sounds;\n- **`ac:AudioManifestation`**, the physical embodiment of an audio expression, e.g., a musical track, a sound, an album; \n- **`ac:AudioItem`**, a single exemplar of an audio manifestation, e.g., a copy of a CD or a specific media file.\n\nThe FRBR class Work, representing a distinct intellectual or artistic creation on a more conceptual level, has not been specialised in Audio Commons.\n\nThe Audio Commons ontology provides a generic schema for audio classification through the property **`ac:audioCategory`** that associates any audio expression, manifestation, or item to some generic **`ac:AudioCategory`**. These two terms can be specialised to provide spefic categorisations.\n\n### Manifestations: audio clips and collections\n\n![A diagram showing the main classes of the Audio Commons ontology](./img/AC-Ontology-Manifestation.png)\n\nThe figure above shows classes and properties related to audio manifestations. An instance of **`ac:AudioClip`**, a subclass of `ac:AudioManifestation`, is any audio segment that has been published in some form or uploaded for consumption, for example, a track in a music label's repository or a sound in an audio repository, library or archive.\n\nThe class **`ac:AudioCollection`**, another subclass of `ac:AudioManifestation`, is used to represent collections of audio clips. The class **`ac:AudioCollectionNode`** is used to represent single nodes of a collection, offering local information like the index in the collection and pointers to previous and next nodes. The separation between the collection node and its actual content (e.g., an `ac:AudioClip`) permits the same content to be shared in multiple collections.\n\nThe content of each node of a collection is not limited to an `ac:AudioClip`, but may contain any `ac:AudioManifestation`. Collections can thus contain other collections to support specific cases, e.g. a mapping to the Music Ontology model where an `mo:Release` can contain multiple `mo:Record`(s) that can in turn contain multiple `mo:Track`(s).\n### Items: audio files\n![A diagram showing ac:Item class and related class and properties](./img/AC-Ontology-Item.png)\n\nAn `ac:AudioItem` is a concrete exemplar of an audio manifestation. In our domain, the main exemplars are the actual audio files. \n\nThe corresponding class **`ac:AudioFile`** is a subclass of `ac:AudioItem`. It is subclass of `ebu:MediaResource` too and the corresponging properties of EBU Core can be used to describe the file (e.g., `ebu:hasEncodingFormat`, `ebu:fileSize`).\n\n### Expressions: audio signals\n![A diagram showing ac:Expression class and related class and properties](./img/AC-Ontology-Expression.png)\n\nWhile `ac:AudioFile` represents a concrete file encoded in a certain format, **`ac:DigitalSignal`** is the representation of the corresponding digital signal. `ac:DigitalSignal` is a subclass of `ac:MusicalExpression`. \n\nThe data properties `ac:sampleRate`, `ac:bitsPerSample`, and `ac:channels`, associate a signal with its basic features specific to digital representations.\n\nThe property `ac:publicationOf` can be used to associate an `ac:AudioClip` with the corresponding digital signal. The property `ac:encodes` instead, associates an `ac:AudioFile` with the encoded digital signal.\n\n### Events: recording/syntesis\n![A diagram showing ac:SignalProduction class and related class and properties!](./img/AC-Ontology-SignalProduction.png)\n\nThe description of temporal events is crucial to formalise and document transitions in the workflow of audio production and publication. The class `event:Event` of the Event Ontology is thus specialised for specific actions that are interesting for the audio domain.\n\nUsing the `event:Event` class, details of an event such as its location in time and space, its factor and its products may be explicitly described. Moreover, events can be composed using the property `event:sub_event`, to build complex events.\n\nThe class `ac:SignalProduction` represents the act of producing a `ac:Signal`, which could be either an `ac:AnalogSignal` or a `ac:DigitalSignal`. This is complemented by **`ac:Recording`**, representing the process of recording a sound (`ac:Sound`) or the product of **`ac:Synthesis`**, in case of artificially generated sounds. \n\n### Events (continued): publication\n![A diagram showing ac:Publication class and related class and properties!](./img/AC-Ontology-Publication.png)\n\nThe event **`ac:AudioPublication`** represents the public release of a piece of work, e.g., the release of a new album by a band.\n\n### Usage Example\n![A diagram showing an example of ontology usage!](./img/AC_Example-AudioClip.png)\n\nThe figure above shows an example of use of the Audio Commons ontology to represent a sound from the Freesound database. For simplicity only the classes `ac:AudioClip`, `ac:AudioFile`, and `ac:AudioCategory` are used in this case.", "example": "AnalogSignal", "homepage": "http://www.audiocommons.org/ac-ontology/aco.html", "keywords": [ "engineering", "nfdi4ing" ], "mappings": { "tib": "n0" }, "name": "The Audio Commons Ontology", "preferred_prefix": "tib.n0", "uri_format": "https://w3id.org/ac-ontology/aco#$1" }, "tib.ofm": { "description": "Ontology for manufacturing and logistics", "example": "Anthropomorphic_Robot", "homepage": "https://github.com/enegri/OFM", "keywords": [ "engineering", "nfdi4ing" ], "mappings": { "tib": "ofm" }, "name": "Ontology for manufacturing and logistics", "preferred_prefix": "tib.ofm", "repository": "https://github.com/enegri/OFM", "uri_format": "http://www.ontologies.com/Ontology3197.owl#$1" }, "tib.re": { "description": "An ontology of the Retail Energy Market of Great Britain created by Lidcast Data Limited.", "example": "Advanced_Meter", "homepage": "https://github.com/DataCreater/GBEnergy", "keywords": [ "nfdi4energy" ], "mappings": { "tib": "re" }, "name": "Retail Energy Market of Great Britain", "preferred_prefix": "tib.re", "repository": "https://github.com/DataCreater/GBEnergy", "uri_format": "https://www.lidcast.co.uk/ontologies/RE#$1" }, "tib.sto": { "description": "An ontology to describe standards related to Industry 4.0 and Smart Manufacturing", "example": "AiiClassification", "homepage": "https://i40-tools.github.io/I40KG/docs/index.html", "keywords": [ "engineering", "nfdi4ing" ], "mappings": { "tib": "sto" }, "name": "Standards Ontology", "preferred_prefix": "tib.sto", "uri_format": "https://w3id.org/i40/sto#$1" }, "tib.ts": { "contact": { "email": "baum@zbmed.de", "github": "rombaum", "name": "Roman Baum", "orcid": "0000-0001-5246-9351" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An instance of the EBI Lookup Service deployed by TIB", "example": "abcd", "homepage": "https://terminology.tib.eu", "name": "TIB Terminology Service", "preferred_prefix": "tib.ts", "uri_format": "https://terminology.tib.eu/ts/ontologies/$1" }, "tib.tso": { "description": "The scope of the TUBES ontology is to explicitly define the topology of interconnected building service system and their relationship to the spatial structure. It has a strong alignment to other ontologies within the W3C community and aims to provide the means to link information at data level within the AEC industry.", "example": "AutomationSystem", "homepage": "https://rwth-e3d.github.io/tso/index.html", "keywords": [ "engineering", "nfdi4ing" ], "mappings": { "tib": "tso" }, "name": "TUBES system ontology", "preferred_prefix": "tib.tso", "uri_format": "https://w3id.org/tso#$1" }, "tigrfam": { "contributor_extras": [ { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" } ], "description": "TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins.", "example": "TIGR00010", "homepage": "http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi", "keywords": [ "protein" ], "mappings": { "biocontext": "TIGRFAM", "edam": "1141", "miriam": "tigrfam", "n2t": "tigrfam", "ncbi": "TIGRFAM", "prefixcommons": "tigrfams" }, "name": "TIGR protein families", "pattern": "^TIGR\\d+$", "preferred_prefix": "tigrfam", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/tigrfams:$1" } ], "references": [ "https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/license_and_availability.txt", "https://github.com/biopragmatics/bioregistry/issues/366" ], "uri_format": "https://www.ncbi.nlm.nih.gov/cdd?term=$1" }, "time": { "contact": { "email": "dr.shorthair@pm.me", "github": "dr-shorthair", "name": "Simon Cox", "orcid": "0000-0002-3884-3420" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Owl-time is an owl-2 dl ontology of temporal concepts, for describing the temporal properties of resources in the world or described in web pages. the ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. time positions and durations may be expressed using either the conventional (gregorian) calendar and clock, or using another temporal reference system such as unix-time, geologic time, or different calendars.", "download_owl": "http://aber-owl.net/media/ontologies/TIME/2/time.owl", "example": "DateTimeDescription", "github_request_issue": 505, "homepage": "https://www.w3.org/TR/owl-time/", "keywords": [ "data coordination", "ess", "fair data spaces", "metadata standardization", "nfdi4chem", "ontology", "resource metadata", "subject agnostic", "time" ], "mappings": { "aberowl": "TIME", "bartoc": "18311", "bioportal": "TIME", "fairsharing": "FAIRsharing.hw3bh2", "lov": "time", "tib": "time", "zazuko": "time" }, "name": "Time Ontology in OWL", "preferred_prefix": "time", "repository": "https://github.com/w3c/sdw", "uri_format": "http://www.w3.org/2006/time#$1" }, "tkg": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells.", "example": "0221", "homepage": "http://www2.idac.tohoku.ac.jp/dep/ccr/", "mappings": { "cellosaurus": "TKG" }, "name": "Tohoku University cell line catalog", "pattern": "^\\d+$", "preferred_prefix": "tkg", "uri_format": "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html" }, "tngb": { "description": "Cell line collections (Providers)", "example": "67035", "homepage": "https://biobanknetwork.telethon.it/", "mappings": { "cellosaurus": "TNGB" }, "name": "Telethon Network of Genetic Biobanks", "pattern": "^\\d+$", "preferred_prefix": "tngb", "uri_format": "https://biobanknetwork.telethon.it/Sample/View?sampleId=$1" }, "to": { "appears_in": [ "agro" ], "contact": { "email": "jaiswalp@science.oregonstate.edu", "github": "jaiswalp", "name": "Pankaj Jaiswal", "orcid": "0000-0002-1005-8383" }, "description": "A controlled vocabulary to describe phenotypic traits in plants.", "download_obo": "http://purl.obolibrary.org/obo/to.obo", "download_owl": "http://purl.obolibrary.org/obo/to.owl", "example": "0000630", "homepage": "http://browser.planteome.org/amigo", "keywords": [ "botany", "dataplant", "earth sciences", "ess", "life cycle", "obo", "ontology", "phenotype", "plant", "structure", "trait" ], "license": "CC-BY-4.0", "logo": "http://planteome.org/sites/default/files/garland_logo.PNG", "mappings": { "aberowl": "TO", "agroportal": "TO", "biocontext": "TO", "bioportal": "PTO", "fairsharing": "FAIRsharing.w69t6r", "obofoundry": "to", "ols": "to", "ontobee": "TO", "prefixcommons": "pto", "tib": "to", "wikidata.entity": "Q81661818" }, "name": "Plant Trait Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "TO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pto:$1" } ], "publications": [ { "doi": "10.1093/nar/gkx1152", "pmc": "PMC5753347", "pubmed": "29186578", "title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics", "year": 2018 }, { "doi": "10.1093/nar/gkad1028", "title": "Planteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology", "year": 2024 } ], "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": "2026-01-14" }, "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_owl": "https://raw.githubusercontent.com/togoid/togoid-config/main/ontology/togoid-ontology.ttl", "example": "AffyProbeset", "homepage": "https://togoid.dbcls.jp/ontology", "keywords": [ "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/#$1" }, "togovar": { "description": "TogoVar (A comprehensive Japanese genetic variation database) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them.", "example": "tgv139393198", "homepage": "https://grch38.togovar.org/", "mappings": { "integbio": "nbdc02359", "miriam": "togovar", "togoid": "Togovar" }, "name": "TogoVar", "pattern": "^tgv[0-9]+$", "preferred_prefix": "togovar", "uri_format": "https://grch38.togovar.org/variant/$1" }, "tokue": { "deprecated": true, "description": "Cell line databases/resources", "homepage": "http://cell-lines.toku-e.com", "mappings": { "cellosaurus": "TOKU-E" }, "name": "TOKU-E Cell-culture Database", "preferred_prefix": "tokue", "uri_format": "http://cell-lines.toku-e.com/Cell-Lines_$1.html" }, "tol": { "contributor_extras": [ { "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" } ], "description": "The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). \n\nEach page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things.", "example": "98034", "homepage": "http://tolweb.org/tree/", "mappings": { "bartoc": "400", "biocontext": "TOL", "miriam": "tol", "n2t": "tol", "wikidata": "P5221", "wikidata.entity": "Q2300489" }, "name": "Tree of Life Web Project", "pattern": "^\\d+$", "preferred_prefix": "tol", "synonyms": [ "tol.webproj" ], "uri_format": "http://tolweb.org/$1" }, "topdb": { "description": "The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases.", "example": "AP00378", "homepage": "http://topdb.enzim.hu/", "keywords": [ "protein" ], "mappings": { "biocontext": "TOPDB", "edam": "2789", "miriam": "topdb", "n2t": "topdb", "prefixcommons": "topdb" }, "name": "Topology Data Bank of Transmembrane Proteins", "pattern": "^[A-Z0-9]+$", "preferred_prefix": "topdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/topdb:$1" } ], "uri_format": "http://topdb.enzim.hu/?m=show&id=$1" }, "topfind": { "contact": { "email": "chris.overall@ubc.ca", "name": "Christopher M. Overall", "orcid": "0000-0001-5844-2731" }, "description": "TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.", "example": "Q9UKQ2", "homepage": "https://topfind.clip.msl.ubc.ca", "keywords": [ "life science" ], "mappings": { "biocontext": "TOPFIND", "fairsharing": "FAIRsharing.rkpmhn", "miriam": "topfind", "n2t": "topfind", "re3data": "r3d100012721" }, "name": "TopFind", "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$", "preferred_prefix": "topfind", "provides": "uniprot", "publications": [ { "doi": "10.1093/nar/gku1012", "pmc": "PMC4383881", "pubmed": "25332401", "title": "Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events", "year": 2014 }, { "doi": "10.1093/nar/gkr1025", "pmc": "PMC3244998", "pubmed": "22102574", "title": "TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function", "year": 2011 }, { "doi": "10.1038/nmeth.1669", "pubmed": "21822272", "title": "TopFIND, a knowledgebase linking protein termini with function", "year": 2011 } ], "uri_format": "http://clipserve.clip.ubc.ca/topfind/proteins/$1" }, "toxoplasma": { "description": "ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "TGME49_053730", "homepage": "http://toxodb.org/toxo/", "mappings": { "biocontext": "TOXOPLASMA", "miriam": "toxoplasma", "n2t": "toxoplasma" }, "name": "ToxoDB", "pattern": "^\\w+$", "preferred_prefix": "toxoplasma", "uri_format": "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" }, "trans": { "contact": { "email": "lynn.schriml@gmail.com", "github": "lschriml", "name": "Lynn Schriml", "orcid": "0000-0001-8910-9851" }, "description": "The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.", "download_obo": "http://purl.obolibrary.org/obo/trans.obo", "download_owl": "http://purl.obolibrary.org/obo/trans.owl", "example": "0000024", "homepage": "https://github.com/DiseaseOntology/PathogenTransmissionOntology", "keywords": [ "health science", "obo", "ontology", "pathogen" ], "license": "CC0-1.0", "mappings": { "aberowl": "TRANS", "biocontext": "TRANS", "bioportal": "TRANS", "fairsharing": "FAIRsharing.nygmp7", "obofoundry": "trans", "ols": "trans", "ontobee": "TRANS", "prefixcommons": "pt", "wikidata.entity": "Q15304508" }, "name": "Pathogen Transmission Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "TRANS", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/pt:$1" } ], "publications": [ { "doi": "10.1093/nar/gkab1063", "pmc": "PMC8728220", "pubmed": "34755882", "title": "The Human Disease Ontology 2022 update", "year": 2022 }, { "doi": "10.1093/nar/gkp832", "pmc": "PMC2808878", "pubmed": "19850722", "title": "GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database", "year": 2009 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/TRANS_$1", "repository": "https://github.com/DiseaseOntology/PathogenTransmissionOntology", "uri_format": "http://purl.obolibrary.org/obo/TRANS_$1", "version": "2022-10-10" }, "transportdb": { "description": "TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available.", "example": "MMP0523", "homepage": "http://www.membranetransport.org", "keywords": [ "protein" ], "mappings": { "pathguide": "105", "prefixcommons": "transportdb" }, "name": "TransportDB", "preferred_prefix": "transportdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/transportdb:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.membranetransport.org/protein.php?pOID=mmar1&pSynonym=$1" }, "transyt": { "description": "The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes.", "example": "TR0000001", "homepage": "https://www.bio.di.uminho.pt/", "mappings": { "miriam": "transyt" }, "name": "Transport Systems Tracker", "pattern": "^T[A-Z]\\d{7}$", "preferred_prefix": "transyt", "uri_format": "https://transyt.bio.di.uminho.pt/reactions/$1" }, "tred": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "Transcriptional Regulatory Element Database (TRED) has been built in response to increasing needs of an integrated repository for both cis- and trans- regulatory elements in mammals, and the lack of such resources at present.", "example": "21552", "homepage": "http://rulai.cshl.edu/TRED", "keywords": [ "dna", "regulation" ], "mappings": { "pathguide": "167", "prefixcommons": "tred" }, "name": "Transcriptional Regulatory Element Database", "preferred_prefix": "tred", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/tred:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid=$1" }, "treebase": { "contact": { "email": "rutgeraldo@gmail.com", "github": "rvosa", "name": "Rutger Vos", "orcid": "0000-0001-9254-7318" }, "deprecated": true, "description": "TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc.", "example": "TB2:S1000", "homepage": "http://treebase.org/", "keywords": [ "classification", "phylogenetics", "phylogenomics" ], "mappings": { "biocontext": "TREEBASE", "fairsharing": "FAIRsharing.zcn4w4", "integbio": "nbdc01882", "miriam": "treebase", "n2t": "treebase", "prefixcommons": "treebase", "re3data": "r3d100010170" }, "name": "TreeBASE", "pattern": "^TB[1,2]?:[A-Z][a-z]?\\d+$", "preferred_prefix": "treebase", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/treebase:$1" } ], "publications": [ { "doi": "10.1186/1471-2148-9-93", "pmc": "PMC2685121", "pubmed": "19426482", "title": "Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment", "year": 2009 } ], "repository": "https://github.com/TreeBASE/treebase/issues", "twitter": "treebase", "uri_format": "http://purl.org/phylo/treebase/phylows/study/$1?format=html" }, "treefam": { "contact": { "email": "Fab.Schreiber@gmail.com", "github": "fabsta", "name": "Fabian Schreiber", "orcid": "0000-0001-9150-5706" }, "description": "TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments.", "example": "TF101014", "homepage": "http://www.treefam.org/", "keywords": [ "classification", "gene" ], "mappings": { "biocontext": "TREEFAM", "integbio": "nbdc01596", "miriam": "treefam", "n2t": "treefam", "prefixcommons": "treefam", "uniprot": "DB-0185" }, "name": "TreeFam", "pattern": "^\\w{1,2}\\d+$", "preferred_prefix": "treefam", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/treefam:$1" } ], "publications": [ { "doi": "10.1093/nar/gkt1055", "pmc": "PMC3965059", "pubmed": "24194607", "title": "TreeFam v9: a new website, more species and orthology-on-the-fly", "year": 2013 } ], "uri_format": "http://www.treefam.org/family/$1" }, "treehub": { "contact": { "email": "wuhui@ibcas.ac.cn", "name": "Hui Wu", "orcid": "0000-0003-2430-9689" }, "contributor": { "email": "maaya.m466@gmail.com", "github": "maayamanoj466", "name": "Maaya Manoj", "orcid": "0009-0000-6974-6386" }, "description": "TreeHub is a taxonomical database for trees. TreeHub contains extracted phylogenetic data and integrates relevant species information for each identifier.", "example": "T00232742", "github_request_issue": 1619, "homepage": "https://www.plantplus.cn/treehub", "keywords": [ "dendrology", "taxonomy", "tree" ], "name": "TreeHub", "pattern": "^T\\d{8}$", "preferred_prefix": "treehub", "publications": [ { "doi": "10.1038/s41597-025-05282-4", "pmc": "PMC12130454", "pubmed": "40456766", "title": "TreeHub: a comprehensive dataset of phylogenetic trees", "year": 2025 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://www.plantplus.cn/treehub/tree/$1" }, "tribain": { "description": "The tribAIn1 ontology aims to formalize knowledge gained from tribological experiments for reuse, comparison and documentation. Therefore, the tribAin ontology provides concepts for the specification of methodological background knowledge of experimental design, the documentation of the experimental setup and the representation of different kinds of results (e.g. measurements series, analysis, interpretation in natural-language). Using the EXPO2 (ontology of scientific experiments) as basis, gives tribAIn a generic background about scientific experimental design, methodology and results representation.", "example": "100Cr6", "homepage": "https://github.com/snow0815/tribAIn", "keywords": [ "engineering", "nfdi4ing" ], "mappings": { "tib": "tai" }, "name": "Tribology Ontology for Artificial Intelligence", "preferred_prefix": "tribain", "repository": "https://github.com/snow0815/tribAIn", "uri_format": "http://ktmfk.de/ontology/tribAIn/$1" }, "tricdb": { "description": "Tri©DB is a newly developed integrated platform functioning as a knowledge base and reporting system for cancer precision medicine. This platform harmonizes and mines cancer-related data from various aspects, presenting them on a centralized platform with enhanced accessibility, rich annotations, and robust analysis capabilities. The development of Tri©DB is aimed at meeting the needs of a broad range of researchers, thereby propelling both foundational and translational research in cancer precision medicine.", "example": "1eec8393-e598-41ed-9d8b-6d5b0db94470", "homepage": "http://www.biomeddb.org/", "mappings": { "miriam": "tricdb" }, "name": "tricdb", "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$", "preferred_prefix": "tricdb", "uri_format": "http://biomeddb.org/Disease/Details?DISEASEID=$1" }, "trichdb": { "contact": { "email": "oharb@pcbi.upenn.edu", "name": "Omar Harb", "orcid": "0000-0003-4446-6200" }, "description": "TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "TVAG_386080", "homepage": "http://trichdb.org/trichdb/", "keywords": [ "genomics" ], "mappings": { "biocontext": "TRICHDB", "fairsharing": "FAIRsharing.pv0ezt", "integbio": "nbdc01785", "miriam": "trichdb", "n2t": "trichdb", "re3data": "r3d100012461" }, "name": "TrichDB", "pattern": "^\\w+$", "preferred_prefix": "trichdb", "publications": [ { "doi": "10.1093/nar/gkn631", "pmc": "PMC2686445", "pubmed": "18824479", "title": "GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis", "year": 2008 } ], "twitter": "eupathdb", "uri_format": "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" }, "tritrypdb": { "contact": { "email": "oharb@pcbi.upenn.edu", "name": "Omar Harb", "orcid": "0000-0003-4446-6200" }, "description": "TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "Tb927.8.620", "homepage": "http://tritrypdb.org/tritrypdb/", "keywords": [ "comparative genomics", "genomics", "infectious disease medicine" ], "mappings": { "biocontext": "TRITRYPDB", "fairsharing": "FAIRsharing.fs1z27", "go": "TriTrypDB", "integbio": "nbdc01786", "miriam": "tritrypdb", "n2t": "tritrypdb", "re3data": "r3d100011479" }, "name": "TriTrypDB", "pattern": "^\\w+(\\.)?\\w+(\\.)?\\w+$", "preferred_prefix": "tritrypdb", "publications": [ { "doi": "10.1093/nar/gkp851", "pmc": "PMC2808979", "pubmed": "19843604", "title": "TriTrypDB: a functional genomic resource for the Trypanosomatidae", "year": 2009 } ], "twitter": "VEuPathDB", "uri_format": "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" }, "trnadbce": { "comment": "requires authentication to access", "description": "The tRNA Gene DataBase Curated by Experts \"tRNADB-CE\" was constructed by analyzing 927 complete and 1301 draft genomes of Bacteria and Archaea, 171 complete virus genomes, 121 complete chloroplast genomes, 12 complete eukaryote (Plant and Fungi) genomes and approximately 230 million DNA sequence entries that originated from environmental metagenomic clones.", "example": "265912", "homepage": "http://trna.nagahama-i-bio.ac.jp", "keywords": [ "dna", "gene", "genome", "rna" ], "mappings": { "integbio": "nbdc00720", "prefixcommons": "trnadbce" }, "name": "tRNA Gene Database", "preferred_prefix": "trnadbce", "proprietary": true, "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/trnadbce:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID=$1" }, "tsc": { "description": "Centralized repository and distribution site for variety of Tetrahymena strains and species. Maintains diverse array of wild type, mutant, and genetically engineered strains of T. thermophila, the most commonly used laboratory species, and variety of other species derived from both laboratory maintained stocks and wild isolates. All stocks are stored in liquid nitrogen to maintain genetic integrity and prevent senescence. In addition to providing worldwide access to strains currently in collection, TSC continually upgrades collection by accepting deposition of newly developed laboratory strains and well characterized wild isolates collected from clearly defined natural sites. [from RRID]", "example": "SD00043", "homepage": "https://tetrahymena.vet.cornell.edu/", "keywords": [ "biology", "cell", "cellular", "culture", "eukaryota", "genetics", "model", "molecular", "protozoan", "repository", "research", "tetrahymena thermophila" ], "mappings": { "rrid": "TSC" }, "name": "Tetrahymena Stock Center", "pattern": "^SD\\d+$", "preferred_prefix": "tsc", "uri_format": "https://tetrahymena.vet.cornell.edu/display.php?stockid=$1" }, "tsrnadisease": { "contact": { "email": "zhenyang@fudan.edu.cn", "name": "Zhen Yang", "orcid": "0000-0002-6782-0316" }, "contributor": { "email": "ji.kang@northeastern.edu", "github": "kanghosaeyo", "name": "Kangho Ji", "orcid": "0009-0009-3402-8013" }, "description": "Identifiers correspond to curated associations between diseases and tRNA-derived small RNAs (tsRNAs) in the tsRNADisease database.", "example": "TRD00001", "github_request_issue": 1700, "homepage": "http://compgenelab.info/tsRNADisease", "keywords": [ "cancer", "disease", "tsrna" ], "name": "tsRNADisease", "pattern": "^TRD\\d{5}$", "preferred_prefix": "tsrnadisease", "publications": [ { "doi": "10.1016/j.jgg.2025.08.001", "pubmed": "40812678", "title": "tsRNADisease: a manually curated database of tsRNAs associated with human disease", "year": 2025 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "http://118.178.132.53/tsRNADisease/detail.php?entry_ID=$1" }, "ttd.drug": { "description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.", "example": "D0N5OV", "homepage": "https://db.idrblab.net/ttd", "mappings": { "biocontext": "TTD.DRUG", "edam": "2653", "miriam": "ttd.drug", "n2t": "ttd.drug" }, "name": "TTD Drug", "pattern": "^\\w+$", "preferred_prefix": "ttd.drug", "uri_format": "https://db.idrblab.net/ttd/data/drug/details/$1" }, "ttd.target": { "description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.", "example": "t59328", "homepage": "https://db.idrblab.net/ttd", "mappings": { "biocontext": "TTD.TARGET", "edam": "2654", "miriam": "ttd.target", "n2t": "ttd.target" }, "name": "TTD Target", "pattern": "^t\\d+$", "preferred_prefix": "ttd.target", "uri_format": "https://db.idrblab.net/ttd/data/target/details/$1" }, "tto": { "contact": { "email": "balhoff@renci.org", "github": "balhoff", "name": "Jim Balhoff", "orcid": "0000-0002-8688-6599" }, "description": "An ontology covering the taxonomy of teleosts (bony fish)", "download_obo": "http://purl.obolibrary.org/obo/tto.obo", "download_owl": "http://purl.obolibrary.org/obo/tto.owl", "example": "1058367", "homepage": "https://github.com/phenoscape/teleost-taxonomy-ontology", "keywords": [ "fish", "life science", "obo", "ontology", "phenotype", "taxonomic classification" ], "license": "CC0-1.0", "mappings": { "aberowl": "TTO", "biocontext": "TTO", "bioportal": "TTO", "fairsharing": "FAIRsharing.1rj558", "obofoundry": "tto", "ols": "tto", "ontobee": "TTO", "prefixcommons": "tto", "wikidata.entity": "Q81661821" }, "name": "Teleost taxonomy ontology", "pattern": "^\\d+$", "preferred_prefix": "TTO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/tto:$1" } ], "publications": [ { "doi": "10.1038/npre.2010.4629.1", "title": "The Teleost Taxonomy Ontology", "year": 2010 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/TTO_$1", "repository": "https://github.com/phenoscape/teleost-taxonomy-ontology", "uri_format": "http://purl.obolibrary.org/obo/TTO_$1" }, "txpo": { "contact": { "email": "yuki.yamagata@riken.jp", "github": "yuki-yamagata", "name": "Yuki Yamagata", "orcid": "0000-0002-9673-1283" }, "description": "Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.\n\nThe TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms.\n\nIn applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp", "download_owl": "http://purl.obolibrary.org/obo/txpo.owl", "example": "0002066", "homepage": "https://toxpilot.nibiohn.go.jp/", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "TXPO", "bioportal": "TXPO", "obofoundry": "txpo", "ols": "txpo", "ontobee": "TXPO", "wikidata.entity": "Q113014440" }, "name": "Toxic Process Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "TXPO", "publications": [ { "doi": "10.1038/s41598-020-71370-7", "pmc": "PMC7471325", "pubmed": "32883995", "title": "Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management", "year": 2020 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/TXPO_$1", "repository": "https://github.com/txpo-ontology/TXPO", "uri_format": "http://purl.obolibrary.org/obo/TXPO_$1", "version": "2022-12-07" }, "uat": { "description": "The Unified Astronomy Thesaurus (UAT) is an open, interoperable and community-supported thesaurus being developed to unify the existing divergent and isolated Astronomy & Astrophysics thesauri into a single high-quality, freely-available open-source thesaurus which will be of immediate value to both research and research support, and provide a mechanism for reviewing, discussing and evaluating the continuous evolution of terminology in these fields.", "example": "0", "homepage": "https://astrothesaurus.org", "keywords": [ "astronomy and astrophysics", "ess", "nfdi4ing", "physics" ], "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBbXNGIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--c891d240862cdbcf96ccc7422197c97d663d82c9/Screenshot%20From%202024-11-20%2013-15-32.png?disposition=inline", "mappings": { "bartoc": "820", "fairsharing": "FAIRsharing.998c4c", "tib": "uat" }, "name": "Unified Astronomy Thesaurus", "preferred_prefix": "uat", "publications": [ { "doi": "10.3847/1538-4365/aab760", "title": "The Unified Astronomy Thesaurus: Semantic Metadata for Astronomy and Astrophysics", "year": 2018 } ], "repository": "https://github.com/astrothesaurus/UAT", "uri_format": "http://astrothesaurus.org/uat/$1" }, "uberon": { "appears_in": [ "aism", "amphx", "chiro", "cl", "clo", "clyh", "colao", "cteno", "ecao", "ecocore", "ecto", "envo", "foodon", "fovt", "genepio", "go", "hso", "lepao", "maxo", "mco", "mfmo", "ons", "pcl", "plana", "poro", "zp" ], "banana": "UBERON", "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "depends_on": [ "bfo", "bspo", "chebi", "cl", "envo", "go", "nbo", "ncbitaxon", "omo", "pato", "pr", "ro" ], "description": "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.", "download_json": "http://purl.obolibrary.org/obo/uberon.json", "download_obo": "http://purl.obolibrary.org/obo/uberon/basic.obo", "download_owl": "http://purl.obolibrary.org/obo/uberon.owl", "example": "2005080", "homepage": "http://uberon.org", "keywords": [ "anatomy", "dataplant", "developmental biology", "life science", "life sciences, biology", "obo", "ontology", "taxonomy" ], "license": "CC-BY-3.0", "logo": "https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/uberon-logos/uberon_logo_black-banner.png", "mappings": { "aberowl": "UBERON", "biocontext": "UBERON", "bioportal": "UBERON", "cellosaurus": "UBERON", "fairsharing": "FAIRsharing.4c0b6b", "go": "UBERON", "miriam": "uberon", "n2t": "uberon", "obofoundry": "uberon", "ols": "uberon", "ontobee": "UBERON", "tib": "uberon", "togoid": "Uberon", "wikidata": "P1554", "wikidata.entity": "Q7876491" }, "name": "Uber Anatomy Ontology", "namespace_in_lui": true, "pattern": "^\\d+$", "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" } ], "publications": [ { "doi": "10.1186/2041-1480-5-21", "pmc": "PMC4089931", "pubmed": "25009735", "title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon", "year": 2014 }, { "doi": "10.1186/gb-2012-13-1-r5", "pmc": "PMC3334586", "pubmed": "22293552", "title": "Uberon, an integrative multi-species anatomy ontology", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/UBERON_$1", "repository": "https://github.com/obophenotype/uberon", "synonyms": [ "UBERON", "Uber-anatomy ontology", "Uberon" ], "twitter": "uberanat", "uri_format": "http://purl.obolibrary.org/obo/UBERON_$1", "version": "2025-12-04" }, "uberon.issue": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An issue on the UBERON GitHub Issue tracker", "example": "530", "github_request_issue": 1553, "homepage": "https://github.com/obophenotype/uberon/issues", "name": "UBERON Issue Tracker", "pattern": "^\\d+$", "preferred_prefix": "uberon.issue", "uri_format": "https://github.com/obophenotype/uberon/issues/$1" }, "ubio.namebank": { "deprecated": true, "description": "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context.", "example": "2555646", "homepage": "http://www.ubio.org", "mappings": { "biocontext": "UBIO.NAMEBANK", "miriam": "ubio.namebank", "n2t": "ubio.namebank" }, "name": "uBio NameBank", "pattern": "^\\d+$", "preferred_prefix": "ubio.namebank", "uri_format": "http://www.ubio.org/browser/details.php?namebankID=$1" }, "ubprop": { "comment": "All of these are typedefs in uberon now", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "name": "Uberon Property", "preferred_prefix": "ubprop", "synonyms": [ "UBPROP", "UBREL" ] }, "ucas": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An identifier for institutions in the United Kingdom, used in GRID and ROR.", "example": "N21", "homepage": "https://www.ucas.com", "keywords": [ "bibliometrics", "institution" ], "name": "UK Universities and Colleges Admissions Service", "pattern": "^\\w\\d+$", "preferred_prefix": "ucas" }, "ucsc": { "contact": { "email": "max@soe.ucsc.edu", "github": "maximilianh", "name": "Maximilian Haeussler", "orcid": "0000-0001-8721-8253" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations.", "example": "uc001rvw.5", "homepage": "https://genome.ucsc.edu/", "mappings": { "biocontext": "UCSC", "uniprot": "DB-0139", "wikidata": "P2576" }, "name": "UCSC Genome Browser", "preferred_prefix": "ucsc", "publications": [ { "doi": "10.1093/nar/gkae974", "pubmed": "39460617" }, { "doi": "10.1093/nar/gky1095", "pmc": "PMC6323953", "pubmed": "30407534", "title": "The UCSC Genome Browser database: 2019 update", "year": 2019 } ], "uri_format": "ftp://hgdownload.cse.ucsc.edu/goldenPath/$1" }, "ucum": { "contact": { "email": "dr.shorthair@pm.me", "github": "dr-shorthair", "name": "Simon Cox", "orcid": "0000-0002-3884-3420" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Unified Code for Units of Measure (UCUM) is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business.", "example": "aBq", "example_extras": [ "%", "/A/s3/cg3/T3", "/g", "/m3", "Cel.d-1", "Em.s-2", "K2", "Wb", "dL/g", "dlm", "dlx", "g.cm-3", "kW/h", "m.s-2", "m/s", "m/s/d", "mmol.mL-1", "mol.L-1", "mol.um", "ng-1", "pA", "ug.mL-1", "umol.L-1", "us" ], "homepage": "https://ucum.org", "keywords": [ "data identity and mapping", "general & upper", "measurement", "subject agnostic", "unit" ], "mappings": { "bartoc": "1895", "fairsharing": "FAIRsharing.27w8k0", "hl7": "2.16.840.1.113883.6.8", "lov": "ucum", "wikidata.entity": "Q2494286" }, "name": "Unified Code for Units of Measure", "preferred_prefix": "ucum", "publications": [ { "doi": "10.1136/jamia.1999.0060151", "pmc": "PMC61354", "pubmed": "10094068", "title": "Units of measure in clinical information systems", "year": 1999 } ], "references": [ "https://units-of-measurement.org/" ], "repository": "https://github.com/ucum-org/ucum", "uri_format": "https://units-of-measurement.org/$1" }, "udsaes.fmi": { "description": "An ontology transcription of definitions in the Functional Mock-up Interface (FMI) standard document from https://fmi-standard.org/ that enables representing Functional Mock-up Units (FMUs) in RDF", "example": "FMU", "homepage": "https://github.com/UdSAES/fmi2rdf", "keywords": [ "mechanical engineering, energy technology", "nfdi4energy" ], "mappings": { "tib": "fmi" }, "name": "Functional Mock-up Interface Ontology", "preferred_prefix": "udsaes.fmi", "repository": "https://github.com/UdSAES/fmi2rdf", "uri_format": "https://purl.org/fmi-ontology#$1" }, "udsaes.sms": { "description": "Ontology for representing systems, models and simulations in RDF.", "example": "CanBeApproximated", "homepage": "https://github.com/UdSAES/sms-ontology", "keywords": [ "mechanical engineering, energy technology", "nfdi4energy" ], "mappings": { "tib": "sms" }, "name": "SMS-Ontology", "preferred_prefix": "udsaes.sms", "repository": "https://github.com/UdSAES/sms-ontology", "uri_format": "https://purl.org/sms-ontology#$1" }, "ukprn": { "comment": "Added because of appearance in ROR", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for an educational organization issued by the UK Register of Learning Providers", "example": "10007835", "homepage": "https://www.ukrlp.co.uk", "mappings": { "wikidata": "P4971" }, "name": "UK Provider Reference Number", "pattern": "^[1-9]\\d*$", "preferred_prefix": "ukprn", "synonyms": [ "ukprns" ], "uri_format": "https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails?x=&pn_p_id=$1&pv_status=VERIFIED&pv_vis_code=L" }, "umbbd.compound": { "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information.", "example": "c0001", "homepage": "http://umbbd.ethz.ch/", "mappings": { "biocontext": "UMBBD.COMPOUND", "miriam": "umbbd.compound", "n2t": "umbbd.compound", "wikidata": "P8121" }, "name": "UM-BBD compound", "pattern": "^c\\d+$", "preferred_prefix": "umbbd.compound", "synonyms": [ "UM-BBD_compID" ], "uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1" }, "umbbd.enzyme": { "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information.", "example": "e0333", "homepage": "http://umbbd.ethz.ch/", "mappings": { "biocontext": "UMBBD.ENZYME", "go": "UM-BBD_enzymeID", "miriam": "umbbd.enzyme", "n2t": "umbbd.enzyme" }, "name": "EAWAG Biocatalysis/Biodegradation Database enzyme", "pattern": "^e\\d+$", "preferred_prefix": "umbbd.enzyme", "synonyms": [ "UM-BBD_enzymeID" ], "uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1" }, "umbbd.pathway": { "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information.", "example": "ala", "homepage": "http://umbbd.ethz.ch/", "mappings": { "biocontext": "UMBBD.PATHWAY", "go": "UM-BBD_pathwayID", "miriam": "umbbd.pathway", "n2t": "umbbd.pathway" }, "name": "EAWAG Biocatalysis/Biodegradation Database pathway", "pattern": "^\\w+$", "preferred_prefix": "umbbd.pathway", "providers": [ { "code": "eawag", "description": "Graphical depiction of pathway", "homepage": "http://eawag-bbd.ethz.ch", "name": "Pathway map diagram", "uri_format": "http://eawag-bbd.ethz.ch/$1/$1_map.html" } ], "synonyms": [ "UM-BBD_pathwayID" ], "uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1" }, "umbbd.reaction": { "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information.", "example": "r0001", "homepage": "http://umbbd.ethz.ch/", "mappings": { "biocontext": "UMBBD.REACTION", "go": "UM-BBD_reactionID", "miriam": "umbbd.reaction", "n2t": "umbbd.reaction", "wikidata.entity": "Q24188985" }, "name": "EAWAG Biocatalysis/Biodegradation Database reaction", "pattern": "^r\\d+$", "preferred_prefix": "umbbd.reaction", "synonyms": [ "UM-BBD_reactionID" ], "uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1" }, "umbbd.rule": { "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules.", "example": "bt0001", "homepage": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules", "mappings": { "biocontext": "UMBBD.RULE", "go": "UM-BBD_ruleID", "miriam": "umbbd.rule", "n2t": "umbbd.rule" }, "name": "EAWAG Biocatalysis/Biodegradation Database rule", "pattern": "^bt\\d+$", "preferred_prefix": "umbbd.rule", "synonyms": [ "UM-BBD_ruleID" ], "uri_format": "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1" }, "uminctr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An additional Japanese clinical trial registry", "example": "UMIN000049383", "homepage": "https://www.umin.ac.jp/ctr/index.htm", "mappings": { "integbio": "nbdc01470" }, "name": "University hospital Medical Information Network Clinical Trial Registry", "pattern": "^UMIN\\d+$|^C\\d+$", "preferred_prefix": "uminctr", "references": [ "https://center6.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000056224" ] }, "umls": { "contact": { "email": "olivier@nlm.nih.gov", "name": "Olivier Bodenreider", "orcid": "0000-0003-4769-4217" }, "description": "The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank.", "example": "C2584994", "homepage": "https://www.nlm.nih.gov/research/umls", "keywords": [ "biomedicine" ], "license": "https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/license_agreement.html", "logo": "https://uts.nlm.nih.gov/uts/assets/images/umls_tree_sm.jpg", "mappings": { "bartoc": "20052", "biocontext": "UMLS", "edam": "1181", "hl7": "2.16.840.1.113883.6.86", "miriam": "umls", "n2t": "umls", "wikidata": "P2892", "wikidata.entity": "Q455338" }, "name": "Unified Medical Language System Concept Unique Identifier", "pattern": "^C\\d+$", "preferred_prefix": "umls", "publications": [ { "doi": "10.1093/nar/gkh061", "pmc": "PMC308795", "pubmed": "14681409", "title": "The Unified Medical Language System (UMLS): integrating biomedical terminology", "year": 2004 } ], "synonyms": [ "UMLS", "UMLS CUI", "UMLS_CUI", "umls.cui" ], "uri_format": "https://uts.nlm.nih.gov/uts/umls/concept/$1" }, "umls.aui": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An identifier for an atom; the smallest unit of naming in a source, viz, a specific string with specific code values and identifiers from a specific source. As such, they can be thought of as representing a single meaning with a source Atoms are the units of terminology that come from sources and form the building blocks of the concepts in the Metathesaurus.", "example": "A0118748", "homepage": "https://www.nlm.nih.gov/research/umls", "name": "Unified Medical Language System Atomic Unique Identifier", "pattern": "^A\\d+$", "preferred_prefix": "umls.aui", "synonyms": [ "UMLS_ICD9CM_2005_AUI" ] }, "unesco.thesaurus": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The UNESCO Thesaurus is a controlled and structured list of terms used in subject analysis and retrieval of documents and publications in the fields of education, culture, natural sciences, social and human sciences, communication and information. Continuously enriched and updated, its multidisciplinary terminology reflects the evolution of UNESCO's programmes and activities. [from homepage]", "example": "585", "homepage": "http://vocabularies.unesco.org/thesaurus", "keywords": [ "communication science", "culture", "education science", "political science", "subject agnostic" ], "license": "CC-BY-3.0-IGO", "mappings": { "fairsharing": "FAIRsharing.81dc5f" }, "name": "UNESCO Thesaurus", "pattern": "^\\d+$", "preferred_prefix": "unesco.thesaurus", "uri_format": "http://vocabularies.unesco.org/thesaurus/concept$1" }, "unicarbdb": { "contact": { "email": "niclas.karlsson@medkem.gu.se", "name": "Niclas Karlsson", "orcid": "0000-0002-3045-2628" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "UniCarb-DB stores structural and mass spectrometry (MS) glycomic data, and has now grown to be one of the largest experimental glycomic MS databases. Identifiers correspond to individual glycan structures and corresponding MS spectra.", "example": "91", "github_request_issue": 1509, "homepage": "https://unicarb-db.expasy.org", "license": "CC-BY-4.0", "name": "UniCarb-DB", "pattern": "^\\d+$", "preferred_prefix": "unicarbdb", "publications": [ { "doi": "10.1016/j.bbapap.2013.04.018", "pubmed": "23624262", "title": "Validation of the curation pipeline of UniCarb-DB: building a global glycan reference MS/MS repository", "year": 2014 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://unicarb-db.expasy.org/msData/$1" }, "unichem": { "description": "identifier of a compound in the UniChem database", "example": "161671", "homepage": "https://chembl.gitbook.io/unichem/downloads", "mappings": { "wikidata": "P11089" }, "name": "UniChem compound", "pattern": "^\\d+$", "preferred_prefix": "unichem", "uri_format": "https://www.ebi.ac.uk/unichem/compoundsources?type=uci&compound=$1" }, "unigene": { "deprecated": true, "description": "A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.", "example": "4900", "homepage": "http://www.ncbi.nlm.nih.gov/unigene", "keywords": [ "dna", "gene", "gene expression", "life science", "protein" ], "mappings": { "biocontext": "UNIGENE", "fairsharing": "FAIRsharing.ge1c3p", "integbio": "nbdc00220", "miriam": "unigene", "n2t": "unigene", "prefixcommons": "unigene", "re3data": "r3d100010774" }, "name": "UniGene", "pattern": "^\\d+$", "preferred_prefix": "unigene", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/unigene:$1" } ], "publications": [ { "doi": "10.1093/nar/gkg033", "pmc": "PMC165480", "pubmed": "12519941", "title": "Database resources of the National Center for Biotechnology", "year": 2003 } ], "uri_format": "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1" }, "unii": { "description": "The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information.", "example": "3G6A5W338E", "homepage": "https://precision.fda.gov/uniisearch", "mappings": { "biocontext": "UNII", "cheminf": "000563", "miriam": "unii", "n2t": "unii", "wikidata": "P652" }, "name": "Unique Ingredient Identifier", "pattern": "^[A-Z0-9]+$", "preferred_prefix": "unii", "uri_format": "https://precision.fda.gov/uniisearch/srs/unii/$1" }, "unimod": { "contact": { "email": "jcottrell@matrixscience.com", "name": "John Cottrell", "orcid": "0000-0003-3843-0818" }, "description": "Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide).", "download_owl": "https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/unimod.owl", "example": "1200", "homepage": "http://www.unimod.org/", "keywords": [ "bioinformatics", "ontology" ], "logo": "https://www.unimod.org/images/logo.gif", "mappings": { "biocontext": "UNIMOD", "edam": "3757", "fairsharing": "FAIRsharing.zZHCUQ", "miriam": "unimod", "n2t": "unimod", "ols": "unimod" }, "name": "Unimod protein modification database for mass spectrometry", "pattern": "^\\d+$", "preferred_prefix": "unimod", "publications": [ { "doi": "10.1002/pmic.200300744", "pubmed": "15174123", "title": "Unimod: Protein modifications for mass spectrometry", "year": 2004 } ], "uri_format": "http://www.unimod.org/modifications_view.php?editid1=$1" }, "uniparc": { "contact": { "email": "agb@ebi.ac.uk", "github": "bateman-research", "name": "Alex Bateman", "orcid": "0000-0002-6982-4660" }, "description": "The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases.", "example": "UPI000000000A", "homepage": "http://www.uniprot.org/uniparc/", "keywords": [ "protein", "structure" ], "mappings": { "biocontext": "UNIPARC", "edam": "2392", "go": "UniParc", "miriam": "uniparc", "n2t": "uniparc", "prefixcommons": "uniparc", "re3data": "r3d100011519" }, "name": "UniProt Archive", "pattern": "^UPI[A-F0-9]{10}$", "preferred_prefix": "uniparc", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/uniparc:$1" } ], "publications": [ { "doi": "10.1093/nar/gkh131", "pmc": "PMC308865", "pubmed": "14681372", "title": "UniProt: the Universal Protein knowledgebase", "year": 2004 } ], "uri_format": "https://www.uniprot.org/uniparc/$1" }, "unipathway.compound": { "description": "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds.", "example": "UPC04349", "homepage": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway", "mappings": { "biocontext": "UNIPATHWAY.COMPOUND", "miriam": "unipathway.compound", "n2t": "unipathway.compound" }, "name": "UniPathway Compound", "pattern": "^UPC\\d{5}$", "preferred_prefix": "unipathway.compound", "uri_format": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1" }, "unipathway.reaction": { "description": "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions.", "example": "UCR00226", "homepage": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway", "mappings": { "biocontext": "UNIPATHWAY.REACTION", "miriam": "unipathway.reaction", "n2t": "unipathway.reaction" }, "name": "UniPathway Reaction", "pattern": "^UCR\\d{5}$", "preferred_prefix": "unipathway.reaction", "uri_format": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1" }, "uniprot": { "contact": { "email": "agb@ebi.ac.uk", "github": "bateman-research", "name": "Alex Bateman", "orcid": "0000-0002-6982-4660" }, "contributor_extras": [ { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" } ], "description": "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. 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The definition of the post-translational modifications usage as well as other information is provided in the following format", "example": "PTM-0450", "homepage": "https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs/ptmlist", "keywords": [ "biochemistry", "post-translational modification", "structural biology" ], "license": "CC-BY-4.0", "logo": "https://www.uniprot.org/uniprot-logo.img.0df091.svg", "name": "UniProt Post-Translational Modification", "pattern": "^PTM-\\d{4}$", "preferred_prefix": "uniprot.ptm", "references": [ "https://twitter.com/cthoyt/status/1510570256619778053", "https://www.uniprot.org/docs/ptmlist.txt" ], "synonyms": [ "PTM" ], "uri_format": "https://biopragmatics.github.io/providers/uniprot.ptm/$1" }, "uniprot.resource": { "contact": { "email": "agb@ebi.ac.uk", "github": "bateman-research", "name": "Alex Bateman", "orcid": "0000-0002-6982-4660" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources.", "example": "DB-0174", "homepage": "https://www.uniprot.org/database/", "logo": "https://www.uniprot.org/og-uniprot-wide-logo-1200x630.png", "name": "UniProt Resource", "pattern": "^DB-\\d{4}$", "preferred_prefix": "uniprot.resource", "synonyms": [ "uniprot.database", "uniprot.db" ], "uri_format": "https://www.uniprot.org/database/$1" }, "uniprot.tissue": { "contact": { "email": "agb@ebi.ac.uk", "github": "bateman-research", "name": "Alex Bateman", "orcid": "0000-0002-6982-4660" }, "description": "The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified.", "example": "TS-0285", "homepage": "https://www.uniprot.org/docs/tisslist.txt", "logo": "https://www.uniprot.org/uniprot-logo.img.0df091.svg", "mappings": { "biocontext": "TISSUELIST", "miriam": "tissuelist", "n2t": "tissuelist" }, "name": "Tissue List", "pattern": "^TS-\\d{4}$", "preferred_prefix": "uniprot.tissue", "uri_format": "https://www.uniprot.org/tissues/$1" }, "uniprot.var": { "contact": { "email": "agb@ebi.ac.uk", "github": "bateman-research", "name": "Alex Bateman", "orcid": "0000-0002-6982-4660" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species.", "example": "068078", "homepage": "https://web.expasy.org/variant_pages", "logo": "https://www.uniprot.org/og-uniprot-wide-logo-1200x630.png", "name": "UniProt Variants", "pattern": "^\\d+$", "preferred_prefix": "uniprot.var", "providers": [ { "code": "expasy", "description": "Expasy external page for protein variant", "homepage": "https://web.expasy.org/variant_pages", "name": "ExPaSy", "uri_format": "https://web.expasy.org/variant_pages/VAR_$1.html" } ], "synonyms": [ "SP_VAR", "UPVAR", "UniProtKB_VAR" ], "uri_format": "http://purl.uniprot.org/annotation/VAR_$1" }, "uniref": { "contact": { "email": "agb@ebi.ac.uk", "github": "bateman-research", "name": "Alex Bateman", "orcid": "0000-0002-6982-4660" }, "description": "The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.", "example": "UniRef90_P00750", "homepage": "https://www.uniprot.org/", "logo": "https://www.uniprot.org/uniprot-logo.img.0df091.svg", "mappings": { "edam": "2346", "miriam": "uniref", "re3data": "r3d100011518" }, "name": "UniRef", "pattern": "^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$", "preferred_prefix": "uniref", "uri_format": "https://www.uniprot.org/uniref/$1" }, "unirule": { "contact": { "email": "agb@ebi.ac.uk", "github": "bateman-research", "name": "Alex Bateman", "orcid": "0000-0002-6982-4660" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates. UniRule rules can annotate protein properties such as the protein name, function, catalytic activity, pathway membership, and subcellular location, along with sequence specific information, such as the positions of post-translational modifications and active sites.", "example": "UR000124451", "homepage": "https://www.uniprot.org/unirule/", "logo": "https://www.uniprot.org/uniprot-logo.img.0df091.svg", "mappings": { "go": "UniRule" }, "name": "UniRule", "preferred_prefix": "unirule", "uri_format": "https://www.uniprot.org/unirule/$1" }, "unists": { "deprecated": true, "description": "UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences.", "example": "456789", "homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists", "keywords": [ "gene", "protein" ], "mappings": { "biocontext": "UNISTS", "edam": "2389", "miriam": "unists", "n2t": "unists", "ncbi": "UniSTS", "prefixcommons": "unists" }, "name": "Database of Sequence Tagged Sites", "pattern": "^\\d+$", "preferred_prefix": "unists", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/unists:$1" } ], "uri_format": "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1" }, "unite": { "contact": { "email": "urmas.koljalg@ut.ee", "name": "Urmas Kõljalg", "orcid": "0000-0002-5171-1668" }, "description": "UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa.", "example": "UDB000691", "homepage": "http://unite.ut.ee/", "keywords": [ "biodiversity", "bioinformatics", "dna", "ecology", "genomics", "metagenomics", "taxonomy" ], "mappings": { "biocontext": "UNITE", "edam": "2390", "fairsharing": "FAIRsharing.cnwx8c", "integbio": "nbdc01905", "miriam": "unite", "n2t": "unite", "ncbi": "UNITE", "prefixcommons": "unite", "re3data": "r3d100011316" }, "name": "Molecular database for the identification of fungi", "pattern": "^UDB\\d{6}$", "preferred_prefix": "unite", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/unite:$1" } ], "publications": [ { "doi": "10.1111/j.1469-8137.2009.03160.x", "pubmed": "20409185", "title": "The UNITE database for molecular identification of fungi--recent updates and future perspectives", "year": 2010 } ], "uri_format": "http://unite.ut.ee/bl_forw.php?nimi=$1" }, "unpd": { "comment": "The website is dead, there are no places to get the source information except inside https://oolonek.github.io/ISDB/.", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "homepage": "http://pkuxxj.pku.edu.cn/UNPD/", "keywords": [ "compound", "natural product", "small molecule" ], "name": "Universal Natural Products Database", "preferred_prefix": "unpd", "publications": [ { "doi": "10.1021/acs.jnatprod.6b01093", "pubmed": "28616931", "title": "Database for Rapid Dereplication of Known Natural Products Using Data from MS and Fast NMR Experiments", "year": 2017 }, { "doi": "10.1371/journal.pone.0062839", "pmc": "PMC3636197", "pubmed": "23638153", "title": "Use of natural products as chemical library for drug discovery and network pharmacology", "year": 2013 } ], "references": [ "http://bioinf-applied.charite.de/supernatural_new/index.php?site=vendor_info&id=Universal%20Natural%20Products%20Database", "https://pharmacognosy.in/the-universal-natural-products-database-unpd/", "https://oolonek.github.io/ISDB/" ] }, "uo": { "appears_in": [ "agro", "ms", "rbo", "scdo" ], "banana": "UO", "contact": { "email": "g.gkoutos@gmail.com", "github": "gkoutos", "name": "George Gkoutos", "orcid": "0000-0002-2061-091X" }, "description": "Ontology of standardized units", "download_json": "http://purl.obolibrary.org/obo/uo.json", "download_obo": "http://purl.obolibrary.org/obo/uo.obo", "download_owl": "http://purl.obolibrary.org/obo/uo.owl", "example": "0000080", "homepage": "https://github.com/bio-ontology-research-group/unit-ontology", "keywords": [ "dataplant", "earth sciences", "ess", "life science", "life sciences, biology", "mathematics", "measurement", "nfdi4chem", "nfdi4ing", "obo", "ontology", "physics", "unit", "units" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "UO", "agroportal": "UO", "biocontext": "UO", "bioportal": "UO", "fairsharing": "FAIRsharing.mjnypw", "miriam": "uo", "n2t": "uo", "obofoundry": "uo", "ols": "uo", "ontobee": "UO", "prefixcommons": "uo", "tib": "uo", "wikidata.entity": "Q81661826" }, "name": "Units of measurement ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "UO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/uo:$1" } ], "publications": [ { "doi": "10.1093/database/bas033", "pmc": "PMC3468815", "pubmed": "23060432", "title": "The Units Ontology: a tool for integrating units of measurement in science", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/UO_$1", "repository": "https://github.com/bio-ontology-research-group/unit-ontology", "uri_format": "http://purl.obolibrary.org/obo/UO_$1", "version": "2026-01-16" }, "upa": { "contact": { "email": "Anne.Morgat@sib.swiss", "github": "amorgat", "name": "Anne Morgat", "orcid": "0000-0002-1216-2969" }, "depends_on": [ "ro" ], "deprecated": true, "description": "A manually curated resource for the representation and annotation of metabolic pathways", "download_obo": "https://raw.githubusercontent.com/geneontology/unipathway/master/upa.obo", "download_owl": "http://purl.obolibrary.org/obo/upa.owl", "example": "UCR00513", "homepage": "https://github.com/geneontology/unipathway", "keywords": [ "obo", "ontology", "pathway" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "UPA", "biocontext": "UNIPATHWAY", "bioportal": "UPA", "edam": "2645", "go": "UniPathway", "obofoundry": "upa", "ols": "upa", "ontobee": "UPA", "pathguide": "414", "prefixcommons": "unipathway", "wikidata.entity": "Q85719315" }, "name": "Unipathway", "pattern": "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\\d{5}$", "preferred_prefix": "UPA", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/unipathway:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr1023", "pmc": "PMC3245108", "pubmed": "22102589", "title": "UniPathway: a resource for the exploration and annotation of metabolic pathways", "year": 2011 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/UPA_$1", "repository": "https://github.com/geneontology/unipathway", "synonyms": [ "UPa", "unipathway", "unipathway.pathway" ], "uri_format": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1", "version": "2024-03-06" }, "upheno": { "contact": { "email": "jmcl@ebi.ac.uk", "github": "jamesamcl", "name": "James McLaughlin", "orcid": "0000-0002-8361-2795" }, "description": "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.", "download_owl": "http://purl.obolibrary.org/obo/upheno.owl", "homepage": "https://github.com/obophenotype/upheno", "keywords": [ "data analysis", "evolutionary biology", "expression data", "obo", "omics", "ontology", "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", "bioportal": "UPHENO", "fairsharing": "FAIRsharing.r41qhx", "obofoundry": "upheno", "ols": "upheno", "ontobee": "UPHENO", "wikidata.entity": "Q81661827" }, "name": "Unified Phenotype Ontology", "no_own_terms": true, "preferred_prefix": "UPHENO", "publications": [ { "doi": "10.1093/genetics/iyaf027", "pubmed": "40048704", "title": "The Unified Phenotype Ontology : a framework for cross-species integrative phenomics", "year": 2025 }, { "doi": "10.1101/2024.09.18.613276", "title": "The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/UPHENO_$1", "repository": "https://github.com/obophenotype/upheno", "uri_format": "http://purl.obolibrary.org/obo/UPHENO_$1", "version": "2025-10-12" }, "urdbms.syndromefinder": { "appears_in": [ "nando" ], "contact": { "email": "naritomi@med.u-ryukyu.ac.jp", "name": "Kenji Naritomi" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "example": "3567", "github_request_issue": 1320, "mappings": { "integbio": "nbdc00728" }, "name": "UR-DBMS Syndrome Finder", "pattern": "^\\d+$", "preferred_prefix": "urdbms.syndromefinder", "publications": [ { "doi": "10.1038/s10038-024-01277-y", "pubmed": "39085458", "title": "An application supporting diagnosis for rare genetic diseases - UR-DBMS and Syndrome Finder", "year": 2024 } ], "uri_format": "http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php?winid=1&recid=$1" }, "usda.cvb.pcn": { "appears_in": [ "vo" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A Product Code Number (PCN) assigned by the Animal and Plant Health Inspection Service (APHIS)'s Center for Veterinary Biologics (CVB) to veterinary biological products such as vaccines, bacterins, antibodies, diagnostic products, antitoxins, bacterin-toxoids, and toxioids approved for veterinary use by the United States Department of Agriculture Veterinary (USDA). A quarterly release, as PDF, can be found [here](https://www.aphis.usda.gov/sites/default/files/currentprodcodebook.pdf).\n\n The PDF document states (verbatim): The alphanumeric system used for product codes provides for a six-digit number of number-letter combination to be assigned to each product, i.e., the first digit denotes product types; second and third, group by agents; fourth, the viability of vaccine, (live, killed, modified live, etc.); fifth, substrates; and sixth, miscellaneous variables", "example": "1011.00", "example_extras": [ "10T1.40", "19O5.D0", "1K11.00", "GA94.00" ], "homepage": "https://www.aphis.usda.gov/veterinary-biologics/licensed-products", "keywords": [ "antitoxin", "bacterin", "bacterin-toxoid", "diagnostic product", "toxoid", "vaccine" ], "name": "United States Department of Agriculture Veterinary Biological Product Code Number", "owners": [ { "name": "Animal and Plant Health Inspection Service", "partnered": false, "ror": "0599wfz09" } ], "pattern": "^[A-Z0-9]{4}\\.[A-Z0-9]{2}$", "preferred_prefix": "usda.cvb.pcn", "references": [ "https://www.aphis.usda.gov/sites/default/files/currentprodcodebook.pdf", "https://www.aphis.usda.gov/veterinary-biologics" ] }, "uspto": { "comment": "Information about the regular expression was derived from examples at https://patft.uspto.gov/netahtml/PTO/srchnum.htm. TODO, make the regular expression work for '100000000'", "contributor_extras": [ { "github": "dhimmel", "name": "Daniel Himmelstein", "orcid": "0000-0002-3012-7446" } ], "description": "The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement.", "example": "4145692", "example_extras": [ "0000001", "10,000,000", "6923014", "AI00007", "D000152", "H001234", "PP07514", "RE12345", "RX00001", "T855019", "X000001" ], "homepage": "http://patft.uspto.gov/netahtml/PTO/index.html", "mappings": { "biocontext": "USPTO", "miriam": "uspto", "n2t": "uspto" }, "name": "United States Patent and Trademark Office", "pattern": "^(\\d{1,2},?\\d{3},?\\d{3}|(PP|RE|AI|RX)\\d{2},?\\d{3}|(D|T|H|X)\\d{3},?\\d{3})$", "preferred_prefix": "uspto", "references": [ "https://github.com/biopragmatics/bioregistry/issues/253" ], "uri_format": "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1" }, "utrdb": { "description": "A curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs. In the current update, the UTR entries are organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets. ", "example": "5UTR_107_ENST00000517291.2", "homepage": "https://utrdb.cloud.ba.infn.it/utrdb/index_107.html", "mappings": { "integbio": "nbdc00730", "miriam": "utrdb" }, "name": "UTRdb", "pattern": "^([3-5][A-Z])\\w+[^A-Z][0-9]$", "preferred_prefix": "utrdb", "uri_format": "https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e=$1" }, "vac": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Vaccine Adjuvant Compendium (VAC) was established in 2020 by the NIAID Division of Allergy, Immunology, and Transplantation to foster collaborations between NIAID-supported adjuvant researchers and the broader scientific community. The VAC displays adjuvant characteristics or metadata defined through NIAID-supported adjuvant studies to help vaccine developers identify suitable adjuvants for various vaccine indications, including immune-mediated and infectious diseases. In addition, the VAC welcomes the inclusion of adjuvant metadata generated by other research programs.", "example": "15", "homepage": "https://vac.niaid.nih.gov", "keywords": [ "biology", "immunology", "vaccines" ], "name": "Vaccine Adjuvant Compendium", "pattern": "^\\d+$", "preferred_prefix": "vac", "uri_format": "https://vac.niaid.nih.gov/view?id=$1" }, "validatordb": { "contact": { "email": "david.sehnal@gmail.com", "name": "David Sehnal", "orcid": "0000-0002-0682-3089" }, "description": "Database of validation results for ligands and non-standard residues in the Protein Data Bank.", "example": "2h6o", "homepage": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/", "keywords": [ "life science" ], "mappings": { "biocontext": "VALIDATORDB", "fairsharing": "FAIRsharing.c9psgb", "integbio": "nbdc02174", "miriam": "validatordb", "n2t": "validatordb" }, "name": "ValidatorDB", "pattern": "^[A-Za-z0-9\\/]+$", "preferred_prefix": "validatordb", "provides": "pdb", "publications": [ { "doi": "10.1093/nar/gku1118", "pmc": "PMC4383933", "pubmed": "25392418", "title": "ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank", "year": 2014 } ], "uri_format": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1" }, "vandf": { "contact": { "email": "michael.lincoln@med.va.gov", "name": "Michael Lincoln" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes.", "example": "4019477", "homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF", "keywords": [ "biomedical science", "drug", "drug interaction", "ontology", "pharmacology" ], "mappings": { "aberowl": "VANDF", "biolink": "VANDF", "bioportal": "VANDF", "fairsharing": "FAIRsharing.xn3pb3", "hl7": "2.16.840.1.113883.6.229" }, "name": "Veterans Administration National Drug File", "pattern": "^\\d+$", "preferred_prefix": "vandf", "publications": [ { "pmc": "PMC2244318", "pubmed": "12463886", "title": "A semantic normal form for clinical drugs in the UMLS: early experiences with the VANDF", "year": 2002 } ], "uri_format": "http://purl.bioontology.org/ontology/VANDF/$1" }, "vann": { "contact": { "email": "nospam@iandavis.com", "github": "iand", "name": "Ian Davis" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This document describes a vocabulary for annotating descriptions of vocabularies with examples and usage notes.", "example": "usageNote", "homepage": "https://vocab.org/vann/", "keywords": [ "computer science", "metadata", "tib" ], "mappings": { "lov": "vann", "tib": "vann", "zazuko": "vann" }, "name": "A vocabulary for annotating vocabulary descriptions", "preferred_prefix": "vann", "rdf_uri_format": "http://purl.org/vocab/vann/$1", "uri_format": "https://vocab.org/vann/#$1" }, "vario": { "banana": "VariO", "contact": { "email": "mauno.vihinen@med.lu.se", "github": "maunov", "name": "Mauno Vihinen", "orcid": "0000-0002-9614-7976" }, "deprecated": true, "description": "The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level.", "download_obo": "http://purl.obolibrary.org/obo/vario.obo", "download_owl": "http://purl.obolibrary.org/obo/vario.owl", "example": "0376", "homepage": "http://variationontology.org", "keywords": [ "chromosome structure variation", "deoxyribonucleic acid", "genetics", "obo", "ontology", "protein", "ribonucleic acid", "sequence variant" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "VARIO", "agroportal": "VARIO", "biocontext": "VARIO", "bioportal": "VARIO", "fairsharing": "FAIRsharing.65xkbs", "miriam": "vario", "n2t": "vario", "obofoundry": "vario", "ols": "vario", "ontobee": "VariO", "wikidata.entity": "Q114677953" }, "name": "Variation Ontology", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "VariO", "publications": [ { "doi": "10.1186/s12864-018-5262-0", "pmc": "PMC6309100", "pubmed": "30591019", "title": "Systematics for types and effects of DNA variations", "year": 2018 }, { "doi": "10.1002/humu.22954", "pubmed": "26773573", "title": "VariOtator, a Software Tool for Variation Annotation with the Variation Ontology", "year": 2016 }, { "doi": "10.1007/s00439-015-1529-6", "pubmed": "25616435", "title": "Types and effects of protein variations", "year": 2015 }, { "doi": "10.1186/2041-1480-5-9", "pmc": "PMC3931275", "pubmed": "24533660", "title": "Variation ontology: annotator guide", "year": 2014 }, { "doi": "10.1101/gr.157495.113", "pmc": "PMC3912426", "pubmed": "24162187", "title": "Variation Ontology for annotation of variation effects and mechanisms", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/VariO_$1", "uri_format": "http://purl.obolibrary.org/obo/VariO_$1", "version": "2018-11-09" }, "vbase2": { "contact": { "email": "wmueller@gbf.de", "name": "Werner Müller", "orcid": "0000-0002-1297-9725" }, "description": "The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes.", "example": "humIGHV025", "homepage": "http://www.vbase2.org/vbase2.php", "keywords": [ "gene", "life science" ], "mappings": { "biocontext": "VBASE2", "fairsharing": "FAIRsharing.qvxhb1", "integbio": "nbdc01897", "miriam": "vbase2", "n2t": "vbase2", "ncbi": "VBASE2", "prefixcommons": "vbase2" }, "name": "Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse", "pattern": "^\\w+$", "preferred_prefix": "vbase2", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/vbase2:$1" } ], "publications": [ { "doi": "10.1093/nar/gki088", "pmc": "PMC540042", "pubmed": "15608286", "title": "VBASE2, an integrative V gene database", "year": 2005 } ], "uri_format": "http://www.vbase2.org/vgene.php?id=$1" }, "vbo": { "contact": { "email": "Sabrina@tislab.org", "github": "sabrinatoro", "name": "Sabrina Toro", "orcid": "0000-0002-4142-7153" }, "depends_on": [ "ncbitaxon" ], "description": "Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.", "download_json": "http://purl.obolibrary.org/obo/vbo.json", "download_obo": "http://purl.obolibrary.org/obo/vbo.obo", "download_owl": "http://purl.obolibrary.org/obo/vbo.owl", "example": "0000038", "homepage": "https://github.com/monarch-initiative/vertebrate-breed-ontology", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "logo": "https://raw.githubusercontent.com/tis-lab/closed-illustrations/master/logos/vbo-logo/VBO-black-logo-stackedv2.png", "mappings": { "aberowl": "VBO", "agroportal": "VBO", "bioportal": "VBO", "cellosaurus": "VBO", "obofoundry": "vbo", "ols": "vbo", "ontobee": "VBO", "wikidata.entity": "Q114296193" }, "name": "Vertebrate Breed Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "VBO", "publications": [ { "doi": "10.1111/jvim.70133", "title": "The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization" } ], "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_$1", "version": "2025-11-07" }, "vbo.issue": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An issue on the Vertebrate Breed Ontology GitHub issue tracker", "example": "126", "github_request_issue": 1553, "homepage": "https://github.com/monarch-initiative/vertebrate-breed-ontology/issues", "name": "Vertebrate Breed Ontology Issue Tracker", "pattern": "^\\d+$", "preferred_prefix": "vbo.issue", "uri_format": "https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/$1" }, "vbrc": { "deprecated": true, "description": "The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis.", "example": "35742", "homepage": "http://vbrc.org/", "mappings": { "biocontext": "VBRC", "miriam": "vbrc", "n2t": "vbrc", "prefixcommons": "vbrc" }, "name": "Viral Bioinformatics Resource Center", "pattern": "^\\d+$", "preferred_prefix": "vbrc", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/vbrc:$1" } ], "uri_format": "http://vbrc.org/gene_detail.asp?gene_id=$1" }, "vcard": { "contact": { "email": "r@iannel.la", "github": "riannella", "name": "Renato Iannella", "orcid": "0000-0001-5547-3508" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "vCard is a specification developed by the Internet Engineering Task Force (IETF) for the description of people and organisations", "download_owl": "https://www.w3.org/2006/vcard/ns", "example": "Agent", "github_request_issue": 1317, "homepage": "https://www.w3.org/TR/vcard-rdf/", "keywords": [ "ontology", "people" ], "mappings": { "lov": "vcard", "zazuko": "vcard" }, "name": "Virtual Contact File", "preferred_prefix": "vcard", "uri_format": "http://www.w3.org/2006/vcard/ns#$1" }, "vcell": { "description": "Models developed with the Virtual Cell (VCell) software prorgam.", "example": "201022999", "homepage": "https://health.uconn.edu/", "mappings": { "miriam": "vcell" }, "name": "VCell Published Models", "pattern": "^\\d{5,}$", "preferred_prefix": "vcell", "uri_format": "https://vcell.org/biomodel-$1" }, "vdrc": { "description": "Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID. [from RRID]", "example": "100291", "homepage": "http://stockcenter.vdrc.at/control/main", "keywords": [ "biomaterial supply resource", "drosophila", "fly lines" ], "mappings": { "rrid": "VDRC" }, "name": "Vienna Drosophila Resource Center", "pattern": "^\\d+$", "preferred_prefix": "vdrc", "uri_format": "https://shop.vbc.ac.at/vdrc_store/$1.html" }, "vectorbase": { "contact": { "email": "d.e.starns@liv.ac.uk", "github": "obsidian83", "name": "David Starns", "orcid": "0000-0001-6583-9067" }, "description": "VectorBase is part of the VEuPathDB, a NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens and related species of interest. Currently, VectorBase contains genome information for approximately 80 organisms: mosquitoes, bed bugs, biting midges, ticks, tsetse flies, mites, sand flies, house flies, body lice, stable flies, kissing bugs, and a snail which is an intermediate host.", "example": "ISCW007415", "homepage": "https://www.vectorbase.org/", "keywords": [ "comparative genomics", "functional genomics", "gene", "genome", "genomics", "population dynamics", "population genetics", "protein" ], "mappings": { "biocontext": "VECTORBASE", "fairsharing": "FAIRsharing.3etvdn", "integbio": "nbdc01909", "miriam": "vectorbase", "n2t": "vectorbase", "ncbi": "VectorBase", "prefixcommons": "vectorbase", "re3data": "r3d100010880" }, "name": "Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens", "pattern": "^\\D{4}\\d{6}(\\-\\D{2})?$", "preferred_prefix": "vectorbase", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/vectorbase:$1" }, { "code": "vectorbase.alt1", "description": "An alternate provider based on the search functionality", "homepage": "https://www.vectorbase.org", "name": "Vectorbase Alt. 1", "uri_format": "https://www.vectorbase.org/search/site/$1?&site=\"Genome\"" }, { "code": "vectorbase.alt2", "description": "An alternate provider based on the app structure", "homepage": "https://www.vectorbase.org", "name": "Vectorbase Alt. 2", "uri_format": "https://vectorbase.org/vectorbase/app/record/gene/$1" } ], "publications": [ { "doi": "10.1093/nar/gku1117", "pmc": "PMC4383932", "pubmed": "25510499", "title": "VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases", "year": 2014 }, { "doi": "10.1093/nar/gkn857", "pmc": "PMC2686483", "pubmed": "19028744", "title": "VectorBase: a data resource for invertebrate vector genomics", "year": 2008 } ], "twitter": "VectorBase", "uri_format": "https://vectorbase.org/gene/$1" }, "vega": { "contact": { "email": "jla1@sanger.ac.uk", "name": "Jennifer L Harrow", "orcid": "0000-0003-0338-3070" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A repository for high-quality gene models produced by the manual annotation of vertebrate genomes.", "example": "OTTHUMG00000169812", "homepage": "https://vega.archive.ensembl.org/index.html", "keywords": [ "genome", "life science" ], "mappings": { "fairsharing": "FAIRsharing.mr293q", "prefixcommons": "vega", "re3data": "r3d100012575" }, "name": "Vertebrate Genome Annotation Database", "preferred_prefix": "vega", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/vega:$1" } ], "publications": [ { "doi": "10.1093/nar/gkt1241", "pmc": "PMC3964964", "pubmed": "24316575", "title": "The Vertebrate Genome Annotation browser 10 years on", "year": 2013 }, { "doi": "10.1093/nar/gkm987", "pmc": "PMC2238886", "pubmed": "18003653", "title": "The vertebrate genome annotation (Vega) database", "year": 2007 } ], "synonyms": [ "VEGA" ], "uri_format": "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1" }, "vegbank": { "description": "VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. ", "example": "VB.Ob.3736.GRSM125", "homepage": "http://vegbank.org/", "mappings": { "miriam": "vegbank", "re3data": "r3d100010153" }, "name": "VegBank", "pattern": "^VB\\.[A-Za-z][A-Za-z]\\..*$", "preferred_prefix": "vegbank", "uri_format": "http://vegbank.org/cite/$1" }, "venom": { "appears_in": [ "vbo" ], "contact": { "email": "DBrodbelt@RVC.AC.UK", "name": "David Brodbelt", "orcid": "0000-0001-5628-4194" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Veterinary Nomenclature (VeNom) is a standard set of clinical veterinary terms for use in referral veterinary hospital electronic patient records and first opinion veterinary practice management systems.", "example": "12969", "homepage": "https://venomcoding.org/", "name": "Veterinary Nomenclature", "pattern": "^\\d+$", "preferred_prefix": "VeNom", "proprietary": true, "references": [ "https://github.com/biopragmatics/bioregistry/pull/724" ] }, "vfb": { "contact": { "email": "r.court@ed.ac.uk", "name": "Robert Court", "orcid": "0000-0002-0173-9080" }, "description": "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster.", "example": "00000001", "homepage": "https://VirtualFlyBrain.org", "keywords": [ "life science", "neurobiology" ], "mappings": { "fairsharing": "FAIRsharing.nzaz6z", "miriam": "vfb", "n2t": "vfb", "re3data": "r3d100011373" }, "name": "Virtual Fly Brain", "pattern": "^[0-9a-zA-Z]{8}$", "preferred_prefix": "vfb", "publications": [ { "doi": "10.1186/1471-2105-13-122", "pmc": "PMC3412715", "pubmed": "22676296", "title": "Web tools for large-scale 3D biological images and atlases", "year": 2012 }, { "doi": "10.1093/bioinformatics/bts113", "pubmed": "22402613", "title": "A strategy for building neuroanatomy ontologies", "year": 2012 }, { "doi": "10.1093/bioinformatics/btr677", "pubmed": "22180411", "title": "The Virtual Fly Brain browser and query interface", "year": 2011 }, { "doi": "doi:10.1186/1471-2105-13-122", "title": "Web tools for large-scale 3D biological images and atlases" } ], "uri_format": "http://virtualflybrain.org/reports/$1" }, "vfdb.gene": { "description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes.", "example": "VFG2154", "homepage": "http://www.mgc.ac.cn/VFs/", "mappings": { "biocontext": "VFDB.GENE", "miriam": "vfdb.gene", "n2t": "vfdb.gene" }, "name": "VFDB Gene", "pattern": "^\\w+$", "preferred_prefix": "vfdb.gene", "uri_format": "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1" }, "vfdb.genus": { "description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus.", "example": "Chlamydia", "homepage": "http://www.mgc.ac.cn/VFs/", "mappings": { "biocontext": "VFDB.GENUS", "miriam": "vfdb.genus", "n2t": "vfdb.genus" }, "name": "VFDB Genus", "pattern": "^\\w+$", "preferred_prefix": "vfdb.genus", "uri_format": "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1" }, "vgnc": { "contact": { "email": "stweedie@ebi.ac.uk", "name": "Susan Tweedie", "orcid": "0000-0003-1818-8243" }, "description": "The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee.", "example": "3792", "homepage": "https://vertebrate.genenames.org", "keywords": [ "life science" ], "mappings": { "cellosaurus": "VGNC", "fairsharing": "FAIRsharing.5NhJFK", "integbio": "nbdc02624", "miriam": "vgnc", "ncbi": "VGNC", "togoid": "Vgnc", "uniprot": "DB-0226" }, "name": "Vertebrate Gene Nomenclature Committee", "pattern": "^\\d{1,9}$", "preferred_prefix": "vgnc", "publications": [ { "doi": "10.1093/nar/gkaa980", "pmc": "PMC7779007", "pubmed": "33152070", "title": "Genenames.org: the HGNC and VGNC resources in 2021", "year": 2021 } ], "uri_format": "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1" }, "vhog": { "contact": { "email": "bgee@isb-sib.ch", "name": "Bgee team" }, "deprecated": true, "description": "vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 \"historical homology\". Each mapping has been manually reviewed, and we provide confidence codes and references when available.", "download_obo": "ftp://ftp.bgee.org/general/ontologies/vHOG.obo", "download_owl": "http://purl.obolibrary.org/obo/vhog.owl", "example": "0000411", "homepage": "http://bgee.unil.ch", "keywords": [ "anatomy", "development", "obo", "ontology" ], "logo": "http://bgee.org/img/logo/bgee13_logo.png", "mappings": { "aberowl": "VHOG", "biocontext": "VHOG", "bioportal": "VHOG", "obofoundry": "vhog", "prefixcommons": "vhog" }, "name": "Vertebrate Homologous Organ Group Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "VHOG", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/vhog:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/VHOG_$1", "synonyms": [ "VHOG_RETIRED" ], "uri_format": "http://purl.obolibrary.org/obo/VHOG_$1" }, "viaf": { "description": "The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web.", "example": "75121530", "homepage": "http://viaf.org", "keywords": [ "centrally registered identifier", "subject agnostic" ], "mappings": { "bartoc": "2053", "fairsharing": "FAIRsharing.a15ac6", "miriam": "viaf", "n2t": "viaf", "wikidata": "P214", "wikidata.entity": "Q19832964" }, "name": "VIAF cluster ID", "pattern": "^\\d+$", "preferred_prefix": "viaf", "providers": [ { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/viaf/$1" }, { "code": "viaf.https", "description": "A duplicate endpoint over HTTPS", "first_party": true, "homepage": "http://viaf.org", "name": "VIAF (https)", "uri_format": "https://viaf.org/$1" } ], "rdf_uri_format": "http://viaf.org/viaf/$1", "uri_format": "http://viaf.org/viaf/$1" }, "vibso": { "contact": { "email": "philip.stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "contributor": { "email": "philip.stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "description": "The Vibration Spectroscopy Ontology defines technical terms with which research data produced in vibrational spectroscopy experiments can be semantically enriched, made machine readable and FAIR.", "example": "0000008", "github_request_issue": 1278, "homepage": "https://nfdi4chem.github.io/VibrationalSpectroscopyOntology/", "keywords": [ "chemistry", "nfdi4chem" ], "license": "CC-BY-4.0", "mappings": { "tib": "vibso" }, "name": "Vibrational Spectroscopy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "vibso", "repository": "https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://purl.obolibrary.org/obo/VIBSO_$1" }, "vido": { "contact": { "email": "johnbeverley2021@u.northwestern.edu", "github": "johnbeve", "name": "John Beverly", "orcid": "0000-0002-1118-1738" }, "description": "The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc.", "download_owl": "https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-virus/master/ontology/vido.owl", "example": "0001114", "homepage": "https://github.com/infectious-disease-ontology-extensions/ido-virus", "keywords": [ "ontology" ], "mappings": { "aberowl": "VIDO", "bioportal": "VIDO", "ols": "vido", "ontobee": "VIDO" }, "name": "The Virus Infectious Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "vido", "providers": [ { "code": "obo.1", "description": "This incorrect encoding was found inside IDO-COVID-19", "homepage": "http://purl.obolibrary.org", "name": "Nonstandard OBO PURL", "uri_format": "http://purl.obolibrary.org/VIDO_$1" } ], "repository": "https://github.com/infectious-disease-ontology-extensions/ido-virus", "uri_format": "http://purl.obolibrary.org/obo/VIDO_$1", "version": "2020-08-25" }, "violinnet": { "appears_in": [ "oae" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "Defunct vaccine information source from the He Lab", "example": "4140", "mappings": { "wikidata": "P1925" }, "name": "ViolinNet", "pattern": "^\\d+$", "preferred_prefix": "violinnet", "synonyms": [ "violinID", "violinId" ], "uri_format": "http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=$1" }, "viperdb": { "description": "VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration.", "example": "2c6s", "homepage": "http://viperdb.scripps.edu/", "keywords": [ "small molecule", "structure" ], "mappings": { "integbio": "nbdc00835", "prefixcommons": "viperdb", "re3data": "r3d100012362" }, "name": "VIPERdb", "preferred_prefix": "viperdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/viperdb:$1" } ], "provides": "pdb", "uri_format": "https://viperdb.org/Info_Page.php?VDB=$1" }, "vipr": { "contact": { "email": "rscheuermann@jcvi.org", "name": "Richard Scheuermann", "orcid": "0000-0003-1355-892X" }, "description": "The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information.", "example": "BeAn 70563", "homepage": "http://www.viprbrc.org/brc/home.do?decorator=vipr", "keywords": [ "biomedical science", "epidemiology", "genomics", "immunology", "life science", "proteomics", "virology" ], "mappings": { "biocontext": "VIPR", "fairsharing": "FAIRsharing.2qx8n8", "miriam": "vipr", "n2t": "vipr", "ncbi": "ViPR", "re3data": "r3d100011931" }, "name": "Virus Pathogen Resource", "pattern": "^[A-Za-z 0-9]+$", "preferred_prefix": "vipr", "publications": [ { "doi": "10.3390/v4113209", "pmc": "PMC3509690", "pubmed": "23202522", "title": "Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community", "year": 2012 }, { "doi": "10.1093/nar/gkr859", "pmc": "PMC3245011", "pubmed": "22006842", "title": "ViPR: an open bioinformatics database and analysis resource for virology research", "year": 2011 }, { "doi": "10.1016/b978-0-12-809633-8.20995-3", "pmc": "PMC7173540", "title": "Database and Analytical Resources for Viral Research Community", "year": 2021 }, { "doi": "10.1016/b978-0-12-801238-3.95728-3", "pmc": "PMC7157461", "title": "Virus Databases ☆", "year": 2017 } ], "repository": "https://github.com/VirusBRC", "uri_format": "http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena" }, "viralzone": { "contact": { "email": "Philippe.Lemercier@sib.swiss", "name": "Philippe Le Mercier", "orcid": "0000-0001-8528-090X" }, "description": "ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.", "example": "992", "homepage": "http://www.expasy.org/viralzone/", "keywords": [ "epidemiology", "life science", "molecular biology", "virology", "virus" ], "mappings": { "biocontext": "VIRALZONE", "fairsharing": "FAIRsharing.tppk10", "go": "VZ", "integbio": "nbdc02226", "miriam": "viralzone", "n2t": "viralzone", "prefixcommons": "vz", "re3data": "r3d100013314", "wikidata.entity": "Q15674507" }, "name": "ViralZone", "pattern": "^\\d+$", "preferred_prefix": "viralzone", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/vz:$1" }, { "code": "viralzone.alt1", "description": "Alternate view", "homepage": "http://viralzone.expasy.org", "name": "Viralzone Alt 1.", "uri_format": "http://viralzone.expasy.org/all_by_protein/$1" } ], "publications": [ { "doi": "10.1093/nar/gks1220", "pmc": "PMC3531065", "pubmed": "23193299", "title": "ViralZone: recent updates to the virus knowledge resource", "year": 2012 }, { "doi": "10.1093/nar/gkq901", "pmc": "PMC3013774", "pubmed": "20947564", "title": "ViralZone: a knowledge resource to understand virus diversity", "year": 2010 } ], "synonyms": [ "vz" ], "uri_format": "https://viralzone.expasy.org/$1" }, "virgen": { "description": "VirGen a comprehensive viral genome resource, which organizes the ‘sequence space’ of viral genomes in a structured fashion. It has been developed with an objective to serve as an annotated and curated database for complete viral genome sequences.", "example": "AY321118", "homepage": "http://bioinfo.ernet.in/virgen/virgen.html", "keywords": [ "genome" ], "mappings": { "prefixcommons": "virgen" }, "name": "VirGen", "preferred_prefix": "virgen", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/virgen:$1" } ] }, "virmirdb": { "description": "A database containing predicted viral miRNA candidate hairpins.", "example": "11002", "homepage": "http://alk.ibms.sinica.edu.tw", "keywords": [ "rna", "structure" ], "mappings": { "prefixcommons": "virmirdb" }, "name": "Vir-Mir db", "preferred_prefix": "virmirdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/virmirdb:$1" } ], "provides": "ncbitaxon", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id=$1" }, "viroligo": { "description": "The VirOligo database (1) is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place.", "example": "BM0456", "homepage": "http://viroligo.okstate.edu", "keywords": [ "small molecule" ], "mappings": { "prefixcommons": "viroligo" }, "name": "VirOligo", "preferred_prefix": "viroligo", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/viroligo:$1" } ], "uri_format": "http://viroligo.okstate.edu/main.php?vid=$1" }, "virsirna": { "description": "The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region.", "example": "virsi1909", "homepage": "http://crdd.osdd.net/servers/virsirnadb", "mappings": { "biocontext": "VIRSIRNA", "miriam": "virsirna", "n2t": "virsirna" }, "name": "VIRsiRNA", "pattern": "^virsi\\d+$", "preferred_prefix": "virsirna", "uri_format": "http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1" }, "virushostdb": { "contact": { "email": "ogata@kuicr.kyoto-u.ac.jp", "name": "Hiroyuki Ogata", "orcid": "0000-0001-6594-377X" }, "description": "Virus-Host DB organizes data about the relationships between viruses and their hosts, represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts. Virus-Host DB covers viruses with complete genomes stored in 1) NCBI/RefSeq and 2) GenBank whose accession numbers are listed in EBI Genomes. The host information is collected from RefSeq, GenBank (in free text format), UniProt, ViralZone, and manually curated with additional information obtained by literature surveys.", "example": "438782", "homepage": "https://www.genome.jp/virushostdb/", "keywords": [ "virus" ], "mappings": { "integbio": "nbdc02395", "prefixcommons": "virushostdb" }, "name": "Virus-HostDB", "preferred_prefix": "virushostdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/virushostdb:$1" } ], "provides": "ncbitaxon", "publications": [ { "doi": "10.3390/v8030066", "pmc": "PMC4810256", "pubmed": "26938550", "title": "Linking Virus Genomes with Host Taxonomy", "year": 2016 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.genome.jp/virushostdb/$1" }, "vita": { "description": "ViTa is a database which collects virus data from miRBase and ICTV, VirGne, VBRC.., etc, including known miRNAs on virus and supporting predicted host miRNA targets by miRanda and TargetScan. ViTa also rovide effective annotations, including human miRNA expression, virus infected tissues, annotation of virus and comparisons.", "example": "AB016785", "homepage": "http://vita.mbc.nctu.edu.tw/", "keywords": [ "gene expression", "rna", "structure" ], "mappings": { "prefixcommons": "vita" }, "name": "Virus' miRNA target", "preferred_prefix": "vita", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/vita:$1" } ], "uri_format": "http://vita.mbc.nctu.edu.tw/search.php?acc=$1" }, "vitro": { "appears_in": [ "fabio", "foaf" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Vitro is a full stack framework for building semantic web applications. It is not domain specific.", "download_owl": "https://raw.githubusercontent.com/vivo-archive/Linked-Data-Indexer/refs/heads/master/src/main/resources/vitro-0.7.owl", "example": "descriptionAnnot", "github_request_issue": 1317, "homepage": "https://github.com/vivo-project/Vitro", "keywords": [ "ontology" ], "name": "Vitro Application Ontology", "preferred_prefix": "vitro", "repository": "https://github.com/vivo-project/Vitro", "uri_format": "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#$1" }, "vivo": { "contact": { "email": "christian.hauschke@tib.eu", "github": "hauschke", "name": "Christian Hauschke", "orcid": "0000-0003-2499-7741" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology about scholarship", "download_owl": "https://raw.githubusercontent.com/vivo-ontologies/vivo-ontology/master/vivo.owl", "example": "Laboratory", "github_request_issue": 1317, "homepage": "https://vivoweb.org", "keywords": [ "academy", "natural science", "ontology", "resource metadata", "study design", "tib" ], "license": "unlicense", "mappings": { "aberowl": "VIVO", "biocontext": "VIVO", "bioportal": "VIVO", "fairsharing": "FAIRsharing.6xfgaq", "lov": "vivo", "tib": "vivo" }, "name": "VIVO Ontology", "preferred_prefix": "vivo", "repository": "https://github.com/vivo-ontologies/vivo-ontology", "uri_format": "http://vivoweb.org/ontology/core#$1" }, "vmc": { "deprecated": true, "mappings": { "biolink": "VMC" }, "name": "Variation Modelling Collaboration", "preferred_prefix": "vmc", "references": [ "https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.67hbe76b6a4z", "https://github.com/ga4gh/vr-spec" ] }, "vmhgene": { "description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.", "example": "8639.1", "homepage": "https://www.vmh.life/", "mappings": { "miriam": "vmhgene" }, "name": "VMH Gene", "pattern": "^[0-9]+\\.[0-9]+$", "preferred_prefix": "vmhgene", "uri_format": "https://www.vmh.life/#gene/$1" }, "vmhmetabolite": { "description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.", "example": "h2o", "homepage": "https://www.vmh.life/", "mappings": { "biocontext": "VMHMETABOLITE", "miriam": "vmhmetabolite", "n2t": "vmhmetabolite" }, "name": "VMH metabolite", "pattern": "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$", "preferred_prefix": "vmhmetabolite", "uri_format": "https://www.vmh.life/#metabolite/$1" }, "vmhreaction": { "description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.", "example": "HEX1", "homepage": "https://www.vmh.life/", "mappings": { "biocontext": "VMHREACTION", "miriam": "vmhreaction", "n2t": "vmhreaction" }, "name": "VMH reaction", "pattern": "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$", "preferred_prefix": "vmhreaction", "uri_format": "https://www.vmh.life/#reaction/$1" }, "vo": { "appears_in": [ "scdo" ], "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqunh He", "orcid": "0000-0001-9189-9661" }, "description": "The Vaccine Ontology (VO) is a community-based biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine types and annotations, integrate various vaccine data, and support computer-assisted reasoning. The VO supports basic vaccine R&D and clinical vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities.", "download_owl": "http://purl.obolibrary.org/obo/vo.owl", "example": "0000093", "homepage": "https://violinet.org/vaccineontology", "keywords": [ "biological_process", "biomedical science", "clinical studies", "immunology", "infection process", "infectious disease medicine", "obo", "ontology", "pathobiochemistry", "pathogen", "preclinical studies", "small molecule", "vaccination", "vaccine" ], "license": "CC-BY-4.0", "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBck1IIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--bcbea6b26f9bd1db48d5f256c3d75bedd6fc2332/Screenshot%20From%202026-01-26%2011-30-20.png?disposition=inline", "mappings": { "aberowl": "VO", "biocontext": "VO", "bioportal": "VO", "fairsharing": "FAIRsharing.zwtww5", "obofoundry": "vo", "ols": "vo", "ontobee": "VO", "prefixcommons": "vo", "wikidata": "P1928", "wikidata.entity": "Q55118646" }, "name": "Vaccine Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "VO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/vo:$1" } ], "publications": [ { "doi": "10.2174/1381612826666201125112131", "pubmed": "33238868", "title": "Ontology-based Precision Vaccinology for Deep Mechanism Understanding and Precision Vaccine Development", "year": 2021 }, { "doi": "10.1186/2041-1480-4-33", "pubmed": "24209834", "title": "Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology", "year": 2013 }, { "doi": "10.1186/2041-1480-3-17", "pmc": "PMC3639077", "pubmed": "23256535", "title": "Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses", "year": 2012 }, { "doi": "10.1038/npre.2009.3553", "pubmed": "21871085", "title": "VO: Vaccine Ontology", "year": 2010 }, { "doi": "10.1186/2041-1480-2-s2-s8", "pmc": "PMC3102897", "pubmed": "21624163", "title": "Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology", "year": 2011 }, { "doi": "10.1186/1745-7580-6-s1-s5", "pmc": "PMC2946783", "pubmed": "20875156", "title": "Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN", "year": 2010 }, { "doi": "10.1101/2025.08.12.669998", "title": "VO: The Vaccine Ontology", "year": 2025 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/VO_$1", "repository": "https://github.com/vaccineontology/VO", "uri_format": "http://purl.obolibrary.org/obo/VO_$1", "version": "2026-01-23" }, "voc4cat": { "comment": "The most current version of a concept can be accessed so * https://w3id.org/nfdi4cat/voc4cat_0000123 other/older versions from releases like so * https://w3id.org/nfdi4cat/voc4cat/v2023-08-17/voc4cat_0000123. This is pretty unique and isn't tracked by the Bioregistry currently.", "contact": { "email": "nikolaos.moustakas@catalysis.de", "github": "nmoust", "name": "Nikolaos Moustakas", "orcid": "0000-0002-6242-2167" }, "contributor": { "email": "David.Linke@catalysis.de", "github": "dalito", "name": "David Linke", "orcid": "0000-0002-5898-1820" }, "description": "Voc4Cat is a [SKOS](https://www.w3.org/TR/2009/REC-skos-reference-20090818/) vocabulary for the catalysis disciplines. The vocabulary was created in the [NFDI4Cat](http://www.nfdi4cat.org/) initiative. The first collection of terms was published in June 2023 with a focus on photo catalysis. Our goal is to continuously extend the vocabulary to other areas of catalysis and related disciplines like chemical engineering or materials science.", "example": "0000123", "github_request_issue": 957, "homepage": "https://nfdi4cat.github.io/voc4cat/", "keywords": [ "chemistry", "fairmat", "nfdi4cat", "nfdi4chem" ], "license": "CC0-1.0", "mappings": { "bartoc": "20501", "tib": "voc4cat" }, "name": "A vocabulary for the catalysis disciplines", "pattern": "^\\d{7,}$", "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": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary.", "example": "feature", "homepage": "http://vocab.deri.ie/void", "keywords": [ "metadata" ], "mappings": { "biocontext": "void", "lov": "void", "zazuko": "void" }, "name": "Vocabulary of Interlinked Datasets", "preferred_prefix": "void", "uri_format": "http://rdfs.org/ns/void#$1" }, "vs": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This vocabulary was created in the FOAF project, based on experience with FOAF, Dublin Core and other early RDF vocabularies. Deployment experience shows that changing namespace URIs is expensive and unrewarding, so this vocabulary provides terms to support in-place evolution of structured data vocabularies. By indicating status at the level of terms rather than vocabularies, dictionary-style, fine grained improvements become easier. Different organizations and parties can agree or disagree on the status of a vocabulary term; however the status published alongside the term may deserve special attention. Future work could include patterns for citing announcements and decisions, or using SKOS to decentralise the extension of the basic status levels. (from artifact)", "download_owl": "https://www.w3.org/2003/06/sw-vocab-status/ns", "example": "term_status", "github_request_issue": 1677, "homepage": "https://www.w3.org/2003/06/sw-vocab-status/ns", "keywords": [ "metadata", "ontology", "semantic web" ], "mappings": { "lov": "vs", "zazuko": "vs" }, "name": "SemWeb Vocab Status ontology", "preferred_prefix": "vs", "rdf_uri_format": "http://www.w3.org/2003/06/sw-vocab-status/ns#$1", "uri_format": "http://www.w3.org/2003/06/sw-vocab-status/ns#$1" }, "vsao": { "contact": { "email": "wasila.dahdul@usd.edu", "name": "Wasila Dahdul", "orcid": "0000-0003-3162-7490" }, "deprecated": true, "description": "Vertebrate skeletal anatomy ontology.", "download_obo": "http://aber-owl.net/media/ontologies/VSAO/20/vsao.obo", "download_owl": "http://purl.obolibrary.org/obo/vsao.owl", "example": "0000183", "homepage": "https://www.nescent.org/phenoscape/Main_Page", "keywords": [ "anatomy", "obo", "ontology", "vertebrate" ], "mappings": { "aberowl": "VSAO", "biocontext": "VSAO", "bioportal": "VSAO", "obofoundry": "vsao", "ols": "vsao", "prefixcommons": "vao", "wikidata.entity": "Q114677916" }, "name": "Vertebrate Skeletal Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "VSAO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/vao:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/VSAO_$1", "synonyms": [ "VSAO_RETIRED" ], "uri_format": "http://purl.obolibrary.org/obo/VSAO_$1", "version": "2012-11-06" }, "vsdb": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source.", "example": "1868", "homepage": "https://sitem.herts.ac.uk/aeru/vsdb", "name": "Veterinary Substances DataBase", "pattern": "^\\d+$", "preferred_prefix": "vsdb", "uri_format": "https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm" }, "vsmo": { "contact": { "email": "lars.eisen@colostate.edu", "name": "Lars Eisen", "orcid": "0000-0002-0094-3186" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems.", "download_json": "https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.json", "download_obo": "https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.obo", "download_owl": "https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.owl", "example": "0000000", "homepage": "https://code.google.com/archive/p/vector-surveillance-and-management-ontology/", "keywords": [ "ontology" ], "license": "New BSD License", "name": "Ontology for vector surveillance and management", "preferred_prefix": "vsmo", "publications": [ { "doi": "10.1603/me12169", "pmc": "PMC3695545", "pubmed": "23427646", "title": "Ontology for vector surveillance and management", "year": 2013 } ], "uri_format": "http://purl.obolibrary.org/obo/VSMO_$1" }, "vso": { "contact": { "email": "albertgoldfain@gmail.com", "name": "Albert Goldfain" }, "description": "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.", "download_owl": "http://aber-owl.net/media/ontologies/VSO/1/vso.owl", "example": "0000041", "homepage": "https://bioportal.bioontology.org/ontologies/VSO", "keywords": [ "biomedical science", "blood", "experimental measurement", "health", "health science", "ontology", "owl" ], "mappings": { "aberowl": "VSO", "bartoc": "18355", "bioportal": "VSO", "fairsharing": "FAIRsharing.jjb2p2", "prefixcommons": "vso", "zazuko": "vso" }, "name": "Vital Sign Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "vso", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/vso:$1" } ], "uri_format": "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1" }, "vssocore": { "description": "This ontology describes the car's attributes, branches and signals defined in the Vehicle Signal Specification.", "example": "VehicleProperty", "homepage": "https://www.w3.org/TR/2022/WD-vsso-core-20220303/", "keywords": [ "fid move", "nfdi4ing", "traffic engineering" ], "mappings": { "tib": "vssocore" }, "name": "Vehicle Signal Specification Core Ontology", "preferred_prefix": "vssocore", "uri_format": "https://github.com/w3c/vsso-core#$1" }, "vt": { "appears_in": [ "scdo" ], "contact": { "email": "caripark@iastate.edu", "github": "caripark", "name": "Carissa Park", "orcid": "0000-0002-2346-5201" }, "description": "The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.", "download_obo": "https://github.com/AnimalGenome/vertebrate-trait-ontology/raw/master/current_release/vt.obo", "download_owl": "http://purl.obolibrary.org/obo/vt.owl", "example": "0000685", "homepage": "https://github.com/AnimalGenome/vertebrate-trait-ontology", "keywords": [ "animal physiology", "biology", "developmental biology", "morphology", "obo", "ontology", "phenotype", "physiology", "trait", "vertebrate" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "VT", "agroportal": "VT", "biocontext": "VT", "bioportal": "VT", "fairsharing": "FAIRsharing.10gr18", "obofoundry": "vt", "ols": "vt", "ontobee": "VT", "prefixcommons": "vt", "wikidata.entity": "Q81661831" }, "name": "Vertebrate trait ontology", "pattern": "^\\d{7}$", "preferred_prefix": "VT", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/vt:$1" } ], "publications": [ { "doi": "10.1186/2041-1480-4-13", "pmc": "PMC3851175", "pubmed": "23937709", "title": "The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/VT_$1", "repository": "https://github.com/AnimalGenome/vertebrate-trait-ontology", "uri_format": "http://purl.obolibrary.org/obo/VT_$1", "version": "2026-01-21" }, "vto": { "contact": { "email": "balhoff@renci.org", "github": "balhoff", "name": "Jim Balhoff", "orcid": "0000-0002-8688-6599" }, "description": "Comprehensive hierarchy of extinct and extant vertebrate taxa.", "download_obo": "http://purl.obolibrary.org/obo/vto.obo", "download_owl": "http://purl.obolibrary.org/obo/vto.owl", "example": "9008500", "homepage": "https://github.com/phenoscape/vertebrate-taxonomy-ontology", "keywords": [ "bone element", "obo", "ontology", "taxonomy" ], "license": "CC0-1.0", "mappings": { "aberowl": "VTO", "biocontext": "VTO", "bioportal": "VTO", "fairsharing": "FAIRsharing.akmeb9", "obofoundry": "vto", "ols": "vto", "ontobee": "VTO", "wikidata.entity": "Q81661832" }, "name": "Vertebrate Taxonomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "VTO", "publications": [ { "doi": "10.1186/2041-1480-4-34", "pmc": "PMC4177199", "pubmed": "24267744", "title": "The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/VTO_$1", "repository": "https://github.com/phenoscape/vertebrate-taxonomy-ontology", "uri_format": "http://purl.obolibrary.org/obo/VTO_$1", "version": "2020-11-13" }, "vuid": { "comment": "The example corresponds to acetaminophen", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Veterans Health Administration is America’s largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year.", "example": "4007166", "homepage": "https://www.va.gov/health", "name": "Veterans Health Administration (VHA) unique identifier", "pattern": "^\\d+$", "preferred_prefix": "vuid", "references": [ "https://academic.oup.com/jamia/article/17/4/432/866953" ] }, "wb.rnai": { "description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes.", "example": "WBRNAi00086878", "homepage": "https://www.wormbase.org/", "mappings": { "biocontext": "WB.RNAI", "miriam": "wb.rnai", "n2t": "wb.rnai" }, "name": "WormBase RNAi", "pattern": "^WBRNAi\\d{8}$", "preferred_prefix": "wb.rnai", "uri_format": "https://www.wormbase.org/species/c_elegans/rnai/$1" }, "wbbt": { "contact": { "email": "raymond@caltech.edu", "github": "raymond91125", "name": "Raymond Lee", "orcid": "0000-0002-8151-7479" }, "description": "Ontology about the gross anatomy of the C. elegans", "download_obo": "http://purl.obolibrary.org/obo/wbbt.obo", "download_owl": "http://purl.obolibrary.org/obo/wbbt.owl", "example": "0001290", "homepage": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology", "keywords": [ "anatomy", "cell", "life science", "obo", "ontology", "worm" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "WBBT", "biocontext": "WBbt", "biolink": "WBbt", "bioportal": "WB-BT", "fairsharing": "FAIRsharing.phk7dd", "go": "WBbt", "obofoundry": "wbbt", "ols": "wbbt", "ontobee": "WBbt", "prefixcommons": "wbbt", "wikidata.entity": "Q81661834" }, "name": "C. elegans Gross Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "WBbt", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/wbbt:$1" } ], "publications": [ { "doi": "10.1002/cfg.248", "pmc": "PMC2447384", "pubmed": "18629098", "title": "Building a cell and anatomy ontology of Caenorhabditis elegans", "year": 2003 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/WBbt_$1", "repository": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology", "synonyms": [ "WBbt" ], "uri_format": "http://purl.obolibrary.org/obo/WBbt_$1", "version": "2025-08-19" }, "wbls": { "contact": { "email": "cgrove@caltech.edu", "github": "chris-grove", "name": "Chris Grove", "orcid": "0000-0001-9076-6015" }, "description": "Ontology about the development and life stages of the C. elegans", "download_obo": "http://purl.obolibrary.org/obo/wbls.obo", "download_owl": "http://purl.obolibrary.org/obo/wbls.owl", "example": "0000690", "homepage": "https://github.com/obophenotype/c-elegans-development-ontology", "keywords": [ "development", "developmental biology", "life cycle", "life cycle stage", "life science", "obo", "ontology", "worm" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "WBLS", "biocontext": "WBLS", "biolink": "WBls", "bioportal": "WB-LS", "fairsharing": "FAIRsharing.sm90nh", "go": "WBls", "obofoundry": "wbls", "ols": "wbls", "ontobee": "WBls", "prefixcommons": "wbls", "wikidata.entity": "Q81661837" }, "name": "C. elegans development ontology", "pattern": "^\\d{7}$", "preferred_prefix": "WBls", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/wbls:$1" } ], "publications": [ { "doi": "10.1093/nar/gkz920", "pmc": "PMC7145598", "pubmed": "31642470", "title": "WormBase: a modern Model Organism Information Resource", "year": 2020 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/WBls_$1", "repository": "https://github.com/obophenotype/c-elegans-development-ontology", "synonyms": [ "WBls" ], "uri_format": "http://purl.obolibrary.org/obo/WBls_$1", "version": "2025-08-12" }, "wbphenotype": { "contact": { "email": "cgrove@caltech.edu", "github": "chris-grove", "name": "Chris Grove", "orcid": "0000-0001-9076-6015" }, "description": "Ontology about C. elegans and other nematode phenotypes", "download_obo": "http://purl.obolibrary.org/obo/wbphenotype.obo", "download_owl": "http://purl.obolibrary.org/obo/wbphenotype.owl", "example": "0000983", "homepage": "https://github.com/obophenotype/c-elegans-phenotype-ontology", "keywords": [ "anatomy", "life science", "obo", "omics", "ontology", "phenomics", "phenotype", "worm" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "WBPHENOTYPE", "biocontext": "WBPhenotype", "bioportal": "WB-PHENOTYPE", "fairsharing": "FAIRsharing.agvc7y", "go": "WBPhenotype", "obofoundry": "wbphenotype", "ols": "wbphenotype", "ontobee": "WBPhenotype", "prefixcommons": "wbphenotype", "wikidata.entity": "Q81660503" }, "name": "C. elegans phenotype", "pattern": "^\\d{7}$", "preferred_prefix": "WBPhenotype", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/wbphenotype:$1" } ], "publications": [ { "doi": "10.1186/1471-2105-12-32", "pmc": "PMC3039574", "pubmed": "21261995", "title": "Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community", "year": 2011 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/WBPhenotype_$1", "repository": "https://github.com/obophenotype/c-elegans-phenotype-ontology", "synonyms": [ "WBPhenotype" ], "uri_format": "http://purl.obolibrary.org/obo/WBPhenotype_$1", "version": "2025-08-12" }, "wdr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Underlying schema for POWDER", "example": "tag", "homepage": "https://www.w3.org/TR/powder-formal/", "name": "Protocol for Web Description Resources (POWDER) Schema", "preferred_prefix": "wdr", "uri_format": "http://www.w3.org/2007/05/powder#$1" }, "wdrs": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Protocol for Web Description Resources (POWDER) allows metadata to be associated with groups of resources such as those found on a Web site. Its main 'unit of information' is the Description Resource (DR), one or more of which are contained in a POWDER document. Processing such a document yields RDF triples describing the resources that are within the scope of the DRs. POWDER documents are written in XML and have relatively loose semantics, however, a GRDDL transform, associated with the root namespace, renders the data in RDF/OWL with more formal semantics. [from homepage]", "example": "structure", "homepage": "https://www.w3.org/2007/05/powder-s", "keywords": [ "api" ], "mappings": { "lov": "wdrs", "zazuko": "wdrs" }, "name": "Protocol for Web Description Resources (POWDER): POWDER-S Vocabulary", "preferred_prefix": "wdrs", "uri_format": "http://www.w3.org/2007/05/powder-s#$1" }, "webelements": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Browser for the periodic table of the elements", "example": "chromium", "homepage": "https://www.webelements.com/", "keywords": [ "chemistry" ], "name": "Web Elements", "pattern": "^\\w+$", "preferred_prefix": "webelements", "uri_format": "https://www.webelements.com/$1" }, "wgs84": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum", "example": "latitude", "homepage": "https://www.w3.org/2003/01/geo/wgs84_pos", "keywords": [ "geography" ], "mappings": { "biolink": "wgs", "lov": "geo", "zazuko": "wgs" }, "name": "WGS84 Geo Positioning", "preferred_prefix": "wgs84", "uri_format": "http://www.w3.org/2003/01/geo/wgs84_pos#$1" }, "who.va": { "contributor": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "Identifiers assigned by the World Health Organization for coding causes of death from verbal autopsy (VA) reports. These codes are produced as outputs in standard VA analysis software.", "example": "VAs-09.01", "example_extras": [ "VAs-09" ], "github_request_issue": 1739, "homepage": "https://www.who.int/publications/m/item/verbal-autopsy-standards-the-2016-who-verbal-autopsy-instrument", "keywords": [ "cause of death", "verbal autopsy" ], "name": "World Health Organization Verbal Autopsy Code", "pattern": "^VAs-\\d{2}(?:\\.\\d{2})?$", "preferred_prefix": "who.va", "publications": [ { "doi": "10.1371/journal.pmed.1002486", "pmc": "PMC5761828", "pubmed": "29320495", "title": "The WHO 2016 verbal autopsy instrument: An international standard suitable for automated analysis by InterVA, InSilicoVA, and Tariff 2.0", "year": 2018 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "wicell": { "description": "Cell line collections (Providers)", "example": "ai10e-kctd13b", "homepage": "https://www.wicell.org", "mappings": { "cellosaurus": "WiCell" }, "name": "WiCell Research Institute Cell Collection", "preferred_prefix": "wicell", "uri_format": "https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true" }, "wikidata": { "contact": { "email": "vrandecic@gmail.com", "github": "vrandezo", "name": "Denny Vrandečić", "orcid": "0000-0002-9593-2294" }, "description": "Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic.", "example": "Q47475003", "example_extras": [ "L704278", "P675" ], "homepage": "https://www.wikidata.org/", "keywords": [ "chemistry", "genomics", "metabolomics", "proteomics", "subject agnostic" ], "license": "CC0-1.0", "mappings": { "bartoc": "1940", "biocontext": "WIKIDATA", "biolink": "WIKIDATA", "cellosaurus": "Wikidata", "cheminf": "000567", "fairsharing": "FAIRsharing.6s749p", "miriam": "wikidata", "n2t": "wikidata", "wikidata.entity": "Q2013" }, "name": "Wikidata", "pattern": "^(Q|P|E|L)\\d+$", "preferred_prefix": "wikidata", "providers": [ { "code": "scholia", "description": "Scholia can generally resolve many Wikidata entries in the biomedical and bibliometric domains", "homepage": "https://scholia.toolforge.org", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/$1" } ], "publications": [ { "doi": "10.1145/2187980.2188242", "title": "Wikidata", "year": 2012 } ], "rdf_uri_format": "http://www.wikidata.org/entity/$1", "synonyms": [ "WD_Entity", "wd", "wdeschema" ], "twitter": "wikidata", "uri_format": "http://www.wikidata.org/entity/$1" }, "wikidata.entity": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Entity in Wikidata", "example": "Q42", "homepage": "https://www.wikidata.org", "license": "CC0-1.0", "name": "Wikidata Entity", "part_of": "wikidata", "pattern": "^Q\\d+$", "preferred_prefix": "wikidata.entity", "providers": [ { "code": "scholia", "description": "Scholia can generally resolve many Wikidata entries in the biomedical and bibliometric domains", "homepage": "https://scholia.toolforge.org", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/$1" } ], "rdf_uri_format": "http://www.wikidata.org/entity/$1", "uri_format": "http://www.wikidata.org/entity/$1" }, "wikidata.property": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Wikidata is a free and open knowledge base that can be read and edited by both humans and machines.\nWikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others.", "example": "P4355", "homepage": "https://www.wikidata.org", "license": "CC0-1.0", "mappings": { "biocontext": "WD_Prop", "biolink": "WIKIDATA_PROPERTY" }, "name": "Wikidata Property", "part_of": "wikidata", "pattern": "^P\\d+$", "preferred_prefix": "wikidata.property", "providers": [ { "code": "scholia", "description": "Scholia can generally resolve many Wikidata entries in the biomedical and bibliometric domains", "homepage": "https://scholia.toolforge.org", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/$1" } ], "rdf_uri_format": "http://www.wikidata.org/entity/$1", "uri_format": "http://www.wikidata.org/entity/$1" }, "wikigenes": { "description": "WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/wikipathways:$1" }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.\n", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/wikipathways/$1" } ], "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", "pubmed": "33211851", "title": "WikiPathways: connecting communities", "year": 2021 }, { "doi": "10.1093/nar/gkx1064", "pmc": "PMC5753270", "pubmed": "29136241", "title": "WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research", "year": 2018 }, { "doi": "10.1093/nar/gkv1024", "pmc": "PMC4702772", "pubmed": "26481357", "title": "WikiPathways: capturing the full diversity of pathway knowledge", "year": 2015 }, { "doi": "10.1093/nar/gkr1074", "pmc": "PMC3245032", "pubmed": "22096230", "title": "WikiPathways: building research communities on biological pathways", "year": 2011 }, { "doi": "10.1371/journal.pbio.0060184", "pmc": "PMC2475545", "pubmed": "18651794", "title": "WikiPathways: pathway editing for the people", "year": 2008 } ], "rdf_uri_format": "http://identifiers.org/wikipathways/$1", "twitter": "WikiPathways", "uri_format": "http://www.wikipathways.org/instance/$1" }, "wikipathways.type": { "contact": { "email": "egon.willighagen@gmail.com", "github": "egonw", "name": "Egon Willighagen", "orcid": "0000-0001-7542-0286" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Types used in WikiPathways RDF", "download_owl": "https://github.com/wikipathways/WpVocabularies/raw/refs/heads/master/docs/wpTypes.owl", "example": "Arrow", "github_request_issue": 1754, "homepage": "https://vocabularies.wikipathways.org/wpTypes", "keywords": [ "ontology" ], "mastodon": "wikipathways@fosstodon.org", "name": "WikiPathways Types", "preferred_prefix": "wikipathways.type", "rdf_uri_format": "http://vocabularies.wikipathways.org/wpTypes#$1", "repository": "https://github.com/wikipathways/WpVocabularies", "synonyms": [ "wikipathways.types", "wptypes" ], "uri_format": "http://vocabularies.wikipathways.org/wpTypes#$1" }, "wikipathways.vocab": { "contact": { "email": "egon.willighagen@gmail.com", "github": "egonw", "name": "Egon Willighagen", "orcid": "0000-0001-7542-0286" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology supporting data modeling in WikiPathways", "download_owl": "https://github.com/wikipathways/WpVocabularies/raw/refs/heads/master/docs/wp.owl", "example": "DataNode", "homepage": "http://www.wikipathways.org", "keywords": [ "ontology" ], "mappings": { "aberowl": "WIKIPATHWAYS", "bioportal": "WIKIPATHWAYS" }, "mastodon": "wikipathways@fosstodon.org", "name": "WikiPathways Ontology", "preferred_prefix": "wikipathways.vocab", "references": [ "https://github.com/biopragmatics/bioregistry/issues/818" ], "repository": "https://github.com/wikipathways/WpVocabularies", "uri_format": "https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/?p=classes&conceptid=http%3A%2F%2Fvocabularies.wikipathways.org%2Fwp%23$1" }, "wikipedia.en": { "contributor_extras": [ { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" } ], "description": "Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay.", "example": "SM_UB-81", "example_extras": [ "Pharyngeal_pouch_(embryology)" ], "homepage": "http://en.wikipedia.org/wiki/Main_Page", "mappings": { "biocontext": "WIKIPEDIA.EN", "go": "Wikipedia", "miriam": "wikipedia.en", "n2t": "wikipedia.en", "prefixcommons": "wikipedia" }, "name": "Wikipedia", "pattern": "^\\S+$", "preferred_prefix": "wikipedia.en", "providers": [ { "code": "", "description": "Wikipedia structured content through DBpedia", "homepage": "http://wiki.dbpedia.org/", "name": "Wikipedia structured content through DBpedia", "uri_format": "http://dbpedia.org/page/$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/wikipedia:$1" }, { "code": "volupedia", "description": "A mix of wikipedia and 3d", "homepage": "http://en.volupedia.org", "name": "Volupedia", "uri_format": "http://en.volupedia.org/wiki/$1" } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/794" ], "synonyms": [ "Wikipedia", "wikipedia" ], "uri_format": "http://en.wikipedia.org/wiki/$1" }, "wiktionary": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A free dictionary", "example": "pharmacist", "github_request_issue": 1310, "homepage": "https://wiktionary.org", "license": "CC BY SA 4.0", "name": "Wiktionary", "preferred_prefix": "wiktionary", "uri_format": "https://en.wiktionary.org/wiki/$1" }, "wlmo": { "description": "The ontology developed for representing wildlife monitoring capture events, the setup within which they were observed and their results.", "example": "Annotation", "homepage": "https://wildlive.senckenberg.de/wlmo/current/", "keywords": [ "earth sciences", "ess" ], "mappings": { "tib": "wlmo" }, "name": "Wildlife Monitoring Ontology", "preferred_prefix": "wlmo", "uri_format": "https://wildlive.senckenberg.de/wlmo/$1" }, "woc.ontology": { "description": "An ontology that represents object-oriented programming languages", "example": "AccessModifier", "homepage": "http://codeontology.org/", "keywords": [ "engineering", "nfdi4ing" ], "mappings": { "tib": "co" }, "name": "Code Ontology", "preferred_prefix": "woc.ontology", "repository": "https://github.com/codeontology/parser", "uri_format": "http://rdf.webofcode.org/woc/$1" }, "worfdb": { "description": "WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/worfdb:$1" } ], "uri_format": "http://worfdb.dfci.harvard.edu/html/index.php?search_type=name&page=showresultrc&race_query=$1" }, "world2dpage": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "A public repository, standards compliant, for proteomics image data published in the literature. This repository currently contains data from 16 published articles, putting together 22 reference maps for 15 species, totalizing nearly 4'400 identified spots.", "example": "0020", "homepage": "http://world-2dpage.expasy.org/repository/", "keywords": [ "2d-page", "protein", "structure" ], "mappings": { "prefixcommons": "world2dpage", "uniprot": "DB-0121" }, "name": "The World-2DPAGE database", "preferred_prefix": "world2dpage", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/world2dpage:$1" } ], "publications": [ { "doi": "10.1016/j.jprot.2008.02.005", "pubmed": "18617148", "title": "The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server", "year": 2008 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://world-2dpage.expasy.org/repository/$1" }, "worldavatar.compchem": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Linked-data framework for connecting species in chemical kinetic reaction mechanisms with quantum calculations. A mechanism can be constructed from thermodynamic, reaction rate, and transport data that has been obtained either experimentally, computationally, or by a combination of both. In order to implement this approach, two existing ontologies, namely OntoKin, for representing chemical kinetic reaction mechanisms, and OntoCompChem, for representing quantum chemistry calculations, are extended. (from https://nfdi4cat.org/services/ontologie-sammlung/)", "download_owl": "http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl", "homepage": "https://como.ceb.cam.ac.uk/preprints/223/", "keywords": [ "chemical and environmental engineering", "chemistry", "nfdi4cat", "nfdi4chem", "ontology" ], "mappings": { "tib": "ontocompchem" }, "name": "Computational Chemistry Ontology", "no_own_terms": true, "preferred_prefix": "worldavatar.compchem", "uri_format": "http://theworldavatar.com/ontology/ontocompchem/ontocompchem.owl#$1" }, "worldavatar.kin": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Represents chemical kinetic reaction mechanisms.", "download_owl": "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl", "example": "ElementNumber", "homepage": "http://www.theworldavatar.com/ontokin/", "keywords": [ "chemical and environmental engineering", "chemistry", "nfdi4cat", "nfdi4chem", "ontology" ], "mappings": { "tib": "ontokin" }, "name": "Ontology for Chemical Kinetic Reaction Mechanisms", "preferred_prefix": "worldavatar.kin", "uri_format": "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#$1" }, "worldavatar.os": { "description": "OntoSpecies is an ontology developed for representing chemical species.", "example": "Charge", "homepage": "https://doi.org/10.17863/CAM.97235.2", "keywords": [ "chemistry", "nfdi4chem" ], "mappings": { "tib": "os" }, "name": "OntoSpecies - Chemical Species Ontology for Data Integration and Knowledge Discovery", "preferred_prefix": "worldavatar.os", "uri_format": "http://www.theworldavatar.com/ontology/ontospecies/OntoSpecies.owl#$1" }, "wormbase": { "contact": { "email": "todd@wormbase.org", "github": "tharris", "name": "Todd W Harris", "orcid": "0000-0003-3406-163X" }, "contributor_extras": [ { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" } ], "description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities.", "example": "WBGene00000001", "homepage": "https://www.wormbase.org/", "keywords": [ "anatomy", "blast", "c elegans", "catalog", "database", "faseb list", "gene", "gene expression", "gene function", "gene mapping", "gene prediction", "geneotype", "genome", "genomic sequence", "genomics", "life science", "ortholog", "orthology assignment", "phenotype", "roundworm", "transposon family", "wormmart" ], "license": "CC0-1.0", "logo": "https://wormbase.org/img/logo/logo_wormbase_gradient.svg", "mappings": { "biocontext": "WormBase", "biolink": "WBVocab", "edam": "1805", "fairsharing": "FAIRsharing.zx1td8", "go": "WB_REF", "integbio": "nbdc00740", "miriam": "wb", "n2t": "wb", "ncbi": "WormBase", "pathguide": "426", "prefixcommons": "wormbase", "re3data": "r3d100010424", "rrid": "WB-STRAIN:WBStrain", "uniprot": "DB-0110", "wikidata": "P3860" }, "name": "WormBase", "pattern": "^(CE[0-9]{5}|WB[A-Z][a-z]+\\d+)$", "preferred_prefix": "WormBase", "providers": [ { "code": "agr", "description": "WormBase through the Alliance of Genome Resources", "homepage": "https://www.alliancegenome.org", "name": "WormBase through the Alliance of Genome Resources", "uri_format": "https://www.alliancegenome.org/gene/WB:$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/wormbase:$1" }, { "code": "wormbase.c_elegans", "description": "Pages describing C. Elegans genes.", "homepage": "http://www.wormbase.org", "name": "WormBase C. Elegans Gene Portal", "uri_format": "http://www.wormbase.org/species/c_elegans/gene/$1" } ], "publications": [ { "doi": "10.1093/nar/gkz920", "pmc": "PMC7145598", "pubmed": "31642470", "title": "WormBase: a modern Model Organism Information Resource", "year": 2020 }, { "doi": "10.1093/nar/gkx998", "pmc": "PMC5753391", "pubmed": "29069413", "title": "WormBase 2017: molting into a new stage", "year": 2018 }, { "pubmed": "24194605" }, { "doi": "10.1186/1471-2105-12-175", "pmc": "PMC3213741", "pubmed": "21595960", "title": "Toward an interactive article: integrating journals and biological databases", "year": 2011 }, { "doi": "10.1093/nar/gkq1116", "pmc": "PMC3013707", "pubmed": "21071413", "title": "The BioGRID Interaction Database: 2011 update", "year": 2010 }, { "doi": "10.1186/1471-2105-11-550", "pmc": "PMC2992068", "pubmed": "21059240", "title": "Localizing triplet periodicity in DNA and cDNA sequences", "year": 2010 }, { "doi": "10.1002/mrd.21130", "pmc": "PMC2830379", "pubmed": "19921742", "title": "Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology", "year": 2010 }, { "doi": "10.1093/nar/gkp1018", "pmc": "PMC2808930", "pubmed": "19920128", "title": "The Gene Ontology in 2010: extensions and refinements", "year": 2009 }, { "doi": "10.1093/nar/gkp952", "pmc": "PMC2808986", "pubmed": "19910365", "title": "WormBase: a comprehensive resource for nematode research", "year": 2009 }, { "doi": "10.1186/1471-2105-10-228", "pmc": "PMC2719631", "pubmed": "19622167", "title": "Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation", "year": 2009 }, { "doi": "10.1371/journal.pcbi.1000431", "pmc": "PMC2699109", "pubmed": "19578431", "title": "The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species", "year": 2009 }, { "doi": "10.1186/1471-2105-9-549", "pmc": "PMC2651883", "pubmed": "19099578", "title": "nGASP--the nematode genome annotation assessment project", "year": 2008 }, { "pubmed": "17991679" }, { "pubmed": "15608221" }, { "doi": "10.1093/nar/29.1.82", "pmc": "PMC29781", "pubmed": "11125056", "title": "WormBase: network access to the genome and biology of Caenorhabditis elegans", "year": 2001 } ], "synonyms": [ "WB", "WB_REF", "wb", "wormbase" ], "twitter": "wormbase", "uri_format": "https://www.wormbase.org/get?name=$1" }, "wormpep": { "description": "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project.", "example": "CE28239", "homepage": "https://www.wormbase.org/db/seq/protein", "keywords": [ "protein", "structure" ], "mappings": { "biocontext": "WORMPEP", "miriam": "wormpep", "n2t": "wormpep", "prefixcommons": "wormpep" }, "name": "Wormpep", "pattern": "^CE\\d{5}$", "preferred_prefix": "wormpep", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/wormpep:$1" } ], "uri_format": "https://www.wormbase.org/db/seq/protein?name=$1" }, "worms": { "contact": { "email": "leen.vandepitte@vliz.be", "name": "Leen Vandepitte", "orcid": "0000-0002-8160-7941" }, "contributor_extras": [ { "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" } ], "description": "The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts.", "example": "146421", "homepage": "http://www.marinespecies.org/", "keywords": [ "biodiversity", "environmental science", "taxonomy" ], "mappings": { "bartoc": "720", "biocontext": "WORMS", "fairsharing": "FAIRsharing.7g1bzj", "miriam": "worms", "n2t": "worms", "wikidata": "P850", "wikidata.entity": "Q604063" }, "name": "WoRMS-ID for taxa", "pattern": "^\\d+$", "preferred_prefix": "worms", "publications": [ { "doi": "10.1371/journal.pone.0194599", "pmc": "PMC5889062", "pubmed": "29624577", "title": "A decade of the World Register of Marine Species - General insights and experiences from the Data Management Team: Where are we, what have we learned and how can we continue?", "year": 2018 } ], "twitter": "WRMarineSpecies", "uri_format": "http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1" }, "wos.researcher": { "description": "identifier for a researcher in a system for scientific authors, redirects to a Web of Science ID, along with P3829", "example": "B-5720-2018", "homepage": "https://access.clarivate.com/login?app=wos", "mappings": { "wikidata": "P1053" }, "name": "ResearcherID", "pattern": "^[A-Z]{1,3}-\\d{4}-(19|20)\\d\\d$", "preferred_prefix": "wos.researcher", "uri_format": "https://www.webofscience.com/wos/author/record/$1" }, "wos.work": { "description": "unique academic work identifier assigned in Web of Science bibliographic database (Web of Science Core Collection only and do not include WOS: prefix)", "example": "000177759000002", "homepage": "https://www.webofscience.com", "mappings": { "wikidata": "P8372" }, "name": "Web of Science work ID", "preferred_prefix": "wos.work", "references": [ "https://github.com/biopragmatics/bioregistry/issues/805" ], "synonyms": [ "wos", "wosid", "wosuid" ], "uri_format": "https://www.webofscience.com/wos/woscc/full-record/WOS:$1" }, "wot": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "he WOT, or Web Of Trust, schema is designed to facilitate the use of Public Key Cryptography tools such as PGP or GPG to sign RDF documents and document these signatures.", "example": "EncryptedDocument", "homepage": "http://xmlns.com/wot/0.1/", "keywords": [ "quality", "security" ], "mappings": { "lov": "wot" }, "name": "XML Web of Trust Ontology", "preferred_prefix": "wot", "rdf_uri_format": "http://xmlns.com/wot/0.1/$1", "uri_format": "http://xmlns.com/wot/0.1/$1" }, "wot.hypermedia": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "an ontology for links and forms, the main hypermedia controls in use on the Web. This ontology offers, among others, a means to reify RDF statements interpreted as links between Web resources. It also provides a versatile exchange format for links and forms in RESTful Web applications. [from homepage]", "example": "AdditionalExpectedResponse", "homepage": "https://www.w3.org/2019/wot/hypermedia#", "name": "Web of Things Hypermedia Controls Ontology", "preferred_prefix": "wot.hypermedia", "rdf_uri_format": "https://www.w3.org/2019/wot/hypermedia#$1", "uri_format": "https://www.w3.org/2019/wot/hypermedia#$1" }, "wot.security": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "an RDF vocabulary for the security metadata definitions", "example": "APIKeySecurityScheme", "homepage": "https://www.w3.org/2019/wot/security", "name": "Web of Things Security Ontology", "preferred_prefix": "wot.security", "rdf_uri_format": "https://www.w3.org/2019/wot/security#$1", "uri_format": "https://www.w3.org/2019/wot/security#$1" }, "wot.td": { "description": "This ontology aims to model the Web of Things domain according to the W3C Interest Group (http://w3c.github.io/wot/)", "example": "description", "homepage": "https://akswnc7.informatik.uni-leipzig.de/dstreitmatter/archivo/w3.org/2019--wot--td/2021.09.22-190316/2019--wot--td_type=pyLodeDoc.html", "keywords": [ "engineering", "nfdi4ing" ], "mappings": { "tib": "td" }, "name": "Thing Description Ontology", "preferred_prefix": "wot.td", "uri_format": "https://www.w3.org/2019/wot/td#$1" }, "wot.tm": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Thing Model (TM) ontology is an RDF axiomatization of the TM concepts, one of the building blocks of the Web of Things (WoT). Besides providing an alternative to the standard JSON representation format for TM documents, the TM ontology can also be used to process contextual information on Things and for alignments with other WoT-related ontologies. [from homepage]", "example": "model", "homepage": "https://www.w3.org/2022/wot/tm", "name": "Web of Things Thing Model", "preferred_prefix": "wot.tm", "rdf_uri_format": "https://www.w3.org/2022/wot/tm#$1", "uri_format": "https://www.w3.org/2022/wot/tm#$1" }, "wwf.ecoregion": { "comment": "ENVO includes xrefs to this resource. See EnvironmentOntology/envo#658", "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions.", "example": "AT1402", "github_request_issue": 153, "homepage": "https://www.worldwildlife.org/biomes", "mappings": { "wikidata": "P1294", "wikidata.entity": "Q6617741" }, "name": "World Wildlife Fund Ecoregion", "pattern": "^AT\\d+$", "preferred_prefix": "wwf.ecoregion", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "WWF" ], "uri_format": "https://www.worldwildlife.org/ecoregions/$1" }, "xao": { "appears_in": [ "xpo" ], "contact": { "email": "Erik.Segerdell@cchmc.org", "github": "seger", "name": "Erik Segerdell", "orcid": "0000-0002-9611-1279" }, "description": "XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis.", "download_obo": "http://purl.obolibrary.org/obo/xao.obo", "download_owl": "http://purl.obolibrary.org/obo/xao.owl", "example": "0004486", "homepage": "http://www.xenbase.org/anatomy/xao.do?method=display", "keywords": [ "anatomy", "developmental biology", "life cycle", "life cycle stage", "life science", "morphology", "obo", "ontology", "structure" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "XAO", "bartoc": "581", "biocontext": "XAO", "bioportal": "XAO", "fairsharing": "FAIRsharing.17zapb", "obofoundry": "xao", "ols": "xao", "ontobee": "XAO", "wikidata": "P4495", "wikidata.entity": "Q42400040" }, "name": "Xenopus Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "XAO", "publications": [ { "doi": "10.1186/2041-1480-4-31", "pmc": "PMC3816597", "pubmed": "24139024", "title": "Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase", "year": 2013 }, { "doi": "10.1186/1471-213x-8-92", "pmc": "PMC2561031", "pubmed": "18817563", "title": "An ontology for Xenopus anatomy and development", "year": 2008 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/XAO_$1", "repository": "https://github.com/xenopus-anatomy/xao", "uri_format": "http://purl.obolibrary.org/obo/XAO_$1", "version": "2024-09-03" }, "xco": { "appears_in": [ "agro", "ecto" ], "contact": { "email": "jrsmith@mcw.edu", "github": "jrsjrs", "name": "Jennifer Smith", "orcid": "0000-0002-6443-9376" }, "description": "Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.", "download_obo": "http://purl.obolibrary.org/obo/xco.obo", "download_owl": "http://purl.obolibrary.org/obo/xco.owl", "example": "0000780", "homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000", "keywords": [ "assay", "biomedical science", "experimental condition", "experimental measurement", "experimentally determined", "life science", "measurement", "obo", "ontology", "study design" ], "license": "CC0-1.0", "logo": "http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif", "mappings": { "aberowl": "XCO", "biocontext": "XCO", "bioportal": "XCO", "fairsharing": "FAIRsharing.x39h5y", "obofoundry": "xco", "ols": "xco", "ontobee": "XCO", "prefixcommons": "xco", "wikidata.entity": "Q81661839" }, "name": "Experimental condition ontology", "pattern": "^\\d{7}$", "preferred_prefix": "XCO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/xco:$1" } ], "publications": [ { "doi": "10.1186/2041-1480-4-26", "pmc": "PMC3882879", "pubmed": "24103152", "title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications", "year": 2013 }, { "doi": "10.3389/fgene.2012.00087", "pmc": "PMC3361058", "pubmed": "22654893", "title": "Three ontologies to define phenotype measurement data", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/XCO_$1", "repository": "https://github.com/rat-genome-database/XCO-experimental-condition-ontology", "twitter": "ratgenome", "uri_format": "http://purl.obolibrary.org/obo/XCO_$1", "version": "4.225" }, "xenbase": { "contact": { "email": "troy_pells@yahoo.ca", "github": "pellst", "name": "Troy Pells", "orcid": "0000-0002-2340-5356" }, "description": "Xenbase is the model organism database for Xenopus laevis and X. 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It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions.", "example": "XB-GENE-922462", "homepage": "https://www.xenbase.org/", "keywords": [ "anatomy", "cell biology", "developmental biology", "expression", "functional genomics", "genetics", "genome", "genomics", "proteomics" ], "logo": "https://www.xenbase.org/xenbase/img/Xenbase-Logo-Small.png", "mappings": { "biocontext": "Xenbase", "biolink": "Xenbase", "edam": "2738", "fairsharing": "FAIRsharing.jrv6wj", "go": "Xenbase", "miriam": "xenbase", "n2t": "xenbase", "ncbi": "Xenbase", "prefixcommons": "xenbase", "re3data": "r3d100011331", "uniprot": "DB-0129" }, "name": "Xenbase", "pattern": "^XB\\-\\w+\\-\\d+$", "preferred_prefix": "xenbase", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/xenbase:$1" } ], "publications": [ { "doi": "10.1093/genetics/iyad018", "pubmed": "36755307" }, { "doi": "10.1186/s12859-022-04636-8", "pmc": "PMC8939077", "pubmed": "35317743", "title": "The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development", "year": 2022 }, { "doi": "10.1093/nar/gkz933", "pmc": "PMC7145613", "pubmed": "31733057", "title": "Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database", "year": 2020 }, { "doi": "10.3389/fphys.2019.00154", "pmc": "PMC6399412", "pubmed": "30863320", "title": "Xenbase: Facilitating the Use of", "year": 2019 }, { "doi": "10.1007/978-1-4939-7737-6_10", "pmc": "PMC6853059", "pubmed": "29761462", "title": "Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database", "year": 2018 }, { "doi": "10.1093/nar/gkx936", "pmc": "PMC5753396", "pubmed": "29059324", "title": "Xenbase: a genomic, epigenomic and transcriptomic model organism database", "year": 2018 }, { "doi": "10.1016/j.ydbio.2016.03.030", "pmc": "PMC5045824", "pubmed": "27039265", "title": "Xenopus genomic data and browser resources", "year": 2016 }, { "doi": "10.1093/database/bau108", "pmc": "PMC4224262", "pubmed": "25380782", "title": "The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud", "year": 2014 }, { "doi": "10.1093/nar/gku956", "pmc": "PMC4384024", "pubmed": "25313157", "title": "Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes", "year": 2014 }, { "doi": "10.1186/2041-1480-4-31", "pmc": "PMC3816597", "pubmed": "24139024", "title": "Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase", "year": 2013 }, { "doi": "10.1093/nar/gkp953", "pmc": "PMC2808955", "pubmed": "19884130", "title": "Xenbase: gene expression and improved integration", "year": 2009 }, { "doi": "doi:10.3389/fphys.2019.00154", "title": "Xenbase: Facilitating the Use of Xenopus to Model Human Disease." }, { "doi": "doi:10.1007/978-1-4939-7737-6_10.", "title": "Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database." } ], "synonyms": [ "Xenbase" ], "twitter": "Xenbase", "uri_format": "https://www.xenbase.org/entry/$1" }, "xhv": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This is a vocabulary collection utilized by XHTML Family modules and document types using XHTML Modularization, including XHTML Role and XHTML + RDFa as defined in rdfa-syntax. The XHTML specifications are developed by the W3C XHTML 2 Working Group as part of the W3C HTML Activity. 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Its goal is to enable generic SGML to be served, received, and processed on the Web in the way that is now possible with HTML. 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