{ "3dmet": { "description": "3DMET is a database collecting three-dimensional structures of natural metabolites.", "example": "B00162", "homepage": "http://www.3dmet.dna.affrc.go.jp/", "mappings": { "biocontext": "3DMET", "edam": "2635", "fairsharing": "FAIRsharing.5ab0n7", "miriam": "3dmet", "n2t": "3dmet", "prefixcommons": "3dmet", "wikidata": "P2796" }, "name": "3D Metabolites", "pattern": "^B\\d{5}$", "preferred_prefix": "3dmet", "publications": [ { "doi": "10.2142/biophysico.15.0_87", "pmc": "PMC5992871", "pubmed": "29892514", "title": "Chemical curation to improve data accuracy: recent development of the 3DMET database.", "year": 2018 }, { "doi": "10.1021/ci300309k", "pmc": null, "pubmed": "23293959", "title": "Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures.", "year": 2013 } ], "uri_format": "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1" }, "4dn.biosource": { "description": "The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. 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This collection references C. elegans genes and expression.", "example": "aap-1", "homepage": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm", "mappings": { "biocontext": "ACEVIEW.WORM", "miriam": "aceview.worm", "n2t": "aceview.worm", "prefixcommons": "aceview.worm" }, "name": "Aceview Worm", "pattern": "^[a-z0-9-]+$", "preferred_prefix": "aceview.worm", "publications": [ { "doi": "10.1186/gb-2006-7-s1-s12", "pmc": "PMC1810549", "pubmed": "16925834", "title": "AceView: a comprehensive cDNA-supported gene and transcripts annotation.", "year": 2006 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1" }, "addexbio": { "description": "Cell line collections", "example": "C0020004/4992", "homepage": "https://www.addexbio.com/productshow?id=4", "mappings": { "cellosaurus": "AddexBio" }, "name": "AddexBio cell line products", "preferred_prefix": "addexbio", "uri_format": "https://www.addexbio.com/productdetail?pid=$1" }, "addgene": { "description": "Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world.", "example": "50943", "homepage": "http://addgene.org/", "mappings": { "fairsharing": "FAIRsharing.8hcczk", "miriam": "addgene", "n2t": "addgene", "prefixcommons": "addgene", "re3data": "r3d100010741" }, "name": "Addgene Plasmid Repository", "pattern": "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$", "preferred_prefix": "addgene", "publications": [ { "doi": "10.1093/nar/gku893", "pmc": "PMC4384007", "pubmed": "25392412", "title": "The Addgene repository: an international nonprofit plasmid and data resource.", "year": 2014 } ], "uri_format": "http://addgene.org/$1" }, "ado": { "contact": { "email": "alpha.tom.kodamullil@scai.fraunhofer.de", "github": "akodamullil", "name": "Alpha Tom Kodamullil", "orcid": "0000-0001-9896-3531" }, "depends_on": [ "bfo" ], "description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining.", "download_owl": "http://purl.obolibrary.org/obo/ado.owl", "example": "0000001", "homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO", "license": "CC BY 4.0", "mappings": { "aberowl": "ADO", "bioportal": "ADO", "fairsharing": "FAIRsharing.ckd4rf", "obofoundry": "ado", "ols": "ado" }, "name": "Alzheimer's Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ADO", "publications": [ { "doi": "10.1016/j.jalz.2013.02.009", "pmc": null, "pubmed": "23830913", "title": "ADO: a disease ontology representing the domain knowledge specific to Alzheimer's disease.", "year": 2013 } ], "repository": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO", "uri_format": "http://purl.obolibrary.org/obo/ADO_$1", "version": "2.0.0" }, "adw": { "contact": { "email": "adw_geeks@umich.edu", "github": null, "name": "Animal Diversity Web technical staff", "orcid": null }, "deprecated": true, "description": "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology.", "download_owl": "http://aber-owl.net/media/ontologies/ADW/2/adw.owl", "example": "Lycalopex_vetulus", "homepage": "http://www.animaldiversity.org", "mappings": { "aberowl": "ADW", "biocontext": "ADW", "bioportal": "ADW", "fairsharing": "FAIRsharing.t9fvdn", "miriam": "adw", "n2t": "adw", "obofoundry": "adw" }, "name": "Animal natural history and life history", "pattern": "^[A-Z_a-z]+$", "preferred_prefix": "ADW", "uri_format": "https://animaldiversity.org/accounts/$1" }, "aeo": { "appears_in": [ "ehdaa2" ], "contact": { "email": "J.Bard@ed.ac.uk", "github": null, "name": "Jonathan Bard", "orcid": null }, "deprecated": true, "description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology", "download_obo": "https://raw.githubusercontent.com/obophenotype/human-developmental-anatomy-ontology/master/src/ontology/aeo.obo", "download_owl": "http://purl.obolibrary.org/obo/aeo.owl", "example": "0001017", "homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology/", "license": "CC BY 4.0", "mappings": { "aberowl": "AEO", "biocontext": "AEO", "bioportal": "AEO", "fairsharing": "FAIRsharing.93ee19", "obofoundry": "aeo", "ols": "aeo", "ontobee": "AEO" }, "name": "Anatomical Entity Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "AEO", "publications": [ { "doi": "10.3389/fgene.2012.00018", "pmc": "PMC3278863", "pubmed": "22347883", "title": "The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs.", "year": 2012 } ], "repository": "https://github.com/obophenotype/human-developmental-anatomy-ontology", "synonyms": [ "AEO_RETIRED" ], "uri_format": "http://purl.obolibrary.org/obo/AEO_$1", "version": "2014-12-05" }, "aero": { "contact": { "email": "mcourtot@gmail.com", "github": null, "name": "Melanie Courtot", "orcid": "0000-0002-9551-6370" }, "deprecated": true, "description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events", "download_owl": "http://purl.obolibrary.org/obo/aero.owl", "example": "0000125", "homepage": "http://purl.obolibrary.org/obo/aero", "license": "CC BY 3.0", "mappings": { "aberowl": "AERO", "biocontext": "AERO", "bioportal": "AERO", "fairsharing": "FAIRsharing.rycy2x", "obofoundry": "aero" }, "name": "Adverse Event Reporting Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "AERO", "uri_format": "http://purl.obolibrary.org/obo/AERO_$1" }, "affy.probeset": { "description": "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration.", "example": "243002_at", "homepage": "http://www.affymetrix.com/", "mappings": { "biocontext": "AFFY.PROBESET", "miriam": "affy.probeset", "n2t": "affy.probeset" }, "name": "Affymetrix Probeset", "pattern": "^\\d{4,}((_[asx])?_at)$", "preferred_prefix": "affy.probeset", "providers": [ { "code": "CURATOR_REVIEW", "description": "Bio2RDF", "homepage": "http://cu.affymetrix.bio2rdf.org/fct/", "name": "Bio2RDF", "uri_format": "http://cu.affymetrix.bio2rdf.org/describe/?url=http://bio2rdf.org/affymetrix:$1" } ], "uri_format": "https://www.affymetrix.com/LinkServlet?probeset=$1" }, "afo": { "contact": { "email": "more.info@allotrope.org", "github": null, "name": "Allotrope Foundation", "orcid": null }, "description": "Allotrope Merged Ontology Suite", "download_owl": "http://purl.allotrope.org/voc/afo/merged-OLS/REC/2019/05/10", "homepage": "https://www.allotrope.org/", "mappings": { "aberowl": "AFO", "bioportal": "AFO", "fairsharing": "FAIRsharing.595710", "ols": "afo" }, "name": "Allotrope Merged Ontology Suite", "no_own_terms": true, "preferred_prefix": "afo", "version": "2019-05-10" }, "aftol.taxonomy": { "contributor_extras": [ { "email": "laylamichan@ciencias.unam.mx", "github": "lmichan", "name": "Layla Michán Aguirre", "orcid": "0000-0002-5798-662X" } ], "description": "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species.", "example": "959", "homepage": "https://aftol.umn.edu", "mappings": { "biocontext": "AFTOL.TAXONOMY", "miriam": "aftol.taxonomy", "n2t": "aftol.taxonomy" }, "name": "Assembling the Fungal Tree of Life - Taxonomy", "pattern": "^\\d+$", "preferred_prefix": "aftol.taxonomy", "uri_format": "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1" }, "agilent.probe": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699.", "example": "A_24_P98555", "homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt", "name": "Agilent Probe", "pattern": "^A_\\d+_.+$", "preferred_prefix": "agilent.probe", "references": [ "http://www.cs.tau.ac.il/cgi-bin/cgiwrap/click/get.cgi/conversionFiles/conversion_human_14850_agilent2entrez.txt" ] }, "agricola": { "contributor_extras": [ { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" } ], "description": "AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century.", "example": "50018", "homepage": "http://agricola.nal.usda.gov/", "mappings": { "biocontext": "AGRICOLA", "go": "AGRICOLA_ID", "miriam": "agricola", "n2t": "agricola" }, "name": "Agricultural Online Access", "pattern": "^\\d+$", "preferred_prefix": "agricola", "synonyms": [ "AGR", "AGRICOLA_ID" ], "uri_format": "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1" }, "agrkb": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor": { "email": null, "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" }, "description": "The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations.\n\nThe Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location:\n\n- [ZFIN](https://zfin.org) - Zebrafish Information Network\n- [WormBase](https://wormbase.org)\n- [MGI](https://www.mgi.org) - Mouse Genome Informatics\n- [RGD](https://rgd.mcw.edu) - Rat Genome Database\n- [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database\n- [FlyBase](https://flybase.org)\n- [Xenbase](https://www.xenbase.org)", "example": "100000000000001", "github_request_issue": 359, "homepage": "https://www.alliancegenome.org", "mappings": { "biolink": "AGRKB" }, "name": "Alliance of Genome Resources Knowledge Base", "pattern": "^[1-9][0-9]{14}$", "preferred_prefix": "agrkb", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.alliancegenome.org/accession/$1" }, "agro": { "contact": { "email": "m.a.laporte@cgiar.org", "github": "marieALaporte", "name": "Marie-Angélique Laporte", "orcid": "0000-0002-8461-9745" }, "depends_on": [ "bfo", "envo", "foodon", "go", "iao", "ncbitaxon", "obi", "pato", "peco", "po", "ro", "to", "uo", "xco" ], "description": "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities", "download_obo": "https://raw.githubusercontent.com/KrishnaTO/agro/master/agro.obo", "download_owl": "http://purl.obolibrary.org/obo/agro.owl", "example": "00020007", "homepage": "https://github.com/AgriculturalSemantics/agro", "license": "CC BY 4.0", "mappings": { "aberowl": "AGRO", "agroportal": "AGRO", "biocontext": "AGRO", "bioportal": "AGRO", "fairsharing": "FAIRsharing.m40bhw", "obofoundry": "agro", "ols": "agro", "ontobee": "AGRO" }, "name": "Agronomy Ontology", "pattern": "^\\d{8}$", "preferred_prefix": "AGRO", "repository": "https://github.com/AgriculturalSemantics/agro", "uri_format": "http://purl.obolibrary.org/obo/AGRO_$1", "version": "2021-11-05" }, "agrovoc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages.", "example": "2842", "homepage": "https://data.apps.fao.org/catalog/organization/agrovoc", "mappings": { "agroportal": "AGROVOC", "ecoportal": "AGROVOC", "fairsharing": "FAIRsharing.anpj91" }, "name": "Agronomy Vocabulary", "pattern": "^[a-z0-9]+$", "preferred_prefix": "agrovoc", "publications": [ { "doi": "https://doi.org/10.4060/cb2838en", "pmc": null, "pubmed": null, "title": "AGROVOC – Semantic data interoperability on food and agriculture", "year": null }, { "doi": "https://doi.org/10.3390/engproc2021009017", "pmc": null, "pubmed": null, "title": "How Agricultural Digital Innovation Can Benefit from Semantics: The Case of the AGROVOC Multilingual Thesaurus", "year": null }, { "doi": "10.1016/j.compag.2020.105965", "pmc": null, "pubmed": null, "title": "AGROVOC: The linked data concept hub for food and agriculture", "year": null } ], "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" ], "uri_format": "http://aims.fao.org/aos/agrovoc/c_$1" }, "aism": { "appears_in": [ "colao", "lepao" ], "contact": { "email": "entiminae@gmail.com", "github": "JCGiron", "name": "Jennifer C. Girón", "orcid": "0000-0002-0851-6883" }, "depends_on": [ "bfo", "bspo", "caro", "pato", "ro", "uberon" ], "description": "The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research.", "download_json": "http://purl.obolibrary.org/obo/aism.json", "download_obo": "http://purl.obolibrary.org/obo/aism.obo", "download_owl": "http://purl.obolibrary.org/obo/aism.owl", "example": "0000027", "homepage": "https://github.com/insect-morphology/aism", "license": "CC BY 4.0", "mappings": { "aberowl": "AISM", "bioportal": "AISM", "obofoundry": "aism", "ols": "aism", "ontobee": "AISM" }, "name": "Ontology for the Anatomy of the Insect SkeletoMuscular system", "pattern": "^\\d{7}$", "preferred_prefix": "AISM", "repository": "https://github.com/insect-morphology/aism", "uri_format": "http://purl.obolibrary.org/obo/AISM_$1", "version": "2022-06-27" }, "allergome": { "description": "Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources.", "example": "1948", "homepage": "http://www.allergome.org/", "mappings": { "biocontext": "ALLERGOME", "fairsharing": "FAIRsharing.w6cxgb", "miriam": "allergome", "n2t": "allergome", "prefixcommons": "allergome", "uniprot": "Allergome" }, "name": "Allergome", "pattern": "^\\d+$", "preferred_prefix": "allergome", "publications": [ { "doi": "10.1016/j.cellimm.2007.02.012", "pmc": null, "pubmed": "17434469", "title": "Bioinformatics applied to allergy: allergen databases, from collecting sequence information to data integration. The Allergome platform as a model.", "year": 2007 }, { "doi": null, "pmc": null, "pubmed": "17393720", "title": "Allergome: a unifying platform.", "year": 2006 } ], "uri_format": "http://www.allergome.org/script/dettaglio.php?id_molecule=$1" }, "alzforum.mutation": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease.", "example": "app-d678n-tottori", "homepage": "https://www.alzforum.org/mutations", "name": "Alzforum Mutations", "preferred_prefix": "alzforum.mutation", "synonyms": [ "Alzforum_mut" ], "uri_format": "https://www.alzforum.org/mutations/$1" }, "amoebadb": { "description": "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "EDI_244000", "homepage": "http://amoebadb.org/amoeba/", "mappings": { "biocontext": "AMOEBADB", "fairsharing": "FAIRsharing.swbypy", "miriam": "amoebadb", "n2t": "amoebadb", "prefixcommons": "amoebadb", "re3data": "r3d100012457" }, "name": "AmoebaDB", "pattern": "^EDI_\\d+$", "preferred_prefix": "amoebadb", "publications": [ { "doi": "10.1093/nar/gkp941", "pmc": "PMC2808945", "pubmed": "19914931", "title": "EuPathDB: a portal to eukaryotic pathogen databases.", "year": 2009 } ], "uri_format": "https://amoebadb.org/amoeba/app/record/gene/$1" }, "amphx": { "contact": { "email": "hescriva@obs-banyuls.fr", "github": "hescriva", "name": "Hector Escriva", "orcid": "0000-0001-7577-5028" }, "depends_on": [ "uberon" ], "description": "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).", "download_obo": "http://purl.obolibrary.org/obo/amphx.obo", "download_owl": "http://purl.obolibrary.org/obo/amphx.owl", "example": "1000160", "homepage": "https://github.com/EBISPOT/amphx_ontology", "license": "CC BY 3.0", "mappings": { "aberowl": "AMPHX", "bioportal": "AMPHX", "obofoundry": "amphx", "ols": "amphx", "ontobee": "AMPHX" }, "name": "The Amphioxus Development and Anatomy Ontology", "pattern": "^\\d+$", "preferred_prefix": "AMPHX", "repository": "https://github.com/EBISPOT/amphx_ontology", "uri_format": "http://purl.obolibrary.org/obo/AMPHX_$1", "version": "2020-12-18" }, "antibodyregistry": { "description": "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.", "example": "493771", "homepage": "http://antibodyregistry.org/", "mappings": { "biocontext": "ANTIBODYREGISTRY", "miriam": "antibodyregistry", "n2t": "antibodyregistry" }, "name": "Antibody Registry", "pattern": "^\\d{6}$", "preferred_prefix": "antibodyregistry", "uri_format": "http://antibodyregistry.org/AB_$1" }, "antweb": { "description": "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures.", "example": "casent0106247", "homepage": "http://www.antweb.org/", "mappings": { "biocontext": "ANTWEB", "fairsharing": "FAIRsharing.yk38tw", "miriam": "antweb", "n2t": "antweb", "ncbi": "AntWeb", "prefixcommons": "antweb", "wikidata": "P5299" }, "name": "AntWeb", "pattern": "^casent\\d+(\\-D\\d+)?$", "preferred_prefix": "antweb", "publications": [ { "doi": "10.1038/424242b", "pmc": null, "pubmed": "12867945", "title": "Ants join online colony to boost conservation efforts.", "year": 2003 } ], "uri_format": "http://www.antweb.org/specimen.do?name=$1" }, "aop": { "description": "International repository of Adverse Outcome Pathways.", "example": "98", "homepage": "https://aopwiki.org/", "mappings": { "biocontext": "AOP", "miriam": "aop", "n2t": "aop" }, "name": "AOPWiki", "pattern": "^\\d+$", "preferred_prefix": "aop", "uri_format": "https://aopwiki.org/aops/$1" }, "aop.events": { "description": "International repository of Adverse Outcome Pathways.", "example": "3", "homepage": "https://aopwiki.org/", "mappings": { "biocontext": "AOP.EVENTS", "miriam": "aop.events", "n2t": "aop.events" }, "name": "AOPWiki (Key Event)", "pattern": "^\\d+$", "preferred_prefix": "aop.events", "uri_format": "https://aopwiki.org/events/$1" }, "aop.relationships": { "description": "International repository of Adverse Outcome Pathways.", "example": "5", "homepage": "https://aopwiki.org/", "mappings": { "biocontext": "AOP.RELATIONSHIPS", "miriam": "aop.relationships", "n2t": "aop.relationships" }, "name": "AOPWiki (Key Event Relationship)", "pattern": "^\\d+$", "preferred_prefix": "aop.relationships", "uri_format": "https://aopwiki.org/relationships/$1" }, "aop.stressor": { "description": "International repository of Adverse Outcome Pathways.", "example": "9", "homepage": "https://aopwiki.org/", "mappings": { "biocontext": "AOP.STRESSOR", "miriam": "aop.stressor", "n2t": "aop.stressor" }, "name": "AOPWiki (Stressor)", "pattern": "^\\d+$", "preferred_prefix": "aop.stressor", "uri_format": "https://aopwiki.org/stressors/$1" }, "apaonto": { "contact": { "email": "awalker@apa.org", "github": null, "name": "Alvin Walker", "orcid": "0000-0003-1082-8760" }, "description": "An ontology developed by the American Psychological Association (APA). Note that URIs in this ontology appear to have been generated with erroneous settings in Protege.", "download_owl": "http://aber-owl.net/media/ontologies/APAONTO/4/apaonto.owl", "example": "Abdomen", "homepage": "https://bioportal.bioontology.org/ontologies/APAONTO", "mappings": { "aberowl": "APAONTO", "bioportal": "APAONTO", "fairsharing": "FAIRsharing.gkw1w8" }, "name": "Psychology Ontology", "preferred_prefix": "apaonto", "references": [ "https://github.com/biopragmatics/bioregistry/issues/528" ], "uri_format": "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1" }, "apd": { "description": "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides.", "example": "01001", "homepage": "http://aps.unmc.edu/AP/", "mappings": { "biocontext": "APD", "fairsharing": "FAIRsharing.ctwd7b", "miriam": "apd", "n2t": "apd", "prefixcommons": "apd" }, "name": "Antimicrobial Peptide Database", "pattern": "^\\d{5}$", "preferred_prefix": "apd", "publications": [ { "doi": "10.1093/nar/gkv1278", "pmc": "PMC4702905", "pubmed": "26602694", "title": "APD3: the antimicrobial peptide database as a tool for research and education.", "year": 2015 } ], "uri_format": "http://aps.unmc.edu/AP/database/query_output.php?ID=$1" }, "aphidbase.transcript": { "description": "AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information.", "example": "ACYPI000159", "homepage": "http://www.aphidbase.com/aphidbase", "mappings": { "biocontext": "APHIDBASE.TRANSCRIPT", "miriam": "aphidbase.transcript", "n2t": "aphidbase.transcript" }, "name": "AphidBase Transcript", "pattern": "^ACYPI\\d{6}(-RA)?$", "preferred_prefix": "aphidbase.transcript", "uri_format": "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1" }, "apid.interactions": { "description": "APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.", "example": "P01116", "homepage": "http://cicblade.dep.usal.es:8080/APID/", "mappings": { "biocontext": "APID.INTERACTIONS", "miriam": "apid.interactions", "n2t": "apid.interactions" }, "name": "APID Interactomes", "pattern": "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$", "preferred_prefix": "apid.interactions", "provides": "uniprot", "uri_format": "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1" }, "apo": { "contact": { "email": "stacia@stanford.edu", "github": "srengel", "name": "Stacia R Engel", "orcid": "0000-0001-5472-917X" }, "description": "A structured controlled vocabulary for the phenotypes of Ascomycete fungi.", "download_obo": "http://purl.obolibrary.org/obo/apo.obo", "download_owl": "http://purl.obolibrary.org/obo/apo.owl", "example": "0000184", "homepage": "http://www.yeastgenome.org/", "license": "CC BY 4.0", "mappings": { "aberowl": "APO", "biocontext": "YPO", "bioportal": "APO", "fairsharing": "FAIRsharing.dyqz3y", "obofoundry": "apo", "ols": "apo", "ontobee": "APO" }, "name": "Ascomycete phenotype ontology", "pattern": "^\\d{7}$", "preferred_prefix": "APO", "publications": [ { "doi": "10.1093/database/bap001", "pmc": "PMC2790299", "pubmed": "20157474", "title": "New mutant phenotype data curation system in the Saccharomyces Genome Database.", "year": 2009 } ], "repository": "https://github.com/obophenotype/ascomycete-phenotype-ontology", "uri_format": "https://www.yeastgenome.org/observable/APO:$1", "version": "2022-07-06" }, "apollosv": { "appears_in": [ "scdo" ], "contact": { "email": "hoganwr@ufl.edu", "github": "hoganwr", "name": "William Hogan", "orcid": "0000-0002-9881-1017" }, "description": "Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models", "download_owl": "http://purl.obolibrary.org/obo/apollo_sv.owl", "example": "00000443", "homepage": "https://github.com/ApolloDev/apollo-sv", "license": "CC BY 4.0", "mappings": { "aberowl": "APOLLO_SV", "bioportal": "APOLLO-SV", "fairsharing": "FAIRsharing.ngv2xx", "obofoundry": "apollo_sv", "ols": "apollo_sv", "ontobee": "APOLLO_SV" }, "name": "Apollo Structured Vocabulary", "pattern": "^\\d{8}$", "preferred_prefix": "APOLLO_SV", "publications": [ { "doi": "10.1186/s13326-016-0092-y", "pmc": "PMC4989460", "pubmed": "27538448", "title": "The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.", "year": 2016 }, { "doi": null, "pmc": "PMC3900155", "pubmed": "24551417", "title": "Apollo: giving application developers a single point of access to public health models using structured vocabularies and Web services.", "year": 2013 } ], "repository": "https://github.com/ApolloDev/apollo-sv", "uri_format": "http://purl.obolibrary.org/obo/APOLLO_SV_$1", "version": "4.1.1" }, "arachnoserver": { "description": "ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information.", "example": "AS000060", "homepage": "http://www.arachnoserver.org/", "mappings": { "biocontext": "ARACHNOSERVER", "edam": "2578", "fairsharing": "FAIRsharing.c54ywe", "miriam": "arachnoserver", "n2t": "arachnoserver", "prefixcommons": "arachnoserver", "re3data": "r3d100012902", "uniprot": "ArachnoServer" }, "name": "ArachnoServer", "pattern": "^AS\\d{6}$", "preferred_prefix": "arachnoserver", "publications": [ { "doi": "10.1093/bioinformatics/btx661", "pmc": null, "pubmed": "29069336", "title": "ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins.", "year": 2018 }, { "doi": "10.1093/nar/gkq1058", "pmc": "PMC3013666", "pubmed": "21036864", "title": "ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures.", "year": 2010 } ], "uri_format": "http://www.arachnoserver.org/toxincard.html?id=$1" }, "araport": { "description": "Website with general information about Arabidopsis and functionalities such as a genomic viewer", "example": "AT1G01010", "homepage": "https://www.araport.org/", "mappings": { "ncbi": "Araport", "uniprot": "Araport" }, "name": "Arabidopsis Information Portal", "preferred_prefix": "araport", "uri_format": "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1" }, "ardb": { "description": "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes.", "example": "CAE46076", "homepage": "http://ardb.cbcb.umd.edu/", "mappings": { "biocontext": "ARDB", "miriam": "ardb", "n2t": "ardb" }, "name": "Antibiotic Resistance Genes Database", "pattern": "^[A-Z_]{3}[0-9]{4,}$", "preferred_prefix": "ardb", "uri_format": "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1" }, "ark": { "banana": "ark", "description": "An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type.", "example": "/12345/fk1234", "homepage": "http://n2t.net/", "mappings": { "biocontext": "ARK", "miriam": "ark", "n2t": "ark" }, "name": "Archival Resource Key", "namespace_in_lui": true, "pattern": "^/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$", "preferred_prefix": "ark", "uri_format": "http://n2t.net/ark:$1" }, "aro": { "appears_in": [ "scdo" ], "contact": { "email": "mcarthua@mcmaster.ca", "github": "agmcarthur", "name": "Andrew G. McArthur", "orcid": "0000-0002-1142-3063" }, "description": "Antibiotic resistance genes and mutations", "download_obo": "http://purl.obolibrary.org/obo/aro.obo", "download_owl": "http://purl.obolibrary.org/obo/aro.owl", "example": "1000001", "homepage": "https://github.com/arpcard/aro", "license": "CC BY 4.0", "mappings": { "aberowl": "ARO", "biocontext": "ARO", "bioportal": "ARO", "obofoundry": "aro", "ols": "aro", "ontobee": "ARO" }, "name": "Antibiotic Resistance Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ARO", "publications": [ { "doi": "10.1093/nar/gkz935", "pmc": "PMC7145624", "pubmed": "31665441", "title": "CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.", "year": 2020 } ], "repository": "https://github.com/arpcard/aro", "uri_format": "http://purl.obolibrary.org/obo/ARO_$1" }, "arrayexpress": { "description": "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.", "example": "E-MEXP-1712", "homepage": "https://www.ebi.ac.uk/arrayexpress/", "mappings": { "biocontext": "ARRAYEXPRESS", "cellosaurus": "ArrayExpress", "fairsharing": "FAIRsharing.6k0kwd", "miriam": "arrayexpress", "n2t": "arrayexpress", "prefixcommons": "arrayexpress", "re3data": "r3d100010222" }, "name": "ArrayExpress", "pattern": "^[AEP]-\\w{4}-\\d+$", "preferred_prefix": "arrayexpress", "providers": [ { "code": "omicsdi", "description": "ArrayExpress through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "ArrayExpress through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/arrayexpress-repository/$1" } ], "publications": [ { "doi": "10.1093/nar/gkg091", "pmc": "PMC165538", "pubmed": "12519949", "title": "ArrayExpress--a public repository for microarray gene expression data at the EBI.", "year": 2003 } ], "uri_format": "https://www.ebi.ac.uk/arrayexpress/experiments/$1" }, "arrayexpress.platform": { "description": "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results.", "example": "A-GEOD-50", "homepage": "https://www.ebi.ac.uk/arrayexpress/", "mappings": { "biocontext": "ARRAYEXPRESS.PLATFORM", "miriam": "arrayexpress.platform", "n2t": "arrayexpress.platform" }, "name": "ArrayExpress Platform", "pattern": "^[AEP]-\\w{4}-\\d+$", "preferred_prefix": "arrayexpress.platform", "uri_format": "https://www.ebi.ac.uk/arrayexpress/arrays/$1" }, "arraymap": { "description": "arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome.", "example": "icdom:8500_3", "homepage": "https://www.arraymap.org", "mappings": { "biocontext": "ARRAYMAP", "fairsharing": "FAIRsharing.1fbc5y", "miriam": "arraymap", "n2t": "arraymap", "re3data": "r3d100012630" }, "name": "ArrayMap", "pattern": "^[\\w\\-:,]{3,64}$", "preferred_prefix": "arraymap", "uri_format": "https://www.arraymap.org/pgx:$1" }, "arxiv": { "description": "arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology.", "example": "0807.4956v1", "homepage": "https://arxiv.org/", "mappings": { "biocontext": "ARXIV", "miriam": "arxiv", "n2t": "arxiv", "prefixcommons": "arxiv" }, "name": "arXiv", "pattern": "^(\\w+(\\-\\w+)?(\\.\\w+)?)?\\d{4,7}(\\.\\d+(v\\d+)?)?$", "preferred_prefix": "arxiv", "providers": [ { "code": "ar5iv", "description": "Articles from arXiv.org as responsive HTML5 web pages.", "homepage": "https://ar5iv.labs.arxiv.org/", "name": "ar5iv", "uri_format": "https://ar5iv.org/abs/$1" }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/arxiv/$1" } ], "uri_format": "https://arxiv.org/abs/$1" }, "asap": { "description": "ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources.", "example": "ABE-0009634", "homepage": "http://asap.ahabs.wisc.edu/asap/home.php", "mappings": { "biocontext": "ASAP", "fairsharing": "FAIRsharing.anpa6", "go": "ASAP", "miriam": "asap", "n2t": "asap", "ncbi": "ASAP", "prefixcommons": "asap", "re3data": "r3d100010666" }, "name": "A Systematic Annotation Package for Community Analysis of Genomes", "pattern": "^[A-Za-z0-9-]+$", "preferred_prefix": "asap", "publications": [ { "doi": "10.1093/nar/gkj164", "pmc": "PMC1347526", "pubmed": "16381899", "title": "ASAP: a resource for annotating, curating, comparing, and disseminating genomic data.", "year": 2006 }, { "doi": "10.1093/nar/gkg125", "pmc": "PMC165572", "pubmed": "12519969", "title": "ASAP, a systematic annotation package for community analysis of genomes.", "year": 2003 } ], "uri_format": "http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1" }, "ascl": { "description": "The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001).", "example": "1801.012", "homepage": "http://ascl.net/", "mappings": { "biocontext": "ASCL", "fairsharing": "FAIRsharing.wb0txg", "miriam": "ascl", "n2t": "ascl" }, "name": "Astrophysics Source Code Library", "pattern": "^[0-9\\.]+$", "preferred_prefix": "ascl", "uri_format": "http://ascl.net/$1" }, "asin": { "description": "Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue.", "example": "0471491039", "homepage": "https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182", "mappings": { "biocontext": "ASIN", "miriam": "asin", "n2t": "asin" }, "name": "Amazon Standard Identification Number", "pattern": "^[0-9]{10}$", "preferred_prefix": "asin", "uri_format": "https://amzn.com/$1" }, "aspgd.locus": { "description": "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information.", "example": "ASPL0000349247", "homepage": "http://www.aspgd.org/", "mappings": { "biocontext": "ASPGD.LOCUS", "go": "AspGD_LOCUS", "miriam": "aspgd.locus", "n2t": "aspgd.locus" }, "name": "Aspergillus Genome Database", "pattern": "^[A-Za-z_0-9]+$", "preferred_prefix": "aspgd.locus", "uri_format": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1" }, "aspgd.protein": { "description": "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information.", "example": "ASPL0000349247", "homepage": "http://www.aspgd.org/", "mappings": { "biocontext": "ASPGD.PROTEIN", "miriam": "aspgd.protein", "n2t": "aspgd.protein" }, "name": "AspGD Protein", "pattern": "^[A-Za-z_0-9]+$", "preferred_prefix": "aspgd.protein", "uri_format": "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1" }, "asrp": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes.", "example": "ASRP1423", "homepage": "https://asrp.danforthcenter.org/", "mappings": { "prefixcommons": "asrp" }, "name": "Arabidopsis Small RNA Project", "preferred_prefix": "asrp", "publications": [ { "doi": "10.1093/nar/gkm997", "pmc": "PMC2238918", "pubmed": "17999994", "title": "Update of ASRP: the Arabidopsis Small RNA Project database.", "year": 2007 }, { "doi": "10.1093/nar/gki127", "pmc": "PMC540081", "pubmed": "15608278", "title": "ASRP: the Arabidopsis Small RNA Project Database.", "year": 2005 } ], "uri_format": "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1" }, "atc": { "contact": { "email": "whocc@fhi.no", "github": null, "name": "WHO Collaborating Centre for Drug Statistics Methodology", "orcid": null }, "description": "The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels.", "example": "A10BA02", "homepage": "http://www.whocc.no/atc_ddd_index/", "mappings": { "aberowl": "ATC", "biocontext": "ATC", "bioportal": "ATC", "edam": "3103", "fairsharing": "FAIRsharing.1a27h8", "hl7": "whoATC", "miriam": "atc", "n2t": "atc", "prefixcommons": "atc", "wikidata": "P267" }, "name": "Anatomical Therapeutic Chemical Classification System", "pattern": "^[A-Z](\\d+([A-Z]{1,2}(\\d+)?)?)?$", "preferred_prefix": "atc", "publications": [ { "doi": null, "pmc": null, "pubmed": "7368387", "title": "[New classification of drugs. The Medical list and the Drug catalogue are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code) in 1981].", "year": 1980 }, { "doi": "10.1007/s002280000200", "pmc": null, "pubmed": "11214783", "title": "Different versions of the anatomical therapeutic chemical classification system and the defined daily dose--are drug utilisation data comparable?", "year": 2000 } ], "synonyms": [ "ATC_code", "ATTC" ], "uri_format": "http://www.whocc.no/atc_ddd_index/?code=$1" }, "atcc": { "description": "The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences.", "example": "11303", "homepage": "https://www.lgcstandards-atcc.org", "mappings": { "biocontext": "ATCC", "cellosaurus": "ATCC", "fairsharing": "FAIRsharing.j0ezpm", "hl7": "2.16.840.1.113883.6.77", "miriam": "atcc", "n2t": "atcc", "ncbi": "ATCC" }, "name": "American Type Culture Collection", "pattern": "^([A-Z]+-)?\\d+$", "preferred_prefix": "atcc", "synonyms": [ "ATCC", "ATCC number", "ATCC(dna)", "ATCC(in host)" ], "uri_format": "https://www.atcc.org/products/$1" }, "atcvet": { "description": "The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use.", "example": "QJ51RV02", "homepage": "http://www.whocc.no/atcvet/atcvet_index/", "mappings": { "biocontext": "ATCVET", "miriam": "atcvet", "n2t": "atcvet" }, "name": "Anatomical Therapeutic Chemical Vetinary", "pattern": "^Q[A-Z0-9]+$", "preferred_prefix": "atcvet", "uri_format": "http://www.whocc.no/atcvet/atcvet_index/?code=$1" }, "atfdb.family": { "description": "The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found.", "example": "CUT", "homepage": "http://www.bioguo.org/AnimalTFDB/family_index.php", "mappings": { "biocontext": "ATFDB.FAMILY", "miriam": "atfdb.family", "n2t": "atfdb.family" }, "name": "Animal TFDB Family", "pattern": "^\\w+$", "preferred_prefix": "atfdb.family", "uri_format": "http://www.bioguo.org/AnimalTFDB/family.php?fam=$1" }, "ato": { "contact": { "email": "david.c.blackburn@gmail.com", "github": null, "name": "David Blackburn", "orcid": null }, "deprecated": true, "description": "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource", "download_obo": "http://aber-owl.net/media/ontologies/ATO/2/ato.obo", "example": "0000000", "homepage": "http://www.amphibanat.org", "mappings": { "aberowl": "ATO", "biocontext": "ATO", "bioportal": "ATO", "fairsharing": "FAIRsharing.ayjdsm", "obofoundry": "ato" }, "name": "Amphibian taxonomy", "pattern": "^\\d{7}$", "preferred_prefix": "ATO", "uri_format": "http://purl.obolibrary.org/obo/ATO_$1" }, "atol": { "contact": { "email": "pylebail@rennes.inra.fr", "github": null, "name": "LeBail Pierre-Yves", "orcid": null }, "description": "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production.", "download_owl": "http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=atol.owl", "example": "0002233", "homepage": "http://www.atol-ontology.com", "mappings": { "aberowl": "ATOL", "agroportal": "ATOL", "bioportal": "ATOL", "fairsharing": "FAIRsharing.wsfk5z", "ols": "atol" }, "name": "Animal Trait Ontology for Livestock", "pattern": "^\\d{7}$", "preferred_prefix": "atol", "uri_format": "http://opendata.inra.fr/ATOL/ATOL_$1", "version": "2018-09-13" }, "autdb": { "description": "AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder.", "example": "ADA", "homepage": "http://autism.mindspec.org/autdb/", "mappings": { "biocontext": "AUTDB", "miriam": "autdb", "n2t": "autdb" }, "name": "AutDB", "pattern": "^[A-Z]+[A-Z-0-9]{2,}$", "preferred_prefix": "autdb", "uri_format": "http://autism.mindspec.org/GeneDetail/$1" }, "bacdive": { "description": "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity.", "example": "131392", "homepage": "https://bacdive.dsmz.de/", "mappings": { "fairsharing": "FAIRsharing.aSszvY", "miriam": "bacdive", "n2t": "bacdive", "re3data": "r3d100013060" }, "name": "Bacterial Diversity Metadatabase", "pattern": "^[0-9]+$", "preferred_prefix": "bacdive", "uri_format": "https://bacdive.dsmz.de/strain/$1" }, "bacmap.biog": { "description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information.", "example": "1050", "homepage": "http://bacmap.wishartlab.com/", "mappings": { "biocontext": "BACMAP.BIOG", "miriam": "bacmap.biog", "n2t": "bacmap.biog" }, "name": "BacMap Biography", "pattern": "^\\d+$", "preferred_prefix": "bacmap.biog", "uri_format": "http://bacmap.wishartlab.com/organisms/$1" }, "bacmap.map": { "description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information.", "example": "AP011135", "homepage": "http://bacmap.wishartlab.com/", "mappings": { "biocontext": "BACMAP.MAP", "miriam": "bacmap.map", "n2t": "bacmap.map" }, "name": "BacMap Map", "pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$", "preferred_prefix": "bacmap.map", "uri_format": "http://bacmap.wishartlab.com/maps/$1/index.html" }, "bactibase": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria.", "example": "BAC045", "homepage": "http://bactibase.hammamilab.org", "mappings": { "fairsharing": "FAIRsharing.5f5mfm", "prefixcommons": "bactibase", "re3data": "r3d100012755" }, "name": "Bactibase", "preferred_prefix": "bactibase", "uri_format": "http://bactibase.hammamilab.org/$1" }, "bams": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions.", "homepage": "https://bams1.org", "name": "Brain Architecture Knowledge Management System Neuroanatomical Ontology", "preferred_prefix": "bams", "references": [ "https://www.frontiersin.org/articles/10.3389/neuro.11.002.2008/full" ] }, "bao": { "contact": { "email": "sschurer@med.miami.edu", "github": null, "name": "Stephan Schurer", "orcid": null }, "description": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.", "download_owl": "http://www.bioassayontology.org/bao/bao_complete.owl", "example": "0002989", "homepage": "http://bioassayontology.org", "mappings": { "aberowl": "BAO", "biocontext": "BAO", "bioportal": "BAO", "fairsharing": "FAIRsharing.mye76w", "miriam": "bao", "n2t": "bao", "ols": "bao", "ontobee": "BAO" }, "name": "BioAssay Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "bao", "publications": [ { "doi": "10.1186/2041-1480-5-s1-s5", "pmc": "PMC4108877", "pubmed": "25093074", "title": "Evolving BioAssay Ontology (BAO): modularization, integration and applications.", "year": 2014 }, { "doi": "10.1371/journal.pone.0049198", "pmc": "PMC3498356", "pubmed": "23155465", "title": "Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO).", "year": 2012 }, { "doi": "10.1186/1471-2105-12-257", "pmc": "PMC3149580", "pubmed": "21702939", "title": "BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results.", "year": 2011 }, { "doi": "10:1371/journal.pone.0049198", "pmc": null, "pubmed": "10", "title": "Digitoxin metabolism by rat liver microsomes.", "year": 1975 } ], "synonyms": [ "BAO" ], "uri_format": "http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1", "version": "2.7.2" }, "bbkg": { "description": "Blue Brain Project's published data as knowledge graphs and Web Studios.", "example": "topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a", "homepage": "https://portal.bluebrain.epfl.ch", "mappings": { "miriam": "bbkg" }, "name": "Blue Brain Project Knowledge Graph", "pattern": "^[-\\w]+(?:\\/[-\\w]+)(?:\\/\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b)$", "preferred_prefix": "bbkg", "uri_format": "https://bbp.epfl.ch/nexus/web/studios/public/$1" }, "bbtp": { "description": "Input data and analysis results for the paper \"Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 ).", "example": "f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a", "homepage": "https://portal.bluebrain.epfl.ch", "mappings": { "miriam": "bbtp" }, "name": "Blue Brain Project Topological sampling Knowledge Graph", "pattern": "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$", "preferred_prefix": "bbtp", "uri_format": "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1" }, "bcgo": { "contact": { "email": "jiezheng@pennmedicine.upenn.edu", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "deprecated": true, "description": "An application ontology built for beta cell genomics studies.", "download_owl": "https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl", "example": "0000015", "homepage": "https://github.com/obi-bcgo/bcgo", "license": "CC BY 3.0", "mappings": { "aberowl": "BCGO", "biocontext": "BCGO", "bioportal": "BCGO", "cellosaurus": "BCGO", "obofoundry": "bcgo", "ontobee": "BCGO" }, "name": "Beta Cell Genomics Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "BCGO", "repository": "https://github.com/obi-bcgo/bcgo", "uri_format": "http://purl.obolibrary.org/obo/BCGO_$1" }, "bcio": { "contact": { "email": "srodriguez@pet.cs.nctu.edu.tw", "github": null, "name": "Sergio José Rodríguez Méndez", "orcid": null }, "description": "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation.", "download_owl": "http://humanbehaviourchange.org/ontology/bcio.owl", "example": "040000", "homepage": "https://www.humanbehaviourchange.org/", "mappings": { "aberowl": "BCI-O", "bioportal": "BCI-O", "ols": "bcio" }, "name": "The Behaviour Change Intervention Ontology", "pattern": "^\\d{6}$", "preferred_prefix": "bcio", "uri_format": "https://w3id.org/BCI-ontology#$1" }, "bco": { "appears_in": [ "fovt" ], "contact": { "email": "rlwalls2008@gmail.com", "github": "ramonawalls", "name": "Ramona Walls", "orcid": "0000-0001-8815-0078" }, "description": "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.", "download_owl": "http://purl.obolibrary.org/obo/bco.owl", "example": "0000081", "homepage": "https://github.com/BiodiversityOntologies/bco", "license": "CC0 1.0", "mappings": { "aberowl": "BCO", "agroportal": "BCO", "biocontext": "BCO", "bioportal": "BCO", "ecoportal": "BCO", "fairsharing": "FAIRsharing.8ktkqy", "obofoundry": "bco", "ols": "bco", "ontobee": "BCO" }, "name": "Biological Collections Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "BCO", "publications": [ { "doi": "10.1371/journal.pone.0089606", "pmc": "PMC3940615", "pubmed": "24595056", "title": "Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.", "year": 2014 } ], "repository": "https://github.com/BiodiversityOntologies/bco", "uri_format": "http://purl.obolibrary.org/obo/BCO_$1", "version": "2021-11-14" }, "bcrc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Cell line collections", "example": "60316", "homepage": "https://catalog.bcrc.firdi.org.tw", "mappings": { "cellosaurus": "BCRC" }, "name": "BCRC Strain Collection Catalog", "pattern": "^\\d+$", "preferred_prefix": "bcrc", "uri_format": "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1" }, "bcrj": { "description": "Cell line collections", "example": "0278", "homepage": "http://bcrj.org.br/celula/bcrj", "mappings": { "cellosaurus": "BCRJ" }, "name": "Banco de Celulas do Rio de Janeiro", "pattern": "^\\d{4}$", "preferred_prefix": "bcrj", "uri_format": "http://bcrj.org.br/celula/$1" }, "bdgp.est": { "description": "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI).", "example": "EY223054.1", "has_canonical": "dbest", "homepage": "https://www.ncbi.nlm.nih.gov/dbEST/index.html", "mappings": { "biocontext": "BDGP.EST", "miriam": "bdgp.est", "n2t": "bdgp.est", "ncbi": "BDGP_EST", "prefixcommons": "flybase.est" }, "name": "Berkeley Drosophila Genome Project EST database", "pattern": "^\\w+(\\.)?(\\d+)?$", "preferred_prefix": "bdgp.est", "uri_format": "https://www.ncbi.nlm.nih.gov/nucest/$1" }, "bdgp.insertion": { "description": "BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element.", "example": "KG09531", "homepage": "http://flypush.imgen.bcm.tmc.edu/pscreen/", "mappings": { "biocontext": "BDGP.INSERTION", "miriam": "bdgp.insertion", "n2t": "bdgp.insertion", "prefixcommons": "bdgp" }, "name": "BDGP insertion DB", "pattern": "^\\w+$", "preferred_prefix": "bdgp.insertion", "publications": [ { "doi": "10.1534/genetics.104.026427", "pmc": "PMC1470905", "pubmed": "15238527", "title": "The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes.", "year": 2004 } ], "uri_format": "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1" }, "bdsc": { "description": "The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research.", "example": "33607", "homepage": "https://bdsc.indiana.edu/about/mission.html", "mappings": { "miriam": "bdsc", "n2t": "bdsc" }, "name": "Bloomington Drosophila Stock Center", "pattern": "^\\d+$", "preferred_prefix": "bdsc", "uri_format": "https://bdsc.indiana.edu/stocks/$1" }, "beetlebase": { "description": "BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications.", "example": "TC010103", "homepage": "http://beetlebase.org/", "mappings": { "biocontext": "BEETLEBASE", "fairsharing": "FAIRsharing.h5f091", "miriam": "beetlebase", "n2t": "beetlebase", "ncbi": "BEETLEBASE", "prefixcommons": "beetlebase", "re3data": "r3d100010921" }, "name": "Tribolium Genome Database -- Insertion", "pattern": "^TC\\d+$", "preferred_prefix": "beetlebase", "publications": [ { "doi": "10.1093/nar/gkp807", "pmc": "PMC2808946", "pubmed": "19820115", "title": "BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum.", "year": 2009 } ], "uri_format": "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1" }, "begdb": { "description": "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. 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This collection refers to anatomical structures.", "example": "EHDAA:2185", "homepage": "http://bgee.unil.ch/bgee/bgee", "mappings": { "biocontext": "BGEE.ORGAN", "miriam": "bgee.organ", "n2t": "bgee.organ" }, "name": "Bgee organ", "pattern": "^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\\:\\d+$", "preferred_prefix": "bgee.organ", "uri_format": "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1" }, "bgee.stage": { "description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages.", "example": "HsapDO:0000004", "homepage": "http://bgee.unil.ch/bgee/bgee", "mappings": { "biocontext": "BGEE.STAGE", "miriam": "bgee.stage", "n2t": "bgee.stage" }, "name": "Bgee stage", "pattern": "^(FBvd|XtroDO|HsapDO|MmusDO)\\:\\d+$", "preferred_prefix": "bgee.stage", "uri_format": "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1" }, "bibo": { "contact": { "email": "fred@fgiasson.com", "github": "fgiasson", "name": "Frédérick Giasson", "orcid": null }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Bibliographic Ontology Specification provides main concepts and properties for describing citations and bibliographic references (i.e. quotes, books, articles, etc) on the Semantic Web.", "example": "authorList", "homepage": "https://bibliontology.com/", "name": "The Bibliographic Ontology", "preferred_prefix": "bibo", "uri_format": "http://purl.org/ontology/bibo/$1" }, "bido": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF.", "example": "CategorialBibliometricData", "homepage": "http://www.sparontologies.net/ontologies/bido", "mappings": { "fairsharing": "FAIRsharing.d7f0a9" }, "name": "Bibliometric Data Ontology", "preferred_prefix": "BiDO", "repository": "https://github.com/sparontologies/bido", "uri_format": "http://purl.org/spar/bido/$1" }, "bigg.compartment": { "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. 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Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes.", "example": "12dgr161", "homepage": "http://bigg.ucsd.edu/universal/metabolites", "mappings": { "biocontext": "BIGG.METABOLITE", "miriam": "bigg.metabolite", "n2t": "bigg.metabolite" }, "name": "BiGG Metabolite", "pattern": "^[a-z_A-Z0-9]+$", "preferred_prefix": "bigg.metabolite", "uri_format": "http://bigg.ucsd.edu/models/universal/metabolites/$1" }, "bigg.model": { "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models.", "example": "iECABU_c1320", "homepage": "http://bigg.ucsd.edu/models", "mappings": { "biocontext": "BIGG.MODEL", "miriam": "bigg.model", "n2t": "bigg.model" }, "name": "BiGG Model", "pattern": "^[a-z_A-Z0-9]+$", "preferred_prefix": "bigg.model", "uri_format": "http://bigg.ucsd.edu/models/$1" }, "bigg.reaction": { "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions.", "example": "13GS", "homepage": "http://bigg.ucsd.edu/universal/reactions", "mappings": { "biocontext": "BIGG.REACTION", "miriam": "bigg.reaction", "n2t": "bigg.reaction" }, "name": "BiGG Reaction", "pattern": "^[a-z_A-Z0-9]+$", "preferred_prefix": "bigg.reaction", "uri_format": "http://bigg.ucsd.edu/models/universal/reactions/$1" }, "bila": { "contact": { "email": "henrich@embl.de", "github": null, "name": "Thorsten Heinrich", "orcid": null }, "deprecated": true, "description": "This is a record of the Bilateria anatomy terminology and ontology. 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It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps.", "example": "h_aktPathway", "homepage": "https://www.biocarta.com/", "mappings": { "biocontext": "BIOCARTA.PATHWAY", "miriam": "biocarta.pathway", "n2t": "biocarta.pathway" }, "name": "BioCarta Pathway", "pattern": "^([hm]\\_)?\\w+Pathway$", "preferred_prefix": "biocarta.pathway", "uri_format": "https://cgap.nci.nih.gov/Pathways/BioCarta/$1" }, "biocatalogue.service": { "description": "The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all.", "example": "614", "homepage": "https://www.biocatalogue.org/", "mappings": { "biocontext": "BIOCATALOGUE.SERVICE", "miriam": "biocatalogue.service", "n2t": "biocatalogue.service" }, "name": "BioCatalogue Service", "pattern": "^\\d+$", "preferred_prefix": "biocatalogue.service", "uri_format": "https://www.biocatalogue.org/services/$1" }, "biocyc": { "description": "BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms.", "example": "ECOLI:CYT-D-UBIOX-CPLX", "homepage": "http://biocyc.org", "mappings": { "biocontext": "BIOCYC", "edam": "2104", "go": "BioCyc", "miriam": "biocyc", "n2t": "biocyc", "prefixcommons": "biocyc", "uniprot": "BioCyc" }, "name": "BioCyc collection of metabolic pathway databases", "pattern": "^[A-Z-0-9]+(\\:)?[A-Za-z0-9+_.%-:]+$", "preferred_prefix": "biocyc", "publications": [ { "doi": "10.1093/nar/gki892", "pmc": 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"contact": { "email": "md.tyers@umontreal.ca", "github": null, "name": "Mike Tyers", "orcid": "0000-0002-9713-9994" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe.", "example": "2649230", "homepage": "https://thebiogrid.org/", "mappings": { "edam": "2628" }, "name": "BioGRID Interactions", "part_of": "biogrid", "pattern": "^\\d+$", "preferred_prefix": "biogrid.interaction", "twitter": "biogrid", "uri_format": "https://thebiogrid.org/interaction/$1" }, "biolegend": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "BioLegend is a life sciences supply vendor.", "example": "3403", "homepage": "https://www.biolegend.com", "name": "BioLegend", "pattern": "^\\d+$", "preferred_prefix": "biolegend", "uri_format": "https://www.biolegend.com/Default.aspx?ID=6664&productid=$1" }, "biolink": { "contact": { "email": "cjmungall@lbl.gov", "github": null, "name": "Chris Mungall", "orcid": null }, "description": "A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations.", "download_owl": "http://aber-owl.net/media/ontologies/BIOLINK/42/biolink.owl", "example": "Gene", "homepage": "https://biolink.github.io/biolink-model/", "mappings": { "aberowl": "BIOLINK", "biolink": "biolink", "bioportal": "BIOLINK", "fairsharing": "FAIRsharing.ad9d85", "miriam": "biolink" }, "name": "Biolink Model", "pattern": "^\\S+$", "preferred_prefix": "biolink", "uri_format": "https://w3id.org/biolink/vocab/$1" }, "biominder": { "description": "Database of the dielectric properties of biological tissues.", "example": "aef4c195-9cf9-46db-a12a-7cfd1ff3eec3", "homepage": "https://datalab.rwth-aachen.de/MINDER", "mappings": { "biocontext": "BIOMINDER", "miriam": "biominder", "n2t": "biominder" }, "name": "Bio-MINDER Tissue Database", "pattern": "^[a-z0-9\\-]+$", "preferred_prefix": "biominder", "uri_format": "https://datalab.rwth-aachen.de/MINDER/resource/$1" }, "biomodels.db": { "description": "BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests.", "example": "BIOMD0000000048", "homepage": "https://www.ebi.ac.uk/biomodels/", "mappings": { "biocontext": "BIOMODELS.DB", "go": "BIOMD", "miriam": "biomodels.db", "n2t": "biomodels.db", "prefixcommons": "biomodels" }, "name": "BioModels Database", "pattern": "^((BIOMD|MODEL)\\d{10})|(BMID\\d{12})$", "preferred_prefix": "biomodels.db", "providers": [ { "code": "CURATOR_REVIEW", "description": "Caltech mirror", "homepage": "http://biomodels.caltech.edu/", "name": "Caltech mirror", "uri_format": "http://biomodels.caltech.edu/$1" }, { "code": "omicsdi", "description": "BioModels through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "BioModels through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/biomodels/$1" } ], "publications": [ { "doi": "10.1093/nar/gkj092", "pmc": "PMC1347454", "pubmed": "16381960", "title": "BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.", "year": 2006 } ], "synonyms": [ "BIOMD" ], "uri_format": "https://www.ebi.ac.uk/biomodels/$1" }, "biomodels.kisao": { "banana": "KISAO", "banana_peel": "_", "contact": { "email": "jonrkarr@gmail.com", "github": "jonrkarr", "name": "Jonathan Karr", "orcid": "0000-0002-2605-5080" }, "description": "The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment.", "download_owl": "http://purl.obolibrary.org/obo/kisao.owl", "example": "0000057", "homepage": "https://github.com/SED-ML/KiSAO", "license": "Artistic License 2.0", "mappings": { "aberowl": "KISAO", "biocontext": "KISAO", "bioportal": "KISAO", "fairsharing": "FAIRsharing.jcg19w", "miriam": "biomodels.kisao", "n2t": "biomodels.kisao", "obofoundry": "kisao", "ols": "kisao", "ontobee": "KISAO", "prefixcommons": "kisao" }, "name": "Kinetic Simulation Algorithm Ontology", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "biomodels.kisao", "providers": [ { "code": "legacy", "description": "This is the URI scheme used in the ontology but it does not resolve.", "homepage": "https://www.biomodels.net", "name": "Legacy Biomodels URL", "uri_format": "https://www.biomodels.net/kisao/KISAO#KISAO_$1" } ], "publications": [ { "doi": "10.1038/msb.2011.77", "pmc": "PMC3261705", "pubmed": "22027554", "title": "Controlled vocabularies and semantics in systems biology.", "year": 2011 } ], "repository": "https://github.com/SED-ML/KiSAO", "synonyms": [ "kisao" ], "uri_format": "https://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=kisao:KISAO_$1", "version": "2.30" }, "biomodels.teddy": { "banana": "TEDDY", "banana_peel": "_", "contact": { "email": "biomodels-net-support@lists.sf.net", "github": null, "name": "BioModels.net team", "orcid": null }, "description": "The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.", "download_owl": "http://svn.code.sf.net/p/teddyontology/code/teddy/tags/current/teddy-inferred.owl", "example": "0000066", "homepage": "http://teddyontology.sourceforge.net/", "mappings": { "aberowl": "TEDDY", "biocontext": "BIOMODELS.TEDDY", "bioportal": "TEDDY", "fairsharing": "FAIRsharing.w9jvbt", "miriam": "biomodels.teddy", "n2t": "biomodels.teddy", "ols": "teddy", "prefixcommons": "teddy" }, "name": "Terminology for Description of Dynamics", "pattern": "^\\d+$", "preferred_prefix": "biomodels.teddy", "publications": [ { "doi": "10.1038/msb.2011.77", "pmc": "PMC3261705", "pubmed": "22027554", "title": "Controlled vocabularies and semantics in systems biology.", "year": 2011 } ], "synonyms": [ "teddy" ], "uri_format": "https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1", "version": "2014-04-24" }, "biomodels.vocabulary": { "description": "Vocabulary used in the RDF representation of SBML models.", "example": "rateRule", "homepage": "http://biomodels.net/rdf/vocabulary.rdf", "mappings": { "biocontext": "BIOMODELS.VOCABULARY", "miriam": "biomodels.vocabulary", "n2t": "biomodels.vocabulary" }, "name": "SBML RDF Vocabulary", "pattern": "^[A-Za-z]+$", "preferred_prefix": "biomodels.vocabulary", "uri_format": "http://biomodels.net/rdf/vocabulary.rdf#$1" }, "bionumbers": { "description": "BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data.", "example": "104674", "homepage": "https://bionumbers.hms.harvard.edu", "mappings": { "biocontext": "BIONUMBERS", "edam": "2660", "miriam": "bionumbers", "n2t": "bionumbers", "prefixcommons": "bionumbers" }, "name": "BioNumbers", "pattern": "^\\d+$", "preferred_prefix": "bionumbers", "uri_format": "https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1" }, "bioportal": { "description": "BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies.", "example": "1046", "homepage": "http://bioportal.bioontology.org/", "mappings": { "biocontext": "BIOPORTAL", "fairsharing": "FAIRsharing.4m97ah", "miriam": "bioportal", "n2t": "bioportal", "prefixcommons": "bioportal", "re3data": "r3d100012344" }, "name": "BioPortal", "pattern": "^\\d+$", "preferred_prefix": "bioportal", "publications": [ { "doi": "10.1093/nar/gkp440", "pmc": "PMC2703982", "pubmed": "19483092", "title": "BioPortal: ontologies and integrated data resources at the click of a mouse.", "year": 2009 } ], "uri_format": "http://bioportal.bioontology.org/ontologies/$1" }, "bioproject": { "description": "BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories.", "example": "PRJDB3", "has_canonical": "ena.embl", "homepage": "http://trace.ddbj.nig.ac.jp/bioproject/", "mappings": { "biocontext": "BIOPROJECT", "fairsharing": "FAIRsharing.aqhv1y", "miriam": "bioproject", "n2t": "bioproject", "re3data": "r3d100013330" }, "name": "BioProject", "pattern": "^PRJ[DEN][A-Z]\\d+$", "preferred_prefix": "bioproject", "providers": [ { "code": "ebi", "description": "BioProject at European Nucleotide Archive (ENA)", "homepage": "https://www.ebi.ac.uk/ena/", "name": "BioProject at European Nucleotide Archive (ENA)", "uri_format": "https://www.ebi.ac.uk/ena/browser/view/$1" }, { "code": "ncbi", "description": "BioProject at NCBI", "homepage": "https://www.ncbi.nlm.nih.gov/bioproject", "name": "BioProject at NCBI", "uri_format": "https://www.ncbi.nlm.nih.gov/bioproject?term=$1" } ], "uri_format": "https://www.ncbi.nlm.nih.gov/bioproject/?term=$1" }, "bioregistry": { "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 is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database.", "example": "bioregistry", "homepage": "https://bioregistry.io", "name": "Bioregistry", "preferred_prefix": "bioregistry", "publications": [ { "doi": "10.1101/2022.07.08.499378", "pmc": null, "pubmed": null, "title": "Unifying the Identification of Biomedical Entities with the Bioregistry", "year": null } ], "repository": "https://github.com/biopragmatics/bioregistry", "uri_format": "https://bioregistry.io/registry/$1" }, "bioregistry.collection": { "contact": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Manually curated collections of resources stored in the bioregistry", "example": "0000001", "homepage": "https://bioregistry.io/collection", "name": "Bioregistry Collections", "pattern": "^\\d{7}$", "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/", "name": "Bioregistry Metaregistry", "preferred_prefix": "bioregistry.registry", "uri_format": "https://bioregistry.io/metaregistry/$1" }, "bioregistry.schema": { "contact": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Schema for the export of the Bioregistry as RDF", "example": "0000001", "homepage": "https://bioregistry.io/schema", "name": "Bioregistry Schema", "pattern": "^\\d{7}$", "preferred_prefix": "bioregistry.schema", "uri_format": "https://bioregistry.io/schema/#$1" }, "biorxiv": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The bioRxiv is a preprint server for biology", "example": "2022.07.08.499378", "example_extras": [ "000091", "000091v1", "2022.07.08.499378v2" ], "homepage": "https://biorxiv.org", "mappings": { "go": "bioRxiv" }, "name": "bioRxiv", "pattern": "^(\\d{4}\\.\\d{2}\\.\\d{2}\\.)?\\d{6,8}(v\\d{1,3})?$", "preferred_prefix": "biorxiv", "providers": [ { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/biorxiv/$1" } ], "uri_format": "https://www.biorxiv.org/content/10.1101/$1" }, "biosample": { "description": "The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation.", "example": "SAMEA2397676", "homepage": "https://www.ebi.ac.uk/biosamples/", "mappings": { "biocontext": "BIOSAMPLE", "cellosaurus": "BioSamples", "fairsharing": "FAIRsharing.qr6pqk", "miriam": "biosample", "n2t": "biosample", "re3data": "r3d100012828" }, "name": "BioSample", "pattern": "^SAM[NED](\\w)?\\d+$", "preferred_prefix": "biosample", "providers": [ { "code": "CURATOR_REVIEW", "description": "BioSample at DNA Data Bank of Japan", "homepage": "http://trace.ddbj.nig.ac.jp/biosample/", "name": "BioSample at DNA Data Bank of Japan", "uri_format": "http://trace.ddbj.nig.ac.jp/BSSearch/biosample?acc=$1" }, { "code": "ncbi", "description": "BioSample at NCBI", "homepage": "http://www.ncbi.nlm.nih.gov/biosample", "name": "BioSample at NCBI", "uri_format": "http://www.ncbi.nlm.nih.gov/biosample?term=$1" } ], "synonyms": [ "biosamples" ], "uri_format": "https://www.ebi.ac.uk/biosamples/sample/$1" }, "biosimulations": { "description": "BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools.", "example": "Yeast-cell-cycle-Irons-J-Theor-Biol-2009", "homepage": "https://icahn.mssm.edu/", "mappings": { "miriam": "biosimulations", "re3data": "r3d100013361" }, "name": "biosimulations", "pattern": "^[a-zA-Z0-9_-]{3,}$", "preferred_prefix": "biosimulations", "uri_format": "https://biosimulations.org/projects/$1" }, "biosimulators": { "description": "BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML).", "example": "vcell", "homepage": "https://biosimulators.org/", "mappings": { "fairsharing": "FAIRsharing.pwEima", "miriam": "biosimulators", "re3data": "r3d100013432" }, "name": "BioSimulators", "pattern": "^[a-zA-Z0-9-_]+$", "preferred_prefix": "biosimulators", "uri_format": "https://biosimulators.org/simulators/$1" }, "biostudies": { "description": "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.", "example": "S-EPMC6266652", "homepage": "https://www.ebi.ac.uk/biostudies/", "mappings": { "fairsharing": "FAIRsharing.mtjvme", "miriam": "biostudies", "n2t": "biostudies", "re3data": "r3d100012627" }, "name": "BioStudies database", "pattern": "^S-[A-Z]{4}[A-Z\\d\\-]+$", "preferred_prefix": "biostudies", "uri_format": "https://www.ebi.ac.uk/biostudies/studies/$1" }, "biosystems": { "description": "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources.", "example": "001", "homepage": "https://www.ncbi.nlm.nih.gov/biosystems/", "mappings": { "biocontext": "BIOSYSTEMS", "fairsharing": "FAIRsharing.w2eeqr", "miriam": "biosystems", "n2t": "biosystems", "prefixcommons": "biosystems" }, "name": "BioSystems", "pattern": "^\\d+$", "preferred_prefix": "biosystems", "publications": [ { "doi": "10.1093/nar/gkp858", "pmc": "PMC2808896", "pubmed": "19854944", "title": "The NCBI BioSystems database.", "year": 2009 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/biosystems/$1" }, "biotools": { "description": "BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research.", "example": "bioregistry", "homepage": "https://bio.tools/", "mappings": { "biocontext": "BIOTOOLS", "fairsharing": "FAIRsharing.63520c", "miriam": "biotools", "n2t": "biotools", "re3data": "r3d100013668" }, "name": "BioTools", "pattern": "^[-A-Za-z0-9\\_]*$", "preferred_prefix": "biotools", "uri_format": "https://bio.tools/$1" }, "biozil": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Redistributor of bilogics and biomedical supplies", "example": "ls-c35719-120", "homepage": "https://www.biozol.de/en", "name": "BIOZIL", "preferred_prefix": "biozil", "uri_format": "https://www.biozol.de/en/product/$1" }, "birnlex": { "comment": "Part of the NeuroLex namespace now", "contact": { "email": "wbug@ncmir.ucsd.edu", "github": null, "name": "William Bug", "orcid": null }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design.", "download_owl": "http://aber-owl.net/media/ontologies/BIRNLEX/1/birnlex.owl", "example": "2023", "homepage": "https://bioportal.bioontology.org/ontologies/BIRNLEX", "mappings": { "aberowl": "BIRNLEX", "bioportal": "BIRNLEX", "fairsharing": "FAIRsharing.jedbbt" }, "name": "Biomedical Informatics Research Network Lexicon", "pattern": "^\\d+$", "preferred_prefix": "birnlex", "uri_format": "http://uri.neuinfo.org/nif/nifstd/birnlex_$1" }, "biro": { "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", "mappings": { "fairsharing": "FAIRsharing.99da5f" }, "name": "Bibliographic Reference Ontology", "preferred_prefix": "BiRO", "repository": "https://github.com/sparontologies/biro", "uri_format": "http://purl.org/spar/biro/$1" }, "bitbucket": { "description": "Bitbucket is a Git-based source code repository hosting service owned by Atlassian.", "example": "andreadega/systems-biology-compiler", "homepage": "https://www.atlassian.com/", "mappings": { "fairsharing": "FAIRsharing.fc3431", "miriam": "bitbucket", "re3data": "r3d100013478" }, "name": "Bitbucket", "pattern": "^[0-9A-Za-z-_\\.]+/[0-9A-Za-z-_\\.]+$", "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=$1" }, "bko": { "comment": "This resource also uses SBO terms and resolves them, e.g., http://www.sbgnbricks.org/BKO/full/entry/all/SBO:0000177/.", "contact": { "email": "adrienrougny@gmail.com", "github": "adrienrougny", "name": "Adrien Rougny", "orcid": "0000-0002-2118-035X" }, "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way.", "download_owl": "http://aber-owl.net/media/ontologies/BKO/1/bko.owl", "example": "0000204", "github_request_issue": 283, "homepage": "http://www.sbgnbricks.org/", "mappings": { "aberowl": "BKO", "bioportal": "BKO" }, "name": "SBGN Bricks data and ontology", "pattern": "^\\d+$", "preferred_prefix": "bko", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1" }, "bmrb": { "description": "BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy.", "example": "15000", "homepage": "http://www.bmrb.wisc.edu/", "mappings": { "fairsharing": "FAIRsharing.p06nme", "miriam": "bmrb", "uniprot": "BMRB" }, "name": "Biological Magnetic Resonance Data Bank", "pattern": "^(bmr|bmse|bmst)?[0-9]{1,6}$", "preferred_prefix": "bmrb", "uri_format": "http://rest.bmrb.wisc.edu/bmrb/$1/html" }, "bmrb.restraint": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively.", "example": "28789", "homepage": "https://restraintsgrid.bmrb.io/NRG/MRGridServlet", "name": "NMR Restraints Grid", "pattern": "^\\d+$", "preferred_prefix": "bmrb.restraint", "uri_format": "https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1" }, "bold.taxonomy": { "description": "The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information.", "example": "27267", "homepage": "http://www.boldsystems.org/", "mappings": { "biocontext": "BOLD.TAXONOMY", "miriam": "bold.taxonomy", "n2t": "bold.taxonomy", "ncbi": "BOLD", "prefixcommons": "bold" }, "name": "Barcode of Life database", "pattern": "^\\d+$", "preferred_prefix": "bold.taxonomy", "publications": [ { "doi": "10.1111/j.1471-8286.2007.01678.x", "pmc": "PMC1890991", "pubmed": "18784790", "title": "bold: The Barcode of Life Data System (http://www.barcodinglife.org).", "year": 2007 } ], "uri_format": "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1" }, "bootstrep": { "contact": { "email": "vlee@ebi.ac.uk", "github": null, "name": "Vivian Lee", "orcid": null }, "deprecated": true, "homepage": "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html", "mappings": { "biocontext": "BOOTSTREP", "obofoundry": "bootstrep" }, "name": "Gene Regulation Ontology", "preferred_prefix": "BOOTSTREP", "uri_format": "http://purl.obolibrary.org/obo/BOOTSTREP_$1" }, "bpdb": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database of biopesticides maintained by the University of Hertfordshire ", "example": "2404", "homepage": "https://sitem.herts.ac.uk/aeru/bpdb/index.htm", "name": "Bio-Pesticides DataBase", "pattern": "^\\d+$", "preferred_prefix": "bpdb", "uri_format": "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm" }, "brenda": { "description": "BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data.", "example": "1.1.1.1", "homepage": "https://www.brenda-enzymes.org/", "mappings": { "biocontext": "BRENDA", "fairsharing": "FAIRsharing.etp533", "go": "BRENDA", "miriam": "brenda", "n2t": "brenda", "prefixcommons": "brenda", "re3data": "r3d100010616", "uniprot": "BRENDA" }, "name": "BRENDA, The Comprehensive Enzyme Information System", "pattern": "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$", "preferred_prefix": "brenda", "publications": [ { "doi": "10.1093/nar/gkn820", "pmc": "PMC2686525", "pubmed": "18984617", "title": "BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009.", "year": 2008 } ], "uri_format": "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1" }, "brenda.ligand": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Information for ligands in the BRENDA database.", "example": "278", "homepage": "https://www.brenda-enzymes.de/ligand.php", "name": "BRENDA Ligand", "pattern": "^\\d+$", "preferred_prefix": "brenda.ligand", "uri_format": "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1" }, "brenda.ligandgroup": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Information for ligand groups (chemical classes).", "example": "18030", "homepage": "https://www.brenda-enzymes.de/ligand.php", "name": "BRENDA Ligand Group", "pattern": "^\\d+$", "preferred_prefix": "brenda.ligandgroup", "uri_format": "https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1" }, "broad": { "description": "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. 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As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae.", "example": "S7000002168151102", "homepage": "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/", "mappings": { "biocontext": "BROAD", "miriam": "broad", "n2t": "broad" }, "name": "Broad Fungal Genome Initiative", "pattern": "^S\\d+$", "preferred_prefix": "broad", "uri_format": "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1" }, "bs": { "comment": "An alernative vocabulary that has been aligned and integrated in Sequence Ontology (SO).", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library.", "download_obo": "https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/subsets/biosapiens.obo", "example": "00042", "homepage": "https://github.com/The-Sequence-Ontology/SO-Ontologies", "name": "Biosapiens Protein Feature Ontology", "pattern": "^\\d+$", "preferred_prefix": "bs", "repository": "https://github.com/The-Sequence-Ontology/SO-Ontologies", "uri_format": "https://biopragmatics.github.io/providers/bs/$1" }, "bspo": { "appears_in": [ "aism", "colao", "fovt", "lepao", "zp" ], "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies.", "download_json": "http://purl.obolibrary.org/obo/bspo.json", "download_obo": "https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo", "download_owl": "http://purl.obolibrary.org/obo/bspo.owl", "example": "0000029", "homepage": "https://github.com/obophenotype/biological-spatial-ontology", "license": "CC BY 3.0", "mappings": { "aberowl": "BSPO", "biocontext": "BSPO", "bioportal": "BSPO", "fairsharing": "FAIRsharing.newa3z", "obofoundry": "bspo", "ols": "bspo", "ontobee": "BSPO" }, "name": "Biological Spatial Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "BSPO", "publications": [ { "doi": "10.1186/2041-1480-5-34", "pmc": "PMC4137724", "pubmed": "25140222", "title": "Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.", "year": 2014 } ], "repository": "https://github.com/obophenotype/biological-spatial-ontology", "uri_format": "http://purl.obolibrary.org/obo/BSPO_$1", "version": "2022-06-28" }, "bto": { "banana": "BTO", "contact": { "email": "c.dudek@tu-braunschweig.de", "github": "chdudek", "name": "Christian-Alexander Dudek", "orcid": "0000-0001-9117-7909" }, "description": "The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.", "download_json": "http://purl.obolibrary.org/obo/bto.json", "download_obo": "http://purl.obolibrary.org/obo/bto.obo", "download_owl": "http://purl.obolibrary.org/obo/bto.owl", "example": "0000590", "homepage": "http://www.brenda-enzymes.org", "license": "CC BY 4.0", "mappings": { "aberowl": "BTO", "biocontext": "BTO", "bioportal": "BTO", "cellosaurus": "BTO", "fairsharing": "FAIRsharing.1414v8", "go": "BTO", "miriam": "bto", "n2t": "bto", "obofoundry": "bto", "ols": "bto", "ontobee": "BTO", "prefixcommons": "bto", "wikidata": "P5501" }, "name": "BRENDA tissue / enzyme source", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "BTO", "publications": [ { "doi": "10.1093/nar/gky1048", "pmc": "PMC6323942", "pubmed": "30395242", "title": "BRENDA in 2019: a European ELIXIR core data resource.", "year": 2019 }, { "doi": "10.1093/nar/gku1068", "pmc": "PMC4383907", "pubmed": "25378310", "title": "BRENDA in 2015: exciting developments in its 25th year of existence.", "year": 2014 }, { "doi": "10.1093/nar/gks1049", "pmc": "PMC3531171", "pubmed": "23203881", "title": "BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.", "year": 2012 }, { "doi": "10.1093/nar/gkq968", "pmc": "PMC3013802", "pubmed": "21030441", "title": "The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources.", "year": 2010 }, { "doi": "10.1093/nar/gkh081", "pmc": "PMC308815", "pubmed": "14681450", "title": "BRENDA, the enzyme database: updates and major new developments.", "year": 2004 } ], "repository": "https://github.com/BRENDA-Enzymes/BTO", "synonyms": [ "BTO" ], "uri_format": "https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=BTO:$1", "version": "2021-10-26" }, "bugbase.expt": { "description": "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments.", "example": "288", "homepage": "http://bugs.sgul.ac.uk/E-BUGS", "mappings": { "biocontext": "BUGBASE.EXPT", "miriam": "bugbase.expt", "n2t": "bugbase.expt" }, "name": "BugBase Expt", "pattern": "^\\d+$", "preferred_prefix": "bugbase.expt", "uri_format": "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view" }, "bugbase.protocol": { "description": "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols.", "example": "67", "homepage": "http://bugs.sgul.ac.uk/E-BUGS", "mappings": { "biocontext": "BUGBASE.PROTOCOL", "miriam": "bugbase.protocol", "n2t": "bugbase.protocol" }, "name": "BugBase Protocol", "pattern": "^\\d+$", "preferred_prefix": "bugbase.protocol", "uri_format": "http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$1&action=view" }, "bykdb": { "description": "The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information.", "example": "A0A009E7X8", "homepage": "https://bykdb.ibcp.fr/BYKdb/", "mappings": { "biocontext": "BYKDB", "fairsharing": "FAIRsharing.jr30xc", "miriam": "bykdb", "n2t": "bykdb", "prefixcommons": "bykdb" }, "name": "Bacterial Tyrosine Kinase Database", "pattern": "^[A-Z0-9]+$", "preferred_prefix": "bykdb", "provides": "uniprot", "publications": [ { "doi": "10.1093/nar/gkr915", "pmc": "PMC3245071", "pubmed": "22080550", "title": "BYKdb: the Bacterial protein tYrosine Kinase database.", "year": 2011 } ], "uri_format": "https://bykdb.ibcp.fr/data/html/annotated/$1.html" }, "c4o": { "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", "mappings": { "fairsharing": "FAIRsharing.beb855" }, "name": "Citation Counting and Context Characterisation Ontology", "preferred_prefix": "C4O", "repository": "https://github.com/sparontologies/c4o", "uri_format": "http://purl.org/spar/c4o/$1" }, "cabri": { "description": "CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it.", "example": "dsmz_mutz-id:ACC 291", "homepage": "http://www.cabri.org/", "mappings": { "biocontext": "CABRI", "edam": "2380", "fairsharing": "FAIRsharing.qx2rvz", "miriam": "cabri", "n2t": "cabri", "ncbi": "CABRI" }, "name": "Common Access to Biological Resources and Information Project", "pattern": "^([A-Za-z]+)?(\\_)?([A-Za-z-]+)\\:([A-Za-z0-9 ]+)$", "preferred_prefix": "cabri", "providers": [ { "code": "CURATOR_REVIEW", "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]" } ], "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=$1]" }, "caloha": { "banana": "TS", "banana_peel": "-", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins.", "download_obo": "https://download.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo", "example": "0001", "homepage": "https://github.com/calipho-sib/controlled-vocabulary", "name": "CALIPHO Group Ontology of Human Anatomy", "pattern": "^\\d+$", "preferred_prefix": "caloha", "references": [ "https://twitter.com/neXtProt_news/status/1350105997633867781" ], "repository": "https://github.com/calipho-sib/controlled-vocabulary", "twitter": "neXtProt_news", "uri_format": "https://biopragmatics.github.io/providers/caloha/$1" }, "cameo": { "description": "The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB.", "example": "2019-08-03_00000089_1", "homepage": "https://cameo3d.org", "mappings": { "biocontext": "CAMEO", "fairsharing": "FAIRsharing.dq34p2", "miriam": "cameo", "n2t": "cameo" }, "name": "Continuous Automated Model Evaluation", "pattern": "^[0-9\\-_]+$", "preferred_prefix": "cameo", "uri_format": "https://www.cameo3d.org/sp/targets/target/$1" }, "caps": { "description": "CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps.", "example": "434", "homepage": "http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home", "mappings": { "biocontext": "CAPS", "miriam": "caps", "n2t": "caps" }, "name": "CAPS-DB", "pattern": "^\\d+$", "preferred_prefix": "caps", "uri_format": "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1" }, "caro": { "appears_in": [ "aism", "colao", "ehdaa2", "lepao", "pco" ], "contact": { "email": "haendel@ohsu.edu", "github": "mellybelly", "name": "Melissa Haendel", "orcid": "0000-0001-9114-8737" }, "description": "None", "download_json": "http://purl.obolibrary.org/obo/caro.json", "download_obo": "http://purl.obolibrary.org/obo/caro.obo", "download_owl": "http://purl.obolibrary.org/obo/caro.owl", "example": "0000000", "homepage": "https://github.com/obophenotype/caro/", "license": "CC BY 3.0", "mappings": { "aberowl": "CARO", "biocontext": "CARO", "bioportal": "CARO", "fairsharing": "FAIRsharing.3kcgmr", "go": "CARO", "obofoundry": "caro", "ols": "caro", "ontobee": "CARO" }, "name": "Common Anatomy Reference Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CARO", "providers": [ { "code": "obo.1", "description": "This incorrect encoding was found inside IDO-COVID-19", "homepage": "http://purl.obolibrary.org", "name": "Nonstandard OBO PURL", "uri_format": "http://purl.obolibrary.org/obo/ido.owl/CARO_$1" } ], "publications": [ { "doi": "10.1007/978-1-84628-885-2_16", "pmc": null, "pubmed": null, "title": "CARO – The Common Anatomy Reference Ontology", "year": null } ], "repository": "https://github.com/obophenotype/caro", "uri_format": "http://purl.obolibrary.org/obo/CARO_$1", "version": "2022-02-18" }, "cas": { "description": "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information.", "example": "50-00-0", "homepage": "https://commonchemistry.cas.org/", "mappings": { "biocontext": "CAS", "cheminf": "000446", "edam": "1002", "fairsharing": "FAIRsharing.r7Kwy7", "go": "CAS", "hl7": "2.16.840.1.113883.6.61", "miriam": "cas", "n2t": "cas", "prefixcommons": "cas", "wikidata": "P231" }, "name": "CAS Chemical Registry", "pattern": "^\\d{1,7}\\-\\d{2}\\-\\d$", "preferred_prefix": "cas", "providers": [ { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/cas/$1" } ], "synonyms": [ "CASID", "CAS_RN", "SECONDARY_CAS_RN", "cas_id" ], "uri_format": "https://commonchemistry.cas.org/detail?ref=$1" }, "casspc": { "comment": "Jim Balhoff said that Catalog of Fishes does not publish their data in a machine readable format, but a long time ago they sent a CSV dump to help in the development of TTO and VTO. These ontologies are effectively retired and CASSPC terms are only also used in Phenoscape.", "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "contributor_extras": [ { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } ], "deprecated": true, "example": "5359", "homepage": "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp", "mappings": { "go": "CASSPC" }, "name": "Eschmeyer's Catalog of Fishes", "pattern": "^\\d+$", "preferred_prefix": "casspc", "uri_format": "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1" }, "cath": { "description": "CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence.", "example": "1.10.8.10", "homepage": "http://www.cathdb.info", "mappings": { "biocontext": "CATH", "edam": "2700", "fairsharing": "FAIRsharing.xgcyyn", "miriam": "cath", "n2t": "cath", "prefixcommons": "cath", "re3data": "r3d100012629" }, "name": "CATH Protein Structural Domain Superfamily", "pattern": "^[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+$", "preferred_prefix": "cath", "publications": [ { "doi": "10.1016/s0969-2126(97)00260-8", "pmc": null, "pubmed": "9309224", "title": "CATH--a hierarchic classification of protein domain structures.", "year": 1997 } ], "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/$1" }, "cattleqtldb": { "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs.", "example": "4685", "homepage": "https://www.animalgenome.org/QTLdb", "mappings": { "biocontext": "CATTLEQTLDB", "miriam": "cattleqtldb", "n2t": "cattleqtldb", "prefixcommons": "cattleqtldb" }, "name": "Animal Genome Cattle QTL", "part_of": "qtldb", "pattern": "^\\d+$", "preferred_prefix": "cattleqtldb", "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" }, "cazy": { "description": "The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features.", "example": "GT10", "homepage": "http://www.cazy.org/", "mappings": { "biocontext": "CAZY", "fairsharing": "FAIRsharing.ntyq70", "go": "CAZY", "miriam": "cazy", "n2t": "cazy", "prefixcommons": "cazy", "uniprot": "CAZy" }, "name": "Carbohydrate Active EnZYmes", "pattern": "^(GT|GH|PL|CE|CBM)\\d+(\\_\\d+)?$", "preferred_prefix": "cazy", "publications": [ { "doi": "10.1093/nar/gkn663", "pmc": "PMC2686590", "pubmed": "18838391", "title": "The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics.", "year": 2008 } ], "uri_format": "http://www.cazy.org/$1.html" }, "cba": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE.", "example": "375364", "homepage": "http://www.cba.ac.cn", "name": "Chinese Biological Abstracts", "pattern": "^\\d+$", "preferred_prefix": "cba", "uri_format": "https://europepmc.org/article/CBA/$1" }, "cbioportal": { "description": "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.", "example": "laml_tcga_pub", "homepage": "http://www.cbioportal.org", "mappings": { "fairsharing": "FAIRsharing.6L6MjA", "miriam": "cbioportal", "n2t": "cbioportal" }, "name": "The cBioPortal for Cancer Genomics", "pattern": "^[a-z0-9\\_]+$", "preferred_prefix": "cbioportal", "uri_format": "https://www.cbioportal.org/study/summary?id=$1" }, "ccdc": { "description": "The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC.", "example": "1829126", "homepage": "https://www.ccdc.cam.ac.uk/", "mappings": { "miriam": "ccdc" }, "name": "CCDC Number", "pattern": "^\\d{6,7}$", "preferred_prefix": "ccdc", "uri_format": "https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG" }, "ccds": { "description": "The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations.", "example": "CCDS13573.1", "homepage": "http://www.ncbi.nlm.nih.gov/CCDS/", "mappings": { "biocontext": "CCDS", "fairsharing": "FAIRsharing.46s4nt", "miriam": "ccds", "n2t": "ccds", "prefixcommons": "ccds", "uniprot": "CCDS" }, "name": "Consensus CDS", "pattern": "^CCDS\\d+\\.\\d+$", "preferred_prefix": "ccds", "publications": [ { "doi": "10.1101/gr.080531.108", "pmc": "PMC2704439", "pubmed": "19498102", "title": "The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.", "year": 2009 } ], "uri_format": "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1" }, "ccle": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Datasets around different cancer cell lines generated by the Broad Institute and Novartis", "example": "BT20_BREAST", "homepage": "https://www.cbioportal.org/study/summary?id=ccle_broad_2019", "mappings": { "cellosaurus": "CCLE" }, "name": "Cancer Cell Line Encyclopedia Cells", "preferred_prefix": "ccle", "synonyms": [ "ccle.cell" ], "uri_format": "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1" }, "cco": { "banana": "CCO", "contact": { "email": "vladimir.n.mironov@gmail.com", "github": null, "name": "Vladimir Mironov", "orcid": null }, "description": "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process.", "download_obo": "https://www.bio.ntnu.no/ontology/CCO/cco.obo", "download_owl": "https://www.bio.ntnu.no/ontology/CCO/cco.owl", "example": "0000003", "homepage": "http://www.semantic-systems-biology.org/apo", "mappings": { "aberowl": "CCO", "biocontext": "CCO", "bioportal": "CCO", "fairsharing": "FAIRsharing.xhwrnr", "miriam": "cco", "n2t": "cco", "ols": "cco", "prefixcommons": "cco" }, "name": "Cell Cycle Ontology", "namespace_in_lui": true, "pattern": "^\\w+$", "preferred_prefix": "cco", "publications": [ { "doi": "10.1186/gb-2009-10-5-r58", "pmc": "PMC2718524", "pubmed": "19480664", "title": "The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process.", "year": 2009 } ], "uri_format": "https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1", "version": "2016-03-23" }, "ccrid": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Cell line databases/resources", "example": "4201PAT-CCTCC00348", "homepage": "http://www.cellresource.cn", "mappings": { "cellosaurus": "CCRID" }, "name": "National Experimental Cell Resource Sharing Platform", "preferred_prefix": "ccrid", "uri_format": "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1" }, "cdao": { "contact": { "email": "balhoff@renci.org", "github": "balhoff", "name": "Jim Balhoff", "orcid": "0000-0002-8688-6599" }, "description": "The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character.", "download_owl": "http://purl.obolibrary.org/obo/cdao.owl", "example": "0000072", "homepage": "https://github.com/evoinfo/cdao", "license": "CC0 1.0", "mappings": { "aberowl": "CDAO", "agroportal": "CDAO", "biocontext": "CDAO", "bioportal": "CDAO", "fairsharing": "FAIRsharing.kay31r", "obofoundry": "cdao", "ols": "cdao", "ontobee": "CDAO" }, "name": "Comparative Data Analysis Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CDAO", "publications": [ { "doi": "10.4137/ebo.s2320", "pmc": "PMC2747124", "pubmed": "19812726", "title": "Initial implementation of a comparative data analysis ontology.", "year": 2009 } ], "repository": "https://github.com/evoinfo/cdao", "uri_format": "http://purl.obolibrary.org/obo/CDAO_$1", "version": "2019-06-26" }, "cdd": { "description": "The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution.", "example": "cd00400", "homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd", "mappings": { "biocontext": "CDD", "edam": "2666", "fairsharing": "FAIRsharing.ea287c", "go": "CDD", "miriam": "cdd", "n2t": "cdd", "ncbi": "CDD", "prefixcommons": "cdd", "uniprot": "CDD" }, "name": "Conserved Domain Database at NCBI", "pattern": "^(cd)?\\d{5}$", "preferred_prefix": "cdd", "publications": [ { "doi": "10.1093/nar/gkn845", "pmc": "PMC2686570", "pubmed": "18984618", "title": "CDD: specific functional annotation with the Conserved Domain Database.", "year": 2008 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1" }, "cdno": { "contact": { "email": "l.andres.hernandez.18@student.scu.edu.au", "github": "LilyAndres", "name": "Liliana Andres Hernandez", "orcid": "0000-0002-7696-731X" }, "depends_on": [ "bfo", "chebi", "envo", "pato", "ro" ], "description": "None", "download_obo": "http://purl.obolibrary.org/obo/cdno.obo", "download_owl": "http://purl.obolibrary.org/obo/cdno.owl", "example": "0000013", "homepage": "https://cdno.info/", "license": "CC BY 3.0", "mappings": { "aberowl": "CDNO", "bioportal": "CDNO", "obofoundry": "cdno", "ols": "cdno", "ontobee": "CDNO" }, "name": "Compositional Dietary Nutrition Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CDNO", "publications": [ { "doi": "10.1002/csc2.20092", "pmc": null, "pubmed": null, "title": "Knowledge representation and data sharing to unlock crop variation for nutritional food security", "year": null } ], "repository": "https://github.com/Southern-Cross-Plant-Science/cdno", "uri_format": "http://purl.obolibrary.org/obo/CDNO_$1", "version": "2022-06-23" }, "cdpd": { "description": "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN).", "example": "63250", "homepage": "http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp", "mappings": { "biocontext": "CDPD", "miriam": "cdpd", "n2t": "cdpd" }, "name": "Canadian Drug Product Database", "pattern": "^\\d+$", "preferred_prefix": "cdpd", "uri_format": "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1" }, "cdt": { "appears_in": [ "ohd" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment.", "download_owl": "https://github.com/oral-health-and-disease-ontologies/ohd-ontology/blob/master/src/ontology/older/CDTCodes%20as%20Classes_pruned.owl", "example": "1000001", "homepage": "https://www.ada.org/publications/CDT", "mappings": { "hl7": "2.16.840.1.113883.6.116" }, "name": "Current Dental Terminology", "pattern": "^\\d{7}$", "preferred_prefix": "cdt" }, "cell_biolabs": { "description": "Cell line collections", "example": "AKR-270", "homepage": "https://www.cellbiolabs.com", "mappings": { "cellosaurus": "Cell_Biolabs" }, "name": "Cell Biolabs cell line products", "preferred_prefix": "cell_biolabs", "uri_format": "https://www.cellbiolabs.com/search?keywords=$1" }, "cell_model_passport": { "description": "Cell line databases/resources", "example": "SIDM01262", "homepage": "https://cellmodelpassports.sanger.ac.uk/", "mappings": { "cellosaurus": "Cell_Model_Passport" }, "name": "Sanger Cell Model Passports", "preferred_prefix": "cell_model_passport", "uri_format": "https://cellmodelpassports.sanger.ac.uk/passports/$1" }, "cellbank.australia": { "description": "CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world.", "example": "ab-1-ha", "homepage": "http://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/", "mappings": { "cellosaurus": "CBA" }, "name": "CellBank Australia", "preferred_prefix": "cellbank.australia", "uri_format": "https://www.cellbankaustralia.com/$1.html" }, "cellimage": { "description": "The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.", "example": "24801", "homepage": "http://cellimagelibrary.org/", "mappings": { "biocontext": "CELLIMAGE", "fairsharing": "FAIRsharing.8t18te", "miriam": "cellimage", "n2t": "cellimage", "prefixcommons": "cellimage" }, "name": "Cell Image Library", "pattern": "^\\d+$", "preferred_prefix": "cellimage", "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/$1" }, "cellosaurus": { "banana": "CVCL", "banana_peel": "_", "contact": { "email": "Amos.Bairoch@sib.swiss", "github": "AmosBairoch", "name": "Amos Bairoch", "orcid": "0000-0003-2826-6444" }, "description": "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.", "download_obo": "https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo", "example": "0440", "homepage": "https://cellosaurus.org", "mappings": { "biocontext": "CELLOSAURUS", "cellosaurus": "Cellosaurus", "fairsharing": "FAIRsharing.hkk309", "miriam": "cellosaurus", "n2t": "cellosaurus", "re3data": "r3d100013293", "wikidata": "P3289" }, "name": "Cellosaurus", "pattern": "^[A-Z0-9]{4}$", "preferred_prefix": "cellosaurus", "providers": [ { "code": "legacy", "description": "The legacy URI for the Cellosaurus website, updated on August 30, 2022 [ref](https://twitter.com/Cellosaurus/status/1564658792691810305).", "homepage": "https://web.expasy.org/cellosaurus", "name": "Legacy Endpoint", "uri_format": "https://web.expasy.org/cellosaurus/CVCL_$1" } ], "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/", "name": "Cellosaurus Registry", "preferred_prefix": "cellosaurus.resource", "uri_format": "https://bioregistry.io/metaregistry/cellosaurus/$1" }, "cellrepo": { "description": "The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines", "example": "82", "homepage": "https://cellrepo.ico2s.org/", "mappings": { "miriam": "cellrepo" }, "name": "Cell Version Control Repository", "pattern": "^[0-9]+$", "preferred_prefix": "cellrepo", "uri_format": "https://cellrepo.ico2s.org/repositories/$1" }, "cemo": { "contact": { "email": "n.queralt_rosinach@lumc.nl", "github": "NuriaQueralt", "name": "Núria Queralt Rosinach", "orcid": "0000-0003-0169-8159" }, "contributor": { "email": null, "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "The covid-19 epidemiology and monitoring ontology (cemo) provides a common ontological model to make epidemiological quantitative data for monitoring the covid-19 outbreak machine-readable and interoperable to facilitate its exchange, integration and analysis, to eventually support evidence-based rapid response.", "download_owl": "https://raw.githubusercontent.com/NuriaQueralt/covid19-epidemiology-ontology/main/owl/cemo.owl", "example": "length_of_intensive_care_unit_(icu)_stay", "github_request_issue": 593, "homepage": "https://github.com/NuriaQueralt/covid19-epidemiology-ontology", "license": "CC0 1.0", "name": "The COVID-19 epidemiology and monitoring ontology", "pattern": "^[()0-9a-z_-]+$", "preferred_prefix": "cemo", "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": "http://purl.obolibrary.org/obo/cemo.owl#$1" }, "ceph": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "deprecated": true, "description": "An anatomical and developmental ontology for cephalopods", "download_obo": "https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo", "download_owl": "http://purl.obolibrary.org/obo/ceph.owl", "example": "0000109", "homepage": "https://github.com/obophenotype/cephalopod-ontology", "license": "CC BY 3.0", "mappings": { "aberowl": "CEPH", "biocontext": "CEPH", "bioportal": "CEPH", "fairsharing": "FAIRsharing.p58bm4", "obofoundry": "ceph", "ols": "ceph", "ontobee": "CEPH" }, "name": "Cephalopod Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CEPH", "repository": "https://github.com/obophenotype/cephalopod-ontology", "uri_format": "http://purl.obolibrary.org/obo/CEPH_$1", "version": "2016-01-12" }, "cgd": { "description": "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.", "example": "CAL0003079", "homepage": "http://www.candidagenome.org/", "mappings": { "biocontext": "CGD", "fairsharing": "FAIRsharing.j7j53", "go": "CGD", "miriam": "cgd", "n2t": "cgd", "ncbi": "CGD", "prefixcommons": "cgd", "uniprot": "CGD" }, "name": "Candida Genome Database", "pattern": "^CAL\\d{7}$", "preferred_prefix": "cgd", "publications": [ { "doi": "10.1093/nar/gki003", "pmc": "PMC539957", "pubmed": "15608216", "title": "The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information.", "year": 2005 } ], "uri_format": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1" }, "cghdb": { "description": "Cell line databases/resources", "example": "300165/p13898_2106T", "homepage": "http://www.cghtmd.jp/CGHDatabase/index_e.jsp", "mappings": { "cellosaurus": "CGH-DB" }, "name": "CGH Data Base", "preferred_prefix": "cghdb", "uri_format": "http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en" }, "cgnc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)", "example": "10087", "homepage": "http://birdgenenames.org/cgnc/", "mappings": { "prefixcommons": "cgnc", "re3data": "r3d100012429" }, "name": "Chicken Gene Nomenclature Consortium", "pattern": "^\\d+$", "preferred_prefix": "cgnc", "publications": [ { "doi": "10.1186/1471-2164-10-s2-s5", "pmc": "PMC2966335", "pubmed": "19607656", "title": "The Chicken Gene Nomenclature Committee report.", "year": 2009 } ], "synonyms": [ "BirdBase", "CGNC" ], "uri_format": "http://birdgenenames.org/cgnc/GeneReport?id=$1" }, "cgsc": { "description": "The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature.", "example": "74", "homepage": "http://cgsc.biology.yale.edu/index.php", "mappings": { "biocontext": "CGSC", "fairsharing": "FAIRsharing.1tbrdz", "go": "CGSC", "miriam": "cgsc", "n2t": "cgsc", "prefixcommons": "cgsc" }, "name": "Coli Genetic Stock Center", "pattern": "^\\d+$", "preferred_prefix": "cgsc", "uri_format": "http://cgsc.biology.yale.edu/Site.php?ID=$1" }, "charprot": { "description": "CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. 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The data is abstracted and curated from the primary scientific literature.", "example": "CHEMBL465070", "homepage": "https://www.ebi.ac.uk/chembldb/", "mappings": { "biocontext": "CHEMBL.COMPOUND", "edam": "2646", "miriam": "chembl.compound", "n2t": "chembl.compound", "wikidata": "P592" }, "name": "ChEMBL", "part_of": "chembl", "pattern": "^CHEMBL\\d+$", "preferred_prefix": "chembl.compound", "providers": [ { "code": "CURATOR_REVIEW", "description": "ChEMBL compound RDF", "homepage": "https://github.com/egonw/chembl.rdf", "name": "ChEMBL compound RDF", "uri_format": "http://linkedchemistry.info/chembl/chemblid/$1" }, { "code": "CURATOR_REVIEW", "description": "ChEMBL compound RDF through EBI RDF Platform", "homepage": "https://www.ebi.ac.uk/rdf/services/chembl/", "name": "ChEMBL compound RDF through EBI RDF Platform", "uri_format": "https://rdf.ebi.ac.uk/resource/chembl/molecule/$1" } ], "uri_format": "https://www.ebi.ac.uk/chembl/compound/inspect/$1" }, "chembl.target": { "description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.", "example": "CHEMBL3467", "homepage": "https://www.ebi.ac.uk/chembldb/", "mappings": { "biocontext": "CHEMBL.TARGET", "cellosaurus": "ChEMBL-Targets", "miriam": "chembl.target", "n2t": "chembl.target" }, "name": "ChEMBL target", "part_of": "chembl", "pattern": "^CHEMBL\\d+$", "preferred_prefix": "chembl.target", "providers": [ { "code": "CURATOR_REVIEW", "description": "ChEMBL target RDF", "homepage": "https://github.com/egonw/chembl.rdf", "name": "ChEMBL target RDF", "uri_format": "http://linkedchemistry.info/chembl/chemblid/$1" }, { "code": "CURATOR_REVIEW", "description": "ChEMBL target RDF through EBI RDF Platform", "homepage": "https://rdf.ebi.ac.uk/resource/chembl/", "name": "ChEMBL target RDF through EBI RDF Platform", "uri_format": "https://rdf.ebi.ac.uk/resource/chembl/target/$1" } ], "synonyms": [ "ChEMBL-Targets" ], "uri_format": "https://www.ebi.ac.uk/chembl/target/inspect/$1" }, "chemdb": { "description": "ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds.", "example": "3966782", "homepage": "http://cdb.ics.uci.edu/", "mappings": { "biocontext": "CHEMDB", "fairsharing": "FAIRsharing.dstf7h", "miriam": "chemdb", "n2t": "chemdb", "prefixcommons": "chemdb" }, "name": "ChemDB", "pattern": "^\\d+$", "preferred_prefix": "chemdb", "publications": [ { "doi": "10.1093/bioinformatics/btm341", "pmc": null, "pubmed": "17599932", "title": "ChemDB update--full-text search and virtual chemical space.", "year": 2007 } ], "uri_format": "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1" }, "chemidplus": { "description": "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. 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This OWL ontology is an automated Translation of the source LinkML schema, https://w3id.org/chemrof", "download_owl": "http://aber-owl.net/media/ontologies/CHEMROF/2/chemrof.owl", "example": "FullySpecifiedAtom", "homepage": "https://chemkg.github.io/chemrof/", "mappings": { "aberowl": "CHEMROF", "bioportal": "CHEMROF" }, "name": "Chemical Entity Materials and Reactions Ontological Framework", "preferred_prefix": "ChEMROF", "uri_format": "https://chemkg.github.io/chemrof/$1" }, "chemspider": { "description": "ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources.", "example": "56586", "homepage": "http://www.chemspider.com/", "mappings": { "biocontext": "CHEMSPIDER", "cheminf": "000405", "edam": "1173", "fairsharing": "FAIRsharing.96f3gm", "miriam": "chemspider", "n2t": "chemspider", "prefixcommons": "chemspider", "re3data": "r3d100010205", "wikidata": "P661" }, "name": "ChemSpider", "pattern": "^\\d+$", "preferred_prefix": "chemspider", "synonyms": [ "ChemSpiderID", "Chemspider" ], "uri_format": "http://www.chemspider.com/Chemical-Structure.$1.html" }, "chickenqtldb": { "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs.", "example": "14362", "homepage": "https://www.animalgenome.org/QTLdb", "mappings": { "biocontext": "CHICKENQTLDB", "miriam": "chickenqtldb", "n2t": "chickenqtldb", "prefixcommons": "chickenqtldb" }, "name": "Animal Genome Chicken QTL", "part_of": "qtldb", "pattern": "^\\d+$", "preferred_prefix": "chickenqtldb", "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" }, "chiro": { "contact": { "email": "vasilevs@ohsu.edu", "github": "nicolevasilevsky", "name": "Nicole Vasilevsky", "orcid": "0000-0001-5208-3432" }, "depends_on": [ "chebi", "go", "hp", "mp", "ncbitaxon", "pr", "uberon" ], "description": "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.", "download_obo": "http://purl.obolibrary.org/obo/chiro.obo", "download_owl": "http://purl.obolibrary.org/obo/chiro.owl", "homepage": "https://github.com/obophenotype/chiro", "license": "CC0 1.0", "mappings": { "aberowl": "CHIRO", "bioportal": "CHIRO", "obofoundry": "chiro", "ols": "chiro", "ontobee": "CHIRO" }, "name": "ChEBI Integrated Role Ontology", "no_own_terms": true, "preferred_prefix": "CHIRO", "publications": [ { "doi": "10.26434/chemrxiv.12591221", "pmc": null, "pubmed": null, "title": "Extension of Roles in the ChEBI Ontology", "year": null } ], "repository": "https://github.com/obophenotype/chiro", "uri_format": "http://purl.obolibrary.org/obo/CHIRO_$1", "version": "2015-11-23" }, "chmo": { "appears_in": [ "rbo", "scdo" ], "contact": { "email": "batchelorc@rsc.org", "github": "batchelorc", "name": "Colin Batchelor", "orcid": "0000-0001-5985-7429" }, "description": "CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI).", "download_obo": "http://purl.obolibrary.org/obo/chmo.obo", "download_owl": "http://purl.obolibrary.org/obo/chmo.owl", "example": "0002902", "homepage": "https://github.com/rsc-ontologies/rsc-cmo", "license": "CC BY 4.0", "mappings": { "aberowl": "CHMO", "biocontext": "CHMO", "bioportal": "CHMO", "fairsharing": "FAIRsharing.9j4wh2", "obofoundry": "chmo", "ols": "chmo", "ontobee": "CHMO" }, "name": "Chemical Methods Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CHMO", "repository": "https://github.com/rsc-ontologies/rsc-cmo", "uri_format": "http://purl.obolibrary.org/obo/CHMO_$1", "version": "2022-04-19" }, "cido": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "description": "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.", "download_owl": "https://github.com/CIDO-ontology/cido/raw/master/cido.owl", "example": "0000005", "homepage": "https://github.com/cido-ontology/cido", "license": "CC BY 4.0", "mappings": { "aberowl": "CIDO", "bioportal": "CIDO", "fairsharing": "FAIRsharing.aVmpKl", "obofoundry": "cido", "ols": "cido", "ontobee": "CIDO" }, "name": "Coronavirus Infectious Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CIDO", "publications": [ { "doi": "10.1038/s41597-020-0523-6", "pmc": "PMC7293349", "pubmed": "32533075", "title": "CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis.", "year": 2020 } ], "repository": "https://github.com/cido-ontology/cido", "uri_format": "http://purl.obolibrary.org/obo/CIDO_$1", "version": "1.0.326" }, "cio": { "contact": { "email": "frederic.bastian@unil.ch", "github": "fbastian", "name": "Frédéric Bastian", "orcid": "0000-0002-9415-5104" }, "description": "An ontology to capture confidence information about annotations.", "download_obo": "http://purl.obolibrary.org/obo/cio.obo", "download_owl": "http://purl.obolibrary.org/obo/cio.owl", "example": "0000040", "homepage": "https://github.com/BgeeDB/confidence-information-ontology", "license": "CC0 1.0", "mappings": { "aberowl": "CIO", "biocontext": "CIO", "bioportal": "CIO", "fairsharing": "FAIRsharing.e3t0yw", "obofoundry": "cio", "ols": "cio", "ontobee": "CIO" }, "name": "Confidence Information Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CIO", "publications": [ { "doi": "10.1093/database/bav043", "pmc": "PMC4425939", "pubmed": "25957950", "title": "The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.", "year": 2015 } ], "repository": "https://github.com/BgeeDB/confidence-information-ontology", "uri_format": "http://purl.obolibrary.org/obo/CIO_$1", "version": "2015-03-10" }, "citexplore": { "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/", "mappings": { "fairsharing": "FAIRsharing.619eqr", "prefixcommons": "citexplore" }, "name": "CiteXplore", "preferred_prefix": "citexplore", "publications": [ { "doi": "10.1097/mol.0b013e328362df13", "pmc": null, "pubmed": "23759795", "title": "Cerebrotendinous xanthomatosis.", "year": 2013 } ], "references": [ "https://www.embl.de/aboutus/communication_outreach/media_relations/2006/061127_hinxton/" ], "synonyms": [ "CTX" ], "uri_format": "https://europepmc.org/article/CTX/$1" }, "cito": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology that enables characterization of the nature or type of citations, both factually and rhetorically.", "example": "sharesAuthorInstitutionWith", "homepage": "http://www.sparontologies.net/ontologies/cito", "mappings": { "fairsharing": "FAIRsharing.b220d4" }, "name": "Citation Typing Ontology", "preferred_prefix": "CiTO", "publications": [ { "doi": "10.1016/j.websem.2012.08.001", "pmc": null, "pubmed": null, "title": "FaBiO and CiTO: Ontologies for describing bibliographic resources and citations", "year": null } ], "repository": "https://github.com/sparontologies/cito", "uri_format": "http://purl.org/spar/cito/$1" }, "civic.aid": { "description": "A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC.", "example": "3", "homepage": "https://civicdb.org/", "mappings": { "miriam": "civic.aid" }, "name": "CIViC Assertion", "pattern": "^[0-9]+$", "preferred_prefix": "civic.aid", "uri_format": "https://civicdb.org/links/assertions/$1" }, "civic.did": { "description": "Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement.", "example": "46", "homepage": "https://civicdb.org/", "mappings": { "miriam": "civic.did" }, "name": "CIViC Disease", "pattern": "^[0-9]+$", "preferred_prefix": "civic.did", "uri_format": "https://civicdb.org/links/diseases/$1" }, "civic.eid": { "description": "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract).", "example": "1199", "homepage": "https://civicdb.org/", "mappings": { "miriam": "civic.eid" }, "name": "CIViC Evidence", "pattern": "^[0-9]+$", "preferred_prefix": "civic.eid", "uri_format": "https://civicdb.org/links/evidence/$1" }, "civic.gid": { "description": "A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus on emphasizing the clinical relevance from a molecular perspective rather than describing the biological function of the gene unless necessary to contextualize its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes, specific treatments for the gene’s associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis", "example": "272", "homepage": "https://civicdb.org/", "mappings": { "miriam": "civic.gid" }, "name": "CIViC Gene", "pattern": "^[0-9]+$", "preferred_prefix": "civic.gid", "uri_format": "https://civicdb.org/links/gene/$1" }, "civic.sid": { "description": "In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source.", "example": "62", "homepage": "https://civicdb.org/", "mappings": { "miriam": "civic.sid" }, "name": "CIViC Source", "pattern": "^[0-9]+$", "preferred_prefix": "civic.sid", "uri_format": "https://civicdb.org/links/sources/$1" }, "civic.tid": { "description": "Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant.", "example": "14", "homepage": "https://civicdb.org/", "mappings": { "miriam": "civic.tid" }, "name": "CIViC Therapy", "pattern": "^[0-9]+$", "preferred_prefix": "civic.tid", "uri_format": "https://civicdb.org/links/drugs/$1" }, "civic.vid": { "description": "CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making.", "example": "12", "homepage": "https://civicdb.org/", "mappings": { "miriam": "civic.vid" }, "name": "CIViC Variant", "pattern": "^[0-9]+$", "preferred_prefix": "civic.vid", "uri_format": "https://civicdb.org/links/variant/$1" }, "cl": { "appears_in": [ "clo", "ecao", "ehdaa2", "go", "mco", "pcl", "uberon", "xpo" ], "banana": "CL", "contact": { "email": "addiehl@buffalo.edu", "github": "addiehl", "name": "Alexander Diehl", "orcid": "0000-0001-9990-8331" }, "depends_on": [ "chebi", "go", "ncbitaxon", "pato", "pr", "ro", "uberon" ], "description": "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.", "download_obo": "https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-full.obo", "download_owl": "http://purl.obolibrary.org/obo/cl.owl", "example": "0000062", "homepage": "https://obophenotype.github.io/cell-ontology/", "license": "CC BY 4.0", "mappings": { "aberowl": "CL", "agroportal": "CL", "biocontext": "CL", "bioportal": "CL", "cellosaurus": "CL", "fairsharing": "FAIRsharing.j9y503", "go": "CL", "miriam": "cl", "n2t": "cl", "obofoundry": "cl", "ols": "cl", "ontobee": "CL", "prefixcommons": "cl", "wikidata": "P7963" }, "name": "Cell Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "CL", "publications": [ { "doi": "10.1186/s13326-016-0088-7", "pmc": "PMC4932724", "pubmed": "27377652", "title": "The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.", "year": 2016 }, { "doi": "10.1186/1471-2105-12-6", "pmc": "PMC3024222", "pubmed": "21208450", "title": "Logical development of the cell ontology.", "year": 2011 } ], "repository": "https://github.com/obophenotype/cell-ontology", "uri_format": "https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:$1", "version": "2022-08-16" }, "clao": { "contact": { "email": "lagonzalezmo@unal.edu.co", "github": "luis-gonzalez-m", "name": "Luis González-Montaña", "orcid": "0000-0002-9136-9932" }, "depends_on": [ "ro" ], "description": "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).", "download_obo": "http://purl.obolibrary.org/obo/clao.obo", "download_owl": "http://purl.obolibrary.org/obo/clao.owl", "example": "0000088", "homepage": "https://github.com/luis-gonzalez-m/Collembola", "license": "CC0 1.0", "mappings": { "aberowl": "CLAO", "bioportal": "CLAO", "obofoundry": "clao", "ols": "clao", "ontobee": "CLAO" }, "name": "Collembola Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CLAO", "repository": "https://github.com/luis-gonzalez-m/Collembola", "uri_format": "http://purl.obolibrary.org/obo/CLAO_$1", "version": "2021-09-27" }, "classyfire": { "banana": "C", "comment": "There's a mismatch between the MIRIAM URI format string, which has a C prefix in front of class identifiers and the ontology which does not use them.", "description": "ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API.", "download_obo": "http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip", "example": "0004828", "homepage": "http://classyfire.wishartlab.com/", "mappings": { "miriam": "classyfire" }, "name": "ClassyFire", "pattern": "^\\d{7}$", "preferred_prefix": "classyfire", "synonyms": [ "CHEMONTID" ], "uri_format": "http://classyfire.wishartlab.com/tax_nodes/C$1" }, "cldb": { "description": "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories.", "example": "cl3603", "homepage": "http://bioinformatics.hsanmartino.it/hypercldb/indexes.html", "mappings": { "biocontext": "CLDB", "cellosaurus": "CLDB", "miriam": "cldb", "n2t": "cldb" }, "name": "Cell Line Database", "pattern": "^(cl|tum)\\d+$", "preferred_prefix": "cldb", "uri_format": "http://bioinformatics.hsanmartino.it/hypercldb/$1.html" }, "clingene": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The allele registry provides and maintains identifiers for genetic variants", "example": "CA981206459", "homepage": "https://reg.clinicalgenome.org", "mappings": { "biolink": "CAID" }, "name": "ClinGen Allele Registry", "preferred_prefix": "clingene", "uri_format": "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1" }, "clinicaltrials": { "description": "ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries", "example": "NCT00222573", "homepage": "https://clinicaltrials.gov/", "mappings": { "biocontext": "CLINICALTRIALS", "miriam": "clinicaltrials", "n2t": "clinicaltrials", "prefixcommons": "clinicaltrials" }, "name": "ClinicalTrials.gov", "pattern": "^NCT\\d{8}$", "preferred_prefix": "clinicaltrials", "providers": [ { "code": "smartpatients", "description": "Smart Patients is an online community for patients and their families. Join us to talk with other patients about the latest research for your condition.", "homepage": "https://www.smartpatients.com", "name": "Smart Patients", "uri_format": "https://www.smartpatients.com/trials/$1" } ], "uri_format": "https://clinicaltrials.gov/ct2/show/$1" }, "clinvar": { "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier.", "example": "12345", "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", "mappings": { "biocontext": "ClinVar", "biolink": "CLINVAR", "cellosaurus": "ClinVar", "fairsharing": "FAIRsharing.wx5r6f", "hl7": "clinVar-V", "miriam": "clinvar", "n2t": "clinvar", "re3data": "r3d100013331", "wikidata": "P1929" }, "name": "ClinVar Variation", "pattern": "^\\d+$", "preferred_prefix": "clinvar", "uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1" }, "clinvar.record": { "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession.", "example": "RCV000033555.3", "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", "mappings": { "biocontext": "CLINVAR.RECORD", "miriam": "clinvar.record", "n2t": "clinvar.record" }, "name": "ClinVar Record", "part_of": "clinvar", "pattern": "^RCV\\d+(\\.\\d+)?$", "preferred_prefix": "clinvar.record", "uri_format": "http://www.ncbi.nlm.nih.gov/clinvar/$1" }, "clinvar.submission": { "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession.", "example": "SCV000151292", "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", "mappings": { "biocontext": "CLINVAR.SUBMISSION", "miriam": "clinvar.submission", "n2t": "clinvar.submission" }, "name": "ClinVar Submission", "pattern": "^SCV\\d+(\\.\\d+)?$", "preferred_prefix": "clinvar.submission", "uri_format": "http://www.ncbi.nlm.nih.gov/clinvar?term=$1" }, "clinvar.submitter": { "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs).", "example": "26957", "homepage": "https://www.ncbi.nlm.nih.gov/clinvar/", "mappings": { "miriam": "clinvar.submitter" }, "name": "ClinVar Submitter", "pattern": "^\\d+$", "preferred_prefix": "clinvar.submitter", "uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1" }, "clo": { "appears_in": [ "mco" ], "contact": { "email": "siiraa@umich.edu", "github": "siiraa", "name": "Sirarat Sarntivijai", "orcid": "0000-0002-2548-641X" }, "depends_on": [ "cl", "doid", "ncbitaxon", "uberon" ], "description": "The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.", "download_owl": "http://purl.obolibrary.org/obo/clo.owl", "example": "0000091", "homepage": "http://www.clo-ontology.org", "license": "CC BY 3.0", "mappings": { "aberowl": "CLO", "biocontext": "CLO", "bioportal": "CLO", "cellosaurus": "CLO", "fairsharing": "FAIRsharing.4dvtcz", "obofoundry": "clo", "ols": "clo", "ontobee": "CLO", "prefixcommons": "clo", "wikidata": "P2158" }, "name": "Cell Line Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CLO", "publications": [ { "doi": "10.1186/2041-1480-5-37", "pmc": "PMC4387853", "pubmed": "25852852", "title": "CLO: The cell line ontology.", "year": 2014 }, { "doi": "10.1186/gb-2005-6-2-r21", "pmc": "PMC551541", "pubmed": "15693950", "title": "An ontology for cell types.", "year": 2005 } ], "repository": "https://github.com/CLO-Ontology/CLO", "synonyms": [ "CLO" ], "uri_format": "http://purl.obolibrary.org/obo/CLO_$1", "version": "2.1.178" }, "cls": { "description": "Cell line collections", "example": "300108/p3934_A-172", "homepage": "https://cls.shop/", "mappings": { "cellosaurus": "CLS" }, "name": "Cell Lines Service", "preferred_prefix": "cls", "uri_format": "https://cls.shop/$1" }, "clyh": { "contact": { "email": "lucas.leclere@obs-vlfr.fr", "github": "L-Leclere", "name": "Lucas Leclere", "orcid": "0000-0002-7440-0467" }, "depends_on": [ "iao", "ro", "uberon" ], "description": "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica.", "download_obo": "http://purl.obolibrary.org/obo/clyh.obo", "download_owl": "http://purl.obolibrary.org/obo/clyh.owl", "example": "1000100", "homepage": "https://github.com/EBISPOT/clyh_ontology", "license": "CC BY 3.0", "mappings": { "aberowl": "CLYH", "bioportal": "CLYH", "obofoundry": "clyh", "ols": "clyh", "ontobee": "CLYH" }, "name": "Clytia hemisphaerica Development and Anatomy Ontology", "pattern": "^\\d+$", "preferred_prefix": "CLYH", "repository": "https://github.com/EBISPOT/clyh_ontology", "uri_format": "http://purl.obolibrary.org/obo/CLYH_$1", "version": "2020-05-29" }, "cmecs": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard.", "example": "595", "homepage": "https://cmecscatalog.org/cmecs", "name": "Costal and Marine Ecological Classification Standard", "pattern": "^\\d+$", "preferred_prefix": "cmecs", "references": [ "http://www.natureserve.org/sites/default/files/publications/files/cmecs_version_06-2012_final.pdf" ], "uri_format": "https://cmecscatalog.org/cmecs/classification/unit/$1.html" }, "cmf": { "contact": { "email": "engelsta@ohsu.edu", "github": null, "name": "Mark Engelstad", "orcid": "0000-0001-5889-4463" }, "deprecated": true, "description": "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain", "homepage": "https://code.google.com/p/craniomaxillofacial-ontology/", "mappings": { "aberowl": "CMF", "biocontext": "CMF", "obofoundry": "cmf", "ontobee": "CMF" }, "name": "CranioMaxilloFacial ontology", "preferred_prefix": "CMF", "uri_format": "http://purl.obolibrary.org/obo/CMF_$1" }, "cmo": { "appears_in": [ "scdo" ], "contact": { "email": "jrsmith@mcw.edu", "github": "jrsjrs", "name": "Jennifer Smith", "orcid": "0000-0002-6443-9376" }, "description": "Morphological and physiological measurement records generated from clinical and model organism research and health programs.", "download_obo": "http://purl.obolibrary.org/obo/cmo.obo", "download_owl": "http://purl.obolibrary.org/obo/cmo.owl", "example": "0001350", "homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html", "license": "CC0 1.0", "mappings": { "aberowl": "CMO", "biocontext": "CMO", "bioportal": "CMO", "fairsharing": "FAIRsharing.dq78pn", "obofoundry": "cmo", "ols": "cmo", "ontobee": "CMO" }, "name": "Clinical measurement ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CMO", "publications": [ { "doi": "10.1186/2041-1480-4-26", "pmc": "PMC3882879", "pubmed": "24103152", "title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.", "year": 2013 }, { "doi": "10.3389/fgene.2012.00087", "pmc": "PMC3361058", "pubmed": "22654893", "title": "Three ontologies to define phenotype measurement data.", "year": 2012 } ], "repository": "https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology", "twitter": "ratgenome", "uri_format": "http://purl.obolibrary.org/obo/CMO_$1", "version": "2019-02-19" }, "cmpo": { "contact": { "email": "jupp@ebi.ac.uk", "github": null, "name": "Simon Jupp", "orcid": null }, "description": "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations.", "download_owl": "http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl", "example": "0000435", "homepage": "http://www.ebi.ac.uk/cmpo", "mappings": { "aberowl": "CMPO", "bioportal": "CMPO", "fairsharing": "FAIRsharing.knp11s", "ols": "cmpo" }, "name": "Cellular Microscopy Phenotype Ontology", "pattern": "^\\d{7}$", "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_$1", "version": "2017-12-19" }, "co_320": { "description": "Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables", "download_owl": "https://cropontology.org/ontology/CO_320/Rice/owl", "example": "0000618", "homepage": "https://cropontology.org/ontology/CO_320/Rice", "mappings": { "agroportal": "CO_320", "cropoct": "CO_320", "fairsharing": "FAIRsharing.2jkxp5", "ols": "co_320" }, "name": "Rice ontology", "pattern": "^\\d{7}$", "preferred_prefix": "co_320", "uri_format": "https://www.cropontology.org/rdf/CO_320:$1", "version": "2019-10-09" }, "co_321": { "description": "July 2018", "download_owl": "https://cropontology.org/ontology/CO_321/Wheat/owl", "example": "0000449", "homepage": "https://cropontology.org/ontology/CO_321/Wheat", "mappings": { "agroportal": "CO_321", "cropoct": "CO_321", "fairsharing": "FAIRsharing.czzmpg", "ols": "co_321" }, "name": "Wheat ontology", "pattern": "^\\d{7}$", "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 } ], "uri_format": "https://www.cropontology.org/rdf/CO_321:$1", "version": "2019-10-09" }, "co_322": { "description": "Maize Trait Dictionary in template 5 - 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Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France).", "download_owl": "https://cropontology.org/ontology/CO_348/Brassica/owl", "example": "1100107", "homepage": "https://cropontology.org/ontology/CO_348/Brassica", "mappings": { "agroportal": "CO_348", "cropoct": "CO_348", "fairsharing": "FAIRsharing.af7a2d", "ols": "co_348" }, "name": "Brassica ontology", "pattern": "^\\d+$", "preferred_prefix": "co_348", "uri_format": "https://www.cropontology.org/rdf/CO_348:$1", "version": "2019-11-29" }, "co_350": { "description": "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo", "download_owl": "https://cropontology.org/ontology/CO_350/Oat/owl", "example": "0000215", "homepage": "https://cropontology.org/ontology/CO_350/Oat", "mappings": { "agroportal": "CO_350", "cropoct": "CO_350", "fairsharing": "FAIRsharing.35e1c3", "ols": "co_350" }, "name": "Oat ontology", "pattern": "^\\d{7}$", "preferred_prefix": "co_350", "uri_format": "https://www.cropontology.org/rdf/CO_350:$1", "version": "2019-10-09" }, "co_356": { "description": "Grape Ontology including OIV and bioversity descriptors. INRA July 2017", "download_owl": "https://cropontology.org/ontology/CO_356/Vitis/owl", "example": "4000027", "homepage": "https://cropontology.org/ontology/CO_356/Vitis", "mappings": { "agroportal": "CO_356", "cropoct": "CO_356", "fairsharing": "FAIRsharing.c7f4d7", "ols": "co_356" }, "name": "Vitis ontology", "pattern": "^\\d+$", "preferred_prefix": "co_356", "uri_format": "https://www.cropontology.org/rdf/CO_356:$1", "version": "2019-11-29" }, "co_357": { "description": "This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE.", "download_owl": "http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology/owl", "example": "1000290", "homepage": "http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology", "mappings": { "agroportal": "CO_357", "cropoct": "CO_357", "fairsharing": "FAIRsharing.2b04ae", "ols": "co_357" }, "name": "Woody Plant Ontology ontology", "pattern": "^\\d+$", "preferred_prefix": "co_357", "uri_format": "https://www.cropontology.org/rdf/CO_357:$1" }, "co_358": { "description": "Cotton ontology from CottonGen database - June 2019", "download_owl": "https://cropontology.org/ontology/CO_358/Cotton/owl", "example": "0000139", "homepage": "https://cropontology.org/ontology/CO_358/Cotton", "mappings": { "agroportal": "CO_358", "cropoct": "CO_358", "ols": "co_358" }, "name": "Cotton ontology", "pattern": "^\\d{7}$", "preferred_prefix": "co_358", "uri_format": "https://www.cropontology.org/rdf/CO_358:$1", "version": "2020-01-03" }, "co_359": { "description": "December 2019", "download_owl": "https://cropontology.org/ontology/CO_359/Sunflower/owl", "example": "0000947", "homepage": "https://cropontology.org/ontology/CO_359/Sunflower", "mappings": { "agroportal": "CO_359", "cropoct": "CO_359", "ols": "co_359" }, "name": "Sunflower ontology", "pattern": "^\\d{7}$", "preferred_prefix": "co_359", "uri_format": "https://www.cropontology.org/rdf/CO_359:$1" }, "co_360": { "description": "Sugar Kelp trait ontology", "download_owl": "http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait/owl", "example": "0000071", "homepage": "http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait", "mappings": { "agroportal": "CO_360", "cropoct": "CO_360", "fairsharing": "FAIRsharing.1c1738", "ols": "co_360" }, "name": "Sugar Kelp trait ontology", "pattern": "^\\d{7}$", "preferred_prefix": "co_360", "uri_format": "https://www.cropontology.org/rdf/CO_360:$1" }, "co_365": { "description": "developed by ICARDA - Dec 2018", "download_owl": "https://cropontology.org/ontology/CO_365/Fababean/owl", "example": "0000205", "homepage": "https://cropontology.org/ontology/CO_365/Fababean", "mappings": { "agroportal": "CO_365", "cropoct": "CO_365", "ols": "co_365" }, "name": "Fababean ontology", "pattern": "^\\d{7}$", "preferred_prefix": "co_365", "uri_format": "https://www.cropontology.org/rdf/CO_365:$1", "version": "2019-10-15" }, "co_366": { "description": "version Dec 2019", "download_owl": "http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut/owl", "example": "0000072", "homepage": "http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut", "mappings": { "agroportal": "CO_366", "cropoct": "CO_366", "ols": "co_366" }, "name": "Bambara groundnut ontology", "pattern": "^\\d{7}$", "preferred_prefix": "co_366", "uri_format": "https://www.cropontology.org/rdf/CO_366:$1" }, "co_367": { "description": "Curator name: Clara S. Stanschewski; Curator Affiliation: King Abdullah University of Science and Technology; Contributing Scientists or Crop expert group: The Salt Lab and the Quinoa Phenotyping Consortium Creation Date: 23.05.2021", "example": "0000004", "homepage": "https://cropontology.org/term/CO_367:ROOT", "mappings": { "cropoct": "CO_367" }, "name": "Quinoa Ontology ontology", "pattern": "^\\d{7}$", "preferred_prefix": "co_367" }, "co_370": { "description": "Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales.", "example": "0000890", "homepage": "https://cropontology.org/term/CO_370:ROOT", "mappings": { "cropoct": "CO_370" }, "name": "Apple ontology", "pattern": "^\\d{7}$", "preferred_prefix": "co_370" }, "cob": { "contact": { "email": "bpeters@lji.org", "github": "bpeters42", "name": "Bjoern Peters", "orcid": "0000-0002-8457-6693" }, "description": "COB brings together key terms from a wide range of OBO projects to improve interoperability.", "download_owl": "http://purl.obolibrary.org/obo/cob.owl", "example": "0000080", "homepage": "https://obofoundry.org/COB/", "license": "CC0 1.0", "mappings": { "aberowl": "COB", "bioportal": "COB", "obofoundry": "cob", "ols": "cob", "ontobee": "COB" }, "name": "Core Ontology for Biology and Biomedicine", "pattern": "^\\d{7}$", "preferred_prefix": "COB", "repository": "https://github.com/OBOFoundry/COB", "uri_format": "http://purl.obolibrary.org/obo/COB_$1", "version": "2022-05-02" }, "coconut": { "comment": "@mSorok is the dev of the resource, hope I got it right!", "contributor": { "email": "adriano.rutz@ik.me", "github": "adafede", "name": "Adriano Rutz", "orcid": "0000-0003-0443-9902" }, "description": "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a \"flat\" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties.", "example": "CNP0171505", "github_request_issue": 221, "homepage": "https://coconut.naturalproducts.net", "name": "COlleCtion of Open Natural ProdUcTs", "pattern": "^CNP\\d{7}$", "preferred_prefix": "coconut", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://coconut.naturalproducts.net/compound/coconut_id/$1" }, "codelink": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release).", "example": "GE86325", "homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt", "name": "GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray", "pattern": "^GE\\d+$", "preferred_prefix": "codelink", "references": [ "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-8060/A-GEOD-8060.adf.txt", "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt" ] }, "cog": { "contact": { "email": "cogs@ncbi.nlm.nih.gov", "github": null, "name": "Michael Y Galperin", "orcid": "0000-0002-2265-5572" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems.", "example": "COG0001", "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/", "mappings": { "biolink": "COG", "fairsharing": "FAIRsharing.djsbw2", "go": "COG_Cluster", "prefixcommons": "cog" }, "name": "Cluster of orthologous genes", "pattern": "^COG\\d+$", "preferred_prefix": "cog", "synonyms": [ "COG_Cluster" ], "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1" }, "cog.category": { "contact": { "email": "cogs@ncbi.nlm.nih.gov", "github": null, "name": "Michael Y Galperin", "orcid": "0000-0002-2265-5572" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Higher-level classifications of COG Pathways", "example": "K", "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/", "name": "COG Categories", "part_of": "cog", "preferred_prefix": "cog.category", "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1" }, "cog.pathway": { "contact": { "email": "cogs@ncbi.nlm.nih.gov", "github": null, "name": "Michael Y Galperin", "orcid": "0000-0002-2265-5572" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera.", "example": "NAD%20biosynthesis", "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/pathways", "mappings": { "go": "COG_Pathway" }, "name": "COG Pathways", "part_of": "cog", "preferred_prefix": "cog.pathway", "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1" }, "cohd": { "comment": "not really sure where the source is. this also links to a system called athena. I was not able to figure out what COHD stands for.", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012", "homepage": "https://github.com/MIT-LCP/mimic-omop", "name": "MIMIC III Database", "no_own_terms": true, "preferred_prefix": "cohd", "repository": "https://github.com/MIT-LCP/mimic-omop" }, "col.taiwan": { "contributor": { "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" }, "description": "Identifier (name code) for a taxon in the catalogue of life in taiwan", "example": "431472", "github_request_issue": 466, "homepage": "http://taibnet.sinica.edu.tw/home.php", "mappings": { "wikidata": "P3088" }, "name": "Catalogue of Life in Taiwan", "pattern": "^[1-9]\\d{5}$", "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=$1" }, "colao": { "contact": { "email": "entiminae@gmail.com", "github": "JCGiron", "name": "Jennifer C. Giron", "orcid": "0000-0002-0851-6883" }, "depends_on": [ "aism", "bfo", "bspo", "caro", "pato", "ro", "uberon" ], "description": "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research.", "download_obo": "http://purl.obolibrary.org/obo/colao.obo", "download_owl": "http://purl.obolibrary.org/obo/colao.owl", "example": "0000000", "homepage": "https://github.com/insect-morphology/colao", "license": "CC BY 4.0", "mappings": { "aberowl": "COLAO", "bioportal": "COLAO", "obofoundry": "colao", "ols": "colao", "ontobee": "COLAO" }, "name": "Coleoptera Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "COLAO", "repository": "https://github.com/insect-morphology/colao", "uri_format": "http://purl.obolibrary.org/obo/COLAO_$1", "version": "2022-06-18" }, "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=$1" }, "combine.specifications": { "description": "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network.", "example": "sbgn.er.level-1.version-1.2", "homepage": "https://co.mbine.org/standards/", "mappings": { "biocontext": "COMBINE.SPECIFICATIONS", "miriam": "combine.specifications", "n2t": "combine.specifications" }, "name": "COMBINE specifications", "pattern": "^\\w+(\\-|\\.|\\w)*$", "preferred_prefix": "combine.specifications", "uri_format": "https://co.mbine.org/specifications/$1" }, "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", "mappings": { "prefixcommons": "come" }, "name": "The Bioinorganic Motif Database", "preferred_prefix": "come", "uri_format": "https://www.flymine.org/come/entry?gn=$1" }, "commoncoreontology": { "contact": { "email": "mpjensen@buffalo.edu", "github": "mark-jensen", "name": "Mark Jensen", "orcid": "0000-0001-9228-8838" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Common Core Ontologies (CCO) comprise twelve ontologies that are designed to represent and integrate taxonomies of generic classes and relations across all domains of interest.\n\nCCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained by the BFO framework, from which it inherits much of its basic semantic relationships.", "example": "DirectiveInformationContentEntity", "homepage": "http://www.ontologyrepository.com", "license": "CC BY 4.0", "name": "Common Core Ontologies", "preferred_prefix": "commoncoreontology", "repository": "https://github.com/CommonCoreOntology/CommonCoreOntologies", "uri_format": "http://www.ontologyrepository.com/CommonCoreOntologies/$1" }, "complexportal": { "description": "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases.", "example": "CPX-263", "homepage": "https://www.ebi.ac.uk/complexportal", "mappings": { "biocontext": "COMPLEXPORTAL", "go": "ComplexPortal", "miriam": "complexportal", "n2t": "complexportal", "re3data": "r3d100013295", "uniprot": "ComplexPortal", "wikidata": "P7718" }, "name": "Complex Portal", "pattern": "^CPX-[0-9]+$", "preferred_prefix": "complexportal", "synonyms": [ "ComplexPortal" ], "uri_format": "https://www.ebi.ac.uk/complexportal/complex/$1" }, "comptox": { "description": "The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks.", "example": "DTXSID2021028", "homepage": "https://comptox.epa.gov/dashboard", "mappings": { "biocontext": "COMPTOX", "miriam": "comptox", "n2t": "comptox", "wikidata": "P3117" }, "name": "CompTox Chemistry Dashboard", "pattern": "^DTXSID\\d+$", "preferred_prefix": "comptox", "uri_format": "https://comptox.epa.gov/dashboard/$1" }, "compulyeast": { "description": "Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record.", "example": "O08709", "homepage": "http://compluyeast2dpage.dacya.ucm.es/", "mappings": { "biocontext": "COMPULYEAST", "fairsharing": "FAIRsharing.rbjs3e", "miriam": "compulyeast", "n2t": "compulyeast" }, "name": "Compluyeast-2D-DB", "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$", "preferred_prefix": "compulyeast", "provides": "uniprot", "uri_format": "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1" }, "confident.event": { "contact": { "email": "Philip.Stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating.", "example": "37af84f2-bfd7-4653-b608-eaff44febba6", "github_request_issue": 519, "homepage": "https://www.confident-conference.org/index.php/Category:Event", "name": "ConfIDent Event", "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$", "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", "name": "ConfIDent Event Series", "preferred_prefix": "confident.series", "uri_format": "https://www.confident-conference.org/index.php/Event_Series:$1" }, "conoserver": { "description": "ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails.", "example": "2639", "homepage": "http://www.conoserver.org/", "mappings": { "biocontext": "CONOSERVER", "fairsharing": "FAIRsharing.y00hz4", "miriam": "conoserver", "n2t": "conoserver", "uniprot": "ConoServer" }, "name": "ConoServer", "pattern": "^\\d+$", "preferred_prefix": "conoserver", "uri_format": "http://www.conoserver.org/?page=card&table=protein&id=$1" }, "conso": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases.", "example": "CONSO00010", "homepage": "https://pharmacome.github.io/conso/", "name": "Curation of Neurodegeneration Supporting Ontology", "pattern": "^CONSO\\d{5}$", "preferred_prefix": "conso", "uri_format": "https://pharmacome.github.io/conso/$1" }, "cordis.article": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).", "example": "436605", "homepage": "https://cordis.europa.eu/", "name": "CORDIS Article", "pattern": "^\\d+$", "preferred_prefix": "cordis.article", "uri_format": "https://cordis.europa.eu/article/id/$1" }, "cordis.project": { "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).", "example": "817732", "github_request_issue": 450, "homepage": "https://cordis.europa.eu/", "name": "CORDIS Project", "pattern": "^\\d+$", "preferred_prefix": "cordis.project", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://cordis.europa.eu/project/id/$1" }, "coriell": { "description": "The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world.", "example": "GM17027", "homepage": "http://ccr.coriell.org/", "mappings": { "biocontext": "Coriell", "cellosaurus": "Coriell", "go": "CORIELL", "miriam": "coriell", "n2t": "coriell" }, "name": "Coriell Institute for Medical Research", "pattern": "^[A-Z]{2}\\d+$", "preferred_prefix": "coriell", "uri_format": "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1" }, "corrdb": { "description": "A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies.", "example": "37232", "homepage": "https://www.animalgenome.org", "mappings": { "fairsharing": "FAIRsharing.IziuCK", "miriam": "corrdb", "re3data": "r3d100011496" }, "name": "CorrDB", "pattern": "^[0-9]+$", "preferred_prefix": "corrdb", "uri_format": "https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1" }, "corum": { "description": "The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded.", "example": "100", "homepage": "https://mips.helmholtz-muenchen.de/genre/proj/corum/", "mappings": { "biocontext": "CORUM", "fairsharing": "FAIRsharing.ohbpNw", "go": "CORUM", "miriam": "corum", "n2t": "corum", "prefixcommons": "corum", "uniprot": "CORUM" }, "name": "Comprehensive Resource of Mammalian protein complexes", "pattern": "^\\d+$", "preferred_prefix": "corum", "uri_format": "https://mips.helmholtz-muenchen.de/corum/?id=$1" }, "cosmic": { "description": "COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes.", "example": "BRAF", "homepage": "http://cancer.sanger.ac.uk/cosmic/", "mappings": { "biocontext": "COSMIC", "cellosaurus": "Cosmic", "edam": "3264", "fairsharing": "FAIRsharing.s5zmbp", "miriam": "cosmic", "n2t": "cosmic" }, "name": "COSMIC Gene", "pattern": "^[A-Z0-9]+$", "preferred_prefix": "cosmic", "uri_format": "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1" }, "cosmic.cell": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer", "example": "906801", "homepage": "https://cancer.sanger.ac.uk/cell_lines/", "mappings": { "cellosaurus": "Cosmic-CLP" }, "name": "COSMIC Cell Lines", "pattern": "^\\d+$", "preferred_prefix": "cosmic.cell", "uri_format": "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1" }, "covid19": { "contact": { "email": "dylan.mcgagh@magd.ox.ac.uk", "github": null, "name": "Dylan McGagh", "orcid": null }, "description": "Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease.", "download_owl": "http://aber-owl.net/media/ontologies/COVID19/3/covid19.owl", "example": "SFB_COVID19_MW286762", "homepage": "https://covid19.sfb.uit.no", "mappings": { "aberowl": "COVID19", "bioportal": "COVID19", "miriam": "covid19" }, "name": "COVID-19 Surveillance Ontology", "pattern": "^\\w+_COVID19_[-\\w]+$", "preferred_prefix": "covid19", "uri_format": "https://covid19.sfb.uit.no/api/records/$1" }, "covoc": { "contact": { "email": "zmp@ebi.ac.uk", "github": "zoependlington", "name": "Zoë May Pendlington", "orcid": "0000-0002-4071-8397" }, "description": "The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.", "download_owl": "http://purl.obolibrary.org/obo/covoc/releases/2020-08-28/covoc.owl", "example": "0010034", "homepage": "https://github.com/EBISPOT/covoc", "mappings": { "ols": "covoc" }, "name": "CoVoc Coronavirus Vocabulary", "pattern": "^\\d{7}$", "preferred_prefix": "covoc", "repository": "https://github.com/EBISPOT/covoc", "uri_format": "http://purl.obolibrary.org/obo/COVOC_$1", "version": "2020-08-28" }, "cp": { "appears_in": [ "cl" ], "comment": "Part of cell ontology but deprecated, see https://github.com/obophenotype/cell-ontology/issues/572", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "name": "Cellular Phenotypes", "preferred_prefix": "cp" }, "cpc": { "description": "The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013.", "example": "A01M1/026", "homepage": "https://worldwide.espacenet.com/classification", "mappings": { "biocontext": "CPC", "fairsharing": "FAIRsharing.e08886", "miriam": "cpc", "n2t": "cpc" }, "name": "Cooperative Patent Classification", "pattern": "^([A-H,Y]|[A-H, Y]\\d{2}|[A-H, Y]\\d{2}[A-Z]|[A-H, Y]\\d{2}[A-Z]\\d{1,3}|[A-H, Y]\\d{2}[A-Z]\\d{1,3}(\\/)?\\d{2,})$", "preferred_prefix": "cpc", "uri_format": "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1" }, "cpga": { "contact": { "email": "po-discuss@plantontology.org", "github": null, "name": "Plant Ontology Administrators", "orcid": null }, "deprecated": true, "description": "A structured controlled vocabulary for the anatomy of Graminae. Please note that this ontology has now been superseded by the Plant Ontology.", "homepage": "http://www.gramene.org/plant_ontology/", "mappings": { "biocontext": "gro.cpga", "bioportal": "GRO-CPGA", "obofoundry": "gro" }, "name": "Cereal Plant Gross Anatomy", "preferred_prefix": "GRO", "uri_format": "http://purl.obolibrary.org/obo/GRO_$1" }, "cpt": { "contact": { "email": "Intellectual.PropertyServices@ama-assn.org", "github": null, "name": "American Medical Association", "orcid": null }, "contributor": { "email": null, "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" }, "contributor_extras": [ { "email": null, "github": "colleenXu", "name": "Colleen Xu", "orcid": "0000-0003-2975-882X" } ], "description": "Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]", "example": "00103", "github_request_issue": 357, "homepage": "https://www.aapc.com", "mappings": { "aberowl": "CPT", "biolink": "CPT", "bioportal": "CPT", "fairsharing": "FAIRsharing.wpxab1" }, "name": "Current Procedural Terminology", "pattern": "^\\d+$", "preferred_prefix": "cpt", "publications": [ { "doi": "10.1136/neurintsurg-2014-011156", "pmc": null, "pubmed": "24589819", "title": "Current procedural terminology; a primer.", "year": 2014 }, { "doi": "10.1016/j.jacr.2007.10.004", "pmc": null, "pubmed": "18359442", "title": "CPT: an open system that describes all that you do.", "year": 2008 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/358", "https://github.com/biolink/biolink-model/pull/993" ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "ama-cpt" ], "uri_format": "https://www.aapc.com/codes/cpt-codes/$1" }, "credit": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output.", "example": "Software", "homepage": "https://casrai.org/credit/", "mappings": { "fairsharing": "FAIRsharing.fe4816" }, "name": "CASRAI Contributor Roles Taxonomy", "preferred_prefix": "credit", "publications": [ { "doi": "10.3789/ansi.niso.z39.104-2022", "pmc": null, "pubmed": null, "title": "ANSI/NISO Z39.104-2022, CRediT, Contributor Roles Taxonomy", "year": null }, { "doi": "10.1087/20150211", "pmc": null, "pubmed": null, "title": "Beyond authorship: attribution, contribution, collaboration, and credit", "year": null }, { "doi": "10.1038/d41586-019-01715-4", "pmc": null, "pubmed": null, "title": "Credit data generators for data reuse", "year": null }, { "doi": "10.1038/508312a", "pmc": null, "pubmed": null, "title": "Publishing: Credit where credit is due", "year": null }, { "doi": "10.1002/leap.1210", "pmc": null, "pubmed": null, "title": "How can we ensure visibility and diversity in research contributions? How the Contributor Role Taxonomy (CRediT) is helping the shift from authorship to contributorship", "year": null } ] }, "crisprdb": { "description": "Repeated CRISPR (\"clustered regularly interspaced short palindromic repeats\") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data.", "example": "551115", "homepage": "http://crispr.i2bc.paris-saclay.fr/", "mappings": { "biocontext": "CRISPRDB", "fairsharing": "FAIRsharing.7sfedh", "miriam": "crisprdb", "n2t": "crisprdb" }, "name": "CRISPRdb", "pattern": "^[0-9]+$", "preferred_prefix": "crisprdb", "uri_format": "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1" }, "cro": { "contact": { "email": "whimar@ohsu.edu", "github": "marijane", "name": "Marijane White", "orcid": "0000-0001-5059-4132" }, "description": "A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability.", "download_obo": "https://raw.githubusercontent.com/data2health/contributor-role-ontology/master/cro.obo", "download_owl": "http://purl.obolibrary.org/obo/cro.owl", "example": "0000038", "homepage": "https://github.com/data2health/contributor-role-ontology", "license": "CC BY 2.0", "mappings": { "aberowl": "CRO", "biocontext": "CRO", "bioportal": "CRO", "obofoundry": "cro", "ols": "cro", "ontobee": "CRO" }, "name": "Contributor Role Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CRO", "repository": "https://github.com/data2health/contributor-role-ontology", "uri_format": "http://purl.obolibrary.org/obo/CRO_$1", "version": "2019-12-11" }, "crop2ml": { "description": "CropMRespository is a database of soil and crop biophysical process models.", "example": "000000001", "homepage": "http://www.crop2ml.org", "mappings": { "miriam": "crop2ml" }, "name": "CropMRepository", "pattern": "^[0-9]{9}$", "preferred_prefix": "crop2ml", "uri_format": "http://www.crop2ml.org/cropmdb/$1" }, "cryoem": { "contact": { "email": "isanchez@cnb.csic.es", "github": null, "name": "Carlos Oscar Sorzano", "orcid": null }, "description": "Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles", "download_owl": "http://scipion.i2pc.es/ontology/cryoem/releases/2021-03-09/cryoem.owl", "example": "0000052", "homepage": "http://scipion.i2pc.es/ontology/cryoem", "mappings": { "aberowl": "CRYOEM", "bioportal": "CRYOEM", "fairsharing": "FAIRsharing.q47I0t", "ols": "cryoem" }, "name": "Cryo Electron Microscopy ontology", "pattern": "^\\d{7}$", "preferred_prefix": "cryoem", "uri_format": "http://scipion.i2pc.es/ontology/CRYOEM_$1", "version": "2021-03-09" }, "cryptodb": { "description": "CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "cgd7_230", "homepage": "https://cryptodb.org/cryptodb/", "mappings": { "biocontext": "CRYPTODB", "fairsharing": "FAIRsharing.t3nprm", "miriam": "cryptodb", "n2t": "cryptodb", "prefixcommons": "cryptodb", "re3data": "r3d100012265" }, "name": "CryptoDB", "pattern": "^\\w+$", "preferred_prefix": "cryptodb", "publications": [ { "doi": "10.1093/nar/gkj078", "pmc": "PMC1347441", "pubmed": "16381902", "title": "CryptoDB: a Cryptosporidium bioinformatics resource update.", "year": 2006 } ], "uri_format": "https://cryptodb.org/cryptodb/app/record/gene/$1" }, "csa": { "description": "The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme.", "example": "1a05", "homepage": "https://www.ebi.ac.uk/thornton-srv/databases/CSA/", "mappings": { "biocontext": "CSA", "fairsharing": "FAIRsharing.2ajtcf", "miriam": "csa", "n2t": "csa", "prefixcommons": "csa" }, "name": "Catalytic Site Atlas", "pattern": "^[0-9][A-Za-z0-9]{3}$", "preferred_prefix": "csa", "publications": [ { "doi": "10.1093/nar/gkh028", "pmc": "PMC308762", "pubmed": "14681376", "title": "The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.", "year": 2004 } ], "uri_format": "https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1" }, "csd": { "description": "The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode.", "example": "PELNAW", "homepage": "https://www.ccdc.cam.ac.uk/", "mappings": { "fairsharing": "FAIRsharing.vs7865", "miriam": "csd" }, "name": "Cambridge Structural Database", "pattern": "^[A-Z]{6}(\\d{2})?$", "preferred_prefix": "csd", "uri_format": "https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG" }, "csp": { "contact": { "email": "af8d@nih.gov", "github": null, "name": "Anita Ghebeles", "orcid": null }, "deprecated": true, "description": "Computer Retrieval of Information on Scientific Projects (CRISP)", "example": "2004-2820", "homepage": "https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm", "mappings": { "aberowl": "CRISP", "bioportal": "CRISP", "hl7": "2.16.840.1.113883.6.120" }, "name": "Computer Retrieval of Information on Science Projects Thesaurus", "preferred_prefix": "csp", "synonyms": [ "CRISP", "CRISP Thesaurus", "CRISP Thesaurus, 2006", "CSP2005" ], "uri_format": "http://purl.bioontology.org/ontology/CSP/$1" }, "cst": { "description": "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways.", "example": "Akt_PKB", "homepage": "http://www.cellsignal.com/pathways/index.html", "mappings": { "biocontext": "CST", "fairsharing": "FAIRsharing.n8pxvx", "hl7": "2.16.840.1.113883.6.62", "miriam": "cst", "n2t": "cst" }, "name": "Cell Signaling Technology Pathways", "pattern": "^[A-Za-z0-9_-]+$", "preferred_prefix": "cst", "uri_format": "http://www.cellsignal.com/reference/pathway/$1.html" }, "cst.ab": { "description": "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products.", "example": "3305", "homepage": "http://www.cellsignal.com/catalog/index.html", "mappings": { "biocontext": "CST.AB", "miriam": "cst.ab", "n2t": "cst.ab", "prefixcommons": "cst" }, "name": "Cell Signaling Technology Antibody", "pattern": "^\\d+$", "preferred_prefix": "cst.ab", "uri_format": "http://www.cellsignal.com/products/$1.html" }, "ctcae": { "appears_in": [ "oae" ], "contact": { "email": "ncictcaehelp@mail.nih.gov", "github": null, "name": "CTCAE Help", "orcid": null }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "The Common Terminology Criteria for Adverse Events (CTCAE),[1] formerly called the Common Toxicity Criteria (CTC or NCI-CTC), are a set of criteria for the standardized classification of adverse effects of drugs used in cancer therapy. The CTCAE system is a product of the US National Cancer Institute (NCI).", "download_owl": "http://aber-owl.net/media/ontologies/CTCAE/2/ctcae.owl", "example": "E12768", "homepage": "https://evs.nci.nih.gov/ftp1/CTCAE/About.html", "mappings": { "aberowl": "CTCAE", "bioportal": "CTCAE" }, "name": "Common Terminology Criteria for Adverse Events", "pattern": "^E\\d+$", "preferred_prefix": "ctcae", "publications": [ { "doi": null, "pmc": "PMC5977606", "pubmed": "29854250", "title": "Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs.", "year": 2018 } ], "references": [ "https://github.com/OAE-ontology/OAE/issues/8", "https://en.wikipedia.org/wiki/Common_Terminology_Criteria_for_Adverse_Events" ], "synonyms": [ "CTCAE" ] }, "ctd.chemical": { "description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.", "example": "D001151", "homepage": "http://ctdbase.org/", "mappings": { "biocontext": "CTD.CHEMICAL", "biolink": "CTD.CHEMICAL", "miriam": "ctd.chemical", "n2t": "ctd.chemical" }, "name": "CTD Chemical", "part_of": "ctd", "pattern": "^[CD]\\d+$", "preferred_prefix": "ctd.chemical", "provides": "mesh", "uri_format": "http://ctdbase.org/detail.go?type=chem&acc=$1" }, "ctd.disease": { "description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.", "example": "D053716", "homepage": "http://ctdbase.org/", "mappings": { "biocontext": "CTD.DISEASE", "biolink": "CTD.DISEASE", "miriam": "ctd.disease", "n2t": "ctd.disease" }, "name": "CTD Disease", "part_of": "ctd", "pattern": "^D\\d+$", "preferred_prefix": "ctd.disease", "provides": "mesh", "uri_format": "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1" }, "ctd.gene": { "description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.", "example": "101", "homepage": "http://ctdbase.org/", "mappings": { "biocontext": "CTD.GENE", "biolink": "CTD.GENE", "miriam": "ctd.gene", "n2t": "ctd.gene" }, "name": "CTD Gene", "part_of": "ctd", "pattern": "^\\d+$", "preferred_prefix": "ctd.gene", "provides": "ncbigene", "uri_format": "http://ctdbase.org/detail.go?type=gene&acc=$1" }, "cteno": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "depends_on": [ "ro", "uberon" ], "description": "An anatomical and developmental ontology for ctenophores (Comb Jellies)", "download_obo": "https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo", "download_owl": "http://purl.obolibrary.org/obo/cteno.owl", "example": "0000047", "homepage": "https://github.com/obophenotype/ctenophore-ontology", "license": "CC BY 3.0", "mappings": { "aberowl": "CTENO", "biocontext": "CTENO", "bioportal": "CTENO", "fairsharing": "FAIRsharing.mgxgza", "obofoundry": "cteno", "ols": "cteno", "ontobee": "CTENO" }, "name": "Ctenophore Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CTENO", "repository": "https://github.com/obophenotype/ctenophore-ontology", "uri_format": "http://purl.obolibrary.org/obo/CTENO_$1", "version": "2016-10-19" }, "cto": { "contact": { "email": "alpha.tom.kodamullil@scai.fraunhofer.de", "github": "akodamullil", "name": "Dr. Alpha Tom Kodamullil", "orcid": "0000-0001-9896-3531" }, "description": "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials.", "download_owl": "http://purl.obolibrary.org/obo/cto.owl", "example": "0000022", "homepage": "https://github.com/ClinicalTrialOntology/CTO/", "license": "CC BY 4.0", "mappings": { "aberowl": "CTO", "bioportal": "CTO", "fairsharing": "FAIRsharing.qp211a", "obofoundry": "cto", "ols": "cto", "ontobee": "CTO" }, "name": "Clinical Trials Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CTO", "repository": "https://github.com/ClinicalTrialOntology/CTO", "uri_format": "http://purl.obolibrary.org/obo/CTO_$1", "version": "1.0.0" }, "cubedb": { "comment": "website down as of 2021-10-04", "deprecated": true, "description": "Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available.", "example": "AKR", "homepage": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html", "mappings": { "biocontext": "CUBEDB", "miriam": "cubedb", "n2t": "cubedb" }, "name": "Cube db", "pattern": "^[A-Za-z_0-9]+$", "preferred_prefix": "cubedb", "uri_format": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/" }, "cvdo": { "contact": { "email": "paul.fabry@usherbrooke.ca", "github": "pfabry", "name": "Paul Fabry", "orcid": "0000-0002-3336-2476" }, "description": "An ontology to describe entities related to cardiovascular diseases", "download_owl": "http://purl.obolibrary.org/obo/cvdo.owl", "example": "0000546", "homepage": "https://github.com/OpenLHS/CVDO", "license": "CC BY 4.0", "mappings": { "aberowl": "CVDO", "biocontext": "CVDO", "bioportal": "CVDO", "fairsharing": "FAIRsharing.2basyz", "obofoundry": "cvdo", "ols": "cvdo", "ontobee": "CVDO" }, "name": "Cardiovascular Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CVDO", "repository": "https://github.com/OpenLHS/CVDO", "uri_format": "http://purl.obolibrary.org/obo/CVDO_$1", "version": "2020-03-05" }, "cvx": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The CDC's National Center of Immunization and Respiratory Diseases (NCIRD) developed and maintains the CVX (vaccine administered) code set. The table below has the most up to date values. It includes both active and inactive vaccines available in the US. CVX codes for inactive vaccines allow transmission of historical immunization records.", "example": "54", "homepage": "https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx", "mappings": { "hl7": "2.16.840.1.113883.6.59" }, "name": "Vaccine administered code set", "pattern": "^\\d+$", "preferred_prefix": "cvx" }, "d1id": { "description": "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences.", "example": "00030692-0FE1-4A1B-955E-A2E55D659267", "homepage": "https://www.dataone.org", "mappings": { "biocontext": "D1ID", "miriam": "d1id", "n2t": "d1id" }, "name": "DataONE", "pattern": "^\\S+$", "preferred_prefix": "d1id", "uri_format": "https://cn.dataone.org/cn/v2/resolve/{$1}" }, "dailymed": { "description": "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read.", "example": "973a9333-fec7-46dd-8eb5-25738f06ee54", "homepage": "https://dailymed.nlm.nih.gov/dailymed/", "mappings": { "biocontext": "DAILYMED", "miriam": "dailymed", "n2t": "dailymed", "prefixcommons": "dailymed" }, "name": "DailyMed", "pattern": "^[A-Za-z0-9-]+$", "preferred_prefix": "dailymed", "uri_format": "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1" }, "dandi": { "description": "DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable).\nDANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data.\nThese data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.", "example": "000017", "homepage": "https://dandiarchive.org/", "mappings": { "miriam": "dandi", "re3data": "r3d100013638" }, "name": "Distributed Archives for Neurophysiology Data Integration", "pattern": "^\\d{6}(\\/\\d+\\.\\d+\\.\\d+)?$", "preferred_prefix": "dandi", "uri_format": "https://dandiarchive.org/dandiset/$1" }, "darc": { "description": "DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.", "example": "1250", "homepage": "http://darcsite.genzentrum.lmu.de/darc/index.php", "mappings": { "biocontext": "DARC", "fairsharing": "FAIRsharing.evfe2s", "miriam": "darc", "n2t": "darc" }, "name": "Database of Aligned Ribosomal Complexes", "pattern": "^\\d+$", "preferred_prefix": "darc", "uri_format": "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1" }, "dashr": { "description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records.", "example": "hsa-mir-200a", "homepage": "http://lisanwanglab.org/DASHR/", "mappings": { "biocontext": "DASHR", "fairsharing": "FAIRsharing.ztvs34", "miriam": "dashr", "n2t": "dashr" }, "name": "Database of small human noncoding RNAs", "pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$", "preferred_prefix": "dashr", "uri_format": "http://lisanwanglab.org/DASHR/entry/$1" }, "dashr.expression": { "description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression.", "example": "hsa-mir-200a", "homepage": "https://dashr1.lisanwanglab.org/show-expression-table.php?start=0", "mappings": { "biocontext": "DASHR.EXPRESSION", "miriam": "dashr.expression", "n2t": "dashr.expression" }, "name": "DASHR expression", "pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$", "preferred_prefix": "dashr.expression", "uri_format": "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable" }, "datacite": { "contact": { "email": "p.vanschayck@maastrichtuniversity.nl", "github": null, "name": "Paul van Schayck", "orcid": null }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF.", "download_owl": "http://aber-owl.net/media/ontologies/DATACITE/2/datacite.owl", "example": "AgentIdentifierScheme", "homepage": "http://www.sparontologies.net/ontologies/datacite", "mappings": { "aberowl": "DATACITE", "bioportal": "DATACITE", "fairsharing": "FAIRsharing.c06f1e" }, "name": "DataCite Ontology", "preferred_prefix": "DataCite", "repository": "https://github.com/sparontologies/datacite", "uri_format": "http://purl.org/spar/datacite/$1" }, "datanator.gene": { "description": "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.", "example": "K00973", "homepage": "https://datanator.info/", "mappings": { "miriam": "datanator.gene" }, "name": "Datanator Gene", "part_of": "datanator", "pattern": "^K[0-9]+$", "preferred_prefix": "datanator.gene", "uri_format": "https://www.datanator.info/gene/$1" }, "datanator.metabolite": { "description": "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.", "example": "OUYCCCASQSFEME-MRVPVSSYSA-N", "homepage": "https://datanator.info/", "mappings": { "miriam": "datanator.metabolite" }, "name": "Datanator Metabolite", "part_of": "datanator", "pattern": "^[A-Z\\-]+$", "preferred_prefix": "datanator.metabolite", "uri_format": "https://www.datanator.info/metabolite/$1" }, "datanator.reaction": { "description": "\tDatanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.", "example": "XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N", "homepage": "https://icahn.mssm.edu/", "mappings": { "miriam": "datanator.reaction" }, "name": "Datanator Reaction", "pattern": "^.*?--%3E.*?$", "preferred_prefix": "datanator.reaction", "uri_format": "https://datanator.info/reaction/$1" }, "datf": { "deprecated": true, "description": "DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals.", "example": "AT1G01030.1", "homepage": "http://datf.cbi.pku.edu.cn/", "mappings": { "biocontext": "DATF", "miriam": "datf", "n2t": "datf", "prefixcommons": "datf" }, "name": "Database of Arabidopsis Transcription Factors", "pattern": "^AT[1-5]G\\d{5}(\\.\\d+)?$", "preferred_prefix": "datf", "uri_format": "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1" }, "dbd": { "description": "The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins.", "example": "0045310", "homepage": "http://www.transcriptionfactor.org/", "mappings": { "biocontext": "DBD", "edam": "2716", "miriam": "dbd", "n2t": "dbd", "prefixcommons": "dbd" }, "name": "Transcription Factor Database", "pattern": "^\\d+$", "preferred_prefix": "dbd", "uri_format": "http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD" }, "dbest": { "description": "The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms.", "example": "BP100000", "homepage": "https://www.ncbi.nlm.nih.gov/nucest", "mappings": { "biocontext": "DBEST", "edam": "1105", "fairsharing": "FAIRsharing.v9fya8", "miriam": "dbest", "n2t": "dbest", "ncbi": "dbEST", "prefixcommons": "dbest" }, "name": "EST database maintained at the NCBI.", "pattern": "^([A-Z]+)?\\d+(\\.\\d+)?$", "preferred_prefix": "dbest", "providers": [ { "code": "CURATOR_REVIEW", "description": "dbEST through DNA Data Bank of Japan (DDBJ)", "homepage": "http://www.ddbj.nig.ac.jp/", "name": "dbEST through DNA Data Bank of Japan (DDBJ)", "uri_format": "http://getentry.ddbj.nig.ac.jp/getentry/na/$1" }, { "code": "ebi", "description": "dbEST through European Nucleotide Archive (ENA)", "homepage": "https://www.ebi.ac.uk/ena", "name": "dbEST through European Nucleotide Archive (ENA)", "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" } ], "uri_format": "https://www.ncbi.nlm.nih.gov/nucest/$1" }, "dbg2introns": { "description": "The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank.", "example": "Cu.me.I1", "homepage": "http://webapps2.ucalgary.ca/~groupii/", "mappings": { "biocontext": "DBG2INTRONS", "miriam": "dbg2introns", "n2t": "dbg2introns", "prefixcommons": "mgiid" }, "name": "DBG2 Introns", "pattern": "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$", "preferred_prefix": "dbg2introns", "publications": [ { "doi": "10.1093/nar/gkr1043", "pmc": "PMC3245105", "pubmed": "22080509", "title": "Database for bacterial group II introns.", "year": 2011 } ], "uri_format": "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1" }, "dbgap": { "description": "The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype.", "example": "phs000768.v2.p1", "homepage": "https://www.ncbi.nlm.nih.gov/projects/gap", "mappings": { "biocontext": "DBGAP", "fairsharing": "FAIRsharing.88v2k0", "miriam": "dbgap", "n2t": "dbgap" }, "name": "Database of Genotypes and Phenotypes", "pattern": "^phs[0-9]{6}(.v\\d+.p\\d+)?$", "preferred_prefix": "dbgap", "uri_format": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1" }, "dbmhc": { "appears_in": [ "cellosaurus" ], "deprecated": true, "description": "Cell line databases/resources", "example": "48439", "homepage": "https://www.ncbi.nlm.nih.gov/gv/mhc/", "mappings": { "cellosaurus": "dbMHC" }, "name": "Database of human Major Histocompatibility Complex", "pattern": "^\\d+$", "preferred_prefix": "dbmhc" }, "dbo": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki.", "example": "careerPrizeMoney", "github_request_issue": 515, "homepage": "https://dbpedia.org/ontology", "name": "DBPedia Ontology", "preferred_prefix": "dbo", "uri_format": "https://dbpedia.org/ontology/$1" }, "dbprobe": { "description": "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.", "example": "1000000", "homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe", "mappings": { "biocontext": "DBPROBE", "edam": "2719", "miriam": "dbprobe", "n2t": "dbprobe", "ncbi": "dbProbe", "prefixcommons": "dbprobe" }, "name": "NCBI Probe database Public registry of nucleic acid reagents", "pattern": "^\\d+$", "preferred_prefix": "dbprobe", "uri_format": "https://www.ncbi.nlm.nih.gov/probe/?term=$1" }, "dbsnp": { "description": "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.", "example": "rs121909098", "homepage": "https://www.ncbi.nlm.nih.gov/snp/", "mappings": { "biocontext": "dbSNP", "cellosaurus": "dbSNP", "edam": "1106", "fairsharing": "FAIRsharing.edxb58", "go": "dbSNP", "hl7": "2.16.840.1.113883.6.284", "miriam": "dbsnp", "n2t": "dbsnp", "ncbi": "dbSNP", "prefixcommons": "dbsnp", "re3data": "r3d100010652", "uniprot": "dbSNP" }, "name": "NCBI dbSNP", "pattern": "^rs\\d+$", "preferred_prefix": "dbsnp", "providers": [ { "code": "sib", "description": "SNP2TFBS", "homepage": "https://ccg.epfl.ch/snp2tfbs/", "name": "SNP2TFBS", "uri_format": "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1" } ], "publications": [ { "doi": "10.1093/nar/29.1.308", "pmc": "PMC29783", "pubmed": "11125122", "title": "dbSNP: the NCBI database of genetic variation.", "year": 2001 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/snp/$1" }, "dbvar.study": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Studies in dbVar.", "example": "nstd102", "homepage": "https://www.ncbi.nlm.nih.gov/dbvar", "name": "Database of Genomic Structural Variation - Study", "preferred_prefix": "dbvar.study", "synonyms": [ "dbvar.studies" ], "uri_format": "https://www.ncbi.nlm.nih.gov/dbvar/studies/$1" }, "dbvar.variant": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Variants in dbVar.", "example": "nsv3875336", "homepage": "https://www.ncbi.nlm.nih.gov/dbvar", "name": "Database of Genomic Structural Variation - Variant", "preferred_prefix": "dbvar.variant", "synonyms": [ "dbvar.variants" ], "uri_format": "https://www.ncbi.nlm.nih.gov/dbvar/variants/$1" }, "dc": { "contact": { "email": "kdurante@stanford.edu", "github": null, "name": "Kim Durante", "orcid": null }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "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/DC/3/dc.owl", "example": "contributor", "homepage": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/", "mappings": { "aberowl": "DC", "biocontext": "dc", "bioportal": "DC", "fairsharing": "FAIRsharing.3nx7t" }, "name": "Dublin Core", "preferred_prefix": "dc", "synonyms": [ "dc11" ], "uri_format": "http://purl.org/dc/elements/1.1/$1" }, "dc_cl": { "contact": { "email": "Lindsay.Cowell@utsouthwestern.edu", "github": null, "name": "Lindsay Cowell", "orcid": "0000-0003-1617-8244" }, "deprecated": true, "example": "0000003", "homepage": "http://www.dukeontologygroup.org/Projects.html", "mappings": { "biocontext": "DC_CL", "obofoundry": "dc_cl" }, "name": "Dendritic cell", "pattern": "^\\d{7}$", "preferred_prefix": "DC_CL", "uri_format": "http://purl.obolibrary.org/obo/DC_CL_$1" }, "dcat": { "contact": { "email": "kdurante@stanford.edu", "github": null, "name": "kdurante", "orcid": null }, "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://aber-owl.net/media/ontologies/DCAT/2/dcat.owl", "example": "Dataset", "homepage": "https://www.w3.org/ns/dcat", "mappings": { "aberowl": "DCAT", "biocontext": "dcat", "biolink": "dcat", "bioportal": "DCAT", "fairsharing": "FAIRsharing.h4j3qm" }, "name": "Data Catalog", "preferred_prefix": "dcat", "uri_format": "http://www.w3.org/ns/dcat#$1" }, "dcterms": { "contact": { "email": "futo@stanford.edu", "github": null, "name": "Michelle Futornick", "orcid": null }, "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", "example": "title", "homepage": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/", "mappings": { "aberowl": "dcterms", "biocontext": "dcterms", "biolink": "dct", "bioportal": "DCTERMS", "fairsharing": "FAIRsharing.9vtwjs" }, "name": "Dublin Core Metadata Vocabulary", "preferred_prefix": "dcterms", "synonyms": [ "dc.terms", "dct" ], "uri_format": "http://purl.org/dc/terms/$1" }, "dctypes": { "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.", "example": "Collection", "homepage": "https://dublincore.org/specifications/dublin-core/dcmi-terms/", "mappings": { "biocontext": "dctypes" }, "name": "Dublin Core Types", "preferred_prefix": "dctypes", "uri_format": "http://purl.org/dc/dcmitype/$1" }, "ddanat": { "contact": { "email": "pfey@northwestern.edu", "github": "pfey03", "name": "Petra Fey", "orcid": "0000-0002-4532-2703" }, "description": "A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum", "download_obo": "http://purl.obolibrary.org/obo/ddanat.obo", "download_owl": "http://purl.obolibrary.org/obo/ddanat.owl", "example": "0000006", "homepage": "http://dictybase.org/", "license": "CC0 1.0", "mappings": { "aberowl": "DDANAT", "biocontext": "DDANAT", "bioportal": "DDANAT", "fairsharing": "FAIRsharing.z656ab", "go": "DDANAT", "obofoundry": "ddanat", "ols": "ddanat", "ontobee": "DDANAT", "prefixcommons": "ddanat" }, "name": "Dictyostelium discoideum anatomy", "pattern": "^\\d{7}$", "preferred_prefix": "DDANAT", "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 } ], "repository": "https://github.com/dictyBase/migration-data", "twitter": "dictybase", "uri_format": "http://purl.obolibrary.org/obo/DDANAT_$1", "version": "2020-04-13" }, "ddinter.drug": { "contact": { "email": "oriental-cds@163.com", "github": null, "name": "Dongsheng Cao", "orcid": "0000-0003-3604-3785" }, "contributor": { "email": null, "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" }, "description": "Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical 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It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene.", "example": "100", "homepage": "http://www.dpvweb.net/", "mappings": { "biocontext": "DPV", "miriam": "dpv", "n2t": "dpv" }, "name": "Description of Plant Viruses", "pattern": "^\\d+$", "preferred_prefix": "dpv", "uri_format": "http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1" }, "dragondb.allele": { "comment": "Deprecated because the website is dead", "deprecated": true, "description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information.", "example": "cho", "homepage": "http://www.antirrhinum.net/", "mappings": { "biocontext": "DRAGONDB.ALLELE", "miriam": "dragondb.allele", "n2t": "dragondb.allele" }, "name": "DragonDB Allele", "part_of": "dragondb", "pattern": "^\\w+$", "preferred_prefix": "dragondb.allele", "uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele" }, "dragondb.dna": { "comment": "Deprecated because the website is dead", "deprecated": true, "description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information.", "example": "3hB06", "homepage": "http://www.antirrhinum.net/", "mappings": { "biocontext": "DRAGONDB.DNA", "miriam": "dragondb.dna", "n2t": "dragondb.dna" }, "name": "DragonDB DNA", "part_of": "dragondb", "pattern": "^\\d\\w+$", "preferred_prefix": "dragondb.dna", "uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA" }, "dragondb.locus": { "comment": "Deprecated because the website is dead", "deprecated": true, "description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information.", "example": "DEF", "homepage": "http://www.antirrhinum.net/", "mappings": { "biocontext": "DRAGONDB.LOCUS", "miriam": "dragondb.locus", "n2t": "dragondb.locus" }, "name": "DragonDB Locus", "part_of": "dragondb", "pattern": "^\\w+$", "preferred_prefix": "dragondb.locus", "uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus" }, "dragondb.protein": { "comment": "Deprecated because the website is dead", "deprecated": true, "description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information.", "example": "AMDEFA", "homepage": "http://www.antirrhinum.net/", "mappings": { "biocontext": "DRAGONDB.PROTEIN", "miriam": "dragondb.protein", "n2t": "dragondb.protein" }, "name": "DragonDB Protein", "part_of": "dragondb", "pattern": "^\\w+$", "preferred_prefix": "dragondb.protein", "uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide" }, "dron": { "appears_in": [ "scdo" ], "contact": { "email": "hoganwr@gmail.com", "github": "hoganwr", "name": "William Hogan", "orcid": "0000-0002-9881-1017" }, "description": "We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive).", "download_json": "http://purl.obolibrary.org/obo/dron.json", "download_obo": "http://purl.obolibrary.org/obo/dron.obo", "download_owl": "http://purl.obolibrary.org/obo/dron.owl", "example": "00023232", "homepage": "https://github.com/ufbmi/dron", "license": "CC BY 3.0", "mappings": { "aberowl": "DRON", "biocontext": "DRON", "bioportal": "DRON", "fairsharing": "FAIRsharing.w5ntfd", "obofoundry": "dron", "ols": "dron", "ontobee": "DRON" }, "name": "The Drug Ontology", "pattern": "^\\d{8}$", "preferred_prefix": "DRON", "publications": [ { "doi": "10.1186/s13326-017-0121-5", "pmc": "PMC5335794", "pubmed": "28253937", "title": "Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request.", "year": 2017 }, { "doi": "10.1186/s13326-016-0048-2", "pmc": "PMC4836073", "pubmed": "27096073", "title": "An accurate and precise representation of drug ingredients.", "year": 2016 }, { "doi": "10.1186/2041-1480-4-44", "pmc": "PMC3931349", "pubmed": "24345026", "title": "Building a drug ontology based on RxNorm and other sources.", "year": 2013 } ], "repository": "https://github.com/ufbmi/dron", "uri_format": "http://purl.obolibrary.org/obo/DRON_$1", "version": "2022-04-22" }, "drsc": { "description": "The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene.", "example": "DRSC05221", "homepage": "http://flyrnai.org/", "mappings": { "biocontext": "DRSC", "miriam": "drsc", "n2t": "drsc" }, "name": "Drosophila RNAi Screening Center", "pattern": "^DRSC\\d+$", "preferred_prefix": "drsc", "uri_format": "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1" }, "drugbank": { "description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information.", "example": "DB14938", "homepage": "http://www.drugbank.ca", "mappings": { "biocontext": "DrugBank", "cellosaurus": "DrugBank", "cheminf": "000406", "edam": "2326", "fairsharing": "FAIRsharing.353yat", "miriam": "drugbank", "n2t": "drugbank", "prefixcommons": "drugbank", "re3data": "r3d100010544", "uniprot": "DrugBank", "wikidata": "P715" }, "name": "DrugBank", "pattern": "^DB\\d{5}$", "preferred_prefix": "drugbank", "publications": [ { "doi": "10.1093/nar/gkt1068", "pmc": "PMC3965102", "pubmed": "24203711", "title": "DrugBank 4.0: shedding new light on drug metabolism.", "year": 2013 }, { "doi": "10.1093/nar/gkq1126", "pmc": "PMC3013709", "pubmed": "21059682", "title": "DrugBank 3.0: a comprehensive resource for 'omics' research on drugs.", "year": 2010 }, { "doi": "10.1093/nar/gkm958", "pmc": "PMC2238889", "pubmed": "18048412", "title": "DrugBank: a knowledgebase for drugs, drug actions and drug targets.", "year": 2007 }, { "doi": "10.1093/nar/gkj067", "pmc": "PMC1347430", "pubmed": "16381955", "title": "DrugBank: a comprehensive resource for in silico drug discovery and exploration.", "year": 2006 } ], "synonyms": [ "DRUGBANK_ID", "DrugBank" ], "uri_format": "http://www.drugbank.ca/drugs/$1" }, "drugbank.category": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Close to 5K Categorizations for drugs, similar to ATCC.", "example": "DBCAT000600", "homepage": "https://go.drugbank.com/categories", "name": "DrugBank Drug Category", "part_of": "drugbank", "pattern": "^DBCAT\\d+$", "preferred_prefix": "drugbank.category", "uri_format": "https://www.drugbank.ca/categories/$1" }, "drugbank.salt": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets.", "example": "DBSALT001211", "homepage": "http://www.drugbank.ca", "mappings": { "biocontext": "DRUGBANK.TARGET" }, "name": "DrugBank Salts", "part_of": "drugbank", "pattern": "^DBSALT\\d{6}$", "preferred_prefix": "drugbank.salt", "synonyms": [ "drugbank.target" ], "uri_format": "https://go.drugbank.com/salts/$1" }, "drugbankv4.target": { "description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database.", "example": "BE0000048", "homepage": "http://www.drugbank.ca/targets", "mappings": { "biocontext": "DRUGBANKV4.TARGET", "miriam": "drugbankv4.target", "n2t": "drugbankv4.target" }, "name": "DrugBank Target v4", "part_of": "drugbank", "pattern": "^BE\\d{7}$", "preferred_prefix": "drugbankv4.target", "uri_format": "http://www.drugbank.ca/biodb/bio_entities/$1" }, "drugcentral": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action.", "example": "307", "homepage": "http://drugcentral.org", "mappings": { "biolink": "DrugCentral", "fairsharing": "FAIRsharing.3me82d", "uniprot": "DrugCentral" }, "name": "Drug Central", "pattern": "^\\d+$", "preferred_prefix": "drugcentral", "synonyms": [ "Drug_Central" ], "uri_format": "http://drugcentral.org/drugcard/$1" }, "dsm4": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]", "example": "315.1", "example_extras": [ "291.89" ], "homepage": "https://en.wikipedia.org/wiki/Diagnostic_and_Statistical_Manual_of_Mental_Disorders#DSM-IV-TR_(2000)", "mappings": { "hl7": "2.16.840.1.113883.6.126", "wikidata": "P663" }, "name": "Diagnostic and Statistical Manual of Mental Disorders (4th Edition)", "pattern": "^\\d+\\.\\d+$", "preferred_prefix": "dsm4", "synonyms": [ "dsm-iv" ] }, "dsm5": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [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).", "example": "ACC-1", "homepage": "https://www.dsmz.de", "mappings": { "cellosaurus": "DSMZ", "re3data": "r3d100010219" }, "name": "Deutsche Sammlung von Mikroorganismen und Zellkulturen", "preferred_prefix": "dsmz", "uri_format": "https://www.dsmz.de/collection/catalogue/details/culture/$1" }, "dso": { "contact": { "email": "evan@epatters.org", "github": "epatters", "name": "Evan Patterson", "orcid": "0000-0002-8600-949X" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Data Science Ontology is a research project of IBM Research AI and Stanford University Statistics. 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We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs).", "example": "90062901", "homepage": "https://www.phe-culturecollections.org.uk/collections/ecacc.aspx", "mappings": { "cellosaurus": "ECACC" }, "name": "European Collection of Authenticated Cell Culture", "pattern": "^\\d+$", "preferred_prefix": "ecacc", "uri_format": "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1" }, "ecao": { "contact": { "email": "ettensohn@cmu.edu", "github": "ettensohn", "name": "Charles Ettensohn", "orcid": "0000-0002-3625-0955" }, "depends_on": [ "cl", "ro", "uberon" ], "description": "None", "download_obo": "http://purl.obolibrary.org/obo/ecao.obo", "download_owl": "http://purl.obolibrary.org/obo/ecao.owl", "example": "0107180", "homepage": "https://github.com/echinoderm-ontology/ecao_ontology", "license": "CC BY 3.0", "mappings": { "aberowl": "ECAO", "bioportal": "ECAO", "obofoundry": "ecao", "ols": "ecao", "ontobee": "ECAO" }, "name": "The Echinoderm Anatomy and Development Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ECAO", "repository": "https://github.com/echinoderm-ontology/ecao_ontology", "uri_format": "http://purl.obolibrary.org/obo/ECAO_$1", "version": "2020-05-22" }, "eccode": { "description": "The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions.", "example": "1.1.1.1", "example_decoys": [ "100", "2.", "2.n1", "2.3.", "2.3.n1", "2.3.1.", "2.3.1.n", "2.3.4.1." ], "example_extras": [ "2", "2.3", "2.3.1", "2.3.1.n12", "3.1.26.n2" ], "homepage": "https://www.ebi.ac.uk/intenz/", "mappings": { "biocontext": "EC-CODE", "edam": "1011", "fairsharing": "FAIRsharing.q1fdkc", "go": "EC", "miriam": "ec-code", "n2t": "ec-code", "prefixcommons": "intenz", "wikidata": "P591" }, "name": "Enzyme Commission Code", "pattern": "^\\d{1,2}(((\\.\\d{1,3}){1,3})|(\\.\\d+){2}\\.n\\d{1,3})?$", "preferred_prefix": "eccode", "providers": [ { "code": "CURATOR_REVIEW", "description": "KEGG Ligand Database for Enzyme Nomenclature", "homepage": "https://www.genome.jp/dbget-bin/www_bfind?enzyme", "name": "KEGG Ligand Database for Enzyme Nomenclature", "uri_format": "https://www.genome.jp/dbget-bin/www_bget?ec:$1" }, { "code": "enzymeportal", "description": "Enzyme Portal through EMBL-EBI", "homepage": "https://www.ebi.ac.uk/enzymeportal", "name": "Enzyme Portal through EMBL-EBI", "uri_format": "https://www.ebi.ac.uk/enzymeportal/ec/$1" }, { "code": "expasy", "description": "Enzyme nomenclature database, ExPASy (Expert Protein Analysis System)", "homepage": "https://enzyme.expasy.org/", "name": "Enzyme nomenclature database, ExPASy (Expert Protein Analysis System)", "uri_format": "https://enzyme.expasy.org/EC/$1" }, { "code": "expenz", "description": "ExploreEnz at Trinity College", "homepage": "http://www.enzyme-database.org/", "name": "ExploreEnz at Trinity College", "uri_format": "http://www.enzyme-database.org/query.php?ec=$1" } ], "synonyms": [ "EC", "EC number", "EC-CODE", "ECCODE", "EC_CODE", "ec-code", "intenz" ], "uri_format": "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1" }, "ecg": { "contact": { "email": "rwinslow@jhu.edu", "github": null, "name": "Raimond L. Winslow, PhD & Stephen Granite", "orcid": null }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms.", "download_owl": "http://aber-owl.net/media/ontologies/ECG/12/ecg.owl", "example": "000000159", "homepage": "https://bioportal.bioontology.org/ontologies/ECG", "mappings": { "aberowl": "ECG", "bioportal": "ECG", "fairsharing": "FAIRsharing.azr389" }, "name": "Electrocardiogram Ontology", "pattern": "^\\d+$", "preferred_prefix": "ecg", "publications": [ { "doi": "10.1016/j.jbi.2010.08.007", "pmc": null, "pubmed": "20800107", "title": "Using an ECG reference ontology for semantic interoperability of ECG data.", "year": 2010 } ], "synonyms": [ "ECGOntology" ], "uri_format": "http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_$1" }, "echobase": { "description": "EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products.", "example": "EB0170", "homepage": "http://www.york.ac.uk/", "mappings": { "biocontext": "ECHOBASE", "go": "EchoBASE", "miriam": "echobase", "n2t": "echobase", "prefixcommons": "echobase", "re3data": "r3d100011646", "uniprot": "EchoBASE" }, "name": "EchoBASE post-genomic database for Escherichia coli", "pattern": "^EB\\d+$", "preferred_prefix": "echobase", "publications": [ { "doi": "10.1093/nar/gki028", "pmc": "PMC539982", "pubmed": "15608209", "title": "EchoBASE: an integrated post-genomic database for Escherichia coli.", "year": 2005 } ], "uri_format": "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1" }, "ecmdb": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes.", "example": "ECMDB00005", "homepage": "https://ecmdb.ca", "name": "E. coli Metabolite Database", "pattern": "^ECMDB\\d+$", "preferred_prefix": "ecmdb", "synonyms": [ "ECMDB" ], "uri_format": "http://ecmdb.ca/compounds/$1" }, "ecn": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A seven-digit identifier for chemical substances for regulatory purposes within the European Union.", "example": "200-003-9", "homepage": "https://echa.europa.eu/information-on-chemicals", "mappings": { "cheminf": "000447" }, "name": "European Community number", "pattern": "^\\d{3}-\\d{3}-\\d$", "preferred_prefix": "ecn", "references": [ "https://github.com/biopragmatics/bioregistry/issues/257", "https://en.wikipedia.org/wiki/European_Community_number" ] }, "eco": { "banana": "ECO", "contact": { "email": "mgiglio@som.umaryland.edu", "github": "mgiglio99", "name": "Michelle Giglio", "orcid": "0000-0001-7628-5565" }, "description": "Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity.", "download_obo": "http://purl.obolibrary.org/obo/eco.obo", "download_owl": "http://purl.obolibrary.org/obo/eco.owl", "example": "0007807", "homepage": "https://www.evidenceontology.org", "license": "CC0 1.0", "mappings": { "aberowl": "ECO", "biocontext": "ECO", "bioportal": "ECO", "fairsharing": "FAIRsharing.wvpgwn", "go": "ECO", "miriam": "eco", "n2t": "eco", "obofoundry": "eco", "ols": "eco", "ontobee": "ECO", "prefixcommons": "eco" }, "name": "Evidence ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "ECO", "publications": [ { "doi": "10.1093/nar/gky1036", "pmc": "PMC6323956", "pubmed": "30407590", "title": "ECO, the Evidence & Conclusion Ontology: community standard for evidence information.", "year": 2019 }, { "doi": "10.1007/978-1-4939-3743-1_18", "pmc": "PMC6377151", "pubmed": "27812948", "title": "The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.", "year": 2017 }, { "doi": "10.1093/database/bau075", "pmc": "PMC4105709", "pubmed": "25052702", "title": "Standardized description of scientific evidence using the Evidence Ontology (ECO).", "year": 2014 }, { "doi": "10.1142/9789812704856_0019", "pmc": null, "pubmed": "14992503", "title": "An evidence ontology for use in pathway/genome databases.", "year": 2004 } ], "repository": "https://github.com/evidenceontology/evidenceontology", "uri_format": "https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1", "version": "2022-08-05" }, "ecocore": { "contact": { "email": "p.buttigieg@gmail.com", "github": "pbuttigieg", "name": "Pier Luigi Buttigieg", "orcid": "0000-0002-4366-3088" }, "depends_on": [ "bfo", "chebi", "envo", "go", "iao", "pato", "pco", "po", "ro", "uberon" ], "description": "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.", "download_obo": "http://purl.obolibrary.org/obo/ecocore.obo", "download_owl": "http://purl.obolibrary.org/obo/ecocore.owl", "example": "00000001", "homepage": "https://github.com/EcologicalSemantics/ecocore", "license": "CC BY 3.0", "mappings": { "aberowl": "ECOCORE", "biocontext": "ECOCORE", "bioportal": "ECOCORE", "obofoundry": "ecocore", "ols": "ecocore", "ontobee": "ECOCORE" }, "name": "An ontology of core ecological entities", "pattern": "^\\d+$", "preferred_prefix": "ECOCORE", "repository": "https://github.com/EcologicalSemantics/ecocore", "uri_format": "http://purl.obolibrary.org/obo/ECOCORE_$1", "version": "2022-03-09" }, "ecocyc": { "description": "EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways.", "example": "AICARTRANSIMPCYCLO-CPLX", "homepage": "http://ecocyc.org/", "mappings": { "fairsharing": "FAIRsharing.65dmtr", "go": "EcoCyc", "ncbi": "ECOCYC" }, "name": "EcoCyc", "preferred_prefix": "ecocyc", "uri_format": "https://biocyc.org/gene?id=$1" }, "ecogene": { "description": "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites.", "example": "EG10173", "homepage": "http://ecogene.org/", "mappings": { "biocontext": "EcoGene", "fairsharing": "FAIRsharing.3q3kvn", "miriam": "ecogene", "n2t": "ecogene", "ncbi": "EcoGene", "prefixcommons": "ecogene", "re3data": "r3d100010546" }, "name": "Database of Escherichia coli Sequence and Function", "pattern": "^EG\\d+$", "preferred_prefix": "ecogene", "publications": [ { "doi": "10.1093/nar/28.1.60", "pmc": "PMC102481", "pubmed": "10592181", "title": "EcoGene: a genome sequence database for Escherichia coli K-12.", "year": 2000 } ], "uri_format": "http://www.ecogene.org/gene/$1" }, "ecolexicon": { "comment": "No resolution - everything is in a single page app", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology.", "example": "canal", "homepage": "http://ecolexicon.ugr.es/en/index.htm", "name": "EcoLexicon", "preferred_prefix": "ecolexicon" }, "ecoliwiki": { "description": "EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes.", "example": "aaeA", "homepage": "http://ecoliwiki.net/colipedia/", "mappings": { "biocontext": "ECOLIWIKI", "fairsharing": "FAIRsharing.tx95wa", "go": "EcoliWiki", "miriam": "ecoliwiki", "n2t": "ecoliwiki" }, "name": "EcoliWiki from EcoliHub", "pattern": "^[A-Za-z0-9-]+$", "preferred_prefix": "ecoliwiki", "uri_format": "http://ecoliwiki.net/colipedia/index.php/$1:Gene" }, "ecto": { "contact": { "email": "annethessen@gmail.com", "github": "diatomsRcool", "name": "Anne Thessen", "orcid": "0000-0002-2908-3327" }, "depends_on": [ "chebi", "envo", "exo", "go", "iao", "maxo", "nbo", "ncbitaxon", "ncit", "pato", "ro", "uberon", "xco" ], "description": "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology).", "download_json": "http://purl.obolibrary.org/obo/ecto.json", "download_obo": "http://purl.obolibrary.org/obo/ecto.obo", "download_owl": "http://purl.obolibrary.org/obo/ecto.owl", "example": "0000001", "homepage": "https://github.com/EnvironmentOntology/environmental-exposure-ontology", "license": "CC0 1.0", "mappings": { "aberowl": "ECTO", "biolink": "ECTO", "bioportal": "ECTO", "obofoundry": "ecto", "ols": "ecto", "ontobee": "ECTO" }, "name": "Environmental conditions, treatments and exposures ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ECTO", "repository": "https://github.com/EnvironmentOntology/environmental-exposure-ontology", "uri_format": "http://purl.obolibrary.org/obo/ECTO_$1", "version": "2022-08-12" }, "ecyano.entity": { "description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities.", "example": "23", "homepage": "http://www.e-cyanobacterium.org/bcs/entity/", "mappings": { "biocontext": "ECYANO.ENTITY", "miriam": "ecyano.entity", "n2t": "ecyano.entity" }, "name": "E-cyanobacterium entity", "part_of": "ecyano", "pattern": "^\\d+$", "preferred_prefix": "ecyano.entity", "uri_format": "https://www.e-cyanobacterium.org/bcs/entity/$1" }, "ecyano.experiment": { "description": "E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments.", "example": "18", "homepage": "https://www.e-cyanobacterium.org/experiments-repository/", "mappings": { "miriam": "ecyano.experiment" }, "name": "E-cyanobacterium Experimental Data", "part_of": "ecyano", "pattern": "^\\d+$", "preferred_prefix": "ecyano.experiment", "uri_format": "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1" }, "ecyano.model": { "description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models.", "example": "26", "homepage": "http://e-cyanobacterium.org/models/", "mappings": { "biocontext": "ECYANO.MODEL", "miriam": "ecyano.model", "n2t": "ecyano.model" }, "name": "E-cyanobacterium model", "pattern": "^\\d+$", "preferred_prefix": "ecyano.model", "uri_format": "https://e-cyanobacterium.org/models/model/$1" }, "ecyano.rule": { "description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules.", "example": "56", "homepage": "http://www.e-cyanobacterium.org/bcs/rule/", "mappings": { "biocontext": "ECYANO.RULE", "miriam": "ecyano.rule", "n2t": "ecyano.rule" }, "name": "E-cyanobacterium rule", "part_of": "ecyano", "pattern": "^\\d+$", "preferred_prefix": "ecyano.rule", "uri_format": "https://e-cyanobacterium.org/bcs/rule/$1" }, "edam": { "contact": { "email": "matus.kalas@uib.no", "github": "matuskalas", "name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981" }, "description": "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "download_owl": "https://raw.githubusercontent.com/edamontology/edamontology/master/releases/EDAM.owl", "example": "data_1664", "homepage": "http://edamontology.org", "mappings": { "aberowl": "EDAM", "agroportal": "EDAM", "biocontext": "EDAM", "bioportal": "EDAM", "fairsharing": "FAIRsharing.a6r7zs", "miriam": "edam", "n2t": "edam", "ols": "edam", "ontobee": "EDAM", "prefixcommons": "edam" }, "name": "Bioinformatics operations, data types, formats, identifiers and topics", "pattern": "^(data|topic|operation|format)\\_\\d{4}$", "preferred_prefix": "edam", "publications": [ { "doi": "10.1093/bioinformatics/btt113", "pmc": "PMC3654706", "pubmed": "23479348", "title": "EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.", "year": 2013 } ], "repository": "https://github.com/edamontology/edamontology", "twitter": "edamontology", "uri_format": "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1", "version": "2019-07-17" }, "edam.data": { "contact": { "email": "matus.kalas@uib.no", "github": "matuskalas", "name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "example": "1664", "homepage": "http://edamontology.org", "mappings": { "biolink": "EDAM-DATA" }, "name": "EDAM Data", "part_of": "edam", "pattern": "^\\d+$", "preferred_prefix": "edam.data", "repository": "https://github.com/edamontology/edamontology", "twitter": "edamontology", "uri_format": "http://edamontology.org/data_$1" }, "edam.format": { "contact": { "email": "matus.kalas@uib.no", "github": "matuskalas", "name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data.", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "example": "1915", "homepage": "http://edamontology.org", "mappings": { "biolink": "EDAM-FORMAT" }, "name": "EDAM Format", "part_of": "edam", "pattern": "^\\d+$", "preferred_prefix": "edam.format", "repository": "https://github.com/edamontology/edamontology", "twitter": "edamontology", "uri_format": "http://edamontology.org/format_$1" }, "edam.operation": { "contact": { "email": "matus.kalas@uib.no", "github": "matuskalas", "name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "example": "0004", "homepage": "http://edamontology.org", "mappings": { "biolink": "EDAM-OPERATION" }, "name": "EDAM Operation", "part_of": "edam", "pattern": "^\\d+$", "preferred_prefix": "edam.operation", "repository": "https://github.com/edamontology/edamontology", "twitter": "edamontology", "uri_format": "http://edamontology.org/operation_$1" }, "edam.topic": { "contact": { "email": "matus.kalas@uib.no", "github": "matuskalas", "name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "example": "0003", "homepage": "http://edamontology.org", "mappings": { "biolink": "EDAM-TOPIC" }, "name": "EDAM Topic", "part_of": "edam", "pattern": "^\\d+$", "preferred_prefix": "edam.topic", "repository": "https://github.com/edamontology/edamontology", "twitter": "edamontology", "uri_format": "http://edamontology.org/topic_$1" }, "edda": { "contact": { "email": "tanja.bekhuis@tcbinfosci.com", "github": null, "name": "Tanja Bekhuis", "orcid": null }, "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", "mappings": { "aberowl": "EDDA", "bioportal": "EDDA", "fairsharing": "FAIRsharing.2ffmsb" }, "name": "EDDA Study Designs Taxonomy", "preferred_prefix": "edda", "uri_format": "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1" }, "efo": { "contact": { "email": "plwhetzel@gmail.com", "github": "twhetzel", "name": "Trish Whetzel", "orcid": "0000-0002-3458-4839" }, "description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.", "download_obo": "http://www.ebi.ac.uk/efo/efo.obo", "download_owl": "http://www.ebi.ac.uk/efo/releases/v3.45.0/efo.owl", "example": "0005147", "homepage": "http://www.ebi.ac.uk/efo", "mappings": { "aberowl": "EFO", "agroportal": "EFO", "biocontext": "EFO", "biolink": "EFO", "bioportal": "EFO", "cellosaurus": "EFO", "fairsharing": "FAIRsharing.1gr4tz", "miriam": "efo", "n2t": "efo", "ols": "efo", "ontobee": "EFO" }, "name": "Experimental Factor Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "EFO", "providers": [ { "code": "ebi", "description": "EFO through Functional Genomics Group (EBI)", "homepage": "https://www.ebi.ac.uk/efo/", "name": "EFO through Functional Genomics Group (EBI)", "uri_format": "https://www.ebi.ac.uk/efo/EFO_$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/btq099", "pmc": "PMC2853691", "pubmed": "20200009", "title": "Modeling sample variables with an Experimental Factor Ontology.", "year": 2010 } ], "repository": "https://github.com/EBISPOT/efo/", "uri_format": "http://www.ebi.ac.uk/efo/EFO_$1", "version": "3.45.0" }, "ega.dataset": { "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.", "example": "EGAD00000000001", "homepage": "https://ega-archive.org/", "mappings": { "biocontext": "EGA.DATASET", "fairsharing": "FAIRsharing.mya1ff", "miriam": "ega.dataset", "n2t": "ega.dataset" }, "name": "European Genome-phenome Archive Dataset", "pattern": "^EGAD\\d{11}$", "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" } ], "uri_format": "https://www.ebi.ac.uk/ega/datasets/$1" }, "ega.study": { "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.", "example": "EGAS00000000001", "homepage": "https://www.ebi.ac.uk/ega/studies", "mappings": { "biocontext": "EGA.STUDY", "miriam": "ega.study", "n2t": "ega.study" }, "name": "European Genome-phenome Archive Study", "pattern": "^EGAS\\d{11}$", "preferred_prefix": "ega.study", "uri_format": "https://www.ebi.ac.uk/ega/studies/$1" }, "eggnog": { "description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).", "example": "veNOG12876", "homepage": "http://eggnog.embl.de/version_3.0/", "mappings": { "biocontext": "EGGNOG", "fairsharing": "FAIRsharing.j1wj7d", "miriam": "eggnog", "n2t": "eggnog", "prefixcommons": "eggnog", "uniprot": "eggNOG" }, "name": "eggNOG", "pattern": "^\\w+$", "preferred_prefix": "eggnog", "publications": [ { "doi": "10.1093/nar/gkp951", "pmc": "PMC2808932", "pubmed": "19900971", "title": "eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.", "year": 2009 } ], "uri_format": "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1" }, "ehda": { "contact": { "email": "J.Bard@ed.ac.uk", "github": null, "name": "Jonathan Bard", "orcid": null }, "deprecated": true, "description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once.", "download_obo": "http://aber-owl.net/media/ontologies/EHDA/6/ehda.obo", "example": "1", "homepage": "http://genex.hgu.mrc.ac.uk/", "mappings": { "aberowl": "EHDA", "biocontext": "EHDA", "bioportal": "EHDA", "obofoundry": "ehda", "prefixcommons": "ehda" }, "name": "Human developmental anatomy, timed version", "pattern": "^\\d+$", "preferred_prefix": "EHDA", "uri_format": "http://purl.obolibrary.org/obo/EHDA_$1" }, "ehdaa": { "contact": { "email": "J.Bard@ed.ac.uk", "github": null, "name": "Jonathan Bard", "orcid": null }, "deprecated": true, "description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). 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More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems.", "download_owl": "http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=eol.owl", "example": "0001927", "homepage": "http://www.atol-ontology.com", "mappings": { "aberowl": "EOL", "agroportal": "EOL", "bioportal": "EOL", "fairsharing": "FAIRsharing.w7bw2y", "ols": "eol", "re3data": "r3d100011663" }, "name": "Environment Ontology for Livestock", "pattern": "^\\d{7}$", "preferred_prefix": "eol", "uri_format": "http://purl.org/obo/owlEOL_$1", "version": "2018-09-13" }, "eolife": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A collaborative project intended to create an encyclopedia documenting all living species known to science", "example": "1044544", "homepage": "https://eol.org", "mappings": { "fairsharing": "FAIRsharing.3J6NYn", "wikidata": "P830" }, "name": "Encyclopedia of Life", "pattern": "^\\d+$", "preferred_prefix": "eolife", "uri_format": "https://eol.org/pages/$1" }, "epcc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Collection of European paediatric cardiac coding files", "homepage": "https://www.aepc.org/european-paediatric-cardiac-coding", "name": "European Paediatric Cardiac Codes", "preferred_prefix": "epcc", "proprietary": true, "references": [ "https://www.cambridge.org/core/journals/cardiology-in-the-young/article/abs/european-paediatric-cardiac-codes-the-long-list-with-icd9-icd10-crossmapping-and-crossmap-to-epcc-short-list/FCA4DFCCB661298294A3D113FC79D5BE" ] }, "epd": { "description": "The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.", "example": "TA_H3", "homepage": "http://epd.vital-it.ch/", "mappings": { "biocontext": "EPD", "edam": "2386", "fairsharing": "FAIRsharing.sym4ne", "miriam": "epd", "n2t": "epd", "ncbi": "EPD", "uniprot": "EPD" }, "name": "Eukaryotic Promoter Database", "pattern": "^[A-Z-_0-9]+$", "preferred_prefix": "epd", "uri_format": "http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1" }, "epio": { "contact": { "email": "alpha.tom.kodamullil@scai.fraunhofer.de", "github": "akodamullil", "name": "Alpha Tom Kodamullil", "orcid": "0000-0001-9896-3531" }, "depends_on": [ "bfo" ], "description": "A application driven Epilepsy Ontology with official terms from the ILAE.", "download_owl": "http://purl.obolibrary.org/obo/epio.owl", "example": "0000011", "homepage": "https://github.com/SCAI-BIO/EpilepsyOntology", "license": "CC BY 4.0", "mappings": { "aberowl": "EPIO", "bioportal": "EPIO", "obofoundry": "epio", "ontobee": "EPIO" }, "name": "Epilepsy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "EPIO", "repository": "https://github.com/SCAI-BIO/EpilepsyOntology", "uri_format": "http://purl.obolibrary.org/obo/EPIO_$1" }, "epo": { "contact": { "email": "ferdinand.dhombres@inserm.fr", "github": null, "name": "Ferdinand Dhombres", "orcid": null }, "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/", "mappings": { "aberowl": "EPO", "biocontext": "EPO", "bioportal": "EPO", "obofoundry": "epo", "ontobee": "EPO" }, "name": "Epidemiology Ontology", "preferred_prefix": "EPO", "uri_format": "http://purl.obolibrary.org/obo/EPO_$1" }, "epso": { "contact": { "email": "satyasahoo@ieee.org", "github": null, "name": "Satya Sahoo", "orcid": null }, "description": "The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. ", "download_owl": "http://aber-owl.net/media/ontologies/EPSO/3/epso.owl", "example": "0000400", "homepage": "http://prism.case.edu/prism/index.php/EpilepsyOntology", "mappings": { "aberowl": "EPSO", "bioportal": "EPSO", "fairsharing": "FAIRsharing.ttprgy", "ontobee": "EPSO" }, "name": "Epilepsy and Seizure Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "epso", "publications": [ { "doi": "10.1136/amiajnl-2013-001696", "pmc": null, "pubmed": null, "title": "Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care", "year": null } ], "uri_format": "http://www.case.edu/EpilepsyOntology.owl#$1" }, "erm": { "contact": { "email": "egon.willighagen@gmail.com", "github": "egonw", "name": "Egon Willighagen", "orcid": "0000-0001-7542-0286" }, "description": "The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project.", "download_rdf": "https://nanocommons.github.io/identifiers/registry", "example": "ERM00000044", "homepage": "https://nanocommons.github.io/identifiers/", "mappings": { "cheminf": "000569", "miriam": "erm", "n2t": "erm" }, "name": "European Registry of Materials", "pattern": "^ERM[0-9]{8}$", "preferred_prefix": "erm", "publications": [ { "doi": "10.1186/s13321-022-00614-7", "pmc": null, "pubmed": null, "title": "European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials", "year": null } ], "twitter": "nanocommons", "uri_format": "https://nanocommons.github.io/identifiers/registry#$1" }, "ero": { "contact": { "email": "Marc_Ciriello@hms.harvard.edu", "github": null, "name": "Marc Ciriello", "orcid": null }, "deprecated": true, "description": "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.", "download_owl": "http://purl.obolibrary.org/obo/ero.owl", "example": "0001655", "homepage": "https://open.med.harvard.edu/wiki/display/eaglei/Ontology", "license": "CC BY 2.0", "mappings": { "aberowl": "ERO", "biocontext": "ERO", "bioportal": "ERO", "fairsharing": "FAIRsharing.nwgynk", "obofoundry": "ero", "ols": "ero", "ontobee": "ERO" }, "name": "eagle-i resource ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ERO", "publications": [ { "doi": "10.1109/jcdl.2017.7991571", "pmc": "PMC5868434", "pubmed": "29599662", "title": "Automating data citation: the eagle-i experience.", "year": 2017 }, { "doi": "10.1093/database/bar067", "pmc": "PMC3308157", "pubmed": "22434835", "title": "Research resources: curating the new eagle-i discovery system.", "year": 2012 } ], "uri_format": "http://purl.obolibrary.org/obo/ERO_$1", "version": "2016-07-27" }, "erv": { "description": "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features.", "example": "THE1B", "homepage": "https://herv.img.cas.cz/", "mappings": { "biocontext": "ERV", "miriam": "erv", "n2t": "erv" }, "name": "Human Endogenous Retrovirus Database", "pattern": "^[A-Za-z0-9\\-\\_]+$", "preferred_prefix": "erv", "uri_format": "https://herv.img.cas.cz/s/$1" }, "estdab": { "comment": "Website is dead", "deprecated": true, "description": "Cell line databases/resources", "example": "046", "homepage": "https://www.ebi.ac.uk/ipd/estdab/", "mappings": { "cellosaurus": "ESTDAB" }, "name": "European Searchable Tumour Line Database", "pattern": "^\\d{3}$", "preferred_prefix": "estdab", "uri_format": "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1" }, "eu89h": { "description": "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union.", "example": "jrc-eurl-ecvam-chemagora", "homepage": "http://data.jrc.ec.europa.eu/", "mappings": { "biocontext": "EU89H", "miriam": "eu89h", "n2t": "eu89h" }, "name": "JRC Data Catalogue", "pattern": "^[a-z0-9\\-_]+$", "preferred_prefix": "eu89h", "uri_format": "http://data.europa.eu/89h/$1" }, "euclinicaltrials": { "description": "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.", "example": "2008-005144-16", "homepage": "https://www.clinicaltrialsregister.eu/", "mappings": { "biocontext": "EUCLINICALTRIALS", "miriam": "euclinicaltrials", "n2t": "euclinicaltrials" }, "name": "EU Clinical Trials", "pattern": "^\\d{4}\\-\\d{6}\\-\\d{2}$", "preferred_prefix": "euclinicaltrials", "uri_format": "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1" }, "eupath": { "appears_in": [ "scdo" ], "contact": { "email": "jiezheng@pennmedicine.upenn.edu", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "description": "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.", "download_owl": "http://purl.obolibrary.org/obo/eupath.owl", "example": "0010316", "homepage": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology", "license": "CC BY 4.0", "mappings": { "aberowl": "EUPATH", "biocontext": "EUPATH", "bioportal": "EUPATH", "fairsharing": "FAIRsharing.9rhr9j", "obofoundry": "eupath", "ols": "eupath", "ontobee": "EUPATH" }, "name": "VEuPathDB ontology", "pattern": "^\\d{7}$", "preferred_prefix": "EUPATH", "publications": [ { "doi": "10.5281/zenodo.6685957", "pmc": null, "pubmed": null, "title": "Malaria study data integration and information retrieval based on OBO Foundry ontologies.", "year": null } ], "repository": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology", "uri_format": "http://purl.obolibrary.org/obo/EUPATH_$1", "version": "2022-06-08" }, "eurofir": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries.", "homepage": "https://www.eurofir.org", "name": "European Food Information Resource Network", "preferred_prefix": "eurofir", "proprietary": true }, "ev": { "appears_in": [ "cl" ], "contact": { "email": "evoc@sanbi.ac.za", "github": null, "name": "eVOC mailing list", "orcid": null }, "deprecated": true, "homepage": "http://www.evocontology.org/", "mappings": { "biocontext": "EV", "obofoundry": "ev", "prefixcommons": "evoc" }, "name": "eVOC (Expressed Sequence Annotation for Humans)", "preferred_prefix": "EV", "references": [ "https://twitter.com/Bgeedb/status/1350124337815281664" ], "uri_format": "http://purl.obolibrary.org/obo/EV_$1" }, "evm": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "name": "eVOC mouse development stage", "preferred_prefix": "evm", "references": [ "https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r229" ] }, "exac.gene": { "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information.", "example": "ENSG00000169174", "homepage": "http://exac.broadinstitute.org/", "mappings": { "biocontext": "EXAC.GENE", "miriam": "exac.gene", "n2t": "exac.gene" }, "name": "ExAC Gene", "pattern": "^ENSG\\d{11}$", "preferred_prefix": "exac.gene", "uri_format": "http://exac.broadinstitute.org/gene/$1" }, "exac.transcript": { "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information.", "example": "ENST00000407236", "homepage": "http://exac.broadinstitute.org/", "mappings": { "biocontext": "EXAC.TRANSCRIPT", "miriam": "exac.transcript", "n2t": "exac.transcript" }, "name": "ExAC Transcript", "pattern": "^ENST\\d{11}$", "preferred_prefix": "exac.transcript", "uri_format": "http://exac.broadinstitute.org/transcript/$1" }, "exac.variant": { "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information.", "example": "22-46615880-T-C", "homepage": "http://exac.broadinstitute.org/", "mappings": { "biocontext": "EXAC.VARIANT", "miriam": "exac.variant", "n2t": "exac.variant" }, "name": "ExAC Variant", "pattern": "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$", "preferred_prefix": "exac.variant", "uri_format": "http://exac.broadinstitute.org/variant/$1" }, "exo": { "appears_in": [ "ecto", "scdo" ], "contact": { "email": "annethessen@gmail.com", "github": "diatomsRcool", "name": "Anne Thessen", "orcid": "0000-0002-2908-3327" }, "description": "ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics.", "download_obo": "http://purl.obolibrary.org/obo/exo.obo", "download_owl": "http://purl.obolibrary.org/obo/exo.owl", "example": "0000078", "homepage": "https://github.com/CTDbase/exposure-ontology", "license": "CC BY 4.0", "mappings": { "aberowl": "EXO", "biocontext": "EXO", "biolink": "ExO", "bioportal": "EXO", "fairsharing": "FAIRsharing.6hna78", "obofoundry": "exo", "ols": "exo", "ontobee": "ExO" }, "name": "Exposure ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ExO", "publications": [ { "doi": "10.1021/es2033857", "pmc": "PMC3314380", "pubmed": "22324457", "title": "Providing the missing link: the exposure science ontology ExO.", "year": 2012 } ], "repository": "https://github.com/CTDbase/exposure-ontology", "synonyms": [ "ExO" ], "uri_format": "http://purl.obolibrary.org/obo/EXO_$1", "version": "2022-06-29" }, "fabio": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references.", "download_owl": "http://aber-owl.net/media/ontologies/FaBiO/1/fabio.owl", "example": "d4e2515", "homepage": "https://github.com/sparontologies/fabio", "mappings": { "aberowl": "FaBiO", "biolink": "fabio", "fairsharing": "FAIRsharing.2f3180" }, "name": "FaBiO, the FRBR-aligned Bibliographic Ontology", "preferred_prefix": "fabio", "providers": [ { "code": "rdf", "description": "A persistent URL for FaBiO", "homepage": "https://github.com/sparontologies/fabio", "name": "FABIO PURL", "uri_format": "http://purl.org/spar/fabio/$1" } ], "publications": [ { "doi": "10.1016/j.websem.2012.08.001", "pmc": null, "pubmed": null, "title": "FaBiO and CiTO: Ontologies for describing bibliographic resources and citations", "year": null } ], "repository": "https://github.com/sparontologies/fabio", "uri_format": "https://sparontologies.github.io/fabio/current/fabio.html#$1" }, "facebase": { "description": "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.", "example": "FB00000917", "homepage": "https://www.facebase.org", "mappings": { "biocontext": "FACEBASE", "fairsharing": "FAIRsharing.mqvqde", "miriam": "facebase", "n2t": "facebase", "re3data": "r3d100013263" }, "name": "FaceBase Data Repository", "pattern": "^FB\\d{8}$", "preferred_prefix": "facebase", "uri_format": "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1" }, "fairsharing": { "description": "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies.", "example": "bsg-000052", "homepage": "https://fairsharing.org/", "mappings": { "biocontext": "FAIRSHARING", "fairsharing": "FAIRsharing.2abjs5", "miriam": "fairsharing", "n2t": "fairsharing", "re3data": "r3d100010142" }, "name": "FAIRsharing", "pattern": "^bsg-[dscp]?\\d{6}$", "preferred_prefix": "fairsharing", "uri_format": "https://fairsharing.org/$1" }, "faldo": { "contact": { "email": "faldo@googlegroups.com", "github": null, "name": "FALDO group", "orcid": null }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources", "download_owl": "http://aber-owl.net/media/ontologies/FALDO/1/faldo.owl", "example": "ForwardStrandPosition", "homepage": "http://biohackathon.org/resource/faldo", "mappings": { "aberowl": "FALDO", "agroportal": "FALDO", "biocontext": "faldo", "bioportal": "FALDO", "fairsharing": "FAIRsharing.haxp7g" }, "name": "Feature Annotation Location Description Ontology ", "preferred_prefix": "faldo", "publications": [ { "doi": "10.1186/s13326-016-0067-z", "pmc": "PMC4907002", "pubmed": "27296299", "title": "FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.", "year": 2016 } ], "uri_format": "http://biohackathon.org/resource/faldo#$1" }, "fao": { "contact": { "email": "vw253@cam.ac.uk", "github": "ValWood", "name": "Val Wood", "orcid": "0000-0001-6330-7526" }, "description": "A structured controlled vocabulary for the anatomy of fungi.", "download_obo": "http://purl.obolibrary.org/obo/fao.obo", "download_owl": "http://purl.obolibrary.org/obo/fao.owl", "example": "0000001", "homepage": "https://github.com/obophenotype/fungal-anatomy-ontology/", "license": "CC0 1.0", "mappings": { "aberowl": "FAO", "biocontext": "FAO", "bioportal": "FAO", "fairsharing": "FAIRsharing.xs6t67", "obofoundry": "fao", "ols": "fao", "ontobee": "FAO", "prefixcommons": "fao" }, "name": "Fungal gross anatomy", "pattern": "^\\d{7}$", "preferred_prefix": "FAO", "repository": "https://github.com/obophenotype/fungal-anatomy-ontology", "uri_format": "http://purl.obolibrary.org/obo/FAO_$1", "version": "2020-05-07" }, "fbbi": { "contact": { "email": "wawong@gmail.com", "github": "wawong", "name": "Willy Wong", "orcid": "0000-0002-8841-5870" }, "description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.", "download_obo": "http://aber-owl.net/media/ontologies/FBbi/14/fbbi.obo", "download_owl": "http://purl.obolibrary.org/obo/fbbi.owl", "example": "00000268", "homepage": "http://cellimagelibrary.org/", "license": "CC BY 4.0", "mappings": { "aberowl": "FBbi", "biocontext": "FBbi", "bioportal": "FBbi", "fairsharing": "FAIRsharing.ny3z9j", "obofoundry": "fbbi", "ols": "fbbi", "ontobee": "FBBI", "prefixcommons": "fbbi" }, "name": "Biological Imaging Methods Ontology", "pattern": "^\\d+$", "preferred_prefix": "FBbi", "repository": "https://github.com/CRBS/Biological_Imaging_Methods_Ontology", "synonyms": [ "FBbi" ], "uri_format": "http://purl.obolibrary.org/obo/FBbi_$1", "version": "2020-11-06" }, "fbbt": { "contact": { "email": "cp390@cam.ac.uk", "github": "Clare72", "name": "Clare Pilgrim", "orcid": "0000-0002-1373-1705" }, "description": "An ontology of Drosophila melanogaster anatomy.", "download_json": "http://purl.obolibrary.org/obo/fbbt.json", "download_obo": "http://purl.obolibrary.org/obo/fbbt.obo", "download_owl": "http://purl.obolibrary.org/obo/fbbt.owl", "example": "00007294", "homepage": "http://purl.obolibrary.org/obo/fbbt", "license": "CC BY 4.0", "mappings": { "aberowl": 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FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world.", "download_owl": "http://aber-owl.net/media/ontologies/foaf/1/foaf.owl", "example": "familyName", "homepage": "http://xmlns.com/foaf/spec/", "mappings": { "aberowl": "foaf", "biocontext": "foaf", "biolink": "foaf", "bioportal": "FOAF" }, "name": "Friend of a Friend", "preferred_prefix": "foaf", "uri_format": "http://xmlns.com/foaf/0.1/$1" }, "fobi": { "contact": { "email": "polcaes@gmail.com", "github": "pcastellanoescuder", "name": "Pol Castellano Escuder", "orcid": "0000-0001-6466-877X" }, "depends_on": [ "chebi", "foodon" ], "description": "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data", "download_owl": "http://purl.obolibrary.org/obo/fobi.owl", "example": "030719", "example_extras": [ "0142", "07504" ], "homepage": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology", "license": "CC BY 3.0", "mappings": { "aberowl": "FOBI", "agroportal": "FOBI", "bioportal": "FOBI", "obofoundry": "fobi", "ols": "fobi", "ontobee": "FOBI" }, "name": "Food-Biomarker Ontology", "pattern": "^\\d{4,6}$", "preferred_prefix": "FOBI", "publications": [ { "doi": "10.1093/bioinformatics/btab626", "pmc": null, "pubmed": "34601570", "title": "The fobitools framework: the first steps towards food enrichment analysis.", "year": 2021 }, { "doi": "10.1093/databa/baaa033", "pmc": "PMC7298227", "pubmed": "32556148", "title": "FOBI: an ontology to represent food intake data and associate it with metabolomic data.", "year": 2020 } ], "repository": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology", "uri_format": "http://purl.obolibrary.org/obo/FOBI_$1" }, "foodb.compound": { "description": "FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds.", "example": "FDB002100", "homepage": "https://foodb.ca/", "mappings": { "biocontext": "FOODB.COMPOUND", "biolink": "foodb.compound", "miriam": "foodb.compound", "n2t": "foodb.compound", "re3data": "r3d100012152" }, "name": "FooDB Compound", "pattern": "^FDB\\d+$", "preferred_prefix": "foodb.compound", "synonyms": [ "foodb" ], "uri_format": "http://foodb.ca/compounds/$1" }, "foodb.food": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Foods in FooDB", "example": "FOOD00020", "homepage": "https://foodb.ca/foods", "mappings": { "biolink": "foodb.food" }, "name": "FooDB Food", "pattern": "^FOOD\\d+$", "preferred_prefix": "foodb.food", "uri_format": "https://foodb.ca/foods/$1" }, "foodex2": { "description": "FoodEx2 is a comprehensive food classification and description system aimed at covering the need to describe food in data collections across different food safety domains.", "example": "A0TMC", "homepage": "http://www.efsa.europa.eu/", "mappings": { "agroportal": "FOODEX2" }, "name": "Food classification and description system", "preferred_prefix": "foodex2", "uri_format": "http://data.food.gov.uk/codes/foodtype/id/$1" }, "foodon": { "appears_in": [ "agro", "envo", "fobi", "maxo", "one", "ons" ], "banana": "FOODON", "contact": { "email": "damion_dooley@sfu.ca", "github": "ddooley", "name": "Damion Dooley", "orcid": "0000-0002-8844-9165" }, "depends_on": [ "bfo", "chebi", "envo", "eo", "ncbitaxon", "obi", "ro", "uberon" ], "description": "FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies.", "download_obo": "http://purl.obolibrary.org/obo/foodon.obo", "download_owl": "http://purl.obolibrary.org/obo/foodon.owl", "example": "03307879", "homepage": "https://foodon.org/", "license": "CC BY 3.0", "mappings": { "aberowl": "FOODON", "agroportal": "FOODON", "biocontext": "FOODON", "bioportal": "FOODON", "fairsharing": "FAIRsharing.dzxae", "miriam": "foodon", "n2t": "foodon", "obofoundry": "foodon", "ols": "foodon", "ontobee": "FOODON" }, "name": "The Food Ontology", "namespace_in_lui": true, "pattern": "^[0-9]{8}$", "preferred_prefix": "FOODON", "publications": [ { "doi": "10.1038/s41538-018-0032-6", "pmc": "PMC6550238", "pubmed": "31304272", "title": "FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration.", "year": 2018 }, { "doi": "10.3389/fmicb.2017.01068", "pmc": "PMC5483436", "pubmed": "28694792", "title": "Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance.", "year": 2017 } ], "repository": "https://github.com/FoodOntology/foodon", "uri_format": "https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1", "version": "2022-02-01" }, "fossilworks.journal": { "contributor": { "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" }, "description": "Identifier for a journal article in the fossilworks website", "example": "61467", "github_request_issue": 468, "homepage": "http://fossilworks.org", "mappings": { "wikidata": "P7720" }, "name": "Fossilworks Journal", "part_of": "fossilworks", "pattern": "^\\d+$", "preferred_prefix": "fossilworks.journal", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://fossilworks.org/?a=referenceInfo&reference_no=$1" }, "fossilworks.taxon": { "contributor": { "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" }, "description": "Identifier for an animal, plant, or microorganism from the fossilworks website", "example": "40565", "github_request_issue": 469, "homepage": "http://www.fossilworks.org", "mappings": { "wikidata": "P842" }, "name": "Fossilworks Taxon", "part_of": "fossilworks", "pattern": "^[1-9]\\d{0,5}$", "preferred_prefix": "fossilworks.taxon", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1" }, "fovt": { "contact": { "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" }, "depends_on": [ "bco", "bfo", "bspo", "iao", "oba", "pato", "ro", "uberon" ], "description": "None", "download_obo": "http://purl.obolibrary.org/obo/fovt.obo", "download_owl": "http://purl.obolibrary.org/obo/fovt.owl", "example": "0000009", "homepage": "https://github.com/futres/fovt", "license": "CC0 1.0", "mappings": { "aberowl": "FOVT", "bioportal": "FOVT", "obofoundry": "fovt", "ols": "fovt", "ontobee": "FOVT" }, "name": "FuTRES Ontology of Vertebrate Traits", "pattern": "^\\d{7}$", "preferred_prefix": "FOVT", "repository": "https://github.com/futres/fovt", "uri_format": "http://purl.obolibrary.org/obo/FOVT_$1", "version": "2021-11-10" }, "fplx": { "contact": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships.", "example": "GPIb_IX_V", "homepage": "https://sorgerlab.github.io/famplex/", "mappings": { "aberowl": "FPLX", "biocontext": "FPLX", "bioportal": "FPLX", "miriam": "fplx", "n2t": "fplx" }, "name": "FamPlex", "pattern": "^[a-zA-Z0-9][A-Za-z0-9_]+$", "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": { "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", "mappings": { "fairsharing": "FAIRsharing.e7e609" }, "name": "FAIR* Reviews Ontology", "preferred_prefix": "FR", "repository": "https://github.com/sparontologies/fr" }, "frapo": { "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", "mappings": { "aberowl": "FRAPO", "fairsharing": "FAIRsharing.0a2576" }, "name": "Funding, Research Administration and Projects Ontology", "preferred_prefix": "FRAPO", "repository": "https://github.com/sparontologies/frapo", "uri_format": "http://purl.org/cerif/frapo/$1" }, "frbr": { "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", "mappings": { "fairsharing": "FAIRsharing.b34b43" }, "name": "Functional Requirements for Bibliographic Records", "preferred_prefix": "FRBR", "repository": "https://github.com/sparontologies/frbr", "uri_format": "http://purl.org/vocab/frbr/core#$1" }, "fsnp": { "description": "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.", "example": "rs17852708", "homepage": "http://compbio.cs.queensu.ca/F-SNP/", "mappings": { "biocontext": "FSNP", "miriam": "fsnp", "n2t": "fsnp", "prefixcommons": "fsnp" }, "name": "F-SNP", "pattern": "^rs\\d+$", "preferred_prefix": "fsnp", "uri_format": "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1" }, "ftt": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific.", "example": "273", "homepage": "https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3", "name": "Feature Type Thesaurus", "pattern": "^\\d+$", "preferred_prefix": "ftt", "references": [ "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200", "https://github.com/EnvironmentOntology/envo/issues/1130" ], "uri_format": "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1" }, "funcbase.fly": { "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data.", "example": "10194", "homepage": "http://func.mshri.on.ca/fly", "mappings": { "biocontext": "FUNCBASE.FLY", "miriam": "funcbase.fly", "n2t": "funcbase.fly" }, "name": "FuncBase Fly", "pattern": "^\\d+$", "preferred_prefix": "funcbase.fly", "uri_format": "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1" }, "funcbase.human": { "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data.", "example": "119514", "homepage": "http://func.mshri.on.ca/human/", "mappings": { "biocontext": "FUNCBASE.HUMAN", "miriam": "funcbase.human", "n2t": "funcbase.human" }, "name": "FuncBase Human", "pattern": "^\\d+$", "preferred_prefix": "funcbase.human", "uri_format": "http://func.mshri.on.ca/human/genes/list_functional_scores/$1" }, "funcbase.mouse": { "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse.", "example": "1351341", "homepage": "http://func.mshri.on.ca/mouse/", "mappings": { "biocontext": "FUNCBASE.MOUSE", "miriam": "funcbase.mouse", "n2t": "funcbase.mouse" }, "name": "FuncBase Mouse", "pattern": "^\\d+$", "preferred_prefix": "funcbase.mouse", "uri_format": "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1" }, "funcbase.yeast": { "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast.", "example": "2701", "homepage": "http://func.mshri.on.ca/yeast", "mappings": { "biocontext": "FUNCBASE.YEAST", "miriam": "funcbase.yeast", "n2t": "funcbase.yeast" }, "name": "FuncBase Yeast", "pattern": "^\\d+$", "preferred_prefix": "funcbase.yeast", "uri_format": "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1" }, "funderregistry": { "description": "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world.", "example": "100000001", "homepage": "https://www.crossref.org/", "mappings": { "miriam": "funderregistry" }, "name": "FunderRegistry", "pattern": "^\\d{9,9}$", "preferred_prefix": "funderregistry", "uri_format": "http://data.crossref.org/fundingdata/funder/10.13039/$1" }, "fungidb": { "description": "FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina.", "example": "CNBG_0001", "homepage": "https://fungidb.org/fungidb", "mappings": { "biocontext": "FUNGIDB", "fairsharing": "FAIRsharing.xf30yc", "miriam": "fungidb", "n2t": "fungidb", "re3data": "r3d100011906" }, "name": "FungiDB", "pattern": "^[A-Za-z_0-9]+$", "preferred_prefix": "fungidb", "uri_format": "https://fungidb.org/fungidb/app/record/gene/$1" }, "fungorum": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for a fungus taxon in Index Fungorum", "example": "154022", "homepage": "http://www.indexfungorum.org", "mappings": { "ncbi": "Fungorum", "wikidata": "P1391" }, "name": "Index Fungorum", "pattern": "^[1-9]\\d{0,5}$", "preferred_prefix": "fungorum", "uri_format": "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1" }, "fyeco": { "comment": "Rather than admitting FYECO to the OBO foundry, we secure the prefix here at bioregistry. The FYECO namespace shows up in a lot of ingests (basically anywhere you ingest PomBase gene-phenotype data). Future work includes mapping FYECO to other OBO ontologies, but this is way ahead in the future.", "contact": { "email": "vw253@cam.ac.uk", "github": "ValWood", "name": "Val Wood", "orcid": "0000-0001-6330-7526" }, "contributor": { "email": "vw253@cam.ac.uk", "github": "ValWood", "name": "Val Wood", "orcid": "0000-0001-6330-7526" }, "description": "PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase.", "example": "0000003", "github_request_issue": 268, "homepage": "https://github.com/pombase/fypo", "mappings": { "biolink": "FYECO" }, "name": "Fission Yeast Experimental Conditions Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "FYECO", "repository": "https://github.com/pombase/fypo", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "fyler": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A hierarchical classification of congenital heart disease ", "example": "4447", "homepage": "https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906", "name": "Fyler", "pattern": "^\\d+$", "preferred_prefix": "fyler", "references": [ "https://github.com/obophenotype/human-phenotype-ontology/issues/2568", "https://github.com/obophenotype/human-phenotype-ontology/issues/2511" ] }, "fypo": { "contact": { "email": "vw253@cam.ac.uk", "github": "ValWood", "name": "Val Wood", "orcid": "0000-0001-6330-7526" }, "description": "A formal ontology of phenotypes observed in fission yeast.", "download_json": "http://purl.obolibrary.org/obo/fypo.json", "download_obo": "http://purl.obolibrary.org/obo/fypo.obo", "download_owl": "http://purl.obolibrary.org/obo/fypo.owl", "example": "0001707", "homepage": "https://github.com/pombase/fypo", "license": "CC BY 4.0", "mappings": { "aberowl": "FYPO", "biocontext": "FYPO", "biolink": "FYPO", "bioportal": "FYPO", "fairsharing": "FAIRsharing.4vr0ys", "go": "FYPO", "obofoundry": "fypo", "ols": "fypo", "ontobee": "FYPO" }, "name": "Fission Yeast Phenotype Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "FYPO", "publications": [ { "doi": "10.1093/bioinformatics/btt266", "pmc": "PMC3694669", "pubmed": "23658422", "title": "FYPO: the fission yeast phenotype ontology.", "year": 2013 } ], "repository": "https://github.com/pombase/fypo", "uri_format": "http://purl.obolibrary.org/obo/FYPO_$1", "version": "2022-07-14" }, "ga4ghdos": { "description": "Assists in resolving data across cloud resources.", "example": "dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d", "homepage": "http://github.com/ga4gh/data-object-service-schemas", "mappings": { "biocontext": "GA4GHDOS", "miriam": "ga4ghdos", "n2t": "ga4ghdos" }, "name": "Data Object Service", "pattern": "^[a-zA-Z0-9\\-:#/\\.]+$", "preferred_prefix": "ga4ghdos", "uri_format": "https://dataguids.org/ga4gh/dos/v1/dataobjects/$1" }, "gabi": { "description": "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'.", "example": "2679240", "homepage": "http://www.gabipd.org/", "mappings": { "biocontext": "GABI", "miriam": "gabi", "n2t": "gabi", "ncbi": "GABI", "prefixcommons": "gabi" }, "name": "Network of Different Plant Genomic Research Projects", "pattern": "^\\w+$", "preferred_prefix": "gabi", "publications": [ { "doi": "10.1093/nar/gkn611", "pmc": "PMC2686513", "pubmed": "18812395", "title": "GabiPD: the GABI primary database--a plant integrative 'omics' database.", "year": 2008 } ], "uri_format": "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject" }, "galen": { "comment": "I really tried, but could not figure out what GALEN stands for", "contact": { "email": "j@deltaflow.com", "github": null, "name": "Julian Seidenberg", "orcid": null }, "deprecated": true, "description": "A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.", "download_owl": "http://aber-owl.net/media/ontologies/GALEN/1/galen.owl", "example": "MagnitudeValueType", "homepage": "https://www.opengalen.org", "mappings": { "aberowl": "GALEN", "bioportal": "GALEN" }, "name": "GALEN", "preferred_prefix": "galen", "uri_format": "http://www.co-ode.org/ontologies/galen#$1" }, "gard": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease.", "example": "6038", "homepage": "https://rarediseases.info.nih.gov/diseases", "mappings": { "wikidata": "P4317" }, "name": "Genetic and Rare Diseases Information Center", "pattern": "^\\d+$", "preferred_prefix": "gard", "synonyms": [ "GARD", "Genetic and Rare Diseases Information Center" ], "uri_format": "https://rarediseases.info.nih.gov/diseases/$1/index" }, "gateway": { "description": "The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access.", "example": "fd8d0743-344a-4758-bb97-f8ad84a37357", "homepage": "https://www.hdruk.ac.uk", "mappings": { "miriam": "gateway" }, "name": "Health Data Research Innovation Gateway", "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "preferred_prefix": "gateway", "uri_format": "https://web.www.healthdatagateway.org/dataset/$1" }, "gaz": { "appears_in": [ "scdo" ], "contact": { "email": "lschriml@som.umaryland.edu", "github": "lschriml", "name": "Lynn Schriml", "orcid": "0000-0001-8910-9851" }, "deprecated": true, "description": "A gazetteer constructed on ontological principles", "download_obo": "http://purl.obolibrary.org/obo/gaz.obo", "download_owl": "http://purl.obolibrary.org/obo/gaz.owl", "example": "00620027", "homepage": "http://environmentontology.github.io/gaz/", "license": "CC0 1.0", "mappings": { "aberowl": "GAZ", "biocontext": "GAZ", "bioportal": "GAZ", "fairsharing": "FAIRsharing.wkdjpb", "obofoundry": "gaz", "ols": "gaz", "ontobee": "GAZ", "wikidata": "P6778" }, "name": "Gazetteer", "pattern": "^\\d{8}$", "preferred_prefix": "GAZ", "repository": "https://github.com/EnvironmentOntology/gaz", "uri_format": "http://purl.obolibrary.org/obo/GAZ_$1" }, "gbif": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth.", "example": "4238", "homepage": "https://www.gbif.org/species", "mappings": { "fairsharing": "FAIRsharing.zv11j3", "wikidata": "P846" }, "name": "Global Biodiversity Information Facility", "pattern": "^\\d+$", "preferred_prefix": "gbif", "twitter": "GBIF", "uri_format": "https://www.gbif.org/species/$1" }, "gc": { "comment": "see comment here: https://github.com/obophenotype/ncbitaxon/issues/47", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries.", "example": "11", "homepage": "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html", "name": "Genetic Code", "pattern": "^\\d+$", "preferred_prefix": "gc", "references": [ "https://github.com/obophenotype/ncbitaxon/issues/47" ], "synonyms": [ "gc_id" ], "uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1" }, "gcst": { "description": "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide.", "example": "GCST000035", "homepage": "https://www.ebi.ac.uk", "mappings": { "miriam": "gcst", "n2t": "gcst" }, "name": "GWAS Catalog", "pattern": "^GCST\\d{6}\\d*$", "preferred_prefix": "gcst", "uri_format": "https://www.ebi.ac.uk/gwas/studies/$1" }, "gdc": { "description": "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis.", "example": "ae8c77fe-e6c8-44d5-8265-4a38c637bbef", "homepage": "https://gdc.cancer.gov", "mappings": { "biocontext": "GDC", "miriam": "gdc", "n2t": "gdc" }, "name": "Genomic Data Commons Data Portal", "pattern": "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$", "preferred_prefix": "gdc", "uri_format": "https://portal.gdc.cancer.gov/cases/$1" }, "gdsc": { "description": "The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies.", "example": "1242", "homepage": "https://www.cancerrxgene.org", "mappings": { "cellosaurus": "GDSC", "miriam": "gdsc", "n2t": "gdsc" }, "name": "Genomics of Drug Sensitivity in Cancer", "pattern": "^[0-9]+$", "preferred_prefix": "gdsc", "uri_format": "https://www.cancerrxgene.org/translation/Drug/$1" }, "gecko": { "contact": { "email": "rbca.jackson@gmail.com", "github": "beckyjackson", "name": "Rebecca Jackson", "orcid": "0000-0003-4871-5569" }, "description": "An ontology to represent genomics cohort attributes.", "download_owl": "http://purl.obolibrary.org/obo/gecko.owl", "example": "0000044", "homepage": "https://github.com/IHCC-cohorts/GECKO", "license": "CC BY 4.0", "mappings": { "aberowl": "GECKO", "bioportal": "GECKO", "fairsharing": "FAIRsharing.3da56b", "obofoundry": "gecko", "ols": "gecko", "ontobee": "GECKO" }, "name": "Genomics Cohorts Knowledge Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "GECKO", "repository": "https://github.com/IHCC-cohorts/GECKO", "uri_format": "http://purl.obolibrary.org/obo/GECKO_$1", "version": "2021-01-18" }, "gemet": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts.", "example": "627", "homepage": "https://www.eionet.europa.eu/gemet/en/themes/", "mappings": { "agroportal": "GEMET" }, "name": "General Multilingual Environmental Thesaurus", "pattern": "^\\d+$", "preferred_prefix": "gemet", "uri_format": "https://www.eionet.europa.eu/gemet/en/concept/$1" }, "genatlas": { "description": "GenAtlas is a database containing information on human genes, markers and phenotypes.", "example": "HBB", "homepage": "http://genatlas.medecine.univ-paris5.fr/", "mappings": { "biocontext": "GENATLAS", "fairsharing": "FAIRsharing.pmg2vd", "miriam": "genatlas", "n2t": "genatlas", "prefixcommons": "genatlas", "uniprot": "GenAtlas" }, "name": "Genatlas", "pattern": "^\\w+$", "preferred_prefix": "genatlas", "publications": [ { "doi": "10.1016/s0764-4469(99)80021-3", "pmc": null, "pubmed": "9835018", "title": "Genatlas database, genes and development defects.", "year": 1998 } ], "uri_format": "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1" }, "genbank": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42).", "example": "U49845", "homepage": "https://www.ncbi.nlm.nih.gov/genbank/", "mappings": { "biocontext": "GenBank", "cheminf": "000304", "edam": "2292", "fairsharing": "FAIRsharing.9kahy4", "go": "GenBank", "prefixcommons": "genbank", "re3data": "r3d100010528", "uniprot": "GenBank" }, "name": "GenBank", "preferred_prefix": "genbank", "uri_format": "https://www.ncbi.nlm.nih.gov/nucleotide/$1" }, "genecards": { "description": "The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene.", "example": "ABL1", "homepage": "http://www.genecards.org/", "mappings": { "biocontext": "GENECARDS", "fairsharing": "FAIRsharing.g7jbvn", "miriam": "genecards", "n2t": "genecards", "prefixcommons": "genecards", "re3data": "r3d100012015", "uniprot": "GeneCards" }, "name": "GeneCards", "pattern": "^[A-Za-z-0-9_]+(\\@)?$", "preferred_prefix": "genecards", "publications": [ { "doi": "10.1093/database/baq020", "pmc": "PMC2938269", "pubmed": "20689021", "title": "GeneCards Version 3: the human gene integrator.", "year": 2010 } ], "uri_format": "https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1" }, "genedb": { "deprecated": true, "description": "GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the \"Pathogen Genomics\" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed.", "example": "LinJ.20.0070", "homepage": "https://www.genedb.org/", "mappings": { "biocontext": "GENEDB", "edam": "1035", "fairsharing": "FAIRsharing.j7esqq", "go": "GeneDB", "miriam": "genedb", "n2t": "genedb", "ncbi": "GeneDB", "prefixcommons": "genedb", "re3data": "r3d100010626", "uniprot": "GeneDB", "wikidata": "P3382" }, "name": "GeneDB", "pattern": "^[\\w\\d\\.-]*$", "preferred_prefix": "genedb", "publications": [ { "doi": "10.1093/nar/gkh007", "pmc": "PMC308742", "pubmed": "14681429", "title": "GeneDB: a resource for prokaryotic and eukaryotic organisms.", "year": 2004 } ], "uri_format": "https://www.genedb.org/gene/$1" }, "genefarm": { "description": "GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products.", "example": "4892", "homepage": "http://urgi.versailles.inra.fr/Genefarm/", "mappings": { "biocontext": "GENEFARM", "fairsharing": "FAIRsharing.2mayq0", "miriam": "genefarm", "n2t": "genefarm", "prefixcommons": "genefarm" }, "name": "GeneFarm", "pattern": "^\\d+$", "preferred_prefix": "genefarm", "publications": [ { "doi": "10.1093/nar/gki115", "pmc": "PMC540069", "pubmed": "15608279", "title": "GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts.", "year": 2005 } ], "uri_format": "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1" }, "genepio": { "contact": { "email": "damion_dooley@sfu.ca", "github": "ddooley", "name": "Damion Dooley", "orcid": "0000-0002-8844-9165" }, "depends_on": [ "chebi", "ncbitaxon", "po", "ro", "uberon" ], "description": "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.", "download_owl": "http://purl.obolibrary.org/obo/genepio.owl", "example": "0001885", "homepage": "http://genepio.org/", "license": "CC BY 3.0", "mappings": { "aberowl": "GENEPIO", "biocontext": "GENEPIO", "fairsharing": "FAIRsharing.y1mmbv", "obofoundry": "genepio", "ols": "genepio", "ontobee": "GENEPIO" }, "name": "Genomic Epidemiology Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "GENEPIO", "repository": "https://github.com/GenEpiO/genepio", "uri_format": "http://purl.obolibrary.org/obo/GENEPIO_$1", "version": "2022-02-06" }, "genetree": { "description": "Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl.", "example": "ENSGT00550000074763", "homepage": "http://www.ensembl.org/", "mappings": { "biocontext": "GENETREE", "miriam": "genetree", "n2t": "genetree", "prefixcommons": "genetree", "uniprot": "GeneTree" }, "name": "GeneTree", "pattern": "^ENSGT\\d+$", "preferred_prefix": "genetree", "publications": [ { "doi": "10.1093/nar/gkj133", "pmc": "PMC1347495", "pubmed": "16381931", "title": "Ensembl 2006.", "year": 2006 } ], "uri_format": "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1" }, "genewiki": { "description": "The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI.", "example": "1017", "homepage": "http://en.wikipedia.org/wiki/Gene_Wiki", "mappings": { "biocontext": "GENEWIKI", "fairsharing": "FAIRsharing.t3snf", "miriam": "genewiki", "n2t": "genewiki", "uniprot": "GeneWiki" }, "name": "Gene Wiki", "pattern": "^\\d+$", "preferred_prefix": "genewiki", "uri_format": "http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1" }, "geno": { "contact": { "email": "mhb120@gmail.com", "github": "mbrush", "name": "Matthew Brush", "orcid": "0000-0002-1048-5019" }, "description": "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013", "download_json": "http://purl.obolibrary.org/obo/geno.json", "download_obo": "https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/develop/geno-full.obo", "download_owl": "http://purl.obolibrary.org/obo/geno.owl", "example": "0000632", "homepage": "https://github.com/monarch-initiative/GENO-ontology/", "license": "CC BY 4.0", "mappings": { "aberowl": "GENO", "biocontext": "GENO", "bioportal": "GENO", "fairsharing": "FAIRsharing.kpbna7", "obofoundry": "geno", "ols": "geno", "ontobee": "GENO" }, "name": "Genotype Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "GENO", "repository": "https://github.com/monarch-initiative/GENO-ontology", "uri_format": "http://purl.obolibrary.org/obo/GENO_$1", "version": "2022-03-05" }, "genpept": { "description": "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank.", "example": "CAA71118.1", "homepage": "https://www.ncbi.nlm.nih.gov/protein", "mappings": { "biocontext": "GENPEPT", "miriam": "genpept", "n2t": "genpept" }, "name": "GenPept", "pattern": "^\\w{3}\\d{5}(\\.\\d+)?$", "preferred_prefix": "genpept", "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept" }, "genprop": { "description": "Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome.", "example": "GenProp0699", "homepage": "https://www.ebi.ac.uk/interpro/genomeproperties/", "mappings": { "biocontext": "GENPROP", "miriam": "genprop", "n2t": "genprop", "prefixcommons": "jcvi.genprop" }, "name": "Genome Properties", "pattern": "^GenProp\\d+$", "preferred_prefix": "genprop", "uri_format": "https://www.ebi.ac.uk/interpro/genomeproperties/#$1" }, "geo": { "banana_peel": "_", "description": "The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval.", "download_owl": "http://aber-owl.net/media/ontologies/GEO/4/geo.owl", "example": "GDS1234", "homepage": "https://www.ncbi.nlm.nih.gov/geo/", "mappings": { "aberowl": "GEO", "biocontext": "GEO", "cellosaurus": "GEO", "edam": "1147", "fairsharing": "FAIRsharing.27rndz", "go": "GEO", "miriam": "geo", "n2t": "geo", "prefixcommons": "geo" }, "name": "NCBI Gene Expression Omnibus", "pattern": "^G(PL|SM|SE|DS)\\d+$", "preferred_prefix": "geo", "publications": [ { "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 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1" }, "geogeo": { "banana": "GEO", "banana_peel": "_", "contact": { "email": "hoganwr@gmail.com", "github": "hoganwr", "name": "Bill Hogan", "orcid": "0000-0002-9881-1017" }, "description": "An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in \"The US declared war on Germany\" vs. the US in \"The plane entered US airspace\".", "download_owl": "http://purl.obolibrary.org/obo/geo.owl", "example": "000000021", "homepage": "https://github.com/ufbmi/geographical-entity-ontology/wiki", "license": "CC BY 4.0", "mappings": { "biocontext": "GEO", "bioportal": "GEO", "miriam": "geogeo", "obofoundry": "geo", "ols": "geo", "ontobee": "GEO" }, "name": "Geographical Entity Ontology", "namespace_in_lui": true, "pattern": "^\\d{9}$", "preferred_prefix": "GEOGEO", "repository": "https://github.com/ufbmi/geographical-entity-ontology", "uri_format": "http://purl.obolibrary.org/obo/GEO_$1", "version": "2016-03-26" }, "geonames": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge.", "example": "3532759", "homepage": "https://www.geonames.org", "mappings": { "fairsharing": "FAIRsharing.6dba71", "re3data": "r3d100010245" }, "name": "GeoNames", "pattern": "^\\d+$", "preferred_prefix": "geonames", "synonyms": [ "Geomames", "Geonamaes" ], "uri_format": "https://www.geonames.org/$1" }, "geonames.feature": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes.", "example": "ADM1", "homepage": "https://www.geonames.org/export/codes.html", "name": "GeoNames Feature Code", "preferred_prefix": "geonames.feature", "uri_format": "https://www.geonames.org/recent-changes/featurecode/$1/" }, "gexo": { "contact": { "email": "vladimir.n.mironov@gmail.com", "github": null, "name": "Vladimir Mironov", "orcid": null }, "description": "Gene Expression Ontology", "download_obo": "https://www.bio.ntnu.no/ontology/GeXO/gexo.obo", "download_owl": "https://www.bio.ntnu.no/ontology/GeXO/gexo.owl", "homepage": "http://www.semantic-systems-biology.org/apo", "mappings": { "aberowl": "GEXO", "bioportal": "GEXO", "fairsharing": "FAIRsharing.3e0sn4", "ols": "gexo" }, "name": "Gene Expression Ontology", "no_own_terms": true, "preferred_prefix": "gexo", "publications": [ { "doi": "10.1186/s12859-014-0386-y", "pmc": "PMC4279962", "pubmed": "25490885", "title": "Finding gene regulatory network candidates using the gene expression knowledge base.", "year": 2014 } ], "version": "2019-09-18" }, "gfo": { "contact": { "email": "heinrich.herre@imise.uni-leipzig.de", "github": null, "name": "Heinrich Herre", "orcid": null }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The General Formal Ontology is a top-level ontology for conceptual modeling, which is being constantly further developed by Onto-Med. It includes elaborations of categories like objects, processes, time and space, properties, relations, roles, functions, facts, and situations. Moreover, we are working on an integration with the notion of levels of reality in order to more appropriately capture entities in the material, mental, and social areas.", "download_owl": "http://www.onto-med.de/ontologies/gfo.owl", "example": "projects_to", "homepage": "https://www.onto-med.de/ontologies/gfo", "mappings": { "aberowl": "GFO", "bioportal": "GFO", "fairsharing": "FAIRsharing.175hsz" }, "name": "General Formal Ontology", "preferred_prefix": "gfo", "uri_format": "http://www.onto-med.de/ontologies/gfo.owl#$1" }, "ghr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA).", "example": "saddan", "homepage": "https://medlineplus.gov/genetics/condition", "name": "Genetics Home Reference", "preferred_prefix": "ghr", "uri_format": "https://medlineplus.gov/genetics/condition/$1" }, "giardiadb": { "description": "GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "GL50803_102438", "homepage": "https://giardiadb.org/giardiadb/", "mappings": { "biocontext": "GIARDIADB", "fairsharing": "FAIRsharing.e7skwg", "miriam": "giardiadb", "n2t": "giardiadb", "prefixcommons": "giardiadb", "re3data": "r3d100012458" }, "name": "GiardiaDB", "pattern": "^\\w+$", "preferred_prefix": "giardiadb", "publications": [ { "doi": "10.1093/nar/gkn631", "pmc": "PMC2686445", "pubmed": "18824479", "title": "GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.", "year": 2008 } ], "uri_format": "https://giardiadb.org/giardiadb/app/record/gene/$1" }, "github": { "description": "GitHub is an online host of Git source code repositories.", "example": "biopragmatics/bioregistry", "example_extras": [ "biopragmatics", "cthoyt" ], "homepage": "https://github.com/", "mappings": { "fairsharing": "FAIRsharing.c55d5e", "miriam": "github", "re3data": "r3d100010375" }, "name": "github", "pattern": "^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$", "preferred_prefix": "github", "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/", "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/", "name": "GitHub Pull Request", "preferred_prefix": "github.pull", "uri_format": "https://bioregistry.io/resolve/github/pull/$1" }, "gitlab": { "description": "GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance. With GitLab, every team in your organization can collaboratively plan, build, secure, and deploy software to drive business outcomes faster with complete transparency, consistency and traceability.", "example": "morpheus.lab/morpheus", "homepage": "https://gitlab.com/", "mappings": { "fairsharing": "FAIRsharing.530e61", "miriam": "gitlab" }, "name": "GitLab", "pattern": "^.*/.*$", "preferred_prefix": "gitlab", "uri_format": "https://gitlab.com/$1" }, "glida.gpcr": { "description": "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors.", "example": "ACM1_HUMAN", "homepage": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/", "mappings": { "biocontext": "GLIDA.GPCR", "miriam": "glida.gpcr", "n2t": "glida.gpcr" }, "name": "GLIDA GPCR", "pattern": "^[A-Z-_0-9]+$", "preferred_prefix": "glida.gpcr", "uri_format": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1" }, "glida.ligand": { "description": "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands.", "example": "L000001", "homepage": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/", "mappings": { "biocontext": "GLIDA.LIGAND", "miriam": "glida.ligand", "n2t": "glida.ligand" }, "name": "GLIDA Ligand", "pattern": "^L\\d+$", "preferred_prefix": "glida.ligand", "uri_format": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1" }, "glycoepitope": { "description": "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes.", "example": "EP0311", "homepage": "https://www.glycoepitope.jp/epitopes/", "mappings": { "biocontext": "GLYCOEPITOPE", "miriam": "glycoepitope", "n2t": "glycoepitope" }, "name": "GlycoEpitope", "pattern": "^EP\\d{4}$", "preferred_prefix": "glycoepitope", "uri_format": "https://www.glycoepitope.jp/epitopes/$1" }, "glycomedb": { "comment": "this is exactly the same as glytoucan. Idk why there are two different ones", "description": "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.", "example": "G77500AY", "has_canonical": "glytoucan", "homepage": "https://glytoucan.org/", "mappings": { "biocontext": "GLYCOMEDB", "edam": "2664", "fairsharing": "FAIRsharing.k5k0yh", "miriam": "glycomedb", "n2t": "glycomedb", "prefixcommons": "glycomedb", "re3data": "r3d100011527" }, "name": "GlycomeDB", "pattern": "^\\w+$", "preferred_prefix": "glycomedb", "publications": [ { "doi": "10.1093/glycob/cwp137", "pmc": null, "pubmed": "19759275", "title": "Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences.", "year": 2009 } ], "uri_format": "https://glytoucan.org/Structures/Glycans/$1" }, "glyconavi": { "description": "GlycoNAVI is a website for carbohydrate research. It consists of the \"GlycoNAVI Database\" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the \"GlycoNAVI tools\" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools.", "example": "GN_G03681DA", "example_extras": [ "GN_GlyTouCan_G03681DA" ], "homepage": "https://www.noguchi.or.jp/", "mappings": { "fairsharing": "FAIRsharing.wvp1t7", "miriam": "glyconavi" }, "name": "GlycoNAVI", "pattern": "^GN_[A-Za-z0-9_:]+$", "preferred_prefix": "glyconavi", "uri_format": "https://glyconavi.org/hub/?id=$1" }, "glycopost": { "description": "GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their \"raw/processed\" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines.", "example": "GPST000024", "homepage": "https://glycopost.glycosmos.org", "mappings": { "fairsharing": "FAIRsharing.2y1KMt", "miriam": "glycopost" }, "name": "GlycoPOST", "pattern": "^GPST[0-9]{6}$", "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": null, "pubmed": null, "title": "Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update)", "year": null } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "glycosciences.db" ], "uri_format": "http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=$1" }, "glygen": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data.", "example": "G24361QY", "homepage": "https://glygen.org/glycan/", "mappings": { "fairsharing": "FAIRsharing.aI1J5W", "uniprot": "GlyGen" }, "name": "Computational and Informatics Resources for Glycoscience", "preferred_prefix": "glygen", "uri_format": "https://glygen.org/glycan/$1" }, "glytoucan": { "description": "GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data.", "example": "G00054MO", "homepage": "https://glytoucan.org", "mappings": { "biocontext": "GLYTOUCAN", "miriam": "glytoucan", "n2t": "glytoucan", "re3data": "r3d100012388" }, "name": "GlyTouCan", "pattern": "^G[0-9]{5}[A-Z]{2}$", "preferred_prefix": "glytoucan", "uri_format": "https://glytoucan.org/Structures/Glycans/$1" }, "gmd": { "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena.", "example": "68513255-fc44-4041-bc4b-4fd2fae7541d", "homepage": "http://gmd.mpimp-golm.mpg.de/", "mappings": { "biocontext": "GMD", "fairsharing": "FAIRsharing.jykmkw", "miriam": "gmd", "n2t": "gmd" }, "name": "Golm Metabolome Database", "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", "preferred_prefix": "gmd", "uri_format": "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx" }, "gmd.analyte": { "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes.", "example": "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80", "homepage": "http://gmd.mpimp-golm.mpg.de/", "mappings": { "biocontext": "GMD.ANALYTE", "miriam": "gmd.analyte", "n2t": "gmd.analyte" }, "name": "Golm Metabolome Database Analyte", "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", "preferred_prefix": "gmd.analyte", "uri_format": "http://gmd.mpimp-golm.mpg.de/Analytes/$1" }, "gmd.gcms": { "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra.", "example": "53d583d8-40c6-40e1-9296-23f821cd77a5", "homepage": "http://gmd.mpimp-golm.mpg.de/", "mappings": { "biocontext": "GMD.GCMS", "miriam": "gmd.gcms", "n2t": "gmd.gcms" }, "name": "Golm Metabolome Database GC-MS spectra", "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", "preferred_prefix": "gmd.gcms", "uri_format": "http://gmd.mpimp-golm.mpg.de/Spectrums/$1" }, "gmd.profile": { "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues.", "example": "10b38aaf-b977-4950-85b8-f4775f66658d", "homepage": "http://gmd.mpimp-golm.mpg.de/", "mappings": { "biocontext": "GMD.PROFILE", "miriam": "gmd.profile", "n2t": "gmd.profile" }, "name": "Golm Metabolome Database Profile", "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", "preferred_prefix": "gmd.profile", "uri_format": "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1" }, "gmd.ref": { "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances.", "example": "8cf84adb-b4db-4807-ac98-0004247c35df", "homepage": "http://gmd.mpimp-golm.mpg.de/", "mappings": { "biocontext": "GMD.REF", "miriam": "gmd.ref", "n2t": "gmd.ref" }, "name": "Golm Metabolome Database Reference Substance", "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", "preferred_prefix": "gmd.ref", "uri_format": "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1" }, "gmelin": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s.", "example": "1466", "homepage": "https://link.springer.com/bookseries/562", "mappings": { "edam": "1004", "wikidata": "P1578" }, "name": "Gmelins Handbuch der anorganischen Chemie", "pattern": "^[1-9][0-9]{3,6}$", "preferred_prefix": "gmelin", "proprietary": true, "references": [ "https://en.wikipedia.org/wiki/Gmelin_database" ] }, "gno": { "contact": { "email": "nje5@georgetown.edu", "github": "edwardsnj", "name": "Nathan Edwards", "orcid": "0000-0001-5168-3196" }, "description": "An ontology for glycans based on GlyTouCan, but organized by subsumption.", "download_json": "http://purl.obolibrary.org/obo/gno.json", "download_obo": "http://purl.obolibrary.org/obo/gno.obo", "download_owl": "http://purl.obolibrary.org/obo/gno.owl", "example": "10004892", "example_extras": [ "G99373GG" ], "homepage": "https://gnome.glyomics.org/", "license": "CC BY 4.0", "mappings": { "aberowl": "GNO", "bioportal": "GNO", "obofoundry": "gno", "ols": "gno", "ontobee": "GNO" }, "name": "Glycan Naming and Subsumption Ontology", "pattern": "^(\\d{8}|(\\w+\\d+\\w+))$", "preferred_prefix": "GNO", "providers": [ { "code": "gno.composition", "description": "GNOme composition browser", "homepage": "https://gnome.glyomics.org/CompositionBrowser.html", "name": "GNOme Composition Browser", "uri_format": "https://gnome.glyomics.org/CompositionBrowser.html?focus=$1" }, { "code": "gno.structure", "description": "GNOme structure browser", "homepage": "https://gnome.glyomics.org/StructureBrowser.html", "name": "GNOme Structure Viewer", "uri_format": "https://gnome.glyomics.org/StructureBrowser.html?focus=$1" } ], "publications": [ { "doi": "10.5281/zenodo.6678278", "pmc": null, "pubmed": null, "title": "GNOme - Glycan Naming and Subsumption Ontology", "year": null } ], "repository": "https://github.com/glygen-glycan-data/GNOme", "synonyms": [ "gnome" ], "uri_format": "http://purl.obolibrary.org/obo/GNO_$1", "version": "1.10.0" }, "gnpis": { "description": "GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest.", "example": "AY109603", "homepage": "https://urgi.versailles.inra.fr/gnpis/", "mappings": { "biocontext": "GNPIS", "fairsharing": "FAIRsharing.dw22y3", "miriam": "gnpis", "n2t": "gnpis", "re3data": "r3d100012647" }, "name": "GnpIS", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "gnpis", "uri_format": "https://urgi.versailles.inra.fr/gnpis/#result/term=$1" }, "go": { "appears_in": [ "agro", "chiro", "cl", "ecocore", "ecto", "envo", "maxo", "pcl", "pco", "planp", "uberon", "xpo", "zp" ], "banana": "GO", "contact": { "email": "suzia@stanford.edu", "github": "suzialeksander", "name": "Suzi Aleksander", "orcid": "0000-0001-6787-2901" }, "depends_on": [ "cl", "ncbitaxon", "ro", "uberon" ], "description": "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.", "download_json": "http://purl.obolibrary.org/obo/go.json", "download_obo": "http://purl.obolibrary.org/obo/go.obo", "download_owl": "http://purl.obolibrary.org/obo/go.owl", "example": "0032571", "homepage": "http://geneontology.org/", "license": "CC BY 4.0", "mappings": { "aberowl": "GO", "agroportal": "GO", "biocontext": "GO", "bioportal": "GO", "edam": "1176", "fairsharing": "FAIRsharing.6xq0ee", "go": "GO", "hl7": "2.16.840.1.113883.6.128", "miriam": "go", "n2t": "go", "ncbi": "GO", "obofoundry": "go", "ols": "go", "ontobee": "GO", "prefixcommons": "go", "uniprot": "GO", "wikidata": "P686" }, "name": "Gene Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "GO", "providers": [ { "code": "CURATOR_REVIEW", "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": "CURATOR_REVIEW", "description": "GO through PANTHER", "homepage": "http://www.pantherdb.org/", "name": "GO through PANTHER", "uri_format": "http://www.pantherdb.org/panther/category.do?categoryAcc=GO:$1" }, { "code": "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": "quickgo", "description": "QuickGO (Gene Ontology browser)", "homepage": "https://www.ebi.ac.uk/QuickGO/", "name": "QuickGO (Gene Ontology browser)", "uri_format": "https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:$1" } ], "publications": [ { "doi": "10.1093/nar/gkaa1113", "pmc": "PMC7779012", "pubmed": "33290552", "title": "The Gene Ontology resource: enriching a GOld mine.", "year": 2021 }, { "doi": "10.1093/nar/gky1055", "pmc": "PMC6323945", "pubmed": "30395331", "title": "The Gene Ontology Resource: 20 years and still GOing strong.", "year": 2019 }, { "doi": "10.1093/nar/gku1179", "pmc": "PMC4383973", "pubmed": "25428369", "title": "Gene Ontology Consortium: going forward.", "year": 2014 }, { "doi": "10.1186/1471-2164-14-513", "pmc": "PMC3733925", "pubmed": "23895341", "title": "Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.", "year": 2013 }, { "doi": "10.1093/nar/gks1050", "pmc": "PMC3531070", "pubmed": "23161678", "title": "Gene Ontology annotations and resources.", "year": 2012 }, { "doi": "10.1093/nar/gkr1028", "pmc": "PMC3245151", "pubmed": "22102568", "title": "The Gene Ontology: enhancements for 2011.", "year": 2011 }, { "doi": "10.1093/nar/gkp1018", "pmc": "PMC2808930", "pubmed": "19920128", "title": "The Gene Ontology in 2010: extensions and refinements.", "year": 2009 }, { "doi": "10.1093/nar/gkh036", "pmc": "PMC308770", "pubmed": "14681407", "title": "The Gene Ontology (GO) database and informatics resource.", "year": 2004 }, { "doi": "10.1038/75556", "pmc": "PMC3037419", "pubmed": "10802651", "title": "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.", "year": 2000 } ], "repository": "https://github.com/geneontology/go-ontology", "synonyms": [ "gobp", "gobpid", "gocc", "goccid", "gomf", "gomfid" ], "twitter": "news4go", "uri_format": "http://amigo.geneontology.org/amigo/term/GO:$1", "version": "2022-07-01" }, "go.model": { "description": "GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform.", "example": "5fce9b7300001250", "homepage": "http://www.geneontology.org/gocam", "mappings": { "go": "gomodel" }, "name": "Gene Ontology Causal Assembly Model", "preferred_prefix": "go.model", "uri_format": "http://noctua.geneontology.org/editor/graph/gomodel:$1" }, "go.ref": { "banana": "GO_REF", "description": "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made.", "example": "0000041", "homepage": "http://www.geneontology.org/cgi-bin/references.cgi", "mappings": { "biocontext": "GO_REF", "go": "GO_REF", "miriam": "go_ref", "n2t": "go.ref" }, "name": "Gene Ontology Database references", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "go.ref", "uri_format": "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-$1.md" }, "go.resource": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A database-specific registry supporting curation in the Gene Ontology", "example": "CHEBI", "homepage": "http://geneontology.org/", "name": "Gene Ontology Registry", "preferred_prefix": "go.resource", "uri_format": "https://bioregistry.io/metaregistry/go/$1" }, "goa": { "description": "The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups.", "example": "P12345", "homepage": "https://www.ebi.ac.uk/GOA/", "mappings": { "biocontext": "GOA", "fairsharing": "FAIRsharing.7zffgc", "miriam": "goa", "n2t": "goa", "ncbi": "GOA", "prefixcommons": "goa" }, "name": "Gene Ontology Annotation Database", "pattern": "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$", "preferred_prefix": "goa", "provides": "uniprot", "publications": [ { "doi": "10.1093/nar/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=$1" }, "goche": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Represent chemical entities having particular CHEBI roles", "download_owl": "https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl", "example": "25512", "homepage": "https://github.com/geneontology/go-ontology", "name": "GO Chemicals", "pattern": "^\\d+$", "preferred_prefix": "GOCHE", "references": [ "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638472847049400", "https://github.com/geneontology/go-ontology/issues/19535" ], "repository": "https://github.com/geneontology/go-ontology", "synonyms": [ "go.chebi", "go.chemical", "go.chemicals" ], "uri_format": "https://biopragmatics.github.io/providers/goche/$1" }, "goeco": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported.", "example": "IPI", "homepage": "http://geneontology.org/docs/guide-go-evidence-codes/", "name": "GO Evidence Code", "preferred_prefix": "goeco" }, "gold": { "description": "The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.", "example": "Gs0000008", "homepage": "https://gold.jgi.doe.gov/", "mappings": { "fairsharing": "FAIRsharing.5q1p14", "miriam": "gold", "prefixcommons": "gold" }, "name": "Genomes Online Database", "pattern": "^[A-Z][a-z][0-9]+$", "preferred_prefix": "gold", "uri_format": "https://gold.jgi.doe.gov/resolver?id=$1" }, "gold.genome": { "description": "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace.\n\nThe GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes.", "example": "Gi07796", "homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi", "mappings": { "biocontext": "GOLD.GENOME", "miriam": "gold.genome", "n2t": "gold.genome" }, "name": "GOLD genome", "pattern": "^(Gi|Gc)\\d+$", "preferred_prefix": "gold.genome", "uri_format": "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1" }, "gold.meta": { "description": "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples.", "example": "Gm00047", "has_canonical": "gold", "homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi", "mappings": { "biocontext": "GOLD.META", "miriam": "gold.meta", "n2t": "gold.meta" }, "name": "GOLD metadata", "pattern": "^Gm\\d+$", "preferred_prefix": "gold.meta", "uri_format": "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1" }, "goldbook": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Compendium is popularly referred to as the \"Gold Book\", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC \"Colour Books\" on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books.\n\nTerminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC's Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry.", "example": "G02681", "homepage": "https://goldbook.iupac.org", "license": "CC BY 4.0-NC-ND", "name": "IUPAC Gold Book Compendium of Chemical Terminology", "preferred_prefix": "goldbook", "uri_format": "https://goldbook.iupac.org/terms/view/$1" }, "google.book": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Search the world's most comprehensive index of full-text books.", "example": "qafeQTWIWmcC", "github_request_issue": 511, "homepage": "https://books.google.com", "mappings": { "wikidata": "P675" }, "name": "Google Books", "preferred_prefix": "google.book", "uri_format": "https://books.google.com/books?id=$1" }, "google.patent": { "contributor_extras": [ { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" } ], "description": "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date.", "example": "US4145692", "example_extras": [ "USRE38117E1" ], "homepage": "https://www.google.com/patents/", "mappings": { "biocontext": "GOOGLE.PATENT", "cellosaurus": "Patent", "miriam": "google.patent", "n2t": "google.patent" }, "name": "Google Patents", "pattern": "^[A-Z]{2,4}\\d+([A-Z])?([0-9])?$", "preferred_prefix": "google.patent", "synonyms": [ "patent" ], "uri_format": "https://www.google.com/patents/$1" }, "google.scholar": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.", "example": "PjrpzUIAAAAJ", "homepage": "https://scholar.google.com/", "mappings": { "biolink": "GSID" }, "name": "Google Scholar Researcher", "preferred_prefix": "google.scholar" }, "gorel": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.", "download_owl": "ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl", "example": "0002005", "homepage": "http://geneontology.org/docs/ontology-relations/", "mappings": { "biolink": "GOREL", "go": "GOREL" }, "name": "GO Relations", "pattern": "^\\d{7}$", "preferred_prefix": "gorel", "providers": [ { "code": "obo.legacy", "description": "Legacy OBO PURLs", "homepage": "http://purl.obolibrary.org/obo/gorel.owl", "name": "Legacy OBO", "uri_format": "http://purl.obolibrary.org/obo/GOREL_$1" } ] }, "gpcrdb": { "description": "The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models.", "example": "RL3R1_HUMAN", "homepage": "http://www.gpcrdb.org/", "mappings": { "biocontext": "GPCRDB", "fairsharing": "FAIRsharing.e4n3an", "miriam": "gpcrdb", "n2t": "gpcrdb", "prefixcommons": "gpcrdb", "uniprot": "GPCRDB" }, "name": "G protein-coupled receptor database", "pattern": "^\\w+$", "preferred_prefix": "gpcrdb", "publications": [ { "doi": "10.1093/nar/gkq1009", "pmc": "PMC3013641", "pubmed": "21045054", "title": "GPCRDB: information system for G protein-coupled receptors.", "year": 2010 } ], "uri_format": "https://gpcrdb.org/protein/$1" }, "gpmdb": { "description": "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns.", "example": "GPM32310002988", "homepage": "http://gpmdb.thegpm.org/", "mappings": { "biocontext": "GPMDB", "fairsharing": "FAIRsharing.fhcmwq", "miriam": "gpmdb", "n2t": "gpmdb" }, "name": "Global Proteome Machine Database", "pattern": "^GPM\\d+$", "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" } ], "uri_format": "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1" }, "graingenes.reference": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A database for Triticeae and Avena references.", "example": "WGS-95-1333", "homepage": "http://wheat.pw.usda.gov", "name": "GrainGenes", "preferred_prefix": "graingenes.reference", "uri_format": "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1" }, "graingenes.symbol": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A database for Triticeae and Avena gene symbols.", "example": "1-FEH+w3", "homepage": "http://wheat.pw.usda.gov", "name": "GrainGenes", "preferred_prefix": "graingenes.symbol", "uri_format": "http://wheat.pw.usda.gov/report?class=gene;name=$1" }, "gramene.gene": { "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene.", "example": "GR:0080039", "homepage": "http://www.gramene.org/", "mappings": { "biocontext": "GRAMENE.GENE", "go": "GR_GENE", "miriam": "gramene.gene", "n2t": "gramene.gene" }, "name": "Gramene Gene", "pattern": "^GR\\:\\d+$", "preferred_prefix": "gramene.gene", "synonyms": [ "GR_GENE" ], "uri_format": "http://www.gramene.org/db/genes/search_gene?acc=$1" }, "gramene.growthstage": { "banana": "GRO", "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.", "example": "0007133", "homepage": "http://www.gramene.org/", "mappings": { "biocontext": "GRAMENE.GROWTHSTAGE", "miriam": "gramene.growthstage", "n2t": "gramene.growthstage" }, "name": "Gramene Growth Stage Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "gramene.growthstage", "uri_format": "http://www.gramene.org/db/ontology/search?id=GRO:$1" }, "gramene.protein": { "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene.", "example": "78073", "homepage": "http://www.gramene.org/", "mappings": { "biocontext": "GRAMENE.PROTEIN", "go": "GR_PROTEIN", "miriam": "gramene.protein", "n2t": "gramene.protein" }, "name": "Gramene protein", "pattern": "^\\d+$", "preferred_prefix": "gramene.protein", "synonyms": [ "GR_PROTEIN" ], "uri_format": "http://www.gramene.org/db/protein/protein_search?protein_id=$1" }, "gramene.qtl": { "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene.", "example": "CQG5", "homepage": "http://www.gramene.org/", "mappings": { "biocontext": "GRAMENE.QTL", "go": "GR_QTL", "miriam": "gramene.qtl", "n2t": "gramene.qtl" }, "name": "Gramene QTL", "pattern": "^\\w+$", "preferred_prefix": "gramene.qtl", "synonyms": [ "GR_QTL" ], "uri_format": "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1" }, "gramene.reference": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Literature references in Gramene", "example": "6200", "homepage": "http://www.gramene.org", "name": "Gramene Reference", "pattern": "^\\d+$", "preferred_prefix": "gramene.reference", "synonyms": [ "gramene.ref" ], "uri_format": "http://www.gramene.org/db/literature/pub_search?ref_id=$1" }, "gramene.taxonomy": { "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene.", "example": "GR_tax:013681", "homepage": "http://www.gramene.org/", "mappings": { "biocontext": "GRAMENE.TAXONOMY", "miriam": "gramene.taxonomy", "n2t": "gramene.taxonomy" }, "name": "Gramene Taxonomy", "pattern": "^GR\\_tax\\:\\d+$", "preferred_prefix": "gramene.taxonomy", "uri_format": "http://www.gramene.org/db/ontology/search?id=$1" }, "grassbase": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species.", "example": "imp10873", "github_request_issue": 218, "homepage": "https://www.kew.org/data/grasses-syn/index.htm", "mappings": { "wikidata": "P1832" }, "name": "GrassBase", "pattern": "^(imp|gen)\\d{5}$", "preferred_prefix": "grassbase", "uri_format": "https://www.kew.org/data/grasses-db/www/$1" }, "greengenes": { "description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.", "example": "100000", "homepage": "http://greengenes.lbl.gov/", "mappings": { "biocontext": "GREENGENES", "fairsharing": "FAIRsharing.bpxgb6", "miriam": "greengenes", "n2t": "greengenes", "ncbi": "Greengenes", "prefixcommons": "greengenes", "re3data": "r3d100010549" }, "name": "16S rRNA gene database", "pattern": "^\\d+$", "preferred_prefix": "greengenes", "publications": [ { "doi": "10.1128/aem.03006-05", "pmc": "PMC1489311", "pubmed": "16820507", "title": "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.", "year": 2006 } ], "uri_format": "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1" }, "grid": { "description": "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally.", "example": "grid.225360.0", "homepage": "https://www.grid.ac/", "mappings": { "biocontext": "GRID", "fairsharing": "FAIRsharing.0pUMYW", "miriam": "grid", "n2t": "grid" }, "name": "Global Research Identifier Database", "pattern": "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$", "preferred_prefix": "grid", "uri_format": "https://www.grid.ac/institutes/$1" }, "grin.taxonomy": { "description": "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact.", "example": "19333", "homepage": "http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en", "mappings": { "biocontext": "GRIN.TAXONOMY", "go": "GRIN", "miriam": "grin.taxonomy", "n2t": "grin.taxonomy", "ncbi": "GRIN" }, "name": "Germplasm Resources Information Network", "pattern": "^\\d+$", "preferred_prefix": "grin.taxonomy", "uri_format": "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1" }, "gro": { "contact": { "email": "vlee@ebi.ac.uk", "github": null, "name": "Vivian Lee", "orcid": null }, "deprecated": true, "description": "The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes.", "download_owl": "http://aber-owl.net/media/ontologies/GRO/5/gro.owl", "example": "Lipid", "homepage": "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html", "mappings": { "aberowl": "GRO", "bioportal": "GRO" }, "name": "Gene Regulation Ontology", "preferred_prefix": "gro", "uri_format": "http://www.bootstrep.eu/ontology/GRO#$1" }, "grsdb": { "description": "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.", "example": "10142", "homepage": "http://bioinformatics.ramapo.edu/GRSDB2/", "mappings": { "biocontext": "GRSDB", "miriam": "grsdb", "n2t": "grsdb", "prefixcommons": "grsdb" }, "name": "G-Rich Sequences Database", "pattern": "^\\d+$", "preferred_prefix": "grsdb", "uri_format": "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1" }, "gsfa": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The \"Codex General Standard for Food Additives\" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database.", "example": "174", "homepage": "http://www.fao.org/gsfaonline", "name": "General Standard for Food Additives Online Database", "pattern": "^\\d+$", "preferred_prefix": "gsfa", "synonyms": [ "FAO/WHO_standards" ], "uri_format": "http://www.fao.org/gsfaonline/additives/details.html?id=$1" }, "gsso": { "appears_in": [ "ontoavida", "scdo" ], "banana": "GSSO", "contact": { "email": "kronkcj@mail.uc.edu", "github": "Superraptor", "name": "Clair Kronk", "orcid": "0000-0001-8397-8810" }, "description": "The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology.", "download_json": "http://purl.obolibrary.org/obo/gsso.json", "download_obo": "http://purl.obolibrary.org/obo/gsso.obo", "download_owl": "http://purl.obolibrary.org/obo/gsso.owl", "example": "002368", "homepage": "https://gsso.research.cchmc.org/", "license": "Apache 2.0 License", "mappings": { "aberowl": "GSSO", "bioportal": "GSSO", "miriam": "gsso", "obofoundry": "gsso", "ols": "gsso", "ontobee": "GSSO" }, "name": "Gender, Sex, and Sexual Orientation Ontology", "namespace_in_lui": true, "pattern": "^\\d{6}$", "preferred_prefix": "GSSO", "repository": "https://github.com/Superraptor/GSSO", "uri_format": "http://purl.obolibrary.org/obo/GSSO_$1", "version": "2.0.5" }, "gtex": { "description": "The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation.", "example": "BRIP1", "homepage": "https://www.gtexportal.org", "mappings": { "biocontext": "GTEX", "biolink": "GTEx", "miriam": "gtex", "n2t": "gtex" }, "name": "Genotype-Tissue Expression", "pattern": "^\\w.+$", "preferred_prefix": "gtex", "uri_format": "https://www.gtexportal.org/home/gene/$1" }, "gtr": { "appears_in": [ "mondo" ], "comment": "Identifiers appearing in MONDO don't match any of the resources apparent endpoints", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease", "example": "AN0097748", "homepage": "https://www.ncbi.nlm.nih.gov/gtr/", "name": "Genetic Testing Registry", "preferred_prefix": "gtr", "synonyms": [ "medgen.gtr" ], "uri_format": "https://www.ncbi.nlm.nih.gov/gtr/conditions/$1" }, "gudmap": { "description": "The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract.", "example": "Q-2958", "homepage": "http://www.gudmap.org/", "mappings": { "biocontext": "GUDMAP", "fairsharing": "FAIRsharing.910c39", "miriam": "gudmap", "n2t": "gudmap", "re3data": "r3d100012193" }, "name": "Genitourinary Development Molecular Anatomy Project", "pattern": "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$", "preferred_prefix": "gudmap", "uri_format": "https://gudmap.org/id/$1" }, "gwascentral.marker": { "description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker.", "example": "HGVM15354", "homepage": "https://www.gwascentral.org/markers", "mappings": { "biocontext": "GWASCENTRAL.MARKER", "miriam": "gwascentral.marker", "n2t": "gwascentral.marker" }, "name": "GWAS Central Marker", "pattern": "^HGVM\\d+$", "preferred_prefix": "gwascentral.marker", "uri_format": "https://www.gwascentral.org/marker/$1" }, "gwascentral.phenotype": { "description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype.", "example": "HGVPM623", "homepage": "https://www.gwascentral.org/phenotypes", "mappings": { "biocontext": "GWASCENTRAL.PHENOTYPE", "miriam": "gwascentral.phenotype", "n2t": "gwascentral.phenotype" }, "name": "GWAS Central Phenotype", "pattern": "^HGVPM\\d+$", "preferred_prefix": "gwascentral.phenotype", "uri_format": "https://www.gwascentral.org/phenotype/$1" }, "gwascentral.study": { "description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study.", "example": "HGVST1828", "homepage": "https://www.gwascentral.org/studies", "mappings": { "biocontext": "GWASCENTRAL.STUDY", "miriam": "gwascentral.study", "n2t": "gwascentral.study" }, "name": "GWAS Central Study", "pattern": "^HGVST\\d+$", "preferred_prefix": "gwascentral.study", "uri_format": "https://www.gwascentral.org/study/$1" }, "gxa.expt": { "description": "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments.", "example": "E-MTAB-2037", "homepage": "https://www.ebi.ac.uk/gxa/", "mappings": { "biocontext": "GXA.EXPT", "miriam": "gxa.expt", "n2t": "gxa.expt" }, "name": "GXA Expt", "pattern": "^[AEP]-\\w{4}-\\d+$", "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/$1" }, "gxa.gene": { "description": "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes.", "example": "AT4G01080", "homepage": "https://www.ebi.ac.uk/gxa/", "mappings": { "biocontext": "GXA.GENE", "miriam": "gxa.gene", "n2t": "gxa.gene" }, "name": "GXA Gene", "pattern": "^\\w+$", "preferred_prefix": "gxa.gene", "uri_format": "https://www.ebi.ac.uk/gxa/genes/$1" }, "habronattus": { "contact": { "email": "peteremidford@yahoo.com", "github": null, "name": "Peter Midford", "orcid": "0000-0001-6512-3296" }, "deprecated": true, "homepage": "http://www.mesquiteproject.org/ontology/Habronattus/index.html", "mappings": { "biocontext": "HABRONATTUS", "obofoundry": "habronattus" }, "name": "Habronattus courtship", "preferred_prefix": "HABRONATTUS", "uri_format": "http://purl.obolibrary.org/obo/HABRONATTUS_$1" }, "hamap": { "description": "HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries.", "example": "MF_01400", "homepage": "https://hamap.expasy.org/", "mappings": { "biocontext": "HAMAP", "edam": "2766", "fairsharing": "FAIRsharing.63m4ss", "go": "HAMAP", "miriam": "hamap", "n2t": "hamap", "prefixcommons": "hamap", "uniprot": "HAMAP" }, "name": "High-quality Automated and Manual Annotation of microbial Proteomes", "pattern": "^MF_\\d+$", "preferred_prefix": "hamap", "uri_format": "https://hamap.expasy.org/unirule/$1" }, "hancestro": { "contact": { "email": "danielle.welter@uni.lu", "github": "daniwelter", "name": "Danielle Welter", "orcid": "0000-0003-1058-2668" }, "description": "Human ancestry ontology for the NHGRI GWAS Catalog", "download_owl": "http://purl.obolibrary.org/obo/hancestro.owl", "example": "0290", "homepage": "https://github.com/EBISPOT/ancestro", "license": "CC BY 4.0", "mappings": { "aberowl": "HANCESTRO", "biolink": "HANCESTRO", "bioportal": "HANCESTRO", "fairsharing": "FAIRsharing.rja8qp", "obofoundry": "hancestro", "ols": "hancestro", "ontobee": "HANCESTRO" }, "name": "Human Ancestry Ontology", "pattern": "^\\d{4}$", "preferred_prefix": "HANCESTRO", "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 } ], "repository": "https://github.com/EBISPOT/ancestro", "uri_format": "http://purl.obolibrary.org/obo/HANCESTRO_$1", "version": "2.6" }, "hao": { "contact": { "email": "diapriid@gmail.com", "github": "mjy", "name": "Matt Yoder", "orcid": "0000-0002-5640-5491" }, "description": "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)", "download_obo": "http://purl.obolibrary.org/obo/hao.obo", "download_owl": "http://purl.obolibrary.org/obo/hao.owl", "example": "0000187", "homepage": "http://hymao.org", "license": "CC0 1.0", "mappings": { "aberowl": "HAO", "biocontext": "HAO", "bioportal": "HAO", "fairsharing": "FAIRsharing.kj3m5n", "obofoundry": "hao", "ols": "hao", "ontobee": "HAO" }, "name": "Hymenoptera Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "HAO", "publications": [ { "doi": "10.1371/journal.pone.0015991", "pmc": "PMC3012123", "pubmed": "21209921", "title": "A gross anatomy ontology for hymenoptera.", "year": 2010 } ], "repository": "https://github.com/hymao/hao", "uri_format": "http://purl.obolibrary.org/obo/HAO_$1", "version": "2021-03-05" }, "hathitrust": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world.", "example": "008893080", "github_request_issue": 510, "homepage": "https://www.hathitrust.org", "name": "Hathi Trust Digital Library", "pattern": "^\\d+$", "preferred_prefix": "hathitrust", "uri_format": "https://catalog.hathitrust.org/Record/$1" }, "hba": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A controlled vocabulary to support the study of transcription in the human brain", "download_obo": "https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-hba.obo", "example": "4005", "example_extras": [ "265504410" ], "homepage": "https://human.brain-map.org", "name": "Human Brain Atlas", "pattern": "^\\d+$", "preferred_prefix": "HBA", "uri_format": "https://biopragmatics.github.io/providers/hba/$1" }, "hc.din": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A Drug Identification Number (DIN) is a computer-generated eight digit number assigned by Health Canada to a drug product prior to being marketed in Canada. It uniquely identifies all drug products sold in a dosage form in Canada and is located on the label of prescription and over-the-counter drug products that have been evaluated and authorized for sale in Canada.", "example": "02069237", "homepage": "https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/fact-sheets/drug-identification-number.html", "mappings": { "hl7": "2.16.840.1.113883.5.1105" }, "name": "Health Canada Drug Identification Number", "pattern": "^\\d{8}$", "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" }, "hcao": { "description": "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas.", "download_owl": "http://ontology.data.humancellatlas.org/ontologies/hcao/releases/2022-06-22/hcao.owl", "homepage": "https://www.humancellatlas.org", "mappings": { "ols": "hcao" }, "name": "Human Cell Atlas Ontology", "no_own_terms": true, "preferred_prefix": "hcao", "version": "2022-06-22" }, "hcpcs": { "contact": { "email": "Cynthia.Hake@cms.hhs.gov", "github": null, "name": "Cynthia Hake", "orcid": null }, "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", "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/$1" }, "hcvdb": { "description": "the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses.", "example": "M58335", "homepage": "http://euhcvdb.ibcp.fr", "mappings": { "biocontext": "HCVDB", "miriam": "hcvdb", "n2t": "hcvdb", "prefixcommons": "euhcvdb" }, "name": "Hepatitis C Virus Database", "pattern": "^M\\d{5}$", "preferred_prefix": "hcvdb", "publications": [ { "doi": "10.1093/nar/gkl970", "pmc": "PMC1669729", "pubmed": "17142229", "title": "euHCVdb: the European hepatitis C virus database.", "year": 2006 } ], "uri_format": "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1" }, "hdr": { "description": "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders.", "example": "63", "homepage": "http://research.nhgri.nih.gov/apps/homeodomain/web/", "mappings": { "biocontext": "HDR", "miriam": "hdr", "n2t": "hdr", "prefixcommons": "hdr" }, "name": "Homeodomain Research", "pattern": "^\\d+$", "preferred_prefix": "hdr", "uri_format": "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1" }, "hgmd": { "description": "The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases.", "example": "CALM1", "homepage": "http://www.hgmd.cf.ac.uk/ac/index.php", "mappings": { "biocontext": "HGMD", "edam": "3265", "miriam": "hgmd", "n2t": "hgmd" }, "name": "Human Gene Mutation Database", "pattern": "^[A-Z_0-9]+$", "preferred_prefix": "hgmd", "uri_format": "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1" }, "hgnc": { "contact": { "email": "hgnc@genenames.org", "github": null, "name": "Dr. Elspeth Bruford", "orcid": null }, "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database.", "download_owl": "http://aber-owl.net/media/ontologies/HGNC/1/hgnc.owl", "example": "16793", "homepage": "http://www.genenames.org", "mappings": { "aberowl": "HGNC", "biocontext": "HGNC", "bioportal": "HGNC", "cellosaurus": "HGNC", "edam": "2298", "fairsharing": "FAIRsharing.amcv1e", "go": "HGNC", "hl7": "2.16.840.1.113883.6.281", "miriam": "hgnc", "n2t": "hgnc", "ncbi": "HGNC", "prefixcommons": "hgnc", "uniprot": "HGNC", "wikidata": "P354" }, "name": "HUGO Gene Nomenclature Committee", "pattern": "^\\d{1,5}$", "preferred_prefix": "hgnc", "providers": [ { "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", "uri_format": "https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@HGNC" } ], "publications": [ { "doi": "10.1093/nar/gky930", "pmc": "PMC6324057", "pubmed": "30304474", "title": "Genenames.org: the HGNC and VGNC resources in 2019.", "year": 2019 }, { "doi": "10.1159/000131404", "pmc": null, "pubmed": "295268", "title": "International system for human gene nomenclature (1979) ISGN (1979).", "year": 1979 } ], "uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1" }, "hgnc.genefamily": { "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.", "example": "2029", "has_canonical": "hgnc.genegroup", "homepage": "http://www.genenames.org", "mappings": { "biocontext": "HGNC.GENEFAMILY", "miriam": "hgnc.genefamily", "n2t": "hgnc.genefamily" }, "name": "HGNC gene family", "pattern": "^\\d+$", "preferred_prefix": "hgnc.genefamily", "synonyms": [ "GFAM", "HGNC_GROUP", "hgnc.family" ], "uri_format": "https://www.genenames.org/cgi-bin/genefamilies/set/$1" }, "hgnc.genegroup": { "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.", "example": "141", "homepage": "https://www.genenames.org", "mappings": { "miriam": "hgnc.genegroup" }, "name": "HGNC Gene Group", "pattern": "^\\d+$", "preferred_prefix": "hgnc.genegroup", "uri_format": "https://www.genenames.org/cgi-bin/genefamilies/set/$1" }, "hgnc.symbol": { "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol.", "example": "DAPK1", "homepage": "https://www.genenames.org/", "mappings": { "biocontext": "HGNC.SYMBOL", "miriam": "hgnc.symbol", "n2t": "hgnc.symbol" }, "name": "HGNC Symbol", "pattern": "^[A-Za-z-0-9_]+(\\@)?$", "preferred_prefix": "hgnc.symbol", "providers": [ { "code": "depmap", "description": "DepMap summary of the given gene", "homepage": "https://depmap.org", "name": "DepMap Gene Summary", "uri_format": "https://depmap.org/portal/gene/$1" }, { "code": "oncomx", "description": "Mutation profiles for a gene", "homepage": "https://oncomx.org", "name": "OncoMX", "uri_format": "https://oncomx.org/searchview/?gene=$1" }, { "code": "pathwaycommons", "description": "Interactions between a given gene and other molecular entities", "homepage": "https://www.pathwaycommons.org/", "name": "Pathway Commons Gene Interations", "uri_format": "https://apps.pathwaycommons.org/interactions?source=$1" } ], "uri_format": "https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1" }, "hinv.locus": { "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view.", "example": "HIX0004394", "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", "mappings": { "biocontext": "HINV.LOCUS", "miriam": "hinv.locus", "n2t": "hinv.locus" }, "name": "H-InvDb Locus", "pattern": "^HIX\\d{7}(\\.\\d+)?$", "preferred_prefix": "hinv.locus", "uri_format": "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1" }, "hinv.protein": { "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view.", "example": "HIP000030660", "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", "mappings": { "biocontext": "HINV.PROTEIN", "miriam": "hinv.protein", "n2t": "hinv.protein" }, "name": "H-InvDb Protein", "pattern": "^HIP\\d{9}(\\.\\d+)?$", "preferred_prefix": "hinv.protein", "uri_format": "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1" }, "hinv.transcript": { "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view.", "example": "HIT000195363", "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", "mappings": { "biocontext": "HINV.TRANSCRIPT", "miriam": "hinv.transcript", "n2t": "hinv.transcript" }, "name": "H-InvDb Transcript", "pattern": "^HIT\\d{9}(\\.\\d+)?$", "preferred_prefix": "hinv.transcript", "uri_format": "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1" }, "hipsci": { "description": "Cell line databases/resources", "example": "HPSI0114i-bezi_1", "homepage": "http://www.hipsci.org", "mappings": { "cellosaurus": "HipSci" }, "name": "Human Induced Pluripotent Stem Cells Initiative", "preferred_prefix": "hipsci", "uri_format": "http://www.hipsci.org/lines/#/lines/$1" }, "hivreagentprogram": { "description": "Cell line collections", "example": "ARP-1513", "homepage": "https://www.hivreagentprogram.org/", "mappings": { "cellosaurus": "HIVReagentProgram" }, "name": "NIH HIV Reagent Program", "preferred_prefix": "hivreagentprogram", "uri_format": "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx" }, "hl7.v2codesystem": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR.", "example": "0778", "homepage": "https://terminology.hl7.org/codesystems-v2.html", "name": "HL7 V2 Code Systems", "pattern": "^\\d+$", "preferred_prefix": "hl7.v2codesystem", "uri_format": "http://terminology.hl7.org/CodeSystem/v2-$1" }, "hl7.v3codesystem": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR.", "example": "AcknowledgementCondition", "homepage": "https://terminology.hl7.org/codesystems-v2.html", "name": "HL7 V2 Code Systems", "pattern": "^\\w+$", "preferred_prefix": "hl7.v3codesystem", "uri_format": "https://terminology.hl7.org/CodeSystem-v3-$1" }, "hmdb": { "description": "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.", "example": "HMDB00001", "homepage": "http://www.hmdb.ca/", "mappings": { "biocontext": "HMDB", "cheminf": "000408", "edam": "2622", "fairsharing": "FAIRsharing.sye5js", "miriam": "hmdb", "n2t": "hmdb", "prefixcommons": "hmdb", "wikidata": "P2057" }, "name": "Human Metabolome Database", "pattern": "^HMDB\\d+$", "preferred_prefix": "hmdb", "publications": [ { "doi": "10.1093/nar/gkl923", "pmc": "PMC1899095", "pubmed": "17202168", "title": "HMDB: the Human Metabolome Database.", "year": 2007 } ], "synonyms": [ "HMDB" ], "uri_format": "http://www.hmdb.ca/metabolites/$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", "homepage": "https://lincs.hms.harvard.edu/db/sm/", "name": "HMS LINCS Compound", "preferred_prefix": "hms.lincs.compound", "synonyms": [ "HMS-LINCS", "hmsl_id" ], "uri_format": "https://lincs.hms.harvard.edu/db/sm/$1" }, "hog": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc.", "download_obo": "ftp://ftp.bgee.org/general/ontologies/HOG.obo", "example": "0000255", "homepage": "https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships", "name": "Homologous Organ Groups", "pattern": "^\\d{7}$", "preferred_prefix": "hog", "uri_format": "https://biopragmatics.github.io/providers/hog/$1" }, "hogenom": { "description": "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.", "example": "HBG284870", "homepage": "http://pbil.univ-lyon1.fr/databases/hogenom/", "mappings": { "biocontext": "HOGENOM", "fairsharing": "FAIRsharing.qe8tz8", "miriam": "hogenom", "n2t": "hogenom", "prefixcommons": "hogenom", "uniprot": "HOGENOM" }, "name": "Database of Complete Genome Homologous Genes Families", "pattern": "^\\w+$", "preferred_prefix": "hogenom", "publications": [ { "doi": "10.1186/1471-2105-10-s6-s3", "pmc": "PMC2697650", "pubmed": "19534752", "title": "Databases of homologous gene families for comparative genomics.", "year": 2009 } ], "uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1" }, "hom": { "contact": { "email": "bgee@sib.swiss", "github": "fbastian", "name": "Frederic Bastian", "orcid": "0000-0002-9415-5104" }, "description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.", "download_owl": "http://purl.obolibrary.org/obo/hom.owl", "example": "0000049", "homepage": "https://github.com/BgeeDB/homology-ontology", "license": "CC0 1.0", "mappings": { "aberowl": "HOM", "biocontext": "HOM", "bioportal": "HOM", "fairsharing": "FAIRsharing.efv7gw", "obofoundry": "hom", "ols": "hom", "ontobee": "HOM" }, "name": "Homology Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "HOM", "publications": [ { "doi": "10.1016/j.tig.2009.12.012", "pmc": null, "pubmed": "20116127", "title": "An ontology to clarify homology-related concepts.", "year": 2010 } ], "repository": "https://github.com/BgeeDB/homology-ontology", "uri_format": "http://purl.obolibrary.org/obo/HOM_$1", "version": "2015-01-07" }, "homd.seq": { "description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.", "example": "SEQF1003", "homepage": "http://www.homd.org/index.php", "mappings": { "biocontext": "HOMD.SEQ", "miriam": "homd.seq", "n2t": "homd.seq", "prefixcommons": "homd.seq" }, "name": "HOMD Sequence Metainformation", "pattern": "^SEQF\\d+$", "preferred_prefix": "homd.seq", "publications": [ { "doi": "10.1093/database/baq013", "pmc": "PMC2911848", "pubmed": "20624719", "title": "The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.", "year": 2010 } ], "uri_format": "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1" }, "homd.taxon": { "description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.", "example": "811", "homepage": "http://www.homd.org/index.php", "mappings": { "biocontext": "HOMD.TAXON", "miriam": "homd.taxon", "n2t": "homd.taxon", "prefixcommons": "homd.taxon" }, "name": "HOMD Taxonomy", "pattern": "^\\d+$", "preferred_prefix": "homd.taxon", "publications": [ { "doi": "10.1093/database/baq013", "pmc": "PMC2911848", "pubmed": "20624719", "title": "The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.", "year": 2010 } ], "uri_format": "http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1" }, "homologene": { "description": "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.", "example": "1000", "homepage": "https://www.ncbi.nlm.nih.gov/homologene/", "mappings": { "biocontext": "HOMOLOGENE", "fairsharing": "FAIRsharing.mzc066", "miriam": "homologene", "n2t": "homologene", "prefixcommons": "homologene", "wikidata": "P593" }, "name": "HomoloGene", "pattern": "^\\d+$", "preferred_prefix": "homologene", "providers": [ { "code": "CURATOR_REVIEW", "description": "Bio2RDF", "homepage": "http://homologene.bio2rdf.org/fct", "name": "Bio2RDF", "uri_format": "http://homologene.bio2rdf.org/describe/?url=http://bio2rdf.org/homologene:$1" } ], "publications": [ { "doi": "10.1093/nar/gkq1172", "pmc": "PMC3013733", "pubmed": "21097890", "title": "Database resources of the National Center for Biotechnology Information.", "year": 2010 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/homologene/$1" }, "horizon_discovery": { "description": "Cell line collections", "example": "HD+118-001", "homepage": "https://horizondiscovery.com/", "mappings": { "cellosaurus": "Horizon_Discovery" }, "name": "Horizon Discovery cell line collection", "preferred_prefix": "horizon_discovery", "uri_format": "https://horizondiscovery.com/en/search?searchterm=$1" }, "hovergen": { "description": "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.", "example": "HBG004341", "homepage": "https://pbil.univ-lyon1.fr/databases/hovergen.php", "mappings": { "biocontext": "HOVERGEN", "fairsharing": "FAIRsharing.dg1f0e", "miriam": "hovergen", "n2t": "hovergen", "prefixcommons": "hovergen" }, "name": "Homologous Vertebrate Genes Database", "pattern": "^HBG\\d+$", "preferred_prefix": "hovergen", "publications": [ { "doi": "10.1093/bioinformatics/bti325", "pmc": null, "pubmed": "15713731", "title": "Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.", "year": 2005 } ], "uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN" }, "hp": { "appears_in": [ "chiro", "scdo" ], "banana": "HP", "contact": { "email": "dr.sebastian.koehler@gmail.com", "github": "drseb", "name": "Sebastian Koehler", "orcid": "0000-0002-5316-1399" }, "description": "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.", "download_json": "http://purl.obolibrary.org/obo/hp.json", "download_obo": "http://purl.obolibrary.org/obo/hp.obo", "download_owl": "http://purl.obolibrary.org/obo/hp.owl", "example": "0011140", "homepage": "http://www.human-phenotype-ontology.org/", "license": "hpo", "mappings": { "aberowl": "HP_O", "biocontext": "HPO", "bioportal": "HP_O", "fairsharing": "FAIRsharing.kbtt7f", "hl7": "2.16.840.1.113883.6.339", "miriam": "hp", "n2t": "hp", "obofoundry": "hp", "ols": "hp", "ontobee": "HP", "wikidata": "P3841" }, "name": "Human Phenotype Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "HP", "publications": [ { "doi": "10.1093/nar/gky1105", "pmc": "PMC6324074", "pubmed": "30476213", "title": "Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.", "year": 2019 }, { "doi": "https://doi.org/10.1093/nar/gkw1039", "pmc": "PMC5210535", "pubmed": "27899602", "title": "The Human Phenotype Ontology in 2017.", "year": null }, { "doi": "10.1093/nar/gkw1039", "pmc": "PMC5210535", "pubmed": "27899602", "title": "The Human Phenotype Ontology in 2017.", "year": 2016 }, { "doi": "10.1016/j.ajhg.2015.05.020", "pmc": "PMC4572507", "pubmed": "26119816", "title": "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.", "year": 2015 }, { "doi": "10.1093/nar/gkt1026", "pmc": "PMC3965098", "pubmed": "24217912", "title": "The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.", "year": 2013 }, { "doi": "10.1111/j.1399-0004.2010.01436.x", "pmc": null, "pubmed": "20412080", "title": "The human phenotype ontology.", "year": 2010 }, { "doi": "10.1016/j.ajhg.2008.09.017", "pmc": "PMC2668030", "pubmed": "18950739", "title": "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.", "year": 2008 } ], "repository": "https://github.com/obophenotype/human-phenotype-ontology", "synonyms": [ "hpo" ], "twitter": "hp_ontology", "uri_format": "https://hpo.jax.org/app/browse/term/HP:$1", "version": "2022-06-11" }, "hpa": { "description": "The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers.", "example": "ENSG00000026508", "homepage": "http://www.proteinatlas.org/", "mappings": { "biocontext": "HPA", "fairsharing": "FAIRsharing.j0t0pe", "go": "HPA", "miriam": "hpa", "n2t": "hpa", "prefixcommons": "hpa", "uniprot": "HPA" }, "name": "Human Protein Atlas tissue profile information", "pattern": "^ENSG\\d{11}$", "preferred_prefix": "hpa", "publications": [ { "doi": "10.1074/mcp.r800013-mcp200", "pmc": null, "pubmed": "18669619", "title": "A genecentric Human Protein Atlas for expression profiles based on antibodies.", "year": 2008 } ], "uri_format": "http://www.proteinatlas.org/$1" }, "hpath": { "description": "An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species.", "download_owl": "https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo", "example": "2000191", "homepage": "https://github.com/Novartis/hpath", "mappings": { "ols": "hpath" }, "name": "Histopathology Ontology", "pattern": "^\\d+$", "preferred_prefix": "hpath", "repository": "https://github.com/Novartis/hpath", "synonyms": [ "MC" ], "uri_format": "http://purl.obolibrary.org/obo/MC_$1", "version": "2019-07-05" }, "hpm.peptide": { "description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra.", "example": "9606117", "homepage": "http://www.humanproteomemap.org/index.php", "mappings": { "biocontext": "HPM.PEPTIDE", "miriam": "hpm.peptide", "n2t": "hpm.peptide" }, "name": "Human Proteome Map Peptide", "pattern": "^\\d+$", "preferred_prefix": "hpm.peptide", "uri_format": "http://www.humanproteomemap.org/spectrum.php?pep_id=$1" }, "hpm.protein": { "description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.", "example": "1968", "homepage": "http://www.humanproteomemap.org/index.php", "mappings": { "biocontext": "HPM.PROTEIN", "miriam": "hpm.protein", "n2t": "hpm.protein" }, "name": "Human Proteome Map Protein", "pattern": "^\\d+$", "preferred_prefix": "hpm.protein", "uri_format": "http://www.humanproteomemap.org/protein.php?hpm_id=$1" }, "hprd": { "description": "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.", "example": "00001", "homepage": "http://www.hprd.org/", "mappings": { "biocontext": "HPRD", "fairsharing": "FAIRsharing.y2qws7", "miriam": "hprd", "n2t": "hprd", "prefixcommons": "hprd" }, "name": "Human Protein Reference Database", "pattern": "^\\d+$", "preferred_prefix": "hprd", "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/$1" }, "hpscreg": { "description": "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines).", "example": "BCRTi001-A", "homepage": "https://hpscreg.eu/", "mappings": { "cellosaurus": "hPSCreg", "fairsharing": "FAIRsharing.7C0aVE", "miriam": "hpscreg", "n2t": "hpscreg", "re3data": "r3d100012863" }, "name": "Human Pluripotent Stem Cell Registry", "pattern": "^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$", "preferred_prefix": "hpscreg", "uri_format": "https://hpscreg.eu/cell-line/$1" }, "hsapdv": { "appears_in": [ "scdo" ], "contact": { "email": "frederic.bastian@unil.ch", "github": "fbastian", "name": "Frédéric Bastian", "orcid": "0000-0002-9415-5104" }, "description": "Life cycle stages for Human", "download_obo": "http://purl.obolibrary.org/obo/hsapdv.obo", "download_owl": "http://purl.obolibrary.org/obo/hsapdv.owl", "example": "0000194", "homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv", "license": "CC BY 3.0", "mappings": { "aberowl": "HSAPDV", "biocontext": "HSAPDV", "biolink": "HsapDv", "bioportal": "HSAPDV", "fairsharing": "FAIRsharing.c6vhm3", "obofoundry": "hsapdv", "ols": "hsapdv", "ontobee": "HSAPDV" }, "name": "Human Developmental Stages", "pattern": "^\\d{7}$", "preferred_prefix": "HsapDv", "repository": "https://github.com/obophenotype/developmental-stage-ontologies", "synonyms": [ "HsapDv" ], "uri_format": "http://purl.obolibrary.org/obo/HSAPDV_$1", "version": "2020-03-10" }, "hsdb": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas.", "example": "5621", "homepage": "https://pubchem.ncbi.nlm.nih.gov/source/hsdb", "mappings": { "wikidata": "P2062" }, "name": "Hazardous Substances Data Bank", "pattern": "^\\d+$", "preferred_prefix": "hsdb", "uri_format": "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1" }, "hso": { "contact": { "email": "fernanda.dorea@sva.se", "github": "nandadorea", "name": "Fernanda Dorea", "orcid": "0000-0001-8638-8525" }, "depends_on": [ "bfo", "ncbitaxon", "obi", "ro", "uberon" ], "description": "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance.", "download_owl": "http://purl.obolibrary.org/obo/hso.owl", "example": "0000062", "homepage": "https://w3id.org/hso", "license": "CC BY 3.0", "mappings": { "aberowl": "HSO", "bioportal": "HSO", "obofoundry": "hso", "ols": "hso", "ontobee": "HSO" }, "name": "Health Surveillance Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "HSO", "repository": "https://github.com/SVA-SE/HSO", "uri_format": "http://purl.obolibrary.org/obo/HSO_$1", "version": "2021-12-13" }, "hssp": { "description": "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.", "example": "102l", "homepage": "http://swift.cmbi.kun.nl/swift/hssp/", "mappings": { "biocontext": "HSSP", "miriam": "hssp", "n2t": "hssp", "ncbi": "HSSP", "prefixcommons": "hssp" }, "name": "Database of homology-derived secondary structure of proteins", "pattern": "^\\w{4}$", "preferred_prefix": "hssp", "providers": [ { "code": "CURATOR_REVIEW", "description": "HSSP at CMBI", "homepage": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/", "name": "HSSP at CMBI", "uri_format": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$1.hssp.bz2" } ], "publications": [ { "doi": "10.1093/nar/24.1.201", "pmc": "PMC145595", "pubmed": "8594579", "title": "The HSSP database of protein structure-sequence alignments.", "year": 1996 }, { "doi": null, "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/$1.hssp.bz2" }, "htn": { "contact": { "email": "aellenhicks@gmail.com", "github": "aellenhicks", "name": "Amanda Hicks", "orcid": "0000-0002-1795-5570" }, "description": "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines", "download_owl": "http://purl.obolibrary.org/obo/htn.owl", "example": "00000014", "homepage": "https://github.com/aellenhicks/htn_owl", "license": "CC BY 4.0", "mappings": { "aberowl": "HTN", "bioportal": "HTN", "obofoundry": "htn", "ols": "htn", "ontobee": "HTN" }, "name": "Hypertension Ontology", "pattern": "^\\d{8}$", "preferred_prefix": "HTN", "repository": "https://github.com/aellenhicks/htn_owl", "uri_format": "http://purl.obolibrary.org/obo/HTN_$1", "version": "2019-06-10" }, "huge": { "description": "The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.", "example": "KIAA0001", "homepage": "http://www.kazusa.or.jp/huge/", "mappings": { "biocontext": "HUGE", "fairsharing": "FAIRsharing.zx2ztd", "miriam": "huge", "n2t": "huge", "prefixcommons": "huge", "uniprot": "HUGE" }, "name": "Human Unidentified Gene-Encoded", "pattern": "^KIAA\\d{4}$", "preferred_prefix": "huge", "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/$1" }, "iao": { "appears_in": [ "agro", "clyh", "duo", "ecocore", "ecto", "fovt", "labo", "maxo", "pco", "psdo", "xpo" ], "contact": { "email": "jiezheng@pennmedicine.upenn.edu", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "description": "An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch.", "download_obo": "http://purl.obolibrary.org/obo/iao.obo", "download_owl": "http://purl.obolibrary.org/obo/iao.owl", "example": "0000030", "homepage": "https://github.com/information-artifact-ontology/IAO/", "license": "CC BY 4.0", "mappings": { "aberowl": "IAO", "biocontext": "IAO", "bioportal": "IAO", "fairsharing": "FAIRsharing.gq1xtx", "go": "IAO", "miriam": "iao", "n2t": "iao", "obofoundry": "iao", "ols": "iao", "ontobee": "IAO" }, "name": "Information Artifact Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "IAO", "publications": [ { "doi": "10.3233/978-1-61499-101-4-68", "pmc": null, "pubmed": "22874154", "title": "An information artifact ontology perspective on data collections and associated representational artifacts.", "year": 2012 } ], "repository": "https://github.com/information-artifact-ontology/IAO", "uri_format": "http://purl.obolibrary.org/obo/IAO_$1", "version": "2020-12-09" }, "icd10": { "contact": { "email": "info@who.int", "github": null, "name": "World Health Organization", "orcid": null }, "contributor_extras": [ { "email": null, "github": "joeflack4", "name": "Joe Flack", "orcid": "0000-0002-2906-7319" }, { "email": null, "github": "matentzn", "name": "Nico Matentzoglu", "orcid": "0000-0002-7356-1779" }, { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } ], "description": "The 10th revision of the International Classification of Diseases (ICD) issued by the World Health Organization (WHO). ICD is formally named 'The International Statistical Classification of Diseases and Related Health Problems'. It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases.\n\nNote that the WHO version of ICD-10 is distinct from the ICD-10-CM (Clinical Modification) issued by the U.S. National Center for Health Statistics for use in the United States.", "example": "C34", "example_decoys": [ "G00X", "C34.90", "C4A.8", "C91.Z", "C91.Z0" ], "example_extras": [ "V20", "G00", "A01.1", "XVIII", "R25-R29", "R25", "R25.3" ], "homepage": "https://icd.who.int/browse10", "mappings": { "aberowl": "ICD10", "biocontext": "ICD", "biolink": "ICD10", "bioportal": "ICD10", "edam": "2611", "fairsharing": "FAIRsharing.nj16g", "hl7": "2.16.840.1.113883.6.3", "miriam": "icd", "n2t": "icd", "prefixcommons": "icd", "wikidata": "P494" }, "name": "International Classification of Diseases, 10th Revision", "pattern": "^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\\.[0-9]))?))$", "preferred_prefix": "icd10", "providers": [ { "code": "icd10_2008", "description": "The 2008 revision of ICD-10", "homepage": "https://icd.who.int/browse10/2008/en#", "name": "ICD-10 Version 2008", "uri_format": "https://icd.who.int/browse10/2008/en#/$1" }, { "code": "icd10_2010", "description": "The 2010 revision of ICD-10", "homepage": "https://icd.who.int/browse10/2010/en#", "name": "ICD-10 Version 2010", "uri_format": "https://icd.who.int/browse10/2010/en#/$1" }, { "code": "icd10_2014", "description": "The 2014 revision of ICD-10", "homepage": "https://icd.who.int/browse10/2014/en#", "name": "ICD-10 Version 2014", "uri_format": "https://icd.who.int/browse10/2014/en#/$1" }, { "code": "icd10_2015", "description": "The 2015 revision of ICD-10", "homepage": "https://icd.who.int/browse10/2015/en#", "name": "ICD-10 Version 2015", "uri_format": "https://icd.who.int/browse10/2015/en#/$1" }, { "code": "icd10_2016", "description": "The 2016 revision of ICD-10", "homepage": "https://icd.who.int/browse10/2016/en#", "name": "ICD-10 Version 2016", "uri_format": "https://icd.who.int/browse10/2016/en#/$1" }, { "code": "icdcodelookup", "description": "This site is dedicated exclusively to helping you look up ICD-10 codes, quickly access the codes you use most, and become more comfortable with the new code set in general.", "homepage": "https://icdcodelookup.com/icd-10/codes", "name": "ICD Code Lookup", "uri_format": "https://icdcodelookup.com/icd-10/codes/$1" } ], "synonyms": [ "ICD", "ICD-10", "ICD10", "ICD10WHO" ], "uri_format": "https://icd.who.int/browse10/2019/en#/$1" }, "icd10cm": { "contact": { "email": "pbrooks@hcfa.gov", "github": null, "name": "Patricia Brooks", "orcid": null }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States issued by the National Center for Health Statistics (NCHS) and Centers for Medicare & Medicaid Services (CMS).", "example": "F45.21", "example_decoys": [ "C000", "c00", "C00-D499", "C00-99", "C34.90000" ], "example_extras": [ "C00-D49", "U49", "C34", "C34.90", "C4A.8", "C91.Z", "C91.Z0", "T37.0X1A" ], "homepage": "https://www.icd10data.com/ICD10CM", "mappings": { "aberowl": "ICD10CM", "bioportal": "ICD10CM", "fairsharing": "FAIRsharing.hpvbxb", "hl7": "2.16.840.1.113883.6.90", "wikidata": "P4229" }, "name": "International Classification of Diseases, 10th Revision, Clinical Modification", "pattern": "^([A-Z][0-9][0-9AB]((-[A-Z][0-9][0-9AB])|(\\.[0-9A-KXZ]([0-9A-EXYZ]([0-9A-HX][0-59A-HJKMNP-S]?)?)?)?))$", "preferred_prefix": "icd10cm", "synonyms": [ "ICD10CM" ], "uri_format": "https://icd.codes/icd10cm/$1" }, "icd10pcs": { "contact": { "email": "patricia.brooks2@cms.hhs.gov", "github": null, "name": "Pat Brooks", "orcid": null }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis.\n\nICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records.", "example": "01N50ZZ", "homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10PCS", "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": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Diagnostic tool for epidemiology, health management and clinical purposes, maintained by the World Health Organization (WHO). It provides a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease.", "example": "RA01.0", "homepage": "https://icd.who.int/", "mappings": { "fairsharing": "FAIRsharing.97805c", "hl7": "2.16.840.1.113883.6.347", "wikidata": "P7807" }, "name": "International Classification of Diseases, 11th Revision", "preferred_prefix": "icd11", "synonyms": [ "ICD-11" ], "uri_format": "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1" }, "icd9": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics.", "example": "277.9", "homepage": "https://www.cdc.gov/nchs/icd/icd9.htm", "mappings": { "biolink": "ICD9", "hl7": "2.16.840.1.113883.6.42", "wikidata": "P493" }, "name": "International Classification of Diseases, 9th Revision", "preferred_prefix": "icd9", "synonyms": [ "ICD9", "ICD9_2005", "MTHICD9_2006" ], "uri_format": "http://www.icd9data.com/getICD9Code.ashx?icd9=$1" }, "icd9cm": { "contact": { "email": "pbrooks@hcfa.gov", "github": null, "name": "Patricia Brooks", "orcid": null }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States.", "example": "784", "homepage": "https://www.cdc.gov/nchs/icd/icd9cm.htm", "mappings": { "aberowl": "ICD9CM", "bioportal": "ICD9CM", "fairsharing": "FAIRsharing.10zsxb", "hl7": "2.16.840.1.113883.6.2", "wikidata": "P1692" }, "name": "International Classification of Diseases, 9th Revision, Clinical Modification", "pattern": "^([\\dA-Z]\\d{2}(\\.\\d{1,3}|))|(\\d{2}(\\.\\d{1,2}|))$", "preferred_prefix": "icd9cm", "synonyms": [ "IC9CM", "ICD9CM", "ICD9CM_2005", "ICD9CM_2006", "ICDCM_2005" ], "uri_format": "http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1" }, "icdc": { "description": "The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer.", "example": "000009", "homepage": "https://caninecommons.cancer.gov/#/", "mappings": { "fairsharing": "FAIRsharing.d95034", "miriam": "icdc" }, "name": "Integrated Canine Data Commons", "pattern": "^\\d{6}$", "preferred_prefix": "icdc", "uri_format": "https://caninecommons.cancer.gov/#/study/$1" }, "icdo": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases", "download_owl": "http://aber-owl.net/media/ontologies/ICDO/10/icdo.owl", "example": "9861/3", "homepage": "https://www.who.int/classifications/icd/adaptations/oncology/en/", "mappings": { "aberowl": "ICDO", "hl7": "2.16.840.1.113883.6.43", "prefixcommons": "icdo", "wikidata": "P563" }, "name": "International Classification of Diseases for Oncology", "pattern": "^[8-9]\\d{3}(/[0-3])?$", "preferred_prefix": "icdo", "synonyms": [ "ICD-O", "ICDO" ], "uri_format": "http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1" }, "iceberg.element": { "description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements.", "example": "100", "homepage": "http://db-mml.sjtu.edu.cn/ICEberg/", "mappings": { "biocontext": "ICEBERG.ELEMENT", "miriam": "iceberg.element", "n2t": "iceberg.element" }, "name": "ICEberg element", "pattern": "^\\d+$", "preferred_prefix": "iceberg.element", "uri_format": "http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1" }, "iceberg.family": { "description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families.", "example": "1", "homepage": "http://db-mml.sjtu.edu.cn/ICEberg/", "mappings": { "biocontext": "ICEBERG.FAMILY", "miriam": "iceberg.family", "n2t": "iceberg.family" }, "name": "ICEberg family", "pattern": "^\\d+$", "preferred_prefix": "iceberg.family", "uri_format": "http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$1" }, "iceo": { "contact": { "email": "liumeng94@sjtu.edu.cn", "github": "Lemon-Liu", "name": "Meng LIU", "orcid": "0000-0003-3781-6962" }, "description": "A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning.", "download_owl": "http://purl.obolibrary.org/obo/iceo.owl", "example": "0000712_1", "example_extras": [ "0000712" ], "homepage": "https://github.com/ontoice/ICEO", "license": "CC BY 4.0", "mappings": { "aberowl": "ICEO", "bioportal": "ICEO", "obofoundry": "iceo", "ols": "iceo", "ontobee": "ICEO" }, "name": "Integrative and Conjugative Element Ontology", "pattern": "^\\d{7}(_\\d)?$", "preferred_prefix": "ICEO", "repository": "https://github.com/ontoice/ICEO", "uri_format": "http://purl.obolibrary.org/obo/ICEO_$1", "version": "2.1" }, "icepo": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. ", "download_obo": "https://download.nextprot.org/pub/current_release/controlled_vocabularies/icepo.obo", "example": "0000002", "homepage": "https://download.nextprot.org/pub/current_release/controlled_vocabularies/", "name": "Ion Channel Electrophysiology Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "icepo", "publications": [ { "doi": null, "pmc": "PMC4823818", "pubmed": null, "title": "ICEPO: the ion channel electrophysiology ontology", "year": null } ], "twitter": "neXtProt_news", "uri_format": "https://biopragmatics.github.io/providers/icepo/$1" }, "icf": { "comment": "This might be possible to roll directly into ICD11", "contact": { "email": "info@who.int", "github": null, "name": "The World Health Organization", "orcid": null }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. As the functioning and disability of an individual occurs in a context, ICF also includes a list of environmental factors. ICF is the WHO framework for measuring health and disability at both individual and population levels.", "download_owl": "http://aber-owl.net/media/ontologies/ICF/3/icf.owl", "example": "326705068", "homepage": "https://icd.who.int/dev11/l-icf/en", "mappings": { "aberowl": "ICF", "bioportal": "ICF", "fairsharing": "FAIRsharing.7rngj0", "hl7": "2.16.840.1.113883.6.254" }, "name": "International Classification of Functioning, Disability and Health", "pattern": "^\\d+$", "preferred_prefix": "icf", "uri_format": "http://id.who.int/icd/entity/$1" }, "iclc": { "description": "Cell line collections", "example": "ATL98012", "homepage": "http://www.iclc.it", "mappings": { "cellosaurus": "ICLC" }, "name": "Interlab Cell Line Collection", "preferred_prefix": "iclc", "uri_format": "http://www.iclc.it/details/det_list.php?line_id=$1" }, "ico": { "appears_in": [ "scdo" ], "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "description": "The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field.", "download_owl": "http://purl.obolibrary.org/obo/ico.owl", "example": "0000066", "homepage": "https://github.com/ICO-ontology/ICO", "license": "CC BY 3.0", "mappings": { "aberowl": "ICO", "biocontext": "ICO", "bioportal": "ICO", "fairsharing": "FAIRsharing.b9znd5", "obofoundry": "ico", "ols": "ico", "ontobee": "ICO" }, "name": "Informed Consent Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ICO", "repository": "https://github.com/ICO-ontology/ICO", "uri_format": "http://purl.obolibrary.org/obo/ICO_$1", "version": "1.0.187" }, "ideal": { "description": "IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments.", "example": "IID00001", "homepage": "https://www.ideal-db.org", "mappings": { "biocontext": "IDEAL", "fairsharing": "FAIRsharing.h3y42f", "miriam": "ideal", "n2t": "ideal", "uniprot": "IDEAL" }, "name": "Intrinsically Disordered proteins with Extensive Annotations and Literature", "pattern": "^IID\\d+$", "preferred_prefix": "ideal", "uri_format": "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1" }, "ido": { "appears_in": [ "scdo" ], "contact": { "email": "Lindsay.Cowell@utsouthwestern.edu", "github": "lgcowell", "name": "Lindsay Cowell", "orcid": "0000-0003-1617-8244" }, "description": "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases.", "download_owl": "http://purl.obolibrary.org/obo/ido.owl", "example": "0000504", "homepage": "http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology", "license": "CC BY 3.0", "mappings": { "aberowl": "IDO", "biocontext": "IDO", "bioportal": "IDO", "fairsharing": "FAIRsharing.aae3v6", "miriam": "ido", "n2t": "ido", "obofoundry": "ido", "ols": "ido", "ontobee": "IDO" }, "name": "Infectious Disease Ontology", "pattern": "^[0-9]+$", "preferred_prefix": "IDO", "providers": [ { "code": "obo.1", "description": "This incorrect encoding was found inside IDO-COVID-19", "homepage": "http://purl.obolibrary.org", "name": "Nonstandard OBO PURL", "uri_format": "http://purl.obolibrary.org/obo/ido.owl/IDO_$1" } ], "repository": "https://github.com/infectious-disease-ontology/infectious-disease-ontology", "uri_format": "https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1", "version": "2017-11-03" }, "idocovid19": { "contact": { "email": "johnbeverley2021@u.northwestern.edu", "github": "johnbeve", "name": "John Beverly", "orcid": "0000-0002-1118-1738" }, "description": "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease.", "download_owl": "https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19", "example": "0001191", "homepage": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19", "mappings": { "aberowl": "IDO-COVID-19", "bioportal": "IDO-COVID-19", "ols": "idocovid19" }, "name": "The COVID-19 Infectious Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "idocovid19", "providers": [ { "code": "obo1", "description": "This variation uses incorrect usage of dashes instead of underscores", "homepage": "http://purl.obolibrary.org", "name": "Incorrect OBO PURL variation 1", "uri_format": "http://purl.obolibrary.org/obo/IDO-COVID-19_$1" } ], "repository": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19", "uri_format": "http://purl.obolibrary.org/obo/COVIDO_$1", "version": "2020-07-21" }, "idoden": { "contact": { "email": "elvira@imbb.forth.gr", "github": null, "name": "Elvira Mitraka", "orcid": null }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology for dengue fever.", "download_owl": "http://aber-owl.net/media/ontologies/IDODEN/6/idoden.owl", "example": "0003463", "homepage": "https://bioportal.bioontology.org/ontologies/IDODEN", "mappings": { "aberowl": "IDODEN", "bioportal": "IDODEN", "fairsharing": "FAIRsharing.askzq4" }, "name": "Dengue Fever Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "idoden", "references": [ "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003479" ], "uri_format": "http://purl.bioontology.org/ontology/IDODEN_$1" }, "idomal": { "appears_in": [ "scdo" ], "contact": { "email": "topalis@imbb.forth.gr", "github": null, "name": "Pantelis Topalis", "orcid": null }, "deprecated": true, "description": "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.", "download_obo": "http://purl.obolibrary.org/obo/idomal.obo", "download_owl": "http://purl.obolibrary.org/obo/idomal.owl", "example": "0002350", "example_extras": [ "50000015" ], "homepage": "https://www.vectorbase.org/ontology-browser", "license": "CC0 1.0", "mappings": { "aberowl": "IDOMAL", "biocontext": "IDOMAL", "bioportal": "IDOMAL", "fairsharing": "FAIRsharing.2q8c28", "obofoundry": "idomal", "ols": "idomal", "ontobee": "IDOMAL" }, "name": "Malaria Ontology", "pattern": "^(5?)\\d{7}$", "preferred_prefix": "IDOMAL", "publications": [ { "doi": "10.1186/2041-1480-4-16", "pmc": "PMC3848731", "pubmed": "24034841", "title": "IDOMAL: the malaria ontology revisited.", "year": 2013 }, { "doi": "10.1186/1475-2875-9-230", "pmc": "PMC2925367", "pubmed": "20698959", "title": "IDOMAL: an ontology for malaria.", "year": 2010 } ], "repository": "https://github.com/VEuPathDB-ontology/IDOMAL", "uri_format": "http://purl.obolibrary.org/obo/IDOMAL_$1", "version": "2015-03-16" }, "idoo": { "description": "Identifiers.org Ontology", "example": "DataCollection", "homepage": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology", "mappings": { "miriam": "idoo", "n2t": "idoo" }, "name": "Identifiers.org Ontology", "pattern": "^[0-9a-zA-Z]+$", "preferred_prefix": "idoo", "uri_format": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1" }, "idot": { "description": "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.", "example": "identifierPattern", "homepage": "http://biomodels.net/vocab/idot.rdf", "mappings": { "biocontext": "idot", "miriam": "idot", "n2t": "idot" }, "name": "Identifiers.org Terms", "pattern": "^[A-Za-z]+$", "preferred_prefix": "idot", "uri_format": "https://biomodels.net/vocab/idot.rdf#$1" }, "idpo": { "contact": { "email": "f.quaglia@ibiom.cnr.it", "github": "federicaquaglia", "name": "Federica Quaglia", "orcid": "0000-0002-0341-4888" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR.", "example": "00056", "homepage": "https://www.disprot.org/ontology", "name": "Intrinsically Disordered Proteins Ontology", "pattern": "^\\d{5}$", "preferred_prefix": "idpo", "uri_format": "https://www.disprot.org/idpo/IDPO:$1" }, "idr": { "description": "Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image\" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools.", "example": "0001", "homepage": "https://idr.openmicroscopy.org", "mappings": { "fairsharing": "FAIRsharing.6wf1zw", "miriam": "idr" }, "name": "Image Data Resource", "pattern": "^[0-9]{4}$", "preferred_prefix": "idr", "uri_format": "https://idr.openmicroscopy.org/search/?query=Name:idr$1" }, "iedb": { "description": "The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes.", "example": "1038233", "homepage": "https://www.lji.org/", "mappings": { "fairsharing": "FAIRsharing.c886cd", "miriam": "iedb" }, "name": "Immune Epitope Database", "pattern": "^[0-9]+$", "preferred_prefix": "iedb", "uri_format": "https://www.iedb.org/reference/$1" }, "ietf.language": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Shorthand representations of languages and their subtypes", "example": "en-GB", "example_extras": [ "en", "ar-SA", "aaf" ], "homepage": "http://www.iana.org/assignments/language-subtag-registry/language-subtag-registry", "mappings": { "wikidata": "P305" }, "name": "Internet Engineering Task Force Language Tag", "pattern": "^\\w{2,3}(-\\w+)?$", "preferred_prefix": "ietf.language", "synonyms": [ "bcp47" ] }, "iev": { "deprecated": true, "example": "0000000", "homepage": "http://www.inoh.org", "mappings": { "biocontext": "IEV", "obofoundry": "iev", "prefixcommons": "iev" }, "name": "Event (INOH pathway ontology)", "pattern": "^\\d{7}$", "preferred_prefix": "IEV", "uri_format": "http://purl.obolibrary.org/obo/IEV_$1" }, "igrhcellid": { "description": "Cell line databases/resources", "example": "ACHN", "homepage": "http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi", "mappings": { "cellosaurus": "IGRhCellID" }, "name": "Integrated Genomic Resources of human Cell Lines for Identification", "preferred_prefix": "igrhcellid", "uri_format": "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1" }, "igsn": { "description": "IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents.", "example": "AU124", "homepage": "http://www.geosamples.org/", "mappings": { "fairsharing": "FAIRsharing.Yvc76F", "miriam": "igsn", "n2t": "igsn" }, "name": "International Geo Sample Number", "pattern": "^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$", "preferred_prefix": "igsn", "uri_format": "http://igsn.org/$1" }, "igsr": { "description": "The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project.", "example": "NA06985", "homepage": "https://www.internationalgenome.org/", "mappings": { "cellosaurus": "IGSR", "fairsharing": "FAIRsharing.4Vs9VM" }, "name": "International Genome Sample Resource", "preferred_prefix": "igsr", "uri_format": "https://www.internationalgenome.org/data-portal/sample/$1" }, "ihw": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics.", "example": "IHW09326", "homepage": "https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html", "mappings": { "cellosaurus": "IHW" }, "name": "International Histocompatibility Workshop cell lines", "pattern": "^IHW\\d+$", "preferred_prefix": "ihw" }, "illumina.probe": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip.", "example": "ILMN_129894", "homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6790/A-GEOD-6790.adf.txt", "name": "Illumina Probe Identifier", "pattern": "^ILMN_\\d+$", "preferred_prefix": "illumina.probe", "references": [ "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-9184/A-GEOD-9184_comments.txt" ] }, "imanis": { "description": "Cell line collections", "example": "CL070", "homepage": "https://www.imanislife.com/collections/cell-lines/", "mappings": { "cellosaurus": "Imanis" }, "name": "Imanis Life Sciences cell line products", "preferred_prefix": "imanis", "uri_format": "https://www.imanislife.com/?s=$1" }, "imdrf": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence.", "homepage": "http://www.imdrf.org/", "name": "International Medical Device Regulators Forum", "no_own_terms": true, "preferred_prefix": "imdrf", "references": [ "https://www.fda.gov/medical-devices/mandatory-reporting-requirements-manufacturers-importers-and-device-user-facilities/mdr-adverse-event-codes" ] }, "imex": { "banana": "IM", "banana_peel": "-", "description": "The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources.", "example": "19210-3", "example_extras": [ "19210" ], "homepage": "https://www.imexconsortium.org/", "mappings": { "biocontext": "IMEX", "miriam": "imex", "n2t": "imex", "prefixcommons": "imex", "re3data": "r3d100010669" }, "name": "International Molecular Exchange", "pattern": "^\\d+(-\\d+)?$", "preferred_prefix": "imex", "providers": [ { "code": "CURATOR_REVIEW", "description": "IMEx Consortium though Intact", "homepage": "https://www.ebi.ac.uk/intact/", "name": "IMEx Consortium though Intact", "uri_format": "https://imexcentral.org/icentral/imex/rec/$1" }, { "code": "intact.search", "description": "Search page on IntAct", "homepage": "https://www.ebi.ac.uk/intact", "name": "IntAct Search", "uri_format": "https://www.ebi.ac.uk/intact/search?query=IM-$1" } ], "publications": [ { "doi": "10.1002/pmic.200700286", "pmc": null, "pubmed": "17893861", "title": "Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition.", "year": 2007 } ], "uri_format": "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-$1" }, "img.gene": { "description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information.", "example": "638309541", "homepage": "http://img.jgi.doe.gov/", "mappings": { "biocontext": "IMG.GENE", "miriam": "img.gene", "n2t": "img.gene", "prefixcommons": "img.gene" }, "name": "Integrated Microbial Genomes Gene", "pattern": "^\\d+$", "preferred_prefix": "img.gene", "publications": [ { "doi": "10.1093/nar/gkm846", "pmc": "PMC2238897", "pubmed": "17933782", "title": "The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.", "year": 2007 } ], "uri_format": "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1" }, "img.taxon": { "description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information.", "example": "648028003", "homepage": "http://img.jgi.doe.gov/", "mappings": { "biocontext": "IMG.TAXON", "miriam": "img.taxon", "n2t": "img.taxon", "prefixcommons": "img.taxon" }, "name": "Integrated Microbial Genomes Taxon", "pattern": "^\\d+$", "preferred_prefix": "img.taxon", "publications": [ { "doi": "10.1093/nar/gkm846", "pmc": "PMC2238897", "pubmed": "17933782", "title": "The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.", "year": 2007 } ], "uri_format": "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1" }, "imgt.hla": { "description": "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature.", "example": "A*01:01:01:01", "homepage": "https://www.ebi.ac.uk/imgt/hla/allele.html", "mappings": { "biocontext": "IMGT.HLA", "cellosaurus": "IPD-IMGT/HLA", "edam": "2773", "fairsharing": "FAIRsharing.e28v7g", "go": "IMGT_HLA", "miriam": "imgt.hla", "n2t": "imgt.hla", "ncbi": "IMGT/HLA", "prefixcommons": "imgthla" }, "name": "IMGT/HLA human major histocompatibility complex sequence database", "pattern": "^[A-Z0-9*:]+$", "preferred_prefix": "imgt.hla", "publications": [ { "doi": "10.1093/nar/gkj088", "pmc": "PMC1347451", "pubmed": "16381979", "title": "IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences.", "year": 2006 } ], "synonyms": [ "IPD-IMGT/HLA" ], "uri_format": "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1" }, "imgt.ligm": { "description": "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates.", "example": "M94112", "homepage": "http://www.imgt.org/", "mappings": { "biocontext": "IMGT.LIGM", "go": "IMGT_LIGM", "miriam": "imgt.ligm", "n2t": "imgt.ligm", "ncbi": "IMGT/LIGM", "prefixcommons": "imgt.ligm" }, "name": "ImMunoGeneTics database covering immunoglobulins and T-cell receptors", "pattern": "^M\\d+$", "preferred_prefix": "imgt.ligm", "providers": [ { "code": "CURATOR_REVIEW", "description": "IMGT LIGM through DKFZ (SRS)", "homepage": "http://genius.embnet.dkfz-heidelberg.de/", "name": "IMGT LIGM through DKFZ (SRS)", "uri_format": "http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-id+4ktAl1fNMTA+-e+[IMGT:'$1']" } ], "publications": [ { "doi": "10.1093/nar/gkj088", "pmc": "PMC1347451", "pubmed": "16381979", "title": "IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences.", "year": 2006 } ], "uri_format": "http://www.imgt.org/ligmdb/view?id=$1" }, "imr": { "contact": { "email": "curator@inoh.org", "github": null, "name": "INOH curators", "orcid": null }, "deprecated": true, "example": "0000001", "homepage": "http://www.inoh.org", "mappings": { "biocontext": "IMR", "obofoundry": "imr", "prefixcommons": "imr" }, "name": "Molecule role (INOH Protein name/family name ontology)", "pattern": "^\\d{7}$", "preferred_prefix": "IMR", "uri_format": "http://purl.obolibrary.org/obo/IMR_$1" }, "inaturalist.observation": { "contributor": { "email": null, "github": "oolonek", "name": "Pierre-Marie Allard", "orcid": "0000-0003-3389-2191" }, "description": "The identifier for an observation in iNaturalist", "example": "36010371", "github_request_issue": 517, "homepage": "https://www.inaturalist.org/observations", "mappings": { "wikidata": "P5683" }, "name": "iNaturalist Observation", "pattern": "^[1-9]\\d*$", "preferred_prefix": "inaturalist.observation", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.inaturalist.org/observations/$1" }, "inaturalist.place": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Identifier for a place in iNaturalist", "example": "7207", "homepage": "https://www.inaturalist.org/places", "mappings": { "wikidata": "P7471" }, "name": "iNaturalist Place", "pattern": "^[1-9]\\d*$", "preferred_prefix": "inaturalist.place", "uri_format": "https://www.inaturalist.org/places/$1" }, "inaturalist.taxon": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Identifier for a species in iNaturalist", "example": "21723", "homepage": "https://www.inaturalist.org/taxa", "mappings": { "wikidata": "P3151" }, "name": "iNaturalist Taxonomy", "pattern": "^[1-9]\\d{0,6}$", "preferred_prefix": "inaturalist.taxon", "uri_format": "https://www.inaturalist.org/taxa/$1" }, "inaturalist.user": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Identifier for a user in iNaturalist", "example": "1426686", "homepage": "https://www.inaturalist.org/users", "name": "iNaturalist User", "pattern": "^[1-9]\\d*$", "preferred_prefix": "inaturalist.user", "uri_format": "https://www.inaturalist.org/users/$1" }, "inchi": { "description": "The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier.", "example": "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3", "homepage": "http://www.chemspider.com/", "mappings": { "biocontext": "INCHI", "fairsharing": "FAIRsharing.ddk9t9", "miriam": "inchi", "n2t": "inchi", "wikidata": "P234" }, "name": "InChI", "pattern": "^InChI\\=1S?\\/[A-Za-z0-9\\.]+(\\+[0-9]+)?(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,\\/\\?\\;\\.]+)*$", "preferred_prefix": "inchi", "providers": [ { "code": "CURATOR_REVIEW", "description": "InChI through NIST", "homepage": "http://webbook.nist.gov/chemistry", "name": "InChI through NIST", "uri_format": "http://webbook.nist.gov/cgi/cbook.cgi?$1" }, { "code": "ebi", "description": "InChI through ChEBI", "homepage": "https://www.ebi.ac.uk/chebi/", "name": "InChI through ChEBI", "uri_format": "https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=$1" }, { "code": "um", "description": "InChI through RDF Open Molecules", "homepage": "http://rdf.openmolecules.net/", "name": "InChI through RDF Open Molecules", "uri_format": "http://rdf.openmolecules.net/?$1" } ], "uri_format": "http://www.chemspider.com/$1" }, "inchikey": { "description": "The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI.", "example": "RYYVLZVUVIJVGH-UHFFFAOYSA-N", "homepage": "http://www.chemspider.com/", "mappings": { "biocontext": "INCHIKEY", "miriam": "inchikey", "n2t": "inchikey", "wikidata": "P235" }, "name": "InChIKey", "pattern": "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-Z])$", "preferred_prefix": "inchikey", "providers": [ { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/inchikey/$1" } ], "uri_format": "http://www.chemspider.com/inchikey=$1" }, "inhand": { "comment": "This nomenclature is available via email. Truly a disgrace.", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology.", "homepage": "https://www.goreni.org/gr3_nomenclature.php", "mappings": { "fairsharing": "FAIRsharing.9gqfpm" }, "name": "The International Harmonization of Nomenclature and Diagnostic criteria", "preferred_prefix": "inhand", "proprietary": true, "publications": [ { "doi": "10.1177/0192623309353423", "pmc": null, "pubmed": "20032296", "title": "Proliferative and nonproliferative lesions of the rat and mouse respiratory tract.", "year": 2009 } ] }, "inn": { "comment": "can not find a place to resolve to", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.", "example": "fluticasone", "homepage": "https://www.who.int/teams/health-product-and-policy-standards/inn", "mappings": { "wikidata": "P2275" }, "name": "International Nonproprietary Names", "preferred_prefix": "inn", "synonyms": [ "INN_ID" ], "uri_format": "https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1" }, "ino": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "description": "he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles.", "download_owl": "http://purl.obolibrary.org/obo/ino.owl", "example": "0000003", "homepage": "https://github.com/INO-ontology/ino", "license": "CC BY 3.0", "mappings": { "aberowl": "INO", "biolink": "INO", "bioportal": "INO", "fairsharing": "FAIRsharing.mm72as", "obofoundry": "ino", "ols": "ino", "ontobee": "INO" }, "name": "Interaction Network Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "INO", "publications": [ { "doi": "10.1186/s13040-016-0118-0", "pmc": "PMC5168857", "pubmed": "28031747", "title": "The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature.", "year": 2016 }, { "doi": "10.1186/2041-1480-6-2", "pmc": "PMC4362819", "pubmed": "25785184", "title": "Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions.", "year": 2015 }, { "doi": "10.1186/2041-1480-2-s2-s8", "pmc": "PMC3102897", "pubmed": "21624163", "title": "Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology.", "year": 2011 } ], "repository": "https://github.com/INO-ontology/ino", "uri_format": "http://purl.obolibrary.org/obo/INO_$1", "version": "1.1.13" }, "insdc": { "description": "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences.", "example": "X58356", "homepage": "https://www.ncbi.nlm.nih.gov/Genbank/", "mappings": { "biocontext": "INSDC", "miriam": "insdc", "n2t": "insdc", "prefixcommons": "insdc" }, "name": "Nucleotide Sequence Database", "pattern": "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$", "preferred_prefix": "insdc", "providers": [ { "code": "CURATOR_REVIEW", "description": "INSDC through DDBJ", "homepage": "http://www.ddbj.nig.ac.jp/", "name": "INSDC through DDBJ", "uri_format": "http://getentry.ddbj.nig.ac.jp/getentry?database=ddbj&accession_number=$1" }, { "code": "ebi", "description": "INSDC through European Nucleotide Archive (ENA)", "homepage": "https://www.ebi.ac.uk/ena/", "name": "INSDC through European Nucleotide Archive (ENA)", "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" }, { "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/18.6.1517", "pmc": "PMC330520", "pubmed": "2326192", "title": "Recent changes in the GenBank On-line Service.", "year": 1990 }, { "doi": "10.1093/nar/gkl986", "pmc": "PMC1781245", "pubmed": "17202161", "title": "GenBank.", "year": 2007 }, { "doi": "10.1093/nar/gkl913", "pmc": "PMC1897316", "pubmed": "17148479", "title": "EMBL Nucleotide Sequence Database in 2006.", "year": 2006 }, { "doi": "10.1126/science.298.5597.1333b", "pmc": null, "pubmed": "12436968", "title": "Nucleotide sequence database policies.", "year": 2002 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" }, "insdc.cds": { "description": "The coding sequence or protein identifiers as maintained in INSDC.", "example": "AAA35559", "has_canonical": "ncbiprotein", "homepage": "http://getentry.ddbj.nig.ac.jp", "mappings": { "biocontext": "INSDC.CDS", "miriam": "insdc.cds", "n2t": "insdc.cds" }, "name": "INSDC CDS", "pattern": "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$", "preferred_prefix": "insdc.cds", "providers": [ { "code": "CURATOR_REVIEW", "description": "INSDC CDS through ENA", "homepage": "https://www.ebi.ac.uk/ena", "name": "INSDC CDS through ENA", "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" }, { "code": "CURATOR_REVIEW", "description": "INSDC CDS through NCBI", "homepage": "https://www.ncbi.nlm.nih.gov/protein/", "name": "INSDC CDS through NCBI", "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1" } ], "uri_format": "http://getentry.ddbj.nig.ac.jp/getentry/dad/$1" }, "insdc.gca": { "description": "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage.", "example": "GCA_000155495.1", "has_canonical": "ncbi.assembly", "homepage": "https://www.ebi.ac.uk/ena/browse/genome-assembly-database", "mappings": { "biocontext": "INSDC.GCA", "miriam": "insdc.gca", "n2t": "insdc.gca" }, "name": "Genome assembly database", "pattern": "^GC[AF]_[0-9]{9}\\.[0-9]+$", "preferred_prefix": "insdc.gca", "providers": [ { "code": "ncbi", "description": "Genome assembly database NCBI", "homepage": "https://www.ncbi.nlm.nih.gov/assembly/", "name": "Genome assembly database NCBI", "uri_format": "https://www.ncbi.nlm.nih.gov/assembly/$1" } ], "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" }, "insdc.run": { "comment": "https://www.insdc.org/ is the authoritative source for INSDC. However, confusingly, they don't mention runs in this table. I think we should ask them to include. ENA is a partner and they have documentation here: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html Runs | (E\\|D\\|S)RR[0-9]{6,} | ERR123456 -- | -- | --", "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "An experimental run, served thrugh the ENA", "example": "ERR436051", "github_request_issue": 131, "has_canonical": "ena.embl", "homepage": "https://www.insdc.org/", "name": "International Nucleotide Sequence Database Collaboration (INSDC) Run", "pattern": "^(E|D|S)RR[0-9]{6,}$", "preferred_prefix": "insdc.run", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.ebi.ac.uk/ena/browser/view/$1" }, "insdc.sra": { "description": "The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.", "example": "SRX000007", "homepage": "https://www.ncbi.nlm.nih.gov/sra", "mappings": { "biocontext": "INSDC.SRA", "fairsharing": "FAIRsharing.g7t2hv", "miriam": "insdc.sra", "n2t": "insdc.sra" }, "name": "Sequence Read Archive", "pattern": "^[SED]R[APRSXZ]\\d+$", "preferred_prefix": "insdc.sra", "providers": [ { "code": "ddbj", "description": "DDBJ Sequence Read Archive (DRA)", "homepage": "http://trace.ddbj.nig.ac.jp/dra/", "name": "DDBJ Sequence Read Archive (DRA)", "uri_format": "http://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc=$1" }, { "code": "ebi", "description": "European Nucleotide Archive (ENA)", "homepage": "https://www.ebi.ac.uk/ena", "name": "European Nucleotide Archive (ENA)", "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" } ], "uri_format": "https://www.ncbi.nlm.nih.gov/sra/$1" }, "intact": { "description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data.", "example": "EBI-2307691", "homepage": "https://www.ebi.ac.uk/intact/", "mappings": { "biocontext": "INTACT", "fairsharing": "FAIRsharing.d05nwx", "go": "IntAct", "miriam": "intact", "n2t": "intact", "prefixcommons": "intact", "re3data": "r3d100010671", "uniprot": "IntAct" }, "name": "IntAct protein interaction database", "pattern": "^EBI\\-[0-9]+$", "preferred_prefix": "intact", "publications": [ { "doi": "10.1093/nar/gkh052", "pmc": "PMC308786", "pubmed": "14681455", "title": "IntAct: an open source molecular interaction database.", "year": 2004 } ], "uri_format": "https://www.ebi.ac.uk/intact/interaction/$1" }, "intact.molecule": { "description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules.", "example": "EBI-366083", "homepage": "https://www.ebi.ac.uk/intact/", "mappings": { "biocontext": "INTACT.MOLECULE", "miriam": "intact.molecule", "n2t": "intact.molecule" }, "name": "IntAct Molecule", "pattern": "^EBI\\-[0-9]+$", "preferred_prefix": "intact.molecule", "uri_format": "https://www.ebi.ac.uk/intact/search?query=$1" }, "interlex": { "description": "InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. ", "example": "0101963", "homepage": "https://www.fdilab.org", "mappings": { "fairsharing": "FAIRsharing.67sssf", "miriam": "ilx" }, "name": "InterLex", "pattern": "^[0-9]+$", "preferred_prefix": "interlex", "publications": [ { "doi": "10.3389/fninf.2013.00018", "pmc": "PMC3757470", "pubmed": "24009581", "title": "NeuroLex.org: an online framework for neuroscience knowledge.", "year": 2013 } ], "references": [ "https://github.com/AllenInstitute/nomenclature" ], "synonyms": [ "ILX" ], "uri_format": "https://scicrunch.org/scicrunch/interlex/view/ilx_$1" }, "interpro": { "contact": { "email": "interhelp@ebi.ac.uk", "github": null, "name": "InterPro Help", "orcid": null }, "description": "InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.", "example": "IPR016380", "homepage": "http://www.ebi.ac.uk/interpro/index.html", "mappings": { "biocontext": "IPR", "biolink": "interpro", "edam": "1133", "fairsharing": "FAIRsharing.pda11d", "go": "InterPro", "miriam": "interpro", "n2t": "interpro", "ncbi": "InterPro", "obofoundry": "ipr", "prefixcommons": "interpro", "re3data": "r3d100010798", "uniprot": "InterPro", "wikidata": "P2926" }, "name": "InterPro", "pattern": "^IPR\\d{6}$", "preferred_prefix": "interpro", "providers": [ { "code": "CURATOR_REVIEW", "description": "Bio2RDF", "homepage": "http://interpro.bio2rdf.org/fct/", "name": "Bio2RDF", "uri_format": "http://interpro.bio2rdf.org/describe/?url=http://bio2rdf.org/interpro:$1" } ], "publications": [ { "doi": "10.1093/nar/gki106", "pmc": "PMC540060", "pubmed": "15608177", "title": "InterPro, progress and status in 2005.", "year": 2005 } ], "synonyms": [ "IP", "IPR", "InterPro" ], "uri_format": "https://www.ebi.ac.uk/interpro/entry/$1" }, "ird.segment": { "description": "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s).", "example": "CY077097", "homepage": "http://www.fludb.org/", "mappings": { "biocontext": "IRD.SEGMENT", "miriam": "ird.segment", "n2t": "ird.segment", "prefixcommons": "ird.segment" }, "name": "IRD Segment Sequence", "pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$", "preferred_prefix": "ird.segment", "publications": [ { "doi": "10.1093/nar/gkm905", "pmc": "PMC2238987", "pubmed": "17965094", "title": "BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence.", "year": 2007 } ], "uri_format": "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1" }, "irefweb": { "description": "iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.", "example": "617102", "homepage": "http://wodaklab.org/iRefWeb/", "mappings": { "biocontext": "IREFWEB", "fairsharing": "FAIRsharing.t31wcb", "miriam": "irefweb", "n2t": "irefweb", "prefixcommons": "irefweb", "re3data": "r3d100012725" }, "name": "iRefWeb", "pattern": "^\\d+$", "preferred_prefix": "irefweb", "uri_format": "http://wodaklab.org/iRefWeb/interaction/show/$1" }, "iro": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "example": "0000008", "name": "Insect Resistance Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "iro", "uri_format": "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1" }, "isbn": { "description": "The International Standard Book Number (ISBN) is for identifying printed books.", "example": "9781584885658", "homepage": "http://isbndb.com/", "mappings": { "biocontext": "ISBN-13", "biolink": "isbn", "edam": "2634", "go": "ISBN", "miriam": "isbn", "n2t": "isbn", "prefixcommons": "isbn" }, "name": "International Standard Book Number", "pattern": "^(ISBN)?(-13|-10)?[:]?[ ]?(\\d{2,3}[ -]?)?\\d{1,5}[ -]?\\d{1,7}[ -]?\\d{1,6}[ -]?(\\d|X)$", "preferred_prefix": "isbn", "providers": [ { "code": "CURATOR_REVIEW", "description": "ISBN database at WorldCat", "homepage": "http://www.worldcat.org/", "name": "ISBN database at WorldCat", "uri_format": "http://www.worldcat.org/isbn/$1" } ], "synonyms": [ "ISBN-10", "ISBN-13" ], "uri_format": "http://isbndb.com/search-all.html?kw=$1" }, "isfinder": { "description": "ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. 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Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. 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It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable.", "example": "ev:E00032", "homepage": "http://www.genome.jp/kegg/drug/environ.html", "mappings": { "biocontext": "KEGG.ENVIRON", "miriam": "kegg.environ", "n2t": "kegg.environ" }, "name": "KEGG Environ", "part_of": "kegg", "pattern": "^(ev\\:)?E\\d+$", "preferred_prefix": "kegg.environ", "synonyms": [ "KEGG.EDRUG" ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.enzyme": { "description": "KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links.", "homepage": "http://www.genome.jp/dbget-bin/www_bfind?enzyme", "mappings": { "biolink": "KEGG.ENZYME", "go": "KEGG_ENZYME" }, "name": "KEGG Enzyme", "part_of": "kegg", "preferred_prefix": "kegg.enzyme", "provides": "eccode", "uri_format": "http://www.genome.jp/dbget-bin/www_bget?ec:$1" }, "kegg.genes": { "description": "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources.", "example": "bsu:BSU01340", "homepage": "http://www.genome.jp/kegg/genes.html", "mappings": { "biocontext": "KEGG.GENES", "biolink": "KEGG.GENE", "miriam": "kegg.genes", "n2t": "kegg.genes", "prefixcommons": "kegg.gene", "wikidata": "P665" }, "name": "KEGG Genes", "part_of": "kegg", "pattern": "^\\w+:[\\w\\d\\.-]*$", "preferred_prefix": "kegg.genes", "publications": [ { "doi": "10.1093/nar/gkj102", "pmc": "PMC1347464", "pubmed": "16381885", "title": "From genomics to chemical genomics: new developments in KEGG.", "year": 2006 } ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.genome": { "description": "KEGG Genome is a collection of organisms whose genomes have been completely sequenced.", "example": "T06648", "homepage": "http://www.genome.jp/kegg/catalog/org_list.html", "mappings": { "biocontext": "KEGG.GENOME", "miriam": "kegg.genome", "n2t": "kegg.genome", "prefixcommons": "kegg.genome", "wikidata": "P665" }, "name": "KEGG Genome", "part_of": "kegg", "pattern": "^(T0\\d+|\\w{3,5})$", "preferred_prefix": "kegg.genome", "publications": [ { "doi": "10.1093/nar/gkr988", "pmc": "PMC3245020", "pubmed": "22080510", "title": "KEGG for integration and interpretation of large-scale molecular data sets.", "year": 2011 } ], "synonyms": [ "kegg_genome", "kegg_genomes" ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.glycan": { "description": "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. 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It now lives inside the compound database", "deprecated": true, "homepage": "http://www.genome.ad.jp/kegg/docs/upd_ligand.html", "mappings": { "go": "KEGG_LIGAND" }, "name": "KEGG LIGAND", "part_of": "kegg", "preferred_prefix": "kegg.ligand", "uri_format": "http://www.genome.jp/dbget-bin/www_bget?cpd:$1" }, "kegg.metagenome": { "description": "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species.", "example": "T30002", "homepage": "http://www.genome.jp/kegg/catalog/org_list3.html", "mappings": { "biocontext": "KEGG.METAGENOME", "miriam": "kegg.metagenome", "n2t": "kegg.metagenome", "prefixcommons": "kegg.metagenome" }, "name": "KEGG Metagenome", "part_of": "kegg", "pattern": "^T3\\d+$", "preferred_prefix": "kegg.metagenome", "publications": [ { "doi": "10.1093/nar/gkr988", "pmc": "PMC3245020", "pubmed": "22080510", "title": "KEGG for integration and interpretation of large-scale molecular data sets.", "year": 2011 } ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.module": { "description": "KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules.", "example": "M00002", "homepage": "http://www.kegg.jp/kegg/module.html", "mappings": { "biocontext": "KEGG.MODULE", "miriam": "kegg.module", "n2t": "kegg.module" }, "name": "KEGG Module", "part_of": "kegg", "pattern": "^([a-z]{3,5}_)?M\\d{5}$", "preferred_prefix": "kegg.module", "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.orthology": { "description": "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms.", "example": "K00001", "homepage": "http://www.genome.jp/kegg/ko.html", "mappings": { "biocontext": "KEGG.ORTHOLOGY", "miriam": "kegg.orthology", "n2t": "kegg.orthology", "prefixcommons": "kegg.orthology" }, "name": "KEGG Orthology", "part_of": "kegg", "pattern": "^K\\d+$", "preferred_prefix": "kegg.orthology", "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.pathway": { "description": "KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.", "example": "rsk00410", "homepage": "https://www.genome.jp/kegg/pathway.html", "mappings": { "biocontext": "KEGG.PATHWAY", "biolink": "KEGG.PATHWAY", "edam": "2343", "go": "KEGG_PATHWAY", "miriam": "kegg.pathway", "n2t": "kegg.pathway", "prefixcommons": "kegg.pathway", "wikidata": "P665" }, "name": "KEGG Pathways Database", "part_of": "kegg", "pattern": "^\\w{2,4}\\d{5}$", "preferred_prefix": "kegg.pathway", "publications": [ { "doi": "10.1002/0471250953.bi0112s38", "pmc": null, "pubmed": "22700311", "title": "Using the KEGG database resource.", "year": 2012 } ], "synonyms": [ "KEGG-path", "KEGG_PATHWAY" ], "uri_format": "https://www.kegg.jp/entry/$1" }, "kegg.rclass": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns.", "example": "RC00001", "homepage": "http://www.genome.jp/kegg/reaction/", "mappings": { "biolink": "KEGG.RCLASS" }, "name": "KEGG Reaction Class", "part_of": "kegg", "pattern": "^RC\\d+$", "preferred_prefix": "kegg.rclass", "references": [ "https://github.com/prefixcommons/prefixes/pull/2" ], "synonyms": [ "KEGG_RCLASS", "KEGG_REACTION_CLASS" ] }, "kegg.reaction": { "description": "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life.", "example": "R00100", "homepage": "https://www.genome.jp/kegg/reaction/", "mappings": { "biocontext": "KEGG.REACTION", "edam": "2608", "go": "KEGG_REACTION", "miriam": "kegg.reaction", "n2t": "kegg.reaction", "prefixcommons": "kegg.reaction", "wikidata": "P665" }, "name": "KEGG Reaction", "part_of": "kegg", "pattern": "^R\\d+$", "preferred_prefix": "kegg.reaction", "publications": [ { "doi": "10.1002/0471250953.bi0112s38", "pmc": null, "pubmed": "22700311", "title": "Using the KEGG database resource.", "year": 2012 } ], "synonyms": [ "KEGG_REACTION" ], "uri_format": "https://www.kegg.jp/entry/$1" }, "kerafast": { "description": "Cell line collections", "example": "EJH014", "homepage": "https://www.kerafast.com/", "mappings": { "cellosaurus": "Kerafast" }, "name": "Kerafast cell lines", "preferred_prefix": "kerafast", "uri_format": "https://www.kerafast.com/Search?SearchTerm="$1"" }, "knapsack": { "description": "KNApSAcK provides information on metabolites and the\ntaxonomic class with which they are associated.", "example": "C00000001", "homepage": "http://www.knapsackfamily.com/KNApSAcK/", "mappings": { "biocontext": "KNAPSACK", "miriam": "knapsack", "n2t": "knapsack", "wikidata": "P2064" }, "name": "KNApSAcK", "pattern": "^C\\d{8}$", "preferred_prefix": "knapsack", "uri_format": "http://www.knapsackfamily.com/knapsack_core/information.php?word=$1" }, "kupo": { "appears_in": [ "cl" ], "comment": "Website is down, now it redirects to something else that is not related", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "example": "0001009", "homepage": "http://www.kupkb.org/", "name": "Kidney and Urinary Pathway Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "kupo", "references": [ "https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-2-S2-S7" ] }, "kyinno": { "description": "Cell line collections", "example": "KC-0979", "homepage": "https://www.kyinno.com/", "mappings": { "cellosaurus": "KYinno" }, "name": "KYinno cell lines", "preferred_prefix": "kyinno", "uri_format": "https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf" }, "labo": { "contact": { "email": "paul.fabry@usherbrooke.ca", "github": "pfabry", "name": "Paul Fabry", "orcid": "0000-0002-3336-2476" }, "depends_on": [ "iao", "obi", "ogms", "omiabis", "omrse", "opmi" ], "description": "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents.", "download_owl": "http://purl.obolibrary.org/obo/labo.owl", "example": "0000124", "homepage": "https://github.com/OpenLHS/LABO", "license": "CC BY 4.0", "mappings": { "aberowl": "LABO", "bioportal": "LABO", "obofoundry": "labo", "ols": "labo", "ontobee": "LABO" }, "name": "clinical LABoratory Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "LABO", "publications": [ { "doi": "10.5281/zenodo.6522019", "pmc": null, "pubmed": null, "title": "LABO: An Ontology for Laboratory Test Prescription and Reporting", "year": null } ], "repository": "https://github.com/OpenLHS/LABO", "uri_format": "http://purl.obolibrary.org/obo/LABO_$1", "version": "2021-06-08" }, "langual": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Langual stands for \"langua alimentaria\" or \"language of food\". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases", "example": "B2067", "github_request_issue": 507, "homepage": "https://www.langual.org", "name": "Langua aLimentaria Thesaurus", "pattern": "^B\\d+$", "preferred_prefix": "langual", "uri_format": "https://www.langual.org/langual_thesaurus.asp?termid=$1" }, "lbo": { "contact": { "email": "caripark@iastate.edu", "github": "caripark", "name": "Carissa Park", "orcid": "0000-0002-2346-5201" }, "description": "A vocabulary for cattle, chicken, horse, pig, and sheep breeds.", "download_obo": "https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.obo", "download_owl": "https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.owl", "example": "0000487", "homepage": "http://bioportal.bioontology.org/ontologies/LBO", "mappings": { "aberowl": "LBO", "agroportal": "LBO", "bioportal": "LBO", "fairsharing": "FAIRsharing.309v57", "ols": "lbo" }, "name": "Livestock Breed Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "lbo", "repository": "https://github.com/AnimalGenome/livestock-breed-ontology", "uri_format": "http://purl.obolibrary.org/obo/LBO_$1" }, "lei": { "description": "Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland.", "example": "HWUPKR0MPOU8FGXBT394", "homepage": "https://www.gleif.org/", "mappings": { "miriam": "lei", "n2t": "lei" }, "name": "Global LEI Index", "pattern": "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$", "preferred_prefix": "lei", "uri_format": "https://www.gleif.org/lei/$1" }, "lepao": { "contact": { "email": "lagonzalezmo@unal.edu.co", "github": "luis-gonzalez-m", "name": "Luis A. Gonzalez-Montana", "orcid": "0000-0002-9136-9932" }, "depends_on": [ "aism", "bfo", "bspo", "caro", "pato", "ro", "uberon" ], "description": "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research.", "download_obo": "http://purl.obolibrary.org/obo/lepao.obo", "download_owl": "http://purl.obolibrary.org/obo/lepao.owl", "example": "0000005", "homepage": "https://github.com/insect-morphology/lepao", "license": "CC BY 4.0", "mappings": { "aberowl": "LEPAO", "bioportal": "LEPAO", "obofoundry": "lepao", "ols": "lepao" }, "name": "Lepidoptera Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "LEPAO", "repository": "https://github.com/insect-morphology/lepao", "uri_format": "http://purl.obolibrary.org/obo/LEPAO_$1", "version": "2021-11-20" }, "lgai.cede": { "description": "LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR).", "example": "LGCEDe-S-000002244", "homepage": "https://www.lgresearch.ai", "mappings": { "miriam": "lgai.cede" }, "name": "LG Chemical Entity Detection Dataset (LGCEDe)", "pattern": "^LGCEDe-S-\\d{9}$", "preferred_prefix": "lgai.cede", "uri_format": "https://s3.us-east-2.amazonaws.com/lg.cede/$1" }, "lgic": { "comment": "Website is gone", "deprecated": true, "description": "The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available.", "example": "5HT3Arano", "homepage": "https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php", "mappings": { "biocontext": "LGIC", "miriam": "lgic", "n2t": "lgic", "prefixcommons": "lgicdb" }, "name": "Ligand-Gated Ion Channel database", "pattern": "^\\w+$", "preferred_prefix": "lgic", "publications": [ { "doi": "10.1093/nar/27.1.340", "pmc": "PMC148177", "pubmed": "9847222", "title": "The Ligand Gated Ion Channel Database.", "year": 1999 } ], "uri_format": "https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php" }, "licebase": { "description": "Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects.", "example": "EMLSAT00000003403", "homepage": "https://licebase.org", "mappings": { "biocontext": "LICEBASE", "fairsharing": "FAIRsharing.c7w81a", "miriam": "licebase", "n2t": "licebase", "re3data": "r3d100013547" }, "name": "LiceBase", "pattern": "^[A-Za-z0-9\\-\\/]+$", "preferred_prefix": "licebase", "uri_format": "https://licebase.org/?q=$1" }, "ligandbook": { "description": "Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community.", "example": "785", "homepage": "https://ligandbook.org/", "mappings": { "miriam": "ligandbook", "n2t": "ligandbook" }, "name": "LigandBook", "pattern": "^[0-9]+$", "preferred_prefix": "ligandbook", "uri_format": "https://ligandbook.org/package/$1" }, "ligandbox": { "description": "LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds.", "example": "D00001", "homepage": "http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en", "mappings": { "biocontext": "LIGANDBOX", "miriam": "ligandbox", "n2t": "ligandbox" }, "name": "LigandBox", "pattern": "^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$", "preferred_prefix": "ligandbox", "uri_format": "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1" }, "ligandexpo": { "description": "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.", "example": "ABC", "homepage": "http://ligand-depot.rutgers.edu/index.html", "mappings": { "biocontext": "LIGANDEXPO", "fairsharing": "FAIRsharing.2ma4gq", "miriam": "ligandexpo", "n2t": "ligandexpo", "prefixcommons": "ligandexpo" }, "name": "Ligand Expo", "pattern": "^(\\w){3}$", "preferred_prefix": "ligandexpo", "providers": [ { "code": "CURATOR_REVIEW", "description": "Ligand Expo at Rutgers", "homepage": "http://ligand-expo.rcsb.org/", "name": "Ligand Expo at Rutgers", "uri_format": "http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid" } ], "publications": [ { "doi": "10.1093/bioinformatics/bth214", "pmc": null, "pubmed": "15059838", "title": "Ligand Depot: a data warehouse for ligands bound to macromolecules.", "year": 2004 } ], "uri_format": "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid" }, "ligea": { "comment": "This might just be a provider for CCLE", "description": "Polymorphism and mutation databases", "example": "CCLE_867", "homepage": "http://hpc-bioinformatics.cineca.it/fusion/main", "mappings": { "cellosaurus": "LiGeA" }, "name": "Cancer cell LInes GEne fusions portAl", "preferred_prefix": "ligea", "uri_format": "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1" }, "limore": { "description": "Cell line databases/resources", "example": "Li7", "homepage": "https://www.picb.ac.cn/limore/home", "mappings": { "cellosaurus": "LIMORE" }, "name": "Liver Cancer Model Repository", "preferred_prefix": "limore", "uri_format": "https://www.picb.ac.cn/limore/cellLines/single?para=$1" }, "lincs.cell": { "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.", "example": "LCL-2085", "homepage": "http://lincsportal.ccs.miami.edu/cells/", "mappings": { "biocontext": "LINCS.CELL", "cellosaurus": "LINCS_LDP", "miriam": "lincs.cell", "n2t": "lincs.cell" }, "name": "LINCS Cell", "pattern": "^(LCL|LDC|ES|LSC|LPC)-\\d+$", "preferred_prefix": "lincs.cell", "synonyms": [ "LINCS_LDP" ], "uri_format": "http://lincsportal.ccs.miami.edu/cells/#/view/$1" }, "lincs.data": { "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level).", "example": "LDS-1110", "homepage": "http://lincsportal.ccs.miami.edu/datasets/", "mappings": { "biocontext": "LINCS.DATA", "miriam": "lincs.data", "n2t": "lincs.data" }, "name": "LINCS Data", "pattern": "^[EL]D[SG]-\\d+$", "preferred_prefix": "lincs.data", "providers": [ { "code": "omicsdi", "description": "Lincs through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "Lincs through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/lincs/$1" } ], "uri_format": "http://lincsportal.ccs.miami.edu/datasets/#/view/$1" }, "lincs.protein": { "description": "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins.", "example": "200282", "homepage": "http://lincs.hms.harvard.edu/db/proteins/", "mappings": { "biocontext": "LINCS.PROTEIN", "miriam": "lincs.protein", "n2t": "lincs.protein" }, "name": "LINCS Protein", "pattern": "^\\d+$", "preferred_prefix": "lincs.protein", "uri_format": "https://lincs.hms.harvard.edu/db/proteins/$1" }, "lincs.smallmolecule": { "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC).", "example": "LSM-6306", "homepage": "http://lincsportal.ccs.miami.edu/SmallMolecules/", "mappings": { "biocontext": "LINCS.SMALLMOLECULE", "miriam": "lincs.smallmolecule", "n2t": "lincs.smallmolecule" }, "name": "LINCS Small Molecule", "pattern": "^LSM-\\d+$", "preferred_prefix": "lincs.smallmolecule", "synonyms": [ "lincs" ], "uri_format": "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1" }, "linguist": { "description": "Registry of programming languages for the Linguist program for detecting and highlighting programming languages.", "example": "Python", "homepage": "https://github.com/github/linguist", "mappings": { "miriam": "linguist" }, "name": "Linguist", "pattern": "^[a-zA-Z0-9 +#'*]+$", "preferred_prefix": "linguist", "repository": "https://github.com/github/linguist", "uri_format": "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1" }, "linkml": { "comment": "Closes #508", "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks.", "example": "SchemaDefinition", "github_request_issue": 512, "homepage": "https://linkml.io/linkml-model/docs/SchemaDefinition/", "mappings": { "biolink": "linkml" }, "name": "LinkML", "preferred_prefix": "linkml", "uri_format": "https://w3id.org/linkml/$1" }, "lipidbank": { "description": "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.", "example": "BBA0001", "homepage": "http://lipidbank.jp/index.html", "mappings": { "biocontext": "LIPIDBANK", "edam": "2665", "fairsharing": "FAIRsharing.bdn9br", "miriam": "lipidbank", "n2t": "lipidbank", "prefixcommons": "lipidbank" }, "name": "LipidBank", "pattern": "^\\w+\\d+$", "preferred_prefix": "lipidbank", "publications": [ { "doi": null, "pmc": null, "pubmed": "12058481", "title": "[LIPIDBANK for Web, the newly developed lipid database].", "year": 2002 } ], "uri_format": "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1" }, "lipidmaps": { "description": "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.", "example": "LMPR0102010012", "homepage": "http://www.lipidmaps.org", "mappings": { "biocontext": "LIPIDMAPS", "cheminf": "000564", "edam": "2625", "fairsharing": "FAIRsharing.cpneh8", "miriam": "lipidmaps", "n2t": "lipidmaps", "prefixcommons": "lipidmaps", "wikidata": "P2063" }, "name": "LIPID MAPS", "pattern": "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$", "preferred_prefix": "lipidmaps", "providers": [ { "code": "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": "10.1093/nar/gkl838", "pmc": "PMC1669719", "pubmed": "17098933", "title": "LMSD: LIPID MAPS structure database.", "year": 2006 }, { "doi": "10.1194/jlr.e400004-jlr200", "pmc": null, "pubmed": "15722563", "title": "A comprehensive classification system for lipids.", "year": 2005 } ], "synonyms": [ "LIPID MAPS", "LIPID_MAPS_class", "LIPID_MAPS_instance" ], "uri_format": "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1" }, "lipro": { "contact": { "email": "bakerc@unb.ca", "github": null, "name": "Christipher Baker", "orcid": null }, "deprecated": true, "description": "An ontology representation of the LIPIDMAPS nomenclature classification.", "download_owl": "http://aber-owl.net/media/ontologies/LIPRO/4/lipro.owl", "mappings": { "aberowl": "LIPRO", "biocontext": "LIPRO", "bioportal": "LIPRO", "obofoundry": "lipro" }, "name": "Lipid Ontology", "preferred_prefix": "LIPRO", "uri_format": "http://purl.obolibrary.org/obo/LIPRO_$1" }, "lncipedia": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A comprehensive compendium of human long non-coding RNAs", "example": "SNHG3", "homepage": "https://lncipedia.org", "mappings": { "fairsharing": "FAIRsharing.84c1a7" }, "name": "LNCipedia", "preferred_prefix": "lncipedia" }, "loggerhead": { "contact": { "email": "peteremidford@yahoo.com", "github": null, "name": "Peter Midford", "orcid": "0000-0001-6512-3296" }, "deprecated": true, "homepage": "http://www.mesquiteproject.org/ontology/Loggerhead/index.html", "mappings": { "biocontext": "LOGGERHEAD", "obofoundry": "loggerhead" }, "name": "Loggerhead nesting", "preferred_prefix": "LOGGERHEAD", "uri_format": "http://purl.obolibrary.org/obo/LOGGERHEAD_$1" }, "loinc": { "contact": { "email": "loinc@regenstrief.org", "github": null, "name": "LOINC Support", "orcid": null }, "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/", "mappings": { "aberowl": "LOINC", "biolink": "LOINC", "bioportal": "LOINC", "fairsharing": "FAIRsharing.2mk2zb", "hl7": "2.16.840.1.113883.6.1" }, "name": "Logical Observation Identifiers Names and Codes", "preferred_prefix": "loinc", "publications": [ { "doi": "10.1016/s1386-5056(98)00089-6", "pmc": null, "pubmed": "9749897", "title": "Combining laboratory data sets from multiple institutions using the logical observation identifier names and codes (LOINC).", "year": 1998 }, { "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 } ], "synonyms": [ "LNC" ], "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=$1" }, "lotus": { "comment": "IDs are actually leading to the structural part of LOTUS only, which might change in the future. Will adapt the regexp in case.", "contact": { "email": "adriano.rutz@ik.me", "github": "adafede", "name": "Adriano Rutz", "orcid": "0000-0003-0443-9902" }, "contributor": { "email": "adriano.rutz@ik.me", "github": "adafede", "name": "Adriano Rutz", "orcid": "0000-0003-0443-9902" }, "description": "LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry.", "example": "LTS0004651", "github_request_issue": 222, "homepage": "https://lotus.naturalproducts.net", "name": "LOTUS Initiative for Open Natural Products Research", "pattern": "^LTS\\d{7}$", "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/$1" }, "lpt": { "contact": { "email": "caripark@iastate.edu", "github": "caripark", "name": "Carissa Park", "orcid": "0000-0002-2346-5201" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.", "download_obo": "https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.obo", "download_owl": "https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.owl", "example": "0000001", "homepage": "https://github.com/AnimalGenome/livestock-product-trait-ontology", "mappings": { "aberowl": "LPT", "agroportal": "LPT", "biocontext": "LPT", "bioportal": "LPT", "fairsharing": "FAIRsharing.g78mbm" }, "name": "Livestock Product Trait Ontology", "pattern": "^\\d+$", "preferred_prefix": "lpt", "repository": "https://github.com/AnimalGenome/livestock-product-trait-ontology", "uri_format": "http://purl.obolibrary.org/obo/LPT_$1" }, "lrg": { "banana": "LRG", "banana_peel": "_", "description": "A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI.", "example": "1", "homepage": "http://www.lrg-sequence.org/", "mappings": { "biocontext": "LRG", "hl7": "2.16.840.1.113883.6.283", "miriam": "lrg", "n2t": "lrg" }, "name": "Locus Reference Genomic", "pattern": "^\\d+$", "preferred_prefix": "lrg", "providers": [ { "code": "CURATOR_REVIEW", "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": "CURATOR_REVIEW", "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": "CURATOR_REVIEW", "description": "Locus Reference Genomic through Ensembl mirror (US west)", "homepage": "http://uswest.ensembl.org/", "name": "Locus Reference Genomic through Ensembl mirror (US west)", "uri_format": "http://uswest.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1" }, { "code": "CURATOR_REVIEW", "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": "ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml" }, "lspci": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)", "example": "1", "homepage": "https://labsyspharm.github.io/lspci/", "name": "Laboratory of Systems Pharmacology Compound", "pattern": "^\\d+$", "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=$1" }, "ma": { "banana": "MA", "contact": { "email": "Terry.Hayamizu@jax.org", "github": "tfhayamizu", "name": "Terry Hayamizu", "orcid": "0000-0002-0956-8634" }, "description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)", "download_obo": "http://purl.obolibrary.org/obo/ma.obo", "download_owl": "http://purl.obolibrary.org/obo/ma.owl", "example": "0002502", "homepage": "https://github.com/obophenotype/mouse-anatomy-ontology", "license": "CC BY 4.0", "mappings": { "aberowl": "MA", "biocontext": "MA", "bioportal": "MA", "fairsharing": "FAIRsharing.pdwqcr", "go": "MA", "miriam": "ma", "n2t": "ma", "obofoundry": "ma", "ols": "ma", "ontobee": "MA", "prefixcommons": "ma" }, "name": "Mouse adult gross anatomy", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "MA", "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 } ], "repository": "https://github.com/obophenotype/mouse-anatomy-ontology", "uri_format": "http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1", "version": "2017-02-07" }, "macie": { "description": "MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved.", "example": "M0001", "homepage": "https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html", "mappings": { "biocontext": "MACIE", "edam": "2641", "fairsharing": "FAIRsharing.7xkx69", "miriam": "macie", "n2t": "macie", "prefixcommons": "macie" }, "name": "Mechanism, Annotation and Classification in Enzymes", "pattern": "^M\\d{4}$", "preferred_prefix": "macie", "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 } ], "uri_format": "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1" }, "maizegdb.locus": { "description": "MaizeGDB is the maize research community's central repository for genetics and genomics information.", "example": "25011", "homepage": "http://www.maizegdb.org/", "mappings": { "biocontext": "MAIZEGDB.LOCUS", "fairsharing": "FAIRsharing.aq280w", "go": "MaizeGDB_Locus", "miriam": "maizegdb.locus", "n2t": "maizegdb.locus", "ncbi": "MaizeGDB", "prefixcommons": "maizegdb", "re3data": "r3d100010795", "uniprot": "MaizeGDB" }, "name": "MaizeGDB Locus", "pattern": "^\\d+$", "preferred_prefix": "maizegdb.locus", "publications": [ { "doi": "10.1155/2008/496957", "pmc": "PMC2518694", "pubmed": "18769488", "title": "MaizeGDB: The maize model organism database for basic, translational, and applied research.", "year": 2008 } ], "synonyms": [ "MaizeGDB" ], "uri_format": "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1" }, "mamo": { "banana": "MAMO", "banana_peel": "_", "contact": { "email": "mamo-ontology-discuss@lists.sourceforge.net", "github": null, "name": "mamo-ontology-discuss", "orcid": null }, "deprecated": true, "description": "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.", "download_owl": "http://purl.obolibrary.org/obo/mamo.owl", "example": "0000026", "homepage": "http://sourceforge.net/p/mamo-ontology/wiki/Home/", "license": "Artistic License 2.0", "mappings": { "aberowl": "MAMO", "biocontext": "MAMO", "bioportal": "MAMO", "fairsharing": "FAIRsharing.kbz5jh", "miriam": "mamo", "n2t": "mamo", "obofoundry": "mamo", "ols": "mamo", "ontobee": "MAMO" }, "name": "Mathematical modeling ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MAMO", "repository": "http://sourceforge.net/p/mamo-ontology", "uri_format": "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1", "version": "2020-08-24" }, "mao": { "contact": { "email": "julie@igbmc.u-strasbg.fr", "github": null, "name": "Julie Thompson", "orcid": null }, "deprecated": true, "homepage": "http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html", "mappings": { "biocontext": "MAO", "obofoundry": "mao", "prefixcommons": "mao" }, "name": "Multiple alignment", "preferred_prefix": "MAO", "uri_format": "http://purl.obolibrary.org/obo/MAO_$1" }, "massbank": { "description": "MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da).", "example": "PB000166", "homepage": "http://www.massbank.jp", "mappings": { "biocontext": "MASSBANK", "fairsharing": "FAIRsharing.dk451a", "miriam": "massbank", "n2t": "massbank", "wikidata": "P6689" }, "name": "MassBank", "pattern": "^[A-Z]{2}[A-Z0-9][0-9]{5}$", "preferred_prefix": "massbank", "providers": [ { "code": "CURATOR_REVIEW", "description": "MassBank in Europe", "homepage": "https://massbank.eu/", "name": "MassBank in Europe", "uri_format": "https://massbank.eu/MassBank/RecordDisplay?id=$1" } ], "uri_format": "http://www.massbank.jp/RecordDisplay?id=$1" }, "massive": { "description": "MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data.", "example": "MSV000082131", "homepage": "https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp", "mappings": { "biocontext": "MASSIVE", "fairsharing": "FAIRsharing.LYsiMd", "miriam": "massive", "n2t": "massive", "uniprot": "MassIVE" }, "name": "MassIVE", "pattern": "^MSV\\d+$", "preferred_prefix": "massive", "providers": [ { "code": "omicsdi", "description": "MassIVE through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "MassIVE through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/massive/$1" } ], "uri_format": "https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1" }, "mat": { "contact": { "email": "j.bard@ed.ac.uk", "github": null, "name": "Jonathan Bard", "orcid": null }, "deprecated": true, "description": "Minimal set of terms for anatomy", "download_obo": "http://aber-owl.net/media/ontologies/MAT/3/mat.obo", "example": "0000000", "mappings": { "aberowl": "MAT", "biocontext": "MAT", "bioportal": "MAT", "obofoundry": "mat" }, "name": "Minimal Anatomical Terminology", "pattern": "^\\d{7}$", "preferred_prefix": "MAT", "uri_format": "http://purl.obolibrary.org/obo/MAT_$1" }, "matrixdb": { "appears_in": [ "complexportal" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "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/", "mappings": { "fairsharing": "FAIRsharing.91yrz6", "prefixcommons": "matrixdb", "re3data": "r3d100010672" }, "name": "MatrixDB", "preferred_prefix": "matrixdb", "publications": [ { "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=$1" }, "matrixdb.association": { "description": "MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations.", "example": "P00747__P07355", "homepage": "http://matrixdb.univ-lyon1.fr/", "mappings": { "biocontext": "MATRIXDB.ASSOCIATION", "miriam": "matrixdb.association", "n2t": "matrixdb.association" }, "name": "MatrixDB Association", "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$", "preferred_prefix": "matrixdb.association", "uri_format": "http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association" }, "maxo": { "appears_in": [ "ecto" ], "contact": { "email": "Leigh.Carmody@jax.org", "github": "LCCarmody", "name": "Leigh Carmody", "orcid": "0000-0001-7941-2961" }, "depends_on": [ "chebi", "foodon", "go", "iao", "ro", "uberon" ], "description": "An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations.", "download_json": "http://purl.obolibrary.org/obo/maxo.json", "download_obo": "http://purl.obolibrary.org/obo/maxo.obo", "download_owl": "http://purl.obolibrary.org/obo/maxo.owl", "example": "0000008", "homepage": "https://github.com/monarch-initiative/MAxO", "license": "CC BY 3.0", "mappings": { "aberowl": "MAXO", "biolink": "MAXO", "bioportal": "MAXO", "obofoundry": "maxo", "ols": "maxo", "ontobee": "MAXO" }, "name": "Medical Action Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MAXO", "repository": "https://github.com/monarch-initiative/MAxO", "twitter": "MonarchInit", "uri_format": "http://purl.obolibrary.org/obo/MAXO_$1", "version": "2022-06-23" }, "mba": { "contact": { "email": "chinhda@alleninstitute.org", "github": null, "name": "Allen Institute for Brain Science", "orcid": null }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A controlled vocabulary to support the study of transcription in the mouse brain", "download_obo": "https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-mba.obo", "example": "688", "homepage": "https://mouse.brain-map.org", "mappings": { "bioportal": "ABA-AMB" }, "name": "Mouse Brain Atlas", "pattern": "^\\d+$", "preferred_prefix": "MBA", "uri_format": "https://biopragmatics.github.io/providers/mba/$1" }, "mcc": { "contact": { "email": "usha@molecularconnections.com", "github": null, "name": "Usha Mahadevan", "orcid": null }, "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", "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#$1" }, "mco": { "contact": { "email": "citlalli.mejiaalmonte@gmail.com", "github": "citmejia", "name": "Citlalli Mejía-Almonte", "orcid": "0000-0002-0142-5591" }, "depends_on": [ "bfo", "chebi", "cl", "clo", "micro", "ncbitaxon", "ncit", "obi", "omit", "omp", "pato", "peco", "uberon", "zeco" ], "description": "Microbial Conditions Ontology is an ontology...", "download_obo": "http://purl.obolibrary.org/obo/mco.obo", "download_owl": "http://purl.obolibrary.org/obo/mco.owl", "example": "0000858", "homepage": "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology", "license": "CC BY 3.0", "mappings": { "aberowl": "MCO", "bioportal": "MCO", "obofoundry": "mco", "ols": "mco", "ontobee": "MCO" }, "name": "Microbial Conditions Ontology", "pattern": "^\\d+$", "preferred_prefix": "MCO", "repository": "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology", "uri_format": "http://purl.obolibrary.org/obo/MCO_$1", "version": "2019-05-15" }, "mdm": { "contact": { "email": "bernd.mueller@zbmed.de", "github": null, "name": "Bernd Müller", "orcid": null }, "description": "The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems.", "download_owl": "http://aber-owl.net/media/ontologies/MDM/4/mdm.owl", "example": "4776", "homepage": "https://medical-data-models.org/", "mappings": { "aberowl": "MDM", "biocontext": "MDM", "bioportal": "MDM", "fairsharing": "FAIRsharing.wnk2eq", "miriam": "mdm", "n2t": "mdm" }, "name": "Medical Data Models", "pattern": "^\\d+$", "preferred_prefix": "mdm", "uri_format": "https://medical-data-models.org/forms/$1" }, "meddra": { "contact": { "email": "mssohelp@meddra.org", "github": null, "name": "MedDRA MSSO", "orcid": null }, "description": "The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT).", "example": "10015919", "homepage": "http://bioportal.bioontology.org/ontologies/MEDDRA", "mappings": { "aberowl": "MEDDRA", "biocontext": "MEDDRA", "bioportal": "MEDDRA", "fairsharing": "FAIRsharing.ad3137", "hl7": "mdr", "miriam": "meddra", "n2t": "meddra", "wikidata": "P3201" }, "name": "Medical Dictionary for Regulatory Activities Terminology", "pattern": "^\\d+$", "preferred_prefix": "meddra", "publications": [ { "doi": "10.1016/s1386-5056(00)00062-9", "pmc": null, "pubmed": "10961570", "title": "The use of a medical dictionary for regulatory activities terminology (MedDRA) in prescription-event monitoring in Japan (J-PEM).", "year": 2000 }, { "doi": "10.2165/00002018-199920020-00002", "pmc": null, "pubmed": "10082069", "title": "The medical dictionary for regulatory activities (MedDRA).", "year": 1999 } ], "synonyms": [ "MEDRA", "MeDRA", "MedDRA", "Medical Dictionary for Regulatory Activities" ], "uri_format": "http://purl.bioontology.org/ontology/MEDDRA/$1" }, "medgen": { "description": "MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder.", "example": "760050", "homepage": "https://www.ncbi.nlm.nih.gov/medgen/", "mappings": { "biocontext": "MedGen", "biolink": "medgen", "miriam": "medgen", "n2t": "medgen", "ncbi": "MedGen" }, "name": "Human Medical Genetics", "pattern": "^[CN]*\\d{4,7}$", "preferred_prefix": "medgen", "uri_format": "https://www.ncbi.nlm.nih.gov/medgen/$1" }, "medlineplus": { "contact": { "email": "custserv@nlm.nih.gov", "github": null, "name": "NLM Customer Service", "orcid": null }, "description": "MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language.", "example": "002804", "homepage": "http://www.nlm.nih.gov/medlineplus/", "mappings": { "aberowl": "MEDLINEPLUS", "biocontext": "MEDLINEPLUS", "bioportal": "MEDLINEPLUS", "fairsharing": "FAIRsharing.bf8dsb", "hl7": "2.16.840.1.113883.6.173", "miriam": "medlineplus", "n2t": "medlineplus" }, "name": "MedlinePlus Health Topics", "pattern": "^\\d+$", "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" }, "merops.clan": { "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", "part_of": "merops", "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=$1" }, "merops.entry": { "description": "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors.", "example": "I31.952", "example_extras": [ "S01.001" ], "homepage": "http://merops.sanger.ac.uk/index.htm", "mappings": { "biocontext": "MEROPS.INHIBITOR", "edam": "2629", "fairsharing": "FAIRsharing.2s4n8r", "go": "MEROPS", "miriam": "merops.inhibitor", "n2t": "merops.inhibitor", "prefixcommons": "merops", "uniprot": "MEROPS" }, "name": "MEROPS Entry", "pattern": "^[SCTAGMNUI]\\d{2}\\.([AB]\\d{2}|\\d{3})$", "preferred_prefix": "merops.entry", "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 }, { "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=$1" }, "merops.family": { "description": "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families.", "example": "S1", "homepage": "http://merops.sanger.ac.uk/index.htm", "mappings": { "biocontext": "MEROPS.FAMILY", "miriam": "merops.family", "n2t": "merops.family" }, "name": "MEROPS Family", "part_of": "merops", "pattern": "^[SCTAGMNU]\\d+$", "preferred_prefix": "merops.family", "publications": [ { "doi": "10.1093/nar/gkx1134", "pmc": "PMC5753285", "pubmed": "29145643", "title": "The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database.", "year": 2018 } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/439" ], "uri_format": "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1" }, "mesh": { "contact": { "email": "custserv@nlm.nih.gov", "github": null, "name": "NLM Customer Service", "orcid": null }, "description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc.", "example": "C063233", "example_extras": [ "D000001" ], "homepage": "http://id.nlm.nih.gov/mesh/", "license": "CC0 1.0", "mappings": { "aberowl": "MESH", "biocontext": "MESH", "biolink": "MESH", "bioportal": "MESH", "cellosaurus": "MeSH", "edam": "1177", "fairsharing": "FAIRsharing.qnkw45", "go": "MeSH", "hl7": "2.16.840.1.113883.6.177", "miriam": "mesh", "n2t": "mesh", "prefixcommons": "mesh", "wikidata": "P486" }, "name": "Medical Subject Headings", "pattern": "^(C|D)\\d{6,9}$", "preferred_prefix": "mesh", "publications": [ { "doi": null, "pmc": "PMC197951", "pubmed": "13982385", "title": "Medical subject headings.", "year": 1963 } ], "synonyms": [ "MESH", "MESHA", "MESHC", "MESHCS", "MESHD", "MESHPP", "MESH_DESCRIPTOR_UI", "MESH_SUPPLEMENTAL_RECORD_UI", "MSH", "MSH2010_2010_02_22" ], "uri_format": "https://meshb.nlm.nih.gov/record/ui?ui=$1" }, "mesh.2012": { "description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012.", "example": "17186", "homepage": "http://www.nlm.nih.gov/mesh/", "mappings": { "biocontext": "MESH.2012", "miriam": "mesh.2012", "n2t": "mesh.2012" }, "name": "MeSH 2012", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "mesh.2012", "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", "uri_format": "http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded" }, "metabolights": { "description": "MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies.", "example": "MTBLS1", "homepage": "https://www.ebi.ac.uk/metabolights/", "mappings": { "biocontext": "METABOLIGHTS", "cellosaurus": "MetaboLights", "miriam": "metabolights", "n2t": "metabolights", "re3data": "r3d100011556", "wikidata": "P3890" }, "name": "MetaboLights Compound", "pattern": "^MTBLS\\d+$", "preferred_prefix": "metabolights", "providers": [ { "code": "omicsdi", "description": "MataboLights through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "MataboLights through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/metabolights_dataset/$1" } ], "uri_format": "https://www.ebi.ac.uk/metabolights/$1" }, "metacyc.compound": { "description": "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.", "example": "CPD-10330", "homepage": "https://metacyc.org", "mappings": { "biocontext": "METACYC.COMPOUND", "biolink": "MetaCyc", "fairsharing": "FAIRsharing.yytevr", "go": "MetaCyc", "miriam": "metacyc.compound", "n2t": "metacyc.compound", "re3data": "r3d100011294" }, "name": "Metabolic Encyclopedia of metabolic and other pathways", "pattern": "^[A-Za-z0-9+_.%-:]+$", "preferred_prefix": "metacyc.compound", "synonyms": [ "MetaCyc" ], "uri_format": "https://metacyc.org/compound?orgid=META&id=$1" }, "metacyc.reaction": { "description": "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.", "example": "RXN-14904", "homepage": "https://metacyc.org", "mappings": { "biocontext": "METACYC.REACTION", "biolink": "metacyc.reaction", "miriam": "metacyc.reaction", "n2t": "metacyc.reaction" }, "name": "MetaCyc Reaction", "pattern": "^[A-Za-z0-9+_.%-:]+$", "preferred_prefix": "metacyc.reaction", "uri_format": "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1" }, "metanetx.chemical": { "description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components.", "example": "MNXM1723", "homepage": "https://www.metanetx.org/", "mappings": { "biocontext": "METANETX.CHEMICAL", "miriam": "metanetx.chemical", "n2t": "metanetx.chemical" }, "name": "MetaNetX chemical", "pattern": "^(MNXM\\d+|BIOMASS|WATER)$", "preferred_prefix": "metanetx.chemical", "uri_format": "https://www.metanetx.org/chem_info/$1" }, "metanetx.compartment": { "description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments.", "example": "MNXC15", "homepage": "https://www.metanetx.org/", "mappings": { "biocontext": "METANETX.COMPARTMENT", "miriam": "metanetx.compartment", "n2t": "metanetx.compartment" }, "name": "MetaNetX compartment", "pattern": "^(MNX[CD]\\d+|BOUNDARY|IN|OUT)$", "preferred_prefix": "metanetx.compartment", "uri_format": "https://www.metanetx.org/comp_info/$1" }, "metanetx.reaction": { "description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions.", "example": "MNXR101574", "homepage": "https://www.metanetx.org/", "mappings": { "biocontext": "METANETX.REACTION", "biolink": "METANETX.REACTION", "miriam": "metanetx.reaction", "n2t": "metanetx.reaction" }, "name": "MetaNetX reaction", "pattern": "^(MNXR\\d+|EMPTY)$", "preferred_prefix": "metanetx.reaction", "uri_format": "https://www.metanetx.org/equa_info/$1" }, "metatlas": { "contact": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "contributor": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "description": "A resource for exploring metabolism, starting with a set of of community-curated genome-scale metabolic models of human and model organisms, enriched with pathway maps and other tools for easy browsing and analysis.", "example": "MAM01234c", "example_decoys": [ "MAR11851c" ], "example_extras": [ "MAR11851" ], "github_request_issue": 495, "homepage": "https://metabolicatlas.org", "mappings": { "miriam": "metatlas" }, "name": "Metabolic Atlas", "pattern": "^(MAM\\d{5}\\w)|(MAR\\d{5})$", "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/$1" }, "metatlas.metabolite": { "contact": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "contributor": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "description": "A subspace of Metabolic Atlas for compartment-specific records for metabolites.", "example": "MAM01234c", "github_request_issue": 495, "homepage": "https://metabolicatlas.org", "name": "Metabolic Atlas Metabolite", "part_of": "metatlas", "pattern": "^MAM\\d{5}\\w$", "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/$1" }, "metatlas.reaction": { "contact": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "contributor": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "description": "A subspace of Metabolic Atlas for reactions.", "example": "MAR11851", "github_request_issue": 495, "homepage": "https://metabolicatlas.org", "name": "Metabolic Atlas Reaction", "part_of": "metatlas", "pattern": "^MAR\\d{5}$", "preferred_prefix": "metatlas.reaction", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://metabolicatlas.org/identifier/MetabolicAtlas/$1" }, "metlin": { "description": "The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry.", "example": "1455", "homepage": "http://masspec.scripps.edu/", "mappings": { "biocontext": "METLIN", "miriam": "metlin", "n2t": "metlin", "re3data": "r3d100012311" }, "name": "Metabolite and Tandem Mass Spectrometry Database", "pattern": "^\\d{4}$", "preferred_prefix": "metlin", "uri_format": "http://metlin.scripps.edu/metabo_info.php?molid=$1" }, "mex": { "description": "A public place to process, interpret and share GC/MS metabolomics datasets.", "example": "36", "homepage": "https://www.metabolome-express.org/", "mappings": { "biocontext": "MEX", "miriam": "mex", "n2t": "mex" }, "name": "Metabolome Express", "pattern": "^\\d+$", "preferred_prefix": "mex", "providers": [ { "code": "omicsdi", "description": "Metabolome Express through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "Metabolome Express through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/metabolome_express/MEX$1" } ], "uri_format": "https://www.metabolome-express.org/datasetview.php?datasetid=$1" }, "mf": { "contact": { "email": "janna.hastings@gmail.com", "github": "jannahastings", "name": "Janna Hastings", "orcid": "0000-0002-3469-4923" }, "description": "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning.", "download_owl": "http://purl.obolibrary.org/obo/mf.owl", "example": "0000091", "homepage": "https://github.com/jannahastings/mental-functioning-ontology", "license": "CC BY 3.0", "mappings": { "aberowl": "MF", "biocontext": "MF", "bioportal": "MF", "fairsharing": "FAIRsharing.4gm9gt", "obofoundry": "mf", "ols": "mf", "ontobee": "MF" }, "name": "Mental Functioning Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MF", "repository": "https://github.com/jannahastings/mental-functioning-ontology", "uri_format": "http://purl.obolibrary.org/obo/MF_$1", "version": "2021-11-17" }, "mfmo": { "contact": { "email": "druzinsk@uic.edu", "github": "RDruzinsky", "name": "Robert Druzinsky", "orcid": "0000-0002-1572-1316" }, "depends_on": [ "uberon" ], "description": "The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors.", "download_owl": "http://purl.obolibrary.org/obo/mfmo.owl", "example": "0000208", "homepage": "https://github.com/rdruzinsky/feedontology", "license": "CC BY 3.0", "mappings": { "aberowl": "MFMO", "biocontext": "MFMO", "bioportal": "MFMO", "fairsharing": "FAIRsharing.669cnk", "obofoundry": "mfmo", "ols": "mfmo", "ontobee": "MFMO" }, "name": "Mammalian Feeding Muscle Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MFMO", "repository": "https://github.com/RDruzinsky/feedontology", "uri_format": "http://purl.obolibrary.org/obo/MFMO_$1", "version": "2013-11-16" }, "mfo": { "contact": { "email": "Thorsten.Henrich@embl-heidelberg.de", "github": null, "name": "Thorsten Henrich", "orcid": null }, "deprecated": true, "description": "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.", "download_obo": "http://aber-owl.net/media/ontologies/MFO/14/mfo.obo", "download_owl": "http://purl.obolibrary.org/obo/mfo.owl", "mappings": { "aberowl": "MFO", "biocontext": "MFO", "bioportal": "MFO", "obofoundry": "mfo", "prefixcommons": "mfo" }, "name": "Medaka fish anatomy and development", "preferred_prefix": "MFO", "uri_format": "http://purl.obolibrary.org/obo/MFO_$1" }, "mfoem": { "contact": { "email": "janna.hastings@gmail.com", "github": "jannahastings", "name": "Janna Hastings", "orcid": "0000-0002-3469-4923" }, "description": "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings.", "download_owl": "http://purl.obolibrary.org/obo/mfoem.owl", "example": "000204", "homepage": "https://github.com/jannahastings/emotion-ontology", "license": "CC BY 3.0", "mappings": { "aberowl": "MFOEM", "biocontext": "MFOEM", "bioportal": "MFOEM", "fairsharing": "FAIRsharing.dx30m8", "obofoundry": "mfoem", "ols": "mfoem", "ontobee": "MFOEM" }, "name": "Emotion Ontology", "pattern": "^\\d{6}$", "preferred_prefix": "MFOEM", "publications": [ { "doi": "10.1186/2041-1480-5-38", "pmc": "PMC4417517", "pubmed": "25937879", "title": "Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference.", "year": 2014 } ], "repository": "https://github.com/jannahastings/emotion-ontology", "uri_format": "http://purl.obolibrary.org/obo/MFOEM_$1", "version": "2021-11-17" }, "mfomd": { "contact": { "email": "janna.hastings@gmail.com", "github": "jannahastings", "name": "Janna Hastings", "orcid": "0000-0002-3469-4923" }, "description": "The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF).", "download_owl": "http://purl.obolibrary.org/obo/mfomd.owl", "example": "0000046", "homepage": "https://github.com/jannahastings/mental-functioning-ontology", "license": "CC BY 3.0", "mappings": { "aberowl": "MFOMD", "biocontext": "MFOMD", "bioportal": "MFOMD", "fairsharing": "FAIRsharing.q053vb", "obofoundry": "mfomd", "ols": "mfomd", "ontobee": "MFOMD" }, "name": "Mental Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MFOMD", "repository": "https://github.com/jannahastings/mental-functioning-ontology", "uri_format": "http://purl.obolibrary.org/obo/MFOMD_$1", "version": "2020-04-26" }, "mge": { "banana": "mge", "description": "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.", "example": "2", "homepage": "http://aclame.ulb.ac.be/", "mappings": { "biocontext": "ACLAME", "edam": "2631", "miriam": "mge", "n2t": "mge", "prefixcommons": "aclame" }, "name": "Aclame", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "mge", "publications": [ { "doi": "10.1093/nar/gkh084", "pmc": "PMC308818", "pubmed": "14681355", "title": "ACLAME: a CLAssification of Mobile genetic Elements.", "year": 2004 } ], "synonyms": [ "aclame" ], "uri_format": "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1" }, "mgi": { "banana": "MGI", "description": "The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.", "example": "6017782", "homepage": "http://www.informatics.jax.org/", "mappings": { "biocontext": "MGI", "cellosaurus": "MGI", "edam": "3274", "fairsharing": "FAIRsharing.fcwyhz", "go": "MGI", "miriam": "mgi", "n2t": "mgi", "ncbi": "MGI", "prefixcommons": "mgi", "uniprot": "MGI", "wikidata": "P671" }, "name": "Mouse Genome Informatics", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "MGI", "providers": [ { "code": "agr", "description": "MGI through the Alliance of Genome Resources", "homepage": "https://www.alliancegenome.org", "name": "MGI through the Alliance of Genome Resources", "uri_format": "https://www.alliancegenome.org/gene/MGI:$1" }, { "code": "bioentitylink", "description": "MGD through BioEntity Link", "homepage": "https://bioentity.link/", "name": "MGD through BioEntity Link", "uri_format": "https://bioentity.link/#/lexicon/public/MGI:$1" }, { "code": "mgi.marker", "description": "MGI Marker", "homepage": "http://www.informatics.jax.org/marker", "name": "MGI Marker", "uri_format": "http://www.informatics.jax.org/marker/MGI:$1" } ], "publications": [ { "doi": "10.1093/nar/gki113", "pmc": "PMC540067", "pubmed": "15608240", "title": "The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology.", "year": 2005 } ], "synonyms": [ "MGD", "MGI" ], "uri_format": "http://www.informatics.jax.org/accession/MGI:$1" }, "mgnify.analysis": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Analyses of microbiome data within MGnify", "example": "MGYA00002270", "homepage": "https://www.ebi.ac.uk/metagenomics/", "name": "MGnify Analysis", "pattern": "^MGYA\\d+$", "preferred_prefix": "mgnify.analysis", "uri_format": "https://www.ebi.ac.uk/metagenomics/analyses/$1" }, "mgnify.proj": { "description": "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.", "example": "ERP004492", "homepage": "https://www.ebi.ac.uk/metagenomics", "mappings": { "miriam": "mgnify.proj", "n2t": "mgnify.proj" }, "name": "MGnify Project", "pattern": "^[A-Z]+[0-9]+$", "preferred_prefix": "mgnify.proj", "uri_format": "https://www.ebi.ac.uk/metagenomics/projects/$1" }, "mgnify.samp": { "description": "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.", "example": "SRS086444", "homepage": "https://www.ebi.ac.uk/metagenomics", "mappings": { "miriam": "mgnify.samp", "n2t": "mgnify.samp" }, "name": "MGnify Sample", "pattern": "^[A-Z]+[0-9]+$", "preferred_prefix": "mgnify.samp", "uri_format": "https://www.ebi.ac.uk/metagenomics/samples/$1" }, "mi": { "banana": "MI", "contact": { "email": "pporras@ebi.ac.uk", "github": "pporrasebi", "name": "Pablo Porras Millán", "orcid": "0000-0002-8429-8793" }, "description": "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.", "download_obo": "http://purl.obolibrary.org/obo/mi.obo", "download_owl": "http://purl.obolibrary.org/obo/mi.owl", "example": "0058", "homepage": "https://github.com/HUPO-PSI/psi-mi-CV", "license": "CC BY 4.0", "mappings": { "aberowl": "MI", "biocontext": "PSIMI", "biolink": "MI", "bioportal": "MI", "fairsharing": "FAIRsharing.8qzmtr", "go": "PSI-MI", "miriam": "mi", "n2t": "psimi", "obofoundry": "mi", "ols": "mi", "ontobee": "MI", "prefixcommons": "psi.mi" }, "name": "Molecular Interactions Controlled Vocabulary", "namespace_in_lui": true, "pattern": "^\\d{4}$", "preferred_prefix": "MI", "publications": [ { "doi": "10.1038/nbt926", "pmc": null, "pubmed": "14755292", "title": "The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.", "year": 2004 } ], "repository": "https://github.com/HUPO-PSI/psi-mi-CV", "synonyms": [ "PSI-MI" ], "uri_format": "https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1" }, "miaa": { "comment": "same as MAT", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "name": "Minimal Information About Anatomy ontology", "preferred_prefix": "miaa", "references": [ "https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/rols/inst/doc/rols.pdf" ] }, "miapa": { "contact": { "email": "hilmar.lapp@duke.edu", "github": "hlapp", "name": "Hilmar Lapp", "orcid": "0000-0001-9107-0714" }, "description": "The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies.\n\nThis ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA.", "download_owl": "http://purl.obolibrary.org/obo/miapa.owl", "example": "0000010", "homepage": "http://www.evoio.org/wiki/MIAPA", "license": "CC0 1.0", "mappings": { "aberowl": "MIAPA", "biocontext": "MIAPA", "bioportal": "MIAPA", "fairsharing": "FAIRsharing.ca48xs", "obofoundry": "miapa", "ols": "miapa", "ontobee": "MIAPA" }, "name": "Minimum Anformation About a Phylogenetic Analysis Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MIAPA", "publications": [ { "doi": "10.1089/omi.2006.10.231", "pmc": null, "pubmed": null, "title": "Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)", "year": null } ], "repository": "https://github.com/evoinfo/miapa", "uri_format": "http://purl.obolibrary.org/obo/MIAPA_$1", "version": "2017-05-09" }, "micro": { "appears_in": [ "mco" ], "contact": { "email": "carrine.blank@umontana.edu", "github": "carrineblank", "name": "Carrine Blank", "orcid": "0000-0002-2100-6351" }, "description": "An ontology of prokaryotic phenotypic and metabolic characters", "download_owl": "http://purl.obolibrary.org/obo/micro.owl", "example": "0002999", "homepage": "https://github.com/carrineblank/MicrO", "license": "CC BY 2.0", "mappings": { "aberowl": "MICRO", "biocontext": "MICRO", "fairsharing": "FAIRsharing.brhpb0", "obofoundry": "micro", "ols": "micro", "ontobee": "MicrO" }, "name": "Ontology of Prokaryotic Phenotypic and Metabolic Characters", "pattern": "^\\d{7}$", "preferred_prefix": "MICRO", "publications": [ { "doi": "10.1186/s13326-016-0060-6", "pmc": "PMC4830071", "pubmed": "27076900", "title": "MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.", "year": 2016 } ], "repository": "https://github.com/carrineblank/MicrO", "uri_format": "http://purl.obolibrary.org/obo/MICRO_$1", "version": "1.5.1" }, "microscope": { "description": "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis.", "example": "5601141", "homepage": "http://www.genoscope.cns.fr/agc/microscope", "mappings": { "biocontext": "MICROSCOPE", "fairsharing": "FAIRsharing.3t5qc3", "miriam": "microscope", "n2t": "microscope", "re3data": "r3d100012928" }, "name": "MicroScope", "pattern": "^\\d+$", "preferred_prefix": "microscope", "uri_format": "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1" }, "microsporidia": { "description": "MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "ECU03_0820i", "homepage": "http://microsporidiadb.org/micro/", "mappings": { "biocontext": "MICROSPORIDIA", "miriam": "microsporidia", "n2t": "microsporidia", "prefixcommons": "microsporidia" }, "name": "MicrosporidiaDB", "pattern": "^\\w+$", "preferred_prefix": "microsporidia", "publications": [ { "doi": "10.1093/nar/gkp941", "pmc": "PMC2808945", "pubmed": "19914931", "title": "EuPathDB: a portal to eukaryotic pathogen databases.", "year": 2009 } ], "uri_format": "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" }, "millipore": { "description": "Cell line collections", "example": "SCC111", "homepage": "https://www.merckmillipore.com/", "mappings": { "cellosaurus": "Millipore" }, "name": "Merck Millipore (EMD Millipore)", "preferred_prefix": "millipore", "uri_format": "https://www.merckmillipore.com/catalogue/item/$1" }, "mimodb": { "description": "MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank.", "example": "1", "homepage": "http://immunet.cn/bdb/", "mappings": { "biocontext": "MIMODB", "fairsharing": "FAIRsharing.bv0zjz", "miriam": "mimodb", "n2t": "mimodb", "prefixcommons": "mimodb" }, "name": "MimoDB", "pattern": "^\\d+$", "preferred_prefix": "mimodb", "publications": [ { "doi": "10.1093/nar/gkr922", "pmc": "PMC3245166", "pubmed": "22053087", "title": "MimoDB 2.0: a mimotope database and beyond.", "year": 2011 } ], "uri_format": "http://immunet.cn/bdb/index.php/mimoset/$1" }, "minid": { "description": "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation.", "example": "b97957", "homepage": "https://fair-research.org", "mappings": { "biocontext": "MINID", "miriam": "minid", "n2t": "minid" }, "name": "Minimal Viable Identifier", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "minid", "uri_format": "https://hdl.handle.net/hdl:20.500.12582/$1" }, "minid.test": { "description": "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. ", "example": "3SBPLMKKVEVR", "homepage": "https://fair-research.org", "mappings": { "miriam": "minid.test" }, "name": "MINID Test", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "minid.test", "uri_format": "https://hdl.handle.net/hdl:20.500.12633/$1" }, "mint": { "banana": "MINT", "banana_peel": "-", "description": "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals.", "example": "6978836", "homepage": "https://mint.bio.uniroma2.it", "mappings": { "biocontext": "MINT", "edam": "2615", "fairsharing": "FAIRsharing.2bdvmk", "miriam": "mint", "n2t": "mint", "prefixcommons": "mint", "uniprot": "MINT" }, "name": "Molecular Interaction Database", "pattern": "^\\d{1,7}$", "preferred_prefix": "mint", "providers": [ { "code": "ebi", "description": "MINT subset through IntAct", "homepage": "https://www.ebi.ac.uk/intact/", "name": "MINT subset through IntAct", "uri_format": "https://www.ebi.ac.uk/intact/query/interaction_id:$1" } ], "publications": [ { "doi": "10.1093/nar/gkl950", "pmc": "PMC1751541", "pubmed": "17135203", "title": "MINT: the Molecular INTeraction database.", "year": 2006 } ], "uri_format": "https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-$1" }, "mipmod": { "description": "MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures.", "example": "HOSAPI0399", "homepage": "http://bioinfo.iitk.ac.in/MIPModDB", "mappings": { "biocontext": "MIPMOD", "miriam": "mipmod", "n2t": "mipmod", "prefixcommons": "mipmod" }, "name": "MIPModDB", "pattern": "^\\w+$", "preferred_prefix": "mipmod", "publications": [ { "doi": "10.1093/nar/gkr914", "pmc": "PMC3245135", "pubmed": "22080560", "title": "MIPModDB: a central resource for the superfamily of major intrinsic proteins.", "year": 2011 } ], "uri_format": "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1" }, "mir": { "banana": "MIR", "description": "The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or \"PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources.", "example": "00100037", "homepage": "https://registry.identifiers.org/registry", "mappings": { "biocontext": "MIR", "miriam": "mir", "n2t": "mir" }, "name": "Identifiers.org Registry", "namespace_in_lui": true, "pattern": "^\\d{8}$", "preferred_prefix": "mir", "uri_format": "https://registry.identifiers.org/registry?query=\"MIR:$1\"" }, "mirbase": { "description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR).", "example": "MI0026471", "homepage": "http://www.mirbase.org/", "mappings": { "biocontext": "MIRBASE", "biolink": "mirbase", "edam": "2642", "fairsharing": "FAIRsharing.hmgte8", "miriam": "mirbase", "n2t": "mirbase", "ncbi": "miRBase", "prefixcommons": "mirbase", "re3data": "r3d100010566", "wikidata": "P2870" }, "name": "miRBase pre-miRNA", "pattern": "^MI\\d{7}$", "preferred_prefix": "mirbase", "publications": [ { "doi": "10.1093/nar/gkh023", "pmc": "PMC308757", "pubmed": "14681370", "title": "The microRNA Registry.", "year": 2004 } ], "uri_format": "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1" }, "mirbase.family": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download.", "example": "MIPF0000002", "homepage": "http://www.mirbase.org/", "name": "miRBase Families", "preferred_prefix": "mirbase.family", "synonyms": [ "MIRBASE_FAMILY" ], "uri_format": "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1" }, "mirbase.mature": { "description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence.", "example": "MIMAT0046872", "homepage": "http://www.mirbase.org/", "mappings": { "biocontext": "MIRBASE.MATURE", "miriam": "mirbase.mature", "n2t": "mirbase.mature", "prefixcommons": "mirbase.mature", "wikidata": "P2871" }, "name": "miRBase mature miRNA", "pattern": "^MIMAT\\d{7}$", "preferred_prefix": "mirbase.mature", "synonyms": [ "MIRBASEM" ], "uri_format": "http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1" }, "mirex": { "description": "mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages.", "example": "165a", "homepage": "http://comgen.pl/mirex/?page=home", "mappings": { "biocontext": "MIREX", "fairsharing": "FAIRsharing.q3b39v", "miriam": "mirex", "n2t": "mirex" }, "name": "mirEX", "pattern": "^\\d+(\\w+)?$", "preferred_prefix": "mirex", "uri_format": "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes" }, "miriam": { "description": "Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain.", "example": "pubmed", "homepage": "https://www.ebi.ac.uk", "mappings": { "edam": "1162", "fairsharing": "FAIRsharing.ap169a", "miriam": "identifiers.namespace" }, "name": "Identifiers.org namespace", "pattern": "^[a-z_\\.]+$", "preferred_prefix": "miriam", "synonyms": [ "identifiers.namespace" ], "uri_format": "https://registry.identifiers.org/registry/$1" }, "miriam.collection": { "banana": "MIR", "deprecated": true, "description": "MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections.", "example": "00000008", "homepage": "https://www.ebi.ac.uk/miriam/", "mappings": { "biocontext": "MIRIAM.COLLECTION", "miriam": "miriam.collection", "n2t": "miriam.collection" }, "name": "MIRIAM Registry collection", "part_of": "miriam", "pattern": "^000\\d{5}$", "preferred_prefix": "miriam.collection", "uri_format": "https://www.ebi.ac.uk/miriam/main/$1" }, "miriam.resource": { "banana": "MIR", "deprecated": true, "description": "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases.", "example": "00100005", "homepage": "https://www.ebi.ac.uk/miriam/", "mappings": { "biocontext": "MIRIAM.RESOURCE", "miriam": "miriam.resource", "n2t": "miriam.resource", "prefixcommons": "miriam.resource" }, "name": "MIRIAM Legacy Registry Identifier", "part_of": "miriam", "pattern": "^001\\d{5}$", "preferred_prefix": "miriam.resource", "publications": [ { "doi": "10.1186/1752-0509-1-58", "pmc": "PMC2259379", "pubmed": "18078503", "title": "MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology.", "year": 2007 } ], "uri_format": "https://www.ebi.ac.uk/miriam/main/resources/$1" }, "mirnao": { "contact": { "email": "topalis@imbb.forth.gr", "github": null, "name": "Pantelis Topalis", "orcid": null }, "deprecated": true, "description": "An application ontology for use with miRNA databases.", "download_owl": "http://purl.obolibrary.org/obo/mirnao.owl", "homepage": "http://code.google.com/p/mirna-ontology/", "license": "CC0 1.0", "mappings": { "aberowl": "MIRNAO", "biocontext": "MIRNAO", "bioportal": "MIRNAO", "obofoundry": "mirnao", "ontobee": "miRNAO" }, "name": "microRNA Ontology", "preferred_prefix": "MIRNAO", "uri_format": "http://purl.obolibrary.org/obo/MIRNAO_$1" }, "mirnest": { "description": "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species.", "example": "MNEST029358", "homepage": "http://rhesus.amu.edu.pl/mirnest/copy/", "mappings": { "biocontext": "MIRNEST", "fairsharing": "FAIRsharing.5pfx4r", "miriam": "mirnest", "n2t": "mirnest", "prefixcommons": "mirnest" }, "name": "miRNEST", "pattern": "^MNEST\\d+$", "preferred_prefix": "mirnest", "publications": [ { "doi": "10.1093/nar/gkr1159", "pmc": "PMC3245016", "pubmed": "22135287", "title": "miRNEST database: an integrative approach in microRNA search and annotation.", "year": 2011 } ], "uri_format": "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1" }, "miro": { "contact": { "email": "louis@imbb.forth.gr", "github": null, "name": "Christos (Kitsos) Louis", "orcid": null }, "deprecated": true, "description": "Application ontology for entities related to insecticide resistance in mosquitos", "download_obo": "http://purl.obolibrary.org/obo/miro.obo", "download_owl": "http://purl.obolibrary.org/obo/miro.owl", "example": "40000617", "homepage": "https://github.com/VEuPathDB-ontology/MIRO", "mappings": { "aberowl": "MIRO", "biocontext": "MIRO", "bioportal": "MIRO", "fairsharing": "FAIRsharing.sjf113", "obofoundry": "miro", "ols": "miro", "ontobee": "MIRO" }, "name": "Mosquito insecticide resistance", "pattern": "^\\d{8}$", "preferred_prefix": "MIRO", "publications": [ { "doi": "10.1371/journal.pntd.0000465", "pmc": "PMC2694272", "pubmed": "19547750", "title": "MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide resistance in mosquito disease vectors.", "year": 2009 } ], "repository": "https://github.com/VEuPathDB-ontology/MIRO", "uri_format": "http://purl.obolibrary.org/obo/MIRO_$1", "version": "2014-05-14" }, "mirtarbase": { "description": "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments.", "example": "MIRT000002", "homepage": "http://mirtarbase.mbc.nctu.edu.tw/", "mappings": { "biocontext": "MIRTARBASE", "fairsharing": "FAIRsharing.f0bxfg", "miriam": "mirtarbase", "n2t": "mirtarbase" }, "name": "miRTarBase", "pattern": "^MIRT\\d{6}$", "preferred_prefix": "mirtarbase", "uri_format": "http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1" }, "mirte": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs", "example": "miR-1", "homepage": "http://www.russelllab.org/miRNAs/", "name": "miRNA Target Prediction at EMBL", "preferred_prefix": "mirte" }, "mlc": { "description": "MLCommons Association artifacts, including benchmark results, datasets, and saved models.", "example": "0.7-123", "homepage": "https://mlcommons.org/en/", "mappings": { "miriam": "mlc" }, "name": "MLCommons Association", "pattern": "^[0-9a-zA-Z\\.\\-\\_]+$", "preferred_prefix": "mlc", "uri_format": "https://www.mlcommons.org/mlc-id/$1" }, "mmdb": { "description": "The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites.", "example": "50885", "homepage": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure", "mappings": { "biocontext": "MMDB", "edam": "2667", "miriam": "mmdb", "n2t": "mmdb", "prefixcommons": "mmdb" }, "name": "Molecular Modeling Database", "pattern": "^\\d{1,5}$", "preferred_prefix": "mmdb", "publications": [ { "doi": "10.1093/nar/gkl952", "pmc": "PMC1751549", "pubmed": "17135201", "title": "MMDB: annotating protein sequences with Entrez's 3D-structure database.", "year": 2006 } ], "uri_format": "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1" }, "mmmp.biomaps": { "description": "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.", "example": "37", "homepage": "http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp", "mappings": { "biocontext": "MMMP:BIOMAPS", "biolink": "mmmp.biomaps", "miriam": "mmmp:biomaps", "n2t": "biomaps" }, "name": "Melanoma Molecular Map Project Biomaps", "pattern": "^\\d+$", "preferred_prefix": "mmmp.biomaps", "synonyms": [ "mmmp:biomaps" ], "uri_format": "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1" }, "mmo": { "contact": { "email": "jrsmith@mcw.edu", "github": "jrsjrs", "name": "Jennifer Smith", "orcid": "0000-0002-6443-9376" }, "description": "A representation of the variety of methods used to make clinical and phenotype measurements. ", "download_obo": "http://purl.obolibrary.org/obo/mmo.obo", "download_owl": "http://purl.obolibrary.org/obo/mmo.owl", "example": "0000574", "homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000", "license": "CC0 1.0", "mappings": { "aberowl": "MMO", "biocontext": "MMO", "bioportal": "MMO", "fairsharing": "FAIRsharing.bgkyd7", "obofoundry": "mmo", "ols": "mmo", "ontobee": "MMO" }, "name": "Measurement method ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MMO", "publications": [ { "doi": "10.1186/2041-1480-4-26", "pmc": "PMC3882879", "pubmed": "24103152", "title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.", "year": 2013 }, { "doi": "10.3389/fgene.2012.00087", "pmc": "PMC3361058", "pubmed": "22654893", "title": "Three ontologies to define phenotype measurement data.", "year": 2012 } ], "repository": "https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology", "twitter": "ratgenome", "uri_format": "http://purl.obolibrary.org/obo/MMO_$1", "version": "2019-03-27" }, "mmp.cat": { "description": "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples.", "example": "MMP743597.11", "homepage": "https://mmp.sfb.uit.no/databases/marcat/", "mappings": { "biocontext": "MMP.CAT", "miriam": "mmp.cat", "n2t": "mmp.cat" }, "name": "MarCat", "pattern": "^MMP\\d+.\\d+$", "preferred_prefix": "mmp.cat", "uri_format": "https://mmp.sfb.uit.no/databases/marcat/#/records/$1" }, "mmp.db": { "description": "MarDB includes all sequenced marine microbial genomes regardless of level of completeness.", "example": "MMP02954345.1", "homepage": "https://mmp.sfb.uit.no/databases/mardb/", "mappings": { "biocontext": "MMP.DB", "miriam": "mmp.db", "n2t": "mmp.db" }, "name": "MarDB", "pattern": "^MMP\\d+.\\d+$", "preferred_prefix": "mmp.db", "uri_format": "https://mmp.sfb.uit.no/databases/mardb/#/records/$1" }, "mmp.fun": { "description": "MarFun is manually curated database for marine fungi which is a part of the MAR databases.", "example": "MMP3888430", "homepage": "https://mmp.sfb.uit.no/databases/marfun", "mappings": { "miriam": "mmp.fun" }, "name": "MarFun", "pattern": "^MMP\\d+.\\d+$", "preferred_prefix": "mmp.fun", "uri_format": "https://mmp.sfb.uit.no/databases/marfun/#/records/$1" }, "mmp.ref": { "description": "MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes.", "example": "MMP3312982.2", "homepage": "https://mmp.sfb.uit.no/databases/marref/", "mappings": { "biocontext": "MMP.REF", "miriam": "mmp.ref", "n2t": "mmp.ref" }, "name": "MarRef", "pattern": "^MMP\\d+.\\d+$", "preferred_prefix": "mmp.ref", "uri_format": "https://mmp.sfb.uit.no/databases/marref/#/records/$1" }, "mmrrc": { "description": "The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections.", "example": "70", "homepage": "https://www.mmrrc.org", "mappings": { "biocontext": "MMRRC", "cellosaurus": "MMRRC", "fairsharing": "FAIRsharing.9dpd18", "miriam": "mmrrc", "n2t": "mmrrc" }, "name": "Mutant Mouse Resource and Research Centers", "pattern": "^\\d+$", "preferred_prefix": "mmrrc", "uri_format": "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1" }, "mmsl": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included.", "example": "3355", "homepage": "https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html", "mappings": { "hl7": "2.16.840.1.113883.6.175" }, "name": "Multum MediSource Lexicon", "pattern": "^\\d+$", "preferred_prefix": "mmsl", "synonyms": [ "MMSL_CODE" ] }, "mmusdv": { "contact": { "email": "frederic.bastian@unil.ch", "github": "fbastian", "name": "Frédéric Bastian", "orcid": "0000-0002-9415-5104" }, "description": "Life cycle stages for Mus Musculus", "download_obo": "http://purl.obolibrary.org/obo/mmusdv.obo", "download_owl": "http://purl.obolibrary.org/obo/mmusdv.owl", "example": "0000066", "homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv", "license": "CC BY 3.0", "mappings": { "aberowl": "MMUSDV", "biocontext": "MMUSDV", "biolink": "MmusDv", "bioportal": "MMUSDV", "fairsharing": "FAIRsharing.zchb68", "obofoundry": "mmusdv", "ols": "mmusdv", "ontobee": "MMUSDV" }, "name": "Mouse Developmental Stages", "pattern": "^\\d{7}$", "preferred_prefix": "MmusDv", "repository": "https://github.com/obophenotype/developmental-stage-ontologies", "synonyms": [ "MmusDv" ], "uri_format": "http://purl.obolibrary.org/obo/MMUSDV_$1", "version": "2020-03-10" }, "mo": { "contact": { "email": "stoeckrt@pcbi.upenn.edu", "github": null, "name": "Chris Stoeckert", "orcid": "0000-0002-5714-991X" }, "deprecated": true, "description": "The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data.", "download_owl": "http://purl.obolibrary.org/obo/mo.owl", "example": "ArrayGroup", "homepage": "http://mged.sourceforge.net/ontologies/MGEDontology.php", "mappings": { "aberowl": "MO", "biocontext": "MO", "bioportal": "MO", "miriam": "mo", "n2t": "mo", "obofoundry": "mo" }, "name": "Microarray experimental conditions", "pattern": "^\\w+$", "preferred_prefix": "MO", "providers": [ { "code": "ebi", "description": "MGED Ontology at SourceForge", "homepage": "https://mged.sourceforge.net/ontologies/MGEDontology.php", "name": "MGED Ontology at SourceForge", "uri_format": "https://mged.sourceforge.net/ontologies/MGEDontology.php#$1" } ], "uri_format": "http://purl.obolibrary.org/obo/MO_$1" }, "mobidb": { "description": "MobiDB is a database of protein disorder and mobility annotations.", "example": "P10636", "homepage": "http://mobidb.bio.unipd.it", "mappings": { "biocontext": "MOBIDB", "fairsharing": "FAIRsharing.jwra3e", "miriam": "mobidb", "n2t": "mobidb", "uniprot": "MobiDB" }, "name": "MobiDB", "pattern": "^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$", "preferred_prefix": "mobidb", "provides": "uniprot", "uri_format": "https://mobidb.org/$1" }, "mod": { "banana": "MOD", "contact": { "email": "pierre-alain.binz@chuv.ch", "github": "pabinz", "name": "Pierre-Alain Binz", "orcid": "0000-0002-0045-7698" }, "description": "The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications.", "download_obo": "http://purl.obolibrary.org/obo/mod.obo", "download_owl": "http://purl.obolibrary.org/obo/mod.owl", "example": "01467", "homepage": "http://www.psidev.info/MOD", "license": "CC BY 4.0", "mappings": { "aberowl": "PSIMOD", "biocontext": "MOD", "bioportal": "PSIMOD", "fairsharing": "FAIRsharing.2m4ms9", "go": "PSI-MOD", "miriam": "mod", "n2t": "mod", "obofoundry": "mod", "ols": "mod", "ontobee": "MOD", "prefixcommons": "psi.mod" }, "name": "Protein modification", "namespace_in_lui": true, "pattern": "^\\d{5}$", "preferred_prefix": "MOD", "publications": [ { "doi": "10.1038/nbt0808-864", "pmc": null, "pubmed": "18688235", "title": "The PSI-MOD community standard for representation of protein modification data.", "year": 2008 } ], "repository": "https://github.com/HUPO-PSI/psi-mod-CV", "synonyms": [ "PSI-MOD" ], "uri_format": "https://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=MOD:$1" }, "modeldb": { "description": "ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment.", "example": "45539", "homepage": "http://senselab.med.yale.edu/ModelDB/", "mappings": { "biocontext": "MODELDB", "edam": "2669", "fairsharing": "FAIRsharing.5rb3fk", "miriam": "modeldb", "n2t": "modeldb", "prefixcommons": "modeldb", "re3data": "r3d100011330" }, "name": "ModelDB", "pattern": "^\\d+$", "preferred_prefix": "modeldb", "publications": [ { "doi": "10.1385/ni:1:1:135", "pmc": "PMC3728921", "pubmed": "15055399", "title": "ModelDB: making models publicly accessible to support computational neuroscience.", "year": 2003 } ], "uri_format": "http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1" }, "modeldb.concept": { "description": "Concept used by ModelDB, an accessible location for storing and efficiently retrieving computational neuroscience models.", "example": "3639", "homepage": "https://www.yale.edu", "mappings": { "miriam": "modeldb.concept" }, "name": "ModelDB concept", "pattern": "^\\d+$", "preferred_prefix": "modeldb.concept", "uri_format": "https://senselab.med.yale.edu/ModelDB/ModelList?id=$1" }, "molbase": { "description": "Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier.", "example": "128796-39-4", "homepage": "http://www.molbase.com/", "mappings": { "biocontext": "MOLBASE", "miriam": "molbase", "n2t": "molbase" }, "name": "Molbase", "pattern": "^(\\d{1,7}\\-\\d{2}\\-\\d)|([A-Za-z0-9\\+\\-\\_]+)$", "preferred_prefix": "molbase", "uri_format": "http://www.molbase.com/en/index.php?app=search&search_keyword=$1" }, "molbase.sheffield": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students.", "example": "1868", "homepage": "https://winter.group.shef.ac.uk/molbase/", "name": "MolBase", "pattern": "^\\d+$", "preferred_prefix": "molbase.sheffield" }, "molmedb": { "contact": { "email": "karel.berka@upol.cz", "github": "KarelBerka", "name": "Karel Berka", "orcid": "0000-0001-9472-2589" }, "contributor_extras": [ { "email": "dominik.martinat@gmail.com", "github": "DominikMartinat", "name": "Dominik Martinat", "orcid": "0000-0001-6611-7883" } ], "description": "MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations. ", "example": "MM00040", "homepage": "http://www.upol.cz/en/", "mappings": { "fairsharing": "FAIRsharing.CWzk3C", "miriam": "molmedb" }, "name": "MolMeDB", "pattern": "^[m,M]{2}[0-9]{5}[0-9]*$", "preferred_prefix": "molmedb", "uri_format": "https://molmedb.upol.cz/mol/$1" }, "mondo": { "contact": { "email": "nicole@tislab.org", "github": "nicolevasilevsky", "name": "Nicole Vasilevsky", "orcid": "0000-0001-5208-3432" }, "description": "A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.", "download_json": "http://purl.obolibrary.org/obo/mondo.json", "download_obo": "http://purl.obolibrary.org/obo/mondo.obo", "download_owl": "http://purl.obolibrary.org/obo/mondo.owl", "example": "0000001", "homepage": "https://monarch-initiative.github.io/mondo", "license": "CC BY 4.0", "mappings": { "aberowl": "MONDO", "biocontext": "MONDO", "bioportal": "MONDO", "fairsharing": "FAIRsharing.b2979t", "obofoundry": "mondo", "ols": "mondo", "ontobee": "MONDO", "wikidata": "P5270" }, "name": "Monarch Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MONDO", "publications": [ { "doi": "10.1101/2022.04.13.22273750", "pmc": null, "pubmed": null, "title": "Mondo: Unifying diseases for the world, by the world", "year": null } ], "repository": "https://github.com/monarch-initiative/mondo", "twitter": "MonarchInit", "uri_format": "http://purl.obolibrary.org/obo/MONDO_$1", "version": "2022-08-01" }, "mop": { "contact": { "email": "batchelorc@rsc.org", "github": "batchelorc", "name": "Colin Batchelor", "orcid": "0000-0001-5985-7429" }, "description": "MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation.", "download_obo": "https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.obo", "download_owl": "http://purl.obolibrary.org/obo/mop.owl", "example": "0000079", "homepage": "https://github.com/rsc-ontologies/rxno", "license": "CC BY 4.0", "mappings": { "aberowl": "MOP", "biocontext": "MOP", "bioportal": "MOP", "fairsharing": "FAIRsharing.mct09a", "obofoundry": "mop", "ols": "mop", "ontobee": "MOP" }, "name": "Molecular Process Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MOP", "repository": "https://github.com/rsc-ontologies/rxno", "uri_format": "http://purl.obolibrary.org/obo/MOP_$1", "version": "2022-02-01" }, "morpheus": { "description": "The Morpheus model repository is an open-access data resource to store, search and retrieve unpublished and published computational models of spatio-temporal and multicellular biological systems, encoded in the MorpheusML language and readily executable with the Morpheus software.\n", "example": "M0001", "homepage": "https://morpheus.gitlab.io/", "mappings": { "miriam": "morpheus" }, "name": "Morpheus model repository", "pattern": "^M[0-9]{4,}$", "preferred_prefix": "morpheus", "uri_format": "https://morpheus.gitlab.io/models/$1" }, "mp": { "appears_in": [ "chiro", "scdo" ], "banana": "MP", "contact": { "email": "drsbello@gmail.com", "github": "sbello", "name": "Sue Bello", "orcid": "0000-0003-4606-0597" }, "description": "The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways.", "download_json": "http://purl.obolibrary.org/obo/mp.json", "download_obo": "http://purl.obolibrary.org/obo/mp.obo", "download_owl": "http://purl.obolibrary.org/obo/mp.owl", "example": "0005452", "homepage": "http://www.informatics.jax.org/searches/MP_form.shtml", "license": "CC BY 4.0", "mappings": { "aberowl": "MP", "biocontext": "MP", "bioportal": "MP", "fairsharing": "FAIRsharing.kg1x4z", "miriam": "mp", "n2t": "mp", "obofoundry": "mp", "ols": "mp", "ontobee": "MP", "prefixcommons": "mp" }, "name": "Mammalian Phenotype Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "MP", "publications": [ { "doi": "10.1186/s13326-015-0009-1", "pmc": "PMC4378007", "pubmed": "25825651", "title": "Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens.", "year": 2015 }, { "doi": "10.1007/s00335-012-9421-3", "pmc": "PMC3463787", "pubmed": "22961259", "title": "The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data.", "year": 2012 }, { "doi": "10.1002/wsbm.44", "pmc": "PMC2801442", "pubmed": "20052305", "title": "The mammalian phenotype ontology: enabling robust annotation and comparative analysis.", "year": null }, { "doi": "10.1186/gb-2004-6-1-r7", "pmc": "PMC549068", "pubmed": "15642099", "title": "The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information.", "year": 2004 } ], "repository": "https://github.com/mgijax/mammalian-phenotype-ontology", "uri_format": "http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1" }, "mpath": { "contact": { "email": "pns12@hermes.cam.ac.uk", "github": "PaulNSchofield", "name": "Paul Schofield", "orcid": "0000-0002-5111-7263" }, "description": "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes", "download_obo": "https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo", "download_owl": "http://purl.obolibrary.org/obo/mpath.owl", "example": "728", "homepage": "http://www.pathbase.net", "license": "CC BY 3.0", "mappings": { "aberowl": "MPATH", "biocontext": "MPATH", "bioportal": "MPATH", "fairsharing": "FAIRsharing.3wbgm0", "obofoundry": "mpath", "ols": "mpath", "ontobee": "MPATH", "prefixcommons": "mpath" }, "name": "Mouse pathology ontology", "pattern": "^\\d+$", "preferred_prefix": "MPATH", "publications": [ { "doi": "10.1177/0300985810374845", "pmc": "PMC3038412", "pubmed": "20587689", "title": "Pathbase and the MPATH ontology. Community resources for mouse histopathology.", "year": 2010 } ], "repository": "https://github.com/PaulNSchofield/mpath", "synonyms": [ "MPATH" ], "uri_format": "http://purl.obolibrary.org/obo/MPATH_$1", "version": "2020-05-19" }, "mpid": { "description": "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts.", "example": "172", "homepage": "http://www.jcvi.org/mpidb/about.php", "mappings": { "biocontext": "MPID", "fairsharing": "FAIRsharing.eyjkws", "miriam": "mpid", "n2t": "mpid", "prefixcommons": "mpi" }, "name": "Microbial Protein Interaction Database", "pattern": "^\\d+$", "preferred_prefix": "mpid", "providers": [ { "code": "ebi", "description": "Microbial Protein Interaction Database subset through IntAct", "homepage": "https://www.ebi.ac.uk/intact/", "name": "Microbial Protein Interaction Database subset through IntAct", "uri_format": "https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/btn285", "pmc": "PMC2638870", "pubmed": "18556668", "title": "MPIDB: the microbial protein interaction database.", "year": 2008 } ], "synonyms": [ "mpidb" ], "uri_format": "http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1" }, "mpio": { "contact": { "email": "mbrochhausen@uams.edu", "github": "mbrochhausen", "name": "Mathias Brochhausen", "orcid": "0000-0003-1834-3856" }, "description": "An ontology of minimum information regarding potential drug-drug interaction information.", "download_owl": "http://purl.obolibrary.org/obo/mpio.owl", "example": "0000004", "homepage": "https://github.com/MPIO-Developers/MPIO", "license": "CC BY 4.0", "mappings": { "aberowl": "MPIO", "biocontext": "MPIO", "bioportal": "MPIO", "obofoundry": "mpio", "ols": "mpio", "ontobee": "MPIO" }, "name": "Minimum PDDI Information Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MPIO", "repository": "https://github.com/MPIO-Developers/MPIO", "uri_format": "http://purl.obolibrary.org/obo/MPIO_$1", "version": "2019-01-30" }, "mro": { "contact": { "email": "bpeters@lji.org", "github": "bpeters42", "name": "Bjoern Peters", "orcid": "0000-0002-8457-6693" }, "description": "The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions.", "download_owl": "http://purl.obolibrary.org/obo/mro.owl", "example": "0000634", "homepage": "https://github.com/IEDB/MRO", "license": "CC BY 3.0", "mappings": { "aberowl": "MRO", "biocontext": "MRO", "bioportal": "MRO", "fairsharing": "FAIRsharing.k893xa", "obofoundry": "mro", "ols": "mro", "ontobee": "MRO" }, "name": "MHC Restriction Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MRO", "publications": [ { "doi": "10.1186/s13326-016-0045-5", "pmc": "PMC4709943", "pubmed": "26759709", "title": "An ontology for major histocompatibility restriction.", "year": 2016 } ], "repository": "https://github.com/IEDB/MRO", "uri_format": "http://purl.obolibrary.org/obo/MRO_$1", "version": "2022-06-17" }, "ms": { "banana": "MS", "contact": { "email": "gerhard.mayer@rub.de", "github": "germa", "name": "Gerhard Mayer", "orcid": "0000-0002-1767-2343" }, "depends_on": [ "pato", "uo" ], "description": "The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance.", "download_obo": "http://purl.obolibrary.org/obo/ms.obo", "download_owl": "http://purl.obolibrary.org/obo/ms.owl", "example": "1000560", "homepage": "http://www.psidev.info/groups/controlled-vocabularies", "license": "CC BY 3.0", "mappings": { "aberowl": "MS", "biocontext": "MS", "bioportal": "MS", "miriam": "ms", "n2t": "ms", "obofoundry": "ms", "ols": "ms", "ontobee": "MS" }, "name": "Mass spectrometry ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "MS", "publications": [ { "doi": "10.1093/database/bat009", "pmc": "PMC3594986", "pubmed": "23482073", "title": "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.", "year": 2013 } ], "repository": "https://github.com/HUPO-PSI/psi-ms-CV", "uri_format": "https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:$1" }, "msigdb": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can", "example": "M1", "homepage": "https://www.gsea-msigdb.org", "mappings": { "biolink": "MSigDB" }, "name": "Molecular Signatures Database", "pattern": "^M\\d+$", "preferred_prefix": "msigdb", "synonyms": [ "msig" ], "uri_format": "https://biopragmatics.github.io/providers/msigdb/$1" }, "msio": { "description": "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.", "download_owl": "https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl", "example": "0000111", "homepage": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO", "mappings": { "ols": "msio" }, "name": "Metabolomics Standards Initiative Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "msio", "repository": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO", "uri_format": "http://purl.obolibrary.org/obo/MSIO_$1", "version": "1.0.1" }, "multicellds": { "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", "mappings": { "fairsharing": "FAIRsharing.pqzyd5" }, "name": "MultiCellDS", "preferred_prefix": "multicellds", "uri_format": "http://multicellds.org/MultiCellDB/$1" }, "multicellds.cell_line": { "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. 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Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections).", "example": "MCDS_C_0000000001", "homepage": "http://multicellds.org/MultiCellDB.php", "mappings": { "biocontext": "MULTICELLDS.COLLECTION", "miriam": "multicellds.collection", "n2t": "multicellds.collection" }, "name": "MultiCellDS collection", "part_of": "multicellds", "pattern": "^MCDS_C_[a-zA-Z0-9]{1,10}$", "preferred_prefix": "multicellds.collection", "uri_format": "http://multicellds.org/MultiCellDB/$1" }, "multicellds.snapshot": { "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data.", "example": "MCDS_S_0000000001", "homepage": "http://multicellds.org/MultiCellDB.php", "mappings": { "biocontext": "MULTICELLDS.SNAPSHOT", "miriam": "multicellds.snapshot", "n2t": "multicellds.snapshot" }, "name": "MultiCellDS Digital snapshot", "part_of": "multicellds", "pattern": "^MCDS_S_[a-zA-Z0-9]{1,10}$", "preferred_prefix": "multicellds.snapshot", "uri_format": "http://multicellds.org/MultiCellDB/$1" }, "mw.project": { "description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).", "example": "PR000001", "homepage": "http://www.metabolomicsworkbench.org/", "mappings": { "biocontext": "MW.PROJECT", "miriam": "mw.project", "n2t": "mw.project" }, "name": "Metabolomics Workbench Project", "pattern": "^PR[0-9]{6}$", "preferred_prefix": "mw.project", "uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1" }, "mw.study": { "description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).", "example": "ST000900", "homepage": "http://www.metabolomicsworkbench.org/", "mappings": { "biocontext": "MW.STUDY", "miriam": "mw.study", "n2t": "mw.study" }, "name": "Metabolomics Workbench Study", "pattern": "^ST[0-9]{6}$", "preferred_prefix": "mw.study", "providers": [ { "code": "omicsdi", "description": "Metabolomics Workbench Study through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "Metabolomics Workbench Study through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/metabolomics_workbench/$1" } ], "uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1" }, "myco.lepra": { "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.", "example": "ML0224", "homepage": "http://mycobrowser.epfl.ch/leprosy.html", "mappings": { "biocontext": "MYCO.LEPRA", "miriam": "myco.lepra", "n2t": "myco.lepra", "prefixcommons": "myco.lepra" }, "name": "MycoBrowser leprae", "pattern": "^ML\\w+$", "preferred_prefix": "myco.lepra", "uri_format": "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1" }, "myco.marinum": { "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information.", "example": "MMAR_2462", "homepage": "http://mycobrowser.epfl.ch/marinolist.html", "mappings": { "biocontext": "MYCO.MARINUM", "miriam": "myco.marinum", "n2t": "myco.marinum", "prefixcommons": "myco.marinum" }, "name": "MycoBrowser marinum", "pattern": "^MMAR\\_\\d+$", "preferred_prefix": "myco.marinum", "uri_format": "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1" }, "myco.smeg": { "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.", "example": "MSMEG_3769", "homepage": "http://mycobrowser.epfl.ch/smegmalist.html", "mappings": { "biocontext": "MYCO.SMEG", "miriam": "myco.smeg", "n2t": "myco.smeg", "prefixcommons": "myco.smeg" }, "name": "MycoBrowser smegmatis", "pattern": "^MSMEG\\w+$", "preferred_prefix": "myco.smeg", "uri_format": "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1" }, "myco.tuber": { "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information.", "example": "Rv1908c", "homepage": "http://tuberculist.epfl.ch/", "mappings": { "biocontext": "MYCO.TUBER", "miriam": "myco.tuber", "n2t": "myco.tuber", "ncbi": "TubercuList", "prefixcommons": "tuberculist", "uniprot": "TubercuList" }, "name": "TubercuList knowledge base", "pattern": "^Rv\\d{4}(A|B|c)?$", "preferred_prefix": "myco.tuber", "synonyms": [ "TubercuList" ], "uri_format": "http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1" }, "mycobank": { "description": "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.", "example": "349124", "homepage": "http://www.mycobank.org/", "mappings": { "biocontext": "MYCOBANK", "fairsharing": "FAIRsharing.v8se8r", "miriam": "mycobank", "n2t": "mycobank", "ncbi": "MycoBank", "prefixcommons": "mycobank", "re3data": "r3d100011222" }, "name": "Fungal Nomenclature and Species Bank", "pattern": "^\\d+$", "preferred_prefix": "mycobank", "uri_format": "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1" }, "mzspec": { "banana": "mzspec", "description": "The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it.", "example": "PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2", "homepage": "http://proteomecentral.proteomexchange.org/", "mappings": { "biocontext": "MZSPEC", "miriam": "mzspec", "n2t": "mzspec" }, "name": "Universal Spectrum Identifier", "namespace_in_lui": true, "pattern": "^.+$", "preferred_prefix": "mzspec", "providers": [ { "code": "CURATOR_REVIEW", "description": "Universal Spectrum Identifier through Peptide Atlas", "homepage": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum", "name": "Universal Spectrum Identifier through Peptide Atlas", "uri_format": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum?usi=mzspec:$1" } ], "uri_format": "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1" }, "n2t": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org", "example": "chebi", "homepage": "https://n2t.net", "name": "Name-to-Thing", "preferred_prefix": "n2t", "uri_format": "https://n2t.net/$1:" }, "namerxn": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO).", "example": "4.2.78", "homepage": "https://www.nextmovesoftware.com/namerxn.html", "name": "NameRXN", "preferred_prefix": "namerxn", "proprietary": true, "publications": [ { "doi": "10.1038/s42256-020-00284-w", "pmc": null, "pubmed": null, "title": "Mapping the space of chemical reactions using attention-based neural networks", "year": null }, { "doi": "10.1021/acs.jmedchem.6b00153", "pmc": null, "pubmed": null, "title": "Big Data from Pharmaceutical Patents: A Computational Analysis of Medicinal Chemists’ Bread and Butter", "year": null } ], "references": [ "https://www.nextmovesoftware.com/products/HazELNutPoster.pdf", "https://twitter.com/cthoyt/status/1443929184745758723" ] }, "napdi": { "description": "The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs).", "example": "28", "homepage": "https://repo.napdi.org/", "mappings": { "biocontext": "NAPDI", "fairsharing": "FAIRsharing.y9x8wk", "miriam": "napdi", "n2t": "napdi" }, "name": "Natural Product-Drug Interaction Research Data Repository", "pattern": "^[0-9]+$", "preferred_prefix": "napdi", "uri_format": "https://repo.napdi.org/study/$1" }, "napp": { "description": "NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters.", "example": "351", "homepage": "http://napp.u-psud.fr/", "mappings": { "biocontext": "NAPP", "fairsharing": "FAIRsharing.vr52p3", "miriam": "napp", "n2t": "napp", "prefixcommons": "napp" }, "name": "Nucleic Acids Phylogenetic Profiling", "pattern": "^\\d+$", "preferred_prefix": "napp", "uri_format": "http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1" }, "narcis": { "description": "NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases.", "example": "oai:cwi.nl:4725", "homepage": "http://www.narcis.nl", "mappings": { "biocontext": "NARCIS", "fairsharing": "FAIRsharing.f63h4k", "miriam": "narcis", "n2t": "narcis" }, "name": "National Academic Research and Collaborations Information System", "pattern": "^oai\\:cwi\\.nl\\:\\d+$", "preferred_prefix": "narcis", "uri_format": "http://www.narcis.nl/publication/RecordID/$1" }, "nasc": { "description": "The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.", "example": "N1899", "homepage": "http://arabidopsis.info/", "mappings": { "biocontext": "NASC", "fairsharing": "FAIRsharing.2sqcxs", "miriam": "nasc", "n2t": "nasc", "prefixcommons": "nasc", "re3data": "r3d100010906" }, "name": "NASC code", "pattern": "^(\\w+)?\\d+$", "preferred_prefix": "nasc", "uri_format": "http://arabidopsis.info/StockInfo?NASC_id=$1" }, "nbn": { "description": "The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier.", "example": "urn:nbn:fi:tkk-004781", "homepage": "http://nbn-resolving.org/resolve_urn.htm", "mappings": { "biocontext": "NBN", "miriam": "nbn", "n2t": "nbn" }, "name": "National Bibliography Number", "pattern": "^urn\\:nbn\\:[A-Za-z_0-9]+\\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$", "preferred_prefix": "nbn", "uri_format": "http://nbn-resolving.org/resolver?identifier=$1&verb=redirect" }, "nbo": { "appears_in": [ "ecto", "pcl", "scdo" ], "contact": { "email": "g.gkoutos@bham.ac.uk", "github": "gkoutos", "name": "George Gkoutos", "orcid": "0000-0002-2061-091X" }, "description": "An ontology of human and animal behaviours and behavioural phenotypes", "download_obo": "https://github.com/obo-behavior/behavior-ontology/raw/master/nbo.obo", "download_owl": "http://purl.obolibrary.org/obo/nbo.owl", "example": "0000564", "homepage": "https://github.com/obo-behavior/behavior-ontology/", "license": "CC BY 3.0", "mappings": { "aberowl": "NBO", "biocontext": "NBO", "bioportal": "NBO", "fairsharing": "FAIRsharing.pktgc6", "obofoundry": "nbo", "ols": "nbo", "ontobee": "NBO" }, "name": "Neuro Behavior Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "NBO", "publications": [ { "doi": "10.1007/s00335-013-9481-z", "pmc": null, "pubmed": "24177753", "title": "Analyzing gene expression data in mice with the Neuro Behavior Ontology.", "year": 2013 }, { "doi": "10.1016/b978-0-12-388408-4.00004-6", "pmc": null, "pubmed": "23195121", "title": "The neurobehavior ontology: an ontology for annotation and integration of behavior and behavioral phenotypes.", "year": 2012 } ], "repository": "https://github.com/obo-behavior/behavior-ontology", "uri_format": "http://purl.obolibrary.org/obo/NBO_$1", "version": "2021-02-15" }, "nbrc": { "description": "NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information.", "example": "00001234", "homepage": "http://www.nbrc.nite.go.jp/e/index.html", "mappings": { "biocontext": "NBRC", "fairsharing": "FAIRsharing.ftamrc", "miriam": "nbrc", "n2t": "nbrc", "ncbi": "NBRC", "prefixcommons": "nbrc" }, "name": "NITE Biological Resource Center", "pattern": "^\\d+$", "preferred_prefix": "nbrc", "uri_format": "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1" }, "ncats.bioplanet": { "contact": { "email": "ruili.huang@nih.gov", "github": null, "name": "Ruili Huang", "orcid": "0000-0001-8886-8311" }, "contributor": { "email": null, "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" }, "description": "The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays.", "example": "3", "github_request_issue": 445, "homepage": "https://tripod.nih.gov/bioplanet/", "mappings": { "biolink": "ncats.bioplanet" }, "name": "National Center for Advancing Translation Sciences BioPlanet", "pattern": "^\\d+$", "preferred_prefix": "ncats.bioplanet", "publications": [ { "doi": "10.3389/fphar.2019.00445", "pmc": null, "pubmed": null, "title": "The NCATS BioPlanet – An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics", "year": null } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "twitter": "ncats_nih_gov", "uri_format": "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1" }, "ncats.drug": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, { "email": null, "github": "vdancik", "name": "Vlado Dancik", "orcid": "0000-0002-5970-6660" }, { "email": null, "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" } ], "description": "The National Center for Advancing Translational Sciences](http://www.ncats.nih.gov/) (NCATS) has developed Inxight Drugs as a comprehensive portal for drug development information. NCATS Inxight Drugs contains information on ingredients in medicinal products, including:\n\n- US Approved Drugs\n- Marketed Drugs\n- Investigational Drugs\n- Other Substances", "example": "44259", "example_extras": [ "1IJV77EI07" ], "homepage": "https://drugs.ncats.io/", "mappings": { "biolink": "ncats.drug" }, "name": "NCATS Drugs", "preferred_prefix": "ncats.drug", "synonyms": [ "inxight", "inxight-drugs" ], "uri_format": "https://drugs.ncats.io/drug/$1" }, "ncbi.assembly": { "description": "A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data.", "example": "GCF_000005845.2", "homepage": "https://www.ncbi.nlm.nih.gov/", "mappings": { "biocontext": "NCBIAssembly", "miriam": "assembly", "re3data": "r3d100012688" }, "name": "Assembly", "pattern": "^[a-zA-Z0-9_\\.]+$", "preferred_prefix": "ncbi.assembly", "uri_format": "https://www.ncbi.nlm.nih.gov/assembly/$1" }, "ncbi.genome": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations.", "example": "51", "homepage": "https://www.ncbi.nlm.nih.gov/genome", "mappings": { "biocontext": "NCBIGenome", "edam": "2787", "re3data": "r3d100010785" }, "name": "NCBI Genome", "pattern": "^\\d+$", "preferred_prefix": "ncbi.genome", "uri_format": "https://www.ncbi.nlm.nih.gov/genome/$1" }, "ncbi.resource": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources", "example": "ECOCYC", "homepage": "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/", "name": "NCBI Registry", "preferred_prefix": "ncbi.resource", "uri_format": "https://bioregistry.io/metaregistry/ncbi/$1" }, "ncbibook": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. 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Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones.", "example": "6b1", "homepage": "http://nematode.lab.nig.ac.jp/", "mappings": { "biocontext": "NEXTDB", "fairsharing": "FAIRsharing.xz5m1a", "miriam": "nextdb", "n2t": "nextdb", "ncbi": "NextDB", "prefixcommons": "nextdb" }, "name": "Nematode Expression Pattern DataBase", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "nextdb", "uri_format": "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1" }, "nextprot": { "description": "neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases.", "example": "NX_O00165", "homepage": "https://www.nextprot.org/", "mappings": { "biocontext": "NEXTPROT", "fairsharing": "FAIRsharing.62evqh", "miriam": "nextprot", "n2t": "nextprot", "uniprot": "neXtProt" }, "name": "nextProt", "pattern": "^NX_\\w+$", "preferred_prefix": "nextprot", "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-$1" }, "ngl": { "description": "NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA.", "example": "GLDS-141", "homepage": "https://genelab-data.ndc.nasa.gov/genelab/", "mappings": { "biocontext": "NGL", "miriam": "ngl", "n2t": "ngl" }, "name": "NASA GeneLab", "pattern": "^GLDS-\\d+$", "preferred_prefix": "ngl", "uri_format": "https://genelab-data.ndc.nasa.gov/genelab/accession/$1" }, "nhcdr": { "description": "Cell line collections", "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=$1" }, "niaest": { "description": "A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones.", "example": "J0705A10", "homepage": "http://lgsun.grc.nia.nih.gov/cDNA/", "mappings": { "biocontext": "NIAEST", "fairsharing": "FAIRsharing.xwqg9h", "miriam": "niaest", "n2t": "niaest", "ncbi": "niaEST", "prefixcommons": "niaest" }, "name": "NIA Mouse cDNA Project", "pattern": "^\\w\\d{4}\\w\\d{2}(\\-[35])?$", "preferred_prefix": "niaest", "uri_format": "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1" }, "nif.cell": { "contact": { "email": "smtifahim@gmail.com", "github": null, "name": "Fahim Imam", "orcid": null }, "deprecated": true, "description": "Neuronal cell types", "download_owl": "http://aber-owl.net/media/ontologies/NIFCELL/15/nifcell.owl", "homepage": "http://neuinfo.org/", "mappings": { "aberowl": "NIFCELL", "biocontext": "NIF_CELL", "bioportal": "NIFCELL", "obofoundry": "nif_cell" }, "name": "NIF Cell", "part_of": "nif", "preferred_prefix": "NIF_CELL", "uri_format": "http://purl.obolibrary.org/obo/NIF_CELL_$1" }, "nif.dysfunction": { "contact": { "email": "smtifahim@gmail.com", "github": null, "name": "Fahim Imam", "orcid": null }, "deprecated": true, "homepage": "http://neuinfo.org/", "mappings": { "biocontext": "NIF_DYSFUNCTION", "obofoundry": "nif_dysfunction" }, "name": "NIF Dysfunction", "part_of": "nif", "preferred_prefix": "NIF_DYSFUNCTION", "uri_format": "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1" }, "nif.ext": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NIFEXT covers IRIs that were \"external\" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed.", "example": "7123", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "license": "CC BY-4.0", "name": "NIF Standard Ontology: External", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nif.ext", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NIFEXT" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nifext_$1" }, "nif.grossanatomy": { "contact": { "email": "smtifahim@gmail.com", "github": null, "name": "Fahim Imam", "orcid": null }, "deprecated": true, "homepage": "http://neuinfo.org/", "mappings": { "biocontext": "NIF_GROSSANATOMY", "obofoundry": "nif_grossanatomy" }, "name": "NIF Gross Anatomy", "part_of": "nif", "preferred_prefix": "NIF_GROSSANATOMY", "uri_format": "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1" }, "nif.std": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing.", "download_owl": "http://aber-owl.net/media/ontologies/NIFSTD/23/nifstd.owl", "example": "BAMSC981", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "license": "CC BY-4.0", "mappings": { "aberowl": "NIFSTD", "bioportal": "NIFSTD", "fairsharing": "FAIRsharing.vgw1m6" }, "name": "NIF Standard Ontology", "part_of": "nif", "pattern": "^BAMSC\\d+$", "preferred_prefix": "nif.std", "publications": [ { "doi": "10.1007/s12021-008-9032-z", "pmc": "PMC2743139", "pubmed": "18975148", "title": "The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.", "year": 2008 } ], "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NIFSTD" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/$1" }, "nihreporter.project": { "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding.", "example": "10343835", "github_request_issue": 400, "homepage": "https://reporter.nih.gov/", "name": "NIH RePORTER", "pattern": "^\\d+$", "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/$1" }, "nist": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species.", "homepage": "https://webbook.nist.gov/chemistry/", "name": "NIST Chemistry WebBook", "no_own_terms": true, "preferred_prefix": "nist", "synonyms": [ "NIST", "NIST Chemistry WebBook" ] }, "nlm": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings.", "example": "101775319", "homepage": "https://www.ncbi.nlm.nih.gov/nlmcatalog", "mappings": { "biolink": "NLMID" }, "name": "National Library of Medicine Catalog", "pattern": "^\\d+$", "preferred_prefix": "nlm", "uri_format": "https://www.ncbi.nlm.nih.gov/nlmcatalog/$1" }, "nlx.anat": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4804" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "NLXANAT covers anatomy terms. Almost all terms are also in Uberon.", "example": "090201", "homepage": "https://scicrunch.org/scicrunch/interlex/dashboard", "name": "NeuroLex Anatomy", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.anat", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1" }, "nlx.br": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4804" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4804" }, "description": "NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999).", "example": "145", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "license": "CC BY-4.0", "name": "NIF Standard Ontology: Brain Regions", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.br", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXBR" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_br_$1" }, "nlx.cell": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4805" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4805" }, "description": "NLXCELL conatins cell types with a focus on neuron types.", "example": "91005", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "license": "CC BY-4.0", "name": "NIF Standard Ontology: Cell Types", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.cell", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXCELL" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1" }, "nlx.chem": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4806" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4806" }, "description": "NLXCHEM covers chemicals. Most classes are also in ChEBI.", "example": "90801", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "license": "CC BY-4.0", "name": "NIF Standard Ontology: Chemical", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.chem", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXCHEM" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1" }, "nlx.dys": { "appears_in": [ "mondo" ], "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4804" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc.", "example": "20090303", "homepage": "https://scicrunch.org/scicrunch/interlex/dashboard", "name": "NeuroLex Dysfunction", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.dys", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1" }, "nlx.func": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4808" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4808" }, "description": "NLXFUNC covers terms for cognitive function.", "example": "90801", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "license": "CC BY-4.0", "name": "NIF Standard Ontology: Cognitive Function", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.func", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXFUNC" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_func_$1" }, "nlx.inv": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4809" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4809" }, "description": "NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis.", "example": "90901", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "license": "CC BY-4.0", "name": "NIF Standard Ontology: Investigations", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.inv", "repository": "https://github.com/SciCrunch/NIF-Ontology", "synonyms": [ "NLXINV" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1" }, "nlx.mol": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4810" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4810" }, "description": "NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system.", "example": "90806", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "license": "CC BY-4.0", "name": "NIF Standard Ontology: Molecules", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.mol", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXMOL" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1" }, "nlx.oen": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4811" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4811" }, "description": "NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results).", "example": "0001000", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "license": "CC BY-4.0", "name": "NIF Standard Ontology: OEN Terms in Neurolex", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.oen", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXOEN" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/oen_$1" }, "nlx.org": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4812" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4812" }, "description": "NLXORG covers organisms.", "example": "090701", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "license": "CC BY-4.0", "name": "NIF Standard Ontology: Organisms", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.org", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXORG" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1" }, "nlx.qual": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4813" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4813" }, "description": "NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO).", "example": "100810", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "license": "CC BY-4.0", "name": "NIF Standard Ontology: Qualities", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.qual", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXQUAL" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1" }, "nlx.res": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4814" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4814" }, "description": "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites", "example": "090924", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "license": "CC BY-4.0", "name": "NIF Standard Ontology: Digital Resources", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.res", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXRES" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_res_$1" }, "nlx.sub": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4815" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4815" }, "description": "NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO).", "example": "090803", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "license": "CC BY-4.0", "mappings": { "go": "NIF_Subcellular" }, "name": "NIF Standard Ontology: Subcellular Entities", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.sub", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXSUB", "nif_subcellular" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1" }, "nmdc": { "contact": { "email": "donny@polyneme.xyz", "github": "dwinston", "name": "Donny Winston", "orcid": "0000-0002-8424-0604" }, "contributor": { "email": "donny@polyneme.xyz", "github": "dwinston", "name": "Donny Winston", "orcid": "0000-0002-8424-0604" }, "description": "An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem.", "example": "y3ax-8bq3-60", "homepage": "https://microbiomedata.org/", "mappings": { "miriam": "nmdc" }, "name": "National Microbiome Data Collaborative", "pattern": "^[\\w\\-.]{3,}$", "preferred_prefix": "nmdc", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://drs.microbiomedata.org/objects/$1" }, "nmr": { "banana": "NMR", "contact": { "email": "schober@imbi.uni-freiburg.de", "github": null, "name": "Schober Daniel", "orcid": null }, "deprecated": true, "description": "nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi.", "download_owl": "https://nmrml.org/cv/stable/nmrCV.owl", "example": "1000003", "homepage": "http://msi-ontology.sourceforge.net/", "mappings": { "aberowl": "NMR", "biocontext": "NMR", "bioportal": "NMR", "miriam": "nmr", "n2t": "nmr", "obofoundry": "nmr", "ols": "nmrcv", "prefixcommons": "nmr" }, "name": "NMR-instrument specific component of metabolomics investigations", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "NMR", "synonyms": [ "nmrcv" ], "uri_format": "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1", "version": "1.1.0" }, "nmrshiftdb2": { "description": "NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties.", "example": "234", "homepage": "https://nmrshiftdb.nmr.uni-koeln.de", "mappings": { "fairsharing": "FAIRsharing.nYaZ1N", "miriam": "nmrshiftdb2" }, "name": "NMR Shift Database", "pattern": "^[0-9]+$", "preferred_prefix": "nmrshiftdb2", "uri_format": "https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1" }, "noaa": { "contributor": { "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" }, "description": "Identifier for a species on the noaa fisheries website", "example": "long-finned-pilot-whale", "github_request_issue": 456, "homepage": "https://www.fisheries.noaa.gov/species-directory", "mappings": { "wikidata": "P6049" }, "name": "NOAA Fisheries Species Directory", "pattern": "^[a-z]+(\\-[a-z]+)*$", "preferred_prefix": "noaa", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.fisheries.noaa.gov/species/$1" }, "nomen": { "contact": { "email": "diapriid@gmail.com", "github": "mjy", "name": "Matt Yoder", "orcid": "0000-0002-5640-5491" }, "description": "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature.", "download_owl": "http://purl.obolibrary.org/obo/nomen.owl", "example": "0000295", "homepage": "https://github.com/SpeciesFileGroup/nomen", "license": "CC0 1.0", "mappings": { "aberowl": "NOMEN", "bioportal": "NOMEN", "obofoundry": "nomen", "ols": "nomen", "ontobee": "NOMEN" }, "name": "A nomenclatural ontology for biological names", "pattern": "^\\d{7}$", "preferred_prefix": "NOMEN", "repository": "https://github.com/SpeciesFileGroup/nomen", "uri_format": "http://purl.obolibrary.org/obo/NOMEN_$1" }, "noncodev3": { "description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4.", "example": "377550", "homepage": "http://www.noncode.org/", "mappings": { "biocontext": "NONCODEV3", "miriam": "noncodev3", "n2t": "noncodev3" }, "name": "NONCODE v3", "pattern": "^\\d+$", "preferred_prefix": "noncodev3", "uri_format": "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1" }, "noncodev4.gene": { "description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions.", "example": "NONHSAG00001", "homepage": "http://www.bioinfo.org/NONCODEv4/", "mappings": { "biocontext": "NONCODEV4.GENE", "miriam": "noncodev4.gene", "n2t": "noncodev4.gene" }, "name": "NONCODE v4 Gene", "pattern": "^NONHSAG\\d{5}$", "preferred_prefix": "noncodev4.gene", "uri_format": "http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1" }, "noncodev4.rna": { "description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts.", "example": "NONHSAT000001", "homepage": "http://www.bioinfo.org/NONCODEv4/", "mappings": { "biocontext": "NONCODEV4.RNA", "miriam": "noncodev4.rna", "n2t": "noncodev4.rna" }, "name": "NONCODE v4 Transcript", "pattern": "^NONHSAT\\d{6}$", "preferred_prefix": "noncodev4.rna", "uri_format": "http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1" }, "norine": { "description": "Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings.", "example": "NOR00681", "homepage": "http://bioinfo.lifl.fr/norine/", "mappings": { "biocontext": "NORINE", "fairsharing": "FAIRsharing.gf8yhy", "miriam": "norine", "n2t": "norine", "prefixcommons": "norine" }, "name": "Nonribosomal Peptides Database", "pattern": "^NOR\\d+$", "preferred_prefix": "norine", "uri_format": "http://bioinfo.lifl.fr/norine/result.jsp?ID=$1" }, "novus": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A vendor of antibodies and other biologics", "example": "nb100-56351", "homepage": "https://www.novusbio.com", "name": "Novus Biologicals", "preferred_prefix": "novus", "uri_format": "https://www.novusbio.com/products/$1" }, "npass": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data.\n", "example": "NPC139585", "homepage": "http://bidd.group/NPASS/", "name": "Natural Product Activity and Species Source Database", "pattern": "^NPC\\d+$", "preferred_prefix": "npass" }, "npo": { "contact": { "email": "nathan.baker@pnnl.gov", "github": "sobolevnrm", "name": "Nathan Baker", "orcid": "0000-0002-5892-6506" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.", "download_owl": "http://aber-owl.net/media/ontologies/NPO/31/npo.owl", "example": "1731", "homepage": "https://bioportal.bioontology.org/ontologies/NPO", "mappings": { "aberowl": "NPO", "bioportal": "NPO", "fairsharing": "FAIRsharing.vy0p71" }, "name": "NanoParticle Ontology", "pattern": "^\\d+$", "preferred_prefix": "npo", "publications": [ { "doi": "10.1016/j.jbi.2010.03.001", "pmc": "PMC3042056", "pubmed": "20211274", "title": "NanoParticle Ontology for cancer nanotechnology research.", "year": 2010 } ], "repository": "https://github.com/sobolevnrm/npo", "uri_format": "http://purl.bioontology.org/ontology/npo#NPO_$1" }, "nsc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Identifier used by the Cancer Chemotherapy National Service Center.", "example": "27223", "homepage": "https://wiki.nci.nih.gov/display/NCIDTPdata/Chemical+Data", "mappings": { "cheminf": "000565" }, "name": "USA National Service Center Number", "pattern": "^\\d+$", "preferred_prefix": "nsc", "references": [ "https://pubchem.ncbi.nlm.nih.gov/source/DTP/NCI" ], "uri_format": "https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist=$1" }, "nsf.award": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Information about research projects that NSF has funded since 1989 can be found by searching the Award Abstracts database. The information includes abstracts that describe the research, and names of principal investigators and their institutions. The database includes both completed and in-process research.", "example": "1458400", "homepage": "https://www.nsf.gov/awards/about.jsp", "name": "National Science Foundation Award", "pattern": "^\\d+$", "preferred_prefix": "nsf.award", "uri_format": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=$1" }, "nucc.characteristic": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Provider Characteristics code set is for use with health care provider information for enrollment and credentialing transactions and their corresponding responses. It is intended to provide codified responses to questions presented to a health care provider applying to or registering with an entity and to report the outcome of such application or registration. It may also be used for responses to inquiries regarding provider participation or registration in a program or plan.", "example": "2A", "example_extras": [ "11", "10" ], "homepage": "https://nucc.org/index.php/code-sets-mainmenu-41/provider-characteristics-mainmenu-39", "name": "National Uniform Claim Committee Characteristic", "pattern": "^\\d(\\d|\\w)$", "preferred_prefix": "nucc.characteristic" }, "nucc.taxonomy": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Health Care Provider Taxonomy code set is an external, nonmedical data code set designed for use in an electronic environment, specifically within the ASC X12N Health Care transactions. This includes the transactions mandated under HIPAA.\n\nThe taxonomy code is a unique alphanumeric code, ten characters in length. The code set is structured into three distinct \"Levels\" including Provider Grouping, Classification, and Area of Specialization.\n\n - **Level I, Provider Grouping** A major grouping of service(s) or occupation(s) of health care providers. For example: Allopathic & Osteopathic Physicians, Dental Providers, Hospitals, etc.\n - **Level II, Classification** A more specific service or occupation related to the Provider Grouping. For example, the Classification for Allopathic & Osteopathic Physicians is based upon the General Specialty Certificates as issued by the appropriate national boards. The following boards will however, have their general certificates appear as Level III areas of specialization strictly due to display limitations of the code set for Boards that have multiple general certificates: Medical Genetics, Preventive Medicine, Psychiatry & Neurology, Radiology, Surgery, Otolaryngology, Pathology.\n - **Level III, Area of Specialization** A more specialized area of the Classification in which a provider chooses to practice or make services available. For example, the Area of Specialization for provider grouping Allopathic & Osteopathic Physicians is based upon the Subspecialty Certificates as issued by the appropriate national boards.", "example": "207LH0002X", "homepage": "https://taxonomy.nucc.org", "name": "National Uniform Claim Committee Taxonomy", "pattern": "^\\d{3}\\w(\\w|\\d_)\\d{4}X$", "preferred_prefix": "nucc.taxonomy", "references": [ "https://www.nucc.org/images/stories/CSV/nucc_taxonomy_221.csv", "https://www.nucc.org" ] }, "nuclearbd": { "description": "NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs.", "example": "prgr_human", "homepage": "http://www.receptors.org/nucleardb/", "mappings": { "biocontext": "NUCLEARBD", "miriam": "nuclearbd", "n2t": "nuclearbd" }, "name": "NucleaRDB", "pattern": "^\\w+\\_\\w+$", "preferred_prefix": "nuclearbd", "uri_format": "http://www.receptors.org/nucleardb/proteins/$1" }, "nucleotide": { "description": "The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.", "example": "880798137", "has_canonical": "insdc", "homepage": "https://www.ncbi.nlm.nih.gov/", "mappings": { "miriam": "nucleotide" }, "name": "Nucleotide", "pattern": "^[a-zA-Z0-9_\\.]+$", "preferred_prefix": "nucleotide", "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" }, "oa": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture.", "download_owl": "http://aber-owl.net/media/ontologies/OA/4/oa.owl", "example": "sourceDateStart", "homepage": "http://www.w3.org/ns/oa", "mappings": { "aberowl": "OA", "biocontext": "oa", "bioportal": "OA" }, "name": "Web Annotation Ontology", "preferred_prefix": "oa", "uri_format": "http://www.w3.org/ns/oa#$1" }, "oae": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqunh He", "orcid": "0000-0001-9189-9661" }, "description": "The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc.", "download_owl": "http://purl.obolibrary.org/obo/oae.owl", "example": "0002959", "homepage": "https://github.com/OAE-ontology/OAE/", "license": "CC BY 3.0", "mappings": { "aberowl": "OAE", "biocontext": "OAE", "bioportal": "OAE", "fairsharing": "FAIRsharing.tw4q8x", "obofoundry": "oae", "ols": "oae", "ontobee": "OAE" }, "name": "Ontology of Adverse Events", "pattern": "^\\d{7}$", "preferred_prefix": "OAE", "publications": [ { "doi": "10.1186/2041-1480-5-29", "pmc": "PMC4120740", "pubmed": "25093068", "title": "OAE: The Ontology of Adverse Events.", "year": 2014 } ], "repository": "https://github.com/OAE-ontology/OAE", "uri_format": "http://purl.obolibrary.org/obo/OAE_$1", "version": "1.2.44" }, "oarcs": { "contact": { "email": "mjyoder@illinois.edu", "github": "mjy", "name": "Matt Yoder", "orcid": "0000-0002-5640-5491" }, "description": "OArCS is an ontology describing the Arthropod ciruclatory system.", "download_owl": "http://purl.obolibrary.org/obo/oarcs.owl", "example": "0000029", "homepage": "https://github.com/aszool/oarcs", "license": "CC BY 3.0", "mappings": { "aberowl": "OARCS", "biocontext": "OARCS", "bioportal": "OARCS", "fairsharing": "FAIRsharing.yqn857", "obofoundry": "oarcs", "ols": "oarcs", "ontobee": "OARCS" }, "name": "Ontology of Arthropod Circulatory Systems", "pattern": "^\\d{7}$", "preferred_prefix": "OARCS", "publications": [ { "doi": "10.1093/sysbio/syw108", "pmc": null, "pubmed": null, "title": "The first organ-based free ontology for arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its integration into a novel formalization scheme for morphological descriptions", "year": null } ], "repository": "https://github.com/aszool/oarcs", "uri_format": "http://purl.obolibrary.org/obo/OARCS_$1", "version": "2019-04-18" }, "oba": { "appears_in": [ "fovt" ], "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO.", "download_json": "http://purl.obolibrary.org/obo/oba.json", "download_obo": "http://purl.obolibrary.org/obo/oba.obo", "download_owl": "http://purl.obolibrary.org/obo/oba.owl", "example": "0000001", "example_extras": [ "VT0003769" ], "homepage": "https://github.com/obophenotype/bio-attribute-ontology", "license": "CC0 1.0", "mappings": { "aberowl": "OBA", "biocontext": "OBA", "bioportal": "OBA", "fairsharing": "FAIRsharing.mp0rwf", "obofoundry": "oba", "ols": "oba", "ontobee": "OBA" }, "name": "Ontology of Biological Attributes", "pattern": "^(VT)?\\d{7}$", "preferred_prefix": "OBA", "repository": "https://github.com/obophenotype/bio-attribute-ontology", "uri_format": "http://purl.obolibrary.org/obo/OBA_$1", "version": "2022-08-03" }, "obcs": { "contact": { "email": "jiezheng@pennmedicine.upenn.edu", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "description": "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. ", "download_owl": "http://purl.obolibrary.org/obo/obcs.owl", "example": "0000121", "homepage": "https://github.com/obcs/obcs", "license": "CC BY 3.0", "mappings": { "aberowl": "OBCS", "biocontext": "OBCS", "bioportal": "OBCS", "fairsharing": "FAIRsharing.5p12xh", "obofoundry": "obcs", "ols": "obcs", "ontobee": "OBCS" }, "name": "Ontology of Biological and Clinical Statistics", "pattern": "^\\d{7}$", "preferred_prefix": "OBCS", "publications": [ { "doi": "10.1186/s13326-016-0100-2", "pmc": "PMC5024438", "pubmed": "27627881", "title": "The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.", "year": 2016 } ], "repository": "https://github.com/obcs/obcs", "uri_format": "http://purl.obolibrary.org/obo/OBCS_$1", "version": "101" }, "obi": { "appears_in": [ "agro", "foodon", "hso", "labo", "mco", "one", "ons", "proco", "rbo", "scdo" ], "banana": "OBI", "banana_peel": ":", "contact": { "email": "bpeters@lji.org", "github": "bpeters42", "name": "Bjoern Peters", "orcid": "0000-0002-8457-6693" }, "description": "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).", "download_obo": "https://github.com/obi-ontology/obi/raw/master/views/obi.obo", "download_owl": "http://purl.obolibrary.org/obo/obi.owl", "example": "0400109", "homepage": "http://obi-ontology.org", "license": "CC BY 4.0", "mappings": { "aberowl": "OBI", "biocontext": "OBI", "bioportal": "OBI", "fairsharing": "FAIRsharing.284e1z", "go": "OBI", "miriam": "obi", "n2t": "obi", "obofoundry": "obi", "ols": "obi", "ontobee": "OBI", "prefixcommons": "obi" }, "name": "Ontology for Biomedical Investigations", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "OBI", "publications": [ { "doi": "10.1371/journal.pone.0154556", "pmc": "PMC4851331", "pubmed": "27128319", "title": "The Ontology for Biomedical Investigations.", "year": 2016 }, { "doi": "10.1093/database/bau132", "pmc": "PMC4309925", "pubmed": "25632945", "title": "Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach.", "year": 2015 }, { "doi": "10.1186/2041-1480-4-s1-s6", "pmc": "PMC3633001", "pubmed": "23734660", "title": "Query enhancement through the practical application of ontology: the IEDB and OBI.", "year": 2013 }, { "doi": "10.4056/sigs.1994602", "pmc": "PMC3235517", "pubmed": "22180825", "title": "Minimum Information about a Genotyping Experiment (MIGEN).", "year": 2011 }, { "doi": "10.1186/2041-1480-1-s1-s7", "pmc": "PMC2903726", "pubmed": "20626927", "title": "Modeling biomedical experimental processes with OBI.", "year": 2010 } ], "repository": "https://github.com/obi-ontology/obi", "uri_format": "http://purl.obolibrary.org/obo/OBI_$1", "version": "2022-07-11" }, "obib": { "contact": { "email": "jiezheng@pennmedicine.upenn.edu", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "description": "The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology.", "download_owl": "http://purl.obolibrary.org/obo/obib.owl", "example": "0000389", "homepage": "https://github.com/biobanking/biobanking", "license": "CC BY 4.0", "mappings": { "aberowl": "OBIB", "biocontext": "OBIB", "bioportal": "OBIB", "fairsharing": "FAIRsharing.bxc508", "obofoundry": "obib", "ols": "obib", "ontobee": "OBIB" }, "name": "Ontology for Biobanking", "pattern": "^\\d{7}$", "preferred_prefix": "OBIB", "publications": [ { "doi": "10.1186/s13326-016-0068-y", "pmc": null, "pubmed": null, "title": "OBIB-a novel ontology for biobanking", "year": null } ], "repository": "https://github.com/biobanking/biobanking", "uri_format": "http://purl.obolibrary.org/obo/OBIB_$1", "version": "2021-11-12" }, "obo": { "description": "The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies.", "homepage": "http://www.obofoundry.org/", "mappings": { "biocontext": "OBO", "fairsharing": "FAIRsharing.847069" }, "name": "Open Biological and Biomedical Ontologies", "preferred_prefix": "obo", "uri_format": "http://purl.obolibrary.org/obo/$1" }, "oboinowl": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties", "download_obo": "https://github.com/geneontology/go-ontology/raw/master/contrib/oboInOwl.obo", "download_owl": "https://github.com/geneontology/go-ontology/raw/master/contrib/oboInOwl.owl", "example": "hasDbXref", "homepage": "https://github.com/geneontology/go-ontology/tree/master/contrib", "mappings": { "biocontext": "oboInOwl", "biolink": "oboformat" }, "name": "OBO in OWL", "preferred_prefix": "oboInOwl", "repository": "https://github.com/geneontology/go-ontology", "synonyms": [ "oboformat", "oio" ], "uri_format": "http://www.geneontology.org/formats/oboInOwl#$1" }, "occ": { "description": "The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law.", "example": "br/1", "homepage": "https://w3id.org/oc/corpus", "mappings": { "miriam": "occ", "n2t": "occ" }, "name": "OpenCitations Corpus", "pattern": "^[a-z][a-z]/[0-9]+$", "preferred_prefix": "occ", "uri_format": "https://w3id.org/oc/corpus/$1" }, "oci": { "description": "Each OCI (Open Citation Identifier) has a simple structure: oci:number-number, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/ for additional information.\r\n\r\nOCIs for citations stored within the OpenCitations Corpus are constructed by combining the OpenCitations Corpus local identifiers for the citing and cited bibliographic resources, separating them with a dash. For example, oci:2544384-7295288 is a valid OCI for the citation between two papers stored within the OpenCitations Corpus.\r\n\r\nOCIs can also be created for bibliographic resources described in an external bibliographic database, if they are similarly identified there by identifiers having a unique numerical part. For example, the OCI for the citation that exists between Wikidata resources Q27931310 and Q22252312 is oci:01027931310–01022252312.\r\n\r\nOCIs can also be created for bibliographic resources described in external bibliographic database such as Crossref or DataCite where they are identified by alphanumeric Digital Object Identifiers (DOIs), rather than purely numerical strings.", "example": "1-18", "homepage": "http://opencitations.net", "mappings": { "biocontext": "OCI", "miriam": "oci", "n2t": "oci" }, "name": "Open Citation Identifier", "pattern": "^[0-9]+-[0-9]+$", "preferred_prefix": "oci", "uri_format": "https://w3id.org/oc/oci/$1" }, "ocid": { "banana": "ocid", "description": "'ocid' stands for \"Ontology Concept Identifiers\" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology.", "example": "190000021540", "homepage": "https://ontochem.com/", "mappings": { "miriam": "ocid" }, "name": "Ontology Concept Identifiers", "namespace_in_lui": true, "pattern": "^[0-9]{12}$", "preferred_prefix": "ocid", "uri_format": "https://ocid.ontochem.com/prefname?ocid=$1" }, "oclc": { "description": "The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information.", "example": "634515043", "homepage": "https://www.oclc.org/en/about.html", "mappings": { "biocontext": "OCLC", "miriam": "oclc", "n2t": "oclc" }, "name": "Online Computer Library Center WorldCat", "pattern": "^[0-9]+$", "preferred_prefix": "oclc", "uri_format": "https://www.worldcat.org/oclc/$1" }, "odam": { "description": "Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed.", "example": "frim1", "homepage": "https://metabolome.cgfb.u-bordeaux.fr/", "mappings": { "miriam": "odam" }, "name": "Open Data for Access and Mining", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "odam", "uri_format": "http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1" }, "odc.sci": { "description": "The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data.", "example": "602", "homepage": "https://odc-sci.org", "mappings": { "fairsharing": "FAIRsharing.M6Ruz3", "miriam": "odc.sci" }, "name": "Open Data Commons for Spinal Cord Injury", "pattern": "^[0-9]*$", "preferred_prefix": "odc.sci", "uri_format": "https://odc-sci.org/data/$1" }, "odc.tbi": { "description": "The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data.", "example": "408", "homepage": "https://odc-tbi.org", "mappings": { "miriam": "odc.tbi" }, "name": "Open Data Commons for Traumatic Brain Injury", "pattern": "^[0-9]*$", "preferred_prefix": "odc.tbi", "uri_format": "https://odc-tbi.org/data/$1" }, "odor": { "description": "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors", "example": "74", "homepage": "http://senselab.med.yale.edu/OdorDB", "mappings": { "biocontext": "ODOR", "miriam": "odor", "n2t": "odor" }, "name": "Odor Molecules DataBase", "pattern": "^\\d+$", "preferred_prefix": "odor", "uri_format": "http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5" }, "ogg": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "description": "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. ", "download_owl": "http://purl.obolibrary.org/obo/ogg.owl", "example": "3000887619", "homepage": "https://bitbucket.org/hegroup/ogg", "license": "CC BY 3.0", "mappings": { "aberowl": "OGG", "biocontext": "OGG", "bioportal": "OGG", "fairsharing": "FAIRsharing.zmx7nn", "obofoundry": "ogg", "ols": "ogg", "ontobee": "OGG" }, "name": "The Ontology of Genes and Genomes", "pattern": "^\\d+$", "preferred_prefix": "OGG", "repository": "https://bitbucket.org/hegroup/ogg", "uri_format": "http://purl.obolibrary.org/obo/OGG_$1", "version": "1.0.59" }, "ogi": { "contact": { "email": "linikujp@gmail.com", "github": "linikujp", "name": "Asiyah Yu Lin", "orcid": "0000-0002-5379-5359" }, "deprecated": true, "description": "OGI formalized the genomic element by defining an upper class 'genetic interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\nYu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI) to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n", "download_owl": "http://purl.obolibrary.org/obo/ogi.owl", "example": "0000019", "homepage": "https://code.google.com/archive/p/ontology-for-genetic-interval/", "mappings": { "aberowl": "OGI", "biocontext": "OGI", "bioportal": "OGI", "obofoundry": "ogi", "ols": "ogi", "ontobee": "OGI" }, "name": "Ontology for genetic interval", "pattern": "^\\d{7}$", "preferred_prefix": "OGI", "synonyms": [ "OGI.owl" ], "uri_format": "http://purl.obolibrary.org/obo/OGI_$1", "version": "2.0" }, "ogms": { "appears_in": [ "labo", "scdo" ], "contact": { "email": "baeverma@jcvi.org", "github": "BAevermann", "name": "Brian Aevermann", "orcid": "0000-0003-1346-1327" }, "description": "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats.\n\nOGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.", "download_obo": "http://purl.obolibrary.org/obo/ogms.obo", "download_owl": "http://purl.obolibrary.org/obo/ogms.owl", "example": "0000031", "homepage": "https://github.com/OGMS/ogms", "license": "CC BY 4.0", "mappings": { "aberowl": "OGMS", "biocontext": "OGMS", "bioportal": "OGMS", "fairsharing": "FAIRsharing.rvz0m9", "obofoundry": "ogms", "ols": "ogms", "ontobee": "OGMS" }, "name": "Ontology for General Medical Science", "pattern": "^\\d{7}$", "preferred_prefix": "OGMS", "publications": [ { "doi": "10.1186/2041-1480-4-42", "pmc": "PMC4028878", "pubmed": "24314207", "title": "The neurological disease ontology.", "year": 2013 } ], "repository": "https://github.com/OGMS/ogms", "synonyms": [ "ogms/OMRE" ], "uri_format": "http://purl.obolibrary.org/obo/OGMS_$1", "version": "2021-08-19" }, "ogsf": { "contact": { "email": "linikujp@gmail.com", "github": "linikujp", "name": "Asiyah Yu Lin", "orcid": "0000-0002-5379-5359" }, "description": "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.", "download_owl": "http://purl.obolibrary.org/obo/ogsf.owl", "example": "0000025", "homepage": "https://github.com/linikujp/OGSF", "license": "CC BY 3.0", "mappings": { "aberowl": "OGSF", "biocontext": "OGSF", "bioportal": "OGSF", "fairsharing": "FAIRsharing.egv2cz", "obofoundry": "ogsf", "ols": "ogsf", "ontobee": "OGSF" }, "name": "Ontology of Genetic Susceptibility Factor", "pattern": "^\\d{7}$", "preferred_prefix": "OGSF", "publications": [ { "doi": "10.1186/2041-1480-5-19", "pmc": "PMC4068904", "pubmed": "24963371", "title": "The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events.", "year": 2014 }, { "doi": null, "pmc": null, "pubmed": "20847592", "title": "Ontology driven modeling for the knowledge of genetic susceptibility to disease.", "year": 2009 } ], "repository": "https://github.com/linikujp/OGSF", "uri_format": "http://purl.obolibrary.org/obo/OGSF_$1", "version": "2.0" }, "ohd": { "contact": { "email": "wdduncan@gmail.com", "github": "wdduncan", "name": "Bill Duncan", "orcid": "0000-0001-9625-1899" }, "description": "The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records.", "download_owl": "http://purl.obolibrary.org/obo/ohd.owl", "example": "0000006", "homepage": "https://purl.obolibrary.org/obo/ohd/home", "license": "CC BY 4.0", "mappings": { "aberowl": "OHD", "biocontext": "OHD", "bioportal": "OHD", "fairsharing": "FAIRsharing.bg7bb6", "obofoundry": "ohd", "ols": "ohd", "ontobee": "OHD" }, "name": "Oral Health and Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "OHD", "publications": [ { "doi": null, "pmc": null, "pubmed": "32819435", "title": "Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology", "year": null } ], "repository": "https://github.com/oral-health-and-disease-ontologies/ohd-ontology", "uri_format": "http://purl.obolibrary.org/obo/OHD_$1", "version": "2016-06-27" }, "ohmi": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "description": "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.", "download_owl": "http://purl.obolibrary.org/obo/ohmi.owl", "example": "0000460", "homepage": "https://github.com/ohmi-ontology/ohmi", "license": "CC BY 4.0", "mappings": { "aberowl": "OHMI", "biocontext": "OHMI", "bioportal": "OHMI", "fairsharing": "FAIRsharing.cz9cnp", "obofoundry": "ohmi", "ols": "ohmi", "ontobee": "OHMI" }, "name": "Ontology of Host-Microbiome Interactions", "pattern": "^\\d{7}$", "preferred_prefix": "OHMI", "repository": "https://github.com/ohmi-ontology/ohmi", "uri_format": "http://purl.obolibrary.org/obo/OHMI_$1", "version": "2019-09-17" }, "ohpi": { "contact": { "email": "edong@umich.edu", "github": "e4ong1031", "name": "Edison Ong", "orcid": "0000-0002-5159-414X" }, "description": "OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration).", "download_owl": "http://purl.obolibrary.org/obo/ohpi.owl", "example": "9001411", "homepage": "https://github.com/OHPI/ohpi", "license": "CC BY 4.0", "mappings": { "aberowl": "OHPI", "bioportal": "OHPI", "fairsharing": "FAIRsharing.vxpUJ6", "obofoundry": "ohpi", "ols": "ohpi", "ontobee": "OHPI" }, "name": "Ontology of Host Pathogen Interactions", "pattern": "^\\d+$", "preferred_prefix": "OHPI", "publications": [ { "doi": "10.1093/nar/gky999", "pmc": "PMC6324020", "pubmed": "30365026", "title": "Victors: a web-based knowledge base of virulence factors in human and animal pathogens.", "year": 2019 } ], "repository": "https://github.com/OHPI/ohpi", "uri_format": "http://purl.obolibrary.org/obo/OHPI_$1", "version": "2019-10-02" }, "oid": { "contributor_extras": [ { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } ], "description": "OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes.", "example": "2.16.840", "example_extras": [ "2", "2.16", "2.16.840.1", "2.16.840.1.113883", "2.16.840.1.113883.6", "2.16.840.1.113883.6.88" ], "homepage": "http://www.oid-info.com/introduction.htm", "mappings": { "miriam": "oid", "n2t": "oid" }, "name": "ISO Object Identifier", "pattern": "^[\\d.]+$", "preferred_prefix": "oid", "providers": [ { "code": "orange", "description": "Mirror of OID site from Orange", "homepage": "https://oid-rep.orange-labs.fr", "name": "Mirror of OID site from Orange", "uri_format": "https://oid-rep.orange-labs.fr/get/$1" } ], "references": [ "https://en.wikipedia.org/wiki/Object_identifier" ], "uri_format": "http://oid-info.com/get/$1" }, "olatdv": { "contact": { "email": "frederic.bastian@unil.ch", "github": "fbastian", "name": "Frédéric Bastian", "orcid": "0000-0002-9415-5104" }, "description": "Life cycle stages for Medaka", "download_obo": "http://purl.obolibrary.org/obo/olatdv.obo", "download_owl": "http://purl.obolibrary.org/obo/olatdv.owl", "example": "0000210", "homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv", "license": "CC BY 3.0", "mappings": { "aberowl": "OLATDV", "biocontext": "OLATDV", "bioportal": "OLATDV", "fairsharing": "FAIRsharing.c86z66", "obofoundry": "olatdv", "ols": "olatdv", "ontobee": "OLATDV" }, "name": "Medaka Developmental Stages", "pattern": "^\\d{7}$", "preferred_prefix": "OlatDv", "repository": "https://github.com/obophenotype/developmental-stage-ontologies", "uri_format": "http://purl.obolibrary.org/obo/OLATDV_$1", "version": "2020-03-10" }, "om": { "contact": { "email": "hajo.rijgersberg@wur.nl", "github": null, "name": "Hajo Rijgersberg", "orcid": null }, "description": "The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units meter and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant: km/s/Mpc, or the quantity vaselife. OM defines the complete set of concepts in the domain as distinguished in the textual standards. As a result the ontology can answer a wider range of competency questions than the existing approaches do. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology; Typography; Shipping; Food engineering; Post-harvest; technology; Dynamics of texture and taste; Packaging", "download_owl": "https://raw.githubusercontent.com/HajoRijgersberg/OM/master/om-2.0.rdf", "example": "Dimension", "homepage": "https://github.com/HajoRijgersberg/OM", "mappings": { "aberowl": "OM", "agroportal": "OM", "bioportal": "OM", "ols": "om" }, "name": "Ontology of units of Measure", "preferred_prefix": "om", "repository": "https://github.com/HajoRijgersberg/OM", "uri_format": "http://www.ontology-of-units-of-measure.org/resource/om-2/$1", "version": "2.0.38" }, "oma.grp": { "description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs.", "example": "LCSCCPN", "homepage": "https://omabrowser.org/cgi-bin/gateway.pl", "mappings": { "biocontext": "OMA.GRP", "miriam": "oma.grp", "n2t": "oma.grp" }, "name": "OMA Group", "pattern": "^[A-Z]+$", "preferred_prefix": "oma.grp", "uri_format": "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1" }, "oma.hog": { "banana": "HOG", "description": "Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. ", "example": "0459895", "homepage": "https://omabrowser.org", "mappings": { "miriam": "oma.hog" }, "name": "OMA HOGs", "namespace_in_lui": true, "pattern": "^[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$", "preferred_prefix": "oma.hog", "uri_format": "https://omabrowser.org/oma/hog/HOG:$1" }, "oma.protein": { "description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records.", "example": "HUMAN16963", "homepage": "https://omabrowser.org/cgi-bin/gateway.pl", "mappings": { "biocontext": "OMA.PROTEIN", "miriam": "oma.protein", "n2t": "oma.protein" }, "name": "OMA Protein", "pattern": "^[A-Z0-9]{5}\\d+$", "preferred_prefix": "oma.protein", "uri_format": "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1" }, "omia": { "comment": "website is down as of 2021-10-04", "deprecated": true, "description": "Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse).", "example": "1000", "homepage": "http://omia.angis.org.au/", "mappings": { "biocontext": "OMIA", "miriam": "omia", "n2t": "omia", "prefixcommons": "omia" }, "name": "Online Mendelian Inheritance in Animals", "pattern": "^\\d+$", "preferred_prefix": "omia", "uri_format": "http://omia.angis.org.au/$1/" }, "omiabis": { "appears_in": [ "labo" ], "contact": { "email": "mbrochhausen@gmail.com", "github": null, "name": "Mathias Brochhausen", "orcid": "0000-0003-1834-3856" }, "deprecated": true, "description": "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)", "download_owl": "http://purl.obolibrary.org/obo/omiabis.owl", "example": "0001079", "homepage": "https://github.com/OMIABIS/omiabis-dev", "license": "CC BY 3.0", "mappings": { "aberowl": "OMIABIS", "biocontext": "OMIABIS", "bioportal": "OMIABIS", "obofoundry": "omiabis", "ols": "omiabis", "ontobee": "OMIABIS" }, "name": "Ontologized MIABIS", "pattern": "^\\d{7}$", "preferred_prefix": "OMIABIS", "repository": "https://github.com/OMIABIS/omiabis-dev", "uri_format": "http://purl.obolibrary.org/obo/OMIABIS_$1", "version": "2014-05-28" }, "omim": { "contact": { "email": "ahamosh@jhmi.edu", "github": "ahamosh", "name": "Ada Hamosh", "orcid": "0000-0002-1780-5230" }, "description": "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.", "example": "603903", "homepage": "https://omim.org/", "mappings": { "aberowl": "OMIM", "biocontext": "OMIM", "bioportal": "OMIM", "edam": "1153", "fairsharing": "FAIRsharing.b084yh", "go": "OMIM", "hl7": "2.16.840.1.113883.6.174", "miriam": "mim", "n2t": "mim", "ncbi": "MIM", "prefixcommons": "omim", "uniprot": "MIM", "wikidata": "P492" }, "name": "Online Mendelian Inheritance in Man", "pattern": "^\\d+$", "preferred_prefix": "omim", "providers": [ { "code": "CURATOR_REVIEW", "description": "OMIM mirror at John Hopkins", "homepage": "http://mirror.omim.org/", "name": "OMIM mirror at John Hopkins", "uri_format": "http://mirror.omim.org/entry/$1" } ], "publications": [ { "doi": "10.1093/nar/gku1205", "pmc": null, "pubmed": "25428349", "title": "OMIM.org: Online Mendelian Inheritance in Man (OMIM(R)), an online catalog of human genes and genetic disorders.", "year": null }, { "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 } ], "synonyms": [ "OMIM", "mim" ], "uri_format": "https://omim.org/entry/$1" }, "omim.ps": { "contact": { "email": "ahamosh@jhmi.edu", "github": "ahamosh", "name": "Ada Hamosh", "orcid": "0000-0002-1780-5230" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": null, "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" } ], "description": "A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.", "example": "PS214100", "homepage": "https://www.omim.org/phenotypicSeriesTitles/all", "mappings": { "biolink": "OMIM.PS" }, "name": "OMIM Phenotypic Series", "part_of": "omim", "pattern": "^PS\\d+$", "preferred_prefix": "omim.ps", "synonyms": [ "MIMPS", "OMIMPS", "PS", "mim.ps" ], "uri_format": "https://omim.org/phenotypicSeries/$1" }, "omit": { "appears_in": [ "mco" ], "contact": { "email": "huang@southalabama.edu", "github": "Huang-OMIT", "name": "Jingshan Huang", "orcid": "0000-0003-2408-2883" }, "description": "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes).", "download_obo": "https://raw.githubusercontent.com/OmniSearch/omit/master/src/ontology/omit.obo", "download_owl": "http://purl.obolibrary.org/obo/omit.owl", "example": "0000069", "homepage": "http://omit.cis.usouthal.edu/", "license": "CC BY 3.0", "mappings": { "aberowl": "OMIT", "biocontext": "OMIT", "bioportal": "OMIT", "fairsharing": "FAIRsharing.mf91p5", "miriam": "omit", "n2t": "omit", "obofoundry": "omit", "ols": "omit", "ontobee": "OMIT" }, "name": "Ontology for MicroRNA Target", "pattern": "^\\d{7}$", "preferred_prefix": "OMIT", "publications": [ { "doi": "10.1186/s13326-016-0064-2", "pmc": "PMC4863347", "pubmed": "27175225", "title": "OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.", "year": 2016 }, { "doi": "10.1371/journal.pone.0100855", "pmc": "PMC4099014", "pubmed": "25025130", "title": "OMIT: dynamic, semi-automated ontology development for the microRNA domain.", "year": 2014 }, { "doi": "10.1007/s11095-011-0573-8", "pmc": null, "pubmed": "21879385", "title": "OMIT: a domain-specific knowledge base for microRNA target prediction.", "year": 2011 } ], "repository": "https://github.com/OmniSearch/omit", "synonyms": [ "OMIT" ], "uri_format": "https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$1", "version": "2019-06-07" }, "omo": { "appears_in": [ "pcl" ], "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO).", "download_owl": "http://purl.obolibrary.org/obo/omo.owl", "homepage": "https://github.com/information-artifact-ontology/ontology-metadata", "license": "CC0 1.0", "mappings": { "aberowl": "OMO", "bioportal": "OMO", "obofoundry": "omo", "ols": "omo", "ontobee": "OMO" }, "name": "OBO Metadata Ontology", "no_own_terms": true, "preferred_prefix": "OMO", "repository": "https://github.com/information-artifact-ontology/ontology-metadata", "uri_format": "http://purl.obolibrary.org/obo/OMO_$1", "version": "2022-04-27" }, "omop": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "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.", "homepage": "https://www.ohdsi.org/data-standardization/the-common-data-model/", "name": "Observational Medical Outcomes Partnership", "no_own_terms": true, "preferred_prefix": "omop", "references": [ "https://github.com/callahantiff/OMOP2OBO" ] }, "omp": { "appears_in": [ "mco" ], "contact": { "email": "jimhu@tamu.edu", "github": "jimhu-tamu", "name": "James C. 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developments.", "year": 2016 } ], "repository": "https://github.com/ufbmi/OMRSE", "uri_format": "http://purl.obolibrary.org/obo/OMRSE_$1", "version": "2022-04-06" }, "oncotree": { "appears_in": [ "efo" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research.", "example": "BLL", "homepage": "http://oncotree.mskcc.org", "name": "OncoTree", "preferred_prefix": "oncotree", "uri_format": "http://oncotree.mskcc.org/api/tumorTypes/search/code/$1" }, "one": { "contact": { "email": "chenyangnutrition@gmail.com", "github": "cyang0128", "name": "Chen Yang", "orcid": "0000-0001-9202-5309" }, "depends_on": [ "foodon", "obi", "ons" ], "description": "An ontology to standardize research output of nutritional epidemiologic studies.", "download_owl": "http://purl.obolibrary.org/obo/one.owl", "example": "0001021", "homepage": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies", "license": "CC BY 4.0", "mappings": { "aberowl": "ONE", "bioportal": "ONE", "fairsharing": "FAIRsharing.USxx0K", "obofoundry": "one", "ols": "one", "ontobee": "ONE" }, "name": "Ontology for Nutritional Epidemiology", "pattern": "^\\d{7}$", "preferred_prefix": "ONE", "publications": [ { "doi": "e1300", "pmc": "PMC6628051", "pubmed": "31181762", "title": "An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content.", "year": null }, { "doi": "10.3390/nu11061300", "pmc": "PMC6628051", "pubmed": "31181762", "title": "An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content.", "year": 2019 } ], "repository": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies", "uri_format": "http://purl.obolibrary.org/obo/ONE_$1" }, "ons": { "appears_in": [ "one" ], "contact": { "email": "francesco.vitali@ibba.cnr.it", "github": "FrancescoVit", "name": "Francesco Vitali", "orcid": "0000-0001-9125-4337" }, "depends_on": [ "bfo", "chebi", "envo", "foodon", "ncbitaxon", "obi", "ro", "uberon" ], "description": "The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies.", "download_owl": "http://purl.obolibrary.org/obo/ons.owl", "example": "0000060", "homepage": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies", "license": "CC BY 4.0", "mappings": { "aberowl": "ONS", "bioportal": "ONS", "fairsharing": "FAIRsharing.rfec93", "obofoundry": "ons", "ols": "ons", "ontobee": "ONS" }, "name": "Ontology for Nutritional Studies", "pattern": "^\\d{7}$", "preferred_prefix": "ONS", "publications": [ { "doi": "10.1186/s12263-018-0601-y", "pmc": "PMC5928560", "pubmed": "29736190", "title": "ONS: an ontology for a standardized description of interventions and observational studies in nutrition.", "year": 2018 } ], "repository": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies", "uri_format": "http://purl.obolibrary.org/obo/ONS_$1", "version": "Release version 1.2.3" }, "ontoavida": { "contact": { "email": "fortuna@ebd.csic.es", "github": "miguelfortuna", "name": "Miguel A. Fortuna", "orcid": "0000-0002-8374-1941" }, "depends_on": [ "fbcv", "gsso", "ncit", "ro", "stato" ], "description": "The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of the most widely used computational approach for performing experimental evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment).\n\nThe lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight.\n\nOntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA).\n\nMore information can be found at https://obofoundry.org/ontology/ontoavida.html", "download_obo": "http://purl.obolibrary.org/obo/ontoavida.obo", "download_owl": "http://purl.obolibrary.org/obo/ontoavida.owl", "example": "00000001", "homepage": "https://gitlab.com/fortunalab/ontoavida", "license": "CC BY 4.0", "mappings": { "aberowl": "ONTOAVIDA", "bioportal": "ONTOAVIDA", "obofoundry": "ontoavida", "ols": "ontoavida", "ontobee": "ONTOAVIDA" }, "name": "Ontology for Avida digital evolution platform", "pattern": "^\\d{8}$", "preferred_prefix": "ONTOAVIDA", "repository": "https://gitlab.com/fortunalab/ontoavida", "uri_format": "http://purl.obolibrary.org/obo/ONTOAVIDA_$1", "version": "2022-03-15" }, "ontoneo": { "contact": { "email": "fernanda.farinelli@gmail.com", "github": "FernandaFarinelli", "name": "Fernanda Farinelli", "orcid": "0000-0003-2338-8872" }, "description": "The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby.", "download_owl": "http://purl.obolibrary.org/obo/ontoneo.owl", "example": "00000098", "homepage": "http://ontoneo.com", "license": "CC BY 3.0", "mappings": { "aberowl": "ONTONEO", "biocontext": "ONTONEO", "bioportal": "ONTONEO", "fairsharing": "FAIRsharing.5a4y1y", "obofoundry": "ontoneo", "ols": "ontoneo", "ontobee": "ONTONEO" }, "name": "Obstetric and Neonatal Ontology", "pattern": "^\\d{8}$", "preferred_prefix": "ONTONEO", "repository": "https://github.com/ontoneo-project/Ontoneo", "uri_format": "http://purl.obolibrary.org/obo/ONTONEO_$1", "version": "v1.6" }, "oostt": { "contact": { "email": "mbrochhausen@gmail.com", "github": "mbrochhausen", "name": "Mathias Brochhausen", "orcid": "0000-0003-1834-3856" }, "description": "An ontology built for representating the organizational components of trauma centers and trauma systems.", "download_owl": "http://purl.obolibrary.org/obo/oostt.owl", "example": "00000099", "homepage": "https://github.com/OOSTT/OOSTT", "license": "CC BY 4.0", "mappings": { "aberowl": "OOSTT", "biocontext": "OOSTT", "bioportal": "OOSTT", "fairsharing": "FAIRsharing.b4sa0w", "obofoundry": "oostt", "ols": "oostt", "ontobee": "OOSTT" }, "name": "Ontology of Organizational Structures of Trauma centers and Trauma systems", "pattern": "^\\d{8}$", "preferred_prefix": "OOSTT", "repository": "https://github.com/OOSTT/OOSTT", "uri_format": "http://purl.obolibrary.org/obo/OOSTT_$1", "version": "2021-01-11" }, "opb": { "banana": "OPB", "banana_peel": "_", "contact": { "email": "maxneal@gmail.com", "github": null, "name": "Max Neal", "orcid": null }, "description": "The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.", "download_owl": "http://aber-owl.net/media/ontologies/OPB/13/opb.owl", "example": "00573", "homepage": "http://bioportal.bioontology.org/ontologies/OPB", "mappings": { "aberowl": "OPB", "biocontext": "OPB", "bioportal": "OPB", "fairsharing": "FAIRsharing.qcceez", "miriam": "opb", "n2t": "opb", "prefixcommons": "opb" }, "name": "Ontology of Physics for Biology", "pattern": "^\\d+$", "preferred_prefix": "opb", "publications": [ { "doi": "10.1186/2041-1480-4-41", "pmc": "PMC3904761", "pubmed": "24295137", "title": "Ontology of physics for biology: representing physical dependencies as a basis for biological processes.", "year": 2013 }, { "doi": "10.1371/journal.pone.0028708", "pmc": "PMC3246444", "pubmed": "22216106", "title": "Physical properties of biological entities: an introduction to the ontology of physics for biology.", "year": 2011 } ], "uri_format": "http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1" }, "openalex": { "contact": { "email": "hpiwowar@gmail.com", "github": "hpiwowar", "name": "Heather Piwowar", "orcid": "0000-0003-1613-5981" }, "contributor": { "email": null, "github": "dhimmel", "name": "Daniel Himmelstein", "orcid": "0000-0002-3012-7446" }, "description": "OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other.", "example": "W2741809807", "github_request_issue": 280, "homepage": "https://openalex.org/", "name": "OpenAlex", "pattern": "^[WAICV]\\d{2,}$", "preferred_prefix": "openalex", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://openalex.org/$1" }, "opl": { "contact": { "email": "jiezheng@pennmedicine.upenn.edu", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "description": "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.", "download_owl": "http://purl.obolibrary.org/obo/opl.owl", "example": "0000319", "homepage": "https://github.com/OPL-ontology/OPL", "license": "CC BY 4.0", "mappings": { "aberowl": "OPL", "biocontext": "OPL", "bioportal": "OPL", "fairsharing": "FAIRsharing.ez2nhb", "obofoundry": "opl", "ols": "opl", "ontobee": "OPL" }, "name": "Ontology for Parasite LifeCycle", "pattern": "^\\d{7}$", "preferred_prefix": "OPL", "publications": [ { "doi": "10.1186/2041-1480-3-5", "pmc": "PMC3488002", "pubmed": "22621763", "title": "The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms.", "year": 2012 } ], "repository": "https://github.com/OPL-ontology/OPL", "uri_format": "http://purl.obolibrary.org/obo/OPL_$1", "version": "2021-01-28" }, "opm": { "description": "The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization.", "example": "1h68", "homepage": "http://opm.phar.umich.edu/", "mappings": { "biocontext": "OPM", "fairsharing": "FAIRsharing.7c683b", "miriam": "opm", "n2t": "opm" }, "name": "Orientations of Proteins in Membranes Database", "pattern": "^[0-9][A-Za-z0-9]{3}$", "preferred_prefix": "opm", "uri_format": "http://opm.phar.umich.edu/protein.php?pdbid=$1" }, "opmi": { "appears_in": [ "labo", "scdo" ], "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "description": "OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles.", "download_owl": "http://purl.obolibrary.org/obo/opmi.owl", "example": "0000101", "homepage": "https://github.com/OPMI/opmi", "license": "CC BY 4.0", "mappings": { "aberowl": "OPMI", "bioportal": "OPMI", "obofoundry": "opmi", "ols": "opmi", "ontobee": "OPMI" }, "name": "Ontology of Precision Medicine and Investigation", "pattern": "^\\d{7}$", "preferred_prefix": "OPMI", "repository": "https://github.com/OPMI/opmi", "uri_format": "http://purl.obolibrary.org/obo/OPMI_$1", "version": "1.0.158" }, "orcid": { "description": "ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities.", "example": "0000-0002-5355-2576", "homepage": "https://orcid.org", "mappings": { "biocontext": "ORCID", "biolink": "ORCID", "miriam": "orcid", "n2t": "orcid", "wikidata": "P496" }, "name": "Open Researcher and Contributor", "pattern": "^\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$", "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" } ], "synonyms": [ "ORCID", "ORCiD" ], "uri_format": "https://orcid.org/$1" }, "ordb": { "description": "The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs).", "example": "8497", "homepage": "http://senselab.med.yale.edu/OrDB/", "mappings": { "biocontext": "ORDB", "fairsharing": "FAIRsharing.6375zh", "miriam": "ordb", "n2t": "ordb", "prefixcommons": "ordb" }, "name": "Olfactory Receptor Database", "pattern": "^\\d+$", "preferred_prefix": "ordb", "uri_format": "http://senselab.med.yale.edu/ORDB/Data/$1" }, "oridb.sacch": { "description": "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae.", "example": "1", "homepage": "http://cerevisiae.oridb.org/index.php", "mappings": { "biocontext": "ORIDB.SACCH", "miriam": "oridb.sacch", "n2t": "oridb.sacch" }, "name": "OriDB Saccharomyces", "pattern": "^\\d+$", "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=$1" }, "ornaseq": { "contact": { "email": "safisher@upenn.edu", "github": "safisher", "name": "Stephen Fisher", "orcid": "0000-0001-8034-7685" }, "description": "An application ontology designed to annotate next-generation sequencing experiments performed on RNA.", "download_obo": "http://purl.obolibrary.org/obo/ornaseq.obo", "download_owl": "http://purl.obolibrary.org/obo/ornaseq.owl", "example": "0000010", "homepage": "http://kim.bio.upenn.edu/software/ornaseq.shtml", "license": "CC BY 4.0", "mappings": { "aberowl": "ORNASEQ", "bioportal": "ORNASEQ", "obofoundry": "ornaseq", "ols": "ornaseq", "ontobee": "ORNASEQ" }, "name": "Ontology of RNA Sequencing", "pattern": "^\\d{7}$", "preferred_prefix": "ORNASEQ", "repository": "https://github.com/safisher/ornaseq", "uri_format": "http://purl.obolibrary.org/obo/ORNASEQ_$1", "version": "2019-07-08" }, "orphanet": { "description": "Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases.", "example": "85163", "homepage": "http://www.orpha.net/consor/", "mappings": { "biocontext": "Orphanet", "fairsharing": "FAIRsharing.6bd5k6", "miriam": "orphanet", "n2t": "orphanet", "prefixcommons": "orphanet", "uniprot": "Orphanet", "wikidata": "P1550" }, "name": "Orphanet", "pattern": "^\\d+$", "preferred_prefix": "orphanet", "providers": [ { "code": "CURATOR_REVIEW", "description": "Bio2RDF", "homepage": "http://orphanet.bio2rdf.org/fct", "name": "Bio2RDF", "uri_format": "http://orphanet.bio2rdf.org/describe/?url=http://bio2rdf.org/orphanet:$1" } ], "publications": [ { "doi": null, "pmc": null, "pubmed": "19058507", "title": "[Orphanet and the Dutch Steering Committee Orphan Drugs. A European and Dutch databank of information on rare diseases].", "year": 2008 } ], "synonyms": [ "ORPHA" ], "uri_format": "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1" }, "orphanet.ordo": { "banana": "Orphanet", "banana_peel": "_", "contact": { "email": "ordo.orphanet@inserm.fr", "github": null, "name": "Ana Rath", "orcid": null }, "description": "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.\r\nIt integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).", "download_owl": "http://www.orphadata.org/data/ORDO/ordo_orphanet.owl", "example": "C023", "example_extras": [ "478" ], "homepage": "https://www.ebi.ac.uk/ols/ontologies/ordo", "mappings": { "aberowl": "ordo", "biocontext": "ORPHANET.ORDO", "biolink": "ORPHA", "bioportal": "ORDO", "cellosaurus": "ORDO", "fairsharing": "FAIRsharing.pbbnwa", "miriam": "orphanet.ordo", "n2t": "orphanet.ordo", "ols": "ordo" }, "name": "Orphanet Rare Disease Ontology", "pattern": "^C?\\d+$", "preferred_prefix": "orphanet.ordo", "publications": [ { "doi": null, "pmc": null, "pubmed": "22874158", "title": "Rare diseases knowledge management: the contribution of proximity measurements in OntoOrpha and OMIM.", "year": 2012 } ], "synonyms": [ "ordo" ], "uri_format": "http://www.orpha.net/ORDO/Orphanet_$1", "version": "4.1" }, "orth": { "contact": { "email": "jfernand@um.es", "github": "jesualdotomasfernandezbreis", "name": "Jesualdo Tomás Fernández-Breis", "orcid": "0000-0002-7558-2880" }, "description": "The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way.", "download_owl": "https://github.com/qfo/OrthologyOntology/raw/master/orthOntology_RC_v2_A.owl", "example": "HomologyRelation", "homepage": "https://github.com/qfo/OrthologyOntology", "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": null, "pubmed": null, "title": "The Orthology Ontology: development and applications", "year": null } ], "repository": "https://github.com/qfo/OrthologyOntology", "uri_format": "http://purl.org/net/orth#$1", "version": "This ontology is the second version of the orthology ontology first published in 2015 and available at http://purl.bioontology.org/ontology/ORTH .\n@authors T.M. de Farias, H. Chiba, J.T. Fernandez-Breis, E. Antezana, D. Kuznetsov, C. Dessimoz and F. Villiers." }, "orthodb": { "description": "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups", "example": "Q9P0K8", "homepage": "https://www.orthodb.org", "mappings": { "biocontext": "ORTHODB", "fairsharing": "FAIRsharing.x989d5", "miriam": "orthodb", "n2t": "orthodb", "prefixcommons": "orthodb", "uniprot": "OrthoDB" }, "name": "OrthoDB", "pattern": "^\\w+$", "preferred_prefix": "orthodb", "provides": "uniprot", "publications": [ { "doi": "10.1093/nar/gkq930", "pmc": "PMC3013786", "pubmed": "20972218", "title": "OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011.", "year": 2010 } ], "uri_format": "http://cegg.unige.ch/orthodb/results?searchtext=$1" }, "oryzabase.gene": { "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information.", "example": "117", "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", "mappings": { "biocontext": "ORYZABASE.GENE", "miriam": "oryzabase.gene", "n2t": "oryzabase.gene" }, "name": "Oryzabase Gene", "pattern": "^\\d+$", "preferred_prefix": "oryzabase.gene", "uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1" }, "oryzabase.mutant": { "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information.", "example": "21393", "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", "mappings": { "biocontext": "ORYZABASE.MUTANT", "miriam": "oryzabase.mutant", "n2t": "oryzabase.mutant" }, "name": "Oryzabase Mutant", "pattern": "^\\d+$", "preferred_prefix": "oryzabase.mutant", "uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1" }, "oryzabase.reference": { "description": "The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan.", "example": "42840", "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", "mappings": { "miriam": "oryzabase.reference", "n2t": "oryzabase.reference" }, "name": "Oryzabase Reference", "pattern": "^\\d+$", "preferred_prefix": "oryzabase.reference", "uri_format": "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1" }, "oryzabase.stage": { "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information.", "example": "34", "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", "mappings": { "biocontext": "ORYZABASE.STAGE", "miriam": "oryzabase.stage", "n2t": "oryzabase.stage" }, "name": "Oryzabase Stage", "pattern": "^\\d+$", "preferred_prefix": "oryzabase.stage", "uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1" }, "oryzabase.strain": { "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information.", "example": "1", "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", "mappings": { "biocontext": "ORYZABASE.STRAIN", "miriam": "oryzabase.strain", "n2t": "oryzabase.strain" }, "name": "Oryzabase Strain", "pattern": "^\\d+$", "preferred_prefix": "oryzabase.strain", "uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1" }, "oslc": { "contact": { "email": "jamsden@us.ibm.com", "github": null, "name": "Jim Amsden", "orcid": null }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains.", "example": "Property", "homepage": "http://open-services.net/ns/core", "name": "OASIS Open Services for Lifecycle Collaboration Core Vocabulary", "preferred_prefix": "oslc", "uri_format": "http://open-services.net/ns/core#$1" }, "otl": { "description": "Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information.", "example": "AADB12", "homepage": "http://oryzatagline.cirad.fr/", "mappings": { "biocontext": "OTL", "fairsharing": "FAIRsharing.61c2x6", "miriam": "otl", "n2t": "otl", "prefixcommons": "otl" }, "name": "Oryza Tag Line", "pattern": "^A[A-Z]+\\d+$", "preferred_prefix": "otl", "uri_format": "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1" }, "otol": { "contributor": { "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" }, "description": "Identifier for an entity in open tree of life", "example": "3905431", "github_request_issue": 470, "homepage": "https://tree.opentreeoflife.org", "mappings": { "wikidata": "P9157" }, "name": "Open Tree of Life", "pattern": "^[1-9]\\d*$", "preferred_prefix": "otol", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://tree.opentreeoflife.org/taxonomy/browse?id=$1" }, "ovae": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqunh He", "orcid": "0000-0001-9189-9661" }, "description": "OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). ", "download_owl": "http://purl.obolibrary.org/obo/ovae.owl", "example": "0000609", "homepage": "http://www.violinet.org/ovae/", "license": "CC BY 3.0", "mappings": { "aberowl": "OVAE", "biocontext": "OVAE", "bioportal": "OVAE", "fairsharing": "FAIRsharing.w4x6n4", "obofoundry": "ovae", "ols": "ovae", "ontobee": "OVAE" }, "name": "Ontology of Vaccine Adverse Events", "pattern": "^\\d{7}$", "preferred_prefix": "OVAE", "publications": [ { "doi": "10.1186/2041-1480-4-40", "pmc": "PMC4177204", "pubmed": "24279920", "title": "The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines.", "year": 2013 } ], "repository": "https://github.com/OVAE-Ontology/ovae", "uri_format": "http://purl.obolibrary.org/obo/OVAE_$1", "version": "1.0.34" }, "owl": { "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/", "mappings": { "biocontext": "owl", "fairsharing": "FAIRsharing.atygwy" }, "name": "Web Ontology Language", "preferred_prefix": "owl", "uri_format": "http://www.w3.org/2002/07/owl#$1" }, "p3db.protein": { "description": "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites.", "example": "70", "homepage": "http://www.p3db.org/", "mappings": { "biocontext": "P3DB.PROTEIN", "miriam": "p3db.protein", "n2t": "p3db.protein" }, "name": "P3DB Protein", "pattern": "^\\d+$", "preferred_prefix": "p3db.protein", "uri_format": "http://www.p3db.org/protein.php?id=$1&ref=0" }, "p3db.site": { "description": "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins.", "example": "65", "homepage": "http://www.p3db.org/", "mappings": { "biocontext": "P3DB.SITE", "miriam": "p3db.site", "n2t": "p3db.site" }, "name": "P3DB Site", "pattern": "^\\d+$", "preferred_prefix": "p3db.site", "uri_format": "http://www.p3db.org/phosphosite.php?id=$1&ref=0" }, "paleodb": { "description": "The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data.", "example": "83088", "homepage": "http://paleodb.org/", "mappings": { "biocontext": "PALEODB", "miriam": "paleodb", "n2t": "paleodb", "prefixcommons": "paleodb" }, "name": "Paleobiology Database", "pattern": "^\\d+$", "preferred_prefix": "paleodb", "uri_format": "http://fossilworks.org/?a=taxonInfo&taxon_no=$1" }, "panorama": { "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", "mappings": { "fairsharing": "FAIRsharing.uBpQ1q" }, "name": "Panorama Public", "preferred_prefix": "panorama", "uri_format": "https://panoramaweb.org/$1.url" }, "panther.family": { "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families.", "example": "PTHR12345", "homepage": "http://www.pantherdb.org/", "mappings": { "biocontext": "PANTHER.FAMILY", "biolink": "PANTHER.FAMILY", "go": "PANTHER", "miriam": "panther.family", "n2t": "panther.family" }, "name": "Protein ANalysis THrough Evolutionary Relationships Classification System", "part_of": "panther", "pattern": "^PTHR\\d{5}(\\:SF\\d{1,3})?$", "preferred_prefix": "panther.family", "uri_format": "http://www.pantherdb.org/panther/family.do?clsAccession=$1" }, "panther.node": { "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes.", "example": "PTN000000026", "homepage": "http://pantree.org/", "mappings": { "biocontext": "PANTHER.NODE", "miriam": "panther.node", "n2t": "panther.node" }, "name": "PANTHER Node", "part_of": "panther", "pattern": "^PTN\\d{9}$", "preferred_prefix": "panther.node", "uri_format": "http://www.pantree.org/node/annotationNode.jsp?id=$1" }, "panther.pathway": { "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components.", "example": "P00024", "homepage": "http://www.pantherdb.org/", "mappings": { "biocontext": "PANTHER.PATHWAY", "edam": "1161", "miriam": "panther.pathway", "n2t": "panther.pathway" }, "name": "PANTHER Pathway", "part_of": "panther", "pattern": "^P\\d{5}$", "preferred_prefix": "panther.pathway", "uri_format": "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1" }, "panther.pthcmp": { "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway\r\ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation.", "example": "P00266", "homepage": "http://www.pantherdb.org/", "mappings": { "biocontext": "PANTHER.PTHCMP", "miriam": "panther.pthcmp", "n2t": "panther.pthcmp" }, "name": "PANTHER Pathway Component", "part_of": "panther", "pattern": "^(G|P|U|C|S)\\d{5}$", "preferred_prefix": "panther.pthcmp", "uri_format": "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1" }, "pao": { "contact": { "email": "jaiswalp@science.oregonstate.edu", "github": "jaiswalp", "name": "Pankaj Jaiswal", "orcid": "0000-0002-1005-8383" }, "deprecated": true, "homepage": "http://www.plantontology.org", "mappings": { "biocontext": "PAO", "obofoundry": "pao" }, "name": "Plant Anatomy Ontology", "preferred_prefix": "PAO", "uri_format": "http://purl.obolibrary.org/obo/PAO_$1" }, "pass2": { "deprecated": true, "description": "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.", "example": "46977", "homepage": "http://caps.ncbs.res.in/pass2", "mappings": { "biocontext": "PASS2", "miriam": "pass2", "n2t": "pass2", "prefixcommons": "pass2" }, "name": "Protein Alignment organised as Structural Superfamily", "pattern": "^\\d+$", "preferred_prefix": "pass2", "ur