{
"3dmet": {
"description": "3DMET is a database collecting three-dimensional structures of natural metabolites.",
"example": "B00162",
"homepage": "http://www.3dmet.dna.affrc.go.jp/",
"keywords": [
"chemical",
"life science",
"metabolite",
"metabolomics",
"structure"
],
"mappings": {
"biocontext": "3DMET",
"edam": "2635",
"fairsharing": "FAIRsharing.5ab0n7",
"miriam": "3dmet",
"n2t": "3dmet",
"prefixcommons": "3dmet",
"wikidata": "P2796"
},
"name": "3D Metabolites",
"pattern": "^B\\d{5}$",
"preferred_prefix": "3dmet",
"publications": [
{
"doi": "10.2142/biophysico.15.0_87",
"pmc": "PMC5992871",
"pubmed": "29892514",
"title": "Chemical curation to improve data accuracy: recent development of the 3DMET database.",
"year": 2018
},
{
"doi": "10.1021/ci300309k",
"pmc": null,
"pubmed": "23293959",
"title": "Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures.",
"year": 2013
}
],
"uri_format": "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1"
},
"4dn.biosource": {
"description": "The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases.",
"example": "4DNSR73BT2A2",
"homepage": "https://data.4dnucleome.org/biosources",
"keywords": [
"dna",
"life science",
"protein"
],
"mappings": {
"cellosaurus": "4DN",
"fairsharing": "FAIRsharing.CugtbQ",
"miriam": "4dn",
"prefixcommons": "4dn"
},
"name": "4D Nucleome Data Portal Biosource",
"pattern": "^4DN[A-Z]{2}[A-Z0-9]{7}$",
"preferred_prefix": "4dn.biosource",
"publications": [
{
"doi": "10.1038/nature23884",
"pmc": "PMC5617335",
"pubmed": "28905911",
"title": "The 4D nucleome project.",
"year": 2017
}
],
"synonyms": [
"4DN"
],
"twitter": "4dn_dcic",
"uri_format": "https://data.4dnucleome.org/biosources/$1"
},
"4dn.replicate": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor_extras": [
{
"email": "laylamichan@ciencias.unam.mx",
"github": "lmichan",
"name": "Layla Michán Aguirre",
"orcid": "0000-0002-5798-662X"
},
{
"email": "mineromero2901@ciencias.unam.mx",
"github": "MinRo60",
"name": "Minerva María Romero Pérez",
"orcid": "0000-0002-6240-9325"
},
{
"email": "victorinolavida@ciencias.unam.mx",
"github": "Victorinolavida",
"name": "José Victorino Ruiz Lavida",
"orcid": "0000-0001-5130-7705"
}
],
"description": "Database portal containing replicate experiments of different assays and samples",
"example": "4DNESWX1J3QU",
"homepage": "https://data.4dnucleome.org/experiment-set-replicates/",
"name": "4D Nucleome Data Portal Experiment Replicate",
"preferred_prefix": "4dn.replicate",
"uri_format": "https://data.4dnucleome.org/experiment-set-replicates/$1"
},
"aaindex": {
"description": "Identifier of an entry from the AAindex database.",
"example": "BUNA790102",
"homepage": "http://www.genome.ad.jp/aaindex/",
"keywords": [
"protein"
],
"mappings": {
"edam": "1128",
"prefixcommons": "aaindex"
},
"name": "AAindex",
"preferred_prefix": "aaindex",
"publications": [
{
"doi": "10.1093/nar/gkm998",
"pmc": "PMC2238890",
"pubmed": "17998252",
"title": "AAindex: amino acid index database, progress report 2008.",
"year": 2007
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?aaindex:$1"
},
"aao": {
"contact": {
"email": "david.c.blackburn@gmail.com",
"github": null,
"name": "David Blackburn",
"orcid": "0000-0002-1810-9886"
},
"deprecated": true,
"description": "A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon.",
"example": "0000138",
"homepage": "http://github.com/seger/aao",
"keywords": [
"anatomy",
"obo",
"ontology"
],
"mappings": {
"biocontext": "AAO",
"fairsharing": "FAIRsharing.mxx5rp",
"obofoundry": "aao",
"prefixcommons": "aao"
},
"name": "Amphibian gross anatomy",
"pattern": "^\\d{7}$",
"preferred_prefix": "AAO",
"publications": [
{
"doi": "10.1186/2041-1480-5-21",
"pmc": "PMC4089931",
"pubmed": "25009735",
"title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.",
"year": 2014
},
{
"doi": "10.1142/9789812772435_0035",
"pmc": null,
"pubmed": "17992749",
"title": "An anatomical ontology for amphibians.",
"year": 2007
}
],
"uri_format": "http://purl.obolibrary.org/obo/AAO_$1"
},
"abcd": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies",
"example": "AD834",
"homepage": "https://web.expasy.org/abcd/",
"keywords": [
"immunology",
"molecular biology"
],
"mappings": {
"cellosaurus": "ABCD",
"fairsharing": "FAIRsharing.Z8OKi5",
"uniprot": "DB-0236"
},
"name": "AntiBodies Chemically Defined database",
"preferred_prefix": "abcd",
"publications": [
{
"doi": "10.1093/nar/gkz714",
"pmc": "PMC6943046",
"pubmed": "31410491",
"title": "The ABCD database: a repository for chemically defined antibodies.",
"year": 2020
}
],
"uri_format": "https://web.expasy.org/abcd/ABCD_$1"
},
"abm": {
"description": "Cell line collections",
"example": "T0599",
"homepage": "https://www.abmgood.com/Cell-Biology.html",
"mappings": {
"cellosaurus": "ABM"
},
"name": "Applied Biological Materials cell line products",
"preferred_prefix": "abm",
"uri_format": "https://www.abmgood.com/catalogsearch/result/?cat=&q=$1"
},
"abs": {
"contact": {
"email": "enrique.blanco@crg.eu",
"github": null,
"name": "Enrique Blanco",
"orcid": "0000-0001-6261-7370"
},
"description": "The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography.",
"example": "A0014",
"homepage": "http://genome.crg.es/datasets/abs2005/",
"keywords": [
"biology",
"gene",
"interaction",
"regulation"
],
"mappings": {
"biocontext": "ABS",
"edam": "2741",
"fairsharing": "FAIRsharing.7mnebr",
"miriam": "abs",
"n2t": "abs",
"prefixcommons": "abs"
},
"name": "Annotated Regulatory Binding Sites",
"pattern": "^A\\d+$",
"preferred_prefix": "abs",
"publications": [
{
"doi": "10.1093/nar/gkj116",
"pmc": "PMC1347478",
"pubmed": "16381947",
"title": "ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.",
"year": 2006
}
],
"uri_format": "http://genome.crg.es/datasets/abs2005/entries/$1.html"
},
"ac": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Activity Streams is an open format specification for activity stream protocols, which are used to syndicate activities taken in social web applications and services, similar to those in Facebook's, Instagram's, and Twitter's. The standard provides a general way to represent activities.",
"example": "Add",
"homepage": "http://www.w3.org/ns/activitystreams",
"keywords": [
"semantic web",
"social media"
],
"name": "Activity Streams",
"preferred_prefix": "ac",
"uri_format": "http://www.w3.org/ns/activitystreams#$1"
},
"aceview.worm": {
"description": "AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression.",
"example": "aap-1",
"homepage": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm",
"keywords": [
"dna",
"gene",
"rna"
],
"mappings": {
"biocontext": "ACEVIEW.WORM",
"miriam": "aceview.worm",
"n2t": "aceview.worm",
"prefixcommons": "aceview.worm"
},
"name": "Aceview Worm",
"pattern": "^[a-z0-9-]+$",
"preferred_prefix": "aceview.worm",
"publications": [
{
"doi": "10.1186/gb-2006-7-s1-s12",
"pmc": "PMC1810549",
"pubmed": "16925834",
"title": "AceView: a comprehensive cDNA-supported gene and transcripts annotation.",
"year": 2006
}
],
"uri_format": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1"
},
"addexbio": {
"description": "Cell line collections",
"example": "C0020004/4992",
"homepage": "https://www.addexbio.com/productshow?id=4",
"mappings": {
"cellosaurus": "AddexBio"
},
"name": "AddexBio cell line products",
"preferred_prefix": "addexbio",
"uri_format": "https://www.addexbio.com/productdetail?pid=$1"
},
"addgene": {
"description": "Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world.",
"example": "50943",
"homepage": "http://addgene.org/",
"keywords": [
"life science",
"plasmid"
],
"mappings": {
"fairsharing": "FAIRsharing.8hcczk",
"miriam": "addgene",
"n2t": "addgene",
"prefixcommons": "addgene",
"re3data": "r3d100010741"
},
"name": "Addgene Plasmid Repository",
"pattern": "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$",
"preferred_prefix": "addgene",
"publications": [
{
"doi": "10.1093/nar/gku893",
"pmc": "PMC4384007",
"pubmed": "25392412",
"title": "The Addgene repository: an international nonprofit plasmid and data resource.",
"year": 2014
},
{
"doi": "10.1038/505272a",
"pmc": null,
"pubmed": "24429608",
"title": "Repositories share key research tools.",
"year": 2014
},
{
"doi": "10.1038/nbt.2177",
"pmc": null,
"pubmed": "22491276",
"title": "Addgene provides an open forum for plasmid sharing.",
"year": 2012
}
],
"twitter": "Addgene",
"uri_format": "http://addgene.org/$1"
},
"ado": {
"contact": {
"email": "alpha.tom.kodamullil@scai.fraunhofer.de",
"github": "akodamullil",
"name": "Alpha Tom Kodamullil",
"orcid": "0000-0001-9896-3531"
},
"depends_on": [
"bfo"
],
"description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining.",
"download_owl": "http://purl.obolibrary.org/obo/ado.owl",
"example": "0000001",
"homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO",
"keywords": [
"health science",
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "ADO",
"bioportal": "ADO",
"fairsharing": "FAIRsharing.ckd4rf",
"obofoundry": "ado",
"ols": "ado",
"ontobee": "ADO"
},
"name": "Alzheimer's Disease Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "ADO",
"publications": [
{
"doi": "10.1016/j.jalz.2013.02.009",
"pmc": null,
"pubmed": "23830913",
"title": "ADO: a disease ontology representing the domain knowledge specific to Alzheimer's disease.",
"year": 2013
}
],
"repository": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO",
"uri_format": "http://purl.obolibrary.org/obo/ADO_$1",
"version": "2.0.0"
},
"adw": {
"contact": {
"email": "adw_geeks@umich.edu",
"github": null,
"name": "Animal Diversity Web technical staff",
"orcid": null
},
"deprecated": true,
"description": "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology.",
"download_owl": "http://aber-owl.net/media/ontologies/ADW/2/adw.owl",
"example": "Lycalopex_vetulus",
"homepage": "http://www.animaldiversity.org",
"keywords": [
"anatomy",
"life science",
"obo",
"ontology"
],
"mappings": {
"aberowl": "ADW",
"biocontext": "ADW",
"bioportal": "ADW",
"fairsharing": "FAIRsharing.t9fvdn",
"miriam": "adw",
"n2t": "adw",
"obofoundry": "adw"
},
"name": "Animal natural history and life history",
"pattern": "^[A-Z_a-z]+$",
"preferred_prefix": "ADW",
"uri_format": "https://animaldiversity.org/accounts/$1"
},
"aeo": {
"appears_in": [
"ehdaa2"
],
"contact": {
"email": "J.Bard@ed.ac.uk",
"github": null,
"name": "Jonathan Bard",
"orcid": null
},
"deprecated": true,
"description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology",
"download_obo": "https://raw.githubusercontent.com/obophenotype/human-developmental-anatomy-ontology/master/src/ontology/aeo.obo",
"download_owl": "http://purl.obolibrary.org/obo/aeo.owl",
"example": "0001017",
"homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology/",
"keywords": [
"anatomy",
"life science",
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "AEO",
"bartoc": "181",
"biocontext": "AEO",
"bioportal": "AEO",
"fairsharing": "FAIRsharing.93ee19",
"obofoundry": "aeo",
"ols": "aeo",
"ontobee": "AEO"
},
"name": "Anatomical Entity Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "AEO",
"publications": [
{
"doi": "10.3389/fgene.2012.00018",
"pmc": "PMC3278863",
"pubmed": "22347883",
"title": "The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs.",
"year": 2012
}
],
"repository": "https://github.com/obophenotype/human-developmental-anatomy-ontology",
"synonyms": [
"AEO_RETIRED"
],
"uri_format": "http://purl.obolibrary.org/obo/AEO_$1",
"version": "2014-12-05"
},
"aeon": {
"contact": {
"email": "Philip.Stroemert@tib.eu",
"github": "StroemPhi",
"name": "Philip Strömert",
"orcid": "0000-0002-1595-3213"
},
"contributor": {
"email": "Philip.Stroemert@tib.eu",
"github": "StroemPhi",
"name": "Philip Strömert",
"orcid": "0000-0002-1595-3213"
},
"description": "The academic event ontology, currently still in development and thus unstable, is an OBO compliant reference ontology for describing academic events such as conferences, workshops or seminars and their series. It is being developed as part of the [ConfIDent project](https://projects.tib.eu/confident/) to allow RDF representations of the academic events and series stored and curated in the [ConfIDent platform](https://www.confident-conference.org/index.php/main_page).",
"download_owl": "https://raw.githubusercontent.com/tibonto/aeon/main/aeon.owl",
"example": "0000001",
"github_request_issue": 617,
"homepage": "https://tibonto.github.io/aeon/",
"keywords": [
"ontology"
],
"license": "CC-BY-4.0",
"name": "Academic Event Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "aeon",
"repository": "https://github.com/tibonto/aeon",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://purl.obolibrary.org/obo/AEON_$1"
},
"aero": {
"contact": {
"email": "mcourtot@gmail.com",
"github": null,
"name": "Melanie Courtot",
"orcid": "0000-0002-9551-6370"
},
"deprecated": true,
"description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events",
"download_owl": "http://purl.obolibrary.org/obo/aero.owl",
"example": "0000125",
"homepage": "http://purl.obolibrary.org/obo/aero",
"keywords": [
"biomedical science",
"health science",
"medicine",
"obo",
"ontology",
"preclinical studies"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "AERO",
"biocontext": "AERO",
"bioportal": "AERO",
"fairsharing": "FAIRsharing.rycy2x",
"obofoundry": "aero"
},
"name": "Adverse Event Reporting Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "AERO",
"uri_format": "http://purl.obolibrary.org/obo/AERO_$1"
},
"affy.probeset": {
"description": "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration.",
"example": "243002_at",
"homepage": "http://www.affymetrix.com/",
"mappings": {
"biocontext": "AFFY.PROBESET",
"miriam": "affy.probeset",
"n2t": "affy.probeset"
},
"name": "Affymetrix Probeset",
"pattern": "^\\d{4,}((_[asx])?_at)$",
"preferred_prefix": "affy.probeset",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "Bio2RDF",
"homepage": "http://cu.affymetrix.bio2rdf.org/fct/",
"name": "Bio2RDF",
"uri_format": "http://cu.affymetrix.bio2rdf.org/describe/?url=http://bio2rdf.org/affymetrix:$1"
}
],
"uri_format": "https://www.affymetrix.com/LinkServlet?probeset=$1"
},
"afo": {
"contact": {
"email": "more.info@allotrope.org",
"github": null,
"name": "Allotrope Foundation",
"orcid": null
},
"description": "Allotrope Merged Ontology Suite",
"download_owl": "http://purl.allotrope.org/voc/afo/merged-OLS/REC/2019/05/10",
"homepage": "https://www.allotrope.org/",
"keywords": [
"agricultural engineering",
"agriculture",
"biology",
"environmental science",
"food chemistry",
"forest management",
"ontology",
"veterinary medicine"
],
"mappings": {
"aberowl": "AFO",
"bioportal": "AFO",
"fairsharing": "FAIRsharing.595710",
"ols": "afo"
},
"name": "Allotrope Merged Ontology Suite",
"no_own_terms": true,
"preferred_prefix": "afo",
"version": "2019-05-10"
},
"aftol.taxonomy": {
"contributor_extras": [
{
"email": "laylamichan@ciencias.unam.mx",
"github": "lmichan",
"name": "Layla Michán Aguirre",
"orcid": "0000-0002-5798-662X"
}
],
"description": "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species.",
"example": "959",
"homepage": "https://aftol.umn.edu",
"mappings": {
"biocontext": "AFTOL.TAXONOMY",
"miriam": "aftol.taxonomy",
"n2t": "aftol.taxonomy"
},
"name": "Assembling the Fungal Tree of Life - Taxonomy",
"pattern": "^\\d+$",
"preferred_prefix": "aftol.taxonomy",
"uri_format": "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1"
},
"agilent.probe": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699.",
"example": "A_24_P98555",
"homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt",
"keywords": [
"transcriptomics"
],
"name": "Agilent Probe",
"pattern": "^A_\\d+_.+$",
"preferred_prefix": "agilent.probe",
"references": [
"http://www.cs.tau.ac.il/cgi-bin/cgiwrap/click/get.cgi/conversionFiles/conversion_human_14850_agilent2entrez.txt"
]
},
"agricola": {
"contributor_extras": [
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
{
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
}
],
"description": "AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century.",
"example": "50018",
"homepage": "http://agricola.nal.usda.gov/",
"mappings": {
"biocontext": "AGRICOLA",
"go": "AGRICOLA_ID",
"miriam": "agricola",
"n2t": "agricola",
"uniprot": "DB-0266"
},
"name": "Agricultural Online Access",
"pattern": "^\\d+$",
"preferred_prefix": "agricola",
"publications": [
{
"doi": "10.1093/nar/gkz813",
"pmc": "PMC6943066",
"pubmed": "31552413",
"title": "Alliance of Genome Resources Portal: unified model organism research platform.",
"year": 2020
}
],
"synonyms": [
"AGR",
"AGRICOLA_ID"
],
"uri_format": "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1"
},
"agrkb": {
"contact": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"contributor": {
"email": null,
"github": "sierra-moxon",
"name": "Sierra Moxon",
"orcid": "0000-0002-8719-7760"
},
"description": "The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations.\n\nThe Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location:\n\n- [ZFIN](https://zfin.org) - Zebrafish Information Network\n- [WormBase](https://wormbase.org)\n- [MGI](https://www.mgi.org) - Mouse Genome Informatics\n- [RGD](https://rgd.mcw.edu) - Rat Genome Database\n- [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database\n- [FlyBase](https://flybase.org)\n- [Xenbase](https://www.xenbase.org)",
"example": "100000000000001",
"github_request_issue": 359,
"homepage": "https://www.alliancegenome.org",
"keywords": [
"model organism database"
],
"mappings": {
"biolink": "AGRKB"
},
"name": "Alliance of Genome Resources Knowledge Base",
"pattern": "^[1-9][0-9]{14}$",
"preferred_prefix": "agrkb",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://www.alliancegenome.org/accession/$1"
},
"agro": {
"contact": {
"email": "m.a.laporte@cgiar.org",
"github": "marieALaporte",
"name": "Marie-Angélique Laporte",
"orcid": "0000-0002-8461-9745"
},
"depends_on": [
"bfo",
"envo",
"foodon",
"go",
"iao",
"ncbitaxon",
"obi",
"pato",
"peco",
"po",
"ro",
"to",
"uo",
"xco"
],
"description": "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities",
"download_obo": "https://raw.githubusercontent.com/KrishnaTO/agro/master/agro.obo",
"download_owl": "http://purl.obolibrary.org/obo/agro.owl",
"example": "00020007",
"homepage": "https://github.com/AgriculturalSemantics/agro",
"keywords": [
"agriculture",
"agronomy",
"farming systems research",
"obo",
"ontology",
"plant breeding"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "AGRO",
"agroportal": "AGRO",
"biocontext": "AGRO",
"bioportal": "AGRO",
"fairsharing": "FAIRsharing.m40bhw",
"obofoundry": "agro",
"ols": "agro",
"ontobee": "AGRO"
},
"name": "Agronomy Ontology",
"pattern": "^\\d{8}$",
"preferred_prefix": "AGRO",
"repository": "https://github.com/AgriculturalSemantics/agro",
"uri_format": "http://purl.obolibrary.org/obo/AGRO_$1",
"version": "2021-11-05"
},
"agrovoc": {
"banana": "c_",
"contact": {
"email": "agrovoc@fao.org",
"github": null,
"name": "AGROVOC Team",
"orcid": null
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages.",
"example": "2842",
"homepage": "https://data.apps.fao.org/catalog/organization/agrovoc",
"keywords": [
"agriculture",
"botany",
"data management",
"environmental science",
"fisheries science",
"forest management",
"nutritional science"
],
"mappings": {
"agroportal": "AGROVOC",
"bartoc": "305",
"ecoportal": "AGROVOC",
"fairsharing": "FAIRsharing.anpj91",
"wikidata": "P8061"
},
"name": "Agronomy Vocabulary",
"pattern": "^[a-z0-9]+$",
"preferred_prefix": "agrovoc",
"publications": [
{
"doi": "10.4060/cb2838en",
"pmc": null,
"pubmed": null,
"title": "AGROVOC",
"year": 2021
},
{
"doi": "10.3390/engproc2021009017",
"pmc": null,
"pubmed": null,
"title": "How Agricultural Digital Innovation Can Benefit from Semantics: The Case of the AGROVOC Multilingual Thesaurus",
"year": 2021
},
{
"doi": "10.1016/j.compag.2020.105965",
"pmc": null,
"pubmed": null,
"title": "AGROVOC: The linked data concept hub for food and agriculture",
"year": 2022
}
],
"references": [
"http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_core.nt.zip",
"http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_lod.nt.zip",
"https://en.wikipedia.org/wiki/AGROVOC"
],
"twitter": "FAOAIMS",
"uri_format": "http://aims.fao.org/aos/agrovoc/c_$1"
},
"agsd": {
"description": "A comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources.",
"example": "4779",
"homepage": "http://www.genomesize.com",
"keywords": [
"dna",
"genome",
"life science"
],
"mappings": {
"fairsharing": "FAIRsharing.efp5v2",
"prefixcommons": "agsd",
"re3data": "r3d100012517"
},
"name": "Animal Genome Size Database",
"preferred_prefix": "agsd",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://www.genomesize.com/result_species.php?id=$1"
},
"aism": {
"appears_in": [
"colao",
"lepao"
],
"contact": {
"email": "entiminae@gmail.com",
"github": "JCGiron",
"name": "Jennifer C. Girón",
"orcid": "0000-0002-0851-6883"
},
"depends_on": [
"bfo",
"bspo",
"caro",
"pato",
"ro",
"uberon"
],
"description": "The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research.",
"download_json": "http://purl.obolibrary.org/obo/aism.json",
"download_obo": "http://purl.obolibrary.org/obo/aism.obo",
"download_owl": "http://purl.obolibrary.org/obo/aism.owl",
"example": "0000027",
"homepage": "https://github.com/insect-morphology/aism",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "AISM",
"bioportal": "AISM",
"obofoundry": "aism",
"ols": "aism",
"ontobee": "AISM"
},
"name": "Ontology for the Anatomy of the Insect SkeletoMuscular system",
"pattern": "^\\d{7}$",
"preferred_prefix": "AISM",
"repository": "https://github.com/insect-morphology/aism",
"uri_format": "http://purl.obolibrary.org/obo/AISM_$1",
"version": "2022-06-27"
},
"alfred": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"description": "ALFRED has been designed to make allele frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases.",
"example": "LO362836C",
"homepage": "http://alfred.med.yale.edu",
"keywords": [
"classification",
"genome"
],
"mappings": {
"prefixcommons": "alfred"
},
"name": "The ALlele FREquency Database",
"preferred_prefix": "alfred",
"publications": [
{
"doi": "10.1093/nar/gkg043",
"pmc": "PMC165490",
"pubmed": "12519999",
"title": "ALFRED: the ALelle FREquency Database. Update.",
"year": 2003
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID=$1"
},
"allergome": {
"description": "Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources.",
"example": "1948",
"homepage": "http://www.allergome.org/",
"keywords": [
"allergen",
"biomedical science",
"health science",
"life science",
"medicine"
],
"mappings": {
"biocontext": "ALLERGOME",
"fairsharing": "FAIRsharing.w6cxgb",
"miriam": "allergome",
"n2t": "allergome",
"prefixcommons": "allergome",
"uniprot": "DB-0160"
},
"name": "Allergome",
"pattern": "^\\d+$",
"preferred_prefix": "allergome",
"publications": [
{
"doi": "10.1007/s11882-009-0055-9",
"pmc": null,
"pubmed": "19671381",
"title": "Allergen databases: current status and perspectives.",
"year": 2009
},
{
"doi": "10.1016/j.cellimm.2007.02.012",
"pmc": null,
"pubmed": "17434469",
"title": "Bioinformatics applied to allergy: allergen databases, from collecting sequence information to data integration. The Allergome platform as a model.",
"year": 2007
},
{
"doi": null,
"pmc": null,
"pubmed": "17393720",
"title": "Allergome: a unifying platform.",
"year": 2006
}
],
"uri_format": "http://www.allergome.org/script/dettaglio.php?id_molecule=$1"
},
"alzforum.mutation": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease.",
"example": "app-d678n-tottori",
"homepage": "https://www.alzforum.org/mutations",
"keywords": [
"alzheimer's disease",
"genes",
"variants"
],
"name": "Alzforum Mutations",
"preferred_prefix": "alzforum.mutation",
"synonyms": [
"Alzforum_mut"
],
"uri_format": "https://www.alzforum.org/mutations/$1"
},
"alzgene": {
"description": "The AlzGene database provides a comprehensive, unbiased and regularly updated field synopsis of genetic association studies performed in Alzheimer’s disease. In addition, hundreds of up-to-date meta-analyses are available for all eligible polymorphisms with sufficient data.",
"example": "88",
"homepage": "http://www.alzgene.org",
"keywords": [
"gene"
],
"mappings": {
"prefixcommons": "alzgene"
},
"name": "Alzheimer Gene Database",
"preferred_prefix": "alzgene",
"publications": [
{
"doi": "10.1038/ng1934",
"pmc": null,
"pubmed": "17192785",
"title": "Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database.",
"year": 2007
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://www.alzgene.org/geneoverview.asp?geneid=$1"
},
"amoebadb": {
"description": "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"example": "EDI_244000",
"homepage": "http://amoebadb.org/amoeba/",
"keywords": [
"functional genomics",
"genomics",
"model organism"
],
"mappings": {
"biocontext": "AMOEBADB",
"fairsharing": "FAIRsharing.swbypy",
"miriam": "amoebadb",
"n2t": "amoebadb",
"prefixcommons": "amoebadb",
"re3data": "r3d100012457"
},
"name": "AmoebaDB",
"pattern": "^EDI_\\d+$",
"preferred_prefix": "amoebadb",
"publications": [
{
"doi": "10.1093/nar/gkp941",
"pmc": "PMC2808945",
"pubmed": "19914931",
"title": "EuPathDB: a portal to eukaryotic pathogen databases.",
"year": 2009
}
],
"twitter": "eupathdb",
"uri_format": "https://amoebadb.org/amoeba/app/record/gene/$1"
},
"amphx": {
"contact": {
"email": "hescriva@obs-banyuls.fr",
"github": "hescriva",
"name": "Hector Escriva",
"orcid": "0000-0001-7577-5028"
},
"depends_on": [
"uberon"
],
"description": "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).",
"download_obo": "http://purl.obolibrary.org/obo/amphx.obo",
"download_owl": "http://purl.obolibrary.org/obo/amphx.owl",
"example": "1000160",
"homepage": "https://github.com/EBISPOT/amphx_ontology",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "AMPHX",
"bioportal": "AMPHX",
"obofoundry": "amphx",
"ols": "amphx",
"ontobee": "AMPHX"
},
"name": "The Amphioxus Development and Anatomy Ontology",
"pattern": "^\\d+$",
"preferred_prefix": "AMPHX",
"repository": "https://github.com/EBISPOT/amphx_ontology",
"uri_format": "http://purl.obolibrary.org/obo/AMPHX_$1",
"version": "2020-12-18"
},
"antibodyregistry": {
"description": "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.",
"example": "493771",
"homepage": "http://antibodyregistry.org/",
"mappings": {
"biocontext": "ANTIBODYREGISTRY",
"miriam": "antibodyregistry",
"n2t": "antibodyregistry"
},
"name": "Antibody Registry",
"pattern": "^\\d{6}$",
"preferred_prefix": "antibodyregistry",
"uri_format": "http://antibodyregistry.org/AB_$1"
},
"antweb": {
"description": "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures.",
"example": "casent0106247",
"homepage": "http://www.antweb.org/",
"keywords": [
"anatomy",
"classification",
"life science"
],
"mappings": {
"biocontext": "ANTWEB",
"fairsharing": "FAIRsharing.yk38tw",
"miriam": "antweb",
"n2t": "antweb",
"ncbi": "AntWeb",
"prefixcommons": "antweb",
"wikidata": "P5299"
},
"name": "AntWeb",
"pattern": "^casent\\d+(\\-D\\d+)?$",
"preferred_prefix": "antweb",
"publications": [
{
"doi": "10.1038/424242b",
"pmc": null,
"pubmed": "12867945",
"title": "Ants join online colony to boost conservation efforts.",
"year": 2003
}
],
"uri_format": "http://www.antweb.org/specimen.do?name=$1"
},
"aop": {
"description": "International repository of Adverse Outcome Pathways.",
"example": "98",
"homepage": "https://aopwiki.org/",
"mappings": {
"biocontext": "AOP",
"miriam": "aop",
"n2t": "aop"
},
"name": "AOPWiki",
"pattern": "^\\d+$",
"preferred_prefix": "aop",
"uri_format": "https://aopwiki.org/aops/$1"
},
"aop.events": {
"description": "International repository of Adverse Outcome Pathways.",
"example": "3",
"homepage": "https://aopwiki.org/",
"mappings": {
"biocontext": "AOP.EVENTS",
"miriam": "aop.events",
"n2t": "aop.events"
},
"name": "AOPWiki (Key Event)",
"pattern": "^\\d+$",
"preferred_prefix": "aop.events",
"uri_format": "https://aopwiki.org/events/$1"
},
"aop.relationships": {
"description": "International repository of Adverse Outcome Pathways.",
"example": "5",
"homepage": "https://aopwiki.org/",
"mappings": {
"biocontext": "AOP.RELATIONSHIPS",
"miriam": "aop.relationships",
"n2t": "aop.relationships"
},
"name": "AOPWiki (Key Event Relationship)",
"pattern": "^\\d+$",
"preferred_prefix": "aop.relationships",
"uri_format": "https://aopwiki.org/relationships/$1"
},
"aop.stressor": {
"description": "International repository of Adverse Outcome Pathways.",
"example": "9",
"homepage": "https://aopwiki.org/",
"mappings": {
"biocontext": "AOP.STRESSOR",
"miriam": "aop.stressor",
"n2t": "aop.stressor"
},
"name": "AOPWiki (Stressor)",
"pattern": "^\\d+$",
"preferred_prefix": "aop.stressor",
"uri_format": "https://aopwiki.org/stressors/$1"
},
"apaonto": {
"contact": {
"email": "awalker@apa.org",
"github": null,
"name": "Alvin Walker",
"orcid": "0000-0003-1082-8760"
},
"description": "An ontology developed by the American Psychological Association (APA). Note that URIs in this ontology appear to have been generated with erroneous settings in Protege.",
"download_owl": "http://aber-owl.net/media/ontologies/APAONTO/4/apaonto.owl",
"example": "Abdomen",
"homepage": "https://bioportal.bioontology.org/ontologies/APAONTO",
"keywords": [
"ontology",
"ontology and terminology",
"psychology"
],
"mappings": {
"aberowl": "APAONTO",
"bioportal": "APAONTO",
"fairsharing": "FAIRsharing.gkw1w8"
},
"name": "Psychology Ontology",
"preferred_prefix": "apaonto",
"references": [
"https://github.com/biopragmatics/bioregistry/issues/528"
],
"uri_format": "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1"
},
"apd": {
"description": "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides.",
"example": "01001",
"homepage": "http://aps.unmc.edu/AP/",
"keywords": [
"biology",
"protein"
],
"mappings": {
"biocontext": "APD",
"fairsharing": "FAIRsharing.ctwd7b",
"miriam": "apd",
"n2t": "apd",
"prefixcommons": "apd",
"re3data": "r3d100012901"
},
"name": "Antimicrobial Peptide Database",
"pattern": "^\\d{5}$",
"preferred_prefix": "apd",
"publications": [
{
"doi": "10.1093/nar/gkv1278",
"pmc": "PMC4702905",
"pubmed": "26602694",
"title": "APD3: the antimicrobial peptide database as a tool for research and education.",
"year": 2015
},
{
"doi": "10.1093/nar/gkn823",
"pmc": "PMC2686604",
"pubmed": "18957441",
"title": "APD2: the updated antimicrobial peptide database and its application in peptide design.",
"year": 2008
},
{
"doi": "10.1093/nar/gkh025",
"pmc": "PMC308759",
"pubmed": "14681488",
"title": "APD: the Antimicrobial Peptide Database.",
"year": 2004
}
],
"uri_format": "http://aps.unmc.edu/AP/database/query_output.php?ID=$1"
},
"aphidbase.transcript": {
"description": "AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information.",
"example": "ACYPI000159",
"homepage": "http://www.aphidbase.com/aphidbase",
"keywords": [
"genome"
],
"mappings": {
"biocontext": "APHIDBASE.TRANSCRIPT",
"miriam": "aphidbase.transcript",
"n2t": "aphidbase.transcript",
"prefixcommons": "aphidbase"
},
"name": "AphidBase Transcript",
"pattern": "^ACYPI\\d{6}(-RA)?$",
"preferred_prefix": "aphidbase.transcript",
"publications": [
{
"doi": "10.1111/j.1365-2583.2009.00930.x",
"pmc": "PMC4372297",
"pubmed": "20482635",
"title": "AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome.",
"year": 2010
}
],
"uri_format": "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1"
},
"apid.interactions": {
"description": "APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.",
"example": "P01116",
"homepage": "http://cicblade.dep.usal.es:8080/APID/",
"mappings": {
"biocontext": "APID.INTERACTIONS",
"miriam": "apid.interactions",
"n2t": "apid.interactions"
},
"name": "APID Interactomes",
"pattern": "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$",
"preferred_prefix": "apid.interactions",
"provides": "uniprot",
"uri_format": "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1"
},
"apo": {
"contact": {
"email": "stacia@stanford.edu",
"github": "srengel",
"name": "Stacia R Engel",
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"download_owl": "http://purl.obolibrary.org/obo/apo.owl",
"example": "0000184",
"homepage": "http://www.yeastgenome.org/",
"keywords": [
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"license": "CC-BY-4.0",
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{
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"pmc": "PMC2790299",
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"year": 2009
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],
"repository": "https://github.com/obophenotype/ascomycete-phenotype-ontology",
"twitter": "yeastgenome",
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"name": "William Hogan",
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"example": "00000443",
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"name": "Apollo Structured Vocabulary",
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{
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{
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{
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{
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"pmc": null,
"pubmed": "29069336",
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"year": 2018
},
{
"doi": "10.1093/nar/gkq1058",
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"pubmed": "21036864",
"title": "ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures.",
"year": 2010
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],
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"description": "Website with general information about Arabidopsis and functionalities such as a genomic viewer",
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{
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],
"uri_format": "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1"
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{
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"pubmed": "14681390",
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"email": "cthoyt@gmail.com",
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"uri_format": "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1"
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"ark": {
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{
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{
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],
"description": "An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type.",
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"pattern": "^/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$",
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"contact": {
"email": "mcarthua@mcmaster.ca",
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"example": "1000001",
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"keywords": [
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"license": "CC-BY-4.0",
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"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",
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"name": "ArrayExpress",
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{
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{
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"title": "ArrayExpress--a public repository for microarray gene expression data at the EBI.",
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],
"twitter": "ArrayExpressEBI",
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},
"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",
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"contact": {
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"github": "mbaudis",
"name": "Michael Baudis",
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"example": "icdom:8500_3",
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{
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{
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"title": "arrayMap 2014: an updated cancer genome resource.",
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{
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{
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],
"twitter": "progenetix",
"uri_format": "https://www.arraymap.org/pgx:$1"
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"arxiv": {
"description": "arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology.",
"example": "0807.4956v1",
"homepage": "https://arxiv.org/",
"keywords": [
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"mappings": {
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"name": "arXiv ID",
"pattern": "^(\\w+(\\-\\w+)?(\\.\\w+)?)?\\d{4,7}(\\.\\d+(v\\d+)?)?$",
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{
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{
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],
"uri_format": "https://arxiv.org/abs/$1"
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"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.",
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"homepage": "http://asap.ahabs.wisc.edu/asap/home.php",
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"name": "A Systematic Annotation Package for Community Analysis of Genomes",
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{
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"title": "ASAP, a systematic annotation package for community analysis of genomes.",
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],
"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).",
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"name": "Astrophysics Source Code Library",
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],
"twitter": "asclnet",
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"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.",
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"name": "Amazon Standard Identification Number",
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"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",
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"preferred_prefix": "aspgd.locus",
"uri_format": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1"
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"name": "AspGD Protein",
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"preferred_prefix": "aspgd.protein",
"uri_format": "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1"
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"asrp": {
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"description": "Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes.",
"example": "ASRP1423",
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"keywords": [
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"mappings": {
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"name": "Arabidopsis Small RNA Project",
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{
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],
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"astd": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"description": "Identifier of an object from the ASTD database.",
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"keywords": [
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"name": "ASTD",
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],
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"atc": {
"contact": {
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"github": null,
"name": "WHO Collaborating Centre for Drug Statistics Methodology",
"orcid": null
},
"description": "The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels.",
"example": "A10BA02",
"homepage": "http://www.whocc.no/atc_ddd_index/",
"keywords": [
"biomedical science",
"chemical",
"chemical biology",
"ontology",
"pharmacology"
],
"mappings": {
"aberowl": "ATC",
"bartoc": "449",
"biocontext": "ATC",
"bioportal": "ATC",
"edam": "3103",
"fairsharing": "FAIRsharing.1a27h8",
"hl7": "2.16.840.1.113883.6.73",
"miriam": "atc",
"n2t": "atc",
"prefixcommons": "atc",
"wikidata": "P267"
},
"name": "Anatomical Therapeutic Chemical Classification System",
"pattern": "^[A-Z](\\d+([A-Z]{1,2}(\\d+)?)?)?$",
"preferred_prefix": "atc",
"publications": [
{
"doi": null,
"pmc": null,
"pubmed": "7368387",
"title": "[New classification of drugs. The Medical list and the Drug catalogue are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code) in 1981].",
"year": 1980
},
{
"doi": "10.1007/s002280000200",
"pmc": null,
"pubmed": "11214783",
"title": "Different versions of the anatomical therapeutic chemical classification system and the defined daily dose--are drug utilisation data comparable?",
"year": 2000
}
],
"synonyms": [
"ATC_code",
"ATTC"
],
"uri_format": "http://www.whocc.no/atc_ddd_index/?code=$1"
},
"atcc": {
"description": "The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences.",
"example": "11303",
"homepage": "https://www.lgcstandards-atcc.org",
"keywords": [
"epidemiology",
"life science",
"virology"
],
"mappings": {
"biocontext": "ATCC",
"cellosaurus": "ATCC",
"fairsharing": "FAIRsharing.j0ezpm",
"hl7": "2.16.840.1.113883.6.77",
"miriam": "atcc",
"n2t": "atcc",
"ncbi": "ATCC"
},
"name": "American Type Culture Collection",
"pattern": "^([A-Z]+-)?\\d+$",
"preferred_prefix": "atcc",
"synonyms": [
"ATCC",
"ATCC number",
"ATCC(dna)",
"ATCC(in host)"
],
"uri_format": "https://www.atcc.org/products/$1"
},
"atcvet": {
"description": "The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use.",
"example": "QJ51RV02",
"homepage": "http://www.whocc.no/atcvet/atcvet_index/",
"mappings": {
"biocontext": "ATCVET",
"miriam": "atcvet",
"n2t": "atcvet"
},
"name": "Anatomical Therapeutic Chemical Vetinary",
"pattern": "^Q[A-Z0-9]+$",
"preferred_prefix": "atcvet",
"uri_format": "http://www.whocc.no/atcvet/atcvet_index/?code=$1"
},
"atfdb.family": {
"description": "The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found.",
"example": "CUT",
"homepage": "http://www.bioguo.org/AnimalTFDB/family_index.php",
"mappings": {
"biocontext": "ATFDB.FAMILY",
"miriam": "atfdb.family",
"n2t": "atfdb.family"
},
"name": "Animal TFDB Family",
"pattern": "^\\w+$",
"preferred_prefix": "atfdb.family",
"uri_format": "http://www.bioguo.org/AnimalTFDB/family.php?fam=$1"
},
"ato": {
"contact": {
"email": "david.c.blackburn@gmail.com",
"github": null,
"name": "David Blackburn",
"orcid": null
},
"deprecated": true,
"description": "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource",
"download_obo": "http://aber-owl.net/media/ontologies/ATO/2/ato.obo",
"example": "0000000",
"homepage": "http://www.amphibanat.org",
"keywords": [
"obo",
"ontology"
],
"mappings": {
"aberowl": "ATO",
"biocontext": "ATO",
"bioportal": "ATO",
"fairsharing": "FAIRsharing.ayjdsm",
"obofoundry": "ato"
},
"name": "Amphibian taxonomy",
"pattern": "^\\d{7}$",
"preferred_prefix": "ATO",
"uri_format": "http://purl.obolibrary.org/obo/ATO_$1"
},
"atol": {
"contact": {
"email": "pylebail@rennes.inra.fr",
"github": null,
"name": "LeBail Pierre-Yves",
"orcid": null
},
"description": "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production.",
"download_owl": "http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=atol.owl",
"example": "0002233",
"homepage": "http://www.atol-ontology.com",
"keywords": [
"agriculture",
"animal husbandry",
"life science",
"ontology"
],
"mappings": {
"aberowl": "ATOL",
"agroportal": "ATOL",
"bioportal": "ATOL",
"fairsharing": "FAIRsharing.wsfk5z",
"ols": "atol"
},
"name": "Animal Trait Ontology for Livestock",
"pattern": "^\\d{7}$",
"preferred_prefix": "atol",
"uri_format": "http://opendata.inra.fr/ATOL/ATOL_$1",
"version": "2018-09-13"
},
"autdb": {
"description": "AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder.",
"example": "ADA",
"homepage": "http://autism.mindspec.org/autdb/",
"mappings": {
"biocontext": "AUTDB",
"miriam": "autdb",
"n2t": "autdb"
},
"name": "AutDB",
"pattern": "^[A-Z]+[A-Z-0-9]{2,}$",
"preferred_prefix": "autdb",
"uri_format": "http://autism.mindspec.org/GeneDetail/$1"
},
"bacdive": {
"contact": {
"email": "contact@bacdive.de",
"github": null,
"name": "Lorenz Reimer",
"orcid": "0000-0002-7805-0660"
},
"description": "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity.",
"example": "131392",
"homepage": "https://bacdive.dsmz.de/",
"keywords": [
"biodiversity",
"life science",
"microbiology"
],
"mappings": {
"fairsharing": "FAIRsharing.aSszvY",
"miriam": "bacdive",
"n2t": "bacdive",
"re3data": "r3d100013060",
"wikidata": "P2946"
},
"name": "BacDive ID",
"pattern": "^[0-9]+$",
"preferred_prefix": "bacdive",
"publications": [
{
"doi": "10.1093/nar/gky879",
"pmc": "PMC6323973",
"pubmed": "30256983",
"title": "BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis.",
"year": 2019
},
{
"doi": "10.1016/j.jbiotec.2017.05.004",
"pmc": null,
"pubmed": "28487186",
"title": "Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase.",
"year": 2017
},
{
"doi": "10.1093/nar/gkv983",
"pmc": "PMC4702946",
"pubmed": "26424852",
"title": "BacDive--The Bacterial Diversity Metadatabase in 2016.",
"year": 2015
},
{
"doi": "10.1093/nar/gkt1058",
"pmc": "PMC3965005",
"pubmed": "24214959",
"title": "BacDive--the Bacterial Diversity Metadatabase.",
"year": 2013
}
],
"uri_format": "https://bacdive.dsmz.de/strain/$1"
},
"bacmap.biog": {
"description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information.",
"example": "1050",
"homepage": "http://bacmap.wishartlab.com/",
"mappings": {
"biocontext": "BACMAP.BIOG",
"miriam": "bacmap.biog",
"n2t": "bacmap.biog"
},
"name": "BacMap Biography",
"pattern": "^\\d+$",
"preferred_prefix": "bacmap.biog",
"uri_format": "http://bacmap.wishartlab.com/organisms/$1"
},
"bacmap.map": {
"description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information.",
"example": "AP011135",
"homepage": "http://bacmap.wishartlab.com/",
"mappings": {
"biocontext": "BACMAP.MAP",
"miriam": "bacmap.map",
"n2t": "bacmap.map"
},
"name": "BacMap Map",
"pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$",
"preferred_prefix": "bacmap.map",
"uri_format": "http://bacmap.wishartlab.com/maps/$1/index.html"
},
"bactibase": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria.",
"example": "BAC045",
"homepage": "http://bactibase.hammamilab.org",
"keywords": [
"life science",
"protein"
],
"mappings": {
"fairsharing": "FAIRsharing.5f5mfm",
"prefixcommons": "bactibase",
"re3data": "r3d100012755"
},
"name": "Bactibase",
"preferred_prefix": "bactibase",
"publications": [
{
"doi": "10.1186/1471-2180-10-22",
"pmc": "PMC2824694",
"pubmed": "20105292",
"title": "BACTIBASE second release: a database and tool platform for bacteriocin characterization.",
"year": 2010
},
{
"doi": "10.1186/1471-2180-7-89",
"pmc": "PMC2211298",
"pubmed": "17941971",
"title": "BACTIBASE: a new web-accessible database for bacteriocin characterization.",
"year": 2007
}
],
"uri_format": "http://bactibase.hammamilab.org/$1"
},
"bams": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"description": "BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions.",
"homepage": "https://bams1.org",
"name": "Brain Architecture Knowledge Management System Neuroanatomical Ontology",
"preferred_prefix": "bams",
"references": [
"https://www.frontiersin.org/articles/10.3389/neuro.11.002.2008/full"
]
},
"bao": {
"contact": {
"email": "sschurer@med.miami.edu",
"github": null,
"name": "Stephan Schurer",
"orcid": null
},
"description": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.",
"download_owl": "http://www.bioassayontology.org/bao/bao_complete.owl",
"example": "0002989",
"homepage": "http://bioassayontology.org",
"keywords": [
"biochemistry",
"biomedical science",
"life science",
"ontology"
],
"mappings": {
"aberowl": "BAO",
"biocontext": "BAO",
"bioportal": "BAO",
"fairsharing": "FAIRsharing.mye76w",
"miriam": "bao",
"n2t": "bao",
"ols": "bao",
"ontobee": "BAO"
},
"name": "BioAssay Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "bao",
"publications": [
{
"doi": "10.1186/2041-1480-5-s1-s5",
"pmc": "PMC4108877",
"pubmed": "25093074",
"title": "Evolving BioAssay Ontology (BAO): modularization, integration and applications.",
"year": 2014
},
{
"doi": "10.1371/journal.pone.0049198",
"pmc": "PMC3498356",
"pubmed": "23155465",
"title": "Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO).",
"year": 2012
},
{
"doi": "10.1186/1471-2105-12-257",
"pmc": "PMC3149580",
"pubmed": "21702939",
"title": "BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results.",
"year": 2011
},
{
"doi": "10:1371/journal.pone.0049198",
"pmc": null,
"pubmed": "10",
"title": "Digitoxin metabolism by rat liver microsomes.",
"year": 1975
}
],
"repository": "https://github.com/BioAssayOntology/BAO/wiki",
"synonyms": [
"BAO"
],
"uri_format": "http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1",
"version": "2.7.2"
},
"bartoc": {
"contact": {
"email": "andreas.ledl1@fhnw.ch",
"github": null,
"name": "Andreas Ledl",
"orcid": "0000-0002-0629-0446"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries.\nThe main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO).",
"example": "241",
"homepage": "https://bartoc.org",
"keywords": [
"knowledge and information systems",
"ontology and terminology"
],
"license": "PDDL 1.0",
"mappings": {
"fairsharing": "FAIRsharing.f1777e",
"wikidata": "P2689"
},
"name": "Basic Register of Thesauri, Ontologies & Classifications",
"pattern": "^[1-9][0-9]*$",
"preferred_prefix": "bartoc",
"repository": "https://github.com/gbv/bartoc.org",
"uri_format": "https://bartoc.org/en/node/$1"
},
"bbkg": {
"description": "Blue Brain Project's published data as knowledge graphs and Web Studios.",
"example": "topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a",
"homepage": "https://portal.bluebrain.epfl.ch",
"mappings": {
"miriam": "bbkg"
},
"name": "Blue Brain Project Knowledge Graph",
"pattern": "^[-\\w]+(?:\\/[-\\w]+)(?:\\/\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b)$",
"preferred_prefix": "bbkg",
"uri_format": "https://bbp.epfl.ch/nexus/web/studios/public/$1"
},
"bbtp": {
"description": "Input data and analysis results for the paper \"Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 ).",
"example": "f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a",
"homepage": "https://portal.bluebrain.epfl.ch",
"mappings": {
"miriam": "bbtp"
},
"name": "Blue Brain Project Topological sampling Knowledge Graph",
"pattern": "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$",
"preferred_prefix": "bbtp",
"uri_format": "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1"
},
"bcgo": {
"contact": {
"email": "jiezheng@pennmedicine.upenn.edu",
"github": "zhengj2007",
"name": "Jie Zheng",
"orcid": "0000-0002-2999-0103"
},
"deprecated": true,
"description": "An application ontology built for beta cell genomics studies.",
"download_owl": "https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl",
"example": "0000015",
"homepage": "https://github.com/obi-bcgo/bcgo",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "BCGO",
"biocontext": "BCGO",
"bioportal": "BCGO",
"cellosaurus": "BCGO",
"obofoundry": "bcgo",
"ontobee": "BCGO"
},
"name": "Beta Cell Genomics Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "BCGO",
"repository": "https://github.com/obi-bcgo/bcgo",
"uri_format": "http://purl.obolibrary.org/obo/BCGO_$1"
},
"bcio": {
"contact": {
"email": "srodriguez@pet.cs.nctu.edu.tw",
"github": null,
"name": "Sergio José Rodríguez Méndez",
"orcid": null
},
"description": "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation.",
"download_owl": "http://humanbehaviourchange.org/ontology/bcio.owl",
"example": "040000",
"homepage": "https://www.humanbehaviourchange.org/",
"keywords": [
"ontology"
],
"mappings": {
"aberowl": "BCI-O",
"bioportal": "BCI-O",
"ols": "bcio"
},
"name": "The Behaviour Change Intervention Ontology",
"pattern": "^\\d{6}$",
"preferred_prefix": "bcio",
"uri_format": "https://w3id.org/BCI-ontology#$1"
},
"bco": {
"appears_in": [
"fovt"
],
"contact": {
"email": "rlwalls2008@gmail.com",
"github": "ramonawalls",
"name": "Ramona Walls",
"orcid": "0000-0001-8815-0078"
},
"description": "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.",
"download_owl": "http://purl.obolibrary.org/obo/bco.owl",
"example": "0000081",
"homepage": "https://github.com/BiodiversityOntologies/bco",
"keywords": [
"biodiversity",
"ecology",
"metagenomics",
"obo",
"ontology",
"taxonomy"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "BCO",
"agroportal": "BCO",
"biocontext": "BCO",
"bioportal": "BCO",
"ecoportal": "BCO",
"fairsharing": "FAIRsharing.8ktkqy",
"obofoundry": "bco",
"ols": "bco",
"ontobee": "BCO"
},
"name": "Biological Collections Ontology",
"pattern": "^\\d{7}$",
"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_$1",
"version": "2021-11-14"
},
"bcrc": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Cell line collections",
"example": "60316",
"homepage": "https://catalog.bcrc.firdi.org.tw",
"keywords": [
"cell lines"
],
"mappings": {
"cellosaurus": "BCRC"
},
"name": "BCRC Strain Collection Catalog",
"pattern": "^\\d+$",
"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/$1"
},
"bdgp.est": {
"description": "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI).",
"example": "EY223054.1",
"has_canonical": "dbest",
"homepage": "https://www.ncbi.nlm.nih.gov/dbEST/index.html",
"keywords": [
"genome"
],
"mappings": {
"biocontext": "BDGP.EST",
"miriam": "bdgp.est",
"n2t": "bdgp.est",
"ncbi": "BDGP_EST",
"prefixcommons": "flybase.est"
},
"name": "Berkeley Drosophila Genome Project EST database",
"pattern": "^\\w+(\\.)?(\\d+)?$",
"preferred_prefix": "bdgp.est",
"uri_format": "https://www.ncbi.nlm.nih.gov/nucest/$1"
},
"bdgp.insertion": {
"description": "BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element.",
"example": "KG09531",
"homepage": "http://flypush.imgen.bcm.tmc.edu/pscreen/",
"keywords": [
"gene",
"sequence"
],
"mappings": {
"biocontext": "BDGP.INSERTION",
"miriam": "bdgp.insertion",
"n2t": "bdgp.insertion",
"prefixcommons": "bdgp"
},
"name": "BDGP insertion DB",
"pattern": "^\\w+$",
"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/$1"
},
"beetlebase": {
"description": "BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications.",
"example": "TC010103",
"homepage": "http://beetlebase.org/",
"keywords": [
"computational biology",
"genome",
"life science"
],
"mappings": {
"biocontext": "BEETLEBASE",
"fairsharing": "FAIRsharing.h5f091",
"miriam": "beetlebase",
"n2t": "beetlebase",
"ncbi": "BEETLEBASE",
"prefixcommons": "beetlebase",
"re3data": "r3d100010921"
},
"name": "Tribolium Genome Database -- Insertion",
"pattern": "^TC\\d+$",
"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=$1"
},
"begdb": {
"description": "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods.",
"example": "4214",
"homepage": "http://www.begdb.com",
"keywords": [
"life science"
],
"mappings": {
"biocontext": "BEGDB",
"fairsharing": "FAIRsharing.nbe4fq",
"miriam": "begdb",
"n2t": "begdb",
"re3data": "r3d100011166"
},
"name": "Benchmark Energy & Geometry Database",
"pattern": "^[0-9]+$",
"preferred_prefix": "begdb",
"publications": [
{
"doi": "10.1135/cccc20081261",
"pmc": null,
"pubmed": null,
"title": "Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples",
"year": 2008
}
],
"uri_format": "http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1"
},
"beiresources": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Cell line collections",
"example": "MRA-253",
"homepage": "https://www.beiresources.org",
"keywords": [
"cell lines"
],
"mappings": {
"cellosaurus": "BEI_Resources"
},
"name": "BEI Resources",
"preferred_prefix": "beiresources",
"synonyms": [
"BEI_Resources"
],
"uri_format": "https://www.beiresources.org/Catalog/cellBanks/$1.aspx"
},
"bel": {
"comment": "INDRA uses bel as a catch-all for scomp/sfam",
"contact": {
"email": "support@bel.bio",
"github": null,
"name": "William Hayes",
"orcid": "0000-0003-0728-781X"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents.",
"example": "9-1-1 Complex",
"homepage": "https://biological-expression-language.github.io/",
"keywords": [
"biology"
],
"mappings": {
"fairsharing": "FAIRsharing.dp0jvd"
},
"name": "Biological Expression Language",
"preferred_prefix": "bel"
},
"bfo": {
"appears_in": [
"ado",
"agro",
"aism",
"cdno",
"colao",
"duo",
"ecocore",
"epio",
"foodon",
"fovt",
"hso",
"lepao",
"mco",
"ons",
"pcl",
"pco",
"psdo",
"rbo",
"xpo",
"zp"
],
"contact": {
"email": "phismith@buffalo.edu",
"github": "phismith",
"name": "Barry Smith",
"orcid": "0000-0003-1384-116X"
},
"description": "The upper level ontology upon which OBO Foundry ontologies are built.",
"download_obo": "http://purl.obolibrary.org/obo/bfo.obo",
"download_owl": "http://purl.obolibrary.org/obo/bfo.owl",
"example": "0000001",
"homepage": "http://ifomis.org/bfo/",
"keywords": [
"obo",
"ontology",
"subject agnostic"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "BFO",
"agroportal": "BFO",
"biocontext": "BFO",
"bioportal": "BFO",
"fairsharing": "FAIRsharing.wcpd6f",
"go": "BFO",
"obofoundry": "bfo",
"ols": "bfo",
"ontobee": "BFO"
},
"name": "Basic Formal Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "BFO",
"repository": "https://github.com/BFO-ontology/BFO",
"uri_format": "http://purl.obolibrary.org/obo/BFO_$1",
"version": "2019-08-26"
},
"bgee.family": {
"description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species.",
"example": "ENSFM00500000270089",
"homepage": "http://bgee.unil.ch/bgee/bgee",
"mappings": {
"biocontext": "BGEE.FAMILY",
"miriam": "bgee.family",
"n2t": "bgee.family"
},
"name": "Bgee family",
"pattern": "^(ENSFM|ENSGTV:)\\d+$",
"preferred_prefix": "bgee.family",
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1"
},
"bgee.gene": {
"description": "Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee.",
"example": "FBgn0000015",
"homepage": "https://bgee.org/",
"keywords": [
"gene expression"
],
"mappings": {
"biocontext": "BGEE.GENE",
"miriam": "bgee.gene",
"n2t": "bgee.gene",
"prefixcommons": "bgee"
},
"name": "Bgee gene",
"pattern": "^[A-Za-z]+\\d+$",
"preferred_prefix": "bgee.gene",
"uri_format": "https://bgee.org/?page=gene&gene_id=$1"
},
"bgee.organ": {
"description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures.",
"example": "EHDAA:2185",
"homepage": "http://bgee.unil.ch/bgee/bgee",
"mappings": {
"biocontext": "BGEE.ORGAN",
"miriam": "bgee.organ",
"n2t": "bgee.organ"
},
"name": "Bgee organ",
"pattern": "^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\\:\\d+$",
"preferred_prefix": "bgee.organ",
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1"
},
"bgee.stage": {
"description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages.",
"example": "HsapDO:0000004",
"homepage": "http://bgee.unil.ch/bgee/bgee",
"mappings": {
"biocontext": "BGEE.STAGE",
"miriam": "bgee.stage",
"n2t": "bgee.stage"
},
"name": "Bgee stage",
"pattern": "^(FBvd|XtroDO|HsapDO|MmusDO)\\:\\d+$",
"preferred_prefix": "bgee.stage",
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1"
},
"bibo": {
"contact": {
"email": "fred@fgiasson.com",
"github": "fgiasson",
"name": "Frédérick Giasson",
"orcid": null
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Bibliographic Ontology Specification provides main concepts and properties for describing citations and bibliographic references (i.e. quotes, books, articles, etc) on the Semantic Web.",
"example": "authorList",
"homepage": "https://bibliontology.com/",
"keywords": [
"bibliometrics"
],
"name": "The Bibliographic Ontology",
"preferred_prefix": "bibo",
"uri_format": "http://purl.org/ontology/bibo/$1"
},
"bido": {
"contact": {
"email": "silvio.peroni@unibo.it",
"github": "essepuntato",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF.",
"example": "CategorialBibliometricData",
"homepage": "http://www.sparontologies.net/ontologies/bido",
"keywords": [
"subject agnostic"
],
"mappings": {
"fairsharing": "FAIRsharing.d7f0a9"
},
"name": "Bibliometric Data Ontology",
"preferred_prefix": "BiDO",
"repository": "https://github.com/sparontologies/bido",
"twitter": "sparontologies",
"uri_format": "http://purl.org/spar/bido/$1"
},
"bigg.compartment": {
"description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments.",
"example": "c",
"homepage": "http://bigg.ucsd.edu/compartments/",
"mappings": {
"biocontext": "BIGG.COMPARTMENT",
"miriam": "bigg.compartment",
"n2t": "bigg.compartment"
},
"name": "BiGG Compartment",
"pattern": "^[a-z_A-Z]+$",
"preferred_prefix": "bigg.compartment",
"uri_format": "http://bigg.ucsd.edu/compartments/$1"
},
"bigg.metabolite": {
"description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes.",
"example": "12dgr161",
"homepage": "http://bigg.ucsd.edu/universal/metabolites",
"mappings": {
"biocontext": "BIGG.METABOLITE",
"miriam": "bigg.metabolite",
"n2t": "bigg.metabolite"
},
"name": "BiGG Metabolite",
"pattern": "^[a-z_A-Z0-9]+$",
"preferred_prefix": "bigg.metabolite",
"uri_format": "http://bigg.ucsd.edu/models/universal/metabolites/$1"
},
"bigg.model": {
"description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models.",
"example": "iECABU_c1320",
"homepage": "http://bigg.ucsd.edu/models",
"mappings": {
"biocontext": "BIGG.MODEL",
"miriam": "bigg.model",
"n2t": "bigg.model"
},
"name": "BiGG Model",
"pattern": "^[a-z_A-Z0-9]+$",
"preferred_prefix": "bigg.model",
"uri_format": "http://bigg.ucsd.edu/models/$1"
},
"bigg.reaction": {
"description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions.",
"example": "13GS",
"homepage": "http://bigg.ucsd.edu/universal/reactions",
"mappings": {
"biocontext": "BIGG.REACTION",
"miriam": "bigg.reaction",
"n2t": "bigg.reaction"
},
"name": "BiGG Reaction",
"pattern": "^[a-z_A-Z0-9]+$",
"preferred_prefix": "bigg.reaction",
"uri_format": "http://bigg.ucsd.edu/models/universal/reactions/$1"
},
"bila": {
"contact": {
"email": "henrich@embl.de",
"github": null,
"name": "Thorsten Heinrich",
"orcid": null
},
"deprecated": true,
"description": "This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource.",
"download_owl": "http://purl.obolibrary.org/obo/bila.owl",
"example": "0000000",
"homepage": "http://4dx.embl.de/4DXpress",
"keywords": [
"anatomy",
"gene expression",
"obo",
"ontology"
],
"mappings": {
"biocontext": "BILA",
"fairsharing": "FAIRsharing.eqgjeq",
"obofoundry": "bila",
"prefixcommons": "4dxpress"
},
"name": "Bilateria anatomy",
"pattern": "^\\d{7}$",
"preferred_prefix": "BILA",
"publications": [
{
"doi": "10.1093/nar/gkm797",
"pmc": "PMC2238840",
"pubmed": "17916571",
"title": "4DXpress: a database for cross-species expression pattern comparisons.",
"year": 2007
}
],
"uri_format": "http://purl.obolibrary.org/obo/BILA_$1"
},
"bind": {
"deprecated": true,
"description": "Accession number of an entry from the BIND database.",
"example": "98346",
"homepage": "http://bind.ca",
"keywords": [
"interaction",
"pathway",
"small molecule"
],
"mappings": {
"biocontext": "BIND",
"edam": "1129",
"prefixcommons": "bind"
},
"name": "BIND accession number",
"preferred_prefix": "bind",
"publications": [
{
"doi": "10.1093/nar/gkg056",
"pmc": "PMC165503",
"pubmed": "12519993",
"title": "BIND: the Biomolecular Interaction Network Database.",
"year": 2003
},
{
"doi": "10.1093/bioinformatics/16.5.465",
"pmc": null,
"pubmed": "10871269",
"title": "BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways.",
"year": 2000
}
],
"uri_format": "http://www.bind.ca/Action?identifier=bindid&idsearch=$1"
},
"bindingdb": {
"contact": {
"email": "mgilson@health.ucsd.edu",
"github": null,
"name": "Michael K. Gilson",
"orcid": "0000-0002-3375-1738"
},
"description": "BindingDB is the first public database of protein-small molecule affinity data.",
"example": "e999",
"homepage": "https://www.bindingdb.org",
"keywords": [
"chemistry",
"computational chemistry",
"drug discovery",
"interaction",
"life science",
"medicinal chemistry",
"protein"
],
"mappings": {
"biocontext": "BINDINGDB",
"fairsharing": "FAIRsharing.3b36hk",
"miriam": "bindingdb",
"n2t": "bindingdb",
"prefixcommons": "bindingdb",
"re3data": "r3d100012074",
"uniprot": "DB-0127"
},
"name": "BindingDB",
"pattern": "^\\w\\d+$",
"preferred_prefix": "bindingdb",
"publications": [
{
"doi": "10.1093/nar/gkv1072",
"pmc": "PMC4702793",
"pubmed": "26481362",
"title": "BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology.",
"year": 2015
},
{
"doi": "10.1093/nar/gkl999",
"pmc": "PMC1751547",
"pubmed": "17145705",
"title": "BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities.",
"year": 2006
}
],
"uri_format": "http://www.bindingdb.org/compact/$1"
},
"biocarta.pathway": {
"description": "BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps.",
"example": "h_aktPathway",
"homepage": "https://www.biocarta.com/",
"mappings": {
"biocontext": "BIOCARTA.PATHWAY",
"miriam": "biocarta.pathway",
"n2t": "biocarta.pathway"
},
"name": "BioCarta Pathway",
"pattern": "^([hm]\\_)?\\w+Pathway$",
"preferred_prefix": "biocarta.pathway",
"uri_format": "https://cgap.nci.nih.gov/Pathways/BioCarta/$1"
},
"biocatalogue.service": {
"description": "The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all.",
"example": "614",
"homepage": "https://www.biocatalogue.org/",
"keywords": [
"registry"
],
"mappings": {
"biocontext": "BIOCATALOGUE.SERVICE",
"miriam": "biocatalogue.service",
"n2t": "biocatalogue.service",
"prefixcommons": "biocatalogue"
},
"name": "BioCatalogue Service",
"pattern": "^\\d+$",
"preferred_prefix": "biocatalogue.service",
"publications": [
{
"doi": "10.1093/nar/gkq394",
"pmc": "PMC2896129",
"pubmed": "20484378",
"title": "BioCatalogue: a universal catalogue of web services for the life sciences.",
"year": 2010
}
],
"uri_format": "https://www.biocatalogue.org/services/$1"
},
"biocyc": {
"description": "BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms.",
"example": "ECOLI:CYT-D-UBIOX-CPLX",
"homepage": "http://biocyc.org",
"keywords": [
"genome",
"pathway",
"sequence"
],
"mappings": {
"biocontext": "BIOCYC",
"edam": "2104",
"go": "BioCyc",
"miriam": "biocyc",
"n2t": "biocyc",
"prefixcommons": "biocyc",
"uniprot": "DB-0005"
},
"name": "BioCyc collection of metabolic pathway databases",
"pattern": "^[A-Z-0-9]+(\\:)?[A-Za-z0-9+_.%-:]+$",
"preferred_prefix": "biocyc",
"publications": [
{
"doi": "10.1093/nar/gkv1164",
"pmc": "PMC4702838",
"pubmed": "26527732",
"title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.",
"year": 2015
},
{
"doi": "10.1093/nar/gki892",
"pmc": "PMC1266070",
"pubmed": "16246909",
"title": "Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.",
"year": 2005
}
],
"uri_format": "http://biocyc.org/getid?id=$1"
},
"biofactoid": {
"contact": {
"email": "jeffvin.wong@utoronto.ca",
"github": "jvwong",
"name": "Jeffrey Wong",
"orcid": "0000-0002-8912-5699"
},
"contributor": {
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"description": "Biofactoid is a web-based system that empowers authors to capture and share machine-readable summaries of molecular-level interactions described in their publications.",
"example": "fdb8a927-45c3-48b7-9743-cbb5e16837fa",
"github_request_issue": 700,
"homepage": "https://biofactoid.org/",
"keywords": [
"biocuration",
"database",
"relationships"
],
"license": "CC0-1.0",
"name": "Biofactoid",
"pattern": "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$",
"preferred_prefix": "biofactoid",
"publications": [
{
"doi": "10.7554/elife.68292",
"pmc": "PMC8683078",
"pubmed": "34860157",
"title": "Author-sourced capture of pathway knowledge in computable form using Biofactoid.",
"year": 2021
}
],
"repository": "https://github.com/PathwayCommons/factoid",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://biofactoid.org/document/$1"
},
"biogrid": {
"description": "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe.",
"example": "31623",
"homepage": "http://thebiogrid.org/",
"keywords": [
"biochemistry",
"bioinformatics",
"chemical biology",
"cheminformatics",
"gene",
"interaction",
"life science",
"protein",
"proteomics",
"systems biology"
],
"mappings": {
"biocontext": "BIOGRID",
"fairsharing": "FAIRsharing.9d5f5r",
"miriam": "biogrid",
"n2t": "biogrid",
"prefixcommons": "biogrid",
"re3data": "r3d100010350",
"uniprot": "DB-0184"
},
"name": "BioGRID",
"pattern": "^\\d+$",
"preferred_prefix": "biogrid",
"publications": [
{
"doi": "10.1002/pro.3978",
"pmc": "PMC7737760",
"pubmed": "33070389",
"title": "The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions.",
"year": 2020
},
{
"doi": "10.1093/nar/gky1079",
"pmc": "PMC6324058",
"pubmed": "30476227",
"title": "The BioGRID interaction database: 2019 update.",
"year": 2019
},
{
"doi": "10.1093/nar/gkq1116",
"pmc": "PMC3013707",
"pubmed": "21071413",
"title": "The BioGRID Interaction Database: 2011 update.",
"year": 2010
},
{
"doi": "10.1093/nar/gkj109",
"pmc": "PMC1347471",
"pubmed": "16381927",
"title": "BioGRID: a general repository for interaction datasets.",
"year": 2006
},
{
"doi": "10.1186/gb-2003-4-3-r23",
"pmc": "PMC153463",
"pubmed": "12620108",
"title": "The GRID: the General Repository for Interaction Datasets.",
"year": 2003
}
],
"repository": "https://github.com/BioGRID",
"twitter": "biogrid",
"uri_format": "http://thebiogrid.org/$1"
},
"biogrid.interaction": {
"contact": {
"email": "md.tyers@umontreal.ca",
"github": null,
"name": "Mike Tyers",
"orcid": "0000-0002-9713-9994"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe.",
"example": "2649230",
"homepage": "https://thebiogrid.org/",
"mappings": {
"edam": "2628"
},
"name": "BioGRID Interactions",
"part_of": "biogrid",
"pattern": "^\\d+$",
"preferred_prefix": "biogrid.interaction",
"twitter": "biogrid",
"uri_format": "https://thebiogrid.org/interaction/$1"
},
"biolegend": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "BioLegend is a life sciences supply vendor.",
"example": "3403",
"homepage": "https://www.biolegend.com",
"keywords": [
"antibodies",
"assays",
"life sciences",
"reagents",
"vendor"
],
"name": "BioLegend",
"pattern": "^\\d+$",
"preferred_prefix": "biolegend",
"uri_format": "https://www.biolegend.com/Default.aspx?ID=6664&productid=$1"
},
"biolink": {
"contact": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"description": "A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations.",
"download_owl": "http://aber-owl.net/media/ontologies/BIOLINK/52/biolink.owl",
"example": "Gene",
"homepage": "https://biolink.github.io/biolink-model/",
"keywords": [
"biomedical science",
"functional genomics",
"medical biotechnology",
"medical informatics",
"ontology",
"translational medicine"
],
"mappings": {
"aberowl": "BIOLINK",
"biolink": "biolink",
"bioportal": "BIOLINK",
"fairsharing": "FAIRsharing.ad9d85",
"miriam": "biolink"
},
"name": "Biolink Model",
"pattern": "^\\S+$",
"preferred_prefix": "biolink",
"repository": "https://github.com/biolink/biolink-model",
"uri_format": "https://w3id.org/biolink/vocab/$1"
},
"biomagresbank": {
"description": "A repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids.",
"example": "10046",
"homepage": "http://www.bmrb.wisc.edu/",
"keywords": [
"protein"
],
"mappings": {
"prefixcommons": "biomagresbank"
},
"name": "BioMagResBank",
"preferred_prefix": "biomagresbank",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId=$1"
},
"biominder": {
"description": "Database of the dielectric properties of biological tissues.",
"example": "aef4c195-9cf9-46db-a12a-7cfd1ff3eec3",
"homepage": "https://datalab.rwth-aachen.de/MINDER",
"mappings": {
"biocontext": "BIOMINDER",
"miriam": "biominder",
"n2t": "biominder"
},
"name": "Bio-MINDER Tissue Database",
"pattern": "^[a-z0-9\\-]+$",
"preferred_prefix": "biominder",
"uri_format": "https://datalab.rwth-aachen.de/MINDER/resource/$1"
},
"biomodels.db": {
"description": "BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests.",
"example": "BIOMD0000000048",
"homepage": "https://www.ebi.ac.uk/biomodels/",
"keywords": [
"model"
],
"mappings": {
"biocontext": "BIOMODELS.DB",
"go": "BIOMD",
"miriam": "biomodels.db",
"n2t": "biomodels.db",
"prefixcommons": "biomodels"
},
"name": "BioModels Database",
"pattern": "^((BIOMD|MODEL)\\d{10})|(BMID\\d{12})$",
"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/$1"
},
"biomodels.kisao": {
"banana": "KISAO",
"banana_peel": "_",
"contact": {
"email": "jonrkarr@gmail.com",
"github": "jonrkarr",
"name": "Jonathan Karr",
"orcid": "0000-0002-2605-5080"
},
"description": "The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment.",
"download_owl": "http://purl.obolibrary.org/obo/kisao.owl",
"example": "0000057",
"homepage": "https://github.com/SED-ML/KiSAO",
"keywords": [
"bioinformatics",
"computer science",
"obo",
"ontology"
],
"license": "Artistic License 2.0",
"mappings": {
"aberowl": "KISAO",
"biocontext": "KISAO",
"bioportal": "KISAO",
"fairsharing": "FAIRsharing.jcg19w",
"miriam": "biomodels.kisao",
"n2t": "biomodels.kisao",
"obofoundry": "kisao",
"ols": "kisao",
"ontobee": "KISAO",
"prefixcommons": "kisao"
},
"name": "Kinetic Simulation Algorithm Ontology",
"namespace_in_lui": true,
"pattern": "^\\d+$",
"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": [
"biomodels.kisao",
"kisao"
],
"uri_format": "https://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=kisao:KISAO_$1",
"version": "2.30"
},
"biomodels.teddy": {
"banana": "TEDDY",
"banana_peel": "_",
"contact": {
"email": "biomodels-net-support@lists.sf.net",
"github": null,
"name": "BioModels.net team",
"orcid": null
},
"description": "The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.",
"download_owl": "http://svn.code.sf.net/p/teddyontology/code/teddy/tags/current/teddy-inferred.owl",
"example": "0000066",
"homepage": "http://teddyontology.sourceforge.net/",
"keywords": [
"neurophysiology",
"ontology",
"synthetic biology",
"systems biology"
],
"mappings": {
"aberowl": "TEDDY",
"biocontext": "BIOMODELS.TEDDY",
"bioportal": "TEDDY",
"fairsharing": "FAIRsharing.w9jvbt",
"miriam": "biomodels.teddy",
"n2t": "biomodels.teddy",
"ols": "teddy",
"prefixcommons": "teddy"
},
"name": "Terminology for Description of Dynamics",
"pattern": "^\\d+$",
"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"
},
"biopixie": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"description": "bioPIXIE is a novel system for biological data integration and visualization. It allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate.",
"example": "12",
"homepage": "http://pixie.princeton.edu/pixie/",
"keywords": [
"gene",
"interaction"
],
"mappings": {
"prefixcommons": "biopixie"
},
"name": "biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology",
"preferred_prefix": "biopixie",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://avis.princeton.edu/pixie/viewgraph.php?graphID=$1"
},
"bioportal": {
"contact": {
"email": "support@bioontology.org",
"github": null,
"name": "John Graybeal",
"orcid": "0000-0001-6875-5360"
},
"description": "BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies.",
"example": "1046",
"example_extras": [
"SEPIO",
"pseudo",
"FBBi"
],
"homepage": "http://bioportal.bioontology.org/",
"keywords": [
"life science",
"ontology",
"ontology and terminology"
],
"mappings": {
"biocontext": "BIOPORTAL",
"fairsharing": "FAIRsharing.4m97ah",
"miriam": "bioportal",
"n2t": "bioportal",
"prefixcommons": "bioportal",
"re3data": "r3d100012344"
},
"name": "BioPortal",
"pattern": "^(\\d+)|(\\w+)$",
"preferred_prefix": "bioportal",
"publications": [
{
"doi": "10.1093/nar/gkr469",
"pmc": "PMC3125807",
"pubmed": "21672956",
"title": "BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.",
"year": 2011
},
{
"doi": "10.1093/nar/gkp440",
"pmc": "PMC2703982",
"pubmed": "19483092",
"title": "BioPortal: ontologies and integrated data resources at the click of a mouse.",
"year": 2009
}
],
"repository": "http://github.com/ncbo",
"twitter": "bioontology",
"uri_format": "http://bioportal.bioontology.org/ontologies/$1"
},
"bioproject": {
"description": "BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories.",
"example": "PRJDB3",
"has_canonical": "ena.embl",
"homepage": "http://trace.ddbj.nig.ac.jp/bioproject/",
"keywords": [
"life science"
],
"mappings": {
"biocontext": "BIOPROJECT",
"fairsharing": "FAIRsharing.aqhv1y",
"miriam": "bioproject",
"n2t": "bioproject",
"re3data": "r3d100013330"
},
"name": "BioProject",
"pattern": "^PRJ[DEN][A-Z]\\d+$",
"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"
}
],
"publications": [
{
"doi": "10.1093/nar/gkr1163",
"pmc": "PMC3245069",
"pubmed": "22139929",
"title": "BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata.",
"year": 2011
}
],
"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",
"keywords": [
"bioinformatics",
"cheminformatics",
"computational biology",
"computational chemistry",
"life science",
"ontology and terminology"
],
"mappings": {
"fairsharing": "FAIRsharing.250a8c"
},
"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": 2022
}
],
"repository": "https://github.com/biopragmatics/bioregistry",
"twitter": "bioregistry",
"uri_format": "https://bioregistry.io/registry/$1"
},
"bioregistry.collection": {
"contact": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Manually curated collections of resources stored in the bioregistry",
"example": "0000001",
"homepage": "https://bioregistry.io/collection",
"keywords": [
"registry"
],
"name": "Bioregistry Collections",
"pattern": "^\\d{7}$",
"preferred_prefix": "bioregistry.collection",
"uri_format": "https://bioregistry.io/collection/$1"
},
"bioregistry.registry": {
"contact": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Bioregistry's meta-registry",
"example": "miriam",
"homepage": "https://bioregistry.io/metaregistry/",
"keywords": [
"data integration",
"data science",
"metaregistry",
"registry"
],
"name": "Bioregistry Metaregistry",
"preferred_prefix": "bioregistry.registry",
"uri_format": "https://bioregistry.io/metaregistry/$1"
},
"bioregistry.schema": {
"contact": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Schema for the export of the Bioregistry as RDF",
"example": "0000001",
"homepage": "https://bioregistry.io/schema",
"keywords": [
"registry"
],
"name": "Bioregistry Schema",
"pattern": "^\\d{7}$",
"preferred_prefix": "bioregistry.schema",
"uri_format": "https://bioregistry.io/schema/#$1"
},
"biorxiv": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The bioRxiv is a preprint server for biology",
"example": "2022.07.08.499378",
"example_extras": [
"000091",
"000091v1",
"2022.07.08.499378v2"
],
"homepage": "https://biorxiv.org",
"keywords": [
"preprints",
"publishing"
],
"mappings": {
"go": "bioRxiv",
"wikidata": "P3951"
},
"name": "bioRxiv",
"pattern": "^(\\d{4}\\.\\d{2}\\.\\d{2}\\.)?\\d{6,8}(v\\d{1,3})?$",
"preferred_prefix": "biorxiv",
"providers": [
{
"code": "scholia",
"description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.",
"homepage": "https://scholia.toolforge.org/",
"name": "Scholia",
"uri_format": "https://scholia.toolforge.org/biorxiv/$1"
}
],
"uri_format": "https://www.biorxiv.org/content/10.1101/$1"
},
"biosample": {
"description": "The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation.",
"example": "SAMEA2397676",
"homepage": "https://www.ebi.ac.uk/biosamples/",
"keywords": [
"biology"
],
"mappings": {
"biocontext": "BIOSAMPLE",
"cellosaurus": "BioSamples",
"fairsharing": "FAIRsharing.qr6pqk",
"miriam": "biosample",
"n2t": "biosample",
"re3data": "r3d100012828"
},
"name": "BioSample",
"pattern": "^SAM[NED](\\w)?\\d+$",
"preferred_prefix": "biosample",
"providers": [
{
"code": "ddbj",
"description": "BioSample at DNA Data Bank of Japan",
"homepage": "http://trace.ddbj.nig.ac.jp/biosample/",
"name": "BioSample at DNA Data Bank of Japan",
"uri_format": "http://trace.ddbj.nig.ac.jp/BSSearch/biosample?acc=$1"
},
{
"code": "ncbi",
"description": "BioSample at NCBI",
"homepage": "http://www.ncbi.nlm.nih.gov/biosample",
"name": "BioSample at NCBI",
"uri_format": "http://www.ncbi.nlm.nih.gov/biosample?term=$1"
}
],
"publications": [
{
"doi": "10.1093/nar/gkr1163",
"pmc": "PMC3245069",
"pubmed": "22139929",
"title": "BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata.",
"year": 2011
}
],
"synonyms": [
"biosamples"
],
"uri_format": "https://www.ebi.ac.uk/biosamples/sample/$1"
},
"biosimulations": {
"description": "BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools.",
"example": "Yeast-cell-cycle-Irons-J-Theor-Biol-2009",
"homepage": "https://icahn.mssm.edu/",
"mappings": {
"miriam": "biosimulations",
"re3data": "r3d100013361"
},
"name": "biosimulations",
"pattern": "^[a-zA-Z0-9_-]{3,}$",
"preferred_prefix": "biosimulations",
"uri_format": "https://biosimulations.org/projects/$1"
},
"biosimulators": {
"contact": {
"email": "karr@mssm.edu",
"github": null,
"name": "Jonathan Karr",
"orcid": "0000-0002-2605-5080"
},
"description": "BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML).",
"example": "vcell",
"homepage": "https://biosimulators.org/",
"keywords": [
"computational biology",
"systems biology"
],
"mappings": {
"fairsharing": "FAIRsharing.pwEima",
"miriam": "biosimulators",
"re3data": "r3d100013432"
},
"name": "BioSimulators",
"pattern": "^[a-zA-Z0-9-_]+$",
"preferred_prefix": "biosimulators",
"repository": "https://github.com/biosimulators/Biosimulators/issues/new/choose",
"uri_format": "https://biosimulators.org/simulators/$1"
},
"biostudies": {
"description": "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.",
"example": "S-EPMC6266652",
"homepage": "https://www.ebi.ac.uk/biostudies/",
"keywords": [
"biomedical science",
"life science"
],
"mappings": {
"fairsharing": "FAIRsharing.mtjvme",
"miriam": "biostudies",
"n2t": "biostudies",
"re3data": "r3d100012627"
},
"name": "BioStudies database",
"pattern": "^S-[A-Z]{4}[\\-\\_A-Z\\d]+$",
"preferred_prefix": "biostudies",
"publications": [
{
"doi": "10.1093/nar/gkx965",
"pmc": "PMC5753238",
"pubmed": "29069414",
"title": "The BioStudies database-one stop shop for all data supporting a life sciences study.",
"year": 2018
},
{
"doi": "10.15252/msb.20156658",
"pmc": "PMC4704487",
"pubmed": "26700850",
"title": "The BioStudies database.",
"year": 2015
}
],
"uri_format": "https://www.ebi.ac.uk/biostudies/studies/$1"
},
"biosystems": {
"description": "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources.",
"example": "001",
"homepage": "https://www.ncbi.nlm.nih.gov/biosystems/",
"keywords": [
"biology",
"molecules",
"pathways",
"systems biology"
],
"mappings": {
"biocontext": "BIOSYSTEMS",
"fairsharing": "FAIRsharing.w2eeqr",
"miriam": "biosystems",
"n2t": "biosystems",
"prefixcommons": "biosystems",
"re3data": "r3d100011033"
},
"name": "BioSystems",
"pattern": "^\\d+$",
"preferred_prefix": "biosystems",
"publications": [
{
"doi": "10.1093/nar/gkp858",
"pmc": "PMC2808896",
"pubmed": "19854944",
"title": "The NCBI BioSystems database.",
"year": 2009
}
],
"uri_format": "https://www.ncbi.nlm.nih.gov/biosystems/$1"
},
"biotools": {
"description": "BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research.",
"example": "bioregistry",
"homepage": "https://bio.tools/",
"keywords": [
"bioinformatics",
"biology",
"biomedical science"
],
"mappings": {
"biocontext": "BIOTOOLS",
"fairsharing": "FAIRsharing.63520c",
"miriam": "biotools",
"n2t": "biotools",
"re3data": "r3d100013668"
},
"name": "BioTools",
"pattern": "^[-A-Za-z0-9\\_]*$",
"preferred_prefix": "biotools",
"publications": [
{
"doi": "10.1093/nar/gkv1116",
"pmc": "PMC4702812",
"pubmed": "26538599",
"title": "Tools and data services registry: a community effort to document bioinformatics resources.",
"year": 2015
}
],
"repository": "http://github.com/bio-tools/biotoolsregistry/",
"uri_format": "https://bio.tools/$1"
},
"biozil": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Redistributor of bilogics and biomedical supplies",
"example": "ls-c35719-120",
"homepage": "https://www.biozol.de/en",
"keywords": [
"biologics",
"life sciences",
"vendor"
],
"name": "BIOZIL",
"preferred_prefix": "biozil",
"uri_format": "https://www.biozol.de/en/product/$1"
},
"birnlex": {
"comment": "Part of the NeuroLex namespace now",
"contact": {
"email": "wbug@ncmir.ucsd.edu",
"github": null,
"name": "William Bug",
"orcid": null
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design.",
"download_owl": "http://aber-owl.net/media/ontologies/BIRNLEX/1/birnlex.owl",
"example": "2023",
"homepage": "https://bioportal.bioontology.org/ontologies/BIRNLEX",
"keywords": [
"ontology"
],
"mappings": {
"aberowl": "BIRNLEX",
"bioportal": "BIRNLEX",
"fairsharing": "FAIRsharing.jedbbt"
},
"name": "Biomedical Informatics Research Network Lexicon",
"pattern": "^\\d+$",
"preferred_prefix": "birnlex",
"uri_format": "http://uri.neuinfo.org/nif/nifstd/birnlex_$1"
},
"biro": {
"contact": {
"email": "silvio.peroni@unibo.it",
"github": "essepuntato",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively.",
"example": "BibliographicRecord",
"homepage": "http://www.sparontologies.net/ontologies/biro",
"keywords": [
"subject agnostic"
],
"mappings": {
"fairsharing": "FAIRsharing.99da5f"
},
"name": "Bibliographic Reference Ontology",
"preferred_prefix": "BiRO",
"repository": "https://github.com/sparontologies/biro",
"twitter": "sparontologies",
"uri_format": "http://purl.org/spar/biro/$1"
},
"bitbucket": {
"description": "Bitbucket is a Git-based source code repository hosting service owned by Atlassian.",
"example": "andreadega/systems-biology-compiler",
"homepage": "https://www.atlassian.com/",
"keywords": [
"knowledge and information systems",
"software engineering",
"subject agnostic"
],
"mappings": {
"fairsharing": "FAIRsharing.fc3431",
"miriam": "bitbucket",
"re3data": "r3d100013478"
},
"name": "Bitbucket",
"pattern": "^[0-9A-Za-z-_\\.]+/[0-9A-Za-z-_\\.]+$",
"preferred_prefix": "bitbucket",
"uri_format": "https://bitbucket.org/$1"
},
"bitterdb.cpd": {
"description": "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds.",
"example": "46",
"homepage": "http://bitterdb.agri.huji.ac.il/dbbitter.php",
"mappings": {
"biocontext": "BITTERDB.CPD",
"miriam": "bitterdb.cpd",
"n2t": "bitterdb.cpd"
},
"name": "BitterDB Compound",
"pattern": "^\\d+$",
"preferred_prefix": "bitterdb.cpd",
"uri_format": "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1"
},
"bitterdb.rec": {
"description": "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors.",
"example": "1",
"homepage": "http://bitterdb.agri.huji.ac.il/dbbitter.php",
"mappings": {
"biocontext": "BITTERDB.REC",
"miriam": "bitterdb.rec",
"n2t": "bitterdb.rec"
},
"name": "BitterDB Receptor",
"pattern": "^\\d+$",
"preferred_prefix": "bitterdb.rec",
"uri_format": "http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1"
},
"bko": {
"comment": "This resource also uses SBO terms and resolves them, e.g., http://www.sbgnbricks.org/BKO/full/entry/all/SBO:0000177/.",
"contact": {
"email": "adrienrougny@gmail.com",
"github": "adrienrougny",
"name": "Adrien Rougny",
"orcid": "0000-0002-2118-035X"
},
"contributor": {
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"description": "SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way.",
"download_owl": "http://aber-owl.net/media/ontologies/BKO/1/bko.owl",
"example": "0000204",
"github_request_issue": 283,
"homepage": "http://www.sbgnbricks.org/",
"keywords": [
"ontology"
],
"mappings": {
"aberowl": "BKO",
"bioportal": "BKO"
},
"name": "SBGN Bricks data and ontology",
"pattern": "^\\d+$",
"preferred_prefix": "bko",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1"
},
"bmrb": {
"description": "BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy.",
"example": "15000",
"homepage": "http://www.bmrb.wisc.edu/",
"keywords": [
"structural biology"
],
"mappings": {
"fairsharing": "FAIRsharing.p06nme",
"miriam": "bmrb",
"re3data": "r3d100010191",
"uniprot": "DB-0256"
},
"name": "Biological Magnetic Resonance Data Bank",
"pattern": "^(bmr|bmse|bmst)?[0-9]{1,6}$",
"preferred_prefix": "bmrb",
"publications": [
{
"doi": "10.1007/s10858-008-9221-y",
"pmc": "PMC2268728",
"pubmed": "18288446",
"title": "BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions.",
"year": 2008
},
{
"doi": "10.1093/nar/gkm957",
"pmc": "PMC2238925",
"pubmed": "17984079",
"title": "BioMagResBank.",
"year": 2007
}
],
"uri_format": "http://rest.bmrb.wisc.edu/bmrb/$1/html"
},
"bmrb.restraint": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively.",
"example": "28789",
"homepage": "https://restraintsgrid.bmrb.io/NRG/MRGridServlet",
"keywords": [
"chemistry",
"nmr",
"spectrometry"
],
"name": "NMR Restraints Grid",
"pattern": "^\\d+$",
"preferred_prefix": "bmrb.restraint",
"uri_format": "https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1"
},
"bold.taxonomy": {
"description": "The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information.",
"example": "27267",
"homepage": "http://www.boldsystems.org/",
"keywords": [
"dna"
],
"mappings": {
"biocontext": "BOLD.TAXONOMY",
"miriam": "bold.taxonomy",
"n2t": "bold.taxonomy",
"ncbi": "BOLD",
"prefixcommons": "bold",
"wikidata": "P3606"
},
"name": "BOLD Systems taxon ID",
"pattern": "^\\d+$",
"preferred_prefix": "bold.taxonomy",
"publications": [
{
"doi": "10.1111/j.1471-8286.2007.01678.x",
"pmc": "PMC1890991",
"pubmed": "18784790",
"title": "bold: The Barcode of Life Data System (http://www.barcodinglife.org).",
"year": 2007
}
],
"uri_format": "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1"
},
"bootstrep": {
"contact": {
"email": "vlee@ebi.ac.uk",
"github": null,
"name": "Vivian Lee",
"orcid": null
},
"deprecated": true,
"homepage": "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html",
"keywords": [
"obo",
"ontology"
],
"mappings": {
"biocontext": "BOOTSTREP",
"obofoundry": "bootstrep"
},
"name": "Gene Regulation Ontology",
"preferred_prefix": "BOOTSTREP",
"uri_format": "http://purl.obolibrary.org/obo/BOOTSTREP_$1"
},
"bpdb": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Database of biopesticides maintained by the University of Hertfordshire ",
"example": "2404",
"homepage": "https://sitem.herts.ac.uk/aeru/bpdb/index.htm",
"keywords": [
"biology",
"biopesticides",
"pesticides"
],
"name": "Bio-Pesticides DataBase",
"pattern": "^\\d+$",
"preferred_prefix": "bpdb",
"uri_format": "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm"
},
"brenda": {
"description": "BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data.",
"example": "1.1.1.1",
"homepage": "https://www.brenda-enzymes.org/",
"keywords": [
"enzyme",
"life science"
],
"mappings": {
"biocontext": "BRENDA",
"fairsharing": "FAIRsharing.etp533",
"go": "BRENDA",
"miriam": "brenda",
"n2t": "brenda",
"prefixcommons": "brenda",
"re3data": "r3d100010616"
},
"name": "BRENDA Enzyme",
"pattern": "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$",
"preferred_prefix": "brenda",
"provides": "eccode",
"publications": [
{
"doi": "s0168-1656(17)30183-9",
"pmc": null,
"pubmed": "28438579",
"title": "The BRENDA enzyme information system-From a database to an expert system.",
"year": null
},
{
"doi": "10.1016/j.jbiotec.2017.04.020",
"pmc": null,
"pubmed": "28438579",
"title": "The BRENDA enzyme information system-From a database to an expert system.",
"year": 2017
},
{
"doi": "10.1093/nar/gku1068",
"pmc": "PMC4383907",
"pubmed": "25378310",
"title": "BRENDA in 2015: exciting developments in its 25th year of existence.",
"year": 2014
},
{
"doi": "10.1093/nar/gks1049",
"pmc": "PMC3531171",
"pubmed": "23203881",
"title": "BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.",
"year": 2012
},
{
"doi": "10.1093/nar/gkq1089",
"pmc": "PMC3013686",
"pubmed": "21062828",
"title": "BRENDA, the enzyme information system in 2011.",
"year": 2010
},
{
"doi": "10.1093/nar/gkn820",
"pmc": "PMC2686525",
"pubmed": "18984617",
"title": "BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009.",
"year": 2008
},
{
"doi": "10.1093/nar/gkl972",
"pmc": "PMC1899097",
"pubmed": "17202167",
"title": "BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.",
"year": 2007
},
{
"doi": "10.1093/nar/gkh081",
"pmc": "PMC308815",
"pubmed": "14681450",
"title": "BRENDA, the enzyme database: updates and major new developments.",
"year": 2004
},
{
"doi": "10.1016/s1096-7176(03)00008-9",
"pmc": null,
"pubmed": "12850129",
"title": "Review of the BRENDA Database.",
"year": 2003
},
{
"doi": "10.1016/s0968-0004(01)02027-8",
"pmc": null,
"pubmed": "11796225",
"title": "BRENDA: a resource for enzyme data and metabolic information.",
"year": 2002
},
{
"doi": "10.1093/nar/30.1.47",
"pmc": "PMC99121",
"pubmed": "11752250",
"title": "BRENDA, enzyme data and metabolic information.",
"year": 2002
}
],
"uri_format": "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1"
},
"brenda.ligand": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Information for ligands in the BRENDA database.",
"example": "278",
"homepage": "https://www.brenda-enzymes.de/ligand.php",
"keywords": [
"chemistry",
"structrual bioinformatics"
],
"name": "BRENDA Ligand",
"pattern": "^\\d+$",
"preferred_prefix": "brenda.ligand",
"uri_format": "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1"
},
"brenda.ligandgroup": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Information for ligand groups (chemical classes).",
"example": "18030",
"homepage": "https://www.brenda-enzymes.de/ligand.php",
"keywords": [
"chemistry",
"grouping",
"structrual bioinformatics"
],
"name": "BRENDA Ligand Group",
"pattern": "^\\d+$",
"preferred_prefix": "brenda.ligandgroup",
"uri_format": "https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1"
},
"broad": {
"description": "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae.",
"example": "S7000002168151102",
"homepage": "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/",
"mappings": {
"biocontext": "BROAD",
"miriam": "broad",
"n2t": "broad"
},
"name": "Broad Fungal Genome Initiative",
"pattern": "^S\\d+$",
"preferred_prefix": "broad",
"uri_format": "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1"
},
"bs": {
"comment": "An alernative vocabulary that has been aligned and integrated in Sequence Ontology (SO).",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library.",
"download_obo": "https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/subsets/biosapiens.obo",
"example": "00042",
"homepage": "https://github.com/The-Sequence-Ontology/SO-Ontologies",
"keywords": [
"ontology"
],
"name": "Biosapiens Protein Feature Ontology",
"pattern": "^\\d+$",
"preferred_prefix": "bs",
"repository": "https://github.com/The-Sequence-Ontology/SO-Ontologies",
"uri_format": "https://biopragmatics.github.io/providers/bs/$1"
},
"bspo": {
"appears_in": [
"aism",
"colao",
"fovt",
"lepao",
"zp"
],
"contact": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"description": "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies.",
"download_json": "http://purl.obolibrary.org/obo/bspo.json",
"download_obo": "https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo",
"download_owl": "http://purl.obolibrary.org/obo/bspo.owl",
"example": "0000029",
"homepage": "https://github.com/obophenotype/biological-spatial-ontology",
"keywords": [
"anatomy",
"life science",
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "BSPO",
"biocontext": "BSPO",
"bioportal": "BSPO",
"fairsharing": "FAIRsharing.newa3z",
"obofoundry": "bspo",
"ols": "bspo",
"ontobee": "BSPO"
},
"name": "Biological Spatial Ontology",
"pattern": "^\\d{7}$",
"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_$1",
"version": "2022-06-28"
},
"bto": {
"banana": "BTO",
"contact": {
"email": "c.dudek@tu-braunschweig.de",
"github": "chdudek",
"name": "Christian-Alexander Dudek",
"orcid": "0000-0001-9117-7909"
},
"description": "The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.",
"download_json": "http://purl.obolibrary.org/obo/bto.json",
"download_obo": "http://purl.obolibrary.org/obo/bto.obo",
"download_owl": "http://purl.obolibrary.org/obo/bto.owl",
"example": "0000590",
"homepage": "http://www.brenda-enzymes.org",
"keywords": [
"enzymology",
"life science",
"obo",
"ontology",
"tissue"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "BTO",
"biocontext": "BTO",
"bioportal": "BTO",
"cellosaurus": "BTO",
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{
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"cbioportal": {
"description": "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.",
"example": "laml_tcga_pub",
"homepage": "http://www.cbioportal.org",
"keywords": [
"biomedical science",
"genomics",
"preclinical studies",
"proteomics"
],
"mappings": {
"fairsharing": "FAIRsharing.6L6MjA",
"miriam": "cbioportal",
"n2t": "cbioportal"
},
"name": "The cBioPortal for Cancer Genomics",
"pattern": "^[a-z0-9\\_]+$",
"preferred_prefix": "cbioportal",
"publications": [
{
"doi": "10.1126/scisignal.2004088",
"pmc": "PMC4160307",
"pubmed": "23550210",
"title": "Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.",
"year": 2013
},
{
"doi": "10.1158/2159-8290.cd-12-0095",
"pmc": "PMC3956037",
"pubmed": "22588877",
"title": "The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.",
"year": 2012
}
],
"repository": "https://github.com/cBioPortal/cbioportal",
"twitter": "cbioportal",
"uri_format": "https://www.cbioportal.org/study/summary?id=$1"
},
"ccdc": {
"description": "The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC.",
"example": "1829126",
"homepage": "https://www.ccdc.cam.ac.uk/",
"mappings": {
"miriam": "ccdc"
},
"name": "CCDC Number",
"pattern": "^\\d{6,7}$",
"preferred_prefix": "ccdc",
"uri_format": "https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG"
},
"ccds": {
"description": "The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations.",
"example": "CCDS13573.1",
"homepage": "http://www.ncbi.nlm.nih.gov/CCDS/",
"keywords": [
"gene",
"life science",
"protein"
],
"mappings": {
"biocontext": "CCDS",
"fairsharing": "FAIRsharing.46s4nt",
"miriam": "ccds",
"n2t": "ccds",
"prefixcommons": "ccds",
"uniprot": "DB-0187"
},
"name": "Consensus CDS",
"pattern": "^CCDS\\d+\\.\\d+$",
"preferred_prefix": "ccds",
"publications": [
{
"doi": "10.1101/gr.080531.108",
"pmc": "PMC2704439",
"pubmed": "19498102",
"title": "The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.",
"year": 2009
}
],
"uri_format": "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1"
},
"ccle": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Datasets around different cancer cell lines generated by the Broad Institute and Novartis",
"example": "BT20_BREAST",
"homepage": "https://www.cbioportal.org/study/summary?id=ccle_broad_2019",
"mappings": {
"cellosaurus": "CCLE"
},
"name": "Cancer Cell Line Encyclopedia Cells",
"preferred_prefix": "ccle",
"synonyms": [
"ccle.cell"
],
"uri_format": "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1"
},
"cco": {
"banana": "CCO",
"contact": {
"email": "kuiper@bio.ntnu.no",
"github": "makuintnu",
"name": "Martin Kuiper",
"orcid": "0000-0002-1171-9876"
},
"description": "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process.",
"download_obo": "https://www.bio.ntnu.no/ontology/CCO/cco.obo",
"download_owl": "https://www.bio.ntnu.no/ontology/CCO/cco.owl",
"example": "0000003",
"homepage": "http://www.semantic-systems-biology.org/apo",
"keywords": [
"cell cycle",
"functional genomics",
"genomics",
"life science",
"obo",
"ontology",
"proteomics"
],
"mappings": {
"aberowl": "CCO",
"biocontext": "CCO",
"bioportal": "CCO",
"fairsharing": "FAIRsharing.xhwrnr",
"miriam": "cco",
"n2t": "cco",
"ols": "cco",
"prefixcommons": "cco"
},
"name": "Cell Cycle Ontology",
"namespace_in_lui": true,
"pattern": "^\\w+$",
"preferred_prefix": "cco",
"publications": [
{
"doi": "10.1186/gb-2009-10-5-r58",
"pmc": "PMC2718524",
"pubmed": "19480664",
"title": "The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process.",
"year": 2009
}
],
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1",
"version": "2016-03-23"
},
"ccrid": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Cell line databases/resources",
"example": "4201PAT-CCTCC00348",
"homepage": "http://www.cellresource.cn",
"mappings": {
"cellosaurus": "CCRID"
},
"name": "National Experimental Cell Resource Sharing Platform",
"preferred_prefix": "ccrid",
"uri_format": "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1"
},
"cdao": {
"contact": {
"email": "balhoff@renci.org",
"github": "balhoff",
"name": "Jim Balhoff",
"orcid": "0000-0002-8688-6599"
},
"description": "The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character.",
"download_owl": "http://purl.obolibrary.org/obo/cdao.owl",
"example": "0000072",
"homepage": "https://github.com/evoinfo/cdao",
"keywords": [
"bioinformatics",
"biomedical science",
"evolutionary biology",
"life science",
"molecular biology",
"obo",
"ontology",
"phylogenetics",
"taxonomy"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "CDAO",
"agroportal": "CDAO",
"biocontext": "CDAO",
"bioportal": "CDAO",
"fairsharing": "FAIRsharing.kay31r",
"obofoundry": "cdao",
"ols": "cdao",
"ontobee": "CDAO"
},
"name": "Comparative Data Analysis Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CDAO",
"publications": [
{
"doi": "10.4137/ebo.s2320",
"pmc": "PMC2747124",
"pubmed": "19812726",
"title": "Initial implementation of a comparative data analysis ontology.",
"year": 2009
}
],
"repository": "https://github.com/evoinfo/cdao",
"uri_format": "http://purl.obolibrary.org/obo/CDAO_$1",
"version": "2019-06-26"
},
"cdd": {
"description": "The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution.",
"example": "cd00400",
"homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd",
"keywords": [
"earth science",
"geology",
"protein",
"structure"
],
"mappings": {
"biocontext": "CDD",
"edam": "2666",
"fairsharing": "FAIRsharing.ea287c",
"go": "CDD",
"miriam": "cdd",
"n2t": "cdd",
"ncbi": "CDD",
"prefixcommons": "cdd",
"re3data": "r3d100012041",
"uniprot": "DB-0214"
},
"name": "Conserved Domain Database at NCBI",
"pattern": "^(cd)?\\d{5}$",
"preferred_prefix": "cdd",
"publications": [
{
"doi": "doi",
"pmc": "PMC4383992",
"pubmed": "25414356",
"title": null,
"year": null
},
{
"doi": "10.1093/nar/gku1221",
"pmc": "PMC4383992",
"pubmed": "25414356",
"title": "CDD: NCBI's conserved domain database.",
"year": 2014
},
{
"doi": "10.1093/nar/gkn845",
"pmc": "PMC2686570",
"pubmed": "18984618",
"title": "CDD: specific functional annotation with the Conserved Domain Database.",
"year": 2008
}
],
"uri_format": "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"
},
"cdno": {
"contact": {
"email": "l.andres.hernandez.18@student.scu.edu.au",
"github": "LilyAndres",
"name": "Liliana Andres Hernandez",
"orcid": "0000-0002-7696-731X"
},
"depends_on": [
"bfo",
"chebi",
"envo",
"pato",
"ro"
],
"description": "None",
"download_obo": "http://purl.obolibrary.org/obo/cdno.obo",
"download_owl": "http://purl.obolibrary.org/obo/cdno.owl",
"example": "0000013",
"homepage": "https://cdno.info/",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "CDNO",
"bioportal": "CDNO",
"obofoundry": "cdno",
"ols": "cdno",
"ontobee": "CDNO"
},
"name": "Compositional Dietary Nutrition Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CDNO",
"publications": [
{
"doi": "10.1002/csc2.20092",
"pmc": null,
"pubmed": null,
"title": "Knowledge representation and data sharing to unlock crop variation for nutritional food security",
"year": 2020
}
],
"repository": "https://github.com/Southern-Cross-Plant-Science/cdno",
"uri_format": "http://purl.obolibrary.org/obo/CDNO_$1",
"version": "2022-06-23"
},
"cdpd": {
"description": "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN).",
"example": "63250",
"homepage": "http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp",
"mappings": {
"biocontext": "CDPD",
"miriam": "cdpd",
"n2t": "cdpd"
},
"name": "Canadian Drug Product Database",
"pattern": "^\\d+$",
"preferred_prefix": "cdpd",
"uri_format": "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1"
},
"cdt": {
"appears_in": [
"ohd"
],
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment.",
"download_owl": "https://github.com/oral-health-and-disease-ontologies/ohd-ontology/blob/master/src/ontology/older/CDTCodes%20as%20Classes_pruned.owl",
"example": "1000001",
"homepage": "https://www.ada.org/publications/CDT",
"keywords": [
"ontology"
],
"mappings": {
"bartoc": "20299",
"hl7": "2.16.840.1.113883.6.116"
},
"name": "Current Dental Terminology",
"pattern": "^\\d{7}$",
"preferred_prefix": "cdt"
},
"cell_biolabs": {
"description": "Cell line collections",
"example": "AKR-270",
"homepage": "https://www.cellbiolabs.com",
"mappings": {
"cellosaurus": "Cell_Biolabs"
},
"name": "Cell Biolabs cell line products",
"preferred_prefix": "cell_biolabs",
"uri_format": "https://www.cellbiolabs.com/search?keywords=$1"
},
"cell_model_passport": {
"description": "Cell line databases/resources",
"example": "SIDM01262",
"homepage": "https://cellmodelpassports.sanger.ac.uk/",
"mappings": {
"cellosaurus": "Cell_Model_Passport"
},
"name": "Sanger Cell Model Passports",
"preferred_prefix": "cell_model_passport",
"uri_format": "https://cellmodelpassports.sanger.ac.uk/passports/$1"
},
"cellbank.australia": {
"description": "CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world.",
"example": "ab-1-ha",
"homepage": "http://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/",
"mappings": {
"cellosaurus": "CBA"
},
"name": "CellBank Australia",
"preferred_prefix": "cellbank.australia",
"uri_format": "https://www.cellbankaustralia.com/$1.html"
},
"cellimage": {
"description": "The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.",
"example": "24801",
"homepage": "http://cellimagelibrary.org/",
"keywords": [
"cell biology",
"image",
"life science"
],
"mappings": {
"biocontext": "CELLIMAGE",
"fairsharing": "FAIRsharing.8t18te",
"miriam": "cellimage",
"n2t": "cellimage",
"prefixcommons": "cellimage",
"re3data": "r3d100000023"
},
"name": "Cell Image Library",
"pattern": "^\\d+$",
"preferred_prefix": "cellimage",
"publications": [
{
"doi": "10.1093/nar/gks1257",
"pmc": "PMC3531121",
"pubmed": "23203874",
"title": "The cell: an image library-CCDB: a curated repository of microscopy data.",
"year": 2012
}
],
"twitter": "CellImageLibrar",
"uri_format": "http://cellimagelibrary.org/images/$1"
},
"cellopub": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Cellosaurus identifeirs for publications, like Pubmed",
"example": "CLPUB00496",
"homepage": "https://web.expasy.org/cellosaurus/",
"mappings": {
"cellosaurus": "CelloPub"
},
"name": "Cellosaurus Publication",
"pattern": "^CLPUB\\d+$",
"preferred_prefix": "cellopub",
"uri_format": "https://web.expasy.org/cellosaurus/cellopub/$1"
},
"cellosaurus": {
"banana": "CVCL",
"banana_peel": "_",
"contact": {
"email": "Amos.Bairoch@sib.swiss",
"github": "AmosBairoch",
"name": "Amos Bairoch",
"orcid": "0000-0003-2826-6444"
},
"description": "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.",
"download_obo": "https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo",
"example": "0440",
"homepage": "https://cellosaurus.org",
"keywords": [
"life science",
"ontology"
],
"mappings": {
"biocontext": "CELLOSAURUS",
"cellosaurus": "Cellosaurus",
"fairsharing": "FAIRsharing.hkk309",
"miriam": "cellosaurus",
"n2t": "cellosaurus",
"re3data": "r3d100013293",
"wikidata": "P3289"
},
"name": "Cellosaurus",
"pattern": "^[A-Z0-9]{4}$",
"preferred_prefix": "cellosaurus",
"providers": [
{
"code": "legacy",
"description": "The legacy URI for the Cellosaurus website, updated on August 30, 2022 [ref](https://twitter.com/Cellosaurus/status/1564658792691810305).",
"homepage": "https://web.expasy.org/cellosaurus",
"name": "Legacy Endpoint",
"uri_format": "https://web.expasy.org/cellosaurus/CVCL_$1"
}
],
"publications": [
{
"doi": "10.1002/ijc.32639",
"pmc": null,
"pubmed": "31444973",
"title": "CLASTR: The Cellosaurus STR similarity search tool - A precious help for cell line authentication.",
"year": 2019
},
{
"doi": "10.7171/jbt.18-2902-002",
"pmc": "PMC5945021",
"pubmed": "29805321",
"title": "The Cellosaurus, a Cell-Line Knowledge Resource.",
"year": 2018
}
],
"synonyms": [
"CVCL"
],
"twitter": "cellosaurus",
"uri_format": "https://www.cellosaurus.org/CVCL_$1"
},
"cellosaurus.resource": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The set of prefixes used in the Cellosaurus resource",
"example": "4DN",
"homepage": "https://web.expasy.org/cellosaurus/",
"keywords": [
"cell lines",
"cells",
"registry"
],
"name": "Cellosaurus Registry",
"preferred_prefix": "cellosaurus.resource",
"uri_format": "https://bioregistry.io/metaregistry/cellosaurus/$1"
},
"cellrepo": {
"description": "The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines",
"example": "82",
"homepage": "https://cellrepo.ico2s.org/",
"mappings": {
"miriam": "cellrepo"
},
"name": "Cell Version Control Repository",
"pattern": "^[0-9]+$",
"preferred_prefix": "cellrepo",
"uri_format": "https://cellrepo.ico2s.org/repositories/$1"
},
"cemo": {
"contact": {
"email": "n.queralt_rosinach@lumc.nl",
"github": "NuriaQueralt",
"name": "Núria Queralt Rosinach",
"orcid": "0000-0003-0169-8159"
},
"contributor": {
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"description": "The covid-19 epidemiology and monitoring ontology (cemo) provides a common ontological model to make epidemiological quantitative data for monitoring the covid-19 outbreak machine-readable and interoperable to facilitate its exchange, integration and analysis, to eventually support evidence-based rapid response.",
"download_json": "https://raw.githubusercontent.com/cthoyt/covid19-epidemiology-ontology/add-artifacts/owl/cemo.json",
"download_owl": "https://raw.githubusercontent.com/NuriaQueralt/covid19-epidemiology-ontology/main/owl/cemo.owl",
"example": "secondary_attack_rate",
"github_request_issue": 593,
"homepage": "https://github.com/NuriaQueralt/covid19-epidemiology-ontology",
"keywords": [
"ontology"
],
"license": "CC0-1.0",
"name": "The COVID-19 epidemiology and monitoring ontology",
"pattern": "^[0-9a-z_-]+$",
"preferred_prefix": "cemo",
"providers": [
{
"code": "obo",
"description": "This represents misconfigured base IRIs, even though this ontology isn't an OBO Foundry ontology",
"homepage": "http://purl.obolibrary.org/obo/",
"name": "Legacy OBO PURL",
"uri_format": "http://purl.obolibrary.org/obo/cemo.owl#$1"
}
],
"repository": "https://github.com/NuriaQueralt/covid19-epidemiology-ontology",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://biopragmatics.github.io/providers/cemo/$1"
},
"ceph": {
"contact": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"deprecated": true,
"description": "An anatomical and developmental ontology for cephalopods",
"download_obo": "https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo",
"download_owl": "http://purl.obolibrary.org/obo/ceph.owl",
"example": "0000109",
"homepage": "https://github.com/obophenotype/cephalopod-ontology",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "CEPH",
"biocontext": "CEPH",
"bioportal": "CEPH",
"fairsharing": "FAIRsharing.p58bm4",
"obofoundry": "ceph",
"ols": "ceph",
"ontobee": "CEPH"
},
"name": "Cephalopod Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CEPH",
"repository": "https://github.com/obophenotype/cephalopod-ontology",
"uri_format": "http://purl.obolibrary.org/obo/CEPH_$1",
"version": "2016-01-12"
},
"cgd": {
"description": "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.",
"example": "CAL0003079",
"homepage": "http://www.candidagenome.org/",
"keywords": [
"eukaryotic",
"genome",
"life science",
"nucleotide"
],
"mappings": {
"biocontext": "CGD",
"fairsharing": "FAIRsharing.j7j53",
"go": "CGD",
"miriam": "cgd",
"n2t": "cgd",
"ncbi": "CGD",
"prefixcommons": "cgd",
"re3data": "r3d100010617",
"uniprot": "DB-0126"
},
"name": "Candida Genome Database",
"pattern": "^CAL\\d{7}$",
"preferred_prefix": "cgd",
"publications": [
{
"doi": "10.1093/nar/gkw924",
"pmc": "PMC5210628",
"pubmed": "27738138",
"title": "The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data.",
"year": 2016
},
{
"doi": "10.1093/nar/gkr945",
"pmc": "PMC3245171",
"pubmed": "22064862",
"title": "The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata.",
"year": 2011
},
{
"doi": "10.1093/nar/gki003",
"pmc": "PMC539957",
"pubmed": "15608216",
"title": "The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information.",
"year": 2005
}
],
"uri_format": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"
},
"cghdb": {
"description": "Cell line databases/resources",
"example": "300165/p13898_2106T",
"homepage": "http://www.cghtmd.jp/CGHDatabase/index_e.jsp",
"mappings": {
"cellosaurus": "CGH-DB"
},
"name": "CGH Data Base",
"preferred_prefix": "cghdb",
"uri_format": "http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en"
},
"cgnc": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)",
"example": "10087",
"homepage": "http://birdgenenames.org/cgnc/",
"keywords": [
"gene"
],
"mappings": {
"prefixcommons": "cgnc",
"re3data": "r3d100012429"
},
"name": "Chicken Gene Nomenclature Consortium",
"pattern": "^\\d+$",
"preferred_prefix": "cgnc",
"publications": [
{
"doi": "10.1186/1471-2164-10-s2-s5",
"pmc": "PMC2966335",
"pubmed": "19607656",
"title": "The Chicken Gene Nomenclature Committee report.",
"year": 2009
}
],
"synonyms": [
"BirdBase",
"CGNC"
],
"uri_format": "http://birdgenenames.org/cgnc/GeneReport?id=$1"
},
"cgsc": {
"description": "The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature.",
"example": "74",
"homepage": "http://cgsc.biology.yale.edu/index.php",
"keywords": [
"gene",
"life science"
],
"mappings": {
"biocontext": "CGSC",
"fairsharing": "FAIRsharing.1tbrdz",
"go": "CGSC",
"miriam": "cgsc",
"n2t": "cgsc",
"prefixcommons": "cgsc",
"re3data": "r3d100010585"
},
"name": "Coli Genetic Stock Center",
"pattern": "^\\d+$",
"preferred_prefix": "cgsc",
"publications": [
{
"doi": "10.1016/s0076-6879(06)21001-2",
"pmc": null,
"pubmed": "17352909",
"title": "Strain collections and genetic nomenclature.",
"year": 2007
}
],
"uri_format": "http://cgsc.biology.yale.edu/Site.php?ID=$1"
},
"charprot": {
"description": "CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession.",
"example": "CH_001923",
"homepage": "http://www.jcvi.org/charprotdb",
"mappings": {
"biocontext": "CHARPROT",
"miriam": "charprot",
"n2t": "charprot"
},
"name": "CharProt",
"pattern": "^CH_\\d+$",
"preferred_prefix": "charprot",
"uri_format": "http://www.jcvi.org/charprotdb/index.cgi/view/$1"
},
"chebi": {
"appears_in": [
"cdno",
"chiro",
"cl",
"ecocore",
"ecto",
"envo",
"fobi",
"foodon",
"genepio",
"maxo",
"mco",
"ons",
"pcl",
"proco",
"scdo",
"uberon",
"xpo"
],
"banana": "CHEBI",
"contact": {
"email": "amalik@ebi.ac.uk",
"github": "amalik01",
"name": "Adnan Malik",
"orcid": "0000-0001-8123-5351"
},
"description": "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds.",
"download_obo": "http://purl.obolibrary.org/obo/chebi.obo",
"download_owl": "http://purl.obolibrary.org/obo/chebi.owl",
"example": "24867",
"homepage": "http://www.ebi.ac.uk/chebi",
"keywords": [
"biochemistry",
"chemical",
"chemistry",
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "CHEBI",
"bartoc": "558",
"biocontext": "CHEBI",
"bioportal": "CHEBI",
"cellosaurus": "ChEBI",
"cheminf": "000407",
"edam": "1174",
"fairsharing": "FAIRsharing.62qk8w",
"go": "CHEBI",
"miriam": "chebi",
"n2t": "chebi",
"obofoundry": "chebi",
"ols": "chebi",
"ontobee": "CHEBI",
"prefixcommons": "chebi",
"re3data": "r3d100012626",
"wikidata": "P683"
},
"name": "Chemical Entities of Biological Interest",
"namespace_in_lui": true,
"pattern": "^\\d+$",
"preferred_prefix": "CHEBI",
"providers": [
{
"code": "chebi-img",
"description": "Image server from chebi",
"homepage": "https://www.ebi.ac.uk/chebi/",
"name": "ChEBI",
"uri_format": "https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=$1"
}
],
"publications": [
{
"doi": "10.1093/nar/gkv1031",
"pmc": "PMC4702775",
"pubmed": "26467479",
"title": "ChEBI in 2016: Improved services and an expanding collection of metabolites.",
"year": 2015
},
{
"doi": "10.1093/nar/gks1146",
"pmc": "PMC3531142",
"pubmed": "23180789",
"title": "The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.",
"year": 2012
},
{
"doi": "10.1093/nar/gkp886",
"pmc": "PMC2808869",
"pubmed": "19854951",
"title": "Chemical Entities of Biological Interest: an update.",
"year": 2009
},
{
"doi": "10.1002/0471250953.bi1409s26",
"pmc": null,
"pubmed": "19496059",
"title": "ChEBI: an open bioinformatics and cheminformatics resource.",
"year": 2009
},
{
"doi": "10.1093/nar/gkm791",
"pmc": "PMC2238832",
"pubmed": "17932057",
"title": "ChEBI: a database and ontology for chemical entities of biological interest.",
"year": 2007
}
],
"repository": "https://github.com/ebi-chebi/ChEBI",
"synonyms": [
"CHEBI",
"CHEBIID",
"ChEBI"
],
"twitter": "chebit",
"uri_format": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1",
"version": "211"
},
"chembank": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"description": "ChemBank is a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG).",
"example": "1000000",
"homepage": "http://chembank.broad.harvard.edu",
"keywords": [
"chemical",
"metabolite"
],
"mappings": {
"biocontext": "CHEMBANK",
"biolink": "ChemBank",
"prefixcommons": "chembank"
},
"name": "ChemBank",
"preferred_prefix": "chembank",
"publications": [
{
"doi": "10.1093/nar/gkm843",
"pmc": "PMC2238881",
"pubmed": "17947324",
"title": "ChemBank: a small-molecule screening and cheminformatics resource database.",
"year": 2007
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$1"
},
"chembl": {
"description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.",
"example": "CHEMBL4303805",
"homepage": "https://www.ebi.ac.uk/chembl",
"keywords": [
"biochemistry",
"drug discovery",
"genomics",
"medicinal chemistry",
"molecules"
],
"mappings": {
"cheminf": "000412",
"fairsharing": "FAIRsharing.m3jtpg",
"miriam": "chembl",
"prefixcommons": "chembl",
"re3data": "r3d100010539",
"uniprot": "DB-0174"
},
"name": "ChEMBL",
"pattern": "^CHEMBL\\d+$",
"preferred_prefix": "chembl",
"publications": [
{
"doi": "10.1093/nar/gky1075",
"pmc": "PMC6323927",
"pubmed": "30398643",
"title": "ChEMBL: towards direct deposition of bioassay data.",
"year": 2019
},
{
"doi": "10.1093/nar/gkw1074",
"pmc": "PMC5210557",
"pubmed": "27899562",
"title": "The ChEMBL database in 2017.",
"year": 2016
},
{
"doi": "10.1093/nar/gkt1031",
"pmc": "PMC3965067",
"pubmed": "24214965",
"title": "The ChEMBL bioactivity database: an update.",
"year": 2013
},
{
"doi": "10.1093/nar/gkr777",
"pmc": "PMC3245175",
"pubmed": "21948594",
"title": "ChEMBL: a large-scale bioactivity database for drug discovery.",
"year": 2011
}
],
"repository": "https://github.com/chembl/GLaDOS",
"synonyms": [
"ChEMBL",
"ChEMBL_ID",
"chembl"
],
"twitter": "chembl",
"uri_format": "https://www.ebi.ac.uk/chembl/entity/$1"
},
"chembl.cell": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Chemistry resources",
"example": "CHEMBL3307800",
"homepage": "https://www.ebi.ac.uk/chembldb",
"keywords": [
"bioactivities",
"cell lines"
],
"mappings": {
"cellosaurus": "ChEMBL-Cells"
},
"name": "ChEMBL database of bioactive drug-like small molecules - Cell lines section",
"part_of": "chembl",
"preferred_prefix": "chembl.cell",
"synonyms": [
"ChEMBL-Cells"
],
"uri_format": "https://www.ebi.ac.uk/chembl/cell_line_report_card/$1"
},
"chembl.compound": {
"description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.",
"example": "CHEMBL465070",
"homepage": "https://www.ebi.ac.uk/chembldb/",
"mappings": {
"biocontext": "CHEMBL.COMPOUND",
"edam": "2646",
"miriam": "chembl.compound",
"n2t": "chembl.compound",
"wikidata": "P592"
},
"name": "ChEMBL",
"part_of": "chembl",
"pattern": "^CHEMBL\\d+$",
"preferred_prefix": "chembl.compound",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "ChEMBL compound RDF",
"homepage": "https://github.com/egonw/chembl.rdf",
"name": "ChEMBL compound RDF",
"uri_format": "http://linkedchemistry.info/chembl/chemblid/$1"
},
{
"code": "CURATOR_REVIEW",
"description": "ChEMBL compound RDF through EBI RDF Platform",
"homepage": "https://www.ebi.ac.uk/rdf/services/chembl/",
"name": "ChEMBL compound RDF through EBI RDF Platform",
"uri_format": "https://rdf.ebi.ac.uk/resource/chembl/molecule/$1"
}
],
"uri_format": "https://www.ebi.ac.uk/chembl/compound/inspect/$1"
},
"chembl.target": {
"description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.",
"example": "CHEMBL3467",
"homepage": "https://www.ebi.ac.uk/chembldb/",
"mappings": {
"biocontext": "CHEMBL.TARGET",
"cellosaurus": "ChEMBL-Targets",
"miriam": "chembl.target",
"n2t": "chembl.target"
},
"name": "ChEMBL target",
"part_of": "chembl",
"pattern": "^CHEMBL\\d+$",
"preferred_prefix": "chembl.target",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "ChEMBL target RDF",
"homepage": "https://github.com/egonw/chembl.rdf",
"name": "ChEMBL target RDF",
"uri_format": "http://linkedchemistry.info/chembl/chemblid/$1"
},
{
"code": "CURATOR_REVIEW",
"description": "ChEMBL target RDF through EBI RDF Platform",
"homepage": "https://rdf.ebi.ac.uk/resource/chembl/",
"name": "ChEMBL target RDF through EBI RDF Platform",
"uri_format": "https://rdf.ebi.ac.uk/resource/chembl/target/$1"
}
],
"synonyms": [
"ChEMBL-Targets"
],
"uri_format": "https://www.ebi.ac.uk/chembl/target/inspect/$1"
},
"chemdb": {
"description": "ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds.",
"example": "3966782",
"homepage": "http://cdb.ics.uci.edu/",
"keywords": [
"biochemistry",
"biomedical science",
"life science",
"preclinical studies",
"small molecule",
"systems biology"
],
"mappings": {
"biocontext": "CHEMDB",
"fairsharing": "FAIRsharing.dstf7h",
"miriam": "chemdb",
"n2t": "chemdb",
"prefixcommons": "chemdb"
},
"name": "ChemDB",
"pattern": "^\\d+$",
"preferred_prefix": "chemdb",
"publications": [
{
"doi": "10.1093/bioinformatics/btm341",
"pmc": null,
"pubmed": "17599932",
"title": "ChemDB update--full-text search and virtual chemical space.",
"year": 2007
},
{
"doi": "10.1093/bioinformatics/bti683",
"pmc": null,
"pubmed": "16174682",
"title": "ChemDB: a public database of small molecules and related chemoinformatics resources.",
"year": 2005
}
],
"uri_format": "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1"
},
"chemidplus": {
"description": "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.",
"example": "57-27-2",
"homepage": "https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp",
"keywords": [
"biomedical science",
"chemistry",
"molecules",
"structure"
],
"mappings": {
"biocontext": "CHEMIDPLUS",
"edam": "2658",
"fairsharing": "FAIRsharing.5949vn",
"miriam": "chemidplus",
"n2t": "chemidplus",
"prefixcommons": "chemidplus"
},
"name": "ChemIDplus",
"pattern": "^\\d+\\-\\d+\\-\\d+$",
"preferred_prefix": "chemidplus",
"publications": [
{
"doi": "10.1300/j115v21n01_04",
"pmc": null,
"pubmed": "11989279",
"title": "ChemIDplus-super source for chemical and drug information.",
"year": 2002
}
],
"synonyms": [
"ChemIDplus"
],
"uri_format": "https://chem.nlm.nih.gov/chemidplus/rn/$1"
},
"cheminf": {
"appears_in": [
"proco"
],
"contact": {
"email": "egon.willighagen@gmail.com",
"github": "egonw",
"name": "Egon Willighagen",
"orcid": "0000-0001-7542-0286"
},
"description": "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.",
"download_owl": "https://github.com/semanticchemistry/semanticchemistry/raw/master/ontology/cheminf.owl",
"example": "000410",
"homepage": "https://github.com/semanticchemistry/semanticchemistry",
"keywords": [
"biochemistry",
"chemistry",
"life science",
"obo",
"ontology"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "CHEMINF",
"biocontext": "CHEMINF",
"bioportal": "CHEMINF",
"fairsharing": "FAIRsharing.sjhvyy",
"obofoundry": "cheminf",
"ols": "cheminf",
"ontobee": "CHEMINF"
},
"name": "Chemical Information Ontology",
"pattern": "^\\d{6}$",
"preferred_prefix": "CHEMINF",
"providers": [
{
"code": "semanticscience",
"description": "Legacy URLs before conversion of CHEMINF to OBO PURLs",
"homepage": "http://semanticscience.org",
"name": "Semantic Science",
"uri_format": "http://semanticscience.org/resource/CHEMINF_$1"
}
],
"publications": [
{
"doi": "10.1371/journal.pone.0025513",
"pmc": "PMC3184996",
"pubmed": "21991315",
"title": "The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.",
"year": 2011
}
],
"repository": "https://github.com/semanticchemistry/semanticchemistry",
"uri_format": "http://purl.obolibrary.org/obo/CHEMINF_$1",
"version": "2.0"
},
"chemrof": {
"contact": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "CHEMROF is an ontological framework for Chemical Entities Mixtures Reactions Ontological Framework. This OWL ontology is an automated Translation of the source LinkML schema, https://w3id.org/chemrof",
"download_owl": "http://aber-owl.net/media/ontologies/CHEMROF/2/chemrof.owl",
"example": "FullySpecifiedAtom",
"homepage": "https://chemkg.github.io/chemrof/",
"keywords": [
"ontology"
],
"mappings": {
"aberowl": "CHEMROF",
"bioportal": "CHEMROF"
},
"name": "Chemical Entity Materials and Reactions Ontological Framework",
"preferred_prefix": "ChEMROF",
"uri_format": "https://chemkg.github.io/chemrof/$1"
},
"chemspider": {
"description": "ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources.",
"example": "56586",
"homepage": "http://www.chemspider.com/",
"keywords": [
"chemistry",
"life science",
"molecules",
"structure"
],
"mappings": {
"biocontext": "CHEMSPIDER",
"cheminf": "000405",
"edam": "1173",
"fairsharing": "FAIRsharing.96f3gm",
"miriam": "chemspider",
"n2t": "chemspider",
"prefixcommons": "chemspider",
"re3data": "r3d100010205",
"wikidata": "P661"
},
"name": "ChemSpider",
"pattern": "^\\d+$",
"preferred_prefix": "chemspider",
"publications": [
{
"doi": "10.1021/ed100697w",
"pmc": null,
"pubmed": null,
"title": "ChemSpider: An Online Chemical Information Resource",
"year": 2010
}
],
"synonyms": [
"ChemSpiderID",
"Chemspider"
],
"twitter": "ChemSpider",
"uri_format": "http://www.chemspider.com/Chemical-Structure.$1.html"
},
"chickenqtldb": {
"description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs.",
"example": "14362",
"homepage": "https://www.animalgenome.org/QTLdb",
"keywords": [
"dna",
"genome"
],
"mappings": {
"biocontext": "CHICKENQTLDB",
"miriam": "chickenqtldb",
"n2t": "chickenqtldb",
"prefixcommons": "chickenqtldb"
},
"name": "Animal Genome Chicken QTL",
"part_of": "qtldb",
"pattern": "^\\d+$",
"preferred_prefix": "chickenqtldb",
"uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"
},
"chiro": {
"contact": {
"email": "vasilevs@ohsu.edu",
"github": "nicolevasilevsky",
"name": "Nicole Vasilevsky",
"orcid": "0000-0001-5208-3432"
},
"depends_on": [
"chebi",
"go",
"hp",
"mp",
"ncbitaxon",
"pr",
"uberon"
],
"description": "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.",
"download_obo": "http://purl.obolibrary.org/obo/chiro.obo",
"download_owl": "http://purl.obolibrary.org/obo/chiro.owl",
"homepage": "https://github.com/obophenotype/chiro",
"keywords": [
"obo",
"ontology"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "CHIRO",
"bioportal": "CHIRO",
"obofoundry": "chiro",
"ols": "chiro",
"ontobee": "CHIRO"
},
"name": "ChEBI Integrated Role Ontology",
"no_own_terms": true,
"preferred_prefix": "CHIRO",
"publications": [
{
"doi": "10.26434/chemrxiv.12591221",
"pmc": null,
"pubmed": null,
"title": "Extension of Roles in the ChEBI Ontology",
"year": 2020
}
],
"repository": "https://github.com/obophenotype/chiro",
"uri_format": "http://purl.obolibrary.org/obo/CHIRO_$1",
"version": "2015-11-23"
},
"chmo": {
"appears_in": [
"rbo",
"scdo"
],
"contact": {
"email": "batchelorc@rsc.org",
"github": "batchelorc",
"name": "Colin Batchelor",
"orcid": "0000-0001-5985-7429"
},
"description": "CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI).",
"download_obo": "http://purl.obolibrary.org/obo/chmo.obo",
"download_owl": "http://purl.obolibrary.org/obo/chmo.owl",
"example": "0002902",
"homepage": "https://github.com/rsc-ontologies/rsc-cmo",
"keywords": [
"chemistry",
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "CHMO",
"biocontext": "CHMO",
"bioportal": "CHMO",
"fairsharing": "FAIRsharing.9j4wh2",
"obofoundry": "chmo",
"ols": "chmo",
"ontobee": "CHMO"
},
"name": "Chemical Methods Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CHMO",
"repository": "https://github.com/rsc-ontologies/rsc-cmo",
"uri_format": "http://purl.obolibrary.org/obo/CHMO_$1",
"version": "2022-04-19"
},
"cido": {
"contact": {
"email": "yongqunh@med.umich.edu",
"github": "yongqunh",
"name": "Yongqun Oliver He",
"orcid": "0000-0001-9189-9661"
},
"description": "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.",
"download_owl": "https://github.com/CIDO-ontology/cido/raw/master/cido.owl",
"example": "0000005",
"homepage": "https://github.com/cido-ontology/cido",
"keywords": [
"bioinformatics",
"drug discovery",
"drug repositioning",
"epidemiology",
"obo",
"ontology",
"virology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "CIDO",
"bioportal": "CIDO",
"fairsharing": "FAIRsharing.aVmpKl",
"obofoundry": "cido",
"ols": "cido",
"ontobee": "CIDO"
},
"name": "Coronavirus Infectious Disease Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CIDO",
"publications": [
{
"doi": "10.1186/s13326-022-00279-z",
"pmc": "PMC9585694",
"pubmed": "36271389",
"title": "A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.",
"year": 2022
},
{
"doi": "10.1038/s41597-020-0523-6",
"pmc": "PMC7293349",
"pubmed": "32533075",
"title": "CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis.",
"year": 2020
}
],
"repository": "https://github.com/cido-ontology/cido",
"uri_format": "http://purl.obolibrary.org/obo/CIDO_$1",
"version": "1.0.337"
},
"cio": {
"contact": {
"email": "frederic.bastian@unil.ch",
"github": "fbastian",
"name": "Frédéric Bastian",
"orcid": "0000-0002-9415-5104"
},
"description": "An ontology to capture confidence information about annotations.",
"download_obo": "http://purl.obolibrary.org/obo/cio.obo",
"download_owl": "http://purl.obolibrary.org/obo/cio.owl",
"example": "0000040",
"homepage": "https://github.com/BgeeDB/confidence-information-ontology",
"keywords": [
"biology",
"obo",
"ontology"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "CIO",
"biocontext": "CIO",
"bioportal": "CIO",
"fairsharing": "FAIRsharing.e3t0yw",
"obofoundry": "cio",
"ols": "cio",
"ontobee": "CIO"
},
"name": "Confidence Information Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CIO",
"publications": [
{
"doi": "10.1093/database/bav043",
"pmc": "PMC4425939",
"pubmed": "25957950",
"title": "The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.",
"year": 2015
}
],
"repository": "https://github.com/BgeeDB/confidence-information-ontology",
"uri_format": "http://purl.obolibrary.org/obo/CIO_$1",
"version": "2015-03-10"
},
"citexplore": {
"contact": {
"email": "maria.taboada@usc.es",
"github": null,
"name": "Maria Taboada",
"orcid": "0000-0002-2353-596X"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes.",
"example": "C6155",
"homepage": "https://www.ebi.ac.uk/citexplore/",
"keywords": [
"biomedical science",
"genetics",
"preclinical studies"
],
"mappings": {
"fairsharing": "FAIRsharing.619eqr",
"prefixcommons": "citexplore"
},
"name": "CiteXplore",
"preferred_prefix": "citexplore",
"publications": [
{
"doi": "10.1097/mol.0b013e328362df13",
"pmc": null,
"pubmed": "23759795",
"title": "Cerebrotendinous xanthomatosis.",
"year": 2013
}
],
"references": [
"https://www.embl.de/aboutus/communication_outreach/media_relations/2006/061127_hinxton/"
],
"synonyms": [
"CTX"
],
"uri_format": "https://europepmc.org/article/CTX/$1"
},
"cito": {
"contact": {
"email": "silvio.peroni@unibo.it",
"github": "essepuntato",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology that enables characterization of the nature or type of citations, both factually and rhetorically.",
"example": "sharesAuthorInstitutionWith",
"homepage": "http://www.sparontologies.net/ontologies/cito",
"keywords": [
"knowledge and information systems"
],
"mappings": {
"fairsharing": "FAIRsharing.b220d4"
},
"name": "Citation Typing Ontology",
"preferred_prefix": "CiTO",
"publications": [
{
"doi": "10.1016/j.websem.2012.08.001",
"pmc": null,
"pubmed": null,
"title": "FaBiO and CiTO: Ontologies for describing bibliographic resources and citations",
"year": 2012
}
],
"repository": "https://github.com/sparontologies/cito",
"twitter": "sparontologies",
"uri_format": "http://purl.org/spar/cito/$1"
},
"civic.aid": {
"description": "A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC.",
"example": "3",
"homepage": "https://civicdb.org/",
"mappings": {
"miriam": "civic.aid"
},
"name": "CIViC Assertion",
"part_of": "civic",
"pattern": "^[0-9]+$",
"preferred_prefix": "civic.aid",
"uri_format": "https://civicdb.org/links/assertions/$1"
},
"civic.did": {
"description": "Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement.",
"example": "46",
"homepage": "https://civicdb.org/",
"mappings": {
"miriam": "civic.did"
},
"name": "CIViC Disease",
"part_of": "civic",
"pattern": "^[0-9]+$",
"preferred_prefix": "civic.did",
"uri_format": "https://civicdb.org/links/diseases/$1"
},
"civic.eid": {
"description": "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract).",
"example": "1199",
"homepage": "https://civicdb.org/",
"mappings": {
"miriam": "civic.eid"
},
"name": "CIViC Evidence",
"part_of": "civic",
"pattern": "^[0-9]+$",
"preferred_prefix": "civic.eid",
"uri_format": "https://civicdb.org/links/evidence/$1"
},
"civic.gid": {
"description": "A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus on emphasizing the clinical relevance from a molecular perspective rather than describing the biological function of the gene unless necessary to contextualize its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes, specific treatments for the gene’s associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis",
"example": "272",
"homepage": "https://civicdb.org/",
"mappings": {
"miriam": "civic.gid",
"wikidata": "P11277"
},
"name": "CIViC gene ID",
"part_of": "civic",
"pattern": "^[0-9]+$",
"preferred_prefix": "civic.gid",
"uri_format": "https://civicdb.org/links/gene/$1"
},
"civic.sid": {
"description": "In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source.",
"example": "62",
"homepage": "https://civicdb.org/",
"mappings": {
"miriam": "civic.sid"
},
"name": "CIViC Source",
"part_of": "civic",
"pattern": "^[0-9]+$",
"preferred_prefix": "civic.sid",
"uri_format": "https://civicdb.org/links/sources/$1"
},
"civic.tid": {
"description": "Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant.",
"example": "14",
"homepage": "https://civicdb.org/",
"mappings": {
"miriam": "civic.tid"
},
"name": "CIViC Therapy",
"part_of": "civic",
"pattern": "^[0-9]+$",
"preferred_prefix": "civic.tid",
"uri_format": "https://civicdb.org/links/drugs/$1"
},
"civic.vid": {
"description": "CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making.",
"example": "12",
"homepage": "https://civicdb.org/",
"mappings": {
"miriam": "civic.vid",
"wikidata": "P3329"
},
"name": "CIViC variant ID",
"part_of": "civic",
"pattern": "^[0-9]+$",
"preferred_prefix": "civic.vid",
"uri_format": "https://civicdb.org/links/variant/$1"
},
"cl": {
"appears_in": [
"clo",
"ecao",
"ehdaa2",
"go",
"mco",
"pcl",
"uberon",
"xpo"
],
"banana": "CL",
"contact": {
"email": "addiehl@buffalo.edu",
"github": "addiehl",
"name": "Alexander Diehl",
"orcid": "0000-0001-9990-8331"
},
"depends_on": [
"chebi",
"go",
"ncbitaxon",
"pato",
"pr",
"ro",
"uberon"
],
"description": "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.",
"download_obo": "https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-full.obo",
"download_owl": "http://purl.obolibrary.org/obo/cl.owl",
"example": "0000062",
"homepage": "https://obophenotype.github.io/cell-ontology/",
"keywords": [
"anatomy",
"cell",
"cell biology",
"life science",
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "CL",
"agroportal": "CL",
"biocontext": "CL",
"bioportal": "CL",
"cellosaurus": "CL",
"fairsharing": "FAIRsharing.j9y503",
"go": "CL",
"miriam": "cl",
"n2t": "cl",
"obofoundry": "cl",
"ols": "cl",
"ontobee": "CL",
"prefixcommons": "cl",
"wikidata": "P7963"
},
"name": "Cell Ontology",
"namespace_in_lui": true,
"pattern": "^\\d{7}$",
"preferred_prefix": "CL",
"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:$1",
"version": "2022-12-15"
},
"clao": {
"contact": {
"email": "lagonzalezmo@unal.edu.co",
"github": "luis-gonzalez-m",
"name": "Luis González-Montaña",
"orcid": "0000-0002-9136-9932"
},
"depends_on": [
"ro"
],
"description": "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).",
"download_obo": "http://purl.obolibrary.org/obo/clao.obo",
"download_owl": "http://purl.obolibrary.org/obo/clao.owl",
"example": "0000088",
"homepage": "https://github.com/luis-gonzalez-m/Collembola",
"keywords": [
"obo",
"ontology"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "CLAO",
"bioportal": "CLAO",
"obofoundry": "clao",
"ols": "clao",
"ontobee": "CLAO"
},
"name": "Collembola Anatomy Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CLAO",
"repository": "https://github.com/luis-gonzalez-m/Collembola",
"uri_format": "http://purl.obolibrary.org/obo/CLAO_$1",
"version": "2021-09-27"
},
"classyfire": {
"banana": "C",
"comment": "There's a mismatch between the MIRIAM URI format string, which has a C prefix in front of class identifiers and the ontology which does not use them.",
"description": "ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API.",
"download_obo": "http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip",
"example": "0004828",
"homepage": "http://classyfire.wishartlab.com/",
"keywords": [
"ontology"
],
"mappings": {
"miriam": "classyfire"
},
"name": "ClassyFire",
"pattern": "^\\d{7}$",
"preferred_prefix": "classyfire",
"synonyms": [
"CHEMONTID"
],
"uri_format": "http://classyfire.wishartlab.com/tax_nodes/C$1"
},
"clb": {
"description": "ChecklistBank is an index and repository for taxonomic and nomenclatural datasets",
"example": "1010",
"homepage": "https://www.checklistbank.org",
"mappings": {
"miriam": "clb"
},
"name": "ChecklistBank",
"pattern": "^[0-9]+(LR)?$",
"preferred_prefix": "clb",
"uri_format": "https://www.checklistbank.org/dataset/$1"
},
"cldb": {
"description": "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories.",
"example": "cl3603",
"homepage": "http://bioinformatics.hsanmartino.it/hypercldb/indexes.html",
"mappings": {
"biocontext": "CLDB",
"cellosaurus": "CLDB",
"miriam": "cldb",
"n2t": "cldb"
},
"name": "Cell Line Database",
"pattern": "^(cl|tum)\\d+$",
"preferred_prefix": "cldb",
"uri_format": "http://bioinformatics.hsanmartino.it/hypercldb/$1.html"
},
"clingene": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor_extras": [
{
"email": null,
"github": "sierra-moxon",
"name": "Sierra Moxon",
"orcid": "0000-0002-8719-7760"
}
],
"description": "The allele registry provides and maintains identifiers for genetic variants",
"example": "CA981206459",
"homepage": "https://reg.clinicalgenome.org",
"keywords": [
"alleles",
"genetics",
"mutations"
],
"mappings": {
"biolink": "CAID"
},
"name": "ClinGen Allele Registry",
"pattern": "^CA\\d+$",
"preferred_prefix": "clingene",
"references": [
"https://github.com/biopragmatics/bioregistry/issues/647"
],
"synonyms": [
"CAID"
],
"uri_format": "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1"
},
"clinicaltrials": {
"description": "ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries",
"example": "NCT00222573",
"homepage": "https://clinicaltrials.gov/",
"keywords": [
"disease",
"drug",
"human"
],
"mappings": {
"biocontext": "CLINICALTRIALS",
"miriam": "clinicaltrials",
"n2t": "clinicaltrials",
"prefixcommons": "clinicaltrials",
"wikidata": "P3098"
},
"name": "ClinicalTrials.gov ID",
"pattern": "^NCT\\d{8}$",
"preferred_prefix": "clinicaltrials",
"providers": [
{
"code": "smartpatients",
"description": "Smart Patients is an online community for patients and their families. Join us to talk with other patients about the latest research for your condition.",
"homepage": "https://www.smartpatients.com",
"name": "Smart Patients",
"uri_format": "https://www.smartpatients.com/trials/$1"
}
],
"synonyms": [
"clinicaltrial"
],
"uri_format": "https://clinicaltrials.gov/ct2/show/$1"
},
"clinvar": {
"description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier.",
"example": "12345",
"homepage": "http://www.ncbi.nlm.nih.gov/clinvar/",
"keywords": [
"biomedical science",
"clinical studies",
"genomics",
"preclinical studies"
],
"mappings": {
"biocontext": "ClinVarVariant",
"biolink": "CLINVAR",
"cellosaurus": "ClinVar",
"fairsharing": "FAIRsharing.wx5r6f",
"hl7": "2.16.840.1.113883.6.319",
"miriam": "clinvar",
"n2t": "clinvar",
"re3data": "r3d100013331",
"wikidata": "P1929"
},
"name": "ClinVar Variation",
"pattern": "^\\d+$",
"preferred_prefix": "clinvar",
"publications": [
{
"doi": "10.1093/nar/gkt1113",
"pmc": "PMC3965032",
"pubmed": "24234437",
"title": "ClinVar: public archive of relationships among sequence variation and human phenotype.",
"year": 2013
}
],
"synonyms": [
"clinvar.variant",
"clinvar.variation"
],
"uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1"
},
"clinvar.record": {
"description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession.",
"example": "RCV000033555.3",
"homepage": "http://www.ncbi.nlm.nih.gov/clinvar/",
"mappings": {
"biocontext": "CLINVAR.RECORD",
"miriam": "clinvar.record",
"n2t": "clinvar.record"
},
"name": "ClinVar Record",
"part_of": "clinvar",
"pattern": "^RCV\\d+(\\.\\d+)?$",
"preferred_prefix": "clinvar.record",
"uri_format": "http://www.ncbi.nlm.nih.gov/clinvar/$1"
},
"clinvar.submission": {
"description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession.",
"example": "SCV000151292",
"homepage": "http://www.ncbi.nlm.nih.gov/clinvar/",
"mappings": {
"biocontext": "CLINVAR.SUBMISSION",
"miriam": "clinvar.submission",
"n2t": "clinvar.submission"
},
"name": "ClinVar Submission",
"pattern": "^SCV\\d+(\\.\\d+)?$",
"preferred_prefix": "clinvar.submission",
"uri_format": "http://www.ncbi.nlm.nih.gov/clinvar?term=$1"
},
"clinvar.submitter": {
"description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs).",
"example": "26957",
"homepage": "https://www.ncbi.nlm.nih.gov/clinvar/",
"mappings": {
"miriam": "clinvar.submitter"
},
"name": "ClinVar Submitter",
"pattern": "^\\d+$",
"preferred_prefix": "clinvar.submitter",
"uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1"
},
"clo": {
"appears_in": [
"mco"
],
"contact": {
"email": "siiraa@umich.edu",
"github": "siiraa",
"name": "Sirarat Sarntivijai",
"orcid": "0000-0002-2548-641X"
},
"depends_on": [
"cl",
"doid",
"ncbitaxon",
"uberon"
],
"description": "The Cell Line Ontology is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.",
"download_owl": "http://purl.obolibrary.org/obo/clo.owl",
"example": "0000091",
"homepage": "http://www.clo-ontology.org",
"keywords": [
"cell biology",
"life science",
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "CLO",
"biocontext": "CLO",
"bioportal": "CLO",
"cellosaurus": "CLO",
"fairsharing": "FAIRsharing.4dvtcz",
"miriam": "clo",
"obofoundry": "clo",
"ols": "clo",
"ontobee": "CLO",
"prefixcommons": "clo",
"wikidata": "P2158"
},
"name": "Cell Line Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CLO",
"providers": [
{
"code": "bioportal",
"description": "Our vision is that all biomedical knowledge and data are disseminated on the Internet using principled ontologies in such a way that the knowledge and data are semantically interoperable and useful for furthering biomedical science and clinical care. Our mission is to create software and support services for the application of principled ontologies in biomedical science and clinical care, ranging from tools for application developers to software for end-users.",
"homepage": "https://bioportal.bioontology.org",
"name": "Center for Biomedical Informatics Research, Stanford",
"uri_format": "https://bioportal.bioontology.org/ontologies/CLO/?p=classes&conceptid=http://purl.obolibrary.org/obo/CLO_$1"
}
],
"publications": [
{
"doi": "10.1186/2041-1480-5-37",
"pmc": "PMC4387853",
"pubmed": "25852852",
"title": "CLO: The cell line ontology.",
"year": 2014
},
{
"doi": "10.1186/gb-2005-6-2-r21",
"pmc": "PMC551541",
"pubmed": "15693950",
"title": "An ontology for cell types.",
"year": 2005
}
],
"repository": "https://github.com/CLO-Ontology/CLO",
"synonyms": [
"CLO"
],
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/clo/terms?short_form=CLO_$1",
"version": "2.1.178"
},
"cls": {
"description": "Cell line collections",
"example": "300108/p3934_A-172",
"homepage": "https://cls.shop/",
"mappings": {
"cellosaurus": "CLS"
},
"name": "Cell Lines Service",
"preferred_prefix": "cls",
"uri_format": "https://cls.shop/$1"
},
"clyh": {
"contact": {
"email": "lucas.leclere@obs-vlfr.fr",
"github": "L-Leclere",
"name": "Lucas Leclere",
"orcid": "0000-0002-7440-0467"
},
"depends_on": [
"iao",
"ro",
"uberon"
],
"description": "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica.",
"download_obo": "http://purl.obolibrary.org/obo/clyh.obo",
"download_owl": "http://purl.obolibrary.org/obo/clyh.owl",
"example": "1000100",
"homepage": "https://github.com/EBISPOT/clyh_ontology",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "CLYH",
"bioportal": "CLYH",
"obofoundry": "clyh",
"ols": "clyh",
"ontobee": "CLYH"
},
"name": "Clytia hemisphaerica Development and Anatomy Ontology",
"pattern": "^\\d+$",
"preferred_prefix": "CLYH",
"repository": "https://github.com/EBISPOT/clyh_ontology",
"uri_format": "http://purl.obolibrary.org/obo/CLYH_$1",
"version": "2020-05-29"
},
"cmecs": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard.",
"example": "595",
"homepage": "https://cmecscatalog.org/cmecs",
"keywords": [
"ecology",
"marine ecology"
],
"name": "Costal and Marine Ecological Classification Standard",
"pattern": "^\\d+$",
"preferred_prefix": "cmecs",
"references": [
"http://www.natureserve.org/sites/default/files/publications/files/cmecs_version_06-2012_final.pdf"
],
"uri_format": "https://cmecscatalog.org/cmecs/classification/unit/$1.html"
},
"cmf": {
"contact": {
"email": "engelsta@ohsu.edu",
"github": null,
"name": "Mark Engelstad",
"orcid": "0000-0001-5889-4463"
},
"deprecated": true,
"description": "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain",
"homepage": "https://code.google.com/p/craniomaxillofacial-ontology/",
"keywords": [
"obo",
"ontology"
],
"mappings": {
"aberowl": "CMF",
"biocontext": "CMF",
"obofoundry": "cmf",
"ontobee": "CMF"
},
"name": "CranioMaxilloFacial ontology",
"preferred_prefix": "CMF",
"uri_format": "http://purl.obolibrary.org/obo/CMF_$1"
},
"cmo": {
"appears_in": [
"scdo"
],
"contact": {
"email": "jrsmith@mcw.edu",
"github": "jrsjrs",
"name": "Jennifer Smith",
"orcid": "0000-0002-6443-9376"
},
"description": "Morphological and physiological measurement records generated from clinical and model organism research and health programs.",
"download_obo": "http://purl.obolibrary.org/obo/cmo.obo",
"download_owl": "http://purl.obolibrary.org/obo/cmo.owl",
"example": "0001350",
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
"keywords": [
"biomedical science",
"life science",
"obo",
"ontology",
"preclinical studies"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "CMO",
"biocontext": "CMO",
"bioportal": "CMO",
"fairsharing": "FAIRsharing.dq78pn",
"obofoundry": "cmo",
"ols": "cmo",
"ontobee": "CMO"
},
"name": "Clinical measurement ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CMO",
"publications": [
{
"doi": "10.1186/2041-1480-4-26",
"pmc": "PMC3882879",
"pubmed": "24103152",
"title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.",
"year": 2013
},
{
"doi": "10.3389/fgene.2012.00087",
"pmc": "PMC3361058",
"pubmed": "22654893",
"title": "Three ontologies to define phenotype measurement data.",
"year": 2012
}
],
"repository": "https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology",
"twitter": "ratgenome",
"uri_format": "http://purl.obolibrary.org/obo/CMO_$1",
"version": "2019-02-19"
},
"cmpo": {
"contact": {
"email": "jupp@ebi.ac.uk",
"github": null,
"name": "Simon Jupp",
"orcid": "0000-0002-0643-3144"
},
"description": "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations.",
"download_owl": "http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl",
"example": "0000435",
"homepage": "http://www.ebi.ac.uk/cmpo",
"keywords": [
"cell biology",
"ontology"
],
"mappings": {
"aberowl": "CMPO",
"bioportal": "CMPO",
"fairsharing": "FAIRsharing.knp11s",
"ols": "cmpo"
},
"name": "Cellular Microscopy Phenotype Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "cmpo",
"publications": [
{
"doi": "10.1186/s13326-016-0074-0",
"pmc": "PMC4870745",
"pubmed": "27195102",
"title": "The cellular microscopy phenotype ontology.",
"year": 2016
}
],
"repository": "https://github.com/EBISPOT/CMPO",
"twitter": "EBIOLS",
"uri_format": "http://www.ebi.ac.uk/cmpo/CMPO_$1",
"version": "2017-12-19"
},
"cnrs": {
"comment": "Motivated to add because of appearance in ROR",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "identifier for an academic research group issued by the CNRS",
"example": "UMR7315",
"homepage": "https://annuaire.cnrs.fr",
"mappings": {
"wikidata": "P4550"
},
"name": "French National Center for Scientific Research - Research Group Identifier",
"pattern": "^(UMR|UMS|UMI|UPR|URA|USR|GDR|EA|FR|SNC|ERL|FRC|FRE|IFR|MOY)\\d+$",
"preferred_prefix": "cnrs",
"uri_format": "https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin?&p_lab=$1&p_origine_appel=u"
},
"co_320": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"github": null,
"name": "Jeffrey A. Detras",
"orcid": null
},
"description": "Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables",
"download_owl": "https://cropontology.org/ontology/CO_320/Rice/owl",
"example": "0000618",
"homepage": "https://cropontology.org/ontology/CO_320/Rice",
"keywords": [
"agriculture",
"botany",
"life science",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_320",
"cropoct": "CO_320",
"fairsharing": "FAIRsharing.2jkxp5",
"ols": "co_320"
},
"name": "Rice ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_320",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_320:$1",
"version": "2019-10-09"
},
"co_321": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"github": null,
"name": "Rosemary Shrestha",
"orcid": "0000-0002-9399-8003"
},
"description": "July 2018",
"download_owl": "https://cropontology.org/ontology/CO_321/Wheat/owl",
"example": "0000449",
"homepage": "https://cropontology.org/ontology/CO_321/Wheat",
"keywords": [
"agriculture",
"life science",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_321",
"cropoct": "CO_321",
"fairsharing": "FAIRsharing.czzmpg",
"ols": "co_321"
},
"name": "Wheat ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_321",
"publications": [
{
"doi": "10.1093/aobpla/plq008",
"pmc": "PMC3000699",
"pubmed": "22476066",
"title": "Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature.",
"year": 2010
}
],
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_321:$1",
"version": "2019-10-09"
},
"co_322": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"github": null,
"name": "Crop Ontology Helpdesk",
"orcid": null
},
"description": "Maize Trait Dictionary in template 5 - CIMMYT- September 2016",
"download_owl": "https://cropontology.org/ontology/CO_322/Maize/owl",
"example": "0000773",
"homepage": "https://cropontology.org/ontology/CO_322/Maize",
"keywords": [
"agriculture",
"botany",
"life science",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_322",
"cropoct": "CO_322",
"fairsharing": "FAIRsharing.eeyne8",
"ols": "co_322"
},
"name": "Maize ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_322",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_322:$1",
"version": "2019-10-09"
},
"co_323": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"github": null,
"name": "Ramesh Verna",
"orcid": null
},
"description": "ICARDA - TDv5 - Sept 2018",
"download_owl": "https://cropontology.org/ontology/CO_323/Barley/owl",
"example": "0000252",
"homepage": "https://cropontology.org/ontology/CO_323/Barley",
"keywords": [
"agriculture",
"botany",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_323",
"cropoct": "CO_323",
"fairsharing": "FAIRsharing.f69084",
"ols": "co_323"
},
"name": "Barley ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_323",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_323:$1",
"version": "2019-11-20"
},
"co_324": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"github": null,
"name": "Crop Ontology Helpdesk",
"orcid": null
},
"description": "Sorghum TDv5 - Oct 2019",
"download_owl": "https://cropontology.org/ontology/CO_324/Sorghum/owl",
"example": "0000111",
"homepage": "https://cropontology.org/ontology/CO_324/Sorghum",
"keywords": [
"agriculture",
"botany",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_324",
"cropoct": "CO_324",
"fairsharing": "FAIRsharing.dxx0c",
"ols": "co_324"
},
"name": "Sorghum ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_324",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_324:$1",
"version": "2019-10-09"
},
"co_325": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"github": null,
"name": "Elizabeth Arnaud",
"orcid": "0000-0002-6020-5919"
},
"description": "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019",
"download_owl": "https://cropontology.org/ontology/CO_325/Banana/owl",
"example": "0000519",
"homepage": "https://cropontology.org/ontology/CO_325/Banana",
"keywords": [
"agriculture",
"life science",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_325",
"cropoct": "CO_325",
"fairsharing": "FAIRsharing.gdszhh",
"ols": "co_325"
},
"name": "Banana ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_325",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_325:$1",
"version": "2019-10-09"
},
"co_326": {
"description": "Draft version",
"download_owl": "https://cropontology.org/ontology/CO_326/Coconut/owl",
"example": "0000254",
"homepage": "https://cropontology.org/ontology/CO_326/Coconut",
"keywords": [
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"cropoct": "CO_326",
"ols": "co_326"
},
"name": "Coconut ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_326",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_326:$1"
},
"co_327": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"github": null,
"name": "Crop Ontology Helpdesk",
"orcid": null
},
"description": "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016",
"download_owl": "http://www.cropontology.org/ontology/CO_327/Pearl%20millet/owl",
"example": "0000095",
"homepage": "http://www.cropontology.org/ontology/CO_327/Pearl%20millet",
"keywords": [
"agriculture",
"botany",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_327",
"cropoct": "CO_327",
"fairsharing": "FAIRsharing.4e3qh9",
"ols": "co_327"
},
"name": "Pearl millet ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_327",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_327:$1"
},
"co_330": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"github": null,
"name": "Crop Ontology Helpdesk",
"orcid": null
},
"description": "CIP - potato ontology - december 2018",
"download_owl": "https://cropontology.org/ontology/CO_330/Potato/owl",
"example": "0000106",
"homepage": "https://cropontology.org/ontology/CO_330/Potato",
"keywords": [
"agriculture",
"botany",
"life science",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_330",
"cropoct": "CO_330",
"fairsharing": "FAIRsharing.4fa657",
"ols": "co_330"
},
"name": "Potato ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_330",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_330:$1",
"version": "2019-10-09"
},
"co_331": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"github": null,
"name": "Vilma Hualla Mamani",
"orcid": "0000-0003-0595-5271"
},
"description": "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019",
"download_owl": "http://www.cropontology.org/ontology/CO_331/Sweet%20Potato/owl",
"example": "0000088",
"homepage": "http://www.cropontology.org/ontology/CO_331/Sweet%20Potato",
"keywords": [
"agriculture",
"botany",
"life science",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_331",
"cropoct": "CO_331",
"fairsharing": "FAIRsharing.4g5qcw",
"ols": "co_331"
},
"name": "Sweet Potato ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_331",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_331:$1"
},
"co_333": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"github": null,
"name": "Crop Ontology Helpdesk",
"orcid": null
},
"description": "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017.",
"download_owl": "http://www.cropontology.org/ontology/CO_333/Beet%20Ontology/owl",
"example": "3000045",
"homepage": "http://www.cropontology.org/ontology/CO_333/Beet%20Ontology",
"keywords": [
"agriculture",
"botany",
"life science",
"ontology",
"plant breeding"
],
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_333",
"cropoct": "CO_333",
"fairsharing": "FAIRsharing.af5655",
"ols": "co_333"
},
"name": "Beet Ontology ontology",
"pattern": "^\\d+$",
"preferred_prefix": "CO_333",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_333:$1"
},
"co_334": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"github": null,
"name": "Crop Ontology Helpdesk",
"orcid": null
},
"description": "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016",
"download_owl": "https://cropontology.org/ontology/CO_334/Cassava/owl",
"example": "0000070",
"homepage": "https://cropontology.org/ontology/CO_334/Cassava",
"keywords": [
"agriculture",
"botany",
"nutritional science",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_334",
"cropoct": "CO_334",
"fairsharing": "FAIRsharing.v06c4q",
"ols": "co_334"
},
"name": "Cassava ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_334",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_334:$1",
"version": "2019-10-09"
},
"co_335": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"github": null,
"name": "Crop Ontology Helpdesk",
"orcid": null
},
"description": "CIAT Common bean trait dictionary - version August 2014",
"download_owl": "http://www.cropontology.org/ontology/CO_335/Common%20Bean/owl",
"example": "0000189",
"homepage": "http://www.cropontology.org/ontology/CO_335/Common%20Bean",
"keywords": [
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"botany",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_335",
"cropoct": "CO_335",
"fairsharing": "FAIRsharing.a14123",
"ols": "co_335"
},
"name": "Common Bean ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_335",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_335:$1"
},
"co_336": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"github": null,
"name": "Elizabeth Arnaud",
"orcid": "0000-0002-6020-5919"
},
"description": "Soybean Trait Dictionary in template v5 - IITA - July 2015",
"download_owl": "https://cropontology.org/ontology/CO_336/Soybean/owl",
"example": "0000339",
"homepage": "https://cropontology.org/ontology/CO_336/Soybean",
"keywords": [
"agriculture",
"life science",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_336",
"cropoct": "CO_336",
"fairsharing": "FAIRsharing.j75srj",
"ols": "co_336"
},
"name": "Soybean ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_336",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_336:$1"
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"preferred_prefix": "codelink",
"references": [
"https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-8060/A-GEOD-8060.adf.txt",
"https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt"
]
},
"cog": {
"contact": {
"email": "cogs@ncbi.nlm.nih.gov",
"github": null,
"name": "Michael Y Galperin",
"orcid": "0000-0002-2265-5572"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems.",
"example": "COG0001",
"homepage": "https://www.ncbi.nlm.nih.gov/research/cog/",
"keywords": [
"genome",
"life science",
"protein"
],
"mappings": {
"biolink": "COG",
"fairsharing": "FAIRsharing.djsbw2",
"go": "COG_Cluster",
"prefixcommons": "cog"
},
"name": "Cluster of orthologous genes",
"pattern": "^COG\\d+$",
"preferred_prefix": "cog",
"publications": [
{
"doi": "10.1126/science.278.5338.631",
"pmc": null,
"pubmed": "9381173",
"title": "A genomic perspective on protein families.",
"year": 1997
},
{
"doi": "10.1093/nar/gku1223",
"pmc": "PMC4383993",
"pubmed": "25428365",
"title": "Expanded microbial genome coverage and improved protein family annotation in the COG database.",
"year": 2014
}
],
"synonyms": [
"COG_Cluster"
],
"uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1"
},
"cog.category": {
"contact": {
"email": "cogs@ncbi.nlm.nih.gov",
"github": null,
"name": "Michael Y Galperin",
"orcid": "0000-0002-2265-5572"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Higher-level classifications of COG Pathways",
"example": "K",
"homepage": "https://www.ncbi.nlm.nih.gov/research/cog/",
"keywords": [
"pathways"
],
"name": "COG Categories",
"part_of": "cog",
"preferred_prefix": "cog.category",
"uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1"
},
"cog.pathway": {
"contact": {
"email": "cogs@ncbi.nlm.nih.gov",
"github": null,
"name": "Michael Y Galperin",
"orcid": "0000-0002-2265-5572"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera.",
"example": "NAD%20biosynthesis",
"homepage": "https://www.ncbi.nlm.nih.gov/research/cog/pathways",
"mappings": {
"go": "COG_Pathway"
},
"name": "COG Pathways",
"part_of": "cog",
"preferred_prefix": "cog.pathway",
"uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1"
},
"cohd": {
"comment": "not really sure where the source is. this also links to a system called athena. I was not able to figure out what COHD stands for.",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012",
"homepage": "https://github.com/MIT-LCP/mimic-omop",
"keywords": [
"clinical data",
"clinical trials",
"health",
"health sciences"
],
"name": "MIMIC III Database",
"no_own_terms": true,
"preferred_prefix": "cohd",
"repository": "https://github.com/MIT-LCP/mimic-omop"
},
"col": {
"description": "Identifier of a taxon or synonym in the Catalogue of Life",
"example": "4QHKG",
"homepage": "https://www.checklistbank.org",
"mappings": {
"bartoc": "1915",
"miriam": "col"
},
"name": "Catalogue of Life",
"pattern": "^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$",
"preferred_prefix": "col",
"providers": [
{
"code": "col",
"description": "The Catalogue of Life website providing a view onto the latest release of the COL Checklist.",
"homepage": "https://www.catalogueoflife.org",
"name": "Catalogue of Life (COL)",
"uri_format": "https://www.catalogueoflife.org/data/taxon/$1"
}
],
"uri_format": "https://www.checklistbank.org/dataset/3LR/taxon/$1"
},
"col.taiwan": {
"contributor": {
"email": "meghan.balk@gmail.com",
"github": "megbalk",
"name": "Meghan Balk",
"orcid": "0000-0003-2699-3066"
},
"description": "Identifier (name code) for a taxon in the catalogue of life in taiwan",
"example": "431472",
"github_request_issue": 466,
"homepage": "http://taibnet.sinica.edu.tw/home.php",
"mappings": {
"wikidata": "P3088"
},
"name": "Catalogue of Life in Taiwan",
"pattern": "^[1-9]\\d{5}$",
"preferred_prefix": "col.taiwan",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1"
},
"colao": {
"contact": {
"email": "entiminae@gmail.com",
"github": "JCGiron",
"name": "Jennifer C. Giron",
"orcid": "0000-0002-0851-6883"
},
"depends_on": [
"aism",
"bfo",
"bspo",
"caro",
"pato",
"ro",
"uberon"
],
"description": "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research.",
"download_obo": "http://purl.obolibrary.org/obo/colao.obo",
"download_owl": "http://purl.obolibrary.org/obo/colao.owl",
"example": "0000000",
"homepage": "https://github.com/insect-morphology/colao",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "COLAO",
"bioportal": "COLAO",
"obofoundry": "colao",
"ols": "colao",
"ontobee": "COLAO"
},
"name": "Coleoptera Anatomy Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "COLAO",
"repository": "https://github.com/insect-morphology/colao",
"uri_format": "http://purl.obolibrary.org/obo/COLAO_$1",
"version": "2022-06-18"
},
"collagenmutdb": {
"description": "This database aims to record all published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP, FKBP10, LEPRE1 and PPIB genes.",
"example": "COL3A1",
"homepage": "http://www.le.ac.uk/genetics/collagen/",
"keywords": [
"gene"
],
"mappings": {
"prefixcommons": "cmd"
},
"name": "Collagen Mutation Database",
"preferred_prefix": "collagenmutdb",
"provides": "hgnc.symbol",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://eds.gene.le.ac.uk/home.php?select_db=$1"
},
"colonatlas": {
"description": "Cell line databases/resources",
"example": "ALA",
"homepage": "http://www.coloncanceratlas.org",
"mappings": {
"cellosaurus": "ColonAtlas"
},
"name": "Colorectal Cancer Atlas",
"preferred_prefix": "colonatlas",
"uri_format": "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1"
},
"combine.specifications": {
"description": "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network.",
"example": "sed-ml.level-1.version-1",
"homepage": "https://co.mbine.org/standards/",
"mappings": {
"biocontext": "COMBINE.SPECIFICATIONS",
"miriam": "combine.specifications",
"n2t": "combine.specifications"
},
"name": "COMBINE specifications",
"pattern": "^\\w+(\\-|\\.|\\w)*$",
"preferred_prefix": "combine.specifications",
"uri_format": "https://github.com/combine-org/combine-specifications/blob/main/specifications/$1.md"
},
"come": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif.",
"example": "MOL000160",
"homepage": "https://www.flymine.org/come",
"keywords": [
"protein"
],
"mappings": {
"prefixcommons": "come"
},
"name": "The Bioinorganic Motif Database",
"preferred_prefix": "come",
"uri_format": "https://www.flymine.org/come/entry?gn=$1"
},
"commoncoreontology": {
"contact": {
"email": "mpjensen@buffalo.edu",
"github": "mark-jensen",
"name": "Mark Jensen",
"orcid": "0000-0001-9228-8838"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Common Core Ontologies (CCO) comprise twelve ontologies that are designed to represent and integrate taxonomies of generic classes and relations across all domains of interest.\n\nCCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained by the BFO framework, from which it inherits much of its basic semantic relationships.",
"example": "DirectiveInformationContentEntity",
"homepage": "http://www.ontologyrepository.com",
"keywords": [
"ontology",
"upper-level ontology"
],
"license": "CC-BY-4.0",
"name": "Common Core Ontologies",
"preferred_prefix": "commoncoreontology",
"repository": "https://github.com/CommonCoreOntology/CommonCoreOntologies",
"uri_format": "http://www.ontologyrepository.com/CommonCoreOntologies/$1"
},
"complexportal": {
"description": "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases.",
"example": "CPX-263",
"homepage": "https://www.ebi.ac.uk/complexportal",
"mappings": {
"biocontext": "COMPLEXPORTAL",
"biolink": "ComplexPortal",
"go": "ComplexPortal",
"miriam": "complexportal",
"n2t": "complexportal",
"re3data": "r3d100013295",
"uniprot": "DB-0228",
"wikidata": "P7718"
},
"name": "Complex Portal",
"pattern": "^CPX-[0-9]+$",
"preferred_prefix": "complexportal",
"publications": [
{
"doi": "10.1093/nar/gku975",
"pmc": "PMC4384031",
"pubmed": "25313161",
"title": "The complex portal--an encyclopaedia of macromolecular complexes.",
"year": 2014
}
],
"synonyms": [
"ComplexPortal"
],
"uri_format": "https://www.ebi.ac.uk/complexportal/complex/$1"
},
"comptox": {
"description": "The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks.",
"example": "DTXSID2021028",
"homepage": "https://comptox.epa.gov/dashboard",
"mappings": {
"biocontext": "COMPTOX",
"miriam": "comptox",
"n2t": "comptox",
"wikidata": "P3117"
},
"name": "DSSTox substance ID",
"pattern": "^DTXSID\\d+$",
"preferred_prefix": "comptox",
"uri_format": "https://comptox.epa.gov/dashboard/$1"
},
"compulyeast": {
"description": "Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record.",
"example": "O08709",
"homepage": "http://compluyeast2dpage.dacya.ucm.es/",
"keywords": [
"protein"
],
"mappings": {
"biocontext": "COMPULYEAST",
"fairsharing": "FAIRsharing.rbjs3e",
"miriam": "compulyeast",
"n2t": "compulyeast",
"prefixcommons": "compluyeast2dpage"
},
"name": "Compluyeast-2D-DB",
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$",
"preferred_prefix": "compulyeast",
"provides": "uniprot",
"uri_format": "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1"
},
"confident.event": {
"contact": {
"email": "Philip.Stroemert@tib.eu",
"github": "StroemPhi",
"name": "Philip Strömert",
"orcid": "0000-0002-1595-3213"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating.",
"example": "37af84f2-bfd7-4653-b608-eaff44febba6",
"github_request_issue": 519,
"homepage": "https://www.confident-conference.org/index.php/Category:Event",
"keywords": [
"conferences",
"meetings",
"metascience"
],
"name": "ConfIDent Event",
"pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$",
"preferred_prefix": "confident.event",
"uri_format": "https://www.confident-conference.org/index.php/Event:$1"
},
"confident.series": {
"contact": {
"email": "Philip.Stroemert@tib.eu",
"github": "StroemPhi",
"name": "Philip Strömert",
"orcid": "0000-0002-1595-3213"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating.",
"example": "AAC",
"github_request_issue": 519,
"homepage": "https://www.confident-conference.org/index.php/Category:Event_Series",
"keywords": [
"conferences",
"grouping",
"meetings",
"metascience"
],
"name": "ConfIDent Event Series",
"preferred_prefix": "confident.series",
"uri_format": "https://www.confident-conference.org/index.php/Event_Series:$1"
},
"conoserver": {
"contact": {
"email": "d.craik@imb.uq.edu.au",
"github": null,
"name": "David Craik",
"orcid": "0000-0003-0007-6796"
},
"description": "ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails.",
"example": "2639",
"homepage": "http://www.conoserver.org/",
"keywords": [
"life science",
"neurophysiology",
"statistics",
"synthetic biology"
],
"mappings": {
"biocontext": "CONOSERVER",
"fairsharing": "FAIRsharing.y00hz4",
"miriam": "conoserver",
"n2t": "conoserver",
"uniprot": "DB-0156"
},
"name": "ConoServer",
"pattern": "^\\d+$",
"preferred_prefix": "conoserver",
"publications": [
{
"doi": "10.1016/j.toxicon.2010.03.002",
"pmc": null,
"pubmed": "20211197",
"title": "Conopeptide characterization and classifications: an analysis using ConoServer.",
"year": 2010
},
{
"doi": "10.1093/bioinformatics/btm596",
"pmc": null,
"pubmed": "18065428",
"title": "ConoServer, a database for conopeptide sequences and structures.",
"year": 2007
},
{
"doi": "10.1021/cb700091j",
"pmc": null,
"pubmed": "17649970",
"title": "Chemical modification of conotoxins to improve stability and activity.",
"year": 2007
},
{
"doi": "10.1152/physrev.00020.2003",
"pmc": null,
"pubmed": "14715910",
"title": "Conus venoms: a rich source of novel ion channel-targeted peptides.",
"year": 2004
}
],
"uri_format": "http://www.conoserver.org/?page=card&table=protein&id=$1"
},
"conso": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases.",
"example": "CONSO00010",
"homepage": "https://pharmacome.github.io/conso/",
"keywords": [
"biology",
"life science",
"neurodegeneration",
"neuroscience",
"ontology"
],
"name": "Curation of Neurodegeneration Supporting Ontology",
"pattern": "^CONSO\\d{5}$",
"preferred_prefix": "conso",
"uri_format": "https://pharmacome.github.io/conso/$1"
},
"cordis.article": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).",
"example": "436605",
"homepage": "https://cordis.europa.eu/",
"name": "CORDIS Article",
"pattern": "^\\d+$",
"preferred_prefix": "cordis.article",
"uri_format": "https://cordis.europa.eu/article/id/$1"
},
"cordis.project": {
"contributor": {
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"description": "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).",
"example": "817732",
"github_request_issue": 450,
"homepage": "https://cordis.europa.eu/",
"name": "CORDIS Project",
"pattern": "^\\d+$",
"preferred_prefix": "cordis.project",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://cordis.europa.eu/project/id/$1"
},
"coriell": {
"description": "The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world.",
"example": "GM17027",
"homepage": "http://ccr.coriell.org/",
"mappings": {
"biocontext": "Coriell",
"cellosaurus": "Coriell",
"go": "CORIELL",
"miriam": "coriell",
"n2t": "coriell"
},
"name": "Coriell Institute for Medical Research",
"pattern": "^[A-Z]{2}\\d+$",
"preferred_prefix": "coriell",
"uri_format": "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1"
},
"corrdb": {
"contact": {
"email": "zhu@iastate.edu",
"github": null,
"name": "Zhiliang Hu",
"orcid": "0000-0002-6704-7538"
},
"description": "A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies.",
"example": "37232",
"homepage": "https://www.animalgenome.org",
"keywords": [
"animal genetics",
"genetics",
"life science",
"systems biology"
],
"mappings": {
"fairsharing": "FAIRsharing.IziuCK",
"miriam": "corrdb",
"re3data": "r3d100011496"
},
"name": "CorrDB",
"pattern": "^[0-9]+$",
"preferred_prefix": "corrdb",
"uri_format": "https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1"
},
"corum": {
"contact": {
"email": "andreas.ruepp@helmholtz-muenchen.de",
"github": null,
"name": "Andreas Ruepp",
"orcid": "0000-0003-1705-3515"
},
"description": "The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded.",
"example": "100",
"homepage": "https://mips.helmholtz-muenchen.de/genre/proj/corum/",
"keywords": [
"bioinformatics",
"biology",
"protein"
],
"mappings": {
"biocontext": "CORUM",
"fairsharing": "FAIRsharing.ohbpNw",
"go": "CORUM",
"miriam": "corum",
"n2t": "corum",
"prefixcommons": "corum",
"uniprot": "DB-0224"
},
"name": "Comprehensive Resource of Mammalian protein complexes",
"pattern": "^\\d+$",
"preferred_prefix": "corum",
"publications": [
{
"doi": "10.1093/nar/gky973",
"pmc": "PMC6323970",
"pubmed": "30357367",
"title": "CORUM: the comprehensive resource of mammalian protein complexes-2019.",
"year": 2019
}
],
"uri_format": "https://mips.helmholtz-muenchen.de/corum/?id=$1"
},
"cosmic": {
"description": "COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes.",
"example": "BRAF",
"homepage": "http://cancer.sanger.ac.uk/cosmic/",
"keywords": [
"biomedical science",
"genetics"
],
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},
"name": "COSMIC Gene",
"pattern": "^[A-Z0-9]+$",
"preferred_prefix": "cosmic",
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"year": 2019
},
{
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"pmc": "PMC4383913",
"pubmed": "25355519",
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{
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"pubmed": "20952405",
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{
"doi": "10.1038/sj.bjc.6601894",
"pmc": "PMC2409828",
"pubmed": "15188009",
"title": "The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website.",
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}
],
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},
"cosmic.cell": {
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
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"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",
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"name": "COSMIC Cell Lines",
"pattern": "^\\d+$",
"preferred_prefix": "cosmic.cell",
"uri_format": "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1"
},
"covid19": {
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"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",
"keywords": [
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],
"mappings": {
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"name": "COVID-19 Surveillance Ontology",
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"preferred_prefix": "covid19",
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"description": "The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.",
"download_json": "https://github.com/EBISPOT/covoc/releases/download/current/covoc.json",
"download_obo": "https://github.com/EBISPOT/covoc/releases/download/current/covoc.obo",
"download_owl": "https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl",
"example": "0010034",
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"keywords": [
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"mappings": {
"ols": "covoc"
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"name": "CoVoc Coronavirus Vocabulary",
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"uri_format": "http://purl.obolibrary.org/obo/COVOC_$1",
"version": "2020-08-28"
},
"cp": {
"appears_in": [
"cl"
],
"comment": "Part of cell ontology but deprecated, see https://github.com/obophenotype/cell-ontology/issues/572",
"contributor": {
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
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"deprecated": true,
"name": "Cellular Phenotypes",
"preferred_prefix": "cp"
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"cpc": {
"description": "The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013.",
"example": "A01M1/026",
"homepage": "https://worldwide.espacenet.com/classification",
"keywords": [
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"earth science",
"geodesy",
"geography",
"hydrogeology",
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"mappings": {
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"fairsharing": "FAIRsharing.e08886",
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"name": "Cooperative Patent Classification",
"pattern": "^([A-H,Y]|[A-H, Y]\\d{2}|[A-H, Y]\\d{2}[A-Z]|[A-H, Y]\\d{2}[A-Z]\\d{1,3}|[A-H, Y]\\d{2}[A-Z]\\d{1,3}(\\/)?\\d{2,})$",
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"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",
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"contributor_extras": [
{
"email": null,
"github": "colleenXu",
"name": "Colleen Xu",
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}
],
"description": "Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]",
"example": "00103",
"github_request_issue": 357,
"homepage": "https://www.aapc.com",
"keywords": [
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"health science",
"medicine",
"ontology"
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"mappings": {
"aberowl": "CPT",
"biolink": "CPT",
"bioportal": "CPT",
"fairsharing": "FAIRsharing.wpxab1"
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"name": "Current Procedural Terminology",
"pattern": "^\\d+$",
"preferred_prefix": "cpt",
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{
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"title": "Current procedural terminology; a primer.",
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},
{
"doi": "10.1016/j.jacr.2007.10.004",
"pmc": null,
"pubmed": "18359442",
"title": "CPT: an open system that describes all that you do.",
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}
],
"references": [
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"https://github.com/biolink/biolink-model/pull/993"
],
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
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"synonyms": [
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"uri_format": "https://www.aapc.com/codes/cpt-codes/$1"
},
"credit": {
"contact": {
"email": "info@casrai.org",
"github": null,
"name": "Liz Allen",
"orcid": "0000-0002-9298-3168"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output.",
"example": "Software",
"homepage": "https://casrai.org/credit/",
"keywords": [
"data quality",
"ontology and terminology",
"subject agnostic"
],
"mappings": {
"fairsharing": "FAIRsharing.fe4816"
},
"name": "CASRAI Contributor Roles Taxonomy",
"preferred_prefix": "credit",
"publications": [
{
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"pmc": null,
"pubmed": "31164773",
"title": "Credit data generators for data reuse.",
"year": 2019
},
{
"doi": "10.1038/508312a",
"pmc": null,
"pubmed": "24745070",
"title": "Publishing: Credit where credit is due.",
"year": 2014
},
{
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"pubmed": null,
"title": "ANSI/NISO Z39.104-2022, CRediT, Contributor Roles Taxonomy",
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},
{
"doi": "10.1087/20150211",
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"title": "Beyond authorship: attribution, contribution, collaboration, and credit",
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},
{
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"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",
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}
],
"twitter": "contrib_roles"
},
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"contact": {
"email": "Christine.Pourcel@u-psud.fr",
"github": null,
"name": "Christine Pourcel",
"orcid": "0000-0002-8951-466X"
},
"description": "Repeated CRISPR (\"clustered regularly interspaced short palindromic repeats\") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data.",
"example": "551115",
"homepage": "http://crispr.i2bc.paris-saclay.fr/",
"keywords": [
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],
"mappings": {
"biocontext": "CRISPRDB",
"fairsharing": "FAIRsharing.7sfedh",
"miriam": "crisprdb",
"n2t": "crisprdb"
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"name": "CRISPRdb",
"pattern": "^[0-9]+$",
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"pmc": "PMC2447796",
"pubmed": "18442988",
"title": "CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats.",
"year": 2008
},
{
"doi": "10.1093/nar/gkm360",
"pmc": "PMC1933234",
"pubmed": "17537822",
"title": "CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.",
"year": 2007
},
{
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"pmc": "PMC1892036",
"pubmed": "17521438",
"title": "The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats.",
"year": 2007
}
],
"uri_format": "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1"
},
"cro": {
"contact": {
"email": "whimar@ohsu.edu",
"github": "marijane",
"name": "Marijane White",
"orcid": "0000-0001-5059-4132"
},
"description": "A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability.",
"download_obo": "https://raw.githubusercontent.com/data2health/contributor-role-ontology/master/cro.obo",
"download_owl": "http://purl.obolibrary.org/obo/cro.owl",
"example": "0000038",
"homepage": "https://github.com/data2health/contributor-role-ontology",
"keywords": [
"obo",
"ontology"
],
"license": "CC BY 2.0",
"mappings": {
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"bioportal": "CRO",
"obofoundry": "cro",
"ols": "cro",
"ontobee": "CRO"
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"name": "Contributor Role Ontology",
"pattern": "^\\d{7}$",
"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/$1"
},
"cryoem": {
"contact": {
"email": "isanchez@cnb.csic.es",
"github": null,
"name": "Carlos Oscar S. Sorzano",
"orcid": "0000-0002-9473-283X"
},
"description": "Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles",
"download_owl": "http://scipion.i2pc.es/ontology/cryoem/releases/2021-03-09/cryoem.owl",
"example": "0000052",
"homepage": "http://scipion.i2pc.es/ontology/cryoem",
"keywords": [
"ontology",
"structural biology"
],
"mappings": {
"aberowl": "CRYOEM",
"bioportal": "CRYOEM",
"fairsharing": "FAIRsharing.q47I0t",
"ols": "cryoem"
},
"name": "Cryo Electron Microscopy ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "cryoem",
"uri_format": "http://scipion.i2pc.es/ontology/CRYOEM_$1",
"version": "2021-03-09"
},
"cryptodb": {
"contact": {
"email": "jkissing@uga.edu",
"github": null,
"name": "Jessica Kissinger",
"orcid": "0000-0003-4446-6200"
},
"description": "CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"example": "cgd7_230",
"homepage": "https://cryptodb.org/cryptodb/",
"keywords": [
"functional genomics",
"genome",
"genomics",
"parasitology"
],
"mappings": {
"biocontext": "CRYPTODB",
"fairsharing": "FAIRsharing.t3nprm",
"miriam": "cryptodb",
"n2t": "cryptodb",
"prefixcommons": "cryptodb",
"re3data": "r3d100012265"
},
"name": "CryptoDB",
"pattern": "^\\w+$",
"preferred_prefix": "cryptodb",
"publications": [
{
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"pubmed": "31452162",
"title": "Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org.",
"year": 2020
},
{
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"pmc": "PMC1347441",
"pubmed": "16381902",
"title": "CryptoDB: a Cryptosporidium bioinformatics resource update.",
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}
],
"twitter": "VEuPathDB",
"uri_format": "https://cryptodb.org/cryptodb/app/record/gene/$1"
},
"csa": {
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"github": null,
"name": "Nicholas Furnham",
"orcid": "0000-0002-7532-1269"
},
"description": "The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme.",
"example": "1a05",
"homepage": "https://www.ebi.ac.uk/thornton-srv/databases/CSA/",
"keywords": [
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"life science",
"structure"
],
"mappings": {
"biocontext": "CSA",
"fairsharing": "FAIRsharing.2ajtcf",
"miriam": "csa",
"n2t": "csa",
"prefixcommons": "csa"
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"name": "Catalytic Site Atlas",
"pattern": "^[0-9][A-Za-z0-9]{3}$",
"preferred_prefix": "csa",
"publications": [
{
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"pmc": "PMC3964973",
"pubmed": "24319146",
"title": "The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.",
"year": 2013
},
{
"doi": "10.1093/nar/gkh028",
"pmc": "PMC308762",
"pubmed": "14681376",
"title": "The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.",
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}
],
"uri_format": "https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1"
},
"csd": {
"contact": {
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"github": null,
"name": "Support Email",
"orcid": "0000-0002-6062-7492"
},
"description": "The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode.",
"example": "PELNAW",
"homepage": "https://www.ccdc.cam.ac.uk/",
"keywords": [
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"chemistry",
"organic chemistry",
"organic molecular chemistry"
],
"mappings": {
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"re3data": "r3d100010197"
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"name": "Cambridge Structural Database",
"pattern": "^[A-Z]{6}(\\d{2})?$",
"preferred_prefix": "csd",
"publications": [
{
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"pubmed": "27048719",
"title": "The Cambridge Structural Database.",
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},
{
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"pubmed": "12037359",
"title": "The Cambridge Structural Database: a quarter of a million crystal structures and rising.",
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}
],
"twitter": "ccdc_cambridge",
"uri_format": "https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG"
},
"csp": {
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"github": null,
"name": "Anita Ghebeles",
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},
"deprecated": true,
"description": "CRISP is a terminology used for indexing biomedical information. CRISP contains over 8,000 preferred terms that are grouped hierarchically into 11 domains.",
"example": "2004-2820",
"homepage": "https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm",
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"chemical biology",
"medicine",
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"mappings": {
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"bioportal": "CRISP",
"fairsharing": "FAIRsharing.1evfpc",
"hl7": "2.16.840.1.113883.6.120"
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"name": "Computer Retrieval of Information on Science Projects Thesaurus",
"preferred_prefix": "csp",
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"title": "Taking a bite out of CRISP. Strategies on using and conducting searches in the Computer Retrieval of Information on Scientific Projects database.",
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}
],
"synonyms": [
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"CRISP Thesaurus",
"CRISP Thesaurus, 2006",
"CSP2005"
],
"uri_format": "http://purl.bioontology.org/ontology/CSP/$1"
},
"cst": {
"description": "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways.",
"example": "Akt_PKB",
"homepage": "http://www.cellsignal.com/pathways/index.html",
"keywords": [
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"life science"
],
"mappings": {
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"miriam": "cst",
"n2t": "cst"
},
"name": "Cell Signaling Technology Pathways",
"pattern": "^[A-Za-z0-9_-]+$",
"preferred_prefix": "cst",
"uri_format": "http://www.cellsignal.com/reference/pathway/$1.html"
},
"cst.ab": {
"description": "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products.",
"example": "3305",
"homepage": "http://www.cellsignal.com/catalog/index.html",
"keywords": [
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],
"mappings": {
"biocontext": "CST.AB",
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"prefixcommons": "cst"
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"name": "Cell Signaling Technology Antibody",
"pattern": "^\\d+$",
"preferred_prefix": "cst.ab",
"uri_format": "http://www.cellsignal.com/products/$1.html"
},
"ctcae": {
"appears_in": [
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],
"contact": {
"email": "ncictcaehelp@mail.nih.gov",
"github": null,
"name": "CTCAE Help",
"orcid": null
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"description": "The Common Terminology Criteria for Adverse Events (CTCAE),[1] formerly called the Common Toxicity Criteria (CTC or NCI-CTC), are a set of criteria for the standardized classification of adverse effects of drugs used in cancer therapy. The CTCAE system is a product of the US National Cancer Institute (NCI).",
"download_owl": "http://aber-owl.net/media/ontologies/CTCAE/2/ctcae.owl",
"example": "E12768",
"homepage": "https://evs.nci.nih.gov/ftp1/CTCAE/About.html",
"keywords": [
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],
"mappings": {
"aberowl": "CTCAE",
"bioportal": "CTCAE"
},
"name": "Common Terminology Criteria for Adverse Events",
"pattern": "^E\\d+$",
"preferred_prefix": "ctcae",
"publications": [
{
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"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.",
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}
],
"references": [
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"https://en.wikipedia.org/wiki/Common_Terminology_Criteria_for_Adverse_Events"
],
"synonyms": [
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]
},
"ctd.chemical": {
"description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.",
"example": "D001151",
"homepage": "http://ctdbase.org/",
"mappings": {
"biocontext": "CTD.CHEMICAL",
"biolink": "CTD.CHEMICAL",
"miriam": "ctd.chemical",
"n2t": "ctd.chemical"
},
"name": "CTD Chemical",
"part_of": "ctd",
"pattern": "^[CD]\\d+$",
"preferred_prefix": "ctd.chemical",
"provides": "mesh",
"uri_format": "http://ctdbase.org/detail.go?type=chem&acc=$1"
},
"ctd.disease": {
"description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.",
"example": "D053716",
"homepage": "http://ctdbase.org/",
"mappings": {
"biocontext": "CTD.DISEASE",
"biolink": "CTD.DISEASE",
"miriam": "ctd.disease",
"n2t": "ctd.disease"
},
"name": "CTD Disease",
"part_of": "ctd",
"pattern": "^D\\d+$",
"preferred_prefix": "ctd.disease",
"provides": "mesh",
"uri_format": "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1"
},
"ctd.gene": {
"description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.",
"example": "101",
"homepage": "http://ctdbase.org/",
"mappings": {
"biocontext": "CTD.GENE",
"biolink": "CTD.GENE",
"miriam": "ctd.gene",
"n2t": "ctd.gene",
"uniprot": "DB-0140"
},
"name": "CTD Gene",
"part_of": "ctd",
"pattern": "^\\d+$",
"preferred_prefix": "ctd.gene",
"provides": "ncbigene",
"publications": [
{
"doi": "10.1093/nar/gkaa891",
"pmc": "PMC7779006",
"pubmed": "33068428",
"title": "Comparative Toxicogenomics Database (CTD): update 2021.",
"year": 2021
}
],
"uri_format": "http://ctdbase.org/detail.go?type=gene&acc=$1"
},
"cteno": {
"contact": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"depends_on": [
"ro",
"uberon"
],
"description": "An anatomical and developmental ontology for ctenophores (Comb Jellies)",
"download_obo": "https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo",
"download_owl": "http://purl.obolibrary.org/obo/cteno.owl",
"example": "0000047",
"homepage": "https://github.com/obophenotype/ctenophore-ontology",
"keywords": [
"anatomy",
"developmental biology",
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "CTENO",
"biocontext": "CTENO",
"bioportal": "CTENO",
"fairsharing": "FAIRsharing.mgxgza",
"obofoundry": "cteno",
"ols": "cteno",
"ontobee": "CTENO"
},
"name": "Ctenophore Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CTENO",
"repository": "https://github.com/obophenotype/ctenophore-ontology",
"uri_format": "http://purl.obolibrary.org/obo/CTENO_$1",
"version": "2016-10-19"
},
"cto": {
"contact": {
"email": "alpha.tom.kodamullil@scai.fraunhofer.de",
"github": "akodamullil",
"name": "Dr. Alpha Tom Kodamullil",
"orcid": "0000-0001-9896-3531"
},
"description": "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials.",
"download_owl": "http://purl.obolibrary.org/obo/cto.owl",
"example": "0000022",
"homepage": "https://github.com/ClinicalTrialOntology/CTO/",
"keywords": [
"biomedical science",
"neurobiology",
"obo",
"ontology",
"preclinical studies"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "CTO",
"bioportal": "CTO",
"fairsharing": "FAIRsharing.qp211a",
"obofoundry": "cto",
"ols": "cto",
"ontobee": "CTO"
},
"name": "Clinical Trials Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CTO",
"repository": "https://github.com/ClinicalTrialOntology/CTO",
"uri_format": "http://purl.obolibrary.org/obo/CTO_$1",
"version": "1.0.0"
},
"cubedb": {
"comment": "website down as of 2021-10-04",
"deprecated": true,
"description": "Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available.",
"example": "AKR",
"homepage": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html",
"mappings": {
"biocontext": "CUBEDB",
"miriam": "cubedb",
"n2t": "cubedb"
},
"name": "Cube db",
"pattern": "^[A-Za-z_0-9]+$",
"preferred_prefix": "cubedb",
"uri_format": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/"
},
"cutg": {
"description": "Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank.",
"example": "9606",
"homepage": "http://www.kazusa.or.jp/codon/",
"keywords": [
"dna",
"gene"
],
"mappings": {
"prefixcommons": "cutg"
},
"name": "Codon Usage Tabulated from GenBank",
"preferred_prefix": "cutg",
"provides": "ncbitaxon",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=$1"
},
"cvdo": {
"contact": {
"email": "paul.fabry@usherbrooke.ca",
"github": "pfabry",
"name": "Paul Fabry",
"orcid": "0000-0002-3336-2476"
},
"description": "An ontology to describe entities related to cardiovascular diseases",
"download_owl": "http://purl.obolibrary.org/obo/cvdo.owl",
"example": "0000546",
"homepage": "https://github.com/OpenLHS/CVDO",
"keywords": [
"cardiology",
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "CVDO",
"biocontext": "CVDO",
"bioportal": "CVDO",
"fairsharing": "FAIRsharing.2basyz",
"obofoundry": "cvdo",
"ols": "cvdo",
"ontobee": "CVDO"
},
"name": "Cardiovascular Disease Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CVDO",
"repository": "https://github.com/OpenLHS/CVDO",
"uri_format": "http://purl.obolibrary.org/obo/CVDO_$1",
"version": "2020-03-05"
},
"cvx": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The CDC's National Center of Immunization and Respiratory Diseases (NCIRD) developed and maintains the CVX (vaccine administered) code set. The table below has the most up to date values. It includes both active and inactive vaccines available in the US. CVX codes for inactive vaccines allow transmission of historical immunization records.",
"example": "54",
"homepage": "https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx",
"mappings": {
"hl7": "2.16.840.1.113883.6.59"
},
"name": "Vaccine administered code set",
"pattern": "^\\d+$",
"preferred_prefix": "cvx"
},
"d1id": {
"description": "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences.",
"example": "00030692-0FE1-4A1B-955E-A2E55D659267",
"homepage": "https://www.dataone.org",
"mappings": {
"biocontext": "D1ID",
"miriam": "d1id",
"n2t": "d1id"
},
"name": "DataONE",
"pattern": "^\\S+$",
"preferred_prefix": "d1id",
"uri_format": "https://cn.dataone.org/cn/v2/resolve/{$1}"
},
"dailymed": {
"description": "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read.",
"example": "973a9333-fec7-46dd-8eb5-25738f06ee54",
"homepage": "https://dailymed.nlm.nih.gov/dailymed/",
"mappings": {
"biocontext": "DAILYMED",
"miriam": "dailymed",
"n2t": "dailymed",
"prefixcommons": "dailymed"
},
"name": "DailyMed",
"pattern": "^[A-Za-z0-9-]+$",
"preferred_prefix": "dailymed",
"uri_format": "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1"
},
"dandi": {
"contact": {
"email": "yoh@dartmouth.edu",
"github": null,
"name": "Yaroslav Halchenko",
"orcid": "0000-0003-3456-2493"
},
"description": "DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable).\nDANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data.\nThese data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.",
"example": "000017",
"homepage": "https://dandiarchive.org/",
"keywords": [
"neurophysiology"
],
"mappings": {
"fairsharing": "FAIRsharing.f2c119",
"miriam": "dandi",
"re3data": "r3d100013638"
},
"name": "Distributed Archives for Neurophysiology Data Integration",
"pattern": "^\\d{6}(\\/\\d+\\.\\d+\\.\\d+)?$",
"preferred_prefix": "dandi",
"repository": "https://github.com/dandi/dandiarchive",
"twitter": "dandiarchive",
"uri_format": "https://dandiarchive.org/dandiset/$1"
},
"darc": {
"description": "DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.",
"example": "1250",
"homepage": "http://darcsite.genzentrum.lmu.de/darc/index.php",
"keywords": [
"life science"
],
"mappings": {
"biocontext": "DARC",
"fairsharing": "FAIRsharing.evfe2s",
"miriam": "darc",
"n2t": "darc"
},
"name": "Database of Aligned Ribosomal Complexes",
"pattern": "^\\d+$",
"preferred_prefix": "darc",
"publications": [
{
"doi": "10.1093/nar/gkr824",
"pmc": "PMC3245104",
"pubmed": "22009674",
"title": "The DARC site: a database of aligned ribosomal complexes.",
"year": 2011
}
],
"uri_format": "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1"
},
"dashr": {
"contact": {
"email": "dashr@lisanwanglab.org",
"github": null,
"name": "Li-San Wang",
"orcid": "0000-0002-3684-0031"
},
"description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records.",
"example": "hsa-mir-200a",
"homepage": "http://lisanwanglab.org/DASHR/",
"keywords": [
"life science"
],
"mappings": {
"biocontext": "DASHR",
"fairsharing": "FAIRsharing.ztvs34",
"miriam": "dashr",
"n2t": "dashr"
},
"name": "Database of small human noncoding RNAs",
"pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$",
"preferred_prefix": "dashr",
"publications": [
{
"doi": "10.1093/nar/gkv1188",
"pmc": "PMC4702848",
"pubmed": "26553799",
"title": "DASHR: database of small human noncoding RNAs.",
"year": 2015
}
],
"uri_format": "http://lisanwanglab.org/DASHR/entry/$1"
},
"dashr.expression": {
"description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression.",
"example": "hsa-mir-200a",
"homepage": "https://dashr1.lisanwanglab.org/show-expression-table.php?start=0",
"mappings": {
"biocontext": "DASHR.EXPRESSION",
"miriam": "dashr.expression",
"n2t": "dashr.expression"
},
"name": "DASHR expression",
"pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$",
"preferred_prefix": "dashr.expression",
"uri_format": "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable"
},
"datacite": {
"contact": {
"email": "silvio.peroni@unibo.it",
"github": "essepuntato",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF.",
"download_owl": "http://aber-owl.net/media/ontologies/DATACITE/2/datacite.owl",
"example": "AgentIdentifierScheme",
"homepage": "http://www.sparontologies.net/ontologies/datacite",
"keywords": [
"ontology",
"subject agnostic"
],
"mappings": {
"aberowl": "DATACITE",
"bioportal": "DATACITE",
"fairsharing": "FAIRsharing.c06f1e"
},
"name": "DataCite Ontology",
"preferred_prefix": "DataCite",
"repository": "https://github.com/sparontologies/datacite",
"twitter": "datacite",
"uri_format": "http://purl.org/spar/datacite/$1"
},
"datanator.gene": {
"description": "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.",
"example": "K00973",
"homepage": "https://datanator.info/",
"mappings": {
"miriam": "datanator.gene"
},
"name": "Datanator Gene",
"part_of": "datanator",
"pattern": "^K[0-9]+$",
"preferred_prefix": "datanator.gene",
"uri_format": "https://www.datanator.info/gene/$1"
},
"datanator.metabolite": {
"description": "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.",
"example": "OUYCCCASQSFEME-MRVPVSSYSA-N",
"homepage": "https://datanator.info/",
"mappings": {
"miriam": "datanator.metabolite"
},
"name": "Datanator Metabolite",
"part_of": "datanator",
"pattern": "^[A-Z\\-]+$",
"preferred_prefix": "datanator.metabolite",
"uri_format": "https://www.datanator.info/metabolite/$1"
},
"datanator.reaction": {
"description": "\tDatanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.",
"example": "XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N",
"homepage": "https://icahn.mssm.edu/",
"mappings": {
"miriam": "datanator.reaction"
},
"name": "Datanator Reaction",
"pattern": "^.*?--%3E.*?$",
"preferred_prefix": "datanator.reaction",
"uri_format": "https://datanator.info/reaction/$1"
},
"datf": {
"deprecated": true,
"description": "DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals.",
"example": "AT1G01030.1",
"homepage": "http://datf.cbi.pku.edu.cn/",
"keywords": [
"regulation"
],
"mappings": {
"biocontext": "DATF",
"miriam": "datf",
"n2t": "datf",
"prefixcommons": "datf"
},
"name": "Database of Arabidopsis Transcription Factors",
"pattern": "^AT[1-5]G\\d{5}(\\.\\d+)?$",
"preferred_prefix": "datf",
"uri_format": "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1"
},
"dbd": {
"description": "The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins.",
"example": "0045310",
"homepage": "http://www.transcriptionfactor.org/",
"keywords": [
"genome",
"regulation"
],
"mappings": {
"biocontext": "DBD",
"edam": "2716",
"miriam": "dbd",
"n2t": "dbd",
"prefixcommons": "dbd"
},
"name": "Transcription Factor Database",
"pattern": "^\\d+$",
"preferred_prefix": "dbd",
"uri_format": "http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD"
},
"dbest": {
"description": "The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms.",
"example": "BP100000",
"homepage": "https://www.ncbi.nlm.nih.gov/nucest",
"keywords": [
"bioinformatics",
"dna",
"life science"
],
"mappings": {
"biocontext": "DBEST",
"edam": "1105",
"fairsharing": "FAIRsharing.v9fya8",
"miriam": "dbest",
"n2t": "dbest",
"ncbi": "dbEST",
"prefixcommons": "dbest",
"re3data": "r3d100010648"
},
"name": "EST database maintained at the NCBI.",
"pattern": "^([A-Z]+)?\\d+(\\.\\d+)?$",
"preferred_prefix": "dbest",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "dbEST through DNA Data Bank of Japan (DDBJ)",
"homepage": "http://www.ddbj.nig.ac.jp/",
"name": "dbEST through DNA Data Bank of Japan (DDBJ)",
"uri_format": "http://getentry.ddbj.nig.ac.jp/getentry/na/$1"
},
{
"code": "ebi",
"description": "dbEST through European Nucleotide Archive (ENA)",
"homepage": "https://www.ebi.ac.uk/ena",
"name": "dbEST through European Nucleotide Archive (ENA)",
"uri_format": "https://www.ebi.ac.uk/ena/data/view/$1"
}
],
"publications": [
{
"doi": "10.1038/ng0893-332",
"pmc": null,
"pubmed": "8401577",
"title": "dbEST--database for \"expressed sequence tags\".",
"year": 1993
}
],
"uri_format": "https://www.ncbi.nlm.nih.gov/nucest/$1"
},
"dbg2introns": {
"description": "The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank.",
"example": "Cu.me.I1",
"homepage": "http://webapps2.ucalgary.ca/~groupii/",
"keywords": [
"dna"
],
"mappings": {
"biocontext": "DBG2INTRONS",
"miriam": "dbg2introns",
"n2t": "dbg2introns",
"prefixcommons": "mgiid"
},
"name": "DBG2 Introns",
"pattern": "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$",
"preferred_prefix": "dbg2introns",
"publications": [
{
"doi": "10.1093/nar/gkr1043",
"pmc": "PMC3245105",
"pubmed": "22080509",
"title": "Database for bacterial group II introns.",
"year": 2011
}
],
"uri_format": "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1"
},
"dbgap": {
"description": "The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype.",
"example": "phs000768.v2.p1",
"homepage": "https://www.ncbi.nlm.nih.gov/projects/gap",
"keywords": [
"biomedical science",
"epigenetics",
"genetics"
],
"mappings": {
"biocontext": "DBGAP",
"cellosaurus": "dbGAP",
"fairsharing": "FAIRsharing.88v2k0",
"miriam": "dbgap",
"n2t": "dbgap"
},
"name": "Database of Genotypes and Phenotypes",
"pattern": "^phs[0-9]{6}(.v\\d+.p\\d+)?$",
"preferred_prefix": "dbgap",
"publications": [
{
"doi": "10.1093/nar/gkt1211",
"pmc": "PMC3965052",
"pubmed": "24297256",
"title": "NCBI's Database of Genotypes and Phenotypes: dbGaP.",
"year": 2013
},
{
"doi": "10.1038/ng1007-1181",
"pmc": "PMC2031016",
"pubmed": "17898773",
"title": "The NCBI dbGaP database of genotypes and phenotypes.",
"year": 2007
}
],
"uri_format": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1"
},
"dbmhc": {
"appears_in": [
"cellosaurus"
],
"deprecated": true,
"description": "Cell line databases/resources",
"example": "48439",
"homepage": "https://www.ncbi.nlm.nih.gov/gv/mhc/",
"mappings": {
"cellosaurus": "dbMHC"
},
"name": "Database of human Major Histocompatibility Complex",
"pattern": "^\\d+$",
"preferred_prefix": "dbmhc"
},
"dbo": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki.",
"example": "careerPrizeMoney",
"github_request_issue": 515,
"homepage": "https://dbpedia.org/ontology",
"keywords": [
"dbpedia",
"ontology"
],
"name": "DBPedia Ontology",
"preferred_prefix": "dbo",
"uri_format": "https://dbpedia.org/ontology/$1"
},
"dbprobe": {
"description": "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.",
"example": "1000000",
"homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe",
"keywords": [
"nucleotide"
],
"mappings": {
"biocontext": "DBPROBE",
"edam": "2719",
"miriam": "dbprobe",
"n2t": "dbprobe",
"ncbi": "dbProbe",
"prefixcommons": "dbprobe"
},
"name": "NCBI Probe database Public registry of nucleic acid reagents",
"pattern": "^\\d+$",
"preferred_prefix": "dbprobe",
"uri_format": "https://www.ncbi.nlm.nih.gov/probe/?term=$1"
},
"dbsnp": {
"description": "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.",
"example": "rs121909098",
"homepage": "https://www.ncbi.nlm.nih.gov/snp/",
"keywords": [
"genome",
"life science"
],
"mappings": {
"biocontext": "dbSNP",
"cellosaurus": "dbSNP",
"edam": "1106",
"fairsharing": "FAIRsharing.edxb58",
"go": "dbSNP",
"hl7": "2.16.840.1.113883.6.284",
"miriam": "dbsnp",
"n2t": "dbsnp",
"ncbi": "dbSNP",
"prefixcommons": "dbsnp",
"re3data": "r3d100010652",
"uniprot": "DB-0013",
"wikidata": "P6861"
},
"name": "dbSNP Reference SNP number",
"pattern": "^rs\\d+$",
"preferred_prefix": "dbsnp",
"providers": [
{
"code": "sib",
"description": "SNP2TFBS",
"homepage": "https://ccg.epfl.ch/snp2tfbs/",
"name": "SNP2TFBS",
"uri_format": "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1"
}
],
"publications": [
{
"doi": "10.1093/nar/gkl1031",
"pmc": "PMC1781113",
"pubmed": "17170002",
"title": "Database resources of the National Center for Biotechnology Information.",
"year": 2006
},
{
"doi": "10.1093/nar/29.1.308",
"pmc": "PMC29783",
"pubmed": "11125122",
"title": "dbSNP: the NCBI database of genetic variation.",
"year": 2001
}
],
"repository": "https://github.com/ncbi/dbsnp/tree/master/tutorials",
"uri_format": "https://www.ncbi.nlm.nih.gov/snp/$1"
},
"dbvar.study": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Studies in dbVar.",
"example": "nstd102",
"homepage": "https://www.ncbi.nlm.nih.gov/dbvar",
"name": "Database of Genomic Structural Variation - Study",
"preferred_prefix": "dbvar.study",
"synonyms": [
"dbvar.studies"
],
"uri_format": "https://www.ncbi.nlm.nih.gov/dbvar/studies/$1"
},
"dbvar.variant": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Variants in dbVar.",
"example": "nsv3875336",
"homepage": "https://www.ncbi.nlm.nih.gov/dbvar",
"name": "Database of Genomic Structural Variation - Variant",
"preferred_prefix": "dbvar.variant",
"synonyms": [
"dbvar.variants"
],
"uri_format": "https://www.ncbi.nlm.nih.gov/dbvar/variants/$1"
},
"dc": {
"contact": {
"email": "kdurante@stanford.edu",
"github": null,
"name": "Kim Durante",
"orcid": "0000-0001-9052-2854"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"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/",
"keywords": [
"biomedical science",
"life science",
"ontology",
"subject agnostic"
],
"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/$1"
},
"dc_cl": {
"contact": {
"email": "Lindsay.Cowell@utsouthwestern.edu",
"github": null,
"name": "Lindsay Cowell",
"orcid": "0000-0003-1617-8244"
},
"deprecated": true,
"example": "0000003",
"homepage": "http://www.dukeontologygroup.org/Projects.html",
"keywords": [
"obo",
"ontology"
],
"mappings": {
"biocontext": "DC_CL",
"obofoundry": "dc_cl"
},
"name": "Dendritic cell",
"pattern": "^\\d{7}$",
"preferred_prefix": "DC_CL",
"uri_format": "http://purl.obolibrary.org/obo/DC_CL_$1"
},
"dcat": {
"contact": {
"email": "kdurante@stanford.edu",
"github": null,
"name": "Kim Durante",
"orcid": "0000-0001-9052-2854"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web",
"download_owl": "http://aber-owl.net/media/ontologies/DCAT/2/dcat.owl",
"example": "Dataset",
"homepage": "https://www.w3.org/ns/dcat",
"keywords": [
"data management",
"ontology",
"subject agnostic"
],
"mappings": {
"aberowl": "DCAT",
"biocontext": "dcat",
"biolink": "dcat",
"bioportal": "DCAT",
"fairsharing": "FAIRsharing.h4j3qm"
},
"name": "Data Catalog",
"preferred_prefix": "dcat",
"repository": "https://github.com/w3c/dxwg/",
"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/",
"keywords": [
"ontology",
"subject agnostic"
],
"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/$1"
},
"ddanat": {
"contact": {
"email": "pfey@northwestern.edu",
"github": "pfey03",
"name": "Petra Fey",
"orcid": "0000-0002-4532-2703"
},
"description": "A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum",
"download_obo": "http://purl.obolibrary.org/obo/ddanat.obo",
"download_owl": "http://purl.obolibrary.org/obo/ddanat.owl",
"example": "0000006",
"homepage": "http://dictybase.org/",
"keywords": [
"anatomy",
"life science",
"obo",
"ontology",
"slime-mould"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "DDANAT",
"biocontext": "DDANAT",
"bioportal": "DDANAT",
"fairsharing": "FAIRsharing.z656ab",
"go": "DDANAT",
"obofoundry": "ddanat",
"ols": "ddanat",
"ontobee": "DDANAT",
"prefixcommons": "ddanat"
},
"name": "Dictyostelium discoideum anatomy",
"pattern": "^\\d{7}$",
"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_$1",
"version": "2020-04-13"
},
"ddinter.drug": {
"contact": {
"email": "oriental-cds@163.com",
"github": null,
"name": "Dongsheng Cao",
"orcid": "0000-0003-3604-3785"
},
"contributor": {
"email": null,
"github": "sierra-moxon",
"name": "Sierra Moxon",
"orcid": "0000-0002-8719-7760"
},
"description": "Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety.",
"example": "DDInter20",
"github_request_issue": 492,
"homepage": "http://ddinter.scbdd.com",
"keywords": [
"chemistry",
"drugs",
"relationships"
],
"license": "CC-BY-NC-SA-4.0",
"name": "Curated Drug-Drug Interactions Database - Drug",
"pattern": "^DDInter\\d+$",
"preferred_prefix": "ddinter.drug",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://ddinter.scbdd.com/ddinter/drug-detail/$1"
},
"ddinter.interaction": {
"contact": {
"email": "oriental-cds@163.com",
"github": null,
"name": "Dongsheng Cao",
"orcid": "0000-0003-3604-3785"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety.",
"example": "1122888",
"github_request_issue": 492,
"homepage": "http://ddinter.scbdd.com",
"keywords": [
"chemistry",
"drug-drug interactions",
"drugs",
"relationships"
],
"license": "CC-BY-NC-SA-4.0",
"name": "Curated Drug-Drug Interactions Database - Interaction",
"pattern": "^\\d+$",
"preferred_prefix": "ddinter.interaction",
"uri_format": "http://ddinter.scbdd.com/ddinter/interact/$1"
},
"ddpheno": {
"contact": {
"email": "pfey@northwestern.edu",
"github": "pfey03",
"name": "Petra Fey",
"orcid": "0000-0002-4532-2703"
},
"description": "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum.",
"download_json": "http://purl.obolibrary.org/obo/ddpheno.json",
"download_obo": "https://raw.githubusercontent.com/obophenotype/dicty-phenotype-ontology/master/ddpheno.obo",
"download_owl": "http://purl.obolibrary.org/obo/ddpheno.owl",
"example": "0001417",
"homepage": "http://dictybase.org/",
"keywords": [
"life science",
"obo",
"ontology"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "DDPHENO",
"biocontext": "DDPHENO",
"bioportal": "DDPHENO",
"fairsharing": "FAIRsharing.9c1p18",
"obofoundry": "ddpheno",
"ols": "ddpheno",
"ontobee": "DDPHENO"
},
"name": "Dictyostelium discoideum phenotype ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "DDPHENO",
"publications": [
{
"doi": "10.1387/ijdb.190226pf",
"pmc": "PMC7409682",
"pubmed": "31840793",
"title": "dictyBase and the Dicty Stock Center (version 2.0) - a progress report.",
"year": 2019
},
{
"doi": "10.1007/978-1-62703-302-2_4",
"pmc": "PMC3762881",
"pubmed": "23494302",
"title": "One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012.",
"year": 2013
}
],
"repository": "https://github.com/obophenotype/dicty-phenotype-ontology",
"twitter": "dictybase",
"uri_format": "http://purl.obolibrary.org/obo/DDPHENO_$1",
"version": "2020-06-19"
},
"debio": {
"contact": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON.",
"download_json": "https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.json",
"download_obo": "https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.obo",
"download_owl": "https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.owl",
"example": "0000001",
"homepage": "https://biopragmatics.github.io/debio",
"keywords": [
"ontology"
],
"name": "Decentralized Biomedical Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "DeBiO",
"providers": [
{
"code": "obo2",
"description": "Because it's not possible to configure the base URI with ROBOT/OWLAPI, this pops out",
"homepage": "http://purl.obolibrary.org",
"name": "Placeholder OBO PURL",
"uri_format": "http://purl.obolibrary.org/obo/debio_$1"
}
],
"uri_format": "https://biopragmatics.github.io/debio/$1"
},
"decipher": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms",
"example": "1",
"homepage": "https://www.deciphergenomics.org/",
"keywords": [
"biomedical science",
"life science"
],
"mappings": {
"biocontext": "DECIPHER",
"fairsharing": "FAIRsharing.l8Sf5x"
},
"name": "DECIPHER CNV Syndromes",
"pattern": "^\\d+$",
"preferred_prefix": "decipher",
"publications": [
{
"doi": "10.1093/nar/gkt937",
"pmc": "PMC3965078",
"pubmed": "24150940",
"title": "DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation.",
"year": 2013
},
{
"doi": "10.1016/j.ajhg.2009.03.010",
"pmc": "PMC2667985",
"pubmed": "19344873",
"title": "DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.",
"year": 2009
}
],
"uri_format": "https://www.deciphergenomics.org/syndrome/$1"
},
"degradome": {
"description": "The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced.",
"example": "Ax1",
"homepage": "http://degradome.uniovi.es/",
"mappings": {
"biocontext": "DEGRADOME",
"miriam": "degradome",
"n2t": "degradome"
},
"name": "Degradome Database",
"pattern": "^[AMCST][0-9x][0-9]$",
"preferred_prefix": "degradome",
"uri_format": "http://degradome.uniovi.es/cgi-bin/protease/$1"
},
"deo": {
"contact": {
"email": "silvio.peroni@unibo.it",
"github": "essepuntato",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology that provides a structured vocabulary for rhetorical elements within documents (e.g., Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix). It is imported by DoCO.",
"example": "Reference",
"homepage": "http://www.sparontologies.net/ontologies/deo",
"keywords": [
"subject agnostic"
],
"mappings": {
"fairsharing": "FAIRsharing.39fd58"
},
"name": "Discourse Elements Ontology",
"preferred_prefix": "DEO",
"publications": [
{
"doi": "10.3233/sw-150177",
"pmc": null,
"pubmed": null,
"title": "The Document Components Ontology (DoCO)",
"year": 2016
}
],
"repository": "https://github.com/sparontologies/deo",
"twitter": "sparontologies",
"uri_format": "http://purl.org/spar/deo/$1"
},
"depmap": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells.",
"example": "ACH-000001",
"homepage": "https://depmap.org/portal",
"mappings": {
"cellosaurus": "DepMap"
},
"name": "DepMap Cell Lines",
"pattern": "^ACH-\\d+$",
"preferred_prefix": "depmap",
"uri_format": "https://depmap.org/portal/cell_line/$1"
},
"depod": {
"contact": {
"email": "depod@embl.de",
"github": null,
"name": "General Enquiries",
"orcid": "0000-0003-3562-7869"
},
"description": "The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources.",
"example": "PTPN1",
"homepage": "http://www.depod.bioss.uni-freiburg.de",
"keywords": [
"life science"
],
"mappings": {
"biocontext": "DEPOD",
"fairsharing": "FAIRsharing.q9j2e3",
"miriam": "depod",
"n2t": "depod",
"re3data": "r3d100011936",
"uniprot": "DB-0190"
},
"name": "Human Dephosphorylation Database",
"pattern": "^[A-Z0-9]+$",
"preferred_prefix": "depod",
"provides": "hgnc.symbol",
"publications": [
{
"doi": "doi",
"pmc": "PMC6911163",
"pubmed": "31836896",
"title": null,
"year": null
},
{
"doi": "10.1093/database/baz133",
"pmc": "PMC6911163",
"pubmed": "31836896",
"title": "The human DEPhOsphorylation Database DEPOD: 2019 update.",
"year": 2019
},
{
"doi": "10.1093/nar/gku1009",
"pmc": "PMC4383878",
"pubmed": "25332398",
"title": "The human DEPhOsphorylation database DEPOD: a 2015 update.",
"year": 2014
},
{
"doi": "10.1126/scisignal.2003203",
"pmc": null,
"pubmed": "23674824",
"title": "Elucidating human phosphatase-substrate networks.",
"year": 2013
}
],
"uri_format": "http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1"
},
"dermo": {
"contact": {
"email": "pns12@cam.ac.uk",
"github": null,
"name": "Paul Schofield",
"orcid": null
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders",
"download_obo": "http://aber-owl.net/media/ontologies/DERMO/10/dermo.obo",
"example": "0000000",
"homepage": "https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x",
"keywords": [
"ontology"
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"mappings": {
"aberowl": "DERMO",
"bioportal": "DERMO",
"fairsharing": "FAIRsharing.k008w7"
},
"name": "Human Dermatological Disease Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "dermo",
"uri_format": "http://purl.obolibrary.org/obo/DERMO_$1"
},
"dev.ga4ghdos": {
"description": "Assists in resolving data across cloud resources.",
"example": "23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00",
"homepage": "http://github.com/ga4gh/data-object-service-schemas",
"mappings": {
"biocontext": "DEV.GA4GHDOS",
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"name": "Development Data Object Service",
"pattern": "^[a-zA-Z0-9\\-:#\\.]+$",
"preferred_prefix": "dev.ga4ghdos",
"uri_format": "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1"
},
"dg.4503": {
"description": "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org",
"example": "0000ffeb-36e0-4a29-b21d-84423bda979d",
"homepage": "https://gen3.biodatacatalyst.nhlbi.nih.gov",
"mappings": {
"miriam": "dg.4503"
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"name": "BioData Catalyst",
"pattern": "^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$",
"preferred_prefix": "dg.4503",
"uri_format": "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/$1"
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"dg.4dfc": {
"description": "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org",
"example": "81944ba1-81d0-436e-8552-33d77a27834b",
"homepage": "https://nci-crdc.datacommons.io/",
"mappings": {
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"name": "NCI Data Commons Framework Services",
"pattern": "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$",
"preferred_prefix": "dg.4dfc",
"uri_format": "https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1"
},
"dg.6vts": {
"description": "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org",
"example": "2afacf00-9a1d-4d80-8c32-69d3923d3913",
"homepage": "https://jcoin.datacommons.io",
"mappings": {
"miriam": "dg.6vts"
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"name": "JCOIN",
"pattern": "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$",
"preferred_prefix": "dg.6vts",
"uri_format": "https://jcoin.datacommons.io/ga4gh/drs/v1/objects/$1"
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"dg.anv0": {
"description": "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org",
"example": "00077f1c-c45a-47ba-8e6c-1bf6b6b43fce",
"homepage": "https://gen3.theanvil.io",
"mappings": {
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"name": "Anvil",
"pattern": "^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$",
"preferred_prefix": "dg.anv0",
"uri_format": "https://gen3.theanvil.io/ga4gh/drs/v1/objects/$1"
},
"dg.f82a1a": {
"description": "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org",
"example": "00026f50-858a-446b-8ed9-b0e3ecd7b20e",
"homepage": "https://kidsfirstdrc.org",
"mappings": {
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"name": "Kids First",
"pattern": "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$",
"preferred_prefix": "dg.f82a1a",
"uri_format": "https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/$1"
},
"dg5b0d": {
"description": "The Blood Profiling Atlas in Cancer (BloodPAC) supports the management, analysis and sharing of liquid biopsy data for the oncology research community and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for cancer treatment and prevention. The data commons supports cross-project analyses by harmonizing data from different projects through the collaborative development of a data dictionary, providing an API for data queries and download, and providing a cloud-based analysis workspace with rich tools and resources.",
"example": "00000d53-99bc-4d3e-8ed7-6dc358baccb7",
"homepage": "https://data.bloodpac.org/.",
"mappings": {
"miriam": "dg.5b0d"
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"name": "BloodPAC",
"pattern": "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$",
"preferred_prefix": "dg5b0d",
"uri_format": "https://data.bloodpac.org/ga4gh/drs/v1/objects/$1"
},
"dgrc": {
"description": "Cell line collections",
"example": "215",
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"mappings": {
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},
"name": "Drosophila Genomics Resource Center",
"pattern": "^\\d+$",
"preferred_prefix": "dgrc",
"uri_format": "https://dgrc.bio.indiana.edu/product/View?product=$1"
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"dhba": {
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A controlled vocabulary to support the study of transcription in the developing human brain",
"download_obo": "https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dhba.obo",
"example": "10153",
"homepage": "https://www.brainspan.org/",
"keywords": [
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],
"name": "Developing Human Brain Atlas",
"pattern": "^\\d+$",
"preferred_prefix": "DHBA",
"uri_format": "https://biopragmatics.github.io/providers/dhba/$1"
},
"dicom": {
"contact": {
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"github": null,
"name": "David Clunie",
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},
"description": "DICOM Controlled Terminology",
"download_owl": "ftp://medical.nema.org/MEDICAL/Dicom/Resources/Ontology/DCM/dcm.owl",
"example": "109082",
"homepage": "http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html",
"keywords": [
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"biomedical science",
"medicine",
"ontology"
],
"mappings": {
"bioportal": "DCM",
"fairsharing": "FAIRsharing.b7z8by",
"hl7": "1.2.840.10008.2.16.4",
"ols": "dicom"
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"name": "DICOM Controlled Terminology",
"pattern": "^\\d+$",
"preferred_prefix": "dicom",
"publications": [
{
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"title": "Multi-series DICOM: an extension of DICOM that stores a whole study in a single object.",
"year": 2013
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{
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"pubmed": "16223609",
"title": "DICOM demystified: a review of digital file formats and their use in radiological practice.",
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],
"uri_format": "http://dicom.nema.org/resources/ontology/DCM/$1",
"version": "2021e_20211122"
},
"dictybase": {
"description": "A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics",
"example": "DDB0191090",
"homepage": "http://dictybase.org",
"keywords": [
"anatomy",
"comparative genomics",
"genome",
"life science"
],
"mappings": {
"biocontext": "dictyBase",
"fairsharing": "FAIRsharing.4shj9c",
"go": "dictyBase",
"ncbi": "dictyBase",
"prefixcommons": "dictybase",
"re3data": "r3d100010586",
"uniprot": "DB-0015"
},
"name": "dictyBase",
"preferred_prefix": "dictybase",
"publications": [
{
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"pmc": "PMC3762881",
"pubmed": "23494302",
"title": "One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012.",
"year": 2013
},
{
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"pmc": "PMC3531180",
"pubmed": "23172289",
"title": "DictyBase 2013: integrating multiple Dictyostelid species.",
"year": 2012
},
{
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"pmc": "PMC308872",
"pubmed": "14681427",
"title": "dictyBase: a new Dictyostelium discoideum genome database.",
"year": 2004
}
],
"synonyms": [
"dictyBase"
],
"uri_format": "http://dictybase.org/gene/$1"
},
"dictybase.est": {
"description": "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information.",
"example": "DDB0016567",
"homepage": "http://dictybase.org/",
"mappings": {
"biocontext": "DICTYBASE.EST",
"miriam": "dictybase.est",
"n2t": "dictybase.est"
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"name": "dictyBase Expressed Sequence Tag",
"part_of": "dictybase",
"pattern": "^DDB\\d+$",
"preferred_prefix": "dictybase.est",
"uri_format": "http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1"
},
"dictybase.gene": {
"description": "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information.",
"example": "DDB_G0267522",
"homepage": "http://dictybase.org/",
"mappings": {
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"miriam": "dictybase.gene",
"n2t": "dictybase.gene"
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"name": "Dictybase Gene",
"part_of": "dictybase",
"pattern": "^DDB_G\\d+$",
"preferred_prefix": "dictybase.gene",
"uri_format": "http://dictybase.org/gene/$1"
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"did": {
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"description": "DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary.",
"example": "sov:WRfXPg8dantKVubE3HX8pw",
"homepage": "https://w3c-ccg.github.io/did-spec/",
"mappings": {
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"n2t": "did"
},
"name": "Decentralized Identifier",
"namespace_in_lui": true,
"pattern": "^[a-z0-9]+:[A-Za-z0-9.\\-:]+$",
"preferred_prefix": "did",
"uri_format": "https://uniresolver.io/#did:$1"
},
"dideo": {
"contact": {
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"github": "mbrochhausen",
"name": "Mathias Brochhausen",
"orcid": "0000-0003-1834-3856"
},
"description": "The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology",
"download_owl": "http://purl.obolibrary.org/obo/dideo.owl",
"example": "00000180",
"homepage": "https://github.com/DIDEO/DIDEO",
"keywords": [
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"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
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"bioportal": "DIDEO",
"fairsharing": "FAIRsharing.9y8f0n",
"obofoundry": "dideo",
"ols": "dideo",
"ontobee": "DIDEO"
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"name": "Drug-drug Interaction and Drug-drug Interaction Evidence Ontology",
"pattern": "^\\d{8}$",
"preferred_prefix": "DIDEO",
"publications": [
{
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"title": "Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse.",
"year": 2018
},
{
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"pmc": "PMC5765984",
"pubmed": "29295242",
"title": "Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies to Improve Evidence Base Curation.",
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},
{
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"title": "Conceptual models of drug-drug interactions: A summary of recent efforts",
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}
],
"repository": "https://github.com/DIDEO/DIDEO",
"uri_format": "http://purl.obolibrary.org/obo/DIDEO_$1",
"version": "2022-06-14"
},
"dinto": {
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"github": null,
"name": "Maria Herrero",
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},
"deprecated": true,
"description": "A formal represention for drug-drug interactions knowledge.",
"download_owl": "http://purl.obolibrary.org/obo/dinto.owl",
"homepage": "http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "DINTO",
"biocontext": "DINTO",
"bioportal": "DINTO",
"obofoundry": "dinto",
"ontobee": "DINTO"
},
"name": "The Drug-Drug Interactions Ontology",
"preferred_prefix": "DINTO",
"publications": [
{
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"pmc": null,
"pubmed": "26147071",
"title": "DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug-Drug Interactions and Their Mechanisms.",
"year": 2015
}
],
"repository": "https://github.com/labda/DINTO",
"uri_format": "http://purl.obolibrary.org/obo/DINTO_$1"
},
"dip": {
"description": "The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions",
"example": "DIP-743N",
"homepage": "https://dip.doe-mbi.ucla.edu/",
"keywords": [
"biology",
"interaction",
"protein"
],
"mappings": {
"biocontext": "DIP",
"edam": "2616",
"fairsharing": "FAIRsharing.qje0v8",
"miriam": "dip",
"n2t": "dip",
"prefixcommons": "dip",
"re3data": "r3d100010670",
"uniprot": "DB-0016"
},
"name": "Database of Interacting Proteins",
"pattern": "^DIP(\\:)?\\-\\d{1,}[ENXS]$",
"preferred_prefix": "dip",
"publications": [
{
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"pmc": "PMC308820",
"pubmed": "14681454",
"title": "The Database of Interacting Proteins: 2004 update.",
"year": 2004
},
{
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"pmc": "PMC99070",
"pubmed": "11752321",
"title": "DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.",
"year": 2002
},
{
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"pmc": "PMC29798",
"pubmed": "11125102",
"title": "DIP: The Database of Interacting Proteins: 2001 update.",
"year": 2001
},
{
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"pmc": "PMC102387",
"pubmed": "10592249",
"title": "DIP: the database of interacting proteins.",
"year": 2000
}
],
"uri_format": "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1"
},
"discoverx": {
"description": "Cell line collections",
"example": "95-0166C6",
"homepage": "https://www.discoverx.com/products-applications/cell-lines",
"mappings": {
"cellosaurus": "DiscoverX"
},
"name": "DiscoverX cell line products",
"preferred_prefix": "discoverx",
"uri_format": "https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact"
},
"disdriv": {
"contact": {
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"github": "lschriml",
"name": "Lynn Schriml",
"orcid": "0000-0001-8910-9851"
},
"description": "Drivers of human diseases including environmental, maternal and social exposures.",
"download_owl": "http://purl.obolibrary.org/obo/disdriv.owl",
"example": "0000000",
"homepage": "http://www.disease-ontology.org",
"keywords": [
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"ontology"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "DISDRIV",
"bioportal": "DISDRIV",
"obofoundry": "disdriv",
"ols": "disdriv",
"ontobee": "DISDRIV"
},
"name": "Disease Drivers Ontology",
"pattern": "^\\d+$",
"preferred_prefix": "DISDRIV",
"repository": "https://github.com/DiseaseOntology/DiseaseDriversOntology",
"twitter": "diseaseontology",
"uri_format": "http://purl.obolibrary.org/obo/DISDRIV_$1"
},
"diseaseclass": {
"appears_in": [
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],
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"description": "Legacy disease classes that later became MONDO",
"download_obo": "https://github.com/obophenotype/human-disease-ontology/raw/master/src/experimental/missing-omc.obo",
"example": "0000598",
"keywords": [
"ontology"
],
"name": "Disease Class",
"pattern": "^\\d{7}$",
"preferred_prefix": "diseaseclass",
"uri_format": "https://biopragmatics.github.io/providers/diseaseclass/$1"
},
"diseasesdb": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities.",
"example": "1784",
"homepage": "http://www.diseasesdatabase.com/",
"mappings": {
"wikidata": "P557"
},
"name": "Diseases Database",
"pattern": "^\\d+$",
"preferred_prefix": "diseasesdb",
"uri_format": "https://www.diseasesdatabase.com/ddb$1.htm"
},
"disprot": {
"contact": {
"email": "silvio.tosatto@unipd.it",
"github": null,
"name": "Silvio C.E. Tosatto",
"orcid": "0000-0003-4525-7793"
},
"description": "DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature.",
"example": "DP00003",
"homepage": "https://disprot.org/",
"keywords": [
"biology",
"biomedical science",
"protein",
"structural biology",
"structure"
],
"mappings": {
"biocontext": "DISPROT",
"edam": "2723",
"fairsharing": "FAIRsharing.dt9z89",
"miriam": "disprot",
"n2t": "disprot",
"prefixcommons": "disprot",
"re3data": "r3d100010561",
"uniprot": "DB-0017"
},
"name": "DisProt",
"pattern": "^DP\\d{5}$",
"preferred_prefix": "disprot",
"publications": [
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"pmc": "PMC8728214",
"pubmed": "34850135",
"title": "DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation.",
"year": 2022
},
{
"doi": "10.1093/nar/gkz975",
"pmc": "PMC7145575",
"pubmed": "31713636",
"title": "DisProt: intrinsic protein disorder annotation in 2020.",
"year": 2020
},
{
"doi": "10.1093/nar/gkw1056",
"pmc": "PMC5210544",
"pubmed": "27899601",
"title": "DisProt 7.0: a major update of the database of disordered proteins.",
"year": 2016
},
{
"doi": "10.1093/nar/gkl893",
"pmc": "PMC1751543",
"pubmed": "17145717",
"title": "DisProt: the Database of Disordered Proteins.",
"year": 2006
},
{
"doi": "10.1093/bioinformatics/bth476",
"pmc": null,
"pubmed": "15310560",
"title": "DisProt: a database of protein disorder.",
"year": 2004
}
],
"repository": "https://disprot.github.io/",
"twitter": "disprot_db",
"uri_format": "https://disprot.org/$1"
},
"disprot.region": {
"description": "DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature.",
"example": "DP00086r013",
"homepage": "https://www.disprot.org",
"mappings": {
"miriam": "disprot.region"
},
"name": "DisProt region",
"part_of": "disprot",
"pattern": "^DP\\d{5}r\\d{3}$",
"preferred_prefix": "disprot.region",
"uri_format": "https://www.disprot.org/$1"
},
"dlxb": {
"description": "DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences.",
"example": "6VDC956",
"homepage": "https://doulix.com",
"mappings": {
"miriam": "dlxb"
},
"name": "Linear double stranded DNA sequences",
"part_of": "dlx",
"pattern": "^[A-Z0-9]{6,7}$",
"preferred_prefix": "dlxb",
"uri_format": "https://doulix.com/biomodules/$1"
},
"dlxc": {
"description": "DOULIX lab-tested standard biological parts, in this case, full length constructs.",
"example": "M77F7JM",
"homepage": "https://doulix.com",
"mappings": {
"miriam": "dlxc"
},
"name": "Circular double stranded DNA sequences composed",
"part_of": "dlx",
"pattern": "^[A-Z0-9]{6,7}$",
"preferred_prefix": "dlxc",
"uri_format": "https://doulix.com/constructs/$1"
},
"dmba": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A controlled vocabulary to support the study of transcription in the developing mouse brain",
"download_obo": "https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dmba.obo",
"example": "15567",
"homepage": "https://developingmouse.brain-map.org/",
"keywords": [
"ontology"
],
"name": "Developing Mouse Brain Atlas",
"pattern": "^\\d+$",
"preferred_prefix": "DMBA",
"uri_format": "https://biopragmatics.github.io/providers/dmba/$1"
},
"doap": {
"contact": {
"email": "edd@usefulinc.com",
"github": "ewilderj",
"name": "Edd Wilder-James",
"orcid": null
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "DOAP is a project to create an XML/RDF vocabulary to describe software projects, and in particular open source projects.",
"download_rdf": "http://usefulinc.com/ns/doap",
"example": "Project",
"homepage": "https://github.com/ewilderj/doap/wiki",
"keywords": [
"metadata",
"rdf",
"semantic web"
],
"name": "Description of a Project",
"preferred_prefix": "doap",
"references": [
"https://en.wikipedia.org/wiki/DOAP"
],
"repository": "https://github.com/ewilderj/doap",
"uri_format": "http://usefulinc.com/ns/doap#$1"
},
"doco": {
"contact": {
"email": "silvio.peroni@unibo.it",
"github": "essepuntato",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology that provides a structured vocabulary written of document components, both structural (e.g., block, inline, paragraph, section, chapter) and rhetorical (e.g., introduction, discussion, acknowledgements, reference list, figure, appendix).",
"example": "Paragraph",
"homepage": "http://www.sparontologies.net/ontologies/doco",
"keywords": [
"subject agnostic"
],
"mappings": {
"fairsharing": "FAIRsharing.162003"
},
"name": "Document Components Ontology",
"preferred_prefix": "DoCO",
"publications": [
{
"doi": "10.3233/sw-150177",
"pmc": null,
"pubmed": null,
"title": "The Document Components Ontology (DoCO)",
"year": 2016
}
],
"repository": "https://github.com/sparontologies/doco",
"twitter": "sparontologies",
"uri_format": "http://purl.org/spar/doco/$1"
},
"doi": {
"banana": "doi",
"comment": "The [DOI resolution factsheet](https://www.doi.org/factsheets/DOIProxy.html) specifies that `https://doi.org/DOI` is the preferred format:\n\n> Users may resolve DOI names that are structured to use the DOI system Proxy Server (https://doi.org (preferred)). The resolution of the DOI name in this case depends on the use of URL syntax: the example DOI name doi:10.10.123/456 would be resolved from the address: \"https://doi.org/10.123/456\". Any standard browser encountering a DOI name in this form will be able to resolve it. The proxy service (both doi.org and the **earlier but no longer preferred** dx.doi.org) is accessible over IPv6, and supports DNSSEC. The proxy servers respond to HTTPS (**preferred**) as well as HTTP requests.",
"contributor_extras": [
{
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
{
"email": null,
"github": "dhimmel",
"name": "Daniel Himmelstein",
"orcid": "0000-0002-3012-7446"
}
],
"description": "The Digital Object Identifier System is for identifying content objects in the digital environment.",
"example": "10.1038/s41597-022-01807-3",
"example_extras": [
"10.21/FQSQT4T3",
"10.1333/s00897980202a",
"10.1139/z02-135",
"10.1016/j.foodchem.2008.11.065",
"10.1093/acprof:oso/9780195159561.001.1"
],
"homepage": "https://www.doi.org/",
"keywords": [
"bibliography",
"knowledge and information systems"
],
"mappings": {
"biocontext": "DOI",
"biolink": "doi",
"cellosaurus": "DOI",
"edam": "1188",
"fairsharing": "FAIRsharing.hFLKCn",
"go": "DOI",
"miriam": "doi",
"n2t": "doi",
"prefixcommons": "doi",
"wikidata": "P356"
},
"name": "Digital Object Identifier",
"pattern": "^10.\\d{2,9}/.*$",
"preferred_prefix": "doi",
"providers": [
{
"code": "doi_http",
"description": "An alternate provider from the DOI website using HTTP",
"homepage": "https://www.doi.org",
"name": "Digital Object Identifier",
"uri_format": "http://doi.org/$1"
},
{
"code": "dx_doi_http",
"description": "An alternate provider from the DOI website using HTTP",
"homepage": "https://www.doi.org",
"name": "Digital Object Identifier",
"uri_format": "http://dx.doi.org/$1"
},
{
"code": "dx_doi_https",
"description": "An alternate provider from the DOI website using HTTPS",
"homepage": "https://www.doi.org",
"name": "Digital Object Identifier",
"uri_format": "https://dx.doi.org/$1"
},
{
"code": "scholia",
"description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.",
"homepage": "https://scholia.toolforge.org/",
"name": "Scholia",
"uri_format": "https://scholia.toolforge.org/doi/$1"
}
],
"references": [
"https://github.com/biopragmatics/bioregistry/issues/287",
"https://github.com/biopragmatics/bioregistry/pull/316"
],
"uri_format": "https://doi.org/$1"
},
"doid": {
"appears_in": [
"clo",
"scdo"
],
"banana": "DOID",
"contact": {
"email": "lynn.schriml@gmail.com",
"github": "lschriml",
"name": "Lynn Schriml",
"orcid": "0000-0001-8910-9851"
},
"description": "The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts.",
"download_json": "http://purl.obolibrary.org/obo/doid.json",
"download_obo": "https://github.com/DiseaseOntology/HumanDiseaseOntology/raw/main/src/ontology/doid.obo",
"download_owl": "http://purl.obolibrary.org/obo/doid.owl",
"example": "0110974",
"homepage": "http://www.disease-ontology.org",
"keywords": [
"biomedical science",
"disease",
"human",
"life science",
"obo",
"ontology"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "DOID",
"bartoc": "576",
"biocontext": "DOID",
"bioportal": "DOID",
"fairsharing": "FAIRsharing.8b6wfq",
"miriam": "doid",
"n2t": "doid",
"obofoundry": "doid",
"ols": "doid",
"ontobee": "DOID",
"prefixcommons": "do",
"wikidata": "P699"
},
"name": "Human Disease Ontology",
"namespace_in_lui": true,
"pattern": "^\\d+$",
"preferred_prefix": "DOID",
"providers": [
{
"code": "hdo",
"description": "Human Disease Ontology at Northwestern University",
"homepage": "http://disease-ontology.org/",
"name": "Human Disease Ontology at Northwestern University",
"uri_format": "http://disease-ontology.org/term/DOID:$1"
},
{
"code": "purl",
"description": "Legacy PURLs found in OAE",
"homepage": "http://purl.org/obo/owl/",
"name": "Legacy PURL",
"uri_format": "http://purl.org/obo/owl/DOID#DOID_$1"
}
],
"publications": [
{
"doi": "10.1093/nar/gkab1063",
"pmc": "PMC8728220",
"pubmed": "34755882",
"title": "The Human Disease Ontology 2022 update.",
"year": 2022
},
{
"doi": "10.1093/bib/bbab191",
"pmc": "PMC8195003",
"pubmed": "34015823",
"title": "COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model.",
"year": 2021
},
{
"doi": "10.7554/elife.52614",
"pmc": "PMC7077981",
"pubmed": "32180547",
"title": "Wikidata as a knowledge graph for the life sciences.",
"year": 2020
},
{
"doi": "10.1093/nar/gky1036",
"pmc": "PMC6323956",
"pubmed": "30407590",
"title": "ECO, the Evidence & Conclusion Ontology: community standard for evidence information.",
"year": 2019
},
{
"doi": "10.1093/nar/gky1032",
"pmc": "PMC6323977",
"pubmed": "30407550",
"title": "Human Disease Ontology 2018 update: classification, content and workflow expansion.",
"year": 2019
},
{
"doi": "10.1242/dmm.032839",
"pmc": "PMC5897730",
"pubmed": "29590633",
"title": "Disease Ontology: improving and unifying disease annotations across species.",
"year": 2018
},
{
"doi": "10.1093/database/baw015",
"pmc": "PMC4795929",
"pubmed": "26989148",
"title": "Wikidata as a semantic framework for the Gene Wiki initiative.",
"year": 2016
},
{
"doi": "10.1016/j.ajhg.2015.05.020",
"pmc": "PMC4572507",
"pubmed": "26119816",
"title": "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.",
"year": 2015
},
{
"doi": "10.1007/s00335-015-9576-9",
"pmc": "PMC4602048",
"pubmed": "26093607",
"title": "The Disease Ontology: fostering interoperability between biological and clinical human disease-related data.",
"year": 2015
},
{
"doi": "10.1093/database/bav032",
"pmc": "PMC4385274",
"pubmed": "25841438",
"title": "Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis.",
"year": 2015
},
{
"doi": "10.1093/nar/gku1011",
"pmc": "PMC4383880",
"pubmed": "25348409",
"title": "Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.",
"year": 2014
},
{
"doi": "10.1093/nar/gkr972",
"pmc": "PMC3245088",
"pubmed": "22080554",
"title": "Disease Ontology: a backbone for disease semantic integration.",
"year": 2011
},
{
"doi": "10.1186/1471-2164-10-s1-s6",
"pmc": "PMC2709267",
"pubmed": "19594883",
"title": "Annotating the human genome with Disease Ontology.",
"year": 2009
},
{
"doi": "10.1093/bioinformatics/btp193",
"pmc": "PMC2687947",
"pubmed": "19478018",
"title": "From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations.",
"year": 2009
}
],
"repository": "https://github.com/DiseaseOntology/HumanDiseaseOntology",
"synonyms": [
"do"
],
"twitter": "diseaseontology",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:$1",
"version": "2022-09-29"
},
"dommino": {
"description": "DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides.",
"example": "2GC4",
"homepage": "http://korkinlab.org/dommino",
"mappings": {
"biocontext": "DOMMINO",
"miriam": "dommino",
"n2t": "dommino"
},
"name": "Database of Macromolecular Interactions",
"pattern": "^[0-9][A-Za-z0-9]{3}$",
"preferred_prefix": "dommino",
"uri_format": "http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1"
},
"door": {
"description": "DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes.",
"example": "1398574",
"homepage": "http://csbl.bmb.uga.edu/DOOR/operon.php",
"keywords": [
"dna"
],
"mappings": {
"biocontext": "DOOR",
"miriam": "door",
"n2t": "door",
"prefixcommons": "door",
"re3data": "r3d100014113"
},
"name": "Database for Prokaryotic Operons",
"pattern": "^\\d+$",
"preferred_prefix": "door",
"uri_format": "http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1"
},
"doqcs.model": {
"description": "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models.",
"example": "57",
"homepage": "http://doqcs.ncbs.res.in/",
"keywords": [
"model"
],
"mappings": {
"biocontext": "DOQCS.MODEL",
"miriam": "doqcs.model",
"n2t": "doqcs.model",
"prefixcommons": "doqcs.model"
},
"name": "Database of Quantitative Cellular Signaling: Model",
"part_of": "doqcs",
"pattern": "^\\d+$",
"preferred_prefix": "doqcs.model",
"publications": [
{
"doi": "10.1093/bioinformatics/btf860",
"pmc": null,
"pubmed": "12584128",
"title": "The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks.",
"year": 2003
}
],
"uri_format": "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1"
},
"doqcs.pathway": {
"description": "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways.",
"example": "131",
"homepage": "http://doqcs.ncbs.res.in/",
"keywords": [
"pathway"
],
"mappings": {
"biocontext": "DOQCS.PATHWAY",
"miriam": "doqcs.pathway",
"n2t": "doqcs.pathway",
"prefixcommons": "doqcs.pathway"
},
"name": "Database of Quantitative Cellular Signaling: Pathway",
"part_of": "doqcs",
"pattern": "^\\d+$",
"preferred_prefix": "doqcs.pathway",
"publications": [
{
"doi": "10.1093/bioinformatics/btf860",
"pmc": null,
"pubmed": "12584128",
"title": "The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks.",
"year": 2003
}
],
"uri_format": "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1"
},
"dpo": {
"comment": "DPO is a subset of terms from FBcv",
"contact": {
"email": "cp390@cam.ac.uk",
"github": "Clare72",
"name": "Clare Pilgrim",
"orcid": "0000-0002-1373-1705"
},
"description": "An ontology for the description of Drosophila melanogaster phenotypes.",
"download_json": "http://purl.obolibrary.org/obo/dpo.json",
"download_obo": "http://purl.obolibrary.org/obo/dpo.obo",
"download_owl": "http://purl.obolibrary.org/obo/dpo.owl",
"homepage": "http://purl.obolibrary.org/obo/fbcv",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "DPO",
"bioportal": "DPO",
"obofoundry": "dpo",
"ols": "dpo",
"ontobee": "DPO"
},
"name": "Drosophila Phenotype Ontology",
"no_own_terms": true,
"part_of": "fbcv",
"preferred_prefix": "DPO",
"publications": [
{
"doi": "10.1186/2041-1480-4-30",
"pmc": "PMC3816596",
"pubmed": "24138933",
"title": "The Drosophila phenotype ontology.",
"year": 2013
}
],
"repository": "https://github.com/FlyBase/drosophila-phenotype-ontology",
"uri_format": "http://purl.obolibrary.org/obo/FBcv_$1",
"version": "2022-08-11"
},
"dpv": {
"description": "Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene.",
"example": "100",
"homepage": "http://www.dpvweb.net/",
"keywords": [
"classification",
"gene"
],
"mappings": {
"biocontext": "DPV",
"miriam": "dpv",
"n2t": "dpv",
"prefixcommons": "dpvweb"
},
"name": "Description of Plant Viruses",
"pattern": "^\\d+$",
"preferred_prefix": "dpv",
"publications": [
{
"doi": "10.1093/nar/gkj023",
"pmc": "PMC1347386",
"pubmed": "16381892",
"title": "DPVweb: a comprehensive database of plant and fungal virus genes and genomes.",
"year": 2006
}
],
"uri_format": "http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1"
},
"dragondb.allele": {
"comment": "Deprecated because the website is dead",
"deprecated": true,
"description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information.",
"example": "cho",
"homepage": "http://www.antirrhinum.net/",
"mappings": {
"biocontext": "DRAGONDB.ALLELE",
"miriam": "dragondb.allele",
"n2t": "dragondb.allele"
},
"name": "DragonDB Allele",
"part_of": "dragondb",
"pattern": "^\\w+$",
"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"
},
"drduke": {
"description": "identifier for chemicals linked to information on occurrence in plants",
"example": "19",
"homepage": "https://phytochem.nal.usda.gov/phytochem/search/list",
"mappings": {
"wikidata": "P10074"
},
"name": "Dr. Duke's Phytochemical and Ethnobotanical Databases chemical ID",
"preferred_prefix": "drduke",
"uri_format": "https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1"
},
"dron": {
"appears_in": [
"scdo"
],
"contact": {
"email": "hoganwr@gmail.com",
"github": "hoganwr",
"name": "William Hogan",
"orcid": "0000-0002-9881-1017"
},
"description": "We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive).",
"download_json": "http://purl.obolibrary.org/obo/dron.json",
"download_obo": "http://purl.obolibrary.org/obo/dron.obo",
"download_owl": "http://purl.obolibrary.org/obo/dron.owl",
"example": "00023232",
"homepage": "https://github.com/ufbmi/dron",
"keywords": [
"biomedical science",
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "DRON",
"biocontext": "DRON",
"bioportal": "DRON",
"fairsharing": "FAIRsharing.w5ntfd",
"obofoundry": "dron",
"ols": "dron",
"ontobee": "DRON"
},
"name": "The Drug Ontology",
"pattern": "^\\d{8}$",
"preferred_prefix": "DRON",
"publications": [
{
"doi": "10.1186/s13326-017-0121-5",
"pmc": "PMC5335794",
"pubmed": "28253937",
"title": "Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request.",
"year": 2017
},
{
"doi": "10.1186/s13326-016-0048-2",
"pmc": "PMC4836073",
"pubmed": "27096073",
"title": "An accurate and precise representation of drug ingredients.",
"year": 2016
},
{
"doi": "10.1186/2041-1480-4-44",
"pmc": "PMC3931349",
"pubmed": "24345026",
"title": "Building a drug ontology based on RxNorm and other sources.",
"year": 2013
}
],
"repository": "https://github.com/ufbmi/dron",
"uri_format": "http://purl.obolibrary.org/obo/DRON_$1",
"version": "2022-04-22"
},
"drsc": {
"description": "The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene.",
"example": "DRSC05221",
"homepage": "http://flyrnai.org/",
"mappings": {
"biocontext": "DRSC",
"miriam": "drsc",
"n2t": "drsc"
},
"name": "Drosophila RNAi Screening Center",
"pattern": "^DRSC\\d+$",
"preferred_prefix": "drsc",
"uri_format": "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1"
},
"drugbank": {
"contact": {
"email": "david.wishart@ualberta.ca",
"github": null,
"name": "David Wishart",
"orcid": "0000-0002-3207-2434"
},
"description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information.",
"example": "DB14938",
"homepage": "http://www.drugbank.ca",
"keywords": [
"biomedical science",
"drug",
"life science",
"protein"
],
"mappings": {
"bartoc": "18377",
"biocontext": "DrugBank",
"cellosaurus": "DrugBank",
"cheminf": "000406",
"edam": "2326",
"fairsharing": "FAIRsharing.353yat",
"miriam": "drugbank",
"n2t": "drugbank",
"prefixcommons": "drugbank",
"re3data": "r3d100010544",
"uniprot": "DB-0019",
"wikidata": "P715"
},
"name": "DrugBank",
"pattern": "^DB\\d{5}$",
"preferred_prefix": "drugbank",
"publications": [
{
"doi": "10.1093/nar/gkt1068",
"pmc": "PMC3965102",
"pubmed": "24203711",
"title": "DrugBank 4.0: shedding new light on drug metabolism.",
"year": 2013
},
{
"doi": "10.1093/nar/gkq1126",
"pmc": "PMC3013709",
"pubmed": "21059682",
"title": "DrugBank 3.0: a comprehensive resource for 'omics' research on drugs.",
"year": 2010
},
{
"doi": "10.1093/nar/gkm958",
"pmc": "PMC2238889",
"pubmed": "18048412",
"title": "DrugBank: a knowledgebase for drugs, drug actions and drug targets.",
"year": 2007
},
{
"doi": "10.1093/nar/gkj067",
"pmc": "PMC1347430",
"pubmed": "16381955",
"title": "DrugBank: a comprehensive resource for in silico drug discovery and exploration.",
"year": 2006
}
],
"synonyms": [
"DRUGBANK_ID",
"DrugBank"
],
"twitter": "DrugBankDB",
"uri_format": "http://www.drugbank.ca/drugs/$1"
},
"drugbank.category": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Close to 5K Categorizations for drugs, similar to ATCC.",
"example": "DBCAT000600",
"homepage": "https://go.drugbank.com/categories",
"keywords": [
"chemistry",
"drugs",
"metascience",
"topics"
],
"name": "DrugBank Drug Category",
"part_of": "drugbank",
"pattern": "^DBCAT\\d+$",
"preferred_prefix": "drugbank.category",
"uri_format": "https://www.drugbank.ca/categories/$1"
},
"drugbank.salt": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets.",
"example": "DBSALT001211",
"homepage": "http://www.drugbank.ca",
"mappings": {
"biocontext": "DRUGBANK.TARGET"
},
"name": "DrugBank Salts",
"part_of": "drugbank",
"pattern": "^DBSALT\\d{6}$",
"preferred_prefix": "drugbank.salt",
"synonyms": [
"drugbank.target"
],
"uri_format": "https://go.drugbank.com/salts/$1"
},
"drugbankv4.target": {
"description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database.",
"example": "BE0000048",
"homepage": "http://www.drugbank.ca/targets",
"mappings": {
"biocontext": "DRUGBANKV4.TARGET",
"miriam": "drugbankv4.target",
"n2t": "drugbankv4.target"
},
"name": "DrugBank Target v4",
"part_of": "drugbank",
"pattern": "^BE\\d{7}$",
"preferred_prefix": "drugbankv4.target",
"uri_format": "http://www.drugbank.ca/biodb/bio_entities/$1"
},
"drugcentral": {
"contact": {
"email": "toprea@salud.unm.edu",
"github": null,
"name": "Tudor Oprea",
"orcid": "0000-0002-6195-6976"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action.",
"example": "307",
"homepage": "http://drugcentral.org",
"keywords": [
"biomedical science",
"drug development",
"drug discovery",
"drug repositioning",
"pharmacology",
"pharmacy"
],
"mappings": {
"biolink": "DrugCentral",
"fairsharing": "FAIRsharing.3me82d",
"miriam": "drugcentral",
"uniprot": "DB-0239",
"wikidata": "P11198"
},
"name": "Drug Central",
"pattern": "^\\d+$",
"preferred_prefix": "drugcentral",
"publications": [
{
"doi": "10.1093/nar/gky963",
"pmc": "PMC6323925",
"pubmed": "30371892",
"title": "DrugCentral 2018: an update.",
"year": 2019
},
{
"doi": "10.1093/nar/gkw993",
"pmc": "PMC5210665",
"pubmed": "27789690",
"title": "DrugCentral: online drug compendium.",
"year": 2016
}
],
"synonyms": [
"Drug_Central"
],
"uri_format": "http://drugcentral.org/drugcard/$1"
},
"dsm4": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]",
"example": "315.1",
"example_extras": [
"291.89"
],
"homepage": "https://en.wikipedia.org/wiki/Diagnostic_and_Statistical_Manual_of_Mental_Disorders#DSM-IV-TR_(2000)",
"mappings": {
"hl7": "2.16.840.1.113883.6.126",
"wikidata": "P663"
},
"name": "Diagnostic and Statistical Manual of Mental Disorders (4th Edition)",
"pattern": "^\\d+\\.\\d+$",
"preferred_prefix": "dsm4",
"synonyms": [
"dsm-iv"
]
},
"dsm5": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [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. Its long-term objective is to improve the efficiency and transparency of collaborative, data-driven science.",
"example": "classification-model",
"homepage": "https://www.datascienceontology.org/",
"keywords": [
"data science",
"ontology"
],
"name": "Data Science Ontology",
"preferred_prefix": "dso",
"repository": "https://github.com/IBM/datascienceontology",
"uri_format": "https://www.datascienceontology.org/concept/$1"
},
"dto": {
"appears_in": [
"pr"
],
"contact": {
"email": "sschurer@med.miami.edu",
"github": null,
"name": "Stephan Schurer",
"orcid": null
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.",
"download_owl": "http://aber-owl.net/media/ontologies/DTO/4/dto.owl",
"example": "90000018",
"homepage": "https://github.com/DrugTargetOntology/DTO",
"keywords": [
"biomedical science",
"drug discovery",
"ontology"
],
"mappings": {
"aberowl": "DTO",
"bioportal": "DTO",
"fairsharing": "FAIRsharing.tke3y2"
},
"name": "Drug Target Ontology",
"pattern": "^\\d+$",
"preferred_prefix": "dto",
"publications": [
{
"doi": "10.1186/s13326-017-0161-x",
"pmc": "PMC5679337",
"pubmed": "29122012",
"title": "Drug target ontology to classify and integrate drug discovery data.",
"year": 2017
}
],
"repository": "https://github.com/DrugTargetOntology/DTO",
"uri_format": "http://www.drugtargetontology.org/dto/DTO_$1"
},
"duo": {
"appears_in": [
"scdo"
],
"contact": {
"email": "mcourtot@gmail.com",
"github": "mcourtot",
"name": "Melanie Courtot",
"orcid": "0000-0002-9551-6370"
},
"depends_on": [
"bfo",
"iao"
],
"description": "DUO is an ontology which represent data use conditions.",
"download_owl": "http://purl.obolibrary.org/obo/duo.owl",
"example": "0000046",
"homepage": "https://github.com/EBISPOT/DUO",
"keywords": [
"biomedical science",
"obo",
"ontology",
"subject agnostic"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "DUO",
"biocontext": "DUO",
"bioportal": "DUO",
"fairsharing": "FAIRsharing.5dnjs2",
"obofoundry": "duo",
"ols": "duo",
"ontobee": "DUO"
},
"name": "Data Use Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "DUO",
"publications": [
{
"doi": "10.1016/j.xgen.2021.100028",
"pmc": "PMC8591903",
"pubmed": "34820659",
"title": "The Data Use Ontology to streamline responsible access to human biomedical datasets.",
"year": 2021
}
],
"repository": "https://github.com/EBISPOT/DUO",
"uri_format": "http://purl.obolibrary.org/obo/DUO_$1",
"version": "2021-02-23"
},
"eaglei": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Discovery tool for biomedical research resources available at institutions throughout the U.S.",
"example": "0000012b-5661-2f63-2f73-b43980000000",
"homepage": "https://hawaii.eagle-i.net",
"mappings": {
"cellosaurus": "eagle-i",
"re3data": "r3d100011564"
},
"name": "eagle-i",
"preferred_prefix": "eaglei",
"uri_format": "http://hawaii.eagle-i.net/i/$1"
},
"easychair.cfp": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Conferences in EasyChair",
"example": "SysBioCancer2022",
"homepage": "https://easychair.org/cfp/",
"keywords": [
"conferences",
"metascience"
],
"name": "EasyChair Call for Paper",
"preferred_prefix": "easychair.cfp",
"uri_format": "https://easychair.org/cfp/$1"
},
"easychair.topic": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Call for paper topics in EasyChair",
"example": "27106865",
"homepage": "https://easychair.org/cfp/",
"keywords": [
"metascience",
"topics"
],
"name": "EasyChair Topic",
"pattern": "^\\d+$",
"preferred_prefix": "easychair.topic",
"uri_format": "https://easychair.org/cfp/topic.cgi?tid=$1"
},
"ebisc": {
"description": "Cell line collections",
"example": "ESi007-A",
"homepage": "https://www.ebisc.org",
"mappings": {
"cellosaurus": "EBiSC"
},
"name": "European Bank for induced pluripotent Stem Cells",
"preferred_prefix": "ebisc",
"uri_format": "https://cells.ebisc.org/$1"
},
"ecacc": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs).",
"example": "90062901",
"homepage": "https://www.phe-culturecollections.org.uk/collections/ecacc.aspx",
"mappings": {
"cellosaurus": "ECACC"
},
"name": "European Collection of Authenticated Cell Culture",
"pattern": "^\\d+$",
"preferred_prefix": "ecacc",
"uri_format": "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1"
},
"ecao": {
"contact": {
"email": "ettensohn@cmu.edu",
"github": "ettensohn",
"name": "Charles Ettensohn",
"orcid": "0000-0002-3625-0955"
},
"depends_on": [
"cl",
"ro",
"uberon"
],
"description": "None",
"download_obo": "http://purl.obolibrary.org/obo/ecao.obo",
"download_owl": "http://purl.obolibrary.org/obo/ecao.owl",
"example": "0107180",
"homepage": "https://github.com/echinoderm-ontology/ecao_ontology",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "ECAO",
"bioportal": "ECAO",
"obofoundry": "ecao",
"ols": "ecao",
"ontobee": "ECAO"
},
"name": "The Echinoderm Anatomy and Development Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "ECAO",
"repository": "https://github.com/echinoderm-ontology/ecao_ontology",
"uri_format": "http://purl.obolibrary.org/obo/ECAO_$1",
"version": "2020-05-22"
},
"eccode": {
"contact": {
"email": "kristian.axelsen@sib.swiss",
"github": "kaxelsen",
"name": "Kristian Axelsen",
"orcid": "0000-0003-3889-2879"
},
"description": "The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions.",
"example": "1.1.1.1",
"example_decoys": [
"100",
"2.",
"2.n1",
"2.3.",
"2.3.n1",
"2.3.1.",
"2.3.1.n",
"2.3.4.1."
],
"example_extras": [
"2",
"2.3",
"2.3.1",
"2.3.1.n12",
"3.1.26.n2"
],
"homepage": "https://www.enzyme-database.org/",
"keywords": [
"biochemistry",
"classification",
"enzyme",
"enzymology"
],
"mappings": {
"bartoc": "671",
"biocontext": "EC-CODE",
"edam": "1011",
"fairsharing": "FAIRsharing.rfLD2u",
"go": "EC",
"miriam": "ec-code",
"n2t": "ec-code",
"prefixcommons": "intenz",
"re3data": "r3d100010803",
"uniprot": "DB-0024",
"wikidata": "P591"
},
"name": "Enzyme Commission Code",
"pattern": "^\\d{1,2}(((\\.\\d{1,3}){1,3})|(\\.\\d+){2}\\.n\\d{1,3})?$",
"preferred_prefix": "eccode",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "KEGG Ligand Database for Enzyme Nomenclature",
"homepage": "https://www.genome.jp/dbget-bin/www_bfind?enzyme",
"name": "KEGG Ligand Database for Enzyme Nomenclature",
"uri_format": "https://www.genome.jp/dbget-bin/www_bget?ec:$1"
},
{
"code": "enzymeportal",
"description": "Enzyme Portal through EMBL-EBI",
"homepage": "https://www.ebi.ac.uk/enzymeportal",
"name": "Enzyme Portal through EMBL-EBI",
"uri_format": "https://www.ebi.ac.uk/enzymeportal/ec/$1"
},
{
"code": "expasy",
"description": "Enzyme nomenclature database, ExPASy (Expert Protein Analysis System)",
"homepage": "https://enzyme.expasy.org/",
"name": "Enzyme nomenclature database, ExPASy (Expert Protein Analysis System)",
"uri_format": "https://enzyme.expasy.org/EC/$1"
},
{
"code": "expenz",
"description": "ExploreEnz at Trinity College",
"homepage": "http://www.enzyme-database.org/",
"name": "ExploreEnz at Trinity College",
"uri_format": "http://www.enzyme-database.org/query.php?ec=$1"
}
],
"publications": [
{
"doi": "10.1093/nar/28.1.304",
"pmc": "PMC102465",
"pubmed": "10592255",
"title": "The ENZYME database in 2000.",
"year": 2000
}
],
"references": [
"https://github.com/biopragmatics/bioregistry/issues/681"
],
"synonyms": [
"EC",
"EC number",
"EC-CODE",
"ECCODE",
"EC_CODE",
"ec-code",
"intenz"
],
"uri_format": "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1"
},
"ecg": {
"contact": {
"email": "rwinslow@jhu.edu",
"github": null,
"name": "Raimond Winslow",
"orcid": "0000-0003-1719-1651"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms.",
"download_owl": "http://aber-owl.net/media/ontologies/ECG/12/ecg.owl",
"example": "000000159",
"homepage": "https://bioportal.bioontology.org/ontologies/ECG",
"keywords": [
"biomedical science",
"ontology"
],
"mappings": {
"aberowl": "ECG",
"bioportal": "ECG",
"fairsharing": "FAIRsharing.azr389"
},
"name": "Electrocardiogram Ontology",
"pattern": "^\\d+$",
"preferred_prefix": "ecg",
"publications": [
{
"doi": "10.1016/j.jbi.2010.08.007",
"pmc": null,
"pubmed": "20800107",
"title": "Using an ECG reference ontology for semantic interoperability of ECG data.",
"year": 2010
}
],
"synonyms": [
"ECGOntology"
],
"uri_format": "http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_$1"
},
"echobase": {
"description": "EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products.",
"example": "EB0170",
"homepage": "http://www.york.ac.uk/",
"keywords": [
"gene",
"gene expression"
],
"mappings": {
"biocontext": "ECHOBASE",
"go": "EchoBASE",
"miriam": "echobase",
"n2t": "echobase",
"prefixcommons": "echobase",
"re3data": "r3d100011646",
"uniprot": "DB-0020"
},
"name": "EchoBASE post-genomic database for Escherichia coli",
"pattern": "^EB\\d+$",
"preferred_prefix": "echobase",
"publications": [
{
"doi": "10.1093/nar/gki028",
"pmc": "PMC539982",
"pubmed": "15608209",
"title": "EchoBASE: an integrated post-genomic database for Escherichia coli.",
"year": 2005
}
],
"uri_format": "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1"
},
"ecmdb": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes.",
"example": "ECMDB00005",
"homepage": "https://ecmdb.ca",
"name": "E. coli Metabolite Database",
"pattern": "^ECMDB\\d+$",
"preferred_prefix": "ecmdb",
"synonyms": [
"ECMDB"
],
"uri_format": "http://ecmdb.ca/compounds/$1"
},
"ecn": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "identifier for a chemical compound per EINECS or ELINCS",
"example": "200-003-9",
"homepage": "https://echa.europa.eu/information-on-chemicals",
"mappings": {
"cheminf": "000447",
"wikidata": "P232"
},
"name": "EC number",
"pattern": "^\\d{3}-\\d{3}-\\d$",
"preferred_prefix": "ecn",
"references": [
"https://github.com/biopragmatics/bioregistry/issues/257",
"https://en.wikipedia.org/wiki/European_Community_number"
]
},
"eco": {
"banana": "ECO",
"contact": {
"email": "mgiglio@som.umaryland.edu",
"github": "mgiglio99",
"name": "Michelle Giglio",
"orcid": "0000-0001-7628-5565"
},
"description": "Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity.",
"download_obo": "http://purl.obolibrary.org/obo/eco.obo",
"download_owl": "http://purl.obolibrary.org/obo/eco.owl",
"example": "0007807",
"homepage": "https://www.evidenceontology.org",
"keywords": [
"computational biology",
"life science",
"obo",
"ontology"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "ECO",
"bartoc": "1028",
"biocontext": "ECO",
"bioportal": "ECO",
"fairsharing": "FAIRsharing.wvpgwn",
"go": "ECO",
"miriam": "eco",
"n2t": "eco",
"obofoundry": "eco",
"ols": "eco",
"ontobee": "ECO",
"prefixcommons": "eco",
"wikidata": "P3811"
},
"name": "Evidence ontology",
"namespace_in_lui": true,
"pattern": "^\\d{7}$",
"preferred_prefix": "ECO",
"publications": [
{
"doi": "10.1093/nar/gkab1025",
"pmc": "PMC8728134",
"pubmed": "34986598",
"title": "ECO: the Evidence and Conclusion Ontology, an update for 2022.",
"year": 2022
},
{
"doi": "10.1093/nar/gky1036",
"pmc": "PMC6323956",
"pubmed": "30407590",
"title": "ECO, the Evidence & Conclusion Ontology: community standard for evidence information.",
"year": 2019
},
{
"doi": "10.1007/978-1-4939-3743-1_18",
"pmc": "PMC6377151",
"pubmed": "27812948",
"title": "The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.",
"year": 2017
},
{
"doi": "10.1093/database/bau075",
"pmc": "PMC4105709",
"pubmed": "25052702",
"title": "Standardized description of scientific evidence using the Evidence Ontology (ECO).",
"year": 2014
},
{
"doi": "10.1142/9789812704856_0019",
"pmc": null,
"pubmed": "14992503",
"title": "An evidence ontology for use in pathway/genome databases.",
"year": 2004
}
],
"repository": "https://github.com/evidenceontology/evidenceontology",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1",
"version": "2022-08-05"
},
"ecocore": {
"contact": {
"email": "p.buttigieg@gmail.com",
"github": "pbuttigieg",
"name": "Pier Luigi Buttigieg",
"orcid": "0000-0002-4366-3088"
},
"depends_on": [
"bfo",
"chebi",
"envo",
"go",
"iao",
"pato",
"pco",
"po",
"ro",
"uberon"
],
"description": "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.",
"download_obo": "http://purl.obolibrary.org/obo/ecocore.obo",
"download_owl": "http://purl.obolibrary.org/obo/ecocore.owl",
"example": "00000001",
"homepage": "https://github.com/EcologicalSemantics/ecocore",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "ECOCORE",
"biocontext": "ECOCORE",
"bioportal": "ECOCORE",
"obofoundry": "ecocore",
"ols": "ecocore",
"ontobee": "ECOCORE"
},
"name": "An ontology of core ecological entities",
"pattern": "^\\d+$",
"preferred_prefix": "ECOCORE",
"repository": "https://github.com/EcologicalSemantics/ecocore",
"uri_format": "http://purl.obolibrary.org/obo/ECOCORE_$1",
"version": "2022-03-09"
},
"ecocyc": {
"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/",
"keywords": [
"biology"
],
"mappings": {
"fairsharing": "FAIRsharing.65dmtr",
"go": "EcoCyc",
"ncbi": "ECOCYC",
"re3data": "r3d100011277"
},
"name": "EcoCyc",
"preferred_prefix": "ecocyc",
"publications": [
{
"doi": "10.3389/fmicb.2021.711077",
"pmc": "PMC8357350",
"pubmed": "34394059",
"title": "The EcoCyc Database in 2021.",
"year": 2021
},
{
"doi": "10.1093/nar/gkw1003",
"pmc": "PMC5210515",
"pubmed": "27899573",
"title": "The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.",
"year": 2016
},
{
"doi": "10.1128/ecosalplus.esp-0009-2013",
"pmc": "PMC4243172",
"pubmed": "26442933",
"title": "The EcoCyc Database.",
"year": 2014
},
{
"doi": "10.1093/nar/gks1027",
"pmc": "PMC3531154",
"pubmed": "23143106",
"title": "EcoCyc: fusing model organism databases with systems biology.",
"year": 2012
}
],
"uri_format": "https://biocyc.org/gene?id=$1"
},
"ecogene": {
"description": "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites.",
"example": "EG10173",
"homepage": "http://ecogene.org/",
"keywords": [
"genome",
"protein"
],
"mappings": {
"biocontext": "EcoGene",
"fairsharing": "FAIRsharing.3q3kvn",
"miriam": "ecogene",
"n2t": "ecogene",
"ncbi": "EcoGene",
"prefixcommons": "ecogene",
"re3data": "r3d100010546"
},
"name": "Database of Escherichia coli Sequence and Function",
"pattern": "^EG\\d+$",
"preferred_prefix": "ecogene",
"publications": [
{
"doi": "10.1093/nar/28.1.60",
"pmc": "PMC102481",
"pubmed": "10592181",
"title": "EcoGene: a genome sequence database for Escherichia coli K-12.",
"year": 2000
}
],
"uri_format": "http://www.ecogene.org/gene/$1"
},
"ecolexicon": {
"comment": "No resolution - everything is in a single page app",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology.",
"example": "canal",
"homepage": "http://ecolexicon.ugr.es/en/index.htm",
"keywords": [
"ecology",
"environmental science"
],
"name": "EcoLexicon",
"preferred_prefix": "ecolexicon"
},
"ecoliwiki": {
"description": "EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes.",
"example": "aaeA",
"homepage": "http://ecoliwiki.net/colipedia/",
"keywords": [
"bioinformatics",
"genomics",
"life science",
"ontology and terminology"
],
"mappings": {
"biocontext": "ECOLIWIKI",
"fairsharing": "FAIRsharing.tx95wa",
"go": "EcoliWiki",
"miriam": "ecoliwiki",
"n2t": "ecoliwiki"
},
"name": "EcoliWiki from EcoliHub",
"pattern": "^[A-Za-z0-9-]+$",
"preferred_prefix": "ecoliwiki",
"publications": [
{
"doi": "10.1016/j.tim.2009.04.004",
"pmc": "PMC3575750",
"pubmed": "19576778",
"title": "What we can learn about Escherichia coli through application of Gene Ontology.",
"year": 2009
}
],
"uri_format": "http://ecoliwiki.net/colipedia/index.php/$1:Gene"
},
"ecto": {
"contact": {
"email": "annethessen@gmail.com",
"github": "diatomsRcool",
"name": "Anne Thessen",
"orcid": "0000-0002-2908-3327"
},
"depends_on": [
"chebi",
"envo",
"exo",
"go",
"iao",
"maxo",
"nbo",
"ncbitaxon",
"ncit",
"pato",
"ro",
"uberon",
"xco"
],
"description": "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology).",
"download_json": "http://purl.obolibrary.org/obo/ecto.json",
"download_obo": "http://purl.obolibrary.org/obo/ecto.obo",
"download_owl": "http://purl.obolibrary.org/obo/ecto.owl",
"example": "0000001",
"homepage": "https://github.com/EnvironmentOntology/environmental-exposure-ontology",
"keywords": [
"obo",
"ontology"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "ECTO",
"biolink": "ECTO",
"bioportal": "ECTO",
"obofoundry": "ecto",
"ols": "ecto",
"ontobee": "ECTO"
},
"name": "Environmental conditions, treatments and exposures ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "ECTO",
"repository": "https://github.com/EnvironmentOntology/environmental-exposure-ontology",
"uri_format": "http://purl.obolibrary.org/obo/ECTO_$1",
"version": "2022-12-12"
},
"ecyano.entity": {
"description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities.",
"example": "23",
"homepage": "http://www.e-cyanobacterium.org/bcs/entity/",
"mappings": {
"biocontext": "ECYANO.ENTITY",
"miriam": "ecyano.entity",
"n2t": "ecyano.entity"
},
"name": "E-cyanobacterium entity",
"part_of": "ecyano",
"pattern": "^\\d+$",
"preferred_prefix": "ecyano.entity",
"uri_format": "https://www.e-cyanobacterium.org/bcs/entity/$1"
},
"ecyano.experiment": {
"description": "E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments.",
"example": "18",
"homepage": "https://www.e-cyanobacterium.org/experiments-repository/",
"mappings": {
"miriam": "ecyano.experiment"
},
"name": "E-cyanobacterium Experimental Data",
"part_of": "ecyano",
"pattern": "^\\d+$",
"preferred_prefix": "ecyano.experiment",
"uri_format": "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1"
},
"ecyano.model": {
"description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models.",
"example": "26",
"homepage": "http://e-cyanobacterium.org/models/",
"mappings": {
"biocontext": "ECYANO.MODEL",
"miriam": "ecyano.model",
"n2t": "ecyano.model"
},
"name": "E-cyanobacterium model",
"pattern": "^\\d+$",
"preferred_prefix": "ecyano.model",
"uri_format": "https://e-cyanobacterium.org/models/model/$1"
},
"ecyano.rule": {
"description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules.",
"example": "56",
"homepage": "http://www.e-cyanobacterium.org/bcs/rule/",
"mappings": {
"biocontext": "ECYANO.RULE",
"miriam": "ecyano.rule",
"n2t": "ecyano.rule"
},
"name": "E-cyanobacterium rule",
"part_of": "ecyano",
"pattern": "^\\d+$",
"preferred_prefix": "ecyano.rule",
"uri_format": "https://e-cyanobacterium.org/bcs/rule/$1"
},
"edam": {
"contact": {
"email": "matus.kalas@uib.no",
"github": "matuskalas",
"name": "Matúš Kalaš",
"orcid": "0000-0002-1509-4981"
},
"description": "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).",
"download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo",
"download_owl": "https://raw.githubusercontent.com/edamontology/edamontology/master/releases/EDAM.owl",
"example": "data_1664",
"homepage": "http://edamontology.org",
"keywords": [
"bioinformatics",
"life science",
"obo",
"ontology"
],
"mappings": {
"aberowl": "EDAM",
"agroportal": "EDAM",
"biocontext": "EDAM",
"bioportal": "EDAM",
"fairsharing": "FAIRsharing.a6r7zs",
"miriam": "edam",
"n2t": "edam",
"ols": "edam",
"ontobee": "EDAM",
"prefixcommons": "edam"
},
"name": "Bioinformatics operations, data types, formats, identifiers and topics",
"pattern": "^(data|topic|operation|format)\\_\\d{4}$",
"preferred_prefix": "edam",
"publications": [
{
"doi": "10.1093/bioinformatics/btt113",
"pmc": "PMC3654706",
"pubmed": "23479348",
"title": "EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.",
"year": 2013
}
],
"repository": "https://github.com/edamontology/edamontology",
"twitter": "edamontology",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1",
"version": "2019-07-17"
},
"edam.data": {
"contact": {
"email": "matus.kalas@uib.no",
"github": "matuskalas",
"name": "Matúš Kalaš",
"orcid": "0000-0002-1509-4981"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.",
"download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo",
"example": "1664",
"homepage": "http://edamontology.org",
"keywords": [
"ontology"
],
"mappings": {
"biolink": "EDAM-DATA"
},
"name": "EDAM Data",
"part_of": "edam",
"pattern": "^\\d+$",
"preferred_prefix": "edam.data",
"repository": "https://github.com/edamontology/edamontology",
"twitter": "edamontology",
"uri_format": "http://edamontology.org/data_$1"
},
"edam.format": {
"contact": {
"email": "matus.kalas@uib.no",
"github": "matuskalas",
"name": "Matúš Kalaš",
"orcid": "0000-0002-1509-4981"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data.",
"download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo",
"example": "1915",
"homepage": "http://edamontology.org",
"keywords": [
"ontology"
],
"mappings": {
"biolink": "EDAM-FORMAT"
},
"name": "EDAM Format",
"part_of": "edam",
"pattern": "^\\d+$",
"preferred_prefix": "edam.format",
"repository": "https://github.com/edamontology/edamontology",
"twitter": "edamontology",
"uri_format": "http://edamontology.org/format_$1"
},
"edam.operation": {
"contact": {
"email": "matus.kalas@uib.no",
"github": "matuskalas",
"name": "Matúš Kalaš",
"orcid": "0000-0002-1509-4981"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.",
"download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo",
"example": "0004",
"homepage": "http://edamontology.org",
"keywords": [
"ontology"
],
"mappings": {
"biolink": "EDAM-OPERATION"
},
"name": "EDAM Operation",
"part_of": "edam",
"pattern": "^\\d+$",
"preferred_prefix": "edam.operation",
"repository": "https://github.com/edamontology/edamontology",
"twitter": "edamontology",
"uri_format": "http://edamontology.org/operation_$1"
},
"edam.topic": {
"contact": {
"email": "matus.kalas@uib.no",
"github": "matuskalas",
"name": "Matúš Kalaš",
"orcid": "0000-0002-1509-4981"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.",
"download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo",
"example": "0003",
"homepage": "http://edamontology.org",
"keywords": [
"ontology"
],
"mappings": {
"biolink": "EDAM-TOPIC"
},
"name": "EDAM Topic",
"part_of": "edam",
"pattern": "^\\d+$",
"preferred_prefix": "edam.topic",
"repository": "https://github.com/edamontology/edamontology",
"twitter": "edamontology",
"uri_format": "http://edamontology.org/topic_$1"
},
"edda": {
"contact": {
"email": "tanja.bekhuis@tcbinfosci.com",
"github": null,
"name": "Tanja Bekhuis",
"orcid": 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",
"keywords": [
"ontology"
],
"mappings": {
"aberowl": "EDDA",
"bioportal": "EDDA",
"fairsharing": "FAIRsharing.2ffmsb"
},
"name": "EDDA Study Designs Taxonomy",
"preferred_prefix": "edda",
"uri_format": "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1"
},
"efo": {
"contact": {
"email": "plwhetzel@gmail.com",
"github": "twhetzel",
"name": "Trish Whetzel",
"orcid": "0000-0002-3458-4839"
},
"description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.",
"download_obo": "http://www.ebi.ac.uk/efo/efo.obo",
"download_owl": "http://www.ebi.ac.uk/efo/efo.owl",
"example": "0005147",
"homepage": "http://www.ebi.ac.uk/efo",
"keywords": [
"functional genomics",
"ontology"
],
"mappings": {
"aberowl": "EFO",
"agroportal": "EFO",
"biocontext": "EFO",
"biolink": "EFO",
"bioportal": "EFO",
"cellosaurus": "EFO",
"fairsharing": "FAIRsharing.1gr4tz",
"miriam": "efo",
"n2t": "efo",
"ols": "efo",
"ontobee": "EFO"
},
"name": "Experimental Factor Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "EFO",
"providers": [
{
"code": "ebi",
"description": "EFO through Functional Genomics Group (EBI)",
"homepage": "https://www.ebi.ac.uk/efo/",
"name": "EFO through Functional Genomics Group (EBI)",
"uri_format": "https://www.ebi.ac.uk/efo/EFO_$1"
}
],
"publications": [
{
"doi": "10.1093/bioinformatics/btq099",
"pmc": "PMC2853691",
"pubmed": "20200009",
"title": "Modeling sample variables with an Experimental Factor Ontology.",
"year": 2010
}
],
"repository": "https://github.com/EBISPOT/efo/",
"uri_format": "http://www.ebi.ac.uk/efo/EFO_$1",
"version": "3.49.0"
},
"ega.dataset": {
"description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.",
"example": "EGAD00000000001",
"homepage": "https://ega-archive.org/",
"keywords": [
"biology",
"biomedical science",
"clinical studies",
"genomics",
"phenomics"
],
"mappings": {
"biocontext": "EGA.DATASET",
"fairsharing": "FAIRsharing.mya1ff",
"miriam": "ega.dataset",
"n2t": "ega.dataset",
"re3data": "r3d100011242"
},
"name": "European Genome-phenome Archive Dataset",
"pattern": "^EGAD\\d{11}$",
"preferred_prefix": "ega.dataset",
"providers": [
{
"code": "omicsdi",
"description": "EGA Dataset through OmicsDI",
"homepage": "https://www.omicsdi.org/",
"name": "EGA Dataset through OmicsDI",
"uri_format": "https://www.omicsdi.org/dataset/ega/$1"
}
],
"publications": [
{
"doi": "10.1093/nar/gkab1059",
"pmc": "PMC8728218",
"pubmed": "34791407",
"title": "The European Genome-phenome Archive in 2021.",
"year": 2022
},
{
"doi": "10.1038/ng.3312",
"pmc": "PMC5426533",
"pubmed": "26111507",
"title": "The European Genome-phenome Archive of human data consented for biomedical research.",
"year": 2015
}
],
"twitter": "EGAarchive",
"uri_format": "https://www.ebi.ac.uk/ega/datasets/$1"
},
"ega.study": {
"description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.",
"example": "EGAS00000000001",
"homepage": "https://www.ebi.ac.uk/ega/studies",
"mappings": {
"biocontext": "EGA.STUDY",
"miriam": "ega.study",
"n2t": "ega.study"
},
"name": "European Genome-phenome Archive Study",
"pattern": "^EGAS\\d{11}$",
"preferred_prefix": "ega.study",
"uri_format": "https://www.ebi.ac.uk/ega/studies/$1"
},
"eggnog": {
"description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).",
"example": "veNOG12876",
"homepage": "http://eggnog.embl.de/version_3.0/",
"keywords": [
"gene",
"life science"
],
"mappings": {
"biocontext": "EGGNOG",
"fairsharing": "FAIRsharing.j1wj7d",
"miriam": "eggnog",
"n2t": "eggnog",
"prefixcommons": "eggnog",
"uniprot": "DB-0152"
},
"name": "eggNOG",
"pattern": "^\\w+$",
"preferred_prefix": "eggnog",
"publications": [
{
"doi": "10.1093/nar/gkp951",
"pmc": "PMC2808932",
"pubmed": "19900971",
"title": "eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.",
"year": 2009
},
{
"doi": "10.1093/nar/gkm796",
"pmc": "PMC2238944",
"pubmed": "17942413",
"title": "eggNOG: automated construction and annotation of orthologous groups of genes.",
"year": 2007
}
],
"uri_format": "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1"
},
"ehda": {
"contact": {
"email": "J.Bard@ed.ac.uk",
"github": null,
"name": "Jonathan Bard",
"orcid": null
},
"deprecated": true,
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once.",
"download_obo": "http://aber-owl.net/media/ontologies/EHDA/6/ehda.obo",
"example": "1",
"homepage": "http://genex.hgu.mrc.ac.uk/",
"keywords": [
"anatomy",
"development",
"human",
"obo",
"ontology"
],
"mappings": {
"aberowl": "EHDA",
"biocontext": "EHDA",
"bioportal": "EHDA",
"obofoundry": "ehda",
"prefixcommons": "ehda"
},
"name": "Human developmental anatomy, timed version",
"pattern": "^\\d+$",
"preferred_prefix": "EHDA",
"uri_format": "http://purl.obolibrary.org/obo/EHDA_$1"
},
"ehdaa": {
"contact": {
"email": "J.Bard@ed.ac.uk",
"github": null,
"name": "Jonathan Bard",
"orcid": null
},
"deprecated": true,
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release.",
"download_obo": "http://aber-owl.net/media/ontologies/EHDAA/6/ehdaa.obo",
"example": "1",
"homepage": "http://genex.hgu.mrc.ac.uk/",
"keywords": [
"anatomy",
"development",
"human",
"obo",
"ontology"
],
"mappings": {
"aberowl": "EHDAA",
"biocontext": "EHDAA",
"bioportal": "EHDAA",
"obofoundry": "ehdaa",
"prefixcommons": "ehdaa"
},
"name": "Human developmental anatomy, abstract version",
"pattern": "^\\d+$",
"preferred_prefix": "EHDAA",
"uri_format": "http://purl.obolibrary.org/obo/EHDAA_$1"
},
"ehdaa2": {
"contact": {
"email": "J.Bard@ed.ac.uk",
"github": null,
"name": "Jonathan Bard",
"orcid": null
},
"depends_on": [
"aeo",
"caro",
"cl"
],
"deprecated": true,
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the developing human.",
"download_obo": "http://purl.obolibrary.org/obo/ehdaa2.obo",
"download_owl": "http://purl.obolibrary.org/obo/ehdaa2.owl",
"example": "0000000",
"homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology",
"keywords": [
"anatomy",
"biomedical science",
"life science",
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "EHDAA2",
"biocontext": "EHDAA2",
"bioportal": "EHDAA2",
"fairsharing": "FAIRsharing.7zxrs6",
"obofoundry": "ehdaa2",
"ols": "ehdaa2",
"ontobee": "EHDAA2"
},
"name": "Human developmental anatomy, abstract",
"pattern": "^\\d{7}$",
"preferred_prefix": "EHDAA2",
"publications": [
{
"doi": "10.1111/j.1469-7580.2012.01566.x",
"pmc": "PMC3482348",
"pubmed": "22973865",
"title": "A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20).",
"year": 2012
}
],
"repository": "https://github.com/obophenotype/human-developmental-anatomy-ontology",
"synonyms": [
"EHDAA2_RETIRED",
"HDAA2",
"RETIRED_EHDAA2"
],
"uri_format": "http://purl.obolibrary.org/obo/EHDAA2_$1",
"version": "2013-07-04"
},
"elm": {
"description": "Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances.",
"example": "CLV_MEL_PAP_1",
"homepage": "http://elm.eu.org/",
"keywords": [
"life science"
],
"mappings": {
"biocontext": "ELM",
"fairsharing": "FAIRsharing.rj3kj5",
"miriam": "elm",
"n2t": "elm",
"uniprot": "DB-0223"
},
"name": "Eukaryotic Linear Motif Resource",
"pattern": "^[A-Za-z_0-9]+$",
"preferred_prefix": "elm",
"publications": [
{
"doi": "10.1093/nar/gkz1030",
"pmc": "PMC7145657",
"pubmed": "31680160",
"title": "ELM-the eukaryotic linear motif resource in 2020.",
"year": 2020
},
{
"doi": "10.1093/nar/gkv1291",
"pmc": "PMC4702912",
"pubmed": "26615199",
"title": "ELM 2016--data update and new functionality of the eukaryotic linear motif resource.",
"year": 2015
},
{
"doi": "10.1093/nar/gkr1064",
"pmc": "PMC3245074",
"pubmed": "22110040",
"title": "ELM--the database of eukaryotic linear motifs.",
"year": 2011
},
{
"doi": "10.1093/nar/gkg545",
"pmc": "PMC168952",
"pubmed": "12824381",
"title": "ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.",
"year": 2003
}
],
"uri_format": "http://elm.eu.org/elms/elmPages/$1.html"
},
"emap": {
"contact": {
"email": "Terry.Hayamizu@jax.org",
"github": "tfhayamizu",
"name": "Terry Hayamizu",
"orcid": "0000-0002-0956-8634"
},
"deprecated": true,
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).",
"download_owl": "http://purl.obolibrary.org/obo/emap.owl",
"example": "1",
"homepage": "http://emouseatlas.org",
"keywords": [
"anatomy",
"development",
"mouse",
"obo",
"ontology"
],
"mappings": {
"biocontext": "EMAP",
"bioportal": "EMAP",
"obofoundry": "emap",
"prefixcommons": "emap.ontology"
},
"name": "Mouse gross anatomy and development, timed",
"pattern": "^\\d+$",
"preferred_prefix": "EMAP",
"uri_format": "http://purl.obolibrary.org/obo/EMAP_$1"
},
"emapa": {
"contact": {
"email": "Terry.Hayamizu@jax.org",
"github": "tfhayamizu",
"name": "Terry Hayamizu",
"orcid": "0000-0002-0956-8634"
},
"description": "An ontology for mouse anatomy covering embryonic development and postnatal stages.",
"download_obo": "http://purl.obolibrary.org/obo/emapa.obo",
"download_owl": "http://purl.obolibrary.org/obo/emapa.owl",
"example": "26753",
"homepage": "http://www.informatics.jax.org/expression.shtml",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "EMAPA",
"bartoc": "549",
"biocontext": "EMAPA",
"bioportal": "EMAPA",
"fairsharing": "FAIRsharing.j0fa1d",
"go": "EMAPA",
"obofoundry": "emapa",
"ols": "emapa",
"ontobee": "EMAPA"
},
"name": "Mouse Developmental Anatomy Ontology",
"pattern": "^\\d+$",
"preferred_prefix": "EMAPA",
"publications": [
{
"doi": "10.1016/s0925-4773(98)00069-0",
"pmc": null,
"pubmed": "9651497",
"title": "An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature.",
"year": 1998
},
{
"doi": "10.1007/s00335-015-9584-9",
"pmc": "PMC4602063",
"pubmed": "26208972",
"title": "Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data.",
"year": 2015
},
{
"doi": "10.1186/2041-1480-4-15",
"pmc": "PMC3851555",
"pubmed": "23972281",
"title": "EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update.",
"year": 2013
},
{
"doi": "10.1016/b978-0-12-800043-4.00023-3",
"pmc": null,
"pubmed": null,
"title": "Textual Anatomics",
"year": 2016
}
],
"repository": "https://github.com/obophenotype/mouse-anatomy-ontology",
"synonyms": [
"EMAPA_RETIRED"
],
"uri_format": "http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:$1",
"version": "2022-07-14"
},
"emdb": {
"contact": {
"email": "help@emdatabank.org",
"github": null,
"name": "Ardan Patwardhan",
"orcid": "0000-0001-7663-9028"
},
"description": "The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community.",
"example": "EMD-1001",
"homepage": "https://www.ebi.ac.uk/pdbe/emdb/",
"keywords": [
"epidemiology",
"structural biology",
"virology"
],
"mappings": {
"biocontext": "EMDB",
"edam": "1146",
"fairsharing": "FAIRsharing.651n9j",
"miriam": "emdb",
"n2t": "emdb",
"re3data": "r3d100010562"
},
"name": "Electron Microscopy Data Bank",
"pattern": "^EMD-\\d{4}$",
"preferred_prefix": "emdb",
"publications": [
{
"doi": "10.1093/nar/gkv1126",
"pmc": "PMC4702818",
"pubmed": "26578576",
"title": "EMDataBank unified data resource for 3DEM.",
"year": 2015
},
{
"doi": "10.1093/nar/gkq880",
"pmc": "PMC3013769",
"pubmed": "20935055",
"title": "EMDataBank.org: unified data resource for CryoEM.",
"year": 2010
},
{
"doi": "10.1016/s0968-0004(02)02176-x",
"pmc": null,
"pubmed": "12417136",
"title": "New electron microscopy database and deposition system.",
"year": 2002
}
],
"uri_format": "https://www.ebi.ac.uk/pdbe/entry/emdb/$1"
},
"emolecules": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Catalog of purchasable reagents and building blocks",
"example": "491187",
"homepage": "https://reaxys.emolecules.com",
"keywords": [
"chemistry",
"reagents",
"vendor"
],
"name": "Reaxys eMolecules",
"pattern": "^\\d+$",
"preferred_prefix": "emolecules",
"uri_format": "https://reaxys.emolecules.com/cgi-bin/more?vid=$1"
},
"empiar": {
"banana": "EMPIAR",
"banana_peel": "-",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure",
"example": "10595",
"homepage": "https://www.ebi.ac.uk/pdbe/emdb",
"keywords": [
"bioinformatics",
"biology"
],
"mappings": {
"fairsharing": "FAIRsharing.dff3ef",
"miriam": "empiar"
},
"name": "Electron Microscopy Public Image Archive",
"pattern": "^\\d+$",
"preferred_prefix": "empiar",
"publications": [
{
"doi": "10.1038/nmeth.3806",
"pmc": null,
"pubmed": "27067018",
"title": "EMPIAR: a public archive for raw electron microscopy image data.",
"year": 2016
}
],
"uri_format": "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1"
},
"ena.embl": {
"contact": {
"email": "datasubs@ebi.ac.uk",
"github": null,
"name": "Guy Cochrane",
"orcid": "0000-0001-7954-7057"
},
"description": "The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers.",
"example": "BN000065",
"homepage": "https://www.ebi.ac.uk/ena/",
"keywords": [
"biodiversity",
"bioinformatics",
"data management",
"dna",
"functional genomics",
"genomics",
"metagenomics",
"transcriptomics"
],
"mappings": {
"biocontext": "ENA.EMBL",
"fairsharing": "FAIRsharing.dj8nt8",
"go": "ENA",
"miriam": "ena.embl",
"n2t": "ena.embl",
"prefixcommons": "ena",
"re3data": "r3d100010527",
"uniprot": "DB-0022"
},
"name": "European Nucleotide Archive",
"pattern": "^[A-Z]+[0-9]+(\\.\\d+)?$",
"preferred_prefix": "ena.embl",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "ENA through GenBank",
"homepage": "https://www.ncbi.nlm.nih.gov/Genbank/",
"name": "ENA through GenBank",
"uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1"
}
],
"publications": [
{
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"pmc": "PMC7778925",
"pubmed": "33175160",
"title": "The European Nucleotide Archive in 2020.",
"year": 2021
},
{
"doi": "10.1093/nar/gkw1106",
"pmc": "PMC5210577",
"pubmed": "27899630",
"title": "European Nucleotide Archive in 2016.",
"year": 2016
},
{
"doi": "10.1093/nar/gkv1323",
"pmc": "PMC4702924",
"pubmed": "26657633",
"title": "The International Nucleotide Sequence Database Collaboration.",
"year": 2015
},
{
"doi": "10.1093/nar/gkv1311",
"pmc": "PMC4702917",
"pubmed": "26615190",
"title": "Biocuration of functional annotation at the European nucleotide archive.",
"year": 2015
},
{
"doi": "10.1093/nar/gku1129",
"pmc": "PMC4383942",
"pubmed": "25404130",
"title": "Content discovery and retrieval services at the European Nucleotide Archive.",
"year": 2014
},
{
"doi": "10.1093/nar/gks1175",
"pmc": "PMC3531187",
"pubmed": "23203883",
"title": "Facing growth in the European Nucleotide Archive.",
"year": 2012
},
{
"doi": "10.1093/nar/gkh120",
"pmc": "PMC308854",
"pubmed": "14681351",
"title": "The EMBL Nucleotide Sequence Database.",
"year": 2004
}
],
"synonyms": [
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],
"twitter": "enasequence",
"uri_format": "https://www.ebi.ac.uk/ena/browser/view/$1"
},
"encode": {
"contact": {
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"github": null,
"name": "Idan Gabdank",
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"description": "The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns.",
"example": "ENCSR163RYW",
"homepage": "https://www.encodeproject.org",
"keywords": [
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],
"mappings": {
"biocontext": "ENCODE",
"cellosaurus": "ENCODE",
"fairsharing": "FAIRsharing.v0hbjs",
"miriam": "encode",
"n2t": "encode",
"re3data": "r3d100013051"
},
"name": "Encyclopedia of DNA Elements",
"pattern": "^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$",
"preferred_prefix": "encode",
"publications": [
{
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"title": "Expanded encyclopaedias of DNA elements in the human and mouse genomes.",
"year": 2020
},
{
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"title": "Perspectives on ENCODE.",
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},
{
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"pmc": "PMC7307447",
"pubmed": "31751002",
"title": "The ENCODE Portal as an Epigenomics Resource.",
"year": 2019
},
{
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"pmc": "PMC7061942",
"pubmed": "31713622",
"title": "New developments on the Encyclopedia of DNA Elements (ENCODE) data portal.",
"year": 2020
},
{
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"title": "The Encyclopedia of DNA elements (ENCODE): data portal update.",
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},
{
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},
{
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"title": "Principles of metadata organization at the ENCODE data coordination center.",
"year": 2016
},
{
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"pmc": "PMC4702836",
"pubmed": "26527727",
"title": "ENCODE data at the ENCODE portal.",
"year": 2015
},
{
"doi": "10.1093/database/bav010",
"pmc": "PMC4360730",
"pubmed": "25776021",
"title": "Ontology application and use at the ENCODE DCC.",
"year": 2015
},
{
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"pmc": "PMC3531152",
"pubmed": "23193274",
"title": "ENCODE data in the UCSC Genome Browser: year 5 update.",
"year": 2012
},
{
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"pmc": "PMC3245183",
"pubmed": "22075998",
"title": "ENCODE whole-genome data in the UCSC Genome Browser: update 2012.",
"year": 2011
},
{
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"pmc": "PMC3013645",
"pubmed": "21037257",
"title": "ENCODE whole-genome data in the UCSC genome browser (2011 update).",
"year": 2010
},
{
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"pmc": "PMC2808953",
"pubmed": "19920125",
"title": "ENCODE whole-genome data in the UCSC Genome Browser.",
"year": 2009
},
{
"doi": "10.1093/nar/gkl1017",
"pmc": "PMC1781110",
"pubmed": "17166863",
"title": "The ENCODE Project at UC Santa Cruz.",
"year": 2006
},
{
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"pmc": null,
"pubmed": "15499007",
"title": "The ENCODE (ENCyclopedia Of DNA Elements) Project.",
"year": 2004
}
],
"uri_format": "https://www.encodeproject.org/$1"
},
"enm": {
"contact": {
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"download_json": "http://purl.obolibrary.org/obo/envo.json",
"download_obo": "http://purl.obolibrary.org/obo/envo.obo",
"download_owl": "http://purl.obolibrary.org/obo/envo.owl",
"example": "09200010",
"homepage": "http://environmentontology.org/",
"keywords": [
"ecology",
"environmental science",
"epidemiology",
"life science",
"nutritional science",
"obo",
"ontology"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "ENVO",
"agroportal": "ENVO",
"biocontext": "ENVO",
"bioportal": "ENVO",
"fairsharing": "FAIRsharing.azqskx",
"miriam": "envo",
"n2t": "envo",
"obofoundry": "envo",
"ols": "envo",
"ontobee": "ENVO"
},
"name": "Environment Ontology",
"namespace_in_lui": true,
"pattern": "^\\d{7,8}$",
"preferred_prefix": "ENVO",
"publications": [
{
"doi": "10.1186/s13326-016-0097-6",
"pmc": "PMC5035502",
"pubmed": "27664130",
"title": "The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.",
"year": 2016
},
{
"doi": "10.1093/database/baw005",
"pmc": "PMC4761108",
"pubmed": "26896844",
"title": "EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.",
"year": 2016
},
{
"doi": "10.7717/peerj.1470",
"pmc": "PMC4690371",
"pubmed": "26713234",
"title": "Emerging semantics to link phenotype and environment.",
"year": 2015
},
{
"doi": "10.1186/2041-1480-4-43",
"pmc": "PMC3904460",
"pubmed": "24330602",
"title": "The environment ontology: contextualising biological and biomedical entities.",
"year": 2013
}
],
"repository": "https://github.com/EnvironmentOntology/envo",
"twitter": "envoTweets",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=ENVO:$1",
"version": "2021-05-14"
},
"enzo": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Enzo Life Sciences is an antibody vendor.",
"example": "ALX-210-175",
"homepage": "https://www.enzolifesciences.com",
"keywords": [
"antibodies",
"life sciences",
"vendor"
],
"name": "Enzo Life Sciences",
"preferred_prefix": "enzo",
"synonyms": [
"Enzo Life Sciences"
],
"uri_format": "https://www.enzolifesciences.com/$1"
},
"eo": {
"appears_in": [
"foodon"
],
"banana": "EO",
"contact": {
"email": "jaiswalp@science.oregonstate.edu",
"github": "jaiswalp",
"name": "Pankaj Jaiswal",
"orcid": "0000-0002-1005-8383"
},
"deprecated": true,
"description": "The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.",
"download_obo": "http://purl.obolibrary.org/obo/eo.obo",
"download_owl": "http://purl.obolibrary.org/obo/eo.owl",
"example": "0007404",
"homepage": "http://planteome.org/",
"keywords": [
"obo",
"ontology",
"plant"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "EO",
"agroportal": "EO",
"biocontext": "EO",
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"n2t": "eo",
"obofoundry": "eo",
"prefixcommons": "eo"
},
"name": "Plant Environment Ontology",
"namespace_in_lui": true,
"pattern": "^\\d{7}$",
"preferred_prefix": "EO",
"publications": [
{
"doi": "10.3732/ajb.1200222",
"pmc": "PMC3492881",
"pubmed": "22847540",
"title": "Ontologies as integrative tools for plant science.",
"year": 2012
}
],
"repository": "https://github.com/Planteome/plant-environment-ontology",
"uri_format": "http://archive.gramene.org/db/ontology/search?query=EO:$1"
},
"eol": {
"contact": {
"email": "pylebail@rennes.inra.fr",
"github": null,
"name": "LeBail Pierre-Yves",
"orcid": null
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems.",
"download_owl": "http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=eol.owl",
"example": "0001927",
"homepage": "http://www.atol-ontology.com",
"keywords": [
"agriculture",
"animal husbandry",
"environmental science",
"ontology"
],
"mappings": {
"aberowl": "EOL",
"agroportal": "EOL",
"bioportal": "EOL",
"fairsharing": "FAIRsharing.w7bw2y",
"ols": "eol",
"re3data": "r3d100011663"
},
"name": "Environment Ontology for Livestock",
"pattern": "^\\d{7}$",
"preferred_prefix": "eol",
"uri_format": "http://purl.org/obo/owlEOL_$1",
"version": "2018-09-13"
},
"eolife": {
"contact": {
"email": "secretariat@eol.org",
"github": null,
"name": "EOL Secretariat",
"orcid": "0000-0002-9943-2342"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A collaborative project intended to create an encyclopedia documenting all living species known to science",
"example": "1044544",
"homepage": "https://eol.org",
"keywords": [
"biodiversity",
"biology",
"ecology",
"taxonomy"
],
"mappings": {
"fairsharing": "FAIRsharing.3J6NYn",
"re3data": "r3d100010229",
"wikidata": "P830"
},
"name": "Encyclopedia of Life",
"pattern": "^\\d+$",
"preferred_prefix": "eolife",
"twitter": "eol",
"uri_format": "https://eol.org/pages/$1"
},
"epcc": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Collection of European paediatric cardiac coding files",
"homepage": "https://www.aepc.org/european-paediatric-cardiac-coding",
"name": "European Paediatric Cardiac Codes",
"preferred_prefix": "epcc",
"proprietary": true,
"references": [
"https://www.cambridge.org/core/journals/cardiology-in-the-young/article/abs/european-paediatric-cardiac-codes-the-long-list-with-icd9-icd10-crossmapping-and-crossmap-to-epcc-short-list/FCA4DFCCB661298294A3D113FC79D5BE"
]
},
"epd": {
"contact": {
"email": "ask-epd@googlegroups.com",
"github": null,
"name": "Philipp Bucher",
"orcid": "0000-0002-0816-7775"
},
"description": "The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.",
"example": "TA_H3",
"homepage": "http://epd.vital-it.ch/",
"keywords": [
"bioinformatics",
"biology"
],
"mappings": {
"biocontext": "EPD",
"edam": "2386",
"fairsharing": "FAIRsharing.yk1krv",
"miriam": "epd",
"n2t": "epd",
"ncbi": "EPD",
"uniprot": "DB-0205"
},
"name": "Eukaryotic Promoter Database",
"pattern": "^[A-Z-_0-9]+$",
"preferred_prefix": "epd",
"publications": [
{
"doi": "10.1093/nar/27.1.307",
"pmc": "PMC148166",
"pubmed": "9847211",
"title": "The Eukaryotic Promoter Database (EPD): recent developments.",
"year": 1999
},
{
"doi": "10.1093/nar/26.1.353",
"pmc": "PMC147208",
"pubmed": "9399872",
"title": "The Eukaryotic Promoter Database EPD.",
"year": 1998
},
{
"doi": "10.1093/nar/14.24.10009",
"pmc": "PMC341352",
"pubmed": "3808945",
"title": "Compilation and analysis of eukaryotic POL II promoter sequences.",
"year": 1986
},
{
"doi": "10.1093/nar/gkx807",
"pmc": "PMC5753345",
"pubmed": "28981707",
"title": "The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics.",
"year": 2018
},
{
"doi": "10.1093/nar/gkw1069",
"pmc": "PMC5210552",
"pubmed": "27899657",
"title": "The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms.",
"year": 2016
},
{
"doi": "10.1093/nar/gku1111",
"pmc": "PMC4383928",
"pubmed": "25378343",
"title": "The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools.",
"year": 2014
},
{
"doi": "10.1093/nar/gks1233",
"pmc": "PMC3531148",
"pubmed": "23193273",
"title": "EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era.",
"year": 2012
},
{
"doi": "10.1093/nar/gkj146",
"pmc": "PMC1347508",
"pubmed": "16381980",
"title": "EPD in its twentieth year: towards complete promoter coverage of selected model organisms.",
"year": 2006
},
{
"doi": "10.1093/nar/gkh122",
"pmc": "PMC308856",
"pubmed": "14681364",
"title": "The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.",
"year": 2004
},
{
"doi": "10.1093/nar/30.1.322",
"pmc": "PMC99099",
"pubmed": "11752326",
"title": "The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data.",
"year": 2002
},
{
"doi": "10.1093/nar/28.1.302",
"pmc": "PMC102462",
"pubmed": "10592254",
"title": "The eukaryotic promoter database (EPD).",
"year": 2000
}
],
"uri_format": "http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1"
},
"epio": {
"contact": {
"email": "alpha.tom.kodamullil@scai.fraunhofer.de",
"github": "akodamullil",
"name": "Alpha Tom Kodamullil",
"orcid": "0000-0001-9896-3531"
},
"depends_on": [
"bfo"
],
"description": "A application driven Epilepsy Ontology with official terms from the ILAE.",
"download_owl": "http://purl.obolibrary.org/obo/epio.owl",
"example": "0000011",
"homepage": "https://github.com/SCAI-BIO/EpilepsyOntology",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "EPIO",
"bioportal": "EPIO",
"obofoundry": "epio",
"ontobee": "EPIO"
},
"name": "Epilepsy Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "EPIO",
"repository": "https://github.com/SCAI-BIO/EpilepsyOntology",
"uri_format": "http://purl.obolibrary.org/obo/EPIO_$1"
},
"epo": {
"contributor_extras": [
{
"email": null,
"github": "djinnome",
"name": "Jeremy Zucker",
"orcid": "0000-0002-7276-9009"
}
],
"deprecated": true,
"description": "An ontology designed to support the semantic annotation of epidemiology resources",
"download_owl": "https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/epidemiology-ontology/epo.owl",
"homepage": "https://code.google.com/p/epidemiology-ontology/",
"keywords": [
"obo",
"ontology"
],
"mappings": {
"biocontext": "EPO",
"obofoundry": "epo",
"ontobee": "EPO"
},
"name": "Epidemiology Ontology",
"preferred_prefix": "EPO",
"uri_format": "http://purl.obolibrary.org/obo/EPO_$1"
},
"epso": {
"contact": {
"email": "satyasahoo@ieee.org",
"github": null,
"name": "Satya Sahoo",
"orcid": null
},
"description": "The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. ",
"download_owl": "http://aber-owl.net/media/ontologies/EPSO/3/epso.owl",
"example": "0000400",
"homepage": "http://prism.case.edu/prism/index.php/EpilepsyOntology",
"keywords": [
"neurology",
"ontology"
],
"mappings": {
"aberowl": "EPSO",
"bioportal": "EPSO",
"fairsharing": "FAIRsharing.ttprgy",
"ontobee": "EPSO"
},
"name": "Epilepsy and Seizure Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "epso",
"publications": [
{
"doi": "10.1136/amiajnl-2013-001696",
"pmc": "PMC3912711",
"pubmed": "23686934",
"title": "Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care.",
"year": 2013
}
],
"uri_format": "http://www.case.edu/EpilepsyOntology.owl#$1"
},
"erm": {
"contact": {
"email": "egon.willighagen@gmail.com",
"github": "egonw",
"name": "Egon Willighagen",
"orcid": "0000-0001-7542-0286"
},
"description": "The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project.",
"download_rdf": "https://nanocommons.github.io/identifiers/registry",
"example": "ERM00000044",
"homepage": "https://nanocommons.github.io/identifiers/",
"keywords": [
"materials informatics",
"nanotechnology"
],
"mappings": {
"cheminf": "000569",
"fairsharing": "FAIRsharing.c26a4e",
"miriam": "erm",
"n2t": "erm"
},
"name": "European Registry of Materials",
"pattern": "^ERM[0-9]{8}$",
"preferred_prefix": "erm",
"publications": [
{
"doi": "10.1186/s13321-022-00614-7",
"pmc": "PMC9400299",
"pubmed": "36002868",
"title": "European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials.",
"year": 2022
}
],
"twitter": "nanocommons",
"uri_format": "https://nanocommons.github.io/identifiers/registry#$1"
},
"ero": {
"contact": {
"email": "Marc_Ciriello@hms.harvard.edu",
"github": null,
"name": "Marc Ciriello",
"orcid": "0000-0002-3734-1859"
},
"deprecated": true,
"description": "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.",
"download_owl": "http://purl.obolibrary.org/obo/ero.owl",
"example": "0001655",
"homepage": "https://open.med.harvard.edu/wiki/display/eaglei/Ontology",
"keywords": [
"biomedical science",
"life science",
"obo",
"ontology"
],
"license": "CC BY 2.0",
"mappings": {
"aberowl": "ERO",
"biocontext": "ERO",
"bioportal": "ERO",
"fairsharing": "FAIRsharing.nwgynk",
"obofoundry": "ero",
"ols": "ero",
"ontobee": "ERO"
},
"name": "eagle-i resource ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "ERO",
"publications": [
{
"doi": "10.1109/jcdl.2017.7991571",
"pmc": "PMC5868434",
"pubmed": "29599662",
"title": "Automating data citation: the eagle-i experience.",
"year": 2017
},
{
"doi": "10.1093/database/bar067",
"pmc": "PMC3308157",
"pubmed": "22434835",
"title": "Research resources: curating the new eagle-i discovery system.",
"year": 2012
}
],
"uri_format": "http://purl.obolibrary.org/obo/ERO_$1",
"version": "2016-07-27"
},
"eropmoscow": {
"description": "EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence database which strives to provide a high level of annotations (such as descriptions of the structure of an oligopeptide, its source and function, post-translational modifications, etc.).",
"example": "E00002",
"homepage": "http://erop.inbi.ras.ru",
"keywords": [
"protein"
],
"mappings": {
"prefixcommons": "eropmoscow"
},
"name": "Endogenous Regulatory OligoPeptide knowledgebase-Moscow",
"preferred_prefix": "eropmoscow",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://erop.inbi.ras.ru/result2.php?PepName=$1"
},
"erv": {
"description": "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features.",
"example": "THE1B",
"homepage": "https://herv.img.cas.cz/",
"mappings": {
"biocontext": "ERV",
"miriam": "erv",
"n2t": "erv"
},
"name": "Human Endogenous Retrovirus Database",
"pattern": "^[A-Za-z0-9\\-\\_]+$",
"preferred_prefix": "erv",
"uri_format": "https://herv.img.cas.cz/s/$1"
},
"esldb": {
"description": "eSLDB is a database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.",
"example": "HS000015122",
"homepage": "http://gpcr.biocomp.unibo.it/esldb",
"keywords": [
"protein"
],
"mappings": {
"prefixcommons": "esldb"
},
"name": "eukaryotic Subcellular Localization database",
"preferred_prefix": "esldb",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice=$1"
},
"estdab": {
"comment": "Website is dead",
"deprecated": true,
"description": "Cell line databases/resources",
"example": "046",
"homepage": "https://www.ebi.ac.uk/ipd/estdab/",
"mappings": {
"cellosaurus": "ESTDAB"
},
"name": "European Searchable Tumour Line Database",
"pattern": "^\\d{3}$",
"preferred_prefix": "estdab",
"uri_format": "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1"
},
"eu89h": {
"description": "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union.",
"example": "jrc-eurl-ecvam-chemagora",
"homepage": "http://data.jrc.ec.europa.eu/",
"mappings": {
"biocontext": "EU89H",
"miriam": "eu89h",
"n2t": "eu89h"
},
"name": "JRC Data Catalogue",
"pattern": "^[a-z0-9\\-_]+$",
"preferred_prefix": "eu89h",
"uri_format": "http://data.europa.eu/89h/$1"
},
"euclinicaltrials": {
"description": "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.",
"example": "2008-005144-16",
"homepage": "https://www.clinicaltrialsregister.eu/",
"mappings": {
"biocontext": "EUCLINICALTRIALS",
"miriam": "euclinicaltrials",
"n2t": "euclinicaltrials"
},
"name": "EU Clinical Trials",
"pattern": "^\\d{4}\\-\\d{6}\\-\\d{2}$",
"preferred_prefix": "euclinicaltrials",
"uri_format": "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1"
},
"eugenes": {
"contact": {
"email": "eugenes@iubio.bio.indiana.edu",
"github": null,
"name": "Don Gilbert",
"orcid": "0000-0002-6646-7274"
},
"description": "euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information.",
"example": "MGgn0008978",
"homepage": "http://eugenes.org/",
"keywords": [
"genome",
"life science",
"ontology"
],
"mappings": {
"fairsharing": "FAIRsharing.7fc5y6",
"prefixcommons": "eugenes"
},
"name": "Eukaryotic Genes",
"preferred_prefix": "eugenes",
"publications": [
{
"doi": "10.1093/nar/30.1.145",
"pmc": "PMC99146",
"pubmed": "11752277",
"title": "euGenes: a eukaryote genome information system.",
"year": 2002
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://eugenes.org:7072/.bin/fbidq.html?$1"
},
"eupath": {
"appears_in": [
"scdo"
],
"contact": {
"email": "jiezheng@pennmedicine.upenn.edu",
"github": "zhengj2007",
"name": "Jie Zheng",
"orcid": "0000-0002-2999-0103"
},
"description": "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.",
"download_owl": "http://purl.obolibrary.org/obo/eupath.owl",
"example": "0010316",
"homepage": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology",
"keywords": [
"biomedical science",
"epidemiology",
"functional genomics",
"obo",
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],
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"mappings": {
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"ols": "eupath",
"ontobee": "EUPATH"
},
"name": "VEuPathDB ontology",
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"preferred_prefix": "EUPATH",
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{
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],
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"uri_format": "http://purl.obolibrary.org/obo/EUPATH_$1",
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},
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"name": "European Food Information Resource Network",
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},
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"name": "eVOC mailing list",
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},
"deprecated": true,
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"deprecated": true,
"name": "eVOC mouse development stage",
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},
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"example": "ENSG00000169174",
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"name": "ExAC Gene",
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"preferred_prefix": "exac.gene",
"uri_format": "http://exac.broadinstitute.org/gene/$1"
},
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"example": "ENST00000407236",
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"example": "22-46615880-T-C",
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"mappings": {
"biocontext": "EXAC.VARIANT",
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"name": "ExAC Variant",
"pattern": "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$",
"preferred_prefix": "exac.variant",
"uri_format": "http://exac.broadinstitute.org/variant/$1"
},
"exo": {
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"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.",
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"download_owl": "http://purl.obolibrary.org/obo/exo.owl",
"example": "0000078",
"homepage": "https://github.com/CTDbase/exposure-ontology",
"keywords": [
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"ontology",
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],
"license": "CC-BY-4.0",
"mappings": {
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"ols": "exo",
"ontobee": "ExO"
},
"name": "Exposure ontology",
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"preferred_prefix": "ExO",
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{
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"pubmed": "22324457",
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}
],
"repository": "https://github.com/CTDbase/exposure-ontology",
"synonyms": [
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],
"uri_format": "http://purl.obolibrary.org/obo/EXO_$1",
"version": "2022-06-29"
},
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"github": "essepuntato",
"name": "Silvio Peroni",
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},
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
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},
"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.",
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"example": "d4e2515",
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"keywords": [
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"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",
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],
"publications": [
{
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"pubmed": null,
"title": "FaBiO and CiTO: Ontologies for describing bibliographic resources and citations",
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}
],
"repository": "https://github.com/sparontologies/fabio",
"twitter": "sparontologies",
"uri_format": "https://sparontologies.github.io/fabio/current/fabio.html#$1"
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"name": "FaceBase Data Repository",
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"preferred_prefix": "facebase",
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{
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],
"uri_format": "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1"
},
"fairsharing": {
"description": "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies.",
"example": "bsg-000052",
"example_extras": [
"FAIRsharing.CugtbQ"
],
"homepage": "https://fairsharing.org/",
"keywords": [
"agriculture",
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"data governance",
"database management",
"earth science",
"environmental science",
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"ontology and terminology",
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],
"mappings": {
"biocontext": "FAIRSHARING",
"fairsharing": "FAIRsharing.2abjs5",
"miriam": "fairsharing",
"n2t": "fairsharing",
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},
"name": "FAIRsharing",
"pattern": "^(bsg-[dscp]?\\d{6})|(FAIRsharing\\.\\w+)$",
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"publications": [
{
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"title": "FAIRsharing as a community approach to standards, repositories and policies.",
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},
{
"doi": "10.1093/database/baw075",
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"title": "BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences.",
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},
{
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"pmc": null,
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"title": "FAIRsharing, a FAIR-enabling service for repositories, standards and policies",
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}
],
"repository": "https://github.com/FAIRsharing",
"twitter": "fairsharing_org",
"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",
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"example": "ForwardStrandPosition",
"homepage": "http://biohackathon.org/resource/faldo",
"keywords": [
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"mappings": {
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},
"name": "Feature Annotation Location Description Ontology ",
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"publications": [
{
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"pubmed": "27296299",
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}
],
"repository": "https://github.com/OBF/FALDO",
"uri_format": "http://biohackathon.org/resource/faldo#$1"
},
"fao": {
"contact": {
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"github": "ValWood",
"name": "Val Wood",
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"description": "A structured controlled vocabulary for the anatomy of fungi.",
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"download_owl": "http://purl.obolibrary.org/obo/fao.owl",
"example": "0000001",
"homepage": "https://github.com/obophenotype/fungal-anatomy-ontology/",
"keywords": [
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"fungi",
"life science",
"microbiology",
"obo",
"ontology"
],
"license": "CC0-1.0",
"mappings": {
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"bioportal": "FAO",
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"ontobee": "FAO",
"prefixcommons": "fao"
},
"name": "Fungal gross anatomy",
"pattern": "^\\d{7}$",
"preferred_prefix": "FAO",
"repository": "https://github.com/obophenotype/fungal-anatomy-ontology",
"uri_format": "http://purl.obolibrary.org/obo/FAO_$1",
"version": "2020-05-07"
},
"fbbi": {
"contact": {
"email": "wawong@gmail.com",
"github": "wawong",
"name": "Willy Wong",
"orcid": "0000-0002-8841-5870"
},
"description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.",
"download_obo": "http://aber-owl.net/media/ontologies/FBbi/14/fbbi.obo",
"download_owl": "http://purl.obolibrary.org/obo/fbbi.owl",
"example": "00000268",
"homepage": "http://cellimagelibrary.org/",
"keywords": [
"biomedical science",
"experiment",
"imaging",
"life science",
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "FBbi",
"biocontext": "FBbi",
"bioportal": "FBbi",
"fairsharing": "FAIRsharing.ny3z9j",
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"ols": "fbbi",
"ontobee": "FBbi",
"prefixcommons": "fbbi"
},
"name": "Biological Imaging Methods Ontology",
"pattern": "^\\d+$",
"preferred_prefix": "FBbi",
"repository": "https://github.com/CRBS/Biological_Imaging_Methods_Ontology",
"synonyms": [
"FBbi"
],
"uri_format": "http://purl.obolibrary.org/obo/FBbi_$1",
"version": "2020-11-06"
},
"fbbt": {
"contact": {
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"github": "Clare72",
"name": "Clare Pilgrim",
"orcid": "0000-0002-1373-1705"
},
"description": "An ontology of Drosophila melanogaster anatomy.",
"download_json": "http://purl.obolibrary.org/obo/fbbt.json",
"download_obo": "http://purl.obolibrary.org/obo/fbbt.obo",
"download_owl": "http://purl.obolibrary.org/obo/fbbt.owl",
"example": "00007294",
"homepage": "http://purl.obolibrary.org/obo/fbbt",
"keywords": [
"anatomy",
"developmental biology",
"fly",
"life science",
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "FBBT",
"biocontext": "FBbt",
"bioportal": "FB-BT",
"fairsharing": "FAIRsharing.y2qkst",
"go": "FBbt",
"obofoundry": "fbbt",
"ols": "fbbt",
"ontobee": "FBbt",
"prefixcommons": "fbbt"
},
"name": "Drosophila gross anatomy",
"part_of": "flybase",
"pattern": "^\\d{8}$",
"preferred_prefix": "FBbt",
"publications": [
{
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"pmc": "PMC4015547",
"pubmed": "24139062",
"title": "The Drosophila anatomy ontology.",
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},
{
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"pmc": null,
"pubmed": "22402613",
"title": "A strategy for building neuroanatomy ontologies.",
"year": 2012
},
{
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"pmc": null,
"pubmed": "22180411",
"title": "The Virtual Fly Brain browser and query interface.",
"year": 2011
},
{
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"pmc": "PMC1347431",
"pubmed": "16381917",
"title": "FlyBase: anatomical data, images and queries.",
"year": 2006
}
],
"repository": "https://github.com/FlyBase/drosophila-anatomy-developmental-ontology",
"synonyms": [
"FBbt",
"FBbt_root"
],
"uri_format": "https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:$1",
"version": "2022-06-09"
},
"fbcv": {
"appears_in": [
"ontoavida"
],
"contact": {
"email": "cp390@cam.ac.uk",
"github": "Clare72",
"name": "Clare Pilgrim",
"orcid": "0000-0002-1373-1705"
},
"description": "A miscellaneous ontology of terms used for curation in FlyBase, including the DPO.",
"download_json": "http://purl.obolibrary.org/obo/fbcv.json",
"download_obo": "https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/fbcv.obo",
"download_owl": "http://purl.obolibrary.org/obo/fbcv.owl",
"example": "0000586",
"homepage": "http://purl.obolibrary.org/obo/fbcv",
"keywords": [
"descriptor",
"fly",
"life science",
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "FBCV",
"biocontext": "FBcv",
"bioportal": "FB-CV",
"fairsharing": "FAIRsharing.6tgyxf",
"obofoundry": "fbcv",
"ols": "fbcv",
"ontobee": "FBcv",
"prefixcommons": "fbcv"
},
"name": "FlyBase Controlled Vocabulary",
"part_of": "flybase",
"pattern": "^\\d{7}$",
"preferred_prefix": "FBcv",
"publications": [
{
"doi": "10.1186/2041-1480-4-30",
"pmc": "PMC3816596",
"pubmed": "24138933",
"title": "The Drosophila phenotype ontology.",
"year": 2013
}
],
"repository": "https://github.com/FlyBase/flybase-controlled-vocabulary",
"synonyms": [
"FBcv"
],
"uri_format": "http://purl.obolibrary.org/obo/FBcv_$1",
"version": "2022-06-09"
},
"fbdv": {
"contact": {
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"github": "Clare72",
"name": "Clare Pilgrim",
"orcid": "0000-0002-1373-1705"
},
"description": "An ontology of Drosophila melanogaster developmental stages.",
"download_json": "http://purl.obolibrary.org/obo/fbdv.json",
"download_obo": "http://purl.obolibrary.org/obo/fbdv.obo",
"download_owl": "http://purl.obolibrary.org/obo/fbdv.owl",
"example": "00000000",
"homepage": "http://purl.obolibrary.org/obo/fbdv",
"keywords": [
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"developmental biology",
"fly",
"life science",
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
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"biocontext": "FBdv",
"bioportal": "FB-DV",
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"obofoundry": "fbdv",
"ols": "fbdv",
"ontobee": "FBdv",
"prefixcommons": "fbdv"
},
"name": "Drosophila development",
"pattern": "^\\d{8}$",
"preferred_prefix": "FBdv",
"repository": "https://github.com/FlyBase/drosophila-developmental-ontology",
"synonyms": [
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],
"uri_format": "http://purl.obolibrary.org/obo/FBdv_$1",
"version": "2022-06-08"
},
"fbol": {
"comment": "Website down, checked on 2021-10-07",
"deprecated": true,
"description": "DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms.",
"example": "2224",
"homepage": "http://www.fungalbarcoding.org/",
"mappings": {
"biocontext": "FBOL",
"miriam": "fbol",
"n2t": "fbol",
"ncbi": "FBOL"
},
"name": "International Fungal Working Group Fungal Barcoding.",
"pattern": "^\\d+$",
"preferred_prefix": "fbol",
"uri_format": "http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T"
},
"fbql": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"example": "00005254",
"name": "FlyBase Qualifiers",
"pattern": "^\\d+$",
"preferred_prefix": "fbql"
},
"fbrf": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "FlyBase internal citation identifiers",
"example": "0187632",
"homepage": "https://flybase.org",
"name": "FlyBase Reference Report",
"part_of": "flybase",
"pattern": "^\\d{7}$",
"preferred_prefix": "fbrf",
"uri_format": "https://flybase.org/reports/FBrf$1"
},
"fbsp": {
"contact": {
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"github": "Clare72",
"name": "Clare Pilgrim",
"orcid": "0000-0002-1373-1705"
},
"deprecated": true,
"description": "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.",
"download_obo": "http://aber-owl.net/media/ontologies/FB-SP/7/fb-sp.obo",
"download_owl": "http://purl.obolibrary.org/obo/fbsp.owl",
"example": "00000000",
"homepage": "http://www.flybase.org/",
"keywords": [
"obo",
"ontology"
],
"mappings": {
"aberowl": "FB-SP",
"biocontext": "FBSP",
"bioportal": "FB-SP",
"obofoundry": "fbsp"
},
"name": "Fly taxonomy",
"part_of": "flybase",
"pattern": "^\\d{8}$",
"preferred_prefix": "FBSP",
"uri_format": "http://purl.obolibrary.org/obo/FBSP_$1"
},
"fbtc": {
"contributor": {
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"description": "The cell line vocabulary inside FlyBase",
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"description": "Traits and phenotypes of flowering plants occurring in digitized Floras",
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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"fobi": {
"contact": {
"email": "polcaes@gmail.com",
"github": "pcastellanoescuder",
"name": "Pol Castellano Escuder",
"orcid": "0000-0001-6466-877X"
},
"depends_on": [
"chebi",
"foodon"
],
"description": "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data",
"download_owl": "http://purl.obolibrary.org/obo/fobi.owl",
"example": "030719",
"example_extras": [
"0142",
"07504"
],
"homepage": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "FOBI",
"agroportal": "FOBI",
"bioportal": "FOBI",
"obofoundry": "fobi",
"ols": "fobi",
"ontobee": "FOBI"
},
"name": "Food-Biomarker Ontology",
"pattern": "^\\d{4,6}$",
"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_$1"
},
"foodb.compound": {
"description": "FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds.",
"example": "FDB002100",
"homepage": "https://foodb.ca/",
"mappings": {
"biocontext": "FOODB.COMPOUND",
"biolink": "foodb.compound",
"miriam": "foodb.compound",
"n2t": "foodb.compound",
"re3data": "r3d100012152",
"wikidata": "P8117"
},
"name": "FooDB compound ID",
"pattern": "^FDB\\d+$",
"preferred_prefix": "foodb.compound",
"synonyms": [
"foodb"
],
"uri_format": "http://foodb.ca/compounds/$1"
},
"foodb.food": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Foods in FooDB",
"example": "FOOD00020",
"homepage": "https://foodb.ca/foods",
"mappings": {
"biolink": "foodb.food"
},
"name": "FooDB Food",
"pattern": "^FOOD\\d+$",
"preferred_prefix": "foodb.food",
"uri_format": "https://foodb.ca/foods/$1"
},
"foodex2": {
"contact": {
"email": "datex@efsa.europa.eu",
"github": null,
"name": "European Food Safety Authority",
"orcid": null
},
"description": "FoodEx2 is a comprehensive food classification and description system aimed at covering the need to describe food in data collections across different food safety domains.",
"example": "A0TMC",
"homepage": "http://www.efsa.europa.eu/",
"mappings": {
"agroportal": "FOODEX2"
},
"name": "Food classification and description system",
"preferred_prefix": "foodex2",
"uri_format": "http://data.food.gov.uk/codes/foodtype/id/$1"
},
"foodon": {
"appears_in": [
"agro",
"envo",
"fobi",
"maxo",
"one",
"ons"
],
"banana": "FOODON",
"contact": {
"email": "damion_dooley@sfu.ca",
"github": "ddooley",
"name": "Damion Dooley",
"orcid": "0000-0002-8844-9165"
},
"depends_on": [
"bfo",
"chebi",
"envo",
"eo",
"ncbitaxon",
"obi",
"ro",
"uberon"
],
"description": "FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies.",
"download_obo": "http://purl.obolibrary.org/obo/foodon.obo",
"download_owl": "http://purl.obolibrary.org/obo/foodon.owl",
"example": "03307879",
"homepage": "https://foodon.org/",
"keywords": [
"agriculture",
"botany",
"environmental science",
"medicine",
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "FOODON",
"agroportal": "FOODON",
"biocontext": "FOODON",
"bioportal": "FOODON",
"fairsharing": "FAIRsharing.dzxae",
"miriam": "foodon",
"n2t": "foodon",
"obofoundry": "foodon",
"ols": "foodon",
"ontobee": "FOODON"
},
"name": "The Food Ontology",
"namespace_in_lui": true,
"pattern": "^[0-9]{8}$",
"preferred_prefix": "FOODON",
"publications": [
{
"doi": "10.1038/s41538-018-0032-6",
"pmc": "PMC6550238",
"pubmed": "31304272",
"title": "FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration.",
"year": 2018
},
{
"doi": "10.3389/fmicb.2017.01068",
"pmc": "PMC5483436",
"pubmed": "28694792",
"title": "Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance.",
"year": 2017
}
],
"repository": "https://github.com/FoodOntology/foodon",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1",
"version": "2022-02-01"
},
"fossilworks.journal": {
"contributor": {
"email": "meghan.balk@gmail.com",
"github": "megbalk",
"name": "Meghan Balk",
"orcid": "0000-0003-2699-3066"
},
"description": "Identifier for a journal article in the fossilworks website",
"example": "61467",
"github_request_issue": 468,
"homepage": "http://fossilworks.org",
"mappings": {
"wikidata": "P7720"
},
"name": "Fossilworks Journal",
"part_of": "fossilworks",
"pattern": "^\\d+$",
"preferred_prefix": "fossilworks.journal",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://fossilworks.org/?a=referenceInfo&reference_no=$1"
},
"fossilworks.taxon": {
"contributor": {
"email": "meghan.balk@gmail.com",
"github": "megbalk",
"name": "Meghan Balk",
"orcid": "0000-0003-2699-3066"
},
"description": "Identifier for an animal, plant, or microorganism from the fossilworks website",
"example": "40565",
"github_request_issue": 469,
"homepage": "http://www.fossilworks.org",
"mappings": {
"wikidata": "P842"
},
"name": "Fossilworks Taxon",
"part_of": "fossilworks",
"pattern": "^[1-9]\\d{0,5}$",
"preferred_prefix": "fossilworks.taxon",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1"
},
"fovt": {
"contact": {
"email": "meghan.balk@gmail.com",
"github": "megbalk",
"name": "Meghan Balk",
"orcid": "0000-0003-2699-3066"
},
"depends_on": [
"bco",
"bfo",
"bspo",
"iao",
"oba",
"pato",
"ro",
"uberon"
],
"description": "None",
"download_obo": "http://purl.obolibrary.org/obo/fovt.obo",
"download_owl": "http://purl.obolibrary.org/obo/fovt.owl",
"example": "0000009",
"homepage": "https://github.com/futres/fovt",
"keywords": [
"obo",
"ontology"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "FOVT",
"bioportal": "FOVT",
"obofoundry": "fovt",
"ols": "fovt",
"ontobee": "FOVT"
},
"name": "FuTRES Ontology of Vertebrate Traits",
"pattern": "^\\d{7}$",
"preferred_prefix": "FOVT",
"repository": "https://github.com/futres/fovt",
"uri_format": "http://purl.obolibrary.org/obo/FOVT_$1",
"version": "2021-11-10"
},
"fplx": {
"contact": {
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"description": "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships.",
"example": "GPIb_IX_V",
"homepage": "https://sorgerlab.github.io/famplex/",
"keywords": [
"ontology"
],
"mappings": {
"aberowl": "FPLX",
"biocontext": "FPLX",
"bioportal": "FPLX",
"miriam": "fplx",
"n2t": "fplx"
},
"name": "FamPlex",
"pattern": "^[a-zA-Z0-9][A-Za-z0-9_]+$",
"preferred_prefix": "fplx",
"publications": [
{
"doi": "10.1186/s12859-018-2211-5",
"pmc": "PMC6022344",
"pubmed": "29954318",
"title": "FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining.",
"year": 2018
}
],
"synonyms": [
"famplex"
],
"uri_format": "https://sorgerlab.github.io/famplex/$1"
},
"fr": {
"contact": {
"email": "silvio.peroni@unibo.it",
"github": "essepuntato",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology that enables the description of reviews of scientific articles and other scholarly resources.",
"example": "ReviewVersion",
"homepage": "http://www.sparontologies.net/ontologies/fr",
"keywords": [
"subject agnostic"
],
"mappings": {
"fairsharing": "FAIRsharing.e7e609"
},
"name": "FAIR* Reviews Ontology",
"preferred_prefix": "FR",
"repository": "https://github.com/sparontologies/fr",
"twitter": "sparontologies"
},
"frapo": {
"contact": {
"email": "silvio.peroni@unibo.it",
"github": "essepuntato",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc.",
"example": "Grant",
"homepage": "http://www.sparontologies.net/ontologies/frapo",
"keywords": [
"subject agnostic"
],
"mappings": {
"aberowl": "FRAPO",
"fairsharing": "FAIRsharing.0a2576"
},
"name": "Funding, Research Administration and Projects Ontology",
"preferred_prefix": "FRAPO",
"repository": "https://github.com/sparontologies/frapo",
"twitter": "sparontologies",
"uri_format": "http://purl.org/cerif/frapo/$1"
},
"frbr": {
"contact": {
"email": "silvio.peroni@unibo.it",
"github": "essepuntato",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO.",
"example": "Expression",
"homepage": "http://www.sparontologies.net/ontologies/frbr",
"keywords": [
"subject agnostic"
],
"mappings": {
"fairsharing": "FAIRsharing.b34b43"
},
"name": "Functional Requirements for Bibliographic Records",
"preferred_prefix": "FRBR",
"repository": "https://github.com/sparontologies/frbr",
"twitter": "sparontologies",
"uri_format": "http://purl.org/vocab/frbr/core#$1"
},
"fsnp": {
"description": "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.",
"example": "rs17852708",
"homepage": "http://compbio.cs.queensu.ca/F-SNP/",
"keywords": [
"dna",
"protein"
],
"mappings": {
"biocontext": "FSNP",
"miriam": "fsnp",
"n2t": "fsnp",
"prefixcommons": "fsnp"
},
"name": "F-SNP",
"pattern": "^rs\\d+$",
"preferred_prefix": "fsnp",
"uri_format": "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1"
},
"ftt": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific.",
"example": "273",
"homepage": "https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3",
"name": "Feature Type Thesaurus",
"pattern": "^\\d+$",
"preferred_prefix": "ftt",
"references": [
"https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200",
"https://github.com/EnvironmentOntology/envo/issues/1130"
],
"uri_format": "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1"
},
"funcbase.fly": {
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data.",
"example": "10194",
"homepage": "http://func.mshri.on.ca/fly",
"mappings": {
"biocontext": "FUNCBASE.FLY",
"miriam": "funcbase.fly",
"n2t": "funcbase.fly"
},
"name": "FuncBase Fly",
"pattern": "^\\d+$",
"preferred_prefix": "funcbase.fly",
"uri_format": "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1"
},
"funcbase.human": {
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data.",
"example": "119514",
"homepage": "http://func.mshri.on.ca/human/",
"mappings": {
"biocontext": "FUNCBASE.HUMAN",
"miriam": "funcbase.human",
"n2t": "funcbase.human"
},
"name": "FuncBase Human",
"pattern": "^\\d+$",
"preferred_prefix": "funcbase.human",
"uri_format": "http://func.mshri.on.ca/human/genes/list_functional_scores/$1"
},
"funcbase.mouse": {
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse.",
"example": "1351341",
"homepage": "http://func.mshri.on.ca/mouse/",
"mappings": {
"biocontext": "FUNCBASE.MOUSE",
"miriam": "funcbase.mouse",
"n2t": "funcbase.mouse"
},
"name": "FuncBase Mouse",
"pattern": "^\\d+$",
"preferred_prefix": "funcbase.mouse",
"uri_format": "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1"
},
"funcbase.yeast": {
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast.",
"example": "2701",
"homepage": "http://func.mshri.on.ca/yeast",
"mappings": {
"biocontext": "FUNCBASE.YEAST",
"miriam": "funcbase.yeast",
"n2t": "funcbase.yeast"
},
"name": "FuncBase Yeast",
"pattern": "^\\d+$",
"preferred_prefix": "funcbase.yeast",
"uri_format": "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1"
},
"funderregistry": {
"description": "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world.",
"example": "100000001",
"homepage": "https://www.crossref.org/",
"mappings": {
"miriam": "funderregistry"
},
"name": "FunderRegistry",
"pattern": "^\\d{9,9}$",
"preferred_prefix": "funderregistry",
"providers": [
{
"code": "crossref.api",
"description": "Access funder data through the Crossref API",
"homepage": "https://api.crossref.org",
"name": "Crossref API",
"uri_format": "https://api.crossref.org/funders/$1"
},
{
"code": "doi",
"description": "Access funder data through a DOI for crossref funders.",
"homepage": "https://doi.org",
"name": "DOI",
"uri_format": "https://dx.doi.org/10.13039/501100000995"
}
],
"synonyms": [
"FundRef",
"crossref.funder"
],
"uri_format": "http://data.crossref.org/fundingdata/funder/10.13039/$1"
},
"fungidb": {
"contact": {
"email": "jason.stajich@ucr.edu",
"github": null,
"name": "Jason E. Stajich",
"orcid": "0000-0002-7591-0020"
},
"description": "FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina.",
"example": "CNBG_0001",
"homepage": "https://fungidb.org/fungidb",
"keywords": [
"genomics"
],
"mappings": {
"biocontext": "FUNGIDB",
"fairsharing": "FAIRsharing.xf30yc",
"miriam": "fungidb",
"n2t": "fungidb",
"re3data": "r3d100011906"
},
"name": "FungiDB",
"pattern": "^[A-Za-z_0-9]+$",
"preferred_prefix": "fungidb",
"publications": [
{
"doi": "10.1016/j.fgb.2016.04.002",
"pmc": null,
"pubmed": "27259951",
"title": "Database whiplash, crowdsourcing, and FungiDB.",
"year": 2016
},
{
"doi": "10.1128/ec.00083-14",
"pmc": "PMC4135733",
"pubmed": "24813190",
"title": "Literature-based gene curation and proposed genetic nomenclature for cryptococcus.",
"year": 2014
},
{
"doi": "10.1093/nar/gkr918",
"pmc": "PMC3245123",
"pubmed": "22064857",
"title": "FungiDB: an integrated functional genomics database for fungi.",
"year": 2011
}
],
"twitter": "fungidb",
"uri_format": "https://fungidb.org/fungidb/app/record/gene/$1"
},
"fungorum": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "identifier for a fungus taxon in Index Fungorum",
"example": "154022",
"homepage": "http://www.indexfungorum.org",
"mappings": {
"ncbi": "Fungorum",
"wikidata": "P1391"
},
"name": "Index Fungorum",
"pattern": "^[1-9]\\d{0,5}$",
"preferred_prefix": "fungorum",
"uri_format": "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1"
},
"fyeco": {
"comment": "Rather than admitting FYECO to the OBO foundry, we secure the prefix here at bioregistry. The FYECO namespace shows up in a lot of ingests (basically anywhere you ingest PomBase gene-phenotype data). Future work includes mapping FYECO to other OBO ontologies, but this is way ahead in the future.",
"contact": {
"email": "vw253@cam.ac.uk",
"github": "ValWood",
"name": "Val Wood",
"orcid": "0000-0001-6330-7526"
},
"contributor": {
"email": "vw253@cam.ac.uk",
"github": "ValWood",
"name": "Val Wood",
"orcid": "0000-0001-6330-7526"
},
"description": "PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase.",
"example": "0000003",
"github_request_issue": 268,
"homepage": "https://github.com/pombase/fypo",
"mappings": {
"biolink": "FYECO"
},
"name": "Fission Yeast Experimental Conditions Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "FYECO",
"repository": "https://github.com/pombase/fypo",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"fyler": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A hierarchical classification of congenital heart disease ",
"example": "4447",
"homepage": "https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906",
"name": "Fyler",
"pattern": "^\\d+$",
"preferred_prefix": "fyler",
"references": [
"https://github.com/obophenotype/human-phenotype-ontology/issues/2568",
"https://github.com/obophenotype/human-phenotype-ontology/issues/2511"
]
},
"fypo": {
"contact": {
"email": "vw253@cam.ac.uk",
"github": "ValWood",
"name": "Val Wood",
"orcid": "0000-0001-6330-7526"
},
"description": "A formal ontology of phenotypes observed in fission yeast.",
"download_json": "http://purl.obolibrary.org/obo/fypo.json",
"download_obo": "http://purl.obolibrary.org/obo/fypo.obo",
"download_owl": "http://purl.obolibrary.org/obo/fypo.owl",
"example": "0001707",
"homepage": "https://github.com/pombase/fypo",
"keywords": [
"genetics",
"life science",
"obo",
"ontology",
"phylogenetics"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "FYPO",
"biocontext": "FYPO",
"biolink": "FYPO",
"bioportal": "FYPO",
"fairsharing": "FAIRsharing.4vr0ys",
"go": "FYPO",
"obofoundry": "fypo",
"ols": "fypo",
"ontobee": "FYPO"
},
"name": "Fission Yeast Phenotype Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "FYPO",
"publications": [
{
"doi": "10.1093/bioinformatics/btt266",
"pmc": "PMC3694669",
"pubmed": "23658422",
"title": "FYPO: the fission yeast phenotype ontology.",
"year": 2013
}
],
"repository": "https://github.com/pombase/fypo",
"uri_format": "http://purl.obolibrary.org/obo/FYPO_$1",
"version": "2022-07-14"
},
"ga4ghdos": {
"description": "Assists in resolving data across cloud resources.",
"example": "dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d",
"homepage": "http://github.com/ga4gh/data-object-service-schemas",
"mappings": {
"biocontext": "GA4GHDOS",
"miriam": "ga4ghdos",
"n2t": "ga4ghdos"
},
"name": "Data Object Service",
"pattern": "^[a-zA-Z0-9\\-:#/\\.]+$",
"preferred_prefix": "ga4ghdos",
"uri_format": "https://dataguids.org/ga4gh/dos/v1/dataobjects/$1"
},
"gabi": {
"description": "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'.",
"example": "2679240",
"homepage": "http://www.gabipd.org/",
"keywords": [
"gene",
"genome",
"plant"
],
"mappings": {
"biocontext": "GABI",
"miriam": "gabi",
"n2t": "gabi",
"ncbi": "GABI",
"prefixcommons": "gabi"
},
"name": "Network of Different Plant Genomic Research Projects",
"pattern": "^\\w+$",
"preferred_prefix": "gabi",
"publications": [
{
"doi": "10.1093/nar/gkn611",
"pmc": "PMC2686513",
"pubmed": "18812395",
"title": "GabiPD: the GABI primary database--a plant integrative 'omics' database.",
"year": 2008
}
],
"uri_format": "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject"
},
"galen": {
"comment": "I really tried, but could not figure out what GALEN stands for",
"contact": {
"email": "j@deltaflow.com",
"github": null,
"name": "Julian Seidenberg",
"orcid": null
},
"deprecated": true,
"description": "A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.",
"download_owl": "http://aber-owl.net/media/ontologies/GALEN/1/galen.owl",
"example": "MagnitudeValueType",
"homepage": "https://www.opengalen.org",
"keywords": [
"ontology"
],
"mappings": {
"aberowl": "GALEN",
"bioportal": "GALEN"
},
"name": "GALEN",
"preferred_prefix": "galen",
"uri_format": "http://www.co-ode.org/ontologies/galen#$1"
},
"gard": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease.",
"example": "6038",
"homepage": "https://rarediseases.info.nih.gov/diseases",
"mappings": {
"wikidata": "P4317"
},
"name": "Genetic and Rare Diseases Information Center",
"pattern": "^\\d+$",
"preferred_prefix": "gard",
"synonyms": [
"GARD",
"Genetic and Rare Diseases Information Center"
],
"uri_format": "https://rarediseases.info.nih.gov/diseases/$1/index"
},
"gateway": {
"description": "The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access.",
"example": "fd8d0743-344a-4758-bb97-f8ad84a37357",
"homepage": "https://www.hdruk.ac.uk",
"mappings": {
"miriam": "gateway"
},
"name": "Health Data Research Innovation Gateway",
"pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$",
"preferred_prefix": "gateway",
"uri_format": "https://web.www.healthdatagateway.org/dataset/$1"
},
"gaz": {
"appears_in": [
"scdo"
],
"contact": {
"email": "lschriml@som.umaryland.edu",
"github": "lschriml",
"name": "Lynn Schriml",
"orcid": "0000-0001-8910-9851"
},
"deprecated": true,
"description": "A gazetteer constructed on ontological principles",
"download_obo": "http://purl.obolibrary.org/obo/gaz.obo",
"download_owl": "http://purl.obolibrary.org/obo/gaz.owl",
"example": "00620027",
"homepage": "http://environmentontology.github.io/gaz/",
"keywords": [
"environmental science",
"obo",
"ontology"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "GAZ",
"biocontext": "GAZ",
"bioportal": "GAZ",
"fairsharing": "FAIRsharing.wkdjpb",
"obofoundry": "gaz",
"ols": "gaz",
"ontobee": "GAZ",
"wikidata": "P6778"
},
"name": "Gazetteer",
"pattern": "^\\d{8}$",
"preferred_prefix": "GAZ",
"repository": "https://github.com/EnvironmentOntology/gaz",
"uri_format": "http://purl.obolibrary.org/obo/GAZ_$1"
},
"gbif": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth.",
"example": "4238",
"homepage": "https://www.gbif.org/species",
"keywords": [
"biodiversity",
"bioinformatics",
"marine biology",
"metagenomics",
"natural history",
"natural science",
"taxonomy"
],
"mappings": {
"fairsharing": "FAIRsharing.zv11j3",
"re3data": "r3d100011343",
"wikidata": "P846"
},
"name": "Global Biodiversity Information Facility",
"pattern": "^\\d+$",
"preferred_prefix": "gbif",
"publications": [
{
"doi": "10.1371/journal.pone.0102623",
"pmc": "PMC4123864",
"pubmed": "25099149",
"title": "The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet.",
"year": 2014
}
],
"repository": "https://github.com/gbif/",
"twitter": "GBIF",
"uri_format": "https://www.gbif.org/species/$1"
},
"gc": {
"comment": "see comment here: https://github.com/obophenotype/ncbitaxon/issues/47",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries.",
"example": "11",
"homepage": "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html",
"name": "Genetic Code",
"pattern": "^\\d+$",
"preferred_prefix": "gc",
"references": [
"https://github.com/obophenotype/ncbitaxon/issues/47"
],
"synonyms": [
"gc_id"
],
"uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1"
},
"gcst": {
"description": "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide.",
"example": "GCST000035",
"homepage": "https://www.ebi.ac.uk",
"mappings": {
"miriam": "gcst",
"n2t": "gcst"
},
"name": "GWAS Catalog",
"pattern": "^GCST\\d{6}\\d*$",
"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/$1"
},
"gecko": {
"contact": {
"email": "rbca.jackson@gmail.com",
"github": "beckyjackson",
"name": "Rebecca Jackson",
"orcid": "0000-0003-4871-5569"
},
"description": "An ontology to represent genomics cohort attributes.",
"download_owl": "http://purl.obolibrary.org/obo/gecko.owl",
"example": "0000044",
"homepage": "https://github.com/IHCC-cohorts/GECKO",
"keywords": [
"genomics",
"life science",
"obo",
"ontology",
"statistics"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "GECKO",
"bioportal": "GECKO",
"fairsharing": "FAIRsharing.3da56b",
"obofoundry": "gecko",
"ols": "gecko",
"ontobee": "GECKO"
},
"name": "Genomics Cohorts Knowledge Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "GECKO",
"repository": "https://github.com/IHCC-cohorts/GECKO",
"uri_format": "http://purl.obolibrary.org/obo/GECKO_$1",
"version": "2021-01-18"
},
"gemet": {
"contact": {
"email": "helpdesk@eionet.europa.eu",
"github": null,
"name": "Eionet Helpdesk",
"orcid": null
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts.",
"example": "627",
"homepage": "https://www.eionet.europa.eu/gemet/en/themes/",
"mappings": {
"agroportal": "GEMET",
"bartoc": "16"
},
"name": "General Multilingual Environmental Thesaurus",
"pattern": "^\\d+$",
"preferred_prefix": "gemet",
"uri_format": "https://www.eionet.europa.eu/gemet/en/concept/$1"
},
"genatlas": {
"description": "GenAtlas is a database containing information on human genes, markers and phenotypes.",
"example": "HBB",
"homepage": "http://genatlas.medecine.univ-paris5.fr/",
"keywords": [
"disorder",
"gene",
"human",
"life science"
],
"mappings": {
"biocontext": "GENATLAS",
"fairsharing": "FAIRsharing.pmg2vd",
"miriam": "genatlas",
"n2t": "genatlas",
"prefixcommons": "genatlas",
"uniprot": "DB-0027"
},
"name": "Genatlas",
"pattern": "^\\w+$",
"preferred_prefix": "genatlas",
"publications": [
{
"doi": "10.1016/s0764-4469(99)80021-3",
"pmc": null,
"pubmed": "9835018",
"title": "Genatlas database, genes and development defects.",
"year": 1998
},
{
"doi": "10.1006/mgme.1999.2867",
"pmc": null,
"pubmed": "10444337",
"title": "Human genes involved in chromatin remodeling in transcription initiation, and associated diseases: An overview using the GENATLAS database.",
"year": 1999
}
],
"uri_format": "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1"
},
"genbank": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42).",
"example": "U49845",
"homepage": "https://www.ncbi.nlm.nih.gov/genbank/",
"keywords": [
"bioinformatics",
"data management",
"dna",
"epidemiology",
"functional genomics",
"genomics",
"metagenomics",
"transcriptomics",
"virology"
],
"mappings": {
"biocontext": "GenBank",
"cheminf": "000304",
"edam": "2292",
"fairsharing": "FAIRsharing.9kahy4",
"go": "GenBank",
"prefixcommons": "genbank",
"re3data": "r3d100010528",
"uniprot": "DB-0028"
},
"name": "GenBank",
"preferred_prefix": "genbank",
"publications": [
{
"doi": "10.1186/s12859-020-3537-3",
"pmc": "PMC7245624",
"pubmed": "32448124",
"title": "VADR: validation and annotation of virus sequence submissions to GenBank.",
"year": 2020
},
{
"doi": "10.1093/nar/gkz956",
"pmc": "PMC7145611",
"pubmed": "31665464",
"title": "GenBank.",
"year": 2020
},
{
"doi": "10.1093/nar/gky989",
"pmc": "PMC6323954",
"pubmed": "30365038",
"title": "GenBank.",
"year": 2019
},
{
"doi": "10.1093/nar/gkx1094",
"pmc": "PMC5753231",
"pubmed": "29140468",
"title": "GenBank.",
"year": 2018
},
{
"doi": "10.1093/nar/gkw1070",
"pmc": "PMC5210553",
"pubmed": "27899564",
"title": "GenBank.",
"year": 2016
},
{
"doi": "10.1093/nar/gkv1276",
"pmc": "PMC4702903",
"pubmed": "26590407",
"title": "GenBank.",
"year": 2015
},
{
"doi": "10.1093/nar/gku1216",
"pmc": "PMC4383990",
"pubmed": "25414350",
"title": "GenBank.",
"year": 2014
},
{
"doi": "10.1093/nar/gkt1030",
"pmc": "PMC3965104",
"pubmed": "24217914",
"title": "GenBank.",
"year": 2013
},
{
"doi": "10.1093/nar/gks1195",
"pmc": "PMC3531190",
"pubmed": "23193287",
"title": "GenBank.",
"year": 2012
},
{
"doi": "10.1093/nar/gkr1202",
"pmc": "PMC3245039",
"pubmed": "22144687",
"title": "GenBank.",
"year": 2011
},
{
"doi": "10.1093/nar/gkq1079",
"pmc": "PMC3013681",
"pubmed": "21071399",
"title": "GenBank.",
"year": 2010
},
{
"doi": "10.1093/nar/gkn723",
"pmc": "PMC2686462",
"pubmed": "18940867",
"title": "GenBank.",
"year": 2008
},
{
"doi": "10.1093/nar/gkm929",
"pmc": "PMC2238942",
"pubmed": "18073190",
"title": "GenBank.",
"year": 2007
},
{
"doi": "10.1093/nar/gkl1031",
"pmc": "PMC1781113",
"pubmed": "17170002",
"title": "Database resources of the National Center for Biotechnology Information.",
"year": 2006
}
],
"uri_format": "https://www.ncbi.nlm.nih.gov/nucleotide/$1"
},
"gendis": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"description": "Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases.",
"example": "46946",
"homepage": "http://caps.ncbs.res.in/gendis/home.html",
"keywords": [
"classification",
"genome"
],
"mappings": {
"prefixcommons": "gendis"
},
"name": "Genomic Distribution of structural Superfamilies",
"preferred_prefix": "gendis",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code=$1"
},
"genecards": {
"contact": {
"email": "marilyn.safran@weizmann.ac.il",
"github": null,
"name": "Marilyn Safran",
"orcid": "0000-0001-5424-1393"
},
"description": "The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene.",
"example": "ABL1",
"homepage": "http://www.genecards.org/",
"keywords": [
"genetics",
"genome",
"life science",
"transcriptomics"
],
"mappings": {
"biocontext": "GENECARDS",
"fairsharing": "FAIRsharing.g7jbvn",
"miriam": "genecards",
"n2t": "genecards",
"prefixcommons": "genecards",
"re3data": "r3d100012015",
"uniprot": "DB-0030"
},
"name": "GeneCards",
"pattern": "^[A-Za-z-0-9_]+(\\@)?$",
"preferred_prefix": "genecards",
"publications": [
{
"doi": "10.1016/s0168-9525(97)01103-7",
"pmc": null,
"pubmed": "9097728",
"title": "GeneCards: integrating information about genes, proteins and diseases.",
"year": 1997
},
{
"doi": "10.1186/s12864-016-2722-2",
"pmc": "PMC4928145",
"pubmed": "27357693",
"title": "VarElect: the phenotype-based variation prioritizer of the GeneCards Suite.",
"year": 2016
},
{
"doi": "10.1002/cpbi.5",
"pmc": null,
"pubmed": "27322403",
"title": "The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses.",
"year": 2016
},
{
"doi": "10.1093/database/baw030",
"pmc": "PMC4820835",
"pubmed": "27048349",
"title": "Genic insights from integrated human proteomics in GeneCards.",
"year": 2016
},
{
"doi": "10.1089/omi.2015.0168",
"pmc": "PMC4799705",
"pubmed": "26983021",
"title": "GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data.",
"year": 2016
},
{
"doi": "10.1093/database/bav006",
"pmc": "PMC4343183",
"pubmed": "25725062",
"title": "PathCards: multi-source consolidation of human biological pathways.",
"year": 2015
},
{
"doi": "10.1093/database/baq020",
"pmc": "PMC2938269",
"pubmed": "20689021",
"title": "GeneCards Version 3: the human gene integrator.",
"year": 2010
},
{
"doi": "10.1093/bioinformatics/18.11.1542",
"pmc": null,
"pubmed": "12424129",
"title": "GeneCards 2002: towards a complete, object-oriented, human gene compendium.",
"year": 2002
}
],
"uri_format": "https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1"
},
"genecards.geneannot": {
"description": "GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Probe-sets are related to GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq and Ensembl mRNA sequences, while assigning sensitivity and specificity scores to each probe-set to gene match.",
"example": "GSTA1",
"homepage": "http://genecards.weizmann.ac.il/geneannot/",
"keywords": [
"gene expression"
],
"mappings": {
"prefixcommons": "geneannot"
},
"name": "GeneAnnot: Microarray Gene Annotation",
"preferred_prefix": "genecards.geneannot"
},
"genecards.geneloc": {
"description": "GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources",
"example": "17503",
"homepage": "http://genecards.weizmann.ac.il/geneloc/",
"keywords": [
"genome"
],
"mappings": {
"prefixcommons": "geneloc"
},
"name": "Gene Location",
"preferred_prefix": "genecards.geneloc",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id=$1"
},
"genecards.genenote": {
"description": "GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E.",
"example": "GC06M052656",
"homepage": "http://genecards.weizmann.ac.il/genenote/",
"keywords": [
"gene expression"
],
"mappings": {
"prefixcommons": "genenote"
},
"name": "Gene Normal Tissue Expression",
"preferred_prefix": "genecards.genenote",
"uri_format": "http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl?keyword_type=2_gc_id&keyword=$1&data_type=norm2&results=yes"
},
"genedb": {
"deprecated": true,
"description": "GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the \"Pathogen Genomics\" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed.",
"example": "LinJ.20.0070",
"homepage": "https://www.genedb.org/",
"keywords": [
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{
"doi": "10.1093/nar/gkh007",
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"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.",
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"homepage": "http://urgi.versailles.inra.fr/Genefarm/",
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{
"doi": "10.1093/nar/gki115",
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"title": "GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts.",
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}
],
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"po",
"ro",
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"example": "0001885",
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"epidemiology",
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},
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"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.",
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"protein"
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{
"doi": "10.1093/database/bav096",
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{
"doi": "10.1093/nar/gkj133",
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"pubmed": "16381931",
"title": "Ensembl 2006.",
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}
],
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},
"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.",
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"homepage": "http://en.wikipedia.org/wiki/Gene_Wiki",
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"genetics",
"life science"
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{
"doi": "10.1093/database/baw015",
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{
"doi": "10.1093/nar/gkr925",
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"title": "The Gene Wiki in 2011: community intelligence applied to human gene annotation.",
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{
"doi": "10.1093/nar/gkp760",
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"title": "The Gene Wiki: community intelligence applied to human gene annotation.",
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},
{
"doi": "10.1371/journal.pbio.0060175",
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"title": "A gene wiki for community annotation of gene function.",
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}
],
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},
"geno": {
"contact": {
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"orcid": "0000-0002-1048-5019"
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"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",
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"keywords": [
"genomics",
"obo",
"ontology"
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"license": "CC-BY-4.0",
"mappings": {
"aberowl": "GENO",
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"ontobee": "GENO"
},
"name": "Genotype Ontology",
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"preferred_prefix": "GENO",
"repository": "https://github.com/monarch-initiative/GENO-ontology",
"uri_format": "http://purl.obolibrary.org/obo/GENO_$1",
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},
"genpept": {
"description": "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank.",
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"biocontext": "GENPEPT",
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"n2t": "genpept"
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},
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"geo": {
"banana_peel": "_",
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"example": "GDS1234",
"homepage": "https://www.ncbi.nlm.nih.gov/geo/",
"keywords": [
"comparative genomics",
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"genome",
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{
"doi": "10.1093/nar/gks1193",
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"title": "NCBI GEO: archive for functional genomics data sets--update.",
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},
{
"doi": "10.1038/nbt1206-1471",
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"pubmed": "17160034",
"title": "NCBI GEO standards and services for microarray data.",
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},
{
"doi": "10.1093/nar/30.1.207",
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"pubmed": "11752295",
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{
"doi": "10.1038/35001676",
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},
{
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"title": "MINSEQE: Minimum Information about a high-throughput Nucleotide SeQuencing Experiment - a proposal for standards in functional genomic data reporting",
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}
],
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},
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"banana": "GEO",
"banana_peel": "_",
"contact": {
"email": "hoganwr@gmail.com",
"github": "hoganwr",
"name": "Bill Hogan",
"orcid": "0000-0002-9881-1017"
},
"description": "An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in \"The US declared war on Germany\" vs. the US in \"The plane entered US airspace\".",
"download_owl": "http://purl.obolibrary.org/obo/geo.owl",
"example": "000000021",
"homepage": "https://github.com/ufbmi/geographical-entity-ontology/wiki",
"keywords": [
"human geography",
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"ontology",
"physical geography"
],
"license": "CC-BY-4.0",
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"ontobee": "GEO"
},
"name": "Geographical Entity Ontology",
"namespace_in_lui": true,
"pattern": "^\\d{9}$",
"preferred_prefix": "GEOGEO",
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},
"geonames": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
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},
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"geography",
"geoinformatics"
],
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"Geonamaes"
],
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},
"geonames.feature": {
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"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
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},
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"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/"
},
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"contact": {
"email": "kuiper@bio.ntnu.no",
"github": "makuintnu",
"name": "Martin Kuiper",
"orcid": "0000-0002-1171-9876"
},
"description": "Gene Expression Ontology",
"download_obo": "https://www.bio.ntnu.no/ontology/GeXO/gexo.obo",
"download_owl": "https://www.bio.ntnu.no/ontology/GeXO/gexo.owl",
"homepage": "http://www.semantic-systems-biology.org/apo",
"keywords": [
"life science",
"ontology"
],
"mappings": {
"aberowl": "GEXO",
"bioportal": "GEXO",
"fairsharing": "FAIRsharing.3e0sn4",
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"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"
},
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"contact": {
"email": "heinrich.herre@imise.uni-leipzig.de",
"github": null,
"name": "Heinrich Herre",
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},
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"name": "Charles Tapley Hoyt",
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"example": "projects_to",
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"keywords": [
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"life science",
"ontology"
],
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"aberowl": "GFO",
"bioportal": "GFO",
"fairsharing": "FAIRsharing.175hsz"
},
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"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",
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},
"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).",
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"name": "Genetics Home Reference",
"preferred_prefix": "ghr",
"uri_format": "https://medlineplus.gov/genetics/condition/$1"
},
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"description": "GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"example": "GL50803_102438",
"homepage": "https://giardiadb.org/giardiadb/",
"keywords": [
"eukaryotic",
"genome",
"genomics"
],
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"biocontext": "GIARDIADB",
"fairsharing": "FAIRsharing.e7skwg",
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"prefixcommons": "giardiadb",
"re3data": "r3d100012458"
},
"name": "GiardiaDB",
"pattern": "^\\w+$",
"preferred_prefix": "giardiadb",
"publications": [
{
"doi": "10.1093/nar/gkn631",
"pmc": "PMC2686445",
"pubmed": "18824479",
"title": "GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.",
"year": 2008
}
],
"twitter": "EuPathDB",
"uri_format": "https://giardiadb.org/giardiadb/app/record/gene/$1"
},
"github": {
"description": "GitHub is an online host of Git source code repositories.",
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"cthoyt"
],
"homepage": "https://github.com/",
"keywords": [
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"software engineering",
"subject agnostic"
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"preferred_prefix": "github",
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},
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
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},
"description": "An issue in any public repository on GitHub.",
"example": "biopragmatics/bioregistry/424",
"homepage": "https://github.com/",
"keywords": [
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"project management",
"software engineering",
"version control"
],
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"github": "cthoyt",
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"keywords": [
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"project management",
"software engineering",
"version control"
],
"name": "GitHub Pull Request",
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"example": "morpheus.lab/morpheus",
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"keywords": [
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"software engineering",
"subject agnostic"
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"twitter": "gitlab",
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"example": "ACM1_HUMAN",
"homepage": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/",
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"biocontext": "GLIDA.GPCR",
"miriam": "glida.gpcr",
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"preferred_prefix": "glida.gpcr",
"uri_format": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1"
},
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"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.",
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"homepage": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/",
"mappings": {
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"preferred_prefix": "glida.ligand",
"uri_format": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1"
},
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"description": "A database of GlycoMaps containing 2585 conformational maps.",
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],
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},
"name": "GlycoMapsDB",
"preferred_prefix": "glycomapsdb",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=$1"
},
"glycomedb": {
"description": "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.",
"example": "G77500AY",
"has_canonical": "glytoucan",
"homepage": "https://glytoucan.org/",
"keywords": [
"life science",
"molecules",
"small molecules",
"structure"
],
"mappings": {
"biocontext": "GLYCOMEDB",
"edam": "2664",
"fairsharing": "FAIRsharing.k5k0yh",
"miriam": "glycomedb",
"n2t": "glycomedb",
"prefixcommons": "glycomedb",
"re3data": "r3d100011527"
},
"name": "GlycomeDB",
"pattern": "^\\w+$",
"preferred_prefix": "glycomedb",
"publications": [
{
"doi": "10.1093/nar/gkq1014",
"pmc": "PMC3013643",
"pubmed": "21045056",
"title": "GlycomeDB--a unified database for carbohydrate structures.",
"year": 2010
},
{
"doi": "10.1093/glycob/cwp137",
"pmc": null,
"pubmed": "19759275",
"title": "Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences.",
"year": 2009
},
{
"doi": "10.1186/1471-2105-9-384",
"pmc": "PMC2567997",
"pubmed": "18803830",
"title": "GlycomeDB - integration of open-access carbohydrate structure databases.",
"year": 2008
}
],
"uri_format": "https://glytoucan.org/Structures/Glycans/$1"
},
"glyconavi": {
"contact": {
"email": "issaku@noguchi.or.jp",
"github": null,
"name": "Issaku Yamada",
"orcid": "0000-0001-9504-189X"
},
"description": "GlycoNAVI is a website for carbohydrate research. It consists of the \"GlycoNAVI Database\" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the \"GlycoNAVI tools\" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools.",
"example": "GN_G03681DA",
"example_extras": [
"GN_GlyTouCan_G03681DA"
],
"homepage": "https://www.noguchi.or.jp/",
"keywords": [
"chemistry",
"glycomics",
"life science",
"organic chemistry"
],
"mappings": {
"fairsharing": "FAIRsharing.wvp1t7",
"miriam": "glyconavi"
},
"name": "GlycoNAVI",
"pattern": "^GN_[A-Za-z0-9_:]+$",
"preferred_prefix": "glyconavi",
"repository": "https://glyconavi.github.io/doc/",
"uri_format": "https://glyconavi.org/hub/?id=$1"
},
"glycopost": {
"description": "GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their \"raw/processed\" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines.",
"example": "GPST000024",
"homepage": "https://glycopost.glycosmos.org",
"keywords": [
"glycomics",
"life science"
],
"mappings": {
"fairsharing": "FAIRsharing.2y1KMt",
"miriam": "glycopost"
},
"name": "GlycoPOST",
"pattern": "^GPST[0-9]{6}$",
"preferred_prefix": "glycopost",
"uri_format": "https://glycopost.glycosmos.org/entry/$1"
},
"glycosciencesdb": {
"contact": {
"email": "thomas@luetteke-online.de",
"github": "glycosciences",
"name": "Thomas Lütteke",
"orcid": "0000-0002-7140-9933"
},
"contributor": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"description": "A database to support glycobiology and glycomics research. Its main focus is on 3D structures, including 3D structure models as well as references to PDB entries that feature carbohydrates.",
"example": "1",
"github_request_issue": 537,
"homepage": "http://www.glycosciences.de/database/",
"name": "Glycosciences.DB",
"pattern": "^\\d+$",
"preferred_prefix": "glycosciencesdb",
"publications": [
{
"doi": "10.1093/nar/gky994",
"pmc": "PMC6323918",
"pubmed": "30357361",
"title": "Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update).",
"year": 2019
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"synonyms": [
"glycosciences.db"
],
"uri_format": "http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=$1"
},
"glygen": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data.",
"example": "G24361QY",
"homepage": "https://glygen.org/glycan/",
"keywords": [
"glycomics",
"life science"
],
"mappings": {
"fairsharing": "FAIRsharing.aI1J5W",
"uniprot": "DB-0254"
},
"name": "Computational and Informatics Resources for Glycoscience",
"preferred_prefix": "glygen",
"publications": [
{
"doi": "cwz080",
"pmc": "PMC7335483",
"pubmed": "31616925",
"title": "GlyGen: Computational and Informatics Resources for Glycoscience.",
"year": null
},
{
"doi": "10.1093/glycob/cwz080",
"pmc": "PMC7335483",
"pubmed": "31616925",
"title": "GlyGen: Computational and Informatics Resources for Glycoscience.",
"year": 2020
}
],
"twitter": "gly_gen",
"uri_format": "https://glygen.org/glycan/$1"
},
"glytoucan": {
"description": "GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data.",
"example": "G00054MO",
"homepage": "https://glytoucan.org",
"keywords": [
"glycomics",
"structural biology"
],
"mappings": {
"biocontext": "GLYTOUCAN",
"fairsharing": "FAIRsharing.5Pze7l",
"miriam": "glytoucan",
"n2t": "glytoucan",
"re3data": "r3d100012388"
},
"name": "GlyTouCan",
"pattern": "^G[0-9]{5}[A-Z]{2}$",
"preferred_prefix": "glytoucan",
"publications": [
{
"doi": "10.1093/glycob/cwx066",
"pmc": "PMC5881658",
"pubmed": "28922742",
"title": "GlyTouCan: an accessible glycan structure repository.",
"year": 2017
},
{
"doi": "10.1093/nar/gkv1041",
"pmc": "PMC4702779",
"pubmed": "26476458",
"title": "GlyTouCan 1.0--The international glycan structure repository.",
"year": 2015
}
],
"twitter": "glytoucan",
"uri_format": "https://glytoucan.org/Structures/Glycans/$1"
},
"gmd": {
"description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena.",
"example": "68513255-fc44-4041-bc4b-4fd2fae7541d",
"homepage": "http://gmd.mpimp-golm.mpg.de/",
"keywords": [
"life science",
"metabolomics"
],
"mappings": {
"biocontext": "GMD",
"fairsharing": "FAIRsharing.jykmkw",
"miriam": "gmd",
"n2t": "gmd",
"re3data": "r3d100011046"
},
"name": "Golm Metabolome Database",
"pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$",
"preferred_prefix": "gmd",
"publications": [
{
"doi": "doi:10.1007/s11306-010-0198-7",
"pmc": "PMC2874469",
"pubmed": "20526350",
"title": "Decision tree supported substructure prediction of metabolites from GC-MS profiles",
"year": null
},
{
"doi": "10.1007/s11306-010-0198-7",
"pmc": "PMC2874469",
"pubmed": "20526350",
"title": "Decision tree supported substructure prediction of metabolites from GC-MS profiles.",
"year": 2010
}
],
"uri_format": "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx"
},
"gmd.analyte": {
"description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes.",
"example": "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80",
"homepage": "http://gmd.mpimp-golm.mpg.de/",
"mappings": {
"biocontext": "GMD.ANALYTE",
"miriam": "gmd.analyte",
"n2t": "gmd.analyte"
},
"name": "Golm Metabolome Database Analyte",
"pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$",
"preferred_prefix": "gmd.analyte",
"uri_format": "http://gmd.mpimp-golm.mpg.de/Analytes/$1"
},
"gmd.gcms": {
"description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra.",
"example": "53d583d8-40c6-40e1-9296-23f821cd77a5",
"homepage": "http://gmd.mpimp-golm.mpg.de/",
"mappings": {
"biocontext": "GMD.GCMS",
"miriam": "gmd.gcms",
"n2t": "gmd.gcms"
},
"name": "Golm Metabolome Database GC-MS spectra",
"pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$",
"preferred_prefix": "gmd.gcms",
"uri_format": "http://gmd.mpimp-golm.mpg.de/Spectrums/$1"
},
"gmd.profile": {
"description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues.",
"example": "10b38aaf-b977-4950-85b8-f4775f66658d",
"homepage": "http://gmd.mpimp-golm.mpg.de/",
"mappings": {
"biocontext": "GMD.PROFILE",
"miriam": "gmd.profile",
"n2t": "gmd.profile"
},
"name": "Golm Metabolome Database Profile",
"pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$",
"preferred_prefix": "gmd.profile",
"uri_format": "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1"
},
"gmd.ref": {
"description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances.",
"example": "8cf84adb-b4db-4807-ac98-0004247c35df",
"homepage": "http://gmd.mpimp-golm.mpg.de/",
"mappings": {
"biocontext": "GMD.REF",
"miriam": "gmd.ref",
"n2t": "gmd.ref"
},
"name": "Golm Metabolome Database Reference Substance",
"pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$",
"preferred_prefix": "gmd.ref",
"uri_format": "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1"
},
"gmelin": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s.",
"example": "1466",
"homepage": "https://link.springer.com/bookseries/562",
"mappings": {
"edam": "1004",
"wikidata": "P1578"
},
"name": "Gmelins Handbuch der anorganischen Chemie",
"pattern": "^[1-9][0-9]{3,6}$",
"preferred_prefix": "gmelin",
"proprietary": true,
"references": [
"https://en.wikipedia.org/wiki/Gmelin_database"
]
},
"gno": {
"contact": {
"email": "nje5@georgetown.edu",
"github": "edwardsnj",
"name": "Nathan Edwards",
"orcid": "0000-0001-5168-3196"
},
"description": "An ontology for glycans based on GlyTouCan, but organized by subsumption.",
"download_json": "http://purl.obolibrary.org/obo/gno.json",
"download_obo": "http://purl.obolibrary.org/obo/gno.obo",
"download_owl": "http://purl.obolibrary.org/obo/gno.owl",
"example": "10004892",
"example_extras": [
"G99373GG"
],
"homepage": "https://gnome.glyomics.org/",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "GNO",
"bioportal": "GNO",
"obofoundry": "gno",
"ols": "gno",
"ontobee": "GNO"
},
"name": "Glycan Naming and Subsumption Ontology",
"pattern": "^(\\d{8}|(\\w+\\d+\\w+))$",
"preferred_prefix": "GNO",
"providers": [
{
"code": "gno.composition",
"description": "GNOme composition browser",
"homepage": "https://gnome.glyomics.org/CompositionBrowser.html",
"name": "GNOme Composition Browser",
"uri_format": "https://gnome.glyomics.org/CompositionBrowser.html?focus=$1"
},
{
"code": "gno.structure",
"description": "GNOme structure browser",
"homepage": "https://gnome.glyomics.org/StructureBrowser.html",
"name": "GNOme Structure Viewer",
"uri_format": "https://gnome.glyomics.org/StructureBrowser.html?focus=$1"
}
],
"publications": [
{
"doi": "10.5281/zenodo.6678278",
"pmc": null,
"pubmed": null,
"title": "GNOme - Glycan Naming and Subsumption Ontology",
"year": 2021
}
],
"repository": "https://github.com/glygen-glycan-data/GNOme",
"synonyms": [
"gnome"
],
"uri_format": "http://purl.obolibrary.org/obo/GNO_$1",
"version": "1.10.0"
},
"gnomad": {
"contact": {
"email": "hrehm@mgh.harvard.edu",
"github": "heidirehm",
"name": "Heidi L. Rehm",
"orcid": "0000-0002-6025-0015"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community (from https://gnomad.broadinstitute.org).",
"example": "1-55516888-G-GA",
"example_extras": [
"M-8602-T-C",
"DUP_2_5708"
],
"github_request_issue": 695,
"homepage": "https://gnomad.broadinstitute.org",
"license": "CC0-1.0",
"name": "Genome Aggregation Database",
"preferred_prefix": "gnomad",
"publications": [
{
"doi": "10.1038/s41586-020-2308-7",
"pmc": "pmc7334197",
"pubmed": "32461654",
"title": "The mutational constraint spectrum quantified from variation in 141,456 humans.",
"year": 2020
},
{
"doi": "10.1038/s41586-020-2287-8",
"pmc": "PMC7334194",
"pubmed": "32461652",
"title": "A structural variation reference for medical and population genetics.",
"year": 2020
}
],
"uri_format": "https://gnomad.broadinstitute.org/variant/$1"
},
"gnpis": {
"contact": {
"email": "urgi-contact@versailles.inra.fr",
"github": null,
"name": "URGI Contact",
"orcid": "0000-0003-3001-4908"
},
"description": "GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest.",
"example": "AY109603",
"homepage": "https://urgi.versailles.inra.fr/gnpis/",
"keywords": [
"life science"
],
"mappings": {
"biocontext": "GNPIS",
"fairsharing": "FAIRsharing.dw22y3",
"miriam": "gnpis",
"n2t": "gnpis",
"re3data": "r3d100012647"
},
"name": "GnpIS",
"pattern": "^[A-Za-z0-9]+$",
"preferred_prefix": "gnpis",
"publications": [
{
"doi": "10.1093/database/bat058",
"pmc": "PMC3746681",
"pubmed": "23959375",
"title": "GnpIS: an information system to integrate genetic and genomic data from plants and fungi.",
"year": 2013
}
],
"uri_format": "https://urgi.versailles.inra.fr/gnpis/#result/term=$1"
},
"go": {
"appears_in": [
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"chiro",
"cl",
"ecocore",
"ecto",
"envo",
"maxo",
"pcl",
"pco",
"planp",
"uberon",
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"zp"
],
"banana": "GO",
"contact": {
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"github": "suzialeksander",
"name": "Suzi Aleksander",
"orcid": "0000-0001-6787-2901"
},
"depends_on": [
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"ncbitaxon",
"ro",
"uberon"
],
"description": "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.",
"download_json": "http://purl.obolibrary.org/obo/go.json",
"download_obo": "http://purl.obolibrary.org/obo/go.obo",
"download_owl": "http://purl.obolibrary.org/obo/go.owl",
"example": "0032571",
"homepage": "http://geneontology.org/",
"keywords": [
"gene",
"life science",
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "GO",
"agroportal": "GO",
"bartoc": "572",
"biocontext": "GO",
"bioportal": "GO",
"edam": "1176",
"fairsharing": "FAIRsharing.6xq0ee",
"go": "GO",
"hl7": "2.16.840.1.113883.6.128",
"miriam": "go",
"n2t": "go",
"ncbi": "GO",
"obofoundry": "go",
"ols": "go",
"ontobee": "GO",
"prefixcommons": "go",
"uniprot": "DB-0037",
"wikidata": "P686"
},
"name": "Gene Ontology",
"namespace_in_lui": true,
"pattern": "^\\d{7}$",
"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": "2022-12-04"
},
"go.model": {
"description": "GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform.",
"example": "5fce9b7300001250",
"homepage": "http://www.geneontology.org/gocam",
"mappings": {
"go": "gomodel"
},
"name": "Gene Ontology Causal Assembly Model",
"preferred_prefix": "go.model",
"uri_format": "http://noctua.geneontology.org/editor/graph/gomodel:$1"
},
"go.ref": {
"banana": "GO_REF",
"description": "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made.",
"example": "0000041",
"homepage": "http://www.geneontology.org/cgi-bin/references.cgi",
"mappings": {
"biocontext": "GO_REF",
"go": "GO_REF",
"miriam": "go_ref",
"n2t": "go.ref"
},
"name": "Gene Ontology Database references",
"namespace_in_lui": true,
"pattern": "^\\d{7}$",
"preferred_prefix": "go.ref",
"uri_format": "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md#goref$1"
},
"go.resource": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A database-specific registry supporting curation in the Gene Ontology",
"example": "CHEBI",
"homepage": "http://geneontology.org/",
"name": "Gene Ontology Registry",
"preferred_prefix": "go.resource",
"uri_format": "https://bioregistry.io/metaregistry/go/$1"
},
"goa": {
"description": "The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups.",
"example": "P12345",
"homepage": "https://www.ebi.ac.uk/GOA/",
"keywords": [
"biology",
"gene",
"life science",
"ontology",
"protein"
],
"mappings": {
"biocontext": "GOA",
"fairsharing": "FAIRsharing.7zffgc",
"miriam": "goa",
"n2t": "goa",
"ncbi": "GOA",
"prefixcommons": "goa"
},
"name": "Gene Ontology Annotation Database",
"pattern": "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$",
"preferred_prefix": "goa",
"provides": "uniprot",
"publications": [
{
"doi": "10.1093/nar/gku1113",
"pmc": "PMC4383930",
"pubmed": "25378336",
"title": "The GOA database: gene Ontology annotation updates for 2015.",
"year": 2014
},
{
"doi": "10.1093/nar/gkn803",
"pmc": "PMC2686469",
"pubmed": "18957448",
"title": "The GOA database in 2009--an integrated Gene Ontology Annotation resource.",
"year": 2008
}
],
"uri_format": "https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1"
},
"goche": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Represent chemical entities having particular CHEBI roles",
"download_owl": "https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl",
"example": "25512",
"homepage": "https://github.com/geneontology/go-ontology",
"keywords": [
"ontology"
],
"name": "GO Chemicals",
"pattern": "^\\d+$",
"preferred_prefix": "GOCHE",
"references": [
"https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638472847049400",
"https://github.com/geneontology/go-ontology/issues/19535"
],
"repository": "https://github.com/geneontology/go-ontology",
"synonyms": [
"go.chebi",
"go.chemical",
"go.chemicals"
],
"uri_format": "https://biopragmatics.github.io/providers/goche/$1"
},
"goeco": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported.",
"example": "IPI",
"homepage": "http://geneontology.org/docs/guide-go-evidence-codes/",
"name": "GO Evidence Code",
"preferred_prefix": "goeco"
},
"gold": {
"description": "The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.",
"example": "Gs0000008",
"homepage": "https://gold.jgi.doe.gov/",
"keywords": [
"genome",
"genomics",
"metabolomics",
"metagenomics",
"ontology and terminology",
"phylogenetics"
],
"mappings": {
"fairsharing": "FAIRsharing.5q1p14",
"miriam": "gold",
"prefixcommons": "gold",
"re3data": "r3d100010808"
},
"name": "Genomes Online Database",
"pattern": "^[A-Z][a-z][0-9]+$",
"preferred_prefix": "gold",
"publications": [
{
"doi": "10.1093/nar/gkaa983",
"pmc": "PMC7778979",
"pubmed": "33152092",
"title": "Genomes OnLine Database (GOLD) v.8: overview and updates.",
"year": 2021
},
{
"doi": "10.1093/nar/gky977",
"pmc": "PMC6323969",
"pubmed": "30357420",
"title": "Genomes OnLine database (GOLD) v.7: updates and new features.",
"year": 2019
},
{
"doi": "10.1093/nar/gkp848",
"pmc": "PMC2808860",
"pubmed": "19914934",
"title": "The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata.",
"year": 2009
},
{
"doi": "10.1093/nar/gkm884",
"pmc": "PMC2238992",
"pubmed": "17981842",
"title": "The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata.",
"year": 2007
},
{
"doi": "11125068",
"pmc": "PMC29859",
"pubmed": "11125068",
"title": "Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.",
"year": null
},
{
"doi": "10.1093/nar/29.1.126",
"pmc": "PMC29859",
"pubmed": "11125068",
"title": "Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.",
"year": 2001
},
{
"doi": "10.1093/bioinformatics/15.9.773",
"pmc": null,
"pubmed": "10498782",
"title": "Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide.",
"year": 1999
}
],
"uri_format": "https://gold.jgi.doe.gov/resolver?id=$1"
},
"gold.genome": {
"description": "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace.\n\nThe GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes.",
"example": "Gi07796",
"homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi",
"mappings": {
"biocontext": "GOLD.GENOME",
"miriam": "gold.genome",
"n2t": "gold.genome"
},
"name": "GOLD genome",
"pattern": "^(Gi|Gc)\\d+$",
"preferred_prefix": "gold.genome",
"uri_format": "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1"
},
"gold.meta": {
"description": "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples.",
"example": "Gm00047",
"has_canonical": "gold",
"homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi",
"mappings": {
"biocontext": "GOLD.META",
"miriam": "gold.meta",
"n2t": "gold.meta"
},
"name": "GOLD metadata",
"pattern": "^Gm\\d+$",
"preferred_prefix": "gold.meta",
"uri_format": "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1"
},
"goldbook": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Compendium is popularly referred to as the \"Gold Book\", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC \"Colour Books\" on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books.\n\nTerminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC's Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry.",
"example": "G02681",
"homepage": "https://goldbook.iupac.org",
"license": "CC BY 4.0-NC-ND",
"mappings": {
"bartoc": "1884",
"wikidata": "P4732"
},
"name": "IUPAC Gold Book Compendium of Chemical Terminology",
"pattern": "^[A-Z]{1,2}\\d{5}$",
"preferred_prefix": "goldbook",
"uri_format": "https://goldbook.iupac.org/terms/view/$1"
},
"google.book": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Search the world's most comprehensive index of full-text books.",
"example": "qafeQTWIWmcC",
"github_request_issue": 511,
"homepage": "https://books.google.com",
"mappings": {
"wikidata": "P675"
},
"name": "Google Books",
"preferred_prefix": "google.book",
"uri_format": "https://books.google.com/books?id=$1"
},
"google.patent": {
"contributor_extras": [
{
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
}
],
"description": "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date.",
"example": "US4145692",
"example_extras": [
"USRE38117E1"
],
"homepage": "https://www.google.com/patents/",
"mappings": {
"biocontext": "GOOGLE.PATENT",
"cellosaurus": "Patent",
"miriam": "google.patent",
"n2t": "google.patent"
},
"name": "Google Patents",
"pattern": "^[A-Z]{2,4}\\d+([A-Z])?([0-9])?$",
"preferred_prefix": "google.patent",
"synonyms": [
"patent"
],
"uri_format": "https://www.google.com/patents/$1"
},
"google.scholar": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.",
"example": "PjrpzUIAAAAJ",
"homepage": "https://scholar.google.com/",
"mappings": {
"biolink": "GSID"
},
"name": "Google Scholar Researcher",
"preferred_prefix": "google.scholar"
},
"gorel": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.",
"download_owl": "ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl",
"example": "0002005",
"homepage": "http://geneontology.org/docs/ontology-relations/",
"keywords": [
"ontology"
],
"mappings": {
"biolink": "GOREL",
"go": "GOREL"
},
"name": "GO Relations",
"pattern": "^\\d{7}$",
"preferred_prefix": "gorel",
"providers": [
{
"code": "obo.legacy",
"description": "Legacy OBO PURLs",
"homepage": "http://purl.obolibrary.org/obo/gorel.owl",
"name": "Legacy OBO",
"uri_format": "http://purl.obolibrary.org/obo/GOREL_$1"
}
]
},
"gpcrdb": {
"contact": {
"email": "david.gloriam@sund.ku.dk",
"github": null,
"name": "David Gloriam",
"orcid": "0000-0002-4299-7561"
},
"description": "The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models.",
"example": "RL3R1_HUMAN",
"homepage": "http://www.gpcrdb.org/",
"keywords": [
"life science",
"molecular biology",
"protein",
"small molecule"
],
"mappings": {
"biocontext": "GPCRDB",
"fairsharing": "FAIRsharing.e4n3an",
"miriam": "gpcrdb",
"n2t": "gpcrdb",
"prefixcommons": "gpcrdb",
"uniprot": "DB-0038"
},
"name": "G protein-coupled receptor database",
"pattern": "^\\w+$",
"preferred_prefix": "gpcrdb",
"publications": [
{
"doi": "10.1093/nar/26.1.275",
"pmc": "PMC147194",
"pubmed": "9399852",
"title": "GPCRDB: an information system for G protein-coupled receptors.",
"year": 1998
},
{
"doi": "10.1093/nar/gkaa1080",
"pmc": "PMC7778909",
"pubmed": "33270898",
"title": "GPCRdb in 2021: integrating GPCR sequence, structure and function.",
"year": 2021
},
{
"doi": "10.1093/nar/gkx1109",
"pmc": "PMC5753179",
"pubmed": "29155946",
"title": "GPCRdb in 2018: adding GPCR structure models and ligands.",
"year": 2018
},
{
"doi": "10.1111/bph.13509",
"pmc": "PMC4919580",
"pubmed": "27155948",
"title": "GPCRdb: the G protein-coupled receptor database - an introduction.",
"year": 2016
},
{
"doi": "10.1093/nar/gkv1178",
"pmc": "PMC4702843",
"pubmed": "26582914",
"title": "GPCRdb: an information system for G protein-coupled receptors.",
"year": 2015
},
{
"doi": "10.1093/nar/gkt1255",
"pmc": "PMC3965068",
"pubmed": "24304901",
"title": "GPCRDB: an information system for G protein-coupled receptors.",
"year": 2013
},
{
"doi": "10.1093/nar/gkq1009",
"pmc": "PMC3013641",
"pubmed": "21045054",
"title": "GPCRDB: information system for G protein-coupled receptors.",
"year": 2010
},
{
"doi": "10.1093/nar/gkg103",
"pmc": "PMC165550",
"pubmed": "12520006",
"title": "GPCRDB information system for G protein-coupled receptors.",
"year": 2003
},
{
"doi": "10.1093/nar/29.1.346",
"pmc": "PMC29816",
"pubmed": "11125133",
"title": "Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems.",
"year": 2001
}
],
"twitter": "gpcrdb",
"uri_format": "https://gpcrdb.org/protein/$1"
},
"gpmdb": {
"description": "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns.",
"example": "GPM32310002988",
"homepage": "http://gpmdb.thegpm.org/",
"keywords": [
"bioinformatics",
"proteomics"
],
"mappings": {
"biocontext": "GPMDB",
"fairsharing": "FAIRsharing.fhcmwq",
"miriam": "gpmdb",
"n2t": "gpmdb"
},
"name": "Global Proteome Machine Database",
"pattern": "^GPM\\d+$",
"preferred_prefix": "gpmdb",
"providers": [
{
"code": "omicsdi",
"description": "GPMDB through OmicsDI",
"homepage": "https://www.omicsdi.org/",
"name": "GPMDB through OmicsDI",
"uri_format": "https://www.omicsdi.org/dataset/gpmdb/$1"
}
],
"publications": [
{
"doi": "10.1021/pr049882h",
"pmc": null,
"pubmed": "15595733",
"title": "Open source system for analyzing, validating, and storing protein identification data.",
"year": 2004
}
],
"twitter": "GPMDB",
"uri_format": "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1"
},
"graingenes.reference": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A database for Triticeae and Avena references.",
"example": "WGS-95-1333",
"homepage": "http://wheat.pw.usda.gov",
"name": "GrainGenes",
"preferred_prefix": "graingenes.reference",
"uri_format": "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1"
},
"graingenes.symbol": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A database for Triticeae and Avena gene symbols.",
"example": "1-FEH+w3",
"homepage": "http://wheat.pw.usda.gov",
"name": "GrainGenes",
"preferred_prefix": "graingenes.symbol",
"uri_format": "http://wheat.pw.usda.gov/report?class=gene;name=$1"
},
"gramene.gene": {
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene.",
"example": "GR:0080039",
"homepage": "http://www.gramene.org/",
"mappings": {
"biocontext": "GRAMENE.GENE",
"go": "GR_GENE",
"miriam": "gramene.gene",
"n2t": "gramene.gene"
},
"name": "Gramene Gene",
"pattern": "^GR\\:\\d+$",
"preferred_prefix": "gramene.gene",
"synonyms": [
"GR_GENE"
],
"uri_format": "http://www.gramene.org/db/genes/search_gene?acc=$1"
},
"gramene.growthstage": {
"banana": "GRO",
"contact": {
"email": "po-discuss@plantontology.org",
"github": null,
"name": "Plant Ontology Administrators",
"orcid": null
},
"deprecated": true,
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.",
"example": "0007133",
"homepage": "http://www.gramene.org/plant_ontology/",
"keywords": [
"anatomy",
"obo",
"ontology"
],
"mappings": {
"biocontext": "GRAMENE.GROWTHSTAGE",
"bioportal": "GRO-CPGA",
"miriam": "gro",
"n2t": "gramene.growthstage",
"obofoundry": "gro",
"prefixcommons": "gramene.po"
},
"name": "Gramene Growth Stage Ontology",
"namespace_in_lui": true,
"pattern": "^\\d{7}$",
"preferred_prefix": "GRO",
"synonyms": [
"cpga",
"gro-cpga"
],
"uri_format": "http://www.gramene.org/db/ontology/search?id=GRO:$1"
},
"gramene.protein": {
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene.",
"example": "78073",
"homepage": "http://www.gramene.org/",
"mappings": {
"biocontext": "GRAMENE.PROTEIN",
"go": "GR_PROTEIN",
"miriam": "gramene.protein",
"n2t": "gramene.protein"
},
"name": "Gramene protein",
"pattern": "^\\d+$",
"preferred_prefix": "gramene.protein",
"synonyms": [
"GR_PROTEIN"
],
"uri_format": "http://www.gramene.org/db/protein/protein_search?protein_id=$1"
},
"gramene.qtl": {
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene.",
"example": "CQG5",
"homepage": "http://www.gramene.org/",
"mappings": {
"biocontext": "GRAMENE.QTL",
"go": "GR_QTL",
"miriam": "gramene.qtl",
"n2t": "gramene.qtl"
},
"name": "Gramene QTL",
"pattern": "^\\w+$",
"preferred_prefix": "gramene.qtl",
"synonyms": [
"GR_QTL"
],
"uri_format": "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1"
},
"gramene.reference": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Literature references in Gramene",
"example": "6200",
"homepage": "http://www.gramene.org",
"name": "Gramene Reference",
"pattern": "^\\d+$",
"preferred_prefix": "gramene.reference",
"synonyms": [
"gramene.ref"
],
"uri_format": "http://www.gramene.org/db/literature/pub_search?ref_id=$1"
},
"gramene.taxonomy": {
"banana": "GR_tax",
"banana_peel": ":",
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene.",
"example": "013681",
"homepage": "http://www.gramene.org/",
"mappings": {
"biocontext": "GRAMENE.TAXONOMY",
"miriam": "gramene.taxonomy",
"n2t": "gramene.taxonomy"
},
"name": "Gramene Taxonomy",
"pattern": "^\\d+$",
"preferred_prefix": "gramene.taxonomy",
"uri_format": "https://archive.gramene.org/db/ontology/search?id=GR_tax:$1"
},
"grassbase": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species.",
"example": "imp10873",
"github_request_issue": 218,
"homepage": "https://www.kew.org/data/grasses-syn/index.htm",
"mappings": {
"wikidata": "P1832"
},
"name": "GrassBase",
"pattern": "^(imp|gen)\\d{5}$",
"preferred_prefix": "grassbase",
"uri_format": "https://www.kew.org/data/grasses-db/www/$1"
},
"greengenes": {
"contact": {
"email": "GLAndersen@lbl.gov",
"github": null,
"name": "Gary L Andersen",
"orcid": "0000-0002-1618-9827"
},
"description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.",
"example": "100000",
"homepage": "http://greengenes.lbl.gov/",
"keywords": [
"genetics",
"life science",
"rna"
],
"mappings": {
"biocontext": "GREENGENES",
"fairsharing": "FAIRsharing.bpxgb6",
"miriam": "greengenes",
"n2t": "greengenes",
"ncbi": "Greengenes",
"prefixcommons": "greengenes",
"re3data": "r3d100010549"
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"name": "16S rRNA gene database",
"pattern": "^\\d+$",
"preferred_prefix": "greengenes",
"publications": [
{
"doi": "10.1128/aem.03006-05",
"pmc": "PMC1489311",
"pubmed": "16820507",
"title": "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.",
"year": 2006
}
],
"uri_format": "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1"
},
"grid": {
"description": "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally.",
"example": "grid.225360.0",
"homepage": "https://www.grid.ac/",
"keywords": [
"data management"
],
"mappings": {
"biocontext": "GRID",
"fairsharing": "FAIRsharing.0pUMYW",
"miriam": "grid",
"n2t": "grid"
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"name": "Global Research Identifier Database",
"pattern": "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$",
"preferred_prefix": "grid",
"twitter": "grid_ac",
"uri_format": "https://www.grid.ac/institutes/$1"
},
"grin": {
"description": "GRIN provides National Genetic Resources Program (NGRP) personnel and germplasm users continuous access to databases for the maintenance of passport, characterization, evaluation, inventory, and distribution data important for the effective management and utilization of national germplasm collections.",
"example": "159787",
"homepage": "http://www.ars-grin.gov/",
"keywords": [
"life science"
],
"mappings": {
"fairsharing": "FAIRsharing.3axym7",
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"name": "Germplasm Resources Information Network",
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"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
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"uri_format": "http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=$1"
},
"grin.taxonomy": {
"description": "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact.",
"example": "19333",
"homepage": "http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en",
"mappings": {
"biocontext": "GRIN.TAXONOMY",
"go": "GRIN",
"miriam": "grin.taxonomy",
"n2t": "grin.taxonomy",
"ncbi": "GRIN",
"wikidata": "P1421"
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"name": "GRIN URL",
"pattern": "^\\d+$",
"preferred_prefix": "grin.taxonomy",
"uri_format": "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1"
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"gro": {
"contact": {
"email": "vlee@ebi.ac.uk",
"github": null,
"name": "Vivian Lee",
"orcid": null
},
"deprecated": true,
"description": "The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes.",
"download_owl": "http://aber-owl.net/media/ontologies/GRO/5/gro.owl",
"example": "Lipid",
"homepage": "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html",
"keywords": [
"ontology"
],
"mappings": {
"aberowl": "GRO",
"bioportal": "GRO"
},
"name": "Gene Regulation Ontology",
"preferred_prefix": "gro",
"uri_format": "http://www.bootstrep.eu/ontology/GRO#$1"
},
"grsdb": {
"description": "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.",
"example": "10142",
"homepage": "http://bioinformatics.ramapo.edu/GRSDB2/",
"keywords": [
"dna",
"rna"
],
"mappings": {
"biocontext": "GRSDB",
"miriam": "grsdb",
"n2t": "grsdb",
"prefixcommons": "grsdb"
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"name": "G-Rich Sequences Database",
"pattern": "^\\d+$",
"preferred_prefix": "grsdb",
"uri_format": "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1"
},
"gsfa": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The \"Codex General Standard for Food Additives\" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database.",
"example": "174",
"homepage": "http://www.fao.org/gsfaonline",
"name": "General Standard for Food Additives Online Database",
"pattern": "^\\d+$",
"preferred_prefix": "gsfa",
"synonyms": [
"FAO/WHO_standards"
],
"uri_format": "http://www.fao.org/gsfaonline/additives/details.html?id=$1"
},
"gsso": {
"appears_in": [
"ontoavida",
"scdo"
],
"banana": "GSSO",
"contact": {
"email": "kronkcj@mail.uc.edu",
"github": "Superraptor",
"name": "Clair Kronk",
"orcid": "0000-0001-8397-8810"
},
"description": "The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology.",
"download_json": "http://purl.obolibrary.org/obo/gsso.json",
"download_obo": "http://purl.obolibrary.org/obo/gsso.obo",
"download_owl": "http://purl.obolibrary.org/obo/gsso.owl",
"example": "002368",
"homepage": "https://gsso.research.cchmc.org/",
"keywords": [
"obo",
"ontology"
],
"license": "Apache 2.0 License",
"mappings": {
"aberowl": "GSSO",
"bioportal": "GSSO",
"miriam": "gsso",
"obofoundry": "gsso",
"ols": "gsso",
"ontobee": "GSSO"
},
"name": "Gender, Sex, and Sexual Orientation Ontology",
"namespace_in_lui": true,
"pattern": "^\\d{6}$",
"preferred_prefix": "GSSO",
"repository": "https://github.com/Superraptor/GSSO",
"uri_format": "http://purl.obolibrary.org/obo/GSSO_$1",
"version": "2.0.5"
},
"gtex": {
"description": "The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation.",
"example": "BRIP1",
"homepage": "https://www.gtexportal.org",
"mappings": {
"biocontext": "GTEX",
"biolink": "GTEx",
"miriam": "gtex",
"n2t": "gtex"
},
"name": "Genotype-Tissue Expression",
"pattern": "^\\w.+$",
"preferred_prefix": "gtex",
"uri_format": "https://www.gtexportal.org/home/gene/$1"
},
"gtr": {
"appears_in": [
"mondo"
],
"comment": "Identifiers appearing in MONDO don't match any of the resources apparent endpoints",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease",
"example": "AN0097748",
"homepage": "https://www.ncbi.nlm.nih.gov/gtr/",
"name": "Genetic Testing Registry",
"preferred_prefix": "gtr",
"synonyms": [
"medgen.gtr"
],
"uri_format": "https://www.ncbi.nlm.nih.gov/gtr/conditions/$1"
},
"gudmap": {
"description": "The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract.",
"example": "Q-2958",
"homepage": "http://www.gudmap.org/",
"keywords": [
"cell biology",
"developmental biology",
"genomics",
"molecular biology"
],
"mappings": {
"biocontext": "GUDMAP",
"fairsharing": "FAIRsharing.910c39",
"miriam": "gudmap",
"n2t": "gudmap",
"re3data": "r3d100012193"
},
"name": "Genitourinary Development Molecular Anatomy Project",
"pattern": "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$",
"preferred_prefix": "gudmap",
"publications": [
{
"doi": "10.1242/dev.063594",
"pmc": "PMC3188593",
"pubmed": "21652655",
"title": "The GUDMAP database--an online resource for genitourinary research.",
"year": 2011
},
{
"doi": "10.1681/asn.2007101078",
"pmc": null,
"pubmed": "18287559",
"title": "GUDMAP: the genitourinary developmental molecular anatomy project.",
"year": 2008
}
],
"twitter": "GUDMAP",
"uri_format": "https://gudmap.org/id/$1"
},
"gwascentral.marker": {
"description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker.",
"example": "HGVM15354",
"homepage": "https://www.gwascentral.org/markers",
"mappings": {
"biocontext": "GWASCENTRAL.MARKER",
"miriam": "gwascentral.marker",
"n2t": "gwascentral.marker"
},
"name": "GWAS Central Marker",
"pattern": "^HGVM\\d+$",
"preferred_prefix": "gwascentral.marker",
"uri_format": "https://www.gwascentral.org/marker/$1"
},
"gwascentral.phenotype": {
"description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype.",
"example": "HGVPM623",
"homepage": "https://www.gwascentral.org/phenotypes",
"mappings": {
"biocontext": "GWASCENTRAL.PHENOTYPE",
"miriam": "gwascentral.phenotype",
"n2t": "gwascentral.phenotype"
},
"name": "GWAS Central Phenotype",
"pattern": "^HGVPM\\d+$",
"preferred_prefix": "gwascentral.phenotype",
"uri_format": "https://www.gwascentral.org/phenotype/$1"
},
"gwascentral.study": {
"description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study.",
"example": "HGVST1828",
"homepage": "https://www.gwascentral.org/studies",
"keywords": [
"gene",
"genome"
],
"mappings": {
"biocontext": "GWASCENTRAL.STUDY",
"miriam": "gwascentral.study",
"n2t": "gwascentral.study",
"prefixcommons": "hgvbase"
},
"name": "GWAS Central Study",
"pattern": "^HGVST\\d+$",
"preferred_prefix": "gwascentral.study",
"uri_format": "https://www.gwascentral.org/study/$1"
},
"gxa.expt": {
"description": "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments.",
"example": "E-MTAB-2037",
"homepage": "https://www.ebi.ac.uk/gxa/",
"mappings": {
"biocontext": "GXA.EXPT",
"miriam": "gxa.expt",
"n2t": "gxa.expt"
},
"name": "GXA Expt",
"pattern": "^[AEP]-\\w{4}-\\d+$",
"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/$1"
},
"gxa.gene": {
"description": "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes.",
"example": "AT4G01080",
"homepage": "https://www.ebi.ac.uk/gxa/",
"mappings": {
"biocontext": "GXA.GENE",
"miriam": "gxa.gene",
"n2t": "gxa.gene"
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"name": "GXA Gene",
"pattern": "^\\w+$",
"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",
"keywords": [
"obo",
"ontology"
],
"mappings": {
"biocontext": "HABRONATTUS",
"obofoundry": "habronattus"
},
"name": "Habronattus courtship",
"preferred_prefix": "HABRONATTUS",
"uri_format": "http://purl.obolibrary.org/obo/HABRONATTUS_$1"
},
"hagr.genage": {
"description": "GenAge is a database of human and model organism genes related to longevity and aging, maintained by the Human Ageing Genomics Resources (HAGR) group.",
"example": "0001",
"homepage": "http://genomics.senescence.info/genes/",
"keywords": [
"aging",
"genes",
"longevity"
],
"mappings": {
"prefixcommons": "genage"
},
"name": "The Ageing Gene Database",
"preferred_prefix": "hagr.genage",
"publications": [
{
"doi": "10.1093/nar/gks1155",
"pmc": "PMC3531213",
"pubmed": "23193293",
"title": "Human Ageing Genomic Resources: integrated databases and tools for the biology and genetics of ageing.",
"year": 2012
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://genomics.senescence.info/genes/details.php?id=$1"
},
"hagr.gendr": {
"description": "GenDR is a database of genes associated with dietary restriction (DR). GenDR includes two datasets: 1) genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of DR; 2) genes robustly altered due to DR, derived from a meta-analysis of microarray DR studies in mammals",
"example": "2",
"homepage": "http://genomics.senescence.info/diet/",
"keywords": [
"aging",
"dietary restriction",
"genes",
"longevity"
],
"mappings": {
"prefixcommons": "gendr"
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"name": "The Dietary Restriction Gene Database",
"preferred_prefix": "hagr.gendr",
"publications": [
{
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"pmc": "PMC3415404",
"pubmed": "22912585",
"title": "Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes.",
"year": 2012
}
],
"reviewer": {
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://genomics.senescence.info/diet/details.php?id=$1"
},
"hamap": {
"contact": {
"email": "alan.bridge@isb-sib.ch",
"github": null,
"name": "Alan Bridge",
"orcid": "0000-0003-2148-9135"
},
"description": "HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries.",
"example": "MF_01400",
"homepage": "https://hamap.expasy.org/",
"keywords": [
"life science",
"protein"
],
"mappings": {
"biocontext": "HAMAP",
"edam": "2766",
"fairsharing": "FAIRsharing.63m4ss",
"go": "HAMAP",
"miriam": "hamap",
"n2t": "hamap",
"prefixcommons": "hamap",
"uniprot": "DB-0041"
},
"name": "High-quality Automated and Manual Annotation of microbial Proteomes",
"pattern": "^MF_\\d+$",
"preferred_prefix": "hamap",
"publications": [
{
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"pmc": "PMC4383873",
"pubmed": "25348399",
"title": "HAMAP in 2015: updates to the protein family classification and annotation system.",
"year": 2014
},
{
"doi": "10.1093/nar/gks1157",
"pmc": "PMC3531088",
"pubmed": "23193261",
"title": "HAMAP in 2013, new developments in the protein family classification and annotation system.",
"year": 2012
}
],
"uri_format": "https://hamap.expasy.org/unirule/$1"
},
"hancestro": {
"contact": {
"email": "danielle.welter@uni.lu",
"github": "daniwelter",
"name": "Danielle Welter",
"orcid": "0000-0003-1058-2668"
},
"description": "Human ancestry ontology for the NHGRI GWAS Catalog",
"download_owl": "http://purl.obolibrary.org/obo/hancestro.owl",
"example": "0290",
"homepage": "https://github.com/EBISPOT/ancestro",
"keywords": [
"demographics",
"human genetics",
"obo",
"ontology",
"population genetics"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "HANCESTRO",
"biolink": "HANCESTRO",
"bioportal": "HANCESTRO",
"fairsharing": "FAIRsharing.rja8qp",
"obofoundry": "hancestro",
"ols": "hancestro",
"ontobee": "HANCESTRO"
},
"name": "Human Ancestry Ontology",
"pattern": "^\\d{4}$",
"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_$1",
"version": "2.6"
},
"hao": {
"contact": {
"email": "diapriid@gmail.com",
"github": "mjy",
"name": "Matt Yoder",
"orcid": "0000-0002-5640-5491"
},
"description": "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)",
"download_obo": "http://purl.obolibrary.org/obo/hao.obo",
"download_owl": "http://purl.obolibrary.org/obo/hao.owl",
"example": "0000187",
"homepage": "http://hymao.org",
"keywords": [
"anatomy",
"life science",
"obo",
"ontology"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "HAO",
"biocontext": "HAO",
"bioportal": "HAO",
"fairsharing": "FAIRsharing.kj3m5n",
"obofoundry": "hao",
"ols": "hao",
"ontobee": "HAO"
},
"name": "Hymenoptera Anatomy Ontology",
"pattern": "^\\d{7}$",
"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/$1"
},
"hba": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A controlled vocabulary to support the study of transcription in the human brain",
"download_obo": "https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-hba.obo",
"example": "4005",
"example_extras": [
"265504410"
],
"homepage": "https://human.brain-map.org",
"keywords": [
"ontology"
],
"name": "Human Brain Atlas",
"pattern": "^\\d+$",
"preferred_prefix": "HBA",
"uri_format": "https://biopragmatics.github.io/providers/hba/$1"
},
"hbvar": {
"description": "This is a relational database of information about hemoglobin variants and mutations that cause thalassemia.",
"example": "2526",
"homepage": "http://globin.cse.psu.edu/globin/hbvar",
"keywords": [
"protein"
],
"mappings": {
"prefixcommons": "hbvar"
},
"name": "A Database of Human Hemoglobin Variants and Thalassemias",
"preferred_prefix": "hbvar",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=$1"
},
"hc.din": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A Drug Identification Number (DIN) is a computer-generated eight digit number assigned by Health Canada to a drug product prior to being marketed in Canada. It uniquely identifies all drug products sold in a dosage form in Canada and is located on the label of prescription and over-the-counter drug products that have been evaluated and authorized for sale in Canada.",
"example": "02069237",
"homepage": "https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/fact-sheets/drug-identification-number.html",
"mappings": {
"hl7": "2.16.840.1.113883.5.1105"
},
"name": "Health Canada Drug Identification Number",
"pattern": "^\\d{8}$",
"preferred_prefix": "hc.din",
"references": [
"http://www.hc-sc.gc.ca/dhp-mps/prodpharma/databasdon/index-eng.php"
]
},
"hc.npn": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Licensed Natural Health Products Database contains information about natural health products that have been issued a product licence by Health Canada.",
"example": "18125",
"homepage": "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/search-rechercheReq.do?lang=eng",
"mappings": {
"hl7": "2.16.840.1.113883.5.1107"
},
"name": "Health Canada Natural Product Number",
"pattern": "^\\d+$",
"preferred_prefix": "hc.npn",
"references": [
"https://www.canada.ca/en/health-canada/services/drugs-health-products/natural-non-prescription/applications-submissions/product-licensing/licensed-natural-health-products-database.html"
],
"uri_format": "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id=$1"
},
"hcao": {
"description": "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas.",
"download_owl": "http://ontology.data.humancellatlas.org/ontologies/hcao/releases/2022-12-16/hcao.owl",
"homepage": "https://www.humancellatlas.org",
"keywords": [
"ontology"
],
"mappings": {
"ols": "hcao"
},
"name": "Human Cell Atlas Ontology",
"no_own_terms": true,
"preferred_prefix": "hcao",
"version": "2022-12-16"
},
"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",
"keywords": [
"biomedical science",
"business administration",
"ontology"
],
"mappings": {
"aberowl": "HCPCS",
"biolink": "HCPCS",
"bioportal": "HCPCS",
"fairsharing": "FAIRsharing.x81wz8"
},
"name": "Healthcare Common Procedure Coding System",
"preferred_prefix": "hcpcs",
"uri_format": "http://purl.bioontology.org/ontology/HCPCS/$1"
},
"hcvdb": {
"description": "the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses.",
"example": "M58335",
"homepage": "http://euhcvdb.ibcp.fr/euHCVdb/",
"keywords": [
"gene"
],
"mappings": {
"biocontext": "HCVDB",
"miriam": "hcvdb",
"n2t": "hcvdb",
"prefixcommons": "hcv"
},
"name": "Hepatitis C Virus Database Project",
"pattern": "^M\\d{5}$",
"preferred_prefix": "hcvdb",
"uri_format": "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1"
},
"hdr": {
"description": "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders.",
"example": "63",
"homepage": "http://research.nhgri.nih.gov/apps/homeodomain/web/",
"keywords": [
"genome"
],
"mappings": {
"biocontext": "HDR",
"miriam": "hdr",
"n2t": "hdr",
"prefixcommons": "hdr"
},
"name": "Homeodomain Research",
"pattern": "^\\d+$",
"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=$1"
},
"hgnc": {
"contact": {
"email": "hgnc@genenames.org",
"github": null,
"name": "Elspeth Bruford",
"orcid": null
},
"description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database.",
"download_owl": "http://aber-owl.net/media/ontologies/HGNC/1/hgnc.owl",
"example": "16793",
"homepage": "http://www.genenames.org",
"keywords": [
"classification",
"gene",
"life science",
"ontology"
],
"mappings": {
"aberowl": "HGNC",
"biocontext": "HGNC",
"bioportal": "HGNC",
"cellosaurus": "HGNC",
"edam": "2298",
"fairsharing": "FAIRsharing.amcv1e",
"go": "HGNC",
"hl7": "2.16.840.1.113883.6.281",
"miriam": "hgnc",
"n2t": "hgnc",
"ncbi": "HGNC",
"prefixcommons": "hgnc",
"uniprot": "DB-0042",
"wikidata": "P354"
},
"name": "HUGO Gene Nomenclature Committee",
"pattern": "^\\d{1,5}$",
"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/gkaa980",
"pmc": "PMC7779007",
"pubmed": "33152070",
"title": "Genenames.org: the HGNC and VGNC resources in 2021.",
"year": 2021
},
{
"doi": "10.1093/nar/gky930",
"pmc": "PMC6324057",
"pubmed": "30304474",
"title": "Genenames.org: the HGNC and VGNC resources in 2019.",
"year": 2019
},
{
"doi": "10.1159/000131404",
"pmc": null,
"pubmed": "295268",
"title": "International system for human gene nomenclature (1979) ISGN (1979).",
"year": 1979
}
],
"uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1"
},
"hgnc.genefamily": {
"description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.",
"example": "2029",
"has_canonical": "hgnc.genegroup",
"homepage": "http://www.genenames.org",
"mappings": {
"biocontext": "HGNC.GENEFAMILY",
"miriam": "hgnc.genefamily",
"n2t": "hgnc.genefamily"
},
"name": "HGNC gene family",
"pattern": "^\\d+$",
"preferred_prefix": "hgnc.genefamily",
"synonyms": [
"GFAM",
"HGNC_GROUP",
"hgnc.family"
],
"uri_format": "https://www.genenames.org/cgi-bin/genefamilies/set/$1"
},
"hgnc.genegroup": {
"description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.",
"example": "141",
"homepage": "https://www.genenames.org",
"mappings": {
"miriam": "hgnc.genegroup"
},
"name": "HGNC Gene Group",
"pattern": "^\\d+$",
"preferred_prefix": "hgnc.genegroup",
"uri_format": "https://www.genenames.org/cgi-bin/genefamilies/set/$1"
},
"hgnc.symbol": {
"description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol.",
"example": "DAPK1",
"homepage": "https://www.genenames.org/",
"mappings": {
"biocontext": "HGNC.SYMBOL",
"miriam": "hgnc.symbol",
"n2t": "hgnc.symbol",
"wikidata": "P353"
},
"name": "HGNC gene symbol",
"pattern": "^[A-Za-z-0-9_]+(\\@)?$",
"preferred_prefix": "hgnc.symbol",
"providers": [
{
"code": "depmap",
"description": "DepMap summary of the given gene",
"homepage": "https://depmap.org",
"name": "DepMap Gene Summary",
"uri_format": "https://depmap.org/portal/gene/$1"
},
{
"code": "oncomx",
"description": "Mutation profiles for a gene",
"homepage": "https://oncomx.org",
"name": "OncoMX",
"uri_format": "https://oncomx.org/searchview/?gene=$1"
},
{
"code": "pathwaycommons",
"description": "Interactions between a given gene and other molecular entities",
"homepage": "https://www.pathwaycommons.org/",
"name": "Pathway Commons Gene Interations",
"uri_format": "https://apps.pathwaycommons.org/interactions?source=$1"
}
],
"uri_format": "https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1"
},
"hinv.locus": {
"description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view.",
"example": "HIX0004394",
"homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp",
"mappings": {
"biocontext": "HINV.LOCUS",
"miriam": "hinv.locus",
"n2t": "hinv.locus"
},
"name": "H-InvDb Locus",
"pattern": "^HIX\\d{7}(\\.\\d+)?$",
"preferred_prefix": "hinv.locus",
"uri_format": "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1"
},
"hinv.protein": {
"description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view.",
"example": "HIP000030660",
"homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp",
"mappings": {
"biocontext": "HINV.PROTEIN",
"miriam": "hinv.protein",
"n2t": "hinv.protein"
},
"name": "H-InvDb Protein",
"pattern": "^HIP\\d{9}(\\.\\d+)?$",
"preferred_prefix": "hinv.protein",
"uri_format": "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1"
},
"hinv.transcript": {
"description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view.",
"example": "HIT000195363",
"homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp",
"mappings": {
"biocontext": "HINV.TRANSCRIPT",
"miriam": "hinv.transcript",
"n2t": "hinv.transcript"
},
"name": "H-InvDb Transcript",
"pattern": "^HIT\\d{9}(\\.\\d+)?$",
"preferred_prefix": "hinv.transcript",
"uri_format": "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1"
},
"hipsci": {
"description": "Cell line databases/resources",
"example": "HPSI0114i-bezi_1",
"homepage": "http://www.hipsci.org",
"mappings": {
"cellosaurus": "HipSci"
},
"name": "Human Induced Pluripotent Stem Cells Initiative",
"preferred_prefix": "hipsci",
"uri_format": "http://www.hipsci.org/lines/#/lines/$1"
},
"hivreagentprogram": {
"description": "Cell line collections",
"example": "ARP-1513",
"homepage": "https://www.hivreagentprogram.org/",
"mappings": {
"cellosaurus": "HIVReagentProgram"
},
"name": "NIH HIV Reagent Program",
"preferred_prefix": "hivreagentprogram",
"uri_format": "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx"
},
"hl7.v2codesystem": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR.",
"example": "0778",
"homepage": "https://terminology.hl7.org/codesystems-v2.html",
"name": "HL7 V2 Code Systems",
"pattern": "^\\d+$",
"preferred_prefix": "hl7.v2codesystem",
"uri_format": "http://terminology.hl7.org/CodeSystem/v2-$1"
},
"hl7.v3codesystem": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR.",
"example": "AcknowledgementCondition",
"homepage": "https://terminology.hl7.org/codesystems-v2.html",
"name": "HL7 V2 Code Systems",
"pattern": "^\\w+$",
"preferred_prefix": "hl7.v3codesystem",
"uri_format": "https://terminology.hl7.org/CodeSystem-v3-$1"
},
"hmdb": {
"description": "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.",
"example": "HMDB00001",
"homepage": "http://www.hmdb.ca/",
"keywords": [
"biochemistry",
"bioinformatics",
"chemical",
"human",
"life science",
"metabolite",
"metabolomics",
"molecular biology",
"omics",
"phenomics",
"proteomics"
],
"mappings": {
"biocontext": "HMDB",
"cheminf": "000408",
"edam": "2622",
"fairsharing": "FAIRsharing.sye5js",
"miriam": "hmdb",
"n2t": "hmdb",
"prefixcommons": "hmdb",
"re3data": "r3d100011285",
"wikidata": "P2057"
},
"name": "Human Metabolome Database",
"pattern": "^HMDB\\d+$",
"preferred_prefix": "hmdb",
"publications": [
{
"doi": "10.1093/nar/gkab1062",
"pmc": "PMC8728138",
"pubmed": "34986597",
"title": "HMDB 5.0: the Human Metabolome Database for 2022.",
"year": 2022
},
{
"doi": "10.1093/nar/gkx1089",
"pmc": "PMC5753273",
"pubmed": "29140435",
"title": "HMDB 4.0: the human metabolome database for 2018.",
"year": 2018
},
{
"doi": "10.1093/nar/gks1065",
"pmc": "PMC3531200",
"pubmed": "23161693",
"title": "HMDB 3.0--The Human Metabolome Database in 2013.",
"year": 2012
},
{
"doi": "10.1093/nar/gkn810",
"pmc": "PMC1899095",
"pubmed": "17202168",
"title": "HMDB: a knowledgebase for the human metabolome",
"year": null
},
{
"doi": "10.1093/nar/gkl923",
"pmc": "PMC1899095",
"pubmed": "17202168",
"title": "HMDB: the Human Metabolome Database.",
"year": 2007
}
],
"synonyms": [
"HMDB"
],
"twitter": "WishartLab",
"uri_format": "http://www.hmdb.ca/metabolites/$1"
},
"hms.lincs.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/$1"
},
"hog": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc.",
"download_obo": "ftp://ftp.bgee.org/general/ontologies/HOG.obo",
"example": "0000255",
"homepage": "https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships",
"keywords": [
"ontology"
],
"name": "Homologous Organ Groups",
"pattern": "^\\d{7}$",
"preferred_prefix": "hog",
"uri_format": "https://biopragmatics.github.io/providers/hog/$1"
},
"hogenom": {
"description": "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.",
"example": "HBG284870",
"homepage": "http://pbil.univ-lyon1.fr/databases/hogenom/",
"keywords": [
"classification",
"life science",
"phylogenetics",
"phylogeny",
"sequence"
],
"mappings": {
"biocontext": "HOGENOM",
"fairsharing": "FAIRsharing.qe8tz8",
"miriam": "hogenom",
"n2t": "hogenom",
"prefixcommons": "hogenom",
"uniprot": "DB-0044"
},
"name": "Database of Complete Genome Homologous Genes Families",
"pattern": "^\\w+$",
"preferred_prefix": "hogenom",
"publications": [
{
"doi": "10.1186/1471-2105-10-s6-s3",
"pmc": "PMC2697650",
"pubmed": "19534752",
"title": "Databases of homologous gene families for comparative genomics.",
"year": 2009
},
{
"doi": "10.1101/gr.10.3.379",
"pmc": "PMC311423",
"pubmed": "10720578",
"title": "HOBACGEN: database system for comparative genomics in bacteria.",
"year": 2000
}
],
"uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1"
},
"hoip": {
"contact": {
"email": "yuki.yamagata@riken.jp",
"github": "yuki-yamagata",
"name": "Yuki Yamagata",
"orcid": "0000-0002-9673-1283"
},
"contributor": {
"email": "j.harry.caufield@gmail.com",
"github": "caufieldjh",
"name": "Harry Caufield",
"orcid": "0000-0001-5705-7831"
},
"description": "An ontology of processes triggered by homeostatic imbalance, with a focus on COVID-19 infectious processes.",
"download_owl": "https://github.com/yuki-yamagata/hoip/raw/master/hoip_0308.owl",
"example": "0040379",
"github_request_issue": 668,
"homepage": "https://knowledge.brc.riken.jp/bioresource/ontology/HOIP",
"keywords": [
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "HOIP",
"bioportal": "HOIP"
},
"name": "Homeostasis imbalance process ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "hoip",
"repository": "https://github.com/yuki-yamagata/hoip",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://purl.bioontology.org/ontology/HOIP/HOIP_$1"
},
"hom": {
"contact": {
"email": "bgee@sib.swiss",
"github": "fbastian",
"name": "Frederic Bastian",
"orcid": "0000-0002-9415-5104"
},
"description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.",
"download_owl": "http://purl.obolibrary.org/obo/hom.owl",
"example": "0000049",
"homepage": "https://github.com/BgeeDB/homology-ontology",
"keywords": [
"anatomy",
"life science",
"obo",
"ontology"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "HOM",
"biocontext": "HOM",
"bioportal": "HOM",
"fairsharing": "FAIRsharing.efv7gw",
"obofoundry": "hom",
"ols": "hom",
"ontobee": "HOM"
},
"name": "Homology Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "HOM",
"publications": [
{
"doi": "10.1016/j.tig.2009.12.012",
"pmc": null,
"pubmed": "20116127",
"title": "An ontology to clarify homology-related concepts.",
"year": 2010
}
],
"repository": "https://github.com/BgeeDB/homology-ontology",
"uri_format": "http://purl.obolibrary.org/obo/HOM_$1",
"version": "2015-01-07"
},
"homd.seq": {
"description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.",
"example": "SEQF1003",
"homepage": "http://www.homd.org/index.php",
"keywords": [
"genome",
"microbial"
],
"mappings": {
"biocontext": "HOMD.SEQ",
"miriam": "homd.seq",
"n2t": "homd.seq",
"prefixcommons": "homd.seq"
},
"name": "HOMD Sequence Metainformation",
"pattern": "^SEQF\\d+$",
"preferred_prefix": "homd.seq",
"publications": [
{
"doi": "10.1093/database/baq013",
"pmc": "PMC2911848",
"pubmed": "20624719",
"title": "The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.",
"year": 2010
}
],
"uri_format": "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1"
},
"homd.taxon": {
"description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.",
"example": "811",
"homepage": "http://www.homd.org/index.php",
"keywords": [
"microbial",
"taxonomy"
],
"mappings": {
"biocontext": "HOMD.TAXON",
"miriam": "homd.taxon",
"n2t": "homd.taxon",
"ncbi": "HOMD",
"prefixcommons": "homd.taxon"
},
"name": "Human Oral Microbiome Database",
"pattern": "^\\d+$",
"preferred_prefix": "homd.taxon",
"publications": [
{
"doi": "10.1093/database/baq013",
"pmc": "PMC2911848",
"pubmed": "20624719",
"title": "The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.",
"year": 2010
}
],
"uri_format": "http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1"
},
"homologene": {
"description": "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.",
"example": "1000",
"homepage": "https://www.ncbi.nlm.nih.gov/homologene/",
"keywords": [
"gene",
"genome",
"life science"
],
"mappings": {
"biocontext": "HOMOLOGENE",
"fairsharing": "FAIRsharing.mzc066",
"miriam": "homologene",
"n2t": "homologene",
"prefixcommons": "homologene",
"wikidata": "P593"
},
"name": "HomoloGene",
"pattern": "^\\d+$",
"preferred_prefix": "homologene",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "Bio2RDF",
"homepage": "http://homologene.bio2rdf.org/fct",
"name": "Bio2RDF",
"uri_format": "http://homologene.bio2rdf.org/describe/?url=http://bio2rdf.org/homologene:$1"
}
],
"publications": [
{
"doi": "10.1093/nar/gkq1172",
"pmc": "PMC3013733",
"pubmed": "21097890",
"title": "Database resources of the National Center for Biotechnology Information.",
"year": 2010
}
],
"uri_format": "https://www.ncbi.nlm.nih.gov/homologene/$1"
},
"horizon_discovery": {
"description": "Cell line collections",
"example": "HD+118-001",
"homepage": "https://horizondiscovery.com/",
"mappings": {
"cellosaurus": "Horizon_Discovery"
},
"name": "Horizon Discovery cell line collection",
"preferred_prefix": "horizon_discovery",
"uri_format": "https://horizondiscovery.com/en/search?searchterm=$1"
},
"hovergen": {
"contact": {
"email": "duret@biomserv.univ-lyon1.fr",
"github": null,
"name": "Laurent Duret",
"orcid": "0000-0003-2836-3463"
},
"description": "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.",
"example": "HBG004341",
"homepage": "https://pbil.univ-lyon1.fr/databases/hovergen.php",
"keywords": [
"dna",
"gene",
"life science",
"protein"
],
"mappings": {
"biocontext": "HOVERGEN",
"fairsharing": "FAIRsharing.dg1f0e",
"miriam": "hovergen",
"n2t": "hovergen",
"prefixcommons": "hovergen"
},
"name": "Homologous Vertebrate Genes Database",
"pattern": "^HBG\\d+$",
"preferred_prefix": "hovergen",
"publications": [
{
"doi": "10.1093/bioinformatics/bti325",
"pmc": null,
"pubmed": "15713731",
"title": "Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.",
"year": 2005
}
],
"uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN"
},
"hp": {
"appears_in": [
"chiro",
"maxo",
"scdo"
],
"banana": "HP",
"contact": {
"email": "dr.sebastian.koehler@gmail.com",
"github": "drseb",
"name": "Sebastian Koehler",
"orcid": "0000-0002-5316-1399"
},
"description": "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.",
"download_json": "http://purl.obolibrary.org/obo/hp.json",
"download_obo": "http://purl.obolibrary.org/obo/hp.obo",
"download_owl": "http://purl.obolibrary.org/obo/hp.owl",
"example": "0011140",
"homepage": "http://www.human-phenotype-ontology.org/",
"keywords": [
"biomedical science",
"genetics",
"obo",
"ontology",
"phenomics",
"preclinical studies"
],
"license": "hpo",
"mappings": {
"aberowl": "HP_O",
"bartoc": "1937",
"biocontext": "HPO",
"bioportal": "HP_O",
"fairsharing": "FAIRsharing.kbtt7f",
"hl7": "2.16.840.1.113883.6.339",
"miriam": "hp",
"n2t": "hp",
"obofoundry": "hp",
"ols": "hp",
"ontobee": "HP",
"wikidata": "P3841"
},
"name": "Human Phenotype Ontology",
"namespace_in_lui": true,
"pattern": "^\\d{7}$",
"preferred_prefix": "HP",
"publications": [
{
"doi": "10.1093/nar/gky1105",
"pmc": "PMC6324074",
"pubmed": "30476213",
"title": "Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.",
"year": 2019
},
{
"doi": "10.1093/nar/gkw1039",
"pmc": "PMC5210535",
"pubmed": "27899602",
"title": "The Human Phenotype Ontology in 2017.",
"year": 2016
},
{
"doi": "10.1016/j.ajhg.2015.05.020",
"pmc": "PMC4572507",
"pubmed": "26119816",
"title": "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.",
"year": 2015
},
{
"doi": "10.1093/nar/gkt1026",
"pmc": "PMC3965098",
"pubmed": "24217912",
"title": "The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.",
"year": 2013
},
{
"doi": "10.1111/j.1399-0004.2010.01436.x",
"pmc": null,
"pubmed": "20412080",
"title": "The human phenotype ontology.",
"year": 2010
},
{
"doi": "10.1016/j.ajhg.2008.09.017",
"pmc": "PMC2668030",
"pubmed": "18950739",
"title": "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.",
"year": 2008
}
],
"repository": "https://github.com/obophenotype/human-phenotype-ontology",
"synonyms": [
"hpo"
],
"twitter": "hp_ontology",
"uri_format": "https://hpo.jax.org/app/browse/term/HP:$1",
"version": "2022-06-11"
},
"hpa": {
"contact": {
"email": "mathias.uhlen@scilifelab.se",
"github": null,
"name": "Mathias Uhlen",
"orcid": "0000-0002-4858-8056"
},
"description": "The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers.",
"example": "ENSG00000026508",
"homepage": "http://www.proteinatlas.org/",
"keywords": [
"biomedical science",
"protein",
"proteomics",
"structure",
"systems biology",
"transcriptomics"
],
"mappings": {
"biocontext": "HPA",
"fairsharing": "FAIRsharing.j0t0pe",
"go": "HPA",
"miriam": "hpa",
"n2t": "hpa",
"prefixcommons": "hpa",
"re3data": "r3d100010931",
"uniprot": "DB-0046"
},
"name": "Human Protein Atlas tissue profile information",
"pattern": "^ENSG\\d{11}$",
"preferred_prefix": "hpa",
"publications": [
{
"doi": "10.1126/science.aan2507",
"pmc": null,
"pubmed": "28818916",
"title": "A pathology atlas of the human cancer transcriptome.",
"year": 2017
},
{
"doi": "eaal3321",
"pmc": null,
"pubmed": "28495876",
"title": "A subcellular map of the human proteome.",
"year": null
},
{
"doi": "10.1126/science.aal3321",
"pmc": null,
"pubmed": "28495876",
"title": "A subcellular map of the human proteome.",
"year": 2017
},
{
"doi": "10.15252/msb.20155865",
"pmc": "PMC4848759",
"pubmed": "27044256",
"title": "Transcriptomics resources of human tissues and organs.",
"year": 2016
},
{
"doi": "10.1126/science.1260419",
"pmc": null,
"pubmed": "25613900",
"title": "Proteomics. Tissue-based map of the human proteome.",
"year": 2015
},
{
"doi": "10.1038/nbt1210-1248",
"pmc": null,
"pubmed": "21139605",
"title": "Towards a knowledge-based Human Protein Atlas.",
"year": 2010
},
{
"doi": "10.1002/path.2440",
"pmc": null,
"pubmed": "18853439",
"title": "The Human Protein Atlas--a tool for pathology.",
"year": 2008
},
{
"doi": "10.1074/mcp.r800013-mcp200",
"pmc": null,
"pubmed": "18669619",
"title": "A genecentric Human Protein Atlas for expression profiles based on antibodies.",
"year": 2008
},
{
"doi": "10.1074/mcp.m500279-mcp200",
"pmc": null,
"pubmed": "16127175",
"title": "A human protein atlas for normal and cancer tissues based on antibody proteomics.",
"year": 2005
}
],
"twitter": "ProteinAtlas",
"uri_format": "http://www.proteinatlas.org/$1"
},
"hpath": {
"description": "An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species.",
"download_owl": "https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo",
"example": "2000191",
"homepage": "https://github.com/Novartis/hpath",
"keywords": [
"ontology"
],
"mappings": {
"fairsharing": "FAIRsharing.kj336a",
"ols": "hpath"
},
"name": "Histopathology Ontology",
"pattern": "^\\d+$",
"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=$1"
},
"hpm.protein": {
"description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.",
"example": "1968",
"homepage": "http://www.humanproteomemap.org/index.php",
"mappings": {
"biocontext": "HPM.PROTEIN",
"miriam": "hpm.protein",
"n2t": "hpm.protein",
"ncbi": "HPM"
},
"name": "Human Proteome Map",
"pattern": "^\\d+$",
"preferred_prefix": "hpm.protein",
"uri_format": "http://www.humanproteomemap.org/protein.php?hpm_id=$1"
},
"hprd": {
"contact": {
"email": "pandey@jhmi.edu",
"github": null,
"name": "Akhilesh Pandey",
"orcid": "0000-0001-9943-6127"
},
"description": "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.",
"example": "00001",
"homepage": "http://www.hprd.org/",
"keywords": [
"protein",
"structure"
],
"mappings": {
"biocontext": "HPRD",
"fairsharing": "FAIRsharing.y2qws7",
"miriam": "hprd",
"n2t": "hprd",
"prefixcommons": "hprd",
"re3data": "r3d100010978"
},
"name": "Human Protein Reference Database",
"pattern": "^\\d+$",
"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/$1"
},
"hpscreg": {
"contact": {
"email": "stefanie.seltmann@ibmt.fraunhofer.de",
"github": null,
"name": "Stefanie Seltmann",
"orcid": "0000-0002-8411-3226"
},
"description": "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines).",
"example": "BCRTi001-A",
"homepage": "https://hpscreg.eu/",
"keywords": [
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"life science"
],
"mappings": {
"cellosaurus": "hPSCreg",
"fairsharing": "FAIRsharing.7C0aVE",
"miriam": "hpscreg",
"n2t": "hpscreg",
"re3data": "r3d100012863"
},
"name": "Human Pluripotent Stem Cell Registry",
"pattern": "^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$",
"preferred_prefix": "hpscreg",
"publications": [
{
"doi": "s1873-5061(20)30188-4",
"pmc": null,
"pubmed": "32707486",
"title": "Access to stem cell data and registration of pluripotent cell lines: The Human Pluripotent Stem Cell Registry (hPSCreg).",
"year": null
},
{
"doi": "10.1016/j.scr.2020.101887",
"pmc": null,
"pubmed": "32707486",
"title": "Access to stem cell data and registration of pluripotent cell lines: The Human Pluripotent Stem Cell Registry (hPSCreg).",
"year": 2020
},
{
"doi": "s2213-6711(20)30235-6",
"pmc": "PMC7419703",
"pubmed": "32679065",
"title": "A Manually Curated Database on Clinical Studies Involving Cell Products Derived from Human Pluripotent Stem Cells.",
"year": null
},
{
"doi": "10.1016/j.stemcr.2020.06.014",
"pmc": "PMC7419703",
"pubmed": "32679065",
"title": "A Manually Curated Database on Clinical Studies Involving Cell Products Derived from Human Pluripotent Stem Cells.",
"year": 2020
},
{
"doi": "s1873-5061(19)30169-2",
"pmc": null,
"pubmed": "31450190",
"title": "A pathway for attesting ethical provenance of cell lines: Lessons from the European human pluripotent stem cell registry (hPSC(reg)).",
"year": null
},
{
"doi": "10.1016/j.scr.2019.101539",
"pmc": null,
"pubmed": "31450190",
"title": "A pathway for attesting ethical provenance of cell lines: Lessons from the European human pluripotent stem cell registry (hPSC",
"year": 2019
},
{
"doi": "s2213-6711(17)30531-3",
"pmc": "PMC5768986",
"pubmed": "29320760",
"title": "A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells.",
"year": null
},
{
"doi": "10.1016/j.stemcr.2017.12.002",
"pmc": "PMC5768986",
"pubmed": "29320760",
"title": "A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells.",
"year": 2018
},
{
"doi": "10.1093/nar/gkv963",
"pmc": "PMC4702942",
"pubmed": "26400179",
"title": "hPSCreg--the human pluripotent stem cell registry.",
"year": 2015
}
],
"uri_format": "https://hpscreg.eu/cell-line/$1"
},
"hsapdv": {
"appears_in": [
"scdo"
],
"contact": {
"email": "frederic.bastian@unil.ch",
"github": "fbastian",
"name": "Frédéric Bastian",
"orcid": "0000-0002-9415-5104"
},
"description": "Life cycle stages for Human",
"download_obo": "http://purl.obolibrary.org/obo/hsapdv.obo",
"download_owl": "http://purl.obolibrary.org/obo/hsapdv.owl",
"example": "0000194",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "HSAPDV",
"biocontext": "HSAPDV",
"biolink": "HsapDv",
"bioportal": "HSAPDV",
"fairsharing": "FAIRsharing.c6vhm3",
"obofoundry": "hsapdv",
"ols": "hsapdv",
"ontobee": "HsapDv"
},
"name": "Human Developmental Stages",
"pattern": "^\\d{7}$",
"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/$1"
},
"hso": {
"contact": {
"email": "fernanda.dorea@sva.se",
"github": "nandadorea",
"name": "Fernanda Dorea",
"orcid": "0000-0001-8638-8525"
},
"depends_on": [
"bfo",
"ncbitaxon",
"obi",
"ro",
"uberon"
],
"description": "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance.",
"download_owl": "http://purl.obolibrary.org/obo/hso.owl",
"example": "0000062",
"homepage": "https://w3id.org/hso",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "HSO",
"bioportal": "HSO",
"obofoundry": "hso",
"ols": "hso",
"ontobee": "HSO"
},
"name": "Health Surveillance Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "HSO",
"repository": "https://github.com/SVA-SE/HSO",
"uri_format": "http://purl.obolibrary.org/obo/HSO_$1",
"version": "2021-12-13"
},
"hssp": {
"description": "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.",
"example": "102l",
"homepage": "http://swift.cmbi.kun.nl/swift/hssp/",
"keywords": [
"clustering",
"protein",
"sequence"
],
"mappings": {
"biocontext": "HSSP",
"miriam": "hssp",
"n2t": "hssp",
"ncbi": "HSSP",
"prefixcommons": "hssp"
},
"name": "Database of homology-derived secondary structure of proteins",
"pattern": "^\\w{4}$",
"preferred_prefix": "hssp",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "HSSP at CMBI",
"homepage": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/",
"name": "HSSP at CMBI",
"uri_format": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$1.hssp.bz2"
}
],
"publications": [
{
"doi": "10.1093/nar/24.1.201",
"pmc": "PMC145595",
"pubmed": "8594579",
"title": "The HSSP database of protein structure-sequence alignments.",
"year": 1996
},
{
"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/$1.hssp.bz2"
},
"htn": {
"contact": {
"email": "aellenhicks@gmail.com",
"github": "aellenhicks",
"name": "Amanda Hicks",
"orcid": "0000-0002-1795-5570"
},
"description": "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines",
"download_owl": "http://purl.obolibrary.org/obo/htn.owl",
"example": "00000014",
"homepage": "https://github.com/aellenhicks/htn_owl",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "HTN",
"bioportal": "HTN",
"obofoundry": "htn",
"ols": "htn",
"ontobee": "HTN"
},
"name": "Hypertension Ontology",
"pattern": "^\\d{8}$",
"preferred_prefix": "HTN",
"repository": "https://github.com/aellenhicks/htn_owl",
"uri_format": "http://purl.obolibrary.org/obo/HTN_$1",
"version": "2019-06-10"
},
"huge": {
"description": "The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.",
"example": "KIAA0001",
"homepage": "http://www.kazusa.or.jp/huge/",
"keywords": [
"computational biology",
"dna",
"life science",
"protein",
"structure"
],
"mappings": {
"biocontext": "HUGE",
"fairsharing": "FAIRsharing.zx2ztd",
"miriam": "huge",
"n2t": "huge",
"prefixcommons": "huge",
"uniprot": "DB-0049"
},
"name": "Human Unidentified Gene-Encoded",
"pattern": "^KIAA\\d{4}$",
"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/$1"
},
"iao": {
"appears_in": [
"agro",
"clyh",
"duo",
"ecocore",
"ecto",
"fovt",
"labo",
"maxo",
"pco",
"psdo",
"xpo"
],
"contact": {
"email": "jiezheng@pennmedicine.upenn.edu",
"github": "zhengj2007",
"name": "Jie Zheng",
"orcid": "0000-0002-2999-0103"
},
"description": "An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch.",
"download_obo": "http://purl.obolibrary.org/obo/iao.obo",
"download_owl": "http://purl.obolibrary.org/obo/iao.owl",
"example": "0000030",
"homepage": "https://github.com/information-artifact-ontology/IAO/",
"keywords": [
"biomedical science",
"data management",
"knowledge and information systems",
"obo",
"ontology",
"subject agnostic"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "IAO",
"biocontext": "IAO",
"bioportal": "IAO",
"fairsharing": "FAIRsharing.gq1xtx",
"go": "IAO",
"miriam": "iao",
"n2t": "iao",
"obofoundry": "iao",
"ols": "iao",
"ontobee": "IAO"
},
"name": "Information Artifact Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "IAO",
"providers": [
{
"code": "legacy",
"description": "A URI from the semanticweb.og",
"homepage": "http://www.semanticweb.org",
"name": "Legacy URI",
"uri_format": "http://www.semanticweb.org/ontologies/2011/9/Ontology1317751904226.owl#IAO_$1"
}
],
"publications": [
{
"doi": "10.3233/978-1-61499-101-4-68",
"pmc": null,
"pubmed": "22874154",
"title": "An information artifact ontology perspective on data collections and associated representational artifacts.",
"year": 2012
}
],
"repository": "https://github.com/information-artifact-ontology/IAO",
"uri_format": "http://purl.obolibrary.org/obo/IAO_$1",
"version": "2020-12-09"
},
"icd10": {
"contact": {
"email": "info@who.int",
"github": null,
"name": "World Health Organization",
"orcid": null
},
"contributor_extras": [
{
"email": null,
"github": "joeflack4",
"name": "Joe Flack",
"orcid": "0000-0002-2906-7319"
},
{
"email": null,
"github": "matentzn",
"name": "Nico Matentzoglu",
"orcid": "0000-0002-7356-1779"
},
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"description": "The 10th revision of the International Classification of Diseases (ICD) issued by the World Health Organization (WHO). ICD is formally named 'The International Statistical Classification of Diseases and Related Health Problems'. It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases.\n\nNote that the WHO version of ICD-10 is distinct from the ICD-10-CM (Clinical Modification) issued by the U.S. National Center for Health Statistics for use in the United States.",
"example": "C34",
"example_decoys": [
"G00X",
"C34.90",
"C4A.8",
"C91.Z",
"C91.Z0"
],
"example_extras": [
"V20",
"G00",
"A01.1",
"XVIII",
"R25-R29",
"R25",
"R25.3"
],
"homepage": "https://icd.who.int/browse10",
"keywords": [
"biomedical science",
"classification",
"disease",
"epidemiology",
"global health",
"health science",
"ontology",
"taxonomy"
],
"mappings": {
"aberowl": "ICD10",
"bartoc": "447",
"biocontext": "ICD",
"biolink": "ICD10",
"bioportal": "ICD10",
"edam": "2611",
"fairsharing": "FAIRsharing.nj16g",
"hl7": "2.16.840.1.113883.6.3",
"miriam": "icd",
"n2t": "icd",
"prefixcommons": "icd",
"wikidata": "P494"
},
"name": "International Classification of Diseases, 10th Revision",
"pattern": "^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\\.[0-9]))?))$",
"preferred_prefix": "icd10",
"providers": [
{
"code": "icd10_2008",
"description": "The 2008 revision of ICD-10",
"homepage": "https://icd.who.int/browse10/2008/en#",
"name": "ICD-10 Version 2008",
"uri_format": "https://icd.who.int/browse10/2008/en#/$1"
},
{
"code": "icd10_2010",
"description": "The 2010 revision of ICD-10",
"homepage": "https://icd.who.int/browse10/2010/en#",
"name": "ICD-10 Version 2010",
"uri_format": "https://icd.who.int/browse10/2010/en#/$1"
},
{
"code": "icd10_2014",
"description": "The 2014 revision of ICD-10",
"homepage": "https://icd.who.int/browse10/2014/en#",
"name": "ICD-10 Version 2014",
"uri_format": "https://icd.who.int/browse10/2014/en#/$1"
},
{
"code": "icd10_2015",
"description": "The 2015 revision of ICD-10",
"homepage": "https://icd.who.int/browse10/2015/en#",
"name": "ICD-10 Version 2015",
"uri_format": "https://icd.who.int/browse10/2015/en#/$1"
},
{
"code": "icd10_2016",
"description": "The 2016 revision of ICD-10",
"homepage": "https://icd.who.int/browse10/2016/en#",
"name": "ICD-10 Version 2016",
"uri_format": "https://icd.who.int/browse10/2016/en#/$1"
},
{
"code": "icdcodelookup",
"description": "This site is dedicated exclusively to helping you look up ICD-10 codes, quickly access the codes you use most, and become more comfortable with the new code set in general.",
"homepage": "https://icdcodelookup.com/icd-10/codes",
"name": "ICD Code Lookup",
"uri_format": "https://icdcodelookup.com/icd-10/codes/$1"
}
],
"synonyms": [
"ICD",
"ICD-10",
"ICD10",
"ICD10WHO"
],
"uri_format": "https://icd.who.int/browse10/2019/en#/$1"
},
"icd10cm": {
"contact": {
"email": "pbrooks@hcfa.gov",
"github": null,
"name": "Patricia Brooks",
"orcid": null
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States issued by the National Center for Health Statistics (NCHS) and Centers for Medicare & Medicaid Services (CMS).",
"example": "F45.21",
"example_decoys": [
"C000",
"c00",
"C00-D499",
"C00-99",
"C34.90000"
],
"example_extras": [
"C00-D49",
"U49",
"C34",
"C34.90",
"C4A.8",
"C91.Z",
"C91.Z0",
"T37.0X1A"
],
"homepage": "https://www.icd10data.com/ICD10CM",
"keywords": [
"biomedical science",
"health science",
"medicine",
"ontology"
],
"mappings": {
"aberowl": "ICD10CM",
"bioportal": "ICD10CM",
"fairsharing": "FAIRsharing.hpvbxb",
"hl7": "2.16.840.1.113883.6.90",
"wikidata": "P4229"
},
"name": "International Classification of Diseases, 10th Revision, Clinical Modification",
"pattern": "^([A-Z][0-9][0-9AB]((-[A-Z][0-9][0-9AB])|(\\.[0-9A-KXZ]([0-9A-EXYZ]([0-9A-HX][0-59A-HJKMNP-S]?)?)?)?))$",
"preferred_prefix": "icd10cm",
"synonyms": [
"ICD10CM"
],
"uri_format": "https://icd.codes/icd10cm/$1"
},
"icd10pcs": {
"contact": {
"email": "patricia.brooks2@cms.hhs.gov",
"github": null,
"name": "Pat Brooks",
"orcid": null
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis.\n\nICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records.",
"example": "01N50ZZ",
"homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10PCS",
"keywords": [
"biomedical science",
"epidemiology",
"health science",
"ontology"
],
"mappings": {
"aberowl": "ICD10PCS",
"bioportal": "ICD10PCS",
"fairsharing": "FAIRsharing.85k1jm",
"hl7": "2.16.840.1.113883.6.4",
"wikidata": "P1690"
},
"name": "International Classification of Diseases, 10th Revision, Procedure Coding System",
"preferred_prefix": "icd10pcs",
"uri_format": "https://www.findacode.com/code.php?set=ICD10PCS&c=$1"
},
"icd11": {
"comment": "The codes, such as RA00.0, need their own namespace.",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Diagnostic tool for epidemiology, health management and clinical purposes, maintained by the World Health Organization (WHO). It provides a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease.",
"example": "402558626",
"homepage": "https://icd.who.int/",
"keywords": [
"biomedical science",
"epidemiology",
"global health",
"health science"
],
"mappings": {
"fairsharing": "FAIRsharing.97805c",
"hl7": "2.16.840.1.113883.6.347",
"wikidata": "P7807"
},
"name": "International Classification of Diseases, 11th Revision",
"pattern": "^[1-9]\\d*$",
"preferred_prefix": "icd11",
"synonyms": [
"ICD-11"
],
"uri_format": "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1"
},
"icd9": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics.",
"example": "277.9",
"homepage": "https://www.cdc.gov/nchs/icd/icd9.htm",
"mappings": {
"biolink": "ICD9",
"hl7": "2.16.840.1.113883.6.42",
"wikidata": "P493"
},
"name": "International Classification of Diseases, 9th Revision",
"pattern": "^(\\d\\d\\d|V\\d\\d|E[8-9]\\d\\d)(\\.\\d{1,2})?$",
"preferred_prefix": "icd9",
"synonyms": [
"ICD9",
"ICD9_2005",
"MTHICD9_2006"
],
"uri_format": "http://www.icd9data.com/getICD9Code.ashx?icd9=$1"
},
"icd9cm": {
"contact": {
"email": "pbrooks@hcfa.gov",
"github": null,
"name": "Patricia Brooks",
"orcid": null
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States.",
"example": "784",
"homepage": "https://www.cdc.gov/nchs/icd/icd9cm.htm",
"keywords": [
"biomedical science",
"epidemiology",
"health science",
"medicine",
"ontology",
"preclinical studies"
],
"mappings": {
"aberowl": "ICD9CM",
"bioportal": "ICD9CM",
"fairsharing": "FAIRsharing.10zsxb",
"hl7": "2.16.840.1.113883.6.2",
"wikidata": "P1692"
},
"name": "International Classification of Diseases, 9th Revision, Clinical Modification",
"pattern": "^([\\dA-Z]\\d{2}(\\.\\d{1,3}|))|(\\d{2}(\\.\\d{1,2}|))$",
"preferred_prefix": "icd9cm",
"synonyms": [
"IC9CM",
"ICD9CM",
"ICD9CM_2005",
"ICD9CM_2006",
"ICDCM_2005"
],
"uri_format": "http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1"
},
"icdc": {
"contact": {
"email": "annika.jahnke-bornemann@uni-hamburg.de",
"github": null,
"name": "Annika Jahnke-Bornemann",
"orcid": "0000-0001-7815-151X"
},
"description": "The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer.",
"example": "000009",
"homepage": "https://caninecommons.cancer.gov/#/",
"keywords": [
"atmospheric science",
"earth science",
"meteorology",
"oceanography",
"remote sensing",
"social science"
],
"mappings": {
"fairsharing": "FAIRsharing.d95034",
"miriam": "icdc"
},
"name": "Integrated Canine Data Commons",
"pattern": "^\\d{6}$",
"preferred_prefix": "icdc",
"twitter": "ICDC_Hamburg",
"uri_format": "https://caninecommons.cancer.gov/#/study/$1"
},
"icdo": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases",
"download_owl": "http://aber-owl.net/media/ontologies/ICDO/12/icdo.owl",
"example": "9861/3",
"homepage": "https://www.who.int/classifications/icd/adaptations/oncology/en/",
"keywords": [
"ontology"
],
"mappings": {
"aberowl": "ICDO",
"bartoc": "445",
"hl7": "2.16.840.1.113883.6.43",
"prefixcommons": "icdo",
"wikidata": "P563"
},
"name": "International Classification of Diseases for Oncology",
"pattern": "^[8-9]\\d{3}(/[0-3])?$",
"preferred_prefix": "icdo",
"synonyms": [
"ICD-O",
"ICDO"
],
"uri_format": "http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1"
},
"iceberg.cime": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements.",
"example": "6",
"homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_CIME.php?type=alpha&alpha=100",
"keywords": [
"biology",
"genomics"
],
"name": "ICEberg cis-integrative and mobilizable element",
"part_of": "iceberg",
"pattern": "^\\d+$",
"preferred_prefix": "iceberg.cime",
"publications": [
{
"doi": "10.1093/nar/gky1123",
"pmc": "PMC6323972",
"pubmed": "30407568",
"title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements.",
"year": 2019
},
{
"doi": "10.1093/nar/gkr846",
"pmc": "PMC3244999",
"pubmed": "22009673",
"title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria.",
"year": 2011
}
],
"uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php?cime_id=$1_CIME"
},
"iceberg.element": {
"description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements.",
"example": "100",
"homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=alpha&alpha=100",
"mappings": {
"biocontext": "ICEBERG.ELEMENT",
"miriam": "iceberg.element",
"n2t": "iceberg.element"
},
"name": "ICEberg integrative and conjugative element",
"part_of": "iceberg",
"pattern": "^\\d+$",
"preferred_prefix": "iceberg.element",
"publications": [
{
"doi": "10.1093/nar/gky1123",
"pmc": "PMC6323972",
"pubmed": "30407568",
"title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements.",
"year": 2019
},
{
"doi": "10.1093/nar/gkr846",
"pmc": "PMC3244999",
"pubmed": "22009673",
"title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria.",
"year": 2011
}
],
"synonyms": [
"iceberg.ice"
],
"uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=$1"
},
"iceberg.family": {
"description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families.",
"example": "1",
"homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_fam.php",
"mappings": {
"biocontext": "ICEBERG.FAMILY",
"miriam": "iceberg.family",
"n2t": "iceberg.family"
},
"name": "ICEberg family",
"part_of": "iceberg",
"pattern": "^\\d+$",
"preferred_prefix": "iceberg.family",
"publications": [
{
"doi": "10.1093/nar/gky1123",
"pmc": "PMC6323972",
"pubmed": "30407568",
"title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements.",
"year": 2019
},
{
"doi": "10.1093/nar/gkr846",
"pmc": "PMC3244999",
"pubmed": "22009673",
"title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria.",
"year": 2011
}
],
"uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id=$1"
},
"iceberg.ime": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements.",
"example": "1",
"homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_IME.php?type=alpha&alpha=100",
"keywords": [
"biology",
"genomics"
],
"name": "ICEberg integrative and mobilizable element",
"part_of": "iceberg",
"pattern": "^\\d+$",
"preferred_prefix": "iceberg.ime",
"publications": [
{
"doi": "10.1093/nar/gky1123",
"pmc": "PMC6323972",
"pubmed": "30407568",
"title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements.",
"year": 2019
},
{
"doi": "10.1093/nar/gkr846",
"pmc": "PMC3244999",
"pubmed": "22009673",
"title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria.",
"year": 2011
}
],
"uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.php?ime_id=$1_IME"
},
"iceo": {
"contact": {
"email": "liumeng94@sjtu.edu.cn",
"github": "Lemon-Liu",
"name": "Meng LIU",
"orcid": "0000-0003-3781-6962"
},
"description": "A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning.",
"download_owl": "http://purl.obolibrary.org/obo/iceo.owl",
"example": "0000712_1",
"example_extras": [
"0000712"
],
"homepage": "https://github.com/ontoice/ICEO",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "ICEO",
"bioportal": "ICEO",
"obofoundry": "iceo",
"ols": "iceo",
"ontobee": "ICEO"
},
"name": "Integrative and Conjugative Element Ontology",
"pattern": "^\\d{7}(_\\d)?$",
"preferred_prefix": "ICEO",
"publications": [
{
"doi": "10.1038/s41597-021-01112-5",
"pmc": "PMC8776819",
"pubmed": "35058462",
"title": "ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements.",
"year": 2022
}
],
"repository": "https://github.com/ontoice/ICEO",
"uri_format": "http://purl.obolibrary.org/obo/ICEO_$1",
"version": "2.1"
},
"icepo": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. ",
"download_obo": "https://download.nextprot.org/pub/current_release/controlled_vocabularies/icepo.obo",
"example": "0000002",
"homepage": "https://download.nextprot.org/pub/current_release/controlled_vocabularies/",
"keywords": [
"ontology"
],
"name": "Ion Channel Electrophysiology Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "icepo",
"publications": [
{
"doi": null,
"pmc": "PMC4823818",
"pubmed": null,
"title": "ICEPO: the ion channel electrophysiology ontology",
"year": null
}
],
"twitter": "neXtProt_news",
"uri_format": "https://biopragmatics.github.io/providers/icepo/$1"
},
"icf": {
"comment": "This might be possible to roll directly into ICD11",
"contact": {
"email": "info@who.int",
"github": null,
"name": "The World Health Organization",
"orcid": null
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. As the functioning and disability of an individual occurs in a context, ICF also includes a list of environmental factors. ICF is the WHO framework for measuring health and disability at both individual and population levels.",
"download_owl": "http://aber-owl.net/media/ontologies/ICF/3/icf.owl",
"example": "326705068",
"homepage": "https://icd.who.int/dev11/l-icf/en",
"keywords": [
"biomedical science",
"health science",
"medicine",
"ontology",
"primary health care"
],
"mappings": {
"aberowl": "ICF",
"bioportal": "ICF",
"fairsharing": "FAIRsharing.7rngj0",
"hl7": "2.16.840.1.113883.6.254"
},
"name": "International Classification of Functioning, Disability and Health",
"pattern": "^\\d+$",
"preferred_prefix": "icf",
"uri_format": "http://id.who.int/icd/entity/$1"
},
"iclc": {
"description": "Cell line collections",
"example": "ATL98012",
"homepage": "http://www.iclc.it",
"mappings": {
"cellosaurus": "ICLC"
},
"name": "Interlab Cell Line Collection",
"preferred_prefix": "iclc",
"uri_format": "http://www.iclc.it/details/det_list.php?line_id=$1"
},
"ico": {
"appears_in": [
"scdo"
],
"contact": {
"email": "yongqunh@med.umich.edu",
"github": "yongqunh",
"name": "Yongqun Oliver He",
"orcid": "0000-0001-9189-9661"
},
"description": "The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field.",
"download_owl": "http://purl.obolibrary.org/obo/ico.owl",
"example": "0000066",
"homepage": "https://github.com/ICO-ontology/ICO",
"keywords": [
"biomedical science",
"clinical studies",
"health science",
"medicine",
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "ICO",
"biocontext": "ICO",
"bioportal": "ICO",
"fairsharing": "FAIRsharing.b9znd5",
"obofoundry": "ico",
"ols": "ico",
"ontobee": "ICO"
},
"name": "Informed Consent Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "ICO",
"repository": "https://github.com/ICO-ontology/ICO",
"uri_format": "http://purl.obolibrary.org/obo/ICO_$1",
"version": "1.0.187"
},
"ideal": {
"description": "IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments.",
"example": "IID00001",
"homepage": "https://www.ideal-db.org",
"keywords": [
"biology"
],
"mappings": {
"biocontext": "IDEAL",
"fairsharing": "FAIRsharing.h3y42f",
"miriam": "ideal",
"n2t": "ideal",
"uniprot": "DB-0251"
},
"name": "Intrinsically Disordered proteins with Extensive Annotations and Literature",
"pattern": "^IID\\d+$",
"preferred_prefix": "ideal",
"publications": [
{
"doi": "10.1093/nar/gkt1010",
"pmc": "PMC3965115",
"pubmed": "24178034",
"title": "IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners.",
"year": 2013
}
],
"uri_format": "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1"
},
"ido": {
"appears_in": [
"scdo"
],
"contact": {
"email": "Lindsay.Cowell@utsouthwestern.edu",
"github": "lgcowell",
"name": "Lindsay Cowell",
"orcid": "0000-0003-1617-8244"
},
"description": "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases.",
"download_owl": "http://purl.obolibrary.org/obo/ido.owl",
"example": "0000504",
"homepage": "http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology",
"keywords": [
"biomedical science",
"molecular infection biology",
"obo",
"ontology",
"preclinical studies"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "IDO",
"biocontext": "IDO",
"bioportal": "IDO",
"fairsharing": "FAIRsharing.aae3v6",
"miriam": "ido",
"n2t": "ido",
"obofoundry": "ido",
"ols": "ido",
"ontobee": "IDO"
},
"name": "Infectious Disease Ontology",
"pattern": "^[0-9]+$",
"preferred_prefix": "IDO",
"providers": [
{
"code": "obo.1",
"description": "This incorrect encoding was found inside IDO-COVID-19",
"homepage": "http://purl.obolibrary.org",
"name": "Nonstandard OBO PURL",
"uri_format": "http://purl.obolibrary.org/obo/ido.owl/IDO_$1"
}
],
"publications": [
{
"doi": "10.1186/s13326-021-00245-1",
"pmc": "PMC8286442",
"pubmed": "34275487",
"title": "The Infectious Disease Ontology in the age of COVID-19.",
"year": 2021
}
],
"repository": "https://github.com/infectious-disease-ontology/infectious-disease-ontology",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1",
"version": "2017-11-03"
},
"idocovid19": {
"contact": {
"email": "johnbeverley2021@u.northwestern.edu",
"github": "johnbeve",
"name": "John Beverly",
"orcid": "0000-0002-1118-1738"
},
"description": "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease.",
"download_owl": "https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19",
"example": "0001191",
"homepage": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19",
"keywords": [
"ontology"
],
"mappings": {
"aberowl": "IDO-COVID-19",
"bioportal": "IDO-COVID-19",
"ols": "idocovid19"
},
"name": "The COVID-19 Infectious Disease Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "idocovid19",
"providers": [
{
"code": "obo1",
"description": "This variation uses incorrect usage of dashes instead of underscores",
"homepage": "http://purl.obolibrary.org",
"name": "Incorrect OBO PURL variation 1",
"uri_format": "http://purl.obolibrary.org/obo/IDO-COVID-19_$1"
}
],
"repository": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19",
"uri_format": "http://purl.obolibrary.org/obo/COVIDO_$1",
"version": "2020-07-21"
},
"idoden": {
"contact": {
"email": "elvira@imbb.forth.gr",
"github": null,
"name": "Elvira Mitraka",
"orcid": null
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology for dengue fever.",
"download_owl": "http://aber-owl.net/media/ontologies/IDODEN/6/idoden.owl",
"example": "0003463",
"homepage": "https://bioportal.bioontology.org/ontologies/IDODEN",
"keywords": [
"ontology"
],
"mappings": {
"aberowl": "IDODEN",
"bioportal": "IDODEN",
"fairsharing": "FAIRsharing.askzq4"
},
"name": "Dengue Fever Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "idoden",
"references": [
"https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003479"
],
"uri_format": "http://purl.bioontology.org/ontology/IDODEN_$1"
},
"idomal": {
"appears_in": [
"scdo"
],
"contact": {
"email": "topalis@imbb.forth.gr",
"github": null,
"name": "Pantelis Topalis",
"orcid": "0000-0002-1635-4810"
},
"deprecated": true,
"description": "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.",
"download_obo": "http://purl.obolibrary.org/obo/idomal.obo",
"download_owl": "http://purl.obolibrary.org/obo/idomal.owl",
"example": "0002350",
"example_extras": [
"50000015"
],
"homepage": "https://www.vectorbase.org/ontology-browser",
"keywords": [
"biomedical science",
"life science",
"molecular infection biology",
"obo",
"ontology"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "IDOMAL",
"biocontext": "IDOMAL",
"bioportal": "IDOMAL",
"fairsharing": "FAIRsharing.2q8c28",
"obofoundry": "idomal",
"ols": "idomal",
"ontobee": "IDOMAL"
},
"name": "Malaria Ontology",
"pattern": "^(5?)\\d{7}$",
"preferred_prefix": "IDOMAL",
"publications": [
{
"doi": "10.1186/2041-1480-4-16",
"pmc": "PMC3848731",
"pubmed": "24034841",
"title": "IDOMAL: the malaria ontology revisited.",
"year": 2013
},
{
"doi": "10.1186/1475-2875-9-230",
"pmc": "PMC2925367",
"pubmed": "20698959",
"title": "IDOMAL: an ontology for malaria.",
"year": 2010
}
],
"repository": "https://github.com/VEuPathDB-ontology/IDOMAL",
"twitter": "VectorBase",
"uri_format": "http://purl.obolibrary.org/obo/IDOMAL_$1",
"version": "2015-03-16"
},
"idoo": {
"description": "Identifiers.org Ontology",
"example": "DataCollection",
"homepage": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology",
"mappings": {
"miriam": "idoo",
"n2t": "idoo"
},
"name": "Identifiers.org Ontology",
"pattern": "^[0-9a-zA-Z]+$",
"preferred_prefix": "idoo",
"uri_format": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1"
},
"idot": {
"description": "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.",
"example": "identifierPattern",
"homepage": "http://biomodels.net/vocab/idot.rdf",
"mappings": {
"biocontext": "idot",
"miriam": "idot",
"n2t": "idot"
},
"name": "Identifiers.org Terms",
"pattern": "^[A-Za-z]+$",
"preferred_prefix": "idot",
"uri_format": "https://biomodels.net/vocab/idot.rdf#$1"
},
"idpo": {
"contact": {
"email": "f.quaglia@ibiom.cnr.it",
"github": "federicaquaglia",
"name": "Federica Quaglia",
"orcid": "0000-0002-0341-4888"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR.",
"example": "00056",
"homepage": "https://www.disprot.org/ontology",
"keywords": [
"protein structure",
"proteins",
"structural biochemistry",
"structural bioinformatics"
],
"name": "Intrinsically Disordered Proteins Ontology",
"pattern": "^\\d{5}$",
"preferred_prefix": "idpo",
"uri_format": "https://www.disprot.org/idpo/IDPO:$1"
},
"idr": {
"contact": {
"email": "j.a.moore@dundee.ac.uk",
"github": null,
"name": "Josh Moore",
"orcid": "0000-0003-4028-811X"
},
"description": "Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image\" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools.",
"example": "0001",
"homepage": "https://idr.openmicroscopy.org",
"keywords": [
"biomedical science",
"botany",
"life science"
],
"mappings": {
"fairsharing": "FAIRsharing.6wf1zw",
"miriam": "idr",
"re3data": "r3d100012435"
},
"name": "Image Data Resource",
"pattern": "^[0-9]{4}$",
"preferred_prefix": "idr",
"publications": [
{
"doi": "10.1038/nmeth.4326",
"pmc": "PMC5536224",
"pubmed": "28775673",
"title": "The Image Data Resource: A Bioimage Data Integration and Publication Platform.",
"year": 2017
}
],
"twitter": "openmicroscopy",
"uri_format": "https://idr.openmicroscopy.org/search/?query=Name:idr$1"
},
"iedb": {
"description": "The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes.",
"example": "1038233",
"homepage": "https://www.lji.org/",
"keywords": [
"bioinformatics",
"immunology",
"life science",
"protein",
"small molecule"
],
"mappings": {
"fairsharing": "FAIRsharing.c886cd",
"miriam": "iedb",
"prefixcommons": "tied",
"re3data": "r3d100012702"
},
"name": "Immune Epitope Database",
"pattern": "^[0-9]+$",
"preferred_prefix": "iedb",
"publications": [
{
"doi": "10.1093/nar/gku938",
"pmc": "PMC4384014",
"pubmed": "25300482",
"title": "The immune epitope database (IEDB) 3.0.",
"year": 2014
},
{
"doi": "10.1111/j.1365-2567.2012.03611.x",
"pmc": "PMC3461392",
"pubmed": "22681406",
"title": "The immune epitope database: a historical retrospective of the first decade.",
"year": 2012
},
{
"doi": "10.1093/nar/gkp1004",
"pmc": "PMC2808938",
"pubmed": "19906713",
"title": "The immune epitope database 2.0.",
"year": 2009
},
{
"doi": null,
"pmc": null,
"pubmed": "16312048",
"title": "The immune epitope database and analysis resource: from vision to blueprint.",
"year": 2004
}
],
"uri_format": "https://www.iedb.org/reference/$1"
},
"ietf.language": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Shorthand representations of languages and their subtypes",
"example": "en-GB",
"example_extras": [
"en",
"ar-SA",
"aaf"
],
"homepage": "http://www.iana.org/assignments/language-subtag-registry/language-subtag-registry",
"mappings": {
"wikidata": "P305"
},
"name": "Internet Engineering Task Force Language Tag",
"pattern": "^\\w{2,3}(-\\w+)?$",
"preferred_prefix": "ietf.language",
"synonyms": [
"bcp47"
]
},
"iev": {
"deprecated": true,
"description": "The Event Ontology is an ontology of pathways. It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure.",
"example": "0000000",
"homepage": "http://www.inoh.org",
"keywords": [
"obo",
"ontology",
"pathway",
"structure"
],
"mappings": {
"biocontext": "IEV",
"obofoundry": "iev",
"prefixcommons": "iev"
},
"name": "Event (INOH pathway ontology)",
"pattern": "^\\d{7}$",
"preferred_prefix": "IEV",
"uri_format": "http://purl.obolibrary.org/obo/IEV_$1"
},
"igrhcellid": {
"description": "Cell line databases/resources",
"example": "ACHN",
"homepage": "http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi",
"mappings": {
"cellosaurus": "IGRhCellID"
},
"name": "Integrated Genomic Resources of human Cell Lines for Identification",
"preferred_prefix": "igrhcellid",
"uri_format": "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1"
},
"igsn": {
"description": "IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents.",
"example": "AU124",
"homepage": "http://www.geosamples.org/",
"keywords": [
"subject agnostic"
],
"mappings": {
"fairsharing": "FAIRsharing.c7f365",
"miriam": "igsn",
"n2t": "igsn"
},
"name": "International Geo Sample Number",
"pattern": "^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$",
"preferred_prefix": "igsn",
"uri_format": "http://igsn.org/$1"
},
"igsr": {
"description": "The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project.",
"example": "NA06985",
"homepage": "https://www.internationalgenome.org/",
"keywords": [
"comparative genomics",
"genomics"
],
"mappings": {
"cellosaurus": "IGSR",
"fairsharing": "FAIRsharing.4Vs9VM",
"re3data": "r3d100010180"
},
"name": "International Genome Sample Resource",
"preferred_prefix": "igsr",
"publications": [
{
"doi": "10.1093/nar/gkz836",
"pmc": "PMC6943028",
"pubmed": "31584097",
"title": "The International Genome Sample Resource (IGSR) collection of open human genomic variation resources.",
"year": 2020
},
{
"doi": "10.1038/nature15393",
"pmc": "PMC4750478",
"pubmed": "26432245",
"title": "A global reference for human genetic variation.",
"year": 2015
}
],
"twitter": "1000genomes",
"uri_format": "https://www.internationalgenome.org/data-portal/sample/$1"
},
"ihw": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics.",
"example": "IHW09326",
"homepage": "https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html",
"mappings": {
"cellosaurus": "IHW"
},
"name": "International Histocompatibility Workshop cell lines",
"pattern": "^IHW\\d+$",
"preferred_prefix": "ihw"
},
"illumina.probe": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip.",
"example": "ILMN_129894",
"homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6790/A-GEOD-6790.adf.txt",
"keywords": [
"transcriptomics"
],
"name": "Illumina Probe Identifier",
"pattern": "^ILMN_\\d+$",
"preferred_prefix": "illumina.probe",
"references": [
"https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-9184/A-GEOD-9184_comments.txt"
]
},
"imanis": {
"description": "Cell line collections",
"example": "CL070",
"homepage": "https://www.imanislife.com/collections/cell-lines/",
"mappings": {
"cellosaurus": "Imanis"
},
"name": "Imanis Life Sciences cell line products",
"preferred_prefix": "imanis",
"uri_format": "https://www.imanislife.com/?s=$1"
},
"imdrf": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence.",
"homepage": "http://www.imdrf.org/",
"name": "International Medical Device Regulators Forum",
"no_own_terms": true,
"preferred_prefix": "imdrf",
"references": [
"https://www.fda.gov/medical-devices/mandatory-reporting-requirements-manufacturers-importers-and-device-user-facilities/mdr-adverse-event-codes"
]
},
"imex": {
"banana": "IM",
"banana_peel": "-",
"description": "The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources.",
"example": "19210-3",
"example_extras": [
"19210"
],
"homepage": "https://www.imexconsortium.org/",
"keywords": [
"interaction",
"molecule"
],
"mappings": {
"biocontext": "IMEX",
"miriam": "imex",
"n2t": "imex",
"prefixcommons": "imex",
"re3data": "r3d100010669"
},
"name": "International Molecular Exchange",
"pattern": "^\\d+(-\\d+)?$",
"preferred_prefix": "imex",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "IMEx Consortium though Intact",
"homepage": "https://www.ebi.ac.uk/intact/",
"name": "IMEx Consortium though Intact",
"uri_format": "https://imexcentral.org/icentral/imex/rec/$1"
},
{
"code": "intact.search",
"description": "Search page on IntAct",
"homepage": "https://www.ebi.ac.uk/intact",
"name": "IntAct Search",
"uri_format": "https://www.ebi.ac.uk/intact/search?query=IM-$1"
}
],
"publications": [
{
"doi": "10.1002/pmic.200700286",
"pmc": null,
"pubmed": "17893861",
"title": "Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition.",
"year": 2007
}
],
"uri_format": "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-$1"
},
"img.gene": {
"description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information.",
"example": "638309541",
"homepage": "http://img.jgi.doe.gov/",
"keywords": [
"gene",
"genome"
],
"mappings": {
"biocontext": "IMG.GENE",
"miriam": "img.gene",
"n2t": "img.gene",
"prefixcommons": "img.gene"
},
"name": "Integrated Microbial Genomes Gene",
"pattern": "^\\d+$",
"preferred_prefix": "img.gene",
"publications": [
{
"doi": "10.1093/nar/gkm846",
"pmc": "PMC2238897",
"pubmed": "17933782",
"title": "The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.",
"year": 2007
}
],
"uri_format": "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1"
},
"img.taxon": {
"description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information.",
"example": "648028003",
"homepage": "http://img.jgi.doe.gov/",
"keywords": [
"genome",
"taxonomy"
],
"mappings": {
"biocontext": "IMG.TAXON",
"miriam": "img.taxon",
"n2t": "img.taxon",
"prefixcommons": "img.taxon"
},
"name": "Integrated Microbial Genomes Taxon",
"pattern": "^\\d+$",
"preferred_prefix": "img.taxon",
"publications": [
{
"doi": "10.1093/nar/gkm846",
"pmc": "PMC2238897",
"pubmed": "17933782",
"title": "The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.",
"year": 2007
}
],
"uri_format": "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1"
},
"imgt.hla": {
"contact": {
"email": "steven.marsh@ucl.ac.uk",
"github": null,
"name": "Steven G. E. Marsh",
"orcid": "0000-0003-2855-4120"
},
"description": "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature.",
"example": "A*01:01:01:01",
"homepage": "https://www.ebi.ac.uk/imgt/hla/allele.html",
"keywords": [
"biomedical science",
"dna",
"immunogenetics",
"immunology",
"protein",
"rna"
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"mappings": {
"biocontext": "IMGT.HLA",
"cellosaurus": "IPD-IMGT/HLA",
"edam": "2773",
"fairsharing": "FAIRsharing.e28v7g",
"go": "IMGT_HLA",
"miriam": "imgt.hla",
"n2t": "imgt.hla",
"ncbi": "IMGT/HLA",
"prefixcommons": "imgthla",
"re3data": "r3d100010804"
},
"name": "IMGT/HLA human major histocompatibility complex sequence database",
"pattern": "^[A-Z0-9*:]+$",
"preferred_prefix": "imgt.hla",
"publications": [
{
"doi": "10.1093/nar/gkz950",
"pmc": "PMC7145640",
"pubmed": "31667505",
"title": "IPD-IMGT/HLA Database.",
"year": 2020
},
{
"doi": "10.1093/nar/gku1161",
"pmc": "PMC4383959",
"pubmed": "25414341",
"title": "The IPD and IMGT/HLA database: allele variant databases.",
"year": 2014
},
{
"doi": "10.1093/nar/gkn662",
"pmc": "PMC2686596",
"pubmed": "18838392",
"title": "The IMGT/HLA database.",
"year": 2008
},
{
"doi": "10.1007/978-1-60327-118-9_3",
"pmc": null,
"pubmed": "18449991",
"title": "The IMGT/HLA database.",
"year": 2007
},
{
"doi": "10.1002/humu.20406",
"pmc": null,
"pubmed": "16944494",
"title": "The IMGT/HLA and IPD databases.",
"year": 2006
},
{
"doi": "10.1093/nar/gkj088",
"pmc": "PMC1347451",
"pubmed": "16381979",
"title": "IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences.",
"year": 2006
},
{
"doi": "10.1093/nar/gkg070",
"pmc": "PMC165517",
"pubmed": "12520010",
"title": "IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex.",
"year": 2003
},
{
"doi": "10.1093/nar/29.1.210",
"pmc": "PMC29780",
"pubmed": "11125094",
"title": "IMGT/HLA Database--a sequence database for the human major histocompatibility complex.",
"year": 2001
},
{
"doi": "10.1034/j.1399-0039.2000.550314.x",
"pmc": null,
"pubmed": "10777106",
"title": "IMGT/HLA database--a sequence database for the human major histocompatibility complex.",
"year": 2000
}
],
"synonyms": [
"IPD-IMGT/HLA"
],
"uri_format": "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1"
},
"imgt.ligm": {
"description": "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates.",
"example": "M94112",
"homepage": "http://www.imgt.org/",
"keywords": [
"dna"
],
"mappings": {
"biocontext": "IMGT.LIGM",
"go": "IMGT_LIGM",
"miriam": "imgt.ligm",
"n2t": "imgt.ligm",
"ncbi": "IMGT/LIGM",
"prefixcommons": "imgt.ligm"
},
"name": "ImMunoGeneTics database covering immunoglobulins and T-cell receptors",
"pattern": "^M\\d+$",
"preferred_prefix": "imgt.ligm",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "IMGT LIGM through DKFZ (SRS)",
"homepage": "http://genius.embnet.dkfz-heidelberg.de/",
"name": "IMGT LIGM through DKFZ (SRS)",
"uri_format": "http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-id+4ktAl1fNMTA+-e+[IMGT:'$1']"
}
],
"publications": [
{
"doi": "10.1093/nar/gkj088",
"pmc": "PMC1347451",
"pubmed": "16381979",
"title": "IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences.",
"year": 2006
}
],
"uri_format": "http://www.imgt.org/ligmdb/view?id=$1"
},
"imgt.primerdb": {
"description": "The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR).",
"example": "IPP900099",
"homepage": "http://imgt.org/IMGTPrimerDB/",
"keywords": [
"dna"
],
"mappings": {
"prefixcommons": "imgt.primerdb",
"re3data": "r3d100012535"
},
"name": "IMGT/PRIMER-DB",
"preferred_prefix": "imgt.primerdb",
"uri_format": "http://imgt.org/IMGTPrimerDB/Check_PrDB.pl?numacc0=$1&origin=view&source=PrList"
},
"imotdb": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"description": "The interacting motif database or iMOTdb , lists interacting motifs thatare identified for all structural entries in the PDB. The conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting the common motifs shared among all superfamily members.",
"example": "53784",
"homepage": "http://caps.ncbs.res.in/imotdb/",
"keywords": [
"interaction",
"protein"
],
"mappings": {
"prefixcommons": "imotdb"
},
"name": "Database of Spatially Interacting Motifs in Proteins",
"preferred_prefix": "imotdb",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode=$1"
},
"imr": {
"contact": {
"email": "curator@inoh.org",
"github": null,
"name": "INOH curators",
"orcid": null
},
"deprecated": true,
"description": "MoleculeRole Ontology is an ontology for proteins/chemicals. It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data.",
"example": "0000001",
"homepage": "http://www.inoh.org",
"keywords": [
"obo",
"ontology",
"protein",
"small molecule"
],
"mappings": {
"biocontext": "IMR",
"obofoundry": "imr",
"prefixcommons": "imr"
},
"name": "Molecule role (INOH Protein name/family name ontology)",
"pattern": "^\\d{7}$",
"preferred_prefix": "IMR",
"uri_format": "http://purl.obolibrary.org/obo/IMR_$1"
},
"inaturalist.observation": {
"contributor": {
"email": null,
"github": "oolonek",
"name": "Pierre-Marie Allard",
"orcid": "0000-0003-3389-2191"
},
"description": "The identifier for an observation in iNaturalist",
"example": "36010371",
"github_request_issue": 517,
"homepage": "https://www.inaturalist.org/observations",
"mappings": {
"wikidata": "P5683"
},
"name": "iNaturalist Observation",
"pattern": "^[1-9]\\d*$",
"preferred_prefix": "inaturalist.observation",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://www.inaturalist.org/observations/$1"
},
"inaturalist.place": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Identifier for a place in iNaturalist",
"example": "7207",
"homepage": "https://www.inaturalist.org/places",
"mappings": {
"wikidata": "P7471"
},
"name": "iNaturalist Place",
"pattern": "^[1-9]\\d*$",
"preferred_prefix": "inaturalist.place",
"uri_format": "https://www.inaturalist.org/places/$1"
},
"inaturalist.taxon": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Identifier for a species in iNaturalist",
"example": "21723",
"homepage": "https://www.inaturalist.org/taxa",
"mappings": {
"wikidata": "P3151"
},
"name": "iNaturalist Taxonomy",
"pattern": "^[1-9]\\d{0,6}$",
"preferred_prefix": "inaturalist.taxon",
"uri_format": "https://www.inaturalist.org/taxa/$1"
},
"inaturalist.user": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Identifier for a user in iNaturalist",
"example": "1426686",
"homepage": "https://www.inaturalist.org/users",
"keywords": [
"person"
],
"name": "iNaturalist User",
"pattern": "^[1-9]\\d*$",
"preferred_prefix": "inaturalist.user",
"uri_format": "https://www.inaturalist.org/users/$1"
},
"inchi": {
"description": "The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier.",
"example": "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3",
"homepage": "http://www.chemspider.com/",
"keywords": [
"cheminformatics",
"chemistry",
"knowledge and information systems"
],
"mappings": {
"biocontext": "INCHI",
"fairsharing": "FAIRsharing.ddk9t9",
"miriam": "inchi",
"n2t": "inchi",
"wikidata": "P234"
},
"name": "InChI",
"pattern": "^InChI\\=1S?\\/[A-Za-z0-9\\.]+(\\+[0-9]+)?(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,\\/\\?\\;\\.]+)*$",
"preferred_prefix": "inchi",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "InChI through NIST",
"homepage": "http://webbook.nist.gov/chemistry",
"name": "InChI through NIST",
"uri_format": "http://webbook.nist.gov/cgi/cbook.cgi?$1"
},
{
"code": "ebi",
"description": "InChI through ChEBI",
"homepage": "https://www.ebi.ac.uk/chebi/",
"name": "InChI through ChEBI",
"uri_format": "https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=$1"
},
{
"code": "um",
"description": "InChI through RDF Open Molecules",
"homepage": "http://rdf.openmolecules.net/",
"name": "InChI through RDF Open Molecules",
"uri_format": "http://rdf.openmolecules.net/?$1"
}
],
"publications": [
{
"doi": "10.1186/s13321-021-00517-z",
"pmc": "PMC8147039",
"pubmed": "34030732",
"title": "InChI version 1.06: now more than 99.99% reliable.",
"year": 2021
},
{
"doi": "10.1186/s13321-015-0068-4",
"pmc": "PMC4486400",
"pubmed": "26136848",
"title": "InChI, the IUPAC International Chemical Identifier.",
"year": 2015
},
{
"doi": "10.1007/s10822-015-9854-3",
"pmc": null,
"pubmed": "26081259",
"title": "Many InChIs and quite some feat.",
"year": 2015
}
],
"twitter": "inchi_trust",
"uri_format": "http://www.chemspider.com/$1"
},
"inchikey": {
"description": "The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI.",
"example": "RYYVLZVUVIJVGH-UHFFFAOYSA-N",
"homepage": "http://www.chemspider.com/",
"mappings": {
"biocontext": "INCHIKEY",
"miriam": "inchikey",
"n2t": "inchikey",
"wikidata": "P235"
},
"name": "InChIKey",
"pattern": "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-Z])$",
"preferred_prefix": "inchikey",
"providers": [
{
"code": "scholia",
"description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.",
"homepage": "https://scholia.toolforge.org/",
"name": "Scholia",
"uri_format": "https://scholia.toolforge.org/inchikey/$1"
}
],
"uri_format": "http://www.chemspider.com/inchikey=$1"
},
"inhand": {
"comment": "This nomenclature is available via email. Truly a disgrace.",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology.",
"homepage": "https://www.goreni.org/gr3_nomenclature.php",
"keywords": [
"biomedical science"
],
"mappings": {
"fairsharing": "FAIRsharing.9gqfpm"
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"name": "The International Harmonization of Nomenclature and Diagnostic criteria",
"preferred_prefix": "inhand",
"proprietary": true,
"publications": [
{
"doi": "10.1177/0192623309353423",
"pmc": null,
"pubmed": "20032296",
"title": "Proliferative and nonproliferative lesions of the rat and mouse respiratory tract.",
"year": 2009
}
]
},
"inn": {
"comment": "can not find a place to resolve to",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.",
"example": "fluticasone",
"homepage": "https://www.who.int/teams/health-product-and-policy-standards/inn",
"mappings": {
"wikidata": "P2275"
},
"name": "International Nonproprietary Names",
"preferred_prefix": "inn",
"synonyms": [
"INN_ID"
],
"uri_format": "https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1"
},
"innatedb": {
"description": "InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactions and signaling responses involved in mammalian innate immunity. InnateDB incorporates information of the whole human, mouse and bovine interactomes by integrating interaction and pathway information from several of the major publicly available databases but aims to capture an improved coverage of the innate immunity interactome through manual curation.",
"example": "20021",
"homepage": "http://www.innatedb.ca/",
"keywords": [
"gene",
"immunology",
"interaction",
"life science",
"pathway",
"protein"
],
"mappings": {
"fairsharing": "FAIRsharing.rb2drw",
"prefixcommons": "innatedb",
"re3data": "r3d100010676"
},
"name": "A Knowledge Resource for Innate Immunity Interactions and Pathways",
"preferred_prefix": "innatedb",
"publications": [
{
"doi": "10.1093/nar/gks1147",
"pmc": "PMC3531080",
"pubmed": "23180781",
"title": "InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation.",
"year": 2012
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"twitter": "innatedb",
"uri_format": "http://www.innatedb.ca/getGeneCard.do?id=$1"
},
"ino": {
"contact": {
"email": "yongqunh@med.umich.edu",
"github": "yongqunh",
"name": "Yongqun Oliver He",
"orcid": "0000-0001-9189-9661"
},
"description": "he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles.",
"download_owl": "http://purl.obolibrary.org/obo/ino.owl",
"example": "0000003",
"homepage": "https://github.com/INO-ontology/ino",
"keywords": [
"life science",
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "INO",
"biolink": "INO",
"bioportal": "INO",
"fairsharing": "FAIRsharing.mm72as",
"obofoundry": "ino",
"ols": "ino",
"ontobee": "INO"
},
"name": "Interaction Network Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "INO",
"publications": [
{
"doi": "10.1186/s13040-016-0118-0",
"pmc": "PMC5168857",
"pubmed": "28031747",
"title": "The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature.",
"year": 2016
},
{
"doi": "10.1186/2041-1480-6-2",
"pmc": "PMC4362819",
"pubmed": "25785184",
"title": "Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions.",
"year": 2015
},
{
"doi": "10.1186/2041-1480-2-s2-s8",
"pmc": "PMC3102897",
"pubmed": "21624163",
"title": "Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology.",
"year": 2011
}
],
"repository": "https://github.com/INO-ontology/ino",
"uri_format": "http://purl.obolibrary.org/obo/INO_$1",
"version": "1.1.13"
},
"insdc": {
"description": "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences.",
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"dna"
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{
"code": "CURATOR_REVIEW",
"description": "INSDC through DDBJ",
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"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)",
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},
{
"code": "ncbi",
"description": "INSDC through Nucleotide database at NCBI",
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}
],
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{
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"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.",
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}
],
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},
"insdc.cds": {
"description": "The coding sequence or protein identifiers as maintained in INSDC.",
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{
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{
"code": "CURATOR_REVIEW",
"description": "INSDC CDS through NCBI",
"homepage": "https://www.ncbi.nlm.nih.gov/protein/",
"name": "INSDC CDS through NCBI",
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}
],
"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.",
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{
"code": "ncbi",
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}
],
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},
"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",
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},
"description": "An experimental run, served thrugh the ENA",
"example": "ERR436051",
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"name": "International Nucleotide Sequence Database Collaboration (INSDC) Run",
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"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",
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{
"code": "ddbj",
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},
{
"code": "ebi",
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}
],
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{
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"title": "Investigation into the annotation of protocol sequencing steps in the sequence read archive.",
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},
{
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"pubmed": "22009675",
"title": "The Sequence Read Archive: explosive growth of sequencing data.",
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{
"doi": "10.1093/nar/gkm1000",
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"title": "Database resources of the National Center for Biotechnology Information.",
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}
],
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},
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{
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{
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{
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{
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}
],
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},
"intact.molecule": {
"description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules.",
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},
"interfil": {
"description": "The Intermediate Filament Database functions as a continuously updated review of the intermediate filament field and it is hoped that users will contribute to the development and expansion of the database on a regular basis. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants.",
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"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. ",
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"anatomy",
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],
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{
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"title": "NeuroLex.org: an online framework for neuroscience knowledge.",
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}
],
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"https://github.com/AllenInstitute/nomenclature"
],
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"ILX"
],
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},
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},
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],
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},
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{
"code": "CURATOR_REVIEW",
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}
],
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{
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"title": "The InterPro protein families and domains database: 20 years on.",
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},
{
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"title": "InterPro in 2019: improving coverage, classification and access to protein sequence annotations.",
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},
{
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"title": "InterPro, progress and status in 2005.",
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}
],
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"IP",
"IPR",
"InterPro"
],
"twitter": "InterProDB",
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},
"ipi": {
"deprecated": true,
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],
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"name": "International Protein Index",
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{
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"title": "The International Protein Index: an integrated database for proteomics experiments.",
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}
],
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},
"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).",
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"keywords": [
"gene",
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],
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{
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"title": "BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence.",
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}
],
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},
"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.",
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"interaction",
"life science",
"protein"
],
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"name": "iRefWeb",
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{
"doi": "10.1093/database/baq023",
"pmc": "PMC2963317",
"pubmed": "20940177",
"title": "iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence.",
"year": 2010
}
],
"twitter": "wodaklab",
"uri_format": "http://wodaklab.org/iRefWeb/interaction/show/$1"
},
"iresite": {
"description": "The IRESite database presents information about experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract the eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure.",
"example": "322",
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"keywords": [
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"regulation",
"rna"
],
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},
"name": "Database of experimentally verified IRES structures",
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{
"doi": "10.1093/nar/gkp981",
"pmc": "PMC2808886",
"pubmed": "19917642",
"title": "IRESite--a tool for the examination of viral and cellular internal ribosome entry sites.",
"year": 2009
},
{
"doi": "10.1093/nar/gkj081",
"pmc": "PMC1347444",
"pubmed": "16381829",
"title": "IRESite: the database of experimentally verified IRES structures (www.iresite.org).",
"year": 2006
}
],
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},
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},
"iro": {
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
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},
"deprecated": true,
"example": "0000008",
"name": "Insect Resistance Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "iro",
"uri_format": "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1"
},
"isbn": {
"description": "The International Standard Book Number (ISBN) is for identifying printed books.",
"example": "9781584885658",
"homepage": "http://isbndb.com/",
"keywords": [
"bibliography"
],
"mappings": {
"biocontext": "ISBN-13",
"biolink": "isbn",
"edam": "2634",
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},
"name": "International Standard Book Number",
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"preferred_prefix": "isbn",
"providers": [
{
"code": "worldcat",
"description": "ISBN database at WorldCat",
"homepage": "http://www.worldcat.org/",
"name": "ISBN database at WorldCat",
"uri_format": "http://www.worldcat.org/isbn/$1"
}
],
"synonyms": [
"ISBN-10",
"ISBN-13"
],
"uri_format": "http://isbndb.com/search-all.html?kw=$1"
},
"ised": {
"description": "ISED catalogues the influenza sequence and epitope information obtained in countries worldwide and currently hosts a total of 49368 influenza A and 4761 influenza B virus sequence data including pandemic A/H1N1 2009 virus sequences collected in 42 countries, and a total of 545 amantadine-resistant influenza virus sequences collected in Korea.",
"example": "AY209920",
"homepage": "http://influenza.korea.ac.kr",
"keywords": [
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],
"mappings": {
"prefixcommons": "ised"
},
"name": "Influenza Sequence and Epitope Database",
"preferred_prefix": "ised"
},
"isfinder": {
"description": "ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available.",
"example": "ISA1083-2",
"homepage": "http://www-is.biotoul.fr/i",
"keywords": [
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"life science",
"sequence"
],
"mappings": {
"biocontext": "ISFINDER",
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"prefixcommons": "isfinder"
},
"name": "Insertion sequence elements database",
"pattern": "^IS\\w+(\\-\\d)?$",
"preferred_prefix": "isfinder",
"publications": [
{
"doi": "10.1093/nar/gkj014",
"pmc": "PMC1347377",
"pubmed": "16381877",
"title": "ISfinder: the reference centre for bacterial insertion sequences.",
"year": 2006
}
],
"uri_format": "https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1"
},
"isni": {
"description": "ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC.\r\n\r\nThe mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described.",
"example": "000000012281955X",
"homepage": "http://www.isni.org",
"mappings": {
"biolink": "isni",
"miriam": "isni",
"n2t": "isni"
},
"name": "International Standard Name Identifier",
"pattern": "^[0-9]{15}[0-9X]{1}$",
"preferred_prefix": "isni",
"uri_format": "http://www.isni.org/isni/$1"
},
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"wikidata": "P299"
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{
"doi": "10.1038/s41597-022-01435-x",
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{
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"IUPHAR_GPCR",
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"dna",
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"prefixcommons": "ivdb"
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"jax": {
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"email": "cthoyt@gmail.com",
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"description": "Information about the C57BL/6J. Includes genetic background and disease data.",
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"life science"
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"biocontext": "JAX",
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"description": "JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc.",
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"name": "Japan Consortium for Glycobiology and Glycotechnology Database",
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"jcm": {
"description": "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2.",
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"keywords": [
"life science",
"microbial",
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"name": "Japan Collection of Microorganisms",
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"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
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"description": "Cell line collections",
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"cellosaurus": "JCRB"
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"name": "JRBC Cell Bank",
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},
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"description": "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST).",
"example": "J55.713G",
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"chemical",
"structure"
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"biocontext": "JCSD",
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"description": "JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration.",
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"biocontext": "JSTOR",
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},
"jws": {
"description": "JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser.",
"example": "achcar11",
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"model",
"pathway"
],
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"prefixcommons": "jws"
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{
"code": "CURATOR_REVIEW",
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"name": "JWS Online Model Repository at Manchester",
"uri_format": "http://jjj.mib.ac.uk/models/$1"
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{
"code": "CURATOR_REVIEW",
"description": "JWS Online Model Repository at Amsterdam",
"homepage": "http://jjj.bio.vu.nl/models/",
"name": "JWS Online Model Repository at Amsterdam",
"uri_format": "http://jjj.bio.vu.nl/models/$1/"
}
],
"publications": [
{
"doi": "10.1093/bioinformatics/bth200",
"pmc": null,
"pubmed": "15072998",
"title": "Web-based kinetic modelling using JWS Online.",
"year": 2004
}
],
"uri_format": "https://jjj.bio.vu.nl/models/$1"
},
"kaggle": {
"description": "Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions.",
"example": "nasa/kepler-exoplanet-search-results",
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"mappings": {
"miriam": "kaggle",
"n2t": "kaggle",
"re3data": "r3d100012705"
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"preferred_prefix": "kaggle",
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},
"kclb": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Cell line collections",
"example": "10020.2",
"homepage": "https://cellbank.snu.ac.kr/english",
"mappings": {
"cellosaurus": "KCLB"
},
"name": "Korean Cell Line Bank",
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"uri_format": "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1"
},
"kegg": {
"comment": "KEGG prefix has been split into several others",
"deprecated": true,
"description": "Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.",
"example": "hsa00190",
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"mappings": {
"biocontext": "KEGG",
"cheminf": "000409",
"go": "KEGG",
"miriam": "kegg",
"n2t": "kegg",
"uniprot": "DB-0053"
},
"name": "Kyoto Encyclopedia of Genes and Genomes",
"pattern": "^([CHDEGTMKR]\\d+)|(\\w+:[\\w\\d\\.-]*)|([a-z]{3,5})|(\\w{2,4}\\d{5})$",
"preferred_prefix": "kegg",
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{
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"pmc": "PMC5210567",
"pubmed": "27899662",
"title": "KEGG: new perspectives on genomes, pathways, diseases and drugs.",
"year": 2016
}
],
"synonyms": [
"KEGG"
],
"uri_format": "http://www.kegg.jp/entry/$1"
},
"kegg.brite": {
"description": "KEGG BRITE is a collection of hierarchical classifications (see new hierarchies and last updates) representing our knowledge on various aspects of biological systems. In contrast to KEGG PATHWAY, which is limited to molecular interactions and reactions, KEGG BRITE incorporates many different types of relationships.",
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"keywords": [
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"ontology",
"pathway"
],
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"uri_format": "http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br$1"
},
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"description": "KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life.",
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"small molecule"
],
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"n2t": "kegg.compound",
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"wikidata": "P665"
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{
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"pmc": null,
"pubmed": "22700311",
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"year": 2012
}
],
"synonyms": [
"KEGG COMPOUND",
"KEGG.COMPOUND"
],
"uri_format": "https://www.kegg.jp/entry/$1"
},
"kegg.dgroup": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": " KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. There are five types of drug groups.\n\n Chemical - grouped as identical chemical structures with minor variations of salts, hydration states, etc.\n Structure - grouped as similar chemical structures having the same skeleton, etc.\n Target - grouped by drug targets\n Class - drug classes often representing similar mechanisms of action\n Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters\n\nChemical groups are often used for identifying essentially the same active ingredients of drugs in different countries.",
"example": "DG00301",
"homepage": "http://www.genome.jp/kegg/reaction/",
"mappings": {
"biolink": "KEGG.DGROUP"
},
"name": "KEGG Drug Group",
"part_of": "kegg",
"pattern": "^DG\\d+$",
"preferred_prefix": "kegg.dgroup",
"references": [
"https://github.com/prefixcommons/prefixes/pull/4"
],
"synonyms": [
"KEGG_DGROUP",
"KEGG_DRUG_GROUP"
]
},
"kegg.disease": {
"description": "The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system.",
"example": "H00076",
"homepage": "http://www.genome.jp/kegg/disease/",
"keywords": [
"classification"
],
"mappings": {
"biocontext": "KEGG.DISEASE",
"miriam": "kegg.disease",
"n2t": "kegg.disease",
"prefixcommons": "kegg.disease"
},
"name": "KEGG Disease",
"part_of": "kegg",
"pattern": "^H\\d+$",
"preferred_prefix": "kegg.disease",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"kegg.drug": {
"description": "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules.",
"example": "D00123",
"homepage": "https://www.genome.jp/kegg/drug/",
"keywords": [
"small molecule"
],
"mappings": {
"biocontext": "KEGG.DRUG",
"edam": "2609",
"miriam": "kegg.drug",
"n2t": "kegg.drug",
"prefixcommons": "kegg.drug",
"wikidata": "P665"
},
"name": "KEGG Drug",
"part_of": "kegg",
"pattern": "^D\\d+$",
"preferred_prefix": "kegg.drug",
"publications": [
{
"doi": "10.1093/nar/gkj102",
"pmc": "PMC1347464",
"pubmed": "16381885",
"title": "From genomics to chemical genomics: new developments in KEGG.",
"year": 2006
}
],
"synonyms": [
"KEGG DRUG",
"KEGG.DRUG"
],
"uri_format": "https://www.kegg.jp/entry/$1"
},
"kegg.environ": {
"deprecated": true,
"description": "KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable.",
"example": "ev:E00032",
"homepage": "http://www.genome.jp/kegg/drug/environ.html",
"mappings": {
"biocontext": "KEGG.ENVIRON",
"miriam": "kegg.environ",
"n2t": "kegg.environ"
},
"name": "KEGG Environ",
"part_of": "kegg",
"pattern": "^(ev\\:)?E\\d+$",
"preferred_prefix": "kegg.environ",
"synonyms": [
"KEGG.EDRUG"
],
"uri_format": "http://www.kegg.jp/entry/$1"
},
"kegg.enzyme": {
"description": "KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links.",
"homepage": "http://www.genome.jp/dbget-bin/www_bfind?enzyme",
"mappings": {
"biolink": "KEGG.ENZYME",
"go": "KEGG_ENZYME"
},
"name": "KEGG Enzyme",
"part_of": "kegg",
"preferred_prefix": "kegg.enzyme",
"provides": "eccode",
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?ec:$1"
},
"kegg.genes": {
"description": "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources.",
"example": "bsu:BSU01340",
"homepage": "http://www.genome.jp/kegg/genes.html",
"keywords": [
"dna",
"gene",
"protein"
],
"mappings": {
"biocontext": "KEGG.GENES",
"biolink": "KEGG.GENE",
"miriam": "kegg.genes",
"n2t": "kegg.genes",
"prefixcommons": "kegg.gene",
"wikidata": "P665"
},
"name": "KEGG Genes",
"part_of": "kegg",
"pattern": "^\\w+:[\\w\\d\\.-]*$",
"preferred_prefix": "kegg.genes",
"publications": [
{
"doi": "10.1093/nar/gkj102",
"pmc": "PMC1347464",
"pubmed": "16381885",
"title": "From genomics to chemical genomics: new developments in KEGG.",
"year": 2006
}
],
"uri_format": "http://www.kegg.jp/entry/$1"
},
"kegg.genome": {
"description": "KEGG Genome is a collection of organisms whose genomes have been completely sequenced.",
"example": "T06648",
"homepage": "http://www.genome.jp/kegg/catalog/org_list.html",
"mappings": {
"biocontext": "KEGG.GENOME",
"miriam": "kegg.genome",
"n2t": "kegg.genome",
"prefixcommons": "kegg.genome",
"wikidata": "P665"
},
"name": "KEGG Genome",
"part_of": "kegg",
"pattern": "^(T0\\d+|\\w{3,5})$",
"preferred_prefix": "kegg.genome",
"publications": [
{
"doi": "10.1093/nar/gkr988",
"pmc": "PMC3245020",
"pubmed": "22080510",
"title": "KEGG for integration and interpretation of large-scale molecular data sets.",
"year": 2011
}
],
"synonyms": [
"kegg_genome",
"kegg_genomes"
],
"uri_format": "http://www.kegg.jp/entry/$1"
},
"kegg.glycan": {
"description": "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways.",
"example": "G00123",
"homepage": "https://www.genome.jp/kegg/glycan/",
"keywords": [
"small molecule"
],
"mappings": {
"biocontext": "KEGG.GLYCAN",
"edam": "2613",
"miriam": "kegg.glycan",
"n2t": "kegg.glycan",
"prefixcommons": "kegg.glycan"
},
"name": "KEGG Glycan",
"part_of": "kegg",
"pattern": "^G\\d+$",
"preferred_prefix": "kegg.glycan",
"publications": [
{
"doi": "10.1093/glycob/cwj010",
"pmc": null,
"pubmed": "16014746",
"title": "KEGG as a glycome informatics resource.",
"year": 2005
}
],
"uri_format": "https://www.kegg.jp/entry/$1"
},
"kegg.ligand": {
"comment": "This database has been discontinued by KEGG. It now lives inside the compound database",
"deprecated": true,
"homepage": "http://www.genome.ad.jp/kegg/docs/upd_ligand.html",
"mappings": {
"go": "KEGG_LIGAND"
},
"name": "KEGG LIGAND",
"part_of": "kegg",
"preferred_prefix": "kegg.ligand",
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?cpd:$1"
},
"kegg.metagenome": {
"description": "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species.",
"example": "T30002",
"homepage": "http://www.genome.jp/kegg/catalog/org_list3.html",
"keywords": [
"genome"
],
"mappings": {
"biocontext": "KEGG.METAGENOME",
"miriam": "kegg.metagenome",
"n2t": "kegg.metagenome",
"prefixcommons": "kegg.metagenome"
},
"name": "KEGG Metagenome",
"part_of": "kegg",
"pattern": "^T3\\d+$",
"preferred_prefix": "kegg.metagenome",
"publications": [
{
"doi": "10.1093/nar/gkr988",
"pmc": "PMC3245020",
"pubmed": "22080510",
"title": "KEGG for integration and interpretation of large-scale molecular data sets.",
"year": 2011
}
],
"uri_format": "http://www.kegg.jp/entry/$1"
},
"kegg.module": {
"description": "KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules.",
"example": "M00002",
"homepage": "http://www.kegg.jp/kegg/module.html",
"mappings": {
"biocontext": "KEGG.MODULE",
"miriam": "kegg.module",
"n2t": "kegg.module"
},
"name": "KEGG Module",
"part_of": "kegg",
"pattern": "^([a-z]{3,5}_)?M\\d{5}$",
"preferred_prefix": "kegg.module",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"kegg.orthology": {
"description": "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms.",
"example": "K00001",
"homepage": "http://www.genome.jp/kegg/ko.html",
"keywords": [
"classification",
"pathway"
],
"mappings": {
"biocontext": "KEGG.ORTHOLOGY",
"miriam": "kegg.orthology",
"n2t": "kegg.orthology",
"prefixcommons": "kegg.orthology"
},
"name": "KEGG Orthology",
"part_of": "kegg",
"pattern": "^K\\d+$",
"preferred_prefix": "kegg.orthology",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"kegg.pathway": {
"description": "KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.",
"example": "rsk00410",
"homepage": "https://www.genome.jp/kegg/pathway.html",
"keywords": [
"pathway"
],
"mappings": {
"biocontext": "KEGG.PATHWAY",
"biolink": "KEGG.PATHWAY",
"edam": "2343",
"go": "KEGG_PATHWAY",
"miriam": "kegg.pathway",
"n2t": "kegg.pathway",
"prefixcommons": "kegg.pathway",
"wikidata": "P665"
},
"name": "KEGG Pathways Database",
"part_of": "kegg",
"pattern": "^\\w{2,4}\\d{5}$",
"preferred_prefix": "kegg.pathway",
"publications": [
{
"doi": "10.1002/0471250953.bi0112s38",
"pmc": null,
"pubmed": "22700311",
"title": "Using the KEGG database resource.",
"year": 2012
}
],
"synonyms": [
"KEGG-path",
"KEGG_PATHWAY"
],
"uri_format": "https://www.kegg.jp/entry/$1"
},
"kegg.rclass": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns.",
"example": "RC00001",
"homepage": "http://www.genome.jp/kegg/reaction/",
"mappings": {
"biolink": "KEGG.RCLASS"
},
"name": "KEGG Reaction Class",
"part_of": "kegg",
"pattern": "^RC\\d+$",
"preferred_prefix": "kegg.rclass",
"references": [
"https://github.com/prefixcommons/prefixes/pull/2"
],
"synonyms": [
"KEGG_RCLASS",
"KEGG_REACTION_CLASS"
]
},
"kegg.reaction": {
"description": "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life.",
"example": "R00100",
"homepage": "https://www.genome.jp/kegg/reaction/",
"keywords": [
"enzyme",
"pathway"
],
"mappings": {
"biocontext": "KEGG.REACTION",
"edam": "2608",
"go": "KEGG_REACTION",
"miriam": "kegg.reaction",
"n2t": "kegg.reaction",
"prefixcommons": "kegg.reaction",
"wikidata": "P665"
},
"name": "KEGG Reaction",
"part_of": "kegg",
"pattern": "^R\\d+$",
"preferred_prefix": "kegg.reaction",
"publications": [
{
"doi": "10.1002/0471250953.bi0112s38",
"pmc": null,
"pubmed": "22700311",
"title": "Using the KEGG database resource.",
"year": 2012
}
],
"synonyms": [
"KEGG_REACTION"
],
"uri_format": "https://www.kegg.jp/entry/$1"
},
"kerafast": {
"description": "Cell line collections",
"example": "EJH014",
"homepage": "https://www.kerafast.com/",
"mappings": {
"cellosaurus": "Kerafast"
},
"name": "Kerafast cell lines",
"preferred_prefix": "kerafast",
"uri_format": "https://www.kerafast.com/Search?SearchTerm="$1""
},
"knapsack": {
"description": "KNApSAcK provides information on metabolites and the\ntaxonomic class with which they are associated.",
"example": "C00000001",
"homepage": "http://www.knapsackfamily.com/KNApSAcK/",
"mappings": {
"biocontext": "KNAPSACK",
"miriam": "knapsack",
"n2t": "knapsack",
"wikidata": "P2064"
},
"name": "KNApSAcK",
"pattern": "^C\\d{8}$",
"preferred_prefix": "knapsack",
"uri_format": "http://www.knapsackfamily.com/knapsack_core/information.php?word=$1"
},
"kupo": {
"appears_in": [
"cl"
],
"comment": "Website is down, now it redirects to something else that is not related",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"example": "0001009",
"homepage": "http://www.kupkb.org/",
"name": "Kidney and Urinary Pathway Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "kupo",
"references": [
"https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-2-S2-S7"
]
},
"kyinno": {
"description": "Cell line collections",
"example": "KC-0979",
"homepage": "https://www.kyinno.com/",
"mappings": {
"cellosaurus": "KYinno"
},
"name": "KYinno cell lines",
"preferred_prefix": "kyinno",
"uri_format": "https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf"
},
"labo": {
"contact": {
"email": "paul.fabry@usherbrooke.ca",
"github": "pfabry",
"name": "Paul Fabry",
"orcid": "0000-0002-3336-2476"
},
"depends_on": [
"iao",
"obi",
"ogms",
"omiabis",
"omrse",
"opmi"
],
"description": "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents.",
"download_owl": "http://purl.obolibrary.org/obo/labo.owl",
"example": "0000124",
"homepage": "https://github.com/OpenLHS/LABO",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "LABO",
"bioportal": "LABO",
"obofoundry": "labo",
"ols": "labo",
"ontobee": "LABO"
},
"name": "clinical LABoratory Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "LABO",
"publications": [
{
"doi": "10.5281/zenodo.6522019",
"pmc": null,
"pubmed": null,
"title": "LABO: An ontology for laboratory test prescription and reporting",
"year": 2019
}
],
"repository": "https://github.com/OpenLHS/LABO",
"uri_format": "http://purl.obolibrary.org/obo/LABO_$1",
"version": "2021-06-08"
},
"langual": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Langual stands for \"langua alimentaria\" or \"language of food\". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases",
"example": "B2067",
"github_request_issue": 507,
"homepage": "https://www.langual.org",
"name": "Langua aLimentaria Thesaurus",
"pattern": "^B\\d+$",
"preferred_prefix": "langual",
"uri_format": "https://www.langual.org/langual_thesaurus.asp?termid=$1"
},
"lbo": {
"contact": {
"email": "caripark@iastate.edu",
"github": "caripark",
"name": "Carissa Park",
"orcid": "0000-0002-2346-5201"
},
"description": "A vocabulary for cattle, chicken, horse, pig, and sheep breeds.",
"download_obo": "https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.obo",
"download_owl": "https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.owl",
"example": "0000487",
"homepage": "http://bioportal.bioontology.org/ontologies/LBO",
"keywords": [
"animal breeding",
"animal husbandry",
"genetics",
"genomics",
"ontology"
],
"mappings": {
"aberowl": "LBO",
"agroportal": "LBO",
"bioportal": "LBO",
"fairsharing": "FAIRsharing.309v57",
"ols": "lbo"
},
"name": "Livestock Breed Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "lbo",
"repository": "https://github.com/AnimalGenome/livestock-breed-ontology",
"uri_format": "http://purl.obolibrary.org/obo/LBO_$1"
},
"leafsnap": {
"description": "identifier for a tree species of the United States and Canada on the Leafsnap electronic field guide",
"example": "Amelanchier laevis",
"homepage": "http://leafsnap.com/",
"mappings": {
"wikidata": "P10538"
},
"name": "Leafsnap ID",
"preferred_prefix": "leafsnap",
"uri_format": "http://leafsnap.com/species/$1/"
},
"lei": {
"description": "Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland.",
"example": "HWUPKR0MPOU8FGXBT394",
"homepage": "https://www.gleif.org/",
"mappings": {
"miriam": "lei",
"n2t": "lei"
},
"name": "Global LEI Index",
"pattern": "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$",
"preferred_prefix": "lei",
"uri_format": "https://www.gleif.org/lei/$1"
},
"lepao": {
"contact": {
"email": "lagonzalezmo@unal.edu.co",
"github": "luis-gonzalez-m",
"name": "Luis A. Gonzalez-Montana",
"orcid": "0000-0002-9136-9932"
},
"depends_on": [
"aism",
"bfo",
"bspo",
"caro",
"pato",
"ro",
"uberon"
],
"description": "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research.",
"download_obo": "http://purl.obolibrary.org/obo/lepao.obo",
"download_owl": "http://purl.obolibrary.org/obo/lepao.owl",
"example": "0000005",
"homepage": "https://github.com/insect-morphology/lepao",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "LEPAO",
"bioportal": "LEPAO",
"obofoundry": "lepao",
"ols": "lepao",
"ontobee": "LEPAO"
},
"name": "Lepidoptera Anatomy Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "LEPAO",
"repository": "https://github.com/insect-morphology/lepao",
"uri_format": "http://purl.obolibrary.org/obo/LEPAO_$1",
"version": "2021-11-20"
},
"lgai.cede": {
"description": "LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR).",
"example": "LGCEDe-S-000002244",
"homepage": "https://www.lgresearch.ai",
"mappings": {
"miriam": "lgai.cede"
},
"name": "LG Chemical Entity Detection Dataset (LGCEDe)",
"pattern": "^LGCEDe-S-\\d{9}$",
"preferred_prefix": "lgai.cede",
"uri_format": "https://s3.us-east-2.amazonaws.com/lg.cede/$1"
},
"lgic": {
"comment": "Website is gone",
"deprecated": true,
"description": "The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available.",
"example": "5HT3Arano",
"homepage": "https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php",
"keywords": [
"gene",
"protein",
"sequence"
],
"mappings": {
"biocontext": "LGIC",
"miriam": "lgic",
"n2t": "lgic",
"prefixcommons": "lgicdb"
},
"name": "Ligand-Gated Ion Channel database",
"pattern": "^\\w+$",
"preferred_prefix": "lgic",
"publications": [
{
"doi": "10.1093/nar/27.1.340",
"pmc": "PMC148177",
"pubmed": "9847222",
"title": "The Ligand Gated Ion Channel Database.",
"year": 1999
}
],
"uri_format": "https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php"
},
"licebase": {
"contact": {
"email": "Inge.Jonassen@uib.no",
"github": null,
"name": "Inge Jonassen",
"orcid": "0000-0003-4110-0748"
},
"description": "Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects.",
"example": "EMLSAT00000003403",
"homepage": "https://licebase.org",
"keywords": [
"life science"
],
"mappings": {
"biocontext": "LICEBASE",
"fairsharing": "FAIRsharing.c7w81a",
"miriam": "licebase",
"n2t": "licebase",
"re3data": "r3d100013547"
},
"name": "LiceBase",
"pattern": "^[A-Za-z0-9\\-\\/]+$",
"preferred_prefix": "licebase",
"uri_format": "https://licebase.org/?q=$1"
},
"ligandbook": {
"description": "Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community.",
"example": "785",
"homepage": "https://ligandbook.org/",
"mappings": {
"miriam": "ligandbook",
"n2t": "ligandbook"
},
"name": "LigandBook",
"pattern": "^[0-9]+$",
"preferred_prefix": "ligandbook",
"uri_format": "https://ligandbook.org/package/$1"
},
"ligandbox": {
"description": "LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds.",
"example": "D00001",
"homepage": "http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en",
"mappings": {
"biocontext": "LIGANDBOX",
"miriam": "ligandbox",
"n2t": "ligandbox"
},
"name": "LigandBox",
"pattern": "^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$",
"preferred_prefix": "ligandbox",
"uri_format": "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1"
},
"ligandexpo": {
"contact": {
"email": "jwest@rcsb.rutgers.edu",
"github": null,
"name": "John Westbrook",
"orcid": "0000-0002-6686-5475"
},
"description": "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.",
"example": "ABC",
"homepage": "http://ligand-depot.rutgers.edu/index.html",
"keywords": [
"chemical",
"interaction",
"life science",
"nucleic acid",
"protein",
"structure"
],
"mappings": {
"biocontext": "LIGANDEXPO",
"fairsharing": "FAIRsharing.2ma4gq",
"miriam": "ligandexpo",
"n2t": "ligandexpo",
"prefixcommons": "ligandexpo"
},
"name": "Ligand Expo",
"pattern": "^(\\w){3}$",
"preferred_prefix": "ligandexpo",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "Ligand Expo at Rutgers",
"homepage": "http://ligand-expo.rcsb.org/",
"name": "Ligand Expo at Rutgers",
"uri_format": "http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid"
}
],
"publications": [
{
"doi": "10.1093/bioinformatics/bth214",
"pmc": null,
"pubmed": "15059838",
"title": "Ligand Depot: a data warehouse for ligands bound to macromolecules.",
"year": 2004
}
],
"uri_format": "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid"
},
"ligea": {
"comment": "This might just be a provider for CCLE",
"description": "Polymorphism and mutation databases",
"example": "CCLE_867",
"homepage": "http://hpc-bioinformatics.cineca.it/fusion/main",
"mappings": {
"cellosaurus": "LiGeA"
},
"name": "Cancer cell LInes GEne fusions portAl",
"preferred_prefix": "ligea",
"uri_format": "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1"
},
"limore": {
"description": "Cell line databases/resources",
"example": "Li7",
"homepage": "https://www.picb.ac.cn/limore/home",
"mappings": {
"cellosaurus": "LIMORE"
},
"name": "Liver Cancer Model Repository",
"preferred_prefix": "limore",
"uri_format": "https://www.picb.ac.cn/limore/cellLines/single?para=$1"
},
"lincs.cell": {
"description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.",
"example": "LCL-2085",
"homepage": "http://lincsportal.ccs.miami.edu/cells/",
"mappings": {
"biocontext": "LINCS.CELL",
"cellosaurus": "LINCS_LDP",
"miriam": "lincs.cell",
"n2t": "lincs.cell"
},
"name": "LINCS Cell",
"pattern": "^(LCL|LDC|ES|LSC|LPC)-\\d+$",
"preferred_prefix": "lincs.cell",
"synonyms": [
"LINCS_LDP"
],
"uri_format": "http://lincsportal.ccs.miami.edu/cells/#/view/$1"
},
"lincs.data": {
"description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level).",
"example": "LDS-1110",
"homepage": "http://lincsportal.ccs.miami.edu/datasets/",
"mappings": {
"biocontext": "LINCS.DATA",
"miriam": "lincs.data",
"n2t": "lincs.data"
},
"name": "LINCS Data",
"pattern": "^[EL]D[SG]-\\d+$",
"preferred_prefix": "lincs.data",
"providers": [
{
"code": "omicsdi",
"description": "Lincs through OmicsDI",
"homepage": "https://www.omicsdi.org/",
"name": "Lincs through OmicsDI",
"uri_format": "https://www.omicsdi.org/dataset/lincs/$1"
}
],
"uri_format": "http://lincsportal.ccs.miami.edu/datasets/#/view/$1"
},
"lincs.protein": {
"description": "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins.",
"example": "200282",
"homepage": "http://lincs.hms.harvard.edu/db/proteins/",
"mappings": {
"biocontext": "LINCS.PROTEIN",
"miriam": "lincs.protein",
"n2t": "lincs.protein"
},
"name": "LINCS Protein",
"pattern": "^\\d+$",
"preferred_prefix": "lincs.protein",
"uri_format": "https://lincs.hms.harvard.edu/db/proteins/$1"
},
"lincs.smallmolecule": {
"description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC).",
"example": "LSM-6306",
"homepage": "http://lincsportal.ccs.miami.edu/SmallMolecules/",
"mappings": {
"biocontext": "LINCS.SMALLMOLECULE",
"miriam": "lincs.smallmolecule",
"n2t": "lincs.smallmolecule"
},
"name": "LINCS Small Molecule",
"pattern": "^LSM-\\d+$",
"preferred_prefix": "lincs.smallmolecule",
"synonyms": [
"lincs"
],
"uri_format": "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1"
},
"linguist": {
"description": "Registry of programming languages for the Linguist program for detecting and highlighting programming languages.",
"example": "Python",
"homepage": "https://github.com/github/linguist",
"mappings": {
"miriam": "linguist"
},
"name": "Linguist",
"pattern": "^[a-zA-Z0-9 +#'*]+$",
"preferred_prefix": "linguist",
"repository": "https://github.com/github/linguist",
"uri_format": "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1"
},
"linkml": {
"comment": "Closes #508",
"contact": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks.",
"example": "SchemaDefinition",
"github_request_issue": 512,
"homepage": "https://linkml.io/linkml-model/docs/SchemaDefinition/",
"keywords": [
"data integration",
"ontology and terminology"
],
"mappings": {
"biolink": "linkml",
"fairsharing": "FAIRsharing.cb7086"
},
"name": "LinkML",
"preferred_prefix": "linkml",
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{
"doi": "10.5281/zenodo.5598314",
"pmc": null,
"pubmed": null,
"title": "linkml/linkml-model: v1.3.1",
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}
],
"repository": "https://github.com/linkml/",
"twitter": "linkml_data",
"uri_format": "https://w3id.org/linkml/$1"
},
"lipidbank": {
"description": "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.",
"example": "BBA0001",
"homepage": "http://lipidbank.jp/index.html",
"keywords": [
"life science",
"lipid",
"molecule",
"structure"
],
"mappings": {
"biocontext": "LIPIDBANK",
"edam": "2665",
"fairsharing": "FAIRsharing.bdn9br",
"miriam": "lipidbank",
"n2t": "lipidbank",
"prefixcommons": "lipidbank"
},
"name": "LipidBank",
"pattern": "^\\w+\\d+$",
"preferred_prefix": "lipidbank",
"publications": [
{
"doi": null,
"pmc": null,
"pubmed": "12058481",
"title": "[LIPIDBANK for Web, the newly developed lipid database].",
"year": 2002
}
],
"uri_format": "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1"
},
"lipidmaps": {
"description": "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.",
"example": "LMPR0102010012",
"homepage": "http://www.lipidmaps.org",
"keywords": [
"biomedical science",
"endocrinology",
"life science",
"lipid",
"structure",
"systems biology",
"taxonomy"
],
"mappings": {
"biocontext": "LIPIDMAPS",
"cheminf": "000564",
"edam": "2625",
"fairsharing": "FAIRsharing.cpneh8",
"miriam": "lipidmaps",
"n2t": "lipidmaps",
"prefixcommons": "lipidmaps",
"re3data": "r3d100012315",
"wikidata": "P2063"
},
"name": "LIPID MAPS ID",
"pattern": "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$",
"preferred_prefix": "lipidmaps",
"providers": [
{
"code": "scholia",
"description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.",
"homepage": "https://scholia.toolforge.org/",
"name": "Scholia",
"uri_format": "https://scholia.toolforge.org/lipidmaps/$1"
}
],
"publications": [
{
"doi": "10.1194/jlr.r800095-jlr200",
"pmc": "PMC2674711",
"pubmed": "19098281",
"title": "Update of the LIPID MAPS comprehensive classification system for lipids.",
"year": 2008
},
{
"doi": "10.1093/nar/gkm324",
"pmc": "PMC1933166",
"pubmed": "17584797",
"title": "LIPID MAPS online tools for lipid research.",
"year": 2007
},
{
"doi": "10.1093/nar/gkl838",
"pmc": "PMC1669719",
"pubmed": "17098933",
"title": "LMSD: LIPID MAPS structure database.",
"year": 2006
},
{
"doi": "10.1194/jlr.e400004-jlr200",
"pmc": null,
"pubmed": "15722563",
"title": "A comprehensive classification system for lipids.",
"year": 2005
}
],
"synonyms": [
"LIPID MAPS",
"LIPID_MAPS_class",
"LIPID_MAPS_instance"
],
"twitter": "lipidmaps",
"uri_format": "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1"
},
"lipro": {
"contact": {
"email": "bakerc@unb.ca",
"github": null,
"name": "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",
"keywords": [
"obo",
"ontology"
],
"mappings": {
"aberowl": "LIPRO",
"biocontext": "LIPRO",
"bioportal": "LIPRO",
"obofoundry": "lipro"
},
"name": "Lipid Ontology",
"preferred_prefix": "LIPRO",
"uri_format": "http://purl.obolibrary.org/obo/LIPRO_$1"
},
"lncipedia": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A comprehensive compendium of human long non-coding RNAs",
"example": "SNHG3",
"homepage": "https://lncipedia.org",
"keywords": [
"life science"
],
"mappings": {
"fairsharing": "FAIRsharing.84c1a7"
},
"name": "LNCipedia",
"preferred_prefix": "lncipedia",
"publications": [
{
"doi": "10.1093/nar/gkv295",
"pmc": "PMC4417186",
"pubmed": "25829178",
"title": "An update on LNCipedia: a database for annotated human lncRNA sequences.",
"year": 2015
},
{
"doi": "10.1093/nar/gku1060",
"pmc": "PMC4383901",
"pubmed": "25378313",
"title": "An update on LNCipedia: a database for annotated human lncRNA sequences.",
"year": 2014
},
{
"doi": "10.1093/nar/gks915",
"pmc": "PMC3531107",
"pubmed": "23042674",
"title": "LNCipedia: a database for annotated human lncRNA transcript sequences and structures.",
"year": 2012
}
]
},
"loggerhead": {
"contact": {
"email": "peteremidford@yahoo.com",
"github": null,
"name": "Peter Midford",
"orcid": "0000-0001-6512-3296"
},
"deprecated": true,
"homepage": "http://www.mesquiteproject.org/ontology/Loggerhead/index.html",
"keywords": [
"obo",
"ontology"
],
"mappings": {
"biocontext": "LOGGERHEAD",
"obofoundry": "loggerhead"
},
"name": "Loggerhead nesting",
"preferred_prefix": "LOGGERHEAD",
"uri_format": "http://purl.obolibrary.org/obo/LOGGERHEAD_$1"
},
"loinc": {
"contact": {
"email": "loinc@regenstrief.org",
"github": null,
"name": "LOINC Support",
"orcid": null
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The international standard for identifying health measurements, observations, and documents.",
"example": "LL379-9",
"homepage": "https://loinc.org/",
"keywords": [
"biomedical science",
"life science",
"ontology",
"preclinical studies"
],
"mappings": {
"aberowl": "LOINC",
"bartoc": "1897",
"biolink": "LOINC",
"bioportal": "LOINC",
"fairsharing": "FAIRsharing.2mk2zb",
"hl7": "2.16.840.1.113883.6.1",
"wikidata": "P4338"
},
"name": "Logical Observation Identifiers Names and Codes",
"pattern": "^(\\d|\\w)+-\\d$",
"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"
],
"twitter": "LOINC",
"uri_format": "https://loinc.org/$1"
},
"lonza": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Contains information about cells and data sheets related to transfection.",
"example": "968",
"homepage": "https://knowledge.lonza.com",
"mappings": {
"cellosaurus": "Lonza"
},
"name": "Lonza",
"pattern": "^\\d+$",
"preferred_prefix": "lonza",
"uri_format": "https://knowledge.lonza.com/cell?id=$1"
},
"loqate": {
"description": "The data presented here is a result of systematically tracking the localization and abundance of 5330 yeast proteins at single-cell resolution under three different stress conditions (DTT, H2O2 and nitrogen starvation) using the GFP-tagged yeast library",
"example": "1001",
"homepage": "http://www.weizmann.ac.il/molgen/loqate/",
"mappings": {
"prefixcommons": "loqate"
},
"name": "The localization and quantitation atlas of the yeast proteome",
"preferred_prefix": "loqate",
"publications": [
{
"doi": "10.1093/nar/gkt933",
"pmc": "PMC3965041",
"pubmed": "24150937",
"title": "LoQAtE--Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast.",
"year": 2013
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://www.weizmann.ac.il/molgen/loqate/gene/view/$1"
},
"lotus": {
"comment": "IDs are actually leading to the structural part of LOTUS only, which might change in the future. Will adapt the regexp in case.",
"contact": {
"email": "adriano.rutz@ik.me",
"github": "adafede",
"name": "Adriano Rutz",
"orcid": "0000-0003-0443-9902"
},
"contributor": {
"email": "adriano.rutz@ik.me",
"github": "adafede",
"name": "Adriano Rutz",
"orcid": "0000-0003-0443-9902"
},
"description": "LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry.",
"example": "LTS0004651",
"github_request_issue": 222,
"homepage": "https://lotus.naturalproducts.net",
"keywords": [
"chemistry",
"drugs",
"metabolites"
],
"name": "LOTUS Initiative for Open Natural Products Research",
"pattern": "^LTS\\d{7}$",
"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/$1"
},
"lpt": {
"contact": {
"email": "caripark@iastate.edu",
"github": "caripark",
"name": "Carissa Park",
"orcid": "0000-0002-2346-5201"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.",
"download_obo": "https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.obo",
"download_owl": "https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.owl",
"example": "0000001",
"homepage": "https://github.com/AnimalGenome/livestock-product-trait-ontology",
"keywords": [
"ontology"
],
"mappings": {
"aberowl": "LPT",
"agroportal": "LPT",
"biocontext": "LPT",
"bioportal": "LPT",
"fairsharing": "FAIRsharing.g78mbm"
},
"name": "Livestock Product Trait Ontology",
"pattern": "^\\d+$",
"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/$1.xml"
},
"lspci": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)",
"example": "1",
"homepage": "https://labsyspharm.github.io/lspci/",
"keywords": [
"chemistry",
"drugs",
"metabolites"
],
"name": "Laboratory of Systems Pharmacology Compound",
"pattern": "^\\d+$",
"preferred_prefix": "lspci",
"uri_format": "https://labsyspharm.github.io/lspci/$1"
},
"lter": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Ecological terms",
"example": "182",
"homepage": "https://vocab.lternet.edu/vocab/vocab/index.php",
"name": "Long Term Ecological Research Controlled Vocabulary",
"pattern": "^\\d+$",
"preferred_prefix": "lter",
"uri_format": "https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1"
},
"ma": {
"banana": "MA",
"contact": {
"email": "Terry.Hayamizu@jax.org",
"github": "tfhayamizu",
"name": "Terry Hayamizu",
"orcid": "0000-0002-0956-8634"
},
"description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)",
"download_obo": "http://purl.obolibrary.org/obo/ma.obo",
"download_owl": "http://purl.obolibrary.org/obo/ma.owl",
"example": "0002502",
"homepage": "https://github.com/obophenotype/mouse-anatomy-ontology",
"keywords": [
"anatomy",
"mouse",
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "MA",
"biocontext": "MA",
"bioportal": "MA",
"fairsharing": "FAIRsharing.pdwqcr",
"go": "MA",
"miriam": "ma",
"n2t": "ma",
"obofoundry": "ma",
"ols": "ma",
"ontobee": "MA",
"prefixcommons": "ma"
},
"name": "Mouse adult gross anatomy",
"namespace_in_lui": true,
"pattern": "^\\d+$",
"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:$1",
"version": "2017-02-07"
},
"macie": {
"description": "MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved.",
"example": "M0001",
"homepage": "https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html",
"keywords": [
"enzyme",
"life science",
"pathway"
],
"mappings": {
"biocontext": "MACIE",
"edam": "2641",
"fairsharing": "FAIRsharing.7xkx69",
"miriam": "macie",
"n2t": "macie",
"prefixcommons": "macie"
},
"name": "Mechanism, Annotation and Classification in Enzymes",
"pattern": "^M\\d{4}$",
"preferred_prefix": "macie",
"publications": [
{
"doi": "10.1093/nar/gkl774",
"pmc": "PMC1634735",
"pubmed": "17082206",
"title": "MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.",
"year": 2006
},
{
"doi": "10.1093/bioinformatics/bti693",
"pmc": "PMC2748267",
"pubmed": "16188925",
"title": "MACiE: a database of enzyme reaction mechanisms.",
"year": 2005
}
],
"uri_format": "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1"
},
"maizegdb.locus": {
"description": "MaizeGDB is the maize research community's central repository for genetics and genomics information.",
"example": "25011",
"homepage": "http://www.maizegdb.org/",
"keywords": [
"dna",
"genetics",
"genome",
"genomics",
"life science"
],
"mappings": {
"biocontext": "MAIZEGDB.LOCUS",
"fairsharing": "FAIRsharing.aq280w",
"go": "MaizeGDB_Locus",
"miriam": "maizegdb.locus",
"n2t": "maizegdb.locus",
"ncbi": "MaizeGDB",
"prefixcommons": "maizegdb",
"re3data": "r3d100010795",
"uniprot": "DB-0058"
},
"name": "MaizeGDB Locus",
"pattern": "^\\d+$",
"preferred_prefix": "maizegdb.locus",
"publications": [
{
"doi": "10.3389/fpls.2019.01050",
"pmc": "PMC6724615",
"pubmed": "31555312",
"title": "MaizeDIG: Maize Database of Images and Genomes.",
"year": 2019
},
{
"doi": "10.1093/nar/gky1046",
"pmc": "PMC6323944",
"pubmed": "30407532",
"title": "MaizeGDB 2018: the maize multi-genome genetics and genomics database.",
"year": 2019
},
{
"doi": "10.1007/978-1-4939-3167-5_9",
"pmc": null,
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},
{
"doi": "10.1042/bj2900205",
"pmc": "PMC1132403",
"pubmed": "8439290",
"title": "Evolutionary families of peptidases.",
"year": 1993
},
{
"doi": "10.1093/nar/gkx1134",
"pmc": "PMC5753285",
"pubmed": "29145643",
"title": "The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database.",
"year": 2018
},
{
"doi": "10.1093/nar/gkv1118",
"pmc": "PMC4702814",
"pubmed": "26527717",
"title": "Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors.",
"year": 2015
},
{
"doi": "10.1016/j.biochi.2015.10.003",
"pmc": "PMC4756867",
"pubmed": "26455268",
"title": "Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation.",
"year": 2015
},
{
"doi": "10.1093/nar/gkr987",
"pmc": "PMC3245014",
"pubmed": "22086950",
"title": "MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.",
"year": 2011
},
{
"doi": "10.1093/nar/gkm954",
"pmc": "PMC2238837",
"pubmed": "17991683",
"title": "MEROPS: the peptidase database.",
"year": 2007
}
],
"references": [
"https://github.com/biopragmatics/bioregistry/issues/439"
],
"synonyms": [
"merops.inhibitor"
],
"uri_format": "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1"
},
"merops.family": {
"description": "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families.",
"example": "S1",
"homepage": "http://merops.sanger.ac.uk/index.htm",
"mappings": {
"biocontext": "MEROPS.FAMILY",
"miriam": "merops.family",
"n2t": "merops.family"
},
"name": "MEROPS Family",
"part_of": "merops",
"pattern": "^[SCTAGMNU]\\d+$",
"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=$1"
},
"mesh": {
"contact": {
"email": "custserv@nlm.nih.gov",
"github": null,
"name": "NLM Customer Service",
"orcid": null
},
"description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc.",
"example": "C063233",
"example_extras": [
"D000001"
],
"homepage": "http://id.nlm.nih.gov/mesh/",
"keywords": [
"bioinformatics",
"biomedical science",
"classification",
"life science",
"metascience",
"ontology",
"topics"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "MESH",
"bartoc": "391",
"biocontext": "MESH",
"biolink": "MESH",
"bioportal": "MESH",
"cellosaurus": "MeSH",
"edam": "1177",
"fairsharing": "FAIRsharing.qnkw45",
"go": "MeSH",
"hl7": "2.16.840.1.113883.6.177",
"miriam": "mesh",
"n2t": "mesh",
"prefixcommons": "mesh",
"wikidata": "P486"
},
"name": "Medical Subject Headings",
"pattern": "^(C|D)\\d{6,9}$",
"preferred_prefix": "mesh",
"publications": [
{
"doi": null,
"pmc": "PMC197951",
"pubmed": "13982385",
"title": "Medical subject headings.",
"year": 1963
}
],
"synonyms": [
"MESH",
"MESHA",
"MESHC",
"MESHCS",
"MESHD",
"MESHPP",
"MESH_DESCRIPTOR_UI",
"MESH_SUPPLEMENTAL_RECORD_UI",
"MSH",
"MSH2010_2010_02_22"
],
"uri_format": "https://meshb.nlm.nih.gov/record/ui?ui=$1"
},
"mesh.2012": {
"description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012.",
"example": "17186",
"homepage": "http://www.nlm.nih.gov/mesh/",
"mappings": {
"biocontext": "MESH.2012",
"miriam": "mesh.2012",
"n2t": "mesh.2012"
},
"name": "MeSH 2012",
"pattern": "^[A-Za-z0-9]+$",
"preferred_prefix": "mesh.2012",
"provides": "mesh",
"uri_format": "http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded"
},
"mesh.2013": {
"description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013.",
"example": "17165",
"homepage": "http://www.nlm.nih.gov/mesh/",
"mappings": {
"biocontext": "MESH.2013",
"miriam": "mesh.2013",
"n2t": "mesh.2013"
},
"name": "MeSH 2013",
"pattern": "^[A-Za-z0-9]+$",
"preferred_prefix": "mesh.2013",
"provides": "mesh",
"uri_format": "http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded"
},
"metabolights": {
"description": "MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies.",
"example": "MTBLS1",
"homepage": "https://www.ebi.ac.uk/metabolights/",
"mappings": {
"biocontext": "METABOLIGHTS",
"cellosaurus": "MetaboLights",
"miriam": "metabolights",
"n2t": "metabolights",
"re3data": "r3d100011556",
"wikidata": "P3890"
},
"name": "MetaboLights Compound",
"pattern": "^MTBLS\\d+$",
"preferred_prefix": "metabolights",
"providers": [
{
"code": "omicsdi",
"description": "MataboLights through OmicsDI",
"homepage": "https://www.omicsdi.org/",
"name": "MataboLights through OmicsDI",
"uri_format": "https://www.omicsdi.org/dataset/metabolights_dataset/$1"
}
],
"uri_format": "https://www.ebi.ac.uk/metabolights/$1"
},
"metacyc.compound": {
"description": "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.",
"example": "CPD-10330",
"homepage": "https://metacyc.org",
"keywords": [
"life science",
"metabolomics",
"systems biology"
],
"mappings": {
"biocontext": "METACYC.COMPOUND",
"biolink": "MetaCyc",
"fairsharing": "FAIRsharing.yytevr",
"go": "MetaCyc",
"miriam": "metacyc.compound",
"n2t": "metacyc.compound",
"re3data": "r3d100011294"
},
"name": "Metabolic Encyclopedia of metabolic and other pathways",
"pattern": "^[A-Za-z0-9+_.%-:]+$",
"preferred_prefix": "metacyc.compound",
"publications": [
{
"doi": "10.1093/nar/gkv1164",
"pmc": "PMC4702838",
"pubmed": "26527732",
"title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.",
"year": 2015
},
{
"doi": "10.1093/nar/gkt1103",
"pmc": "PMC3964957",
"pubmed": "24225315",
"title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.",
"year": 2013
},
{
"doi": "10.1093/nar/gkr1014",
"pmc": "PMC3245006",
"pubmed": "22102576",
"title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.",
"year": 2011
}
],
"synonyms": [
"MetaCyc"
],
"twitter": "BioCyc",
"uri_format": "https://metacyc.org/compound?orgid=META&id=$1"
},
"metacyc.reaction": {
"description": "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.",
"example": "RXN-14904",
"homepage": "https://metacyc.org",
"mappings": {
"biocontext": "METACYC.REACTION",
"biolink": "metacyc.reaction",
"miriam": "metacyc.reaction",
"n2t": "metacyc.reaction"
},
"name": "MetaCyc Reaction",
"pattern": "^[A-Za-z0-9+_.%-:]+$",
"preferred_prefix": "metacyc.reaction",
"uri_format": "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1"
},
"metanetx.chemical": {
"description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components.",
"example": "MNXM1723",
"homepage": "https://www.metanetx.org/",
"mappings": {
"biocontext": "METANETX.CHEMICAL",
"miriam": "metanetx.chemical",
"n2t": "metanetx.chemical"
},
"name": "MetaNetX chemical",
"pattern": "^(MNXM\\d+|BIOMASS|WATER)$",
"preferred_prefix": "metanetx.chemical",
"uri_format": "https://www.metanetx.org/chem_info/$1"
},
"metanetx.compartment": {
"description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments.",
"example": "MNXC15",
"homepage": "https://www.metanetx.org/",
"mappings": {
"biocontext": "METANETX.COMPARTMENT",
"miriam": "metanetx.compartment",
"n2t": "metanetx.compartment"
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"name": "MetaNetX compartment",
"pattern": "^(MNX[CD]\\d+|BOUNDARY|IN|OUT)$",
"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/$1"
},
"metatlas": {
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"github": "mihai-sysbio",
"name": "Mihail Anton",
"orcid": "0000-0002-7753-9042"
},
"contributor": {
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"github": "mihai-sysbio",
"name": "Mihail Anton",
"orcid": "0000-0002-7753-9042"
},
"description": "A resource for exploring metabolism, starting with a set of of community-curated genome-scale metabolic models of human and model organisms, enriched with pathway maps and other tools for easy browsing and analysis.",
"example": "MAM01234c",
"example_decoys": [
"MAR11851c"
],
"example_extras": [
"MAR11851"
],
"github_request_issue": 495,
"homepage": "https://metabolicatlas.org",
"keywords": [
"chemistry",
"metabolites",
"reactions"
],
"mappings": {
"miriam": "metatlas"
},
"name": "Metabolic Atlas",
"pattern": "^(MAM\\d{5}\\w)|(MAR\\d{5})$",
"preferred_prefix": "metatlas",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://metabolicatlas.org/identifier/MetabolicAtlas/$1"
},
"metatlas.metabolite": {
"contact": {
"email": "mihail.anton@chalmers.se",
"github": "mihai-sysbio",
"name": "Mihail Anton",
"orcid": "0000-0002-7753-9042"
},
"contributor": {
"email": "mihail.anton@chalmers.se",
"github": "mihai-sysbio",
"name": "Mihail Anton",
"orcid": "0000-0002-7753-9042"
},
"description": "A subspace of Metabolic Atlas for compartment-specific records for metabolites.",
"example": "MAM01234c",
"github_request_issue": 495,
"homepage": "https://metabolicatlas.org",
"keywords": [
"chemistry",
"metabolites"
],
"name": "Metabolic Atlas Metabolite",
"part_of": "metatlas",
"pattern": "^MAM\\d{5}\\w$",
"preferred_prefix": "metatlas.metabolite",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://metabolicatlas.org/identifier/MetabolicAtlas/$1"
},
"metatlas.reaction": {
"contact": {
"email": "mihail.anton@chalmers.se",
"github": "mihai-sysbio",
"name": "Mihail Anton",
"orcid": "0000-0002-7753-9042"
},
"contributor": {
"email": "mihail.anton@chalmers.se",
"github": "mihai-sysbio",
"name": "Mihail Anton",
"orcid": "0000-0002-7753-9042"
},
"description": "A subspace of Metabolic Atlas for reactions.",
"example": "MAR11851",
"github_request_issue": 495,
"homepage": "https://metabolicatlas.org",
"keywords": [
"chemistry",
"reactions"
],
"name": "Metabolic Atlas Reaction",
"part_of": "metatlas",
"pattern": "^MAR\\d{5}$",
"preferred_prefix": "metatlas.reaction",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://metabolicatlas.org/identifier/MetabolicAtlas/$1"
},
"metlin": {
"description": "The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry.",
"example": "1455",
"homepage": "http://masspec.scripps.edu/",
"mappings": {
"biocontext": "METLIN",
"miriam": "metlin",
"n2t": "metlin",
"re3data": "r3d100012311"
},
"name": "Metabolite and Tandem Mass Spectrometry Database",
"pattern": "^\\d{4}$",
"preferred_prefix": "metlin",
"uri_format": "http://metlin.scripps.edu/metabo_info.php?molid=$1"
},
"metnetdb": {
"description": "The MetNet database (MetNetDB) contains information on networks of metabolic and regulatory and interactions in Arabidopsis. Types of interactions in MetNetDB include transcription, translation, protein modification, assembly, allosteric regulation, translocation from one subcellular compartment to another.",
"example": "377369",
"homepage": "http://www.metnetdb.org/MetNet_db.htm",
"keywords": [
"dna",
"interaction",
"pathway",
"protein",
"regulation",
"rna",
"small molecule"
],
"mappings": {
"prefixcommons": "metnetdb"
},
"name": "Metabolic Network Exchange Database",
"preferred_prefix": "metnetdb",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://metnetonline.org/browse_pathway2.php?pthID=$1"
},
"mex": {
"description": "A public place to process, interpret and share GC/MS metabolomics datasets.",
"example": "36",
"homepage": "https://www.metabolome-express.org/",
"mappings": {
"biocontext": "MEX",
"miriam": "mex",
"n2t": "mex"
},
"name": "Metabolome Express",
"pattern": "^\\d+$",
"preferred_prefix": "mex",
"providers": [
{
"code": "omicsdi",
"description": "Metabolome Express through OmicsDI",
"homepage": "https://www.omicsdi.org/",
"name": "Metabolome Express through OmicsDI",
"uri_format": "https://www.omicsdi.org/dataset/metabolome_express/MEX$1"
}
],
"uri_format": "https://www.metabolome-express.org/datasetview.php?datasetid=$1"
},
"mf": {
"contact": {
"email": "janna.hastings@gmail.com",
"github": "jannahastings",
"name": "Janna Hastings",
"orcid": "0000-0002-3469-4923"
},
"description": "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning.",
"download_owl": "http://purl.obolibrary.org/obo/mf.owl",
"example": "0000091",
"homepage": "https://github.com/jannahastings/mental-functioning-ontology",
"keywords": [
"biomedical science",
"cognitive neuroscience",
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "MF",
"biocontext": "MF",
"bioportal": "MF",
"fairsharing": "FAIRsharing.4gm9gt",
"obofoundry": "mf",
"ols": "mf",
"ontobee": "MF"
},
"name": "Mental Functioning Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "MF",
"repository": "https://github.com/jannahastings/mental-functioning-ontology",
"uri_format": "http://purl.obolibrary.org/obo/MF_$1",
"version": "2021-11-17"
},
"mfmo": {
"contact": {
"email": "druzinsk@uic.edu",
"github": "RDruzinsky",
"name": "Robert Druzinsky",
"orcid": "0000-0002-1572-1316"
},
"depends_on": [
"uberon"
],
"description": "The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors.",
"download_owl": "http://purl.obolibrary.org/obo/mfmo.owl",
"example": "0000208",
"homepage": "https://github.com/rdruzinsky/feedontology",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "MFMO",
"biocontext": "MFMO",
"bioportal": "MFMO",
"fairsharing": "FAIRsharing.669cnk",
"obofoundry": "mfmo",
"ols": "mfmo",
"ontobee": "MFMO"
},
"name": "Mammalian Feeding Muscle Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "MFMO",
"providers": [
{
"code": "conflated",
"description": "A conflated URL with parts.",
"homepage": "http://purl.obolibrary.org",
"name": "OBO PURL Parts",
"uri_format": "http://purl.obolibrary.org/obo/mfmo.owl#MFMO_$1"
}
],
"repository": "https://github.com/RDruzinsky/feedontology",
"uri_format": "http://purl.obolibrary.org/obo/MFMO_$1",
"version": "2013-11-16"
},
"mfo": {
"contact": {
"email": "Thorsten.Henrich@embl-heidelberg.de",
"github": null,
"name": "Thorsten Henrich",
"orcid": null
},
"deprecated": true,
"description": "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.",
"download_obo": "http://aber-owl.net/media/ontologies/MFO/14/mfo.obo",
"download_owl": "http://purl.obolibrary.org/obo/mfo.owl",
"example": "MFO_0000001",
"homepage": "http://ani.embl.de:8080/mepd/",
"keywords": [
"anatomy",
"development",
"fish",
"obo",
"ontology"
],
"mappings": {
"aberowl": "MFO",
"biocontext": "MFO",
"bioportal": "MFO",
"obofoundry": "mfo",
"prefixcommons": "mfo"
},
"name": "Medaka fish anatomy and development",
"preferred_prefix": "MFO",
"uri_format": "http://purl.obolibrary.org/obo/MFO_$1"
},
"mfoem": {
"contact": {
"email": "janna.hastings@gmail.com",
"github": "jannahastings",
"name": "Janna Hastings",
"orcid": "0000-0002-3469-4923"
},
"description": "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings.",
"download_owl": "http://purl.obolibrary.org/obo/mfoem.owl",
"example": "000204",
"homepage": "https://github.com/jannahastings/emotion-ontology",
"keywords": [
"biomedical science",
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "MFOEM",
"biocontext": "MFOEM",
"bioportal": "MFOEM",
"fairsharing": "FAIRsharing.dx30m8",
"obofoundry": "mfoem",
"ols": "mfoem",
"ontobee": "MFOEM"
},
"name": "Emotion Ontology",
"pattern": "^\\d{6}$",
"preferred_prefix": "MFOEM",
"publications": [
{
"doi": "10.1186/2041-1480-5-38",
"pmc": "PMC4417517",
"pubmed": "25937879",
"title": "Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference.",
"year": 2014
}
],
"repository": "https://github.com/jannahastings/emotion-ontology",
"uri_format": "http://purl.obolibrary.org/obo/MFOEM_$1",
"version": "2021-11-17"
},
"mfomd": {
"contact": {
"email": "janna.hastings@gmail.com",
"github": "jannahastings",
"name": "Janna Hastings",
"orcid": "0000-0002-3469-4923"
},
"description": "The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF).",
"download_owl": "http://purl.obolibrary.org/obo/mfomd.owl",
"example": "0000046",
"homepage": "https://github.com/jannahastings/mental-functioning-ontology",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "MFOMD",
"biocontext": "MFOMD",
"bioportal": "MFOMD",
"fairsharing": "FAIRsharing.q053vb",
"obofoundry": "mfomd",
"ols": "mfomd",
"ontobee": "MFOMD"
},
"name": "Mental Disease Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "MFOMD",
"repository": "https://github.com/jannahastings/mental-functioning-ontology",
"uri_format": "http://purl.obolibrary.org/obo/MFOMD_$1",
"version": "2020-04-26"
},
"mge": {
"banana": "mge",
"deprecated": true,
"description": "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.",
"example": "2",
"homepage": "http://aclame.ulb.ac.be/",
"keywords": [
"gene",
"genome",
"life science"
],
"mappings": {
"biocontext": "ACLAME",
"edam": "2631",
"fairsharing": "FAIRsharing.5tfcy8",
"miriam": "mge",
"n2t": "mge",
"prefixcommons": "aclame"
},
"name": "Aclame",
"namespace_in_lui": true,
"pattern": "^\\d+$",
"preferred_prefix": "mge",
"publications": [
{
"doi": "10.1093/nar/gkp938",
"pmc": "PMC2808911",
"pubmed": "19933762",
"title": "ACLAME: a CLAssification of Mobile genetic Elements, update 2010.",
"year": 2009
},
{
"doi": "10.1093/nar/gkh084",
"pmc": "PMC308818",
"pubmed": "14681355",
"title": "ACLAME: a CLAssification of Mobile genetic Elements.",
"year": 2004
}
],
"synonyms": [
"aclame"
],
"uri_format": "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1"
},
"mgi": {
"banana": "MGI",
"description": "The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.",
"example": "6017782",
"homepage": "http://www.informatics.jax.org/",
"keywords": [
"expression",
"life science",
"ontology and terminology",
"phenotype",
"sequence"
],
"mappings": {
"biocontext": "MGI",
"cellosaurus": "MGI",
"edam": "3274",
"fairsharing": "FAIRsharing.fcwyhz",
"go": "MGI",
"miriam": "mgi",
"n2t": "mgi",
"ncbi": "MGI",
"prefixcommons": "mgi",
"re3data": "r3d100010266",
"uniprot": "DB-0060",
"wikidata": "P671"
},
"name": "Mouse Genome Informatics",
"namespace_in_lui": true,
"pattern": "^\\d+$",
"preferred_prefix": "MGI",
"providers": [
{
"code": "agr",
"description": "MGI through the Alliance of Genome Resources",
"homepage": "https://www.alliancegenome.org",
"name": "MGI through the Alliance of Genome Resources",
"uri_format": "https://www.alliancegenome.org/gene/MGI:$1"
},
{
"code": "mgi.marker",
"description": "MGI Marker",
"homepage": "http://www.informatics.jax.org/marker",
"name": "MGI Marker",
"uri_format": "http://www.informatics.jax.org/marker/MGI:$1"
}
],
"publications": [
{
"doi": "10.1126/science.8091224",
"pmc": null,
"pubmed": "8091224",
"title": "A database for mouse development.",
"year": 1994
},
{
"doi": "10.1093/nar/gky1056",
"pmc": "PMC6323923",
"pubmed": "30407599",
"title": "Mouse Genome Database (MGD) 2019.",
"year": 2019
},
{
"doi": "10.1093/nar/gky922",
"pmc": "PMC6324054",
"pubmed": "30335138",
"title": "The mouse Gene Expression Database (GXD): 2019 update.",
"year": 2019
},
{
"doi": "10.1093/ilar/ilx013",
"pmc": "PMC5886341",
"pubmed": "28838066",
"title": "Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse.",
"year": 2017
},
{
"doi": "10.1007/978-1-4939-6427-7_3",
"pmc": null,
"pubmed": "27933520",
"title": "Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research.",
"year": 2017
},
{
"doi": "10.1093/nar/gkw1040",
"pmc": "PMC5210536",
"pubmed": "27899570",
"title": "Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse.",
"year": 2016
},
{
"doi": "10.1093/nar/gkt1225",
"pmc": "PMC3964950",
"pubmed": "24285300",
"title": "The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse.",
"year": 2013
},
{
"doi": "10.1093/nar/gks1115",
"pmc": "PMC3531104",
"pubmed": "23175610",
"title": "The mouse genome database: genotypes, phenotypes, and models of human disease.",
"year": 2012
},
{
"doi": "10.1093/nar/gkr974",
"pmc": "PMC3245042",
"pubmed": "22075990",
"title": "The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse.",
"year": 2011
},
{
"doi": "10.1093/nar/gki113",
"pmc": "PMC540067",
"pubmed": "15608240",
"title": "The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology.",
"year": 2005
}
],
"synonyms": [
"MGD",
"MGI"
],
"twitter": "mgi_mouse",
"uri_format": "http://www.informatics.jax.org/accession/MGI:$1"
},
"mgnify.analysis": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Analyses of microbiome data within MGnify",
"example": "MGYA00002270",
"homepage": "https://www.ebi.ac.uk/metagenomics/",
"name": "MGnify Analysis",
"pattern": "^MGYA\\d+$",
"preferred_prefix": "mgnify.analysis",
"uri_format": "https://www.ebi.ac.uk/metagenomics/analyses/$1"
},
"mgnify.proj": {
"description": "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.",
"example": "ERP004492",
"homepage": "https://www.ebi.ac.uk/metagenomics",
"mappings": {
"miriam": "mgnify.proj",
"n2t": "mgnify.proj"
},
"name": "MGnify Project",
"pattern": "^[A-Z]+[0-9]+$",
"preferred_prefix": "mgnify.proj",
"uri_format": "https://www.ebi.ac.uk/metagenomics/projects/$1"
},
"mgnify.samp": {
"description": "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.",
"example": "SRS086444",
"homepage": "https://www.ebi.ac.uk/metagenomics",
"mappings": {
"miriam": "mgnify.samp",
"n2t": "mgnify.samp"
},
"name": "MGnify Sample",
"pattern": "^[A-Z]+[0-9]+$",
"preferred_prefix": "mgnify.samp",
"uri_format": "https://www.ebi.ac.uk/metagenomics/samples/$1"
},
"mi": {
"banana": "MI",
"contact": {
"email": "pporras@ebi.ac.uk",
"github": "pporrasebi",
"name": "Pablo Porras Millán",
"orcid": "0000-0002-8429-8793"
},
"description": "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.",
"download_obo": "http://purl.obolibrary.org/obo/mi.obo",
"download_owl": "http://purl.obolibrary.org/obo/mi.owl",
"example": "0058",
"homepage": "https://github.com/HUPO-PSI/psi-mi-CV",
"keywords": [
"interaction",
"life science",
"molecule",
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "MI",
"biocontext": "PSIMI",
"biolink": "MI",
"bioportal": "MI",
"fairsharing": "FAIRsharing.8qzmtr",
"go": "PSI-MI",
"miriam": "mi",
"n2t": "psimi",
"obofoundry": "mi",
"ols": "mi",
"ontobee": "MI",
"prefixcommons": "psi.mi"
},
"name": "Molecular Interactions Controlled Vocabulary",
"namespace_in_lui": true,
"pattern": "^\\d{4}$",
"preferred_prefix": "MI",
"publications": [
{
"doi": "10.1038/nbt926",
"pmc": null,
"pubmed": "14755292",
"title": "The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.",
"year": 2004
}
],
"repository": "https://github.com/HUPO-PSI/psi-mi-CV",
"synonyms": [
"PSI-MI"
],
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1"
},
"miaa": {
"comment": "same as MAT",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"name": "Minimal Information About Anatomy ontology",
"preferred_prefix": "miaa",
"references": [
"https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/rols/inst/doc/rols.pdf"
]
},
"miapa": {
"contact": {
"email": "hilmar.lapp@duke.edu",
"github": "hlapp",
"name": "Hilmar Lapp",
"orcid": "0000-0001-9107-0714"
},
"description": "The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata