3dmet: description: 3DMET is a database collecting three-dimensional structures of natural metabolites. example: B00162 homepage: http://www.3dmet.dna.affrc.go.jp/ mappings: biocontext: 3DMET edam: '2635' fairsharing: FAIRsharing.5ab0n7 miriam: 3dmet n2t: 3dmet prefixcommons: 3dmet wikidata: P2796 name: 3D Metabolites pattern: ^B\d{5}$ preferred_prefix: 3dmet publications: - doi: 10.2142/biophysico.15.0_87 pmc: PMC5992871 pubmed: '29892514' title: 'Chemical curation to improve data accuracy: recent development of the 3DMET database.' year: 2018 - doi: 10.1021/ci300309k pmc: null pubmed: '23293959' title: 'Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures.' year: 2013 uri_format: http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1 4dn.biosource: description: The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases. example: 4DNSR73BT2A2 homepage: https://data.4dnucleome.org/biosources mappings: cellosaurus: 4DN fairsharing: FAIRsharing.CugtbQ miriam: 4dn prefixcommons: 4dn name: 4D Nucleome Data Portal Biosource pattern: ^4DN[A-Z]{2}[A-Z0-9]{7}$ preferred_prefix: 4dn.biosource publications: - doi: 10.1038/nature23884 pmc: PMC5617335 pubmed: '28905911' title: The 4D nucleome project. year: 2017 synonyms: - 4DN 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 aao: contact: email: david.c.blackburn@gmail.com github: null name: David Blackburn orcid: null deprecated: true description: A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon. homepage: http://github.com/seger/aao mappings: biocontext: AAO fairsharing: FAIRsharing.mxx5rp obofoundry: aao prefixcommons: aao name: Amphibian gross anatomy no_own_terms: true 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/ mappings: cellosaurus: ABCD fairsharing: FAIRsharing.Z8OKi5 uniprot: ABCD name: AntiBodies Chemically Defined database preferred_prefix: abcd 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=$1 abs: description: The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. example: A0014 homepage: http://genome.crg.es/datasets/abs2005/ mappings: biocontext: ABS edam: '2741' fairsharing: FAIRsharing.7mnebr miriam: abs n2t: abs prefixcommons: abs name: Annotated Regulatory Binding Sites pattern: ^A\d+$ 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 name: Activity Streams preferred_prefix: ac uri_format: http://www.w3.org/ns/activitystreams#$1 aceview.worm: description: AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression. example: aap-1 homepage: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm mappings: biocontext: ACEVIEW.WORM miriam: aceview.worm n2t: aceview.worm prefixcommons: aceview.worm name: Aceview Worm pattern: ^[a-z0-9-]+$ preferred_prefix: aceview.worm publications: - doi: 10.1186/gb-2006-7-s1-s12 pmc: PMC1810549 pubmed: '16925834' title: 'AceView: a comprehensive cDNA-supported gene and transcripts annotation.' year: 2006 uri_format: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1 addexbio: description: Cell line collections example: C0020004/4992 homepage: https://www.addexbio.com/productshow?id=4 mappings: cellosaurus: AddexBio name: AddexBio cell line products preferred_prefix: addexbio uri_format: https://www.addexbio.com/productdetail?pid=$1 addgene: description: Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world. example: '50943' homepage: http://addgene.org/ mappings: fairsharing: FAIRsharing.8hcczk miriam: addgene n2t: addgene prefixcommons: addgene re3data: r3d100010741 name: Addgene Plasmid Repository pattern: ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$ preferred_prefix: addgene publications: - doi: 10.1093/nar/gku893 pmc: PMC4384007 pubmed: '25392412' title: 'The Addgene repository: an international nonprofit plasmid and data resource.' year: 2014 uri_format: http://addgene.org/$1 ado: contact: email: alpha.tom.kodamullil@scai.fraunhofer.de github: akodamullil name: Alpha Tom Kodamullil orcid: 0000-0001-9896-3531 depends_on: - bfo description: Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining. download_owl: http://purl.obolibrary.org/obo/ado.owl example: '0000001' homepage: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO license: CC BY 4.0 mappings: aberowl: ADO bioportal: ADO fairsharing: FAIRsharing.ckd4rf obofoundry: ado ols: ado name: Alzheimer's Disease Ontology pattern: ^\d{7}$ preferred_prefix: ADO publications: - doi: 10.1016/j.jalz.2013.02.009 pmc: null pubmed: '23830913' title: 'ADO: a disease ontology representing the domain knowledge specific to Alzheimer''s disease.' year: 2013 repository: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO uri_format: http://purl.obolibrary.org/obo/ADO_$1 version: 2.0.0 adw: contact: email: adw_geeks@umich.edu github: null name: Animal Diversity Web technical staff orcid: null deprecated: true description: Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology. download_owl: http://aber-owl.net/media/ontologies/ADW/2/adw.owl example: Lycalopex_vetulus homepage: http://www.animaldiversity.org mappings: aberowl: ADW biocontext: ADW bioportal: ADW fairsharing: FAIRsharing.t9fvdn miriam: adw n2t: adw obofoundry: adw name: Animal natural history and life history pattern: ^[A-Z_a-z]+$ preferred_prefix: ADW uri_format: https://animaldiversity.org/accounts/$1 aeo: appears_in: - ehdaa2 contact: email: J.Bard@ed.ac.uk github: null name: Jonathan Bard orcid: null deprecated: true description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology download_obo: https://raw.githubusercontent.com/obophenotype/human-developmental-anatomy-ontology/master/src/ontology/aeo.obo download_owl: http://purl.obolibrary.org/obo/aeo.owl example: '0001017' homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/ license: CC BY 4.0 mappings: aberowl: AEO biocontext: AEO bioportal: AEO fairsharing: FAIRsharing.93ee19 obofoundry: aeo ols: aeo ontobee: AEO name: Anatomical Entity Ontology pattern: ^\d{7}$ preferred_prefix: AEO publications: - doi: 10.3389/fgene.2012.00018 pmc: PMC3278863 pubmed: '22347883' title: The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs. year: 2012 repository: https://github.com/obophenotype/human-developmental-anatomy-ontology synonyms: - AEO_RETIRED uri_format: http://purl.obolibrary.org/obo/AEO_$1 version: '2014-12-05' aero: contact: email: mcourtot@gmail.com github: null name: Melanie Courtot orcid: 0000-0002-9551-6370 deprecated: true description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events download_owl: http://purl.obolibrary.org/obo/aero.owl example: '0000125' homepage: http://purl.obolibrary.org/obo/aero license: CC BY 3.0 mappings: aberowl: AERO biocontext: AERO bioportal: AERO fairsharing: FAIRsharing.rycy2x obofoundry: aero name: Adverse Event Reporting Ontology pattern: ^\d{7}$ preferred_prefix: AERO uri_format: http://purl.obolibrary.org/obo/AERO_$1 affy.probeset: description: An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration. example: 243002_at homepage: http://www.affymetrix.com/ mappings: biocontext: AFFY.PROBESET miriam: affy.probeset n2t: affy.probeset name: Affymetrix Probeset pattern: ^\d{4,}((_[asx])?_at)$ preferred_prefix: affy.probeset providers: - code: CURATOR_REVIEW description: Bio2RDF homepage: http://cu.affymetrix.bio2rdf.org/fct/ name: Bio2RDF uri_format: http://cu.affymetrix.bio2rdf.org/describe/?url=http://bio2rdf.org/affymetrix:$1 uri_format: https://www.affymetrix.com/LinkServlet?probeset=$1 afo: contact: email: more.info@allotrope.org github: null name: Allotrope Foundation orcid: null description: Allotrope Merged Ontology Suite download_owl: http://purl.allotrope.org/voc/afo/merged-OLS/REC/2019/05/10 homepage: https://www.allotrope.org/ mappings: aberowl: AFO bioportal: AFO fairsharing: FAIRsharing.595710 ols: afo name: Allotrope Merged Ontology Suite no_own_terms: true preferred_prefix: afo version: '2019-05-10' aftol.taxonomy: contributor_extras: - email: laylamichan@ciencias.unam.mx github: lmichan name: Layla Michán Aguirre orcid: 0000-0002-5798-662X description: The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species. example: '959' homepage: https://aftol.umn.edu mappings: biocontext: AFTOL.TAXONOMY miriam: aftol.taxonomy n2t: aftol.taxonomy name: Assembling the Fungal Tree of Life - Taxonomy pattern: ^\d+$ preferred_prefix: aftol.taxonomy uri_format: http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1 agilent.probe: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699.' example: A_24_P98555 homepage: https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt name: Agilent Probe pattern: ^A_\d+_.+$ preferred_prefix: agilent.probe references: - http://www.cs.tau.ac.il/cgi-bin/cgiwrap/click/get.cgi/conversionFiles/conversion_human_14850_agilent2entrez.txt agricola: contributor_extras: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 - email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century. example: '50018' homepage: http://agricola.nal.usda.gov/ mappings: biocontext: AGRICOLA go: AGRICOLA_ID miriam: agricola n2t: agricola name: Agricultural Online Access pattern: ^\d+$ preferred_prefix: agricola synonyms: - AGR - AGRICOLA_ID uri_format: https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1 agrkb: contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 contributor: email: null github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 description: 'The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations. The Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location: - [ZFIN](https://zfin.org) - Zebrafish Information Network - [WormBase](https://wormbase.org) - [MGI](https://www.mgi.org) - Mouse Genome Informatics - [RGD](https://rgd.mcw.edu) - Rat Genome Database - [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database - [FlyBase](https://flybase.org) - [Xenbase](https://www.xenbase.org)' example: '100000000000001' github_request_issue: 359 homepage: https://www.alliancegenome.org mappings: biolink: AGRKB name: Alliance of Genome Resources Knowledge Base pattern: ^[1-9][0-9]{14}$ preferred_prefix: agrkb reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.alliancegenome.org/accession/$1 agro: contact: email: m.a.laporte@cgiar.org github: marieALaporte name: Marie-Angélique Laporte orcid: 0000-0002-8461-9745 depends_on: - bfo - envo - foodon - go - iao - ncbitaxon - obi - pato - peco - po - ro - to - uo - xco description: AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities download_obo: https://raw.githubusercontent.com/KrishnaTO/agro/master/agro.obo download_owl: http://purl.obolibrary.org/obo/agro.owl example: '00020007' homepage: https://github.com/AgriculturalSemantics/agro license: CC BY 4.0 mappings: aberowl: AGRO agroportal: AGRO biocontext: AGRO bioportal: AGRO fairsharing: FAIRsharing.m40bhw obofoundry: agro ols: agro ontobee: AGRO name: Agronomy Ontology pattern: ^\d{8}$ preferred_prefix: AGRO repository: https://github.com/AgriculturalSemantics/agro uri_format: http://purl.obolibrary.org/obo/AGRO_$1 version: '2021-11-05' agrovoc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages. example: '2842' homepage: https://data.apps.fao.org/catalog/organization/agrovoc mappings: agroportal: AGROVOC ecoportal: AGROVOC fairsharing: FAIRsharing.anpj91 name: Agronomy Vocabulary pattern: ^[a-z0-9]+$ preferred_prefix: agrovoc publications: - doi: https://doi.org/10.4060/cb2838en pmc: null pubmed: null title: AGROVOC – Semantic data interoperability on food and agriculture year: null - doi: https://doi.org/10.3390/engproc2021009017 pmc: null pubmed: null title: 'How Agricultural Digital Innovation Can Benefit from Semantics: The Case of the AGROVOC Multilingual Thesaurus' year: null - doi: 10.1016/j.compag.2020.105965 pmc: null pubmed: null title: 'AGROVOC: The linked data concept hub for food and agriculture' year: null references: - http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_core.nt.zip - http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_lod.nt.zip - https://en.wikipedia.org/wiki/AGROVOC uri_format: http://aims.fao.org/aos/agrovoc/c_$1 aism: appears_in: - colao - lepao contact: email: entiminae@gmail.com github: JCGiron name: Jennifer C. Girón orcid: 0000-0002-0851-6883 depends_on: - bfo - bspo - caro - pato - ro - uberon description: The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research. download_json: http://purl.obolibrary.org/obo/aism.json download_obo: http://purl.obolibrary.org/obo/aism.obo download_owl: http://purl.obolibrary.org/obo/aism.owl example: '0000027' homepage: https://github.com/insect-morphology/aism license: CC BY 4.0 mappings: aberowl: AISM bioportal: AISM obofoundry: aism ols: aism ontobee: AISM name: Ontology for the Anatomy of the Insect SkeletoMuscular system pattern: ^\d{7}$ preferred_prefix: AISM repository: https://github.com/insect-morphology/aism uri_format: http://purl.obolibrary.org/obo/AISM_$1 version: '2022-06-27' allergome: description: Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources. example: '1948' homepage: http://www.allergome.org/ mappings: biocontext: ALLERGOME fairsharing: FAIRsharing.w6cxgb miriam: allergome n2t: allergome prefixcommons: allergome uniprot: Allergome name: Allergome pattern: ^\d+$ preferred_prefix: allergome publications: - doi: 10.1016/j.cellimm.2007.02.012 pmc: null pubmed: '17434469' title: 'Bioinformatics applied to allergy: allergen databases, from collecting sequence information to data integration. The Allergome platform as a model.' year: 2007 - doi: null pmc: null pubmed: '17393720' title: 'Allergome: a unifying platform.' year: 2006 uri_format: http://www.allergome.org/script/dettaglio.php?id_molecule=$1 alzforum.mutation: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease. example: app-d678n-tottori homepage: https://www.alzforum.org/mutations name: Alzforum Mutations preferred_prefix: alzforum.mutation synonyms: - Alzforum_mut uri_format: https://www.alzforum.org/mutations/$1 amoebadb: description: AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: EDI_244000 homepage: http://amoebadb.org/amoeba/ mappings: biocontext: AMOEBADB fairsharing: FAIRsharing.swbypy miriam: amoebadb n2t: amoebadb prefixcommons: amoebadb re3data: r3d100012457 name: AmoebaDB pattern: ^EDI_\d+$ preferred_prefix: amoebadb publications: - doi: 10.1093/nar/gkp941 pmc: PMC2808945 pubmed: '19914931' title: 'EuPathDB: a portal to eukaryotic pathogen databases.' year: 2009 uri_format: https://amoebadb.org/amoeba/app/record/gene/$1 amphx: contact: email: hescriva@obs-banyuls.fr github: hescriva name: Hector Escriva orcid: 0000-0001-7577-5028 depends_on: - uberon description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). download_obo: http://purl.obolibrary.org/obo/amphx.obo download_owl: http://purl.obolibrary.org/obo/amphx.owl example: '1000160' homepage: https://github.com/EBISPOT/amphx_ontology license: CC BY 3.0 mappings: aberowl: AMPHX bioportal: AMPHX obofoundry: amphx ols: amphx ontobee: AMPHX name: The Amphioxus Development and Anatomy Ontology pattern: ^\d+$ preferred_prefix: AMPHX repository: https://github.com/EBISPOT/amphx_ontology uri_format: http://purl.obolibrary.org/obo/AMPHX_$1 version: '2020-12-18' antibodyregistry: description: The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information. example: '493771' homepage: http://antibodyregistry.org/ mappings: biocontext: ANTIBODYREGISTRY miriam: antibodyregistry n2t: antibodyregistry name: Antibody Registry pattern: ^\d{6}$ preferred_prefix: antibodyregistry uri_format: http://antibodyregistry.org/AB_$1 antweb: description: AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures. example: casent0106247 homepage: http://www.antweb.org/ mappings: biocontext: ANTWEB fairsharing: FAIRsharing.yk38tw miriam: antweb n2t: antweb ncbi: AntWeb prefixcommons: antweb wikidata: P5299 name: AntWeb pattern: ^casent\d+(\-D\d+)?$ preferred_prefix: antweb publications: - doi: 10.1038/424242b pmc: null pubmed: '12867945' title: Ants join online colony to boost conservation efforts. year: 2003 uri_format: http://www.antweb.org/specimen.do?name=$1 aop: description: International repository of Adverse Outcome Pathways. example: '98' homepage: https://aopwiki.org/ mappings: biocontext: AOP miriam: aop n2t: aop name: AOPWiki pattern: ^\d+$ preferred_prefix: aop uri_format: https://aopwiki.org/aops/$1 aop.events: description: International repository of Adverse Outcome Pathways. example: '3' homepage: https://aopwiki.org/ mappings: biocontext: AOP.EVENTS miriam: aop.events n2t: aop.events name: AOPWiki (Key Event) pattern: ^\d+$ preferred_prefix: aop.events uri_format: https://aopwiki.org/events/$1 aop.relationships: description: International repository of Adverse Outcome Pathways. example: '5' homepage: https://aopwiki.org/ mappings: biocontext: AOP.RELATIONSHIPS miriam: aop.relationships n2t: aop.relationships name: AOPWiki (Key Event Relationship) pattern: ^\d+$ preferred_prefix: aop.relationships uri_format: https://aopwiki.org/relationships/$1 aop.stressor: description: International repository of Adverse Outcome Pathways. example: '9' homepage: https://aopwiki.org/ mappings: biocontext: AOP.STRESSOR miriam: aop.stressor n2t: aop.stressor name: AOPWiki (Stressor) pattern: ^\d+$ preferred_prefix: aop.stressor uri_format: https://aopwiki.org/stressors/$1 apaonto: contact: email: awalker@apa.org github: null name: Alvin Walker orcid: 0000-0003-1082-8760 description: An ontology developed by the American Psychological Association (APA). Note that URIs in this ontology appear to have been generated with erroneous settings in Protege. download_owl: http://aber-owl.net/media/ontologies/APAONTO/4/apaonto.owl example: Abdomen homepage: https://bioportal.bioontology.org/ontologies/APAONTO mappings: aberowl: APAONTO bioportal: APAONTO fairsharing: FAIRsharing.gkw1w8 name: Psychology Ontology preferred_prefix: apaonto references: - https://github.com/biopragmatics/bioregistry/issues/528 uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1 apd: description: The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides. example: '01001' homepage: http://aps.unmc.edu/AP/ mappings: biocontext: APD fairsharing: FAIRsharing.ctwd7b miriam: apd n2t: apd prefixcommons: apd name: Antimicrobial Peptide Database pattern: ^\d{5}$ preferred_prefix: apd publications: - doi: 10.1093/nar/gkv1278 pmc: PMC4702905 pubmed: '26602694' title: 'APD3: the antimicrobial peptide database as a tool for research and education.' year: 2015 uri_format: http://aps.unmc.edu/AP/database/query_output.php?ID=$1 aphidbase.transcript: description: AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information. example: ACYPI000159 homepage: http://www.aphidbase.com/aphidbase mappings: biocontext: APHIDBASE.TRANSCRIPT miriam: aphidbase.transcript n2t: aphidbase.transcript name: AphidBase Transcript pattern: ^ACYPI\d{6}(-RA)?$ preferred_prefix: aphidbase.transcript uri_format: http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1 apid.interactions: description: APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier. example: P01116 homepage: http://cicblade.dep.usal.es:8080/APID/ mappings: biocontext: APID.INTERACTIONS miriam: apid.interactions n2t: apid.interactions name: APID Interactomes pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ preferred_prefix: apid.interactions provides: uniprot uri_format: http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1 apo: contact: email: stacia@stanford.edu github: srengel name: Stacia R Engel orcid: 0000-0001-5472-917X description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi. download_obo: http://purl.obolibrary.org/obo/apo.obo download_owl: http://purl.obolibrary.org/obo/apo.owl example: 0000184 homepage: http://www.yeastgenome.org/ license: CC BY 4.0 mappings: aberowl: APO biocontext: YPO bioportal: APO fairsharing: FAIRsharing.dyqz3y obofoundry: apo ols: apo ontobee: APO name: Ascomycete phenotype ontology pattern: ^\d{7}$ preferred_prefix: APO publications: - doi: 10.1093/database/bap001 pmc: PMC2790299 pubmed: '20157474' title: New mutant phenotype data curation system in the Saccharomyces Genome Database. year: 2009 repository: https://github.com/obophenotype/ascomycete-phenotype-ontology uri_format: https://www.yeastgenome.org/observable/APO:$1 version: '2022-07-06' apollosv: appears_in: - scdo contact: email: hoganwr@ufl.edu github: hoganwr name: William Hogan orcid: 0000-0002-9881-1017 description: Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models download_owl: http://purl.obolibrary.org/obo/apollo_sv.owl example: '00000443' homepage: https://github.com/ApolloDev/apollo-sv license: CC BY 4.0 mappings: aberowl: APOLLO_SV bioportal: APOLLO-SV fairsharing: FAIRsharing.ngv2xx obofoundry: apollo_sv ols: apollo_sv ontobee: APOLLO_SV name: Apollo Structured Vocabulary pattern: ^\d{8}$ preferred_prefix: APOLLO_SV publications: - doi: 10.1186/s13326-016-0092-y pmc: PMC4989460 pubmed: '27538448' title: 'The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.' year: 2016 - doi: null pmc: PMC3900155 pubmed: '24551417' title: 'Apollo: giving application developers a single point of access to public health models using structured vocabularies and Web services.' year: 2013 repository: https://github.com/ApolloDev/apollo-sv uri_format: http://purl.obolibrary.org/obo/APOLLO_SV_$1 version: 4.1.1 arachnoserver: description: ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information. example: AS000060 homepage: http://www.arachnoserver.org/ mappings: biocontext: ARACHNOSERVER edam: '2578' fairsharing: FAIRsharing.c54ywe miriam: arachnoserver n2t: arachnoserver prefixcommons: arachnoserver re3data: r3d100012902 uniprot: ArachnoServer name: ArachnoServer pattern: ^AS\d{6}$ preferred_prefix: arachnoserver publications: - doi: 10.1093/bioinformatics/btx661 pmc: null pubmed: '29069336' title: 'ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins.' year: 2018 - doi: 10.1093/nar/gkq1058 pmc: PMC3013666 pubmed: '21036864' title: ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures. year: 2010 uri_format: http://www.arachnoserver.org/toxincard.html?id=$1 araport: description: Website with general information about Arabidopsis and functionalities such as a genomic viewer example: AT1G01010 homepage: https://www.araport.org/ mappings: ncbi: Araport uniprot: Araport name: Arabidopsis Information Portal preferred_prefix: araport uri_format: https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1 ardb: description: The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes. example: CAE46076 homepage: http://ardb.cbcb.umd.edu/ mappings: biocontext: ARDB miriam: ardb n2t: ardb name: Antibiotic Resistance Genes Database pattern: ^[A-Z_]{3}[0-9]{4,}$ preferred_prefix: ardb uri_format: http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1 ark: banana: ark description: An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type. example: /12345/fk1234 homepage: http://n2t.net/ mappings: biocontext: ARK miriam: ark n2t: ark name: Archival Resource Key namespace_in_lui: true pattern: ^/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$ preferred_prefix: ark uri_format: http://n2t.net/ark:$1 aro: appears_in: - scdo contact: email: mcarthua@mcmaster.ca github: agmcarthur name: Andrew G. McArthur orcid: 0000-0002-1142-3063 description: Antibiotic resistance genes and mutations download_obo: http://purl.obolibrary.org/obo/aro.obo download_owl: http://purl.obolibrary.org/obo/aro.owl example: '1000001' homepage: https://github.com/arpcard/aro license: CC BY 4.0 mappings: aberowl: ARO biocontext: ARO bioportal: ARO obofoundry: aro ols: aro ontobee: ARO name: Antibiotic Resistance Ontology pattern: ^\d{7}$ preferred_prefix: ARO publications: - doi: 10.1093/nar/gkz935 pmc: PMC7145624 pubmed: '31665441' title: 'CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.' year: 2020 repository: https://github.com/arpcard/aro uri_format: http://purl.obolibrary.org/obo/ARO_$1 arrayexpress: description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations. example: E-MEXP-1712 homepage: https://www.ebi.ac.uk/arrayexpress/ mappings: biocontext: ARRAYEXPRESS cellosaurus: ArrayExpress fairsharing: FAIRsharing.6k0kwd miriam: arrayexpress n2t: arrayexpress prefixcommons: arrayexpress re3data: r3d100010222 name: ArrayExpress pattern: ^[AEP]-\w{4}-\d+$ preferred_prefix: arrayexpress providers: - code: omicsdi description: ArrayExpress through OmicsDI homepage: https://www.omicsdi.org/ name: ArrayExpress through OmicsDI uri_format: https://www.omicsdi.org/dataset/arrayexpress-repository/$1 publications: - doi: 10.1093/nar/gkg091 pmc: PMC165538 pubmed: '12519949' title: ArrayExpress--a public repository for microarray gene expression data at the EBI. year: 2003 uri_format: https://www.ebi.ac.uk/arrayexpress/experiments/$1 arrayexpress.platform: description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results. example: A-GEOD-50 homepage: https://www.ebi.ac.uk/arrayexpress/ mappings: biocontext: ARRAYEXPRESS.PLATFORM miriam: arrayexpress.platform n2t: arrayexpress.platform name: ArrayExpress Platform pattern: ^[AEP]-\w{4}-\d+$ preferred_prefix: arrayexpress.platform uri_format: https://www.ebi.ac.uk/arrayexpress/arrays/$1 arraymap: description: arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome. example: icdom:8500_3 homepage: https://www.arraymap.org mappings: biocontext: ARRAYMAP fairsharing: FAIRsharing.1fbc5y miriam: arraymap n2t: arraymap re3data: r3d100012630 name: ArrayMap pattern: ^[\w\-:,]{3,64}$ preferred_prefix: arraymap uri_format: https://www.arraymap.org/pgx:$1 arxiv: description: arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology. example: 0807.4956v1 homepage: https://arxiv.org/ mappings: biocontext: ARXIV miriam: arxiv n2t: arxiv prefixcommons: arxiv name: arXiv pattern: ^(\w+(\-\w+)?(\.\w+)?)?\d{4,7}(\.\d+(v\d+)?)?$ preferred_prefix: arxiv providers: - code: ar5iv description: Articles from arXiv.org as responsive HTML5 web pages. homepage: https://ar5iv.labs.arxiv.org/ name: ar5iv uri_format: https://ar5iv.org/abs/$1 - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/arxiv/$1 uri_format: https://arxiv.org/abs/$1 asap: description: ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. example: ABE-0009634 homepage: http://asap.ahabs.wisc.edu/asap/home.php mappings: biocontext: ASAP fairsharing: FAIRsharing.anpa6 go: ASAP miriam: asap n2t: asap ncbi: ASAP prefixcommons: asap re3data: r3d100010666 name: A Systematic Annotation Package for Community Analysis of Genomes pattern: ^[A-Za-z0-9-]+$ preferred_prefix: asap publications: - doi: 10.1093/nar/gkj164 pmc: PMC1347526 pubmed: '16381899' title: 'ASAP: a resource for annotating, curating, comparing, and disseminating genomic data.' year: 2006 - doi: 10.1093/nar/gkg125 pmc: PMC165572 pubmed: '12519969' title: ASAP, a systematic annotation package for community analysis of genomes. year: 2003 uri_format: http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1 ascl: description: The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001). example: '1801.012' homepage: http://ascl.net/ mappings: biocontext: ASCL fairsharing: FAIRsharing.wb0txg miriam: ascl n2t: ascl name: Astrophysics Source Code Library pattern: ^[0-9\.]+$ preferred_prefix: ascl uri_format: http://ascl.net/$1 asin: description: Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue. example: 0471491039 homepage: https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182 mappings: biocontext: ASIN miriam: asin n2t: asin name: Amazon Standard Identification Number pattern: ^[0-9]{10}$ preferred_prefix: asin uri_format: https://amzn.com/$1 aspgd.locus: description: The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information. example: ASPL0000349247 homepage: http://www.aspgd.org/ mappings: biocontext: ASPGD.LOCUS go: AspGD_LOCUS miriam: aspgd.locus n2t: aspgd.locus name: Aspergillus Genome Database pattern: ^[A-Za-z_0-9]+$ preferred_prefix: aspgd.locus uri_format: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1 aspgd.protein: description: The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information. example: ASPL0000349247 homepage: http://www.aspgd.org/ mappings: biocontext: ASPGD.PROTEIN miriam: aspgd.protein n2t: aspgd.protein name: AspGD Protein pattern: ^[A-Za-z_0-9]+$ preferred_prefix: aspgd.protein uri_format: http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1 asrp: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes. example: ASRP1423 homepage: https://asrp.danforthcenter.org/ mappings: prefixcommons: asrp name: Arabidopsis Small RNA Project preferred_prefix: asrp publications: - doi: 10.1093/nar/gkm997 pmc: PMC2238918 pubmed: '17999994' title: 'Update of ASRP: the Arabidopsis Small RNA Project database.' year: 2007 - doi: 10.1093/nar/gki127 pmc: PMC540081 pubmed: '15608278' title: 'ASRP: the Arabidopsis Small RNA Project Database.' year: 2005 uri_format: http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1 atc: contact: email: whocc@fhi.no github: null name: WHO Collaborating Centre for Drug Statistics Methodology orcid: null description: The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels. example: A10BA02 homepage: http://www.whocc.no/atc_ddd_index/ mappings: aberowl: ATC biocontext: ATC bioportal: ATC edam: '3103' fairsharing: FAIRsharing.1a27h8 hl7: whoATC miriam: atc n2t: atc prefixcommons: atc wikidata: P267 name: Anatomical Therapeutic Chemical Classification System pattern: ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$ preferred_prefix: atc publications: - doi: null pmc: null pubmed: '7368387' title: '[New classification of drugs. The Medical list and the Drug catalogue are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code) in 1981].' year: 1980 - doi: 10.1007/s002280000200 pmc: null pubmed: '11214783' title: Different versions of the anatomical therapeutic chemical classification system and the defined daily dose--are drug utilisation data comparable? year: 2000 synonyms: - ATC_code - ATTC uri_format: http://www.whocc.no/atc_ddd_index/?code=$1 atcc: description: The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences. example: '11303' homepage: https://www.lgcstandards-atcc.org mappings: biocontext: ATCC cellosaurus: ATCC fairsharing: FAIRsharing.j0ezpm hl7: 2.16.840.1.113883.6.77 miriam: atcc n2t: atcc ncbi: ATCC name: American Type Culture Collection pattern: ^([A-Z]+-)?\d+$ preferred_prefix: atcc synonyms: - ATCC - ATCC number - ATCC(dna) - ATCC(in host) uri_format: https://www.atcc.org/products/$1 atcvet: description: The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use. example: QJ51RV02 homepage: http://www.whocc.no/atcvet/atcvet_index/ mappings: biocontext: ATCVET miriam: atcvet n2t: atcvet name: Anatomical Therapeutic Chemical Vetinary pattern: ^Q[A-Z0-9]+$ preferred_prefix: atcvet uri_format: http://www.whocc.no/atcvet/atcvet_index/?code=$1 atfdb.family: description: The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found. example: CUT homepage: http://www.bioguo.org/AnimalTFDB/family_index.php mappings: biocontext: ATFDB.FAMILY miriam: atfdb.family n2t: atfdb.family name: Animal TFDB Family pattern: ^\w+$ preferred_prefix: atfdb.family uri_format: http://www.bioguo.org/AnimalTFDB/family.php?fam=$1 ato: contact: email: david.c.blackburn@gmail.com github: null name: David Blackburn orcid: null deprecated: true description: Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource download_obo: http://aber-owl.net/media/ontologies/ATO/2/ato.obo example: '0000000' homepage: http://www.amphibanat.org mappings: aberowl: ATO biocontext: ATO bioportal: ATO fairsharing: FAIRsharing.ayjdsm obofoundry: ato name: Amphibian taxonomy pattern: ^\d{7}$ preferred_prefix: ATO uri_format: http://purl.obolibrary.org/obo/ATO_$1 atol: contact: email: pylebail@rennes.inra.fr github: null name: LeBail Pierre-Yves orcid: null description: 'ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production.' download_owl: http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=atol.owl example: '0002233' homepage: http://www.atol-ontology.com mappings: aberowl: ATOL agroportal: ATOL bioportal: ATOL fairsharing: FAIRsharing.wsfk5z ols: atol name: Animal Trait Ontology for Livestock pattern: ^\d{7}$ preferred_prefix: atol uri_format: http://opendata.inra.fr/ATOL/ATOL_$1 version: '2018-09-13' autdb: description: AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder. example: ADA homepage: http://autism.mindspec.org/autdb/ mappings: biocontext: AUTDB miriam: autdb n2t: autdb name: AutDB pattern: ^[A-Z]+[A-Z-0-9]{2,}$ preferred_prefix: autdb uri_format: http://autism.mindspec.org/GeneDetail/$1 bacdive: description: BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. example: '131392' homepage: https://bacdive.dsmz.de/ mappings: fairsharing: FAIRsharing.aSszvY miriam: bacdive n2t: bacdive re3data: r3d100013060 name: Bacterial Diversity Metadatabase pattern: ^[0-9]+$ preferred_prefix: bacdive uri_format: https://bacdive.dsmz.de/strain/$1 bacmap.biog: description: BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information. example: '1050' homepage: http://bacmap.wishartlab.com/ mappings: biocontext: BACMAP.BIOG miriam: bacmap.biog n2t: bacmap.biog name: BacMap Biography pattern: ^\d+$ preferred_prefix: bacmap.biog uri_format: http://bacmap.wishartlab.com/organisms/$1 bacmap.map: description: BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information. example: AP011135 homepage: http://bacmap.wishartlab.com/ mappings: biocontext: BACMAP.MAP miriam: bacmap.map n2t: bacmap.map name: BacMap Map pattern: ^\w+(\_)?\d+(\.\d+)?$ preferred_prefix: bacmap.map uri_format: http://bacmap.wishartlab.com/maps/$1/index.html bactibase: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria. example: BAC045 homepage: http://bactibase.hammamilab.org mappings: fairsharing: FAIRsharing.5f5mfm prefixcommons: bactibase re3data: r3d100012755 name: Bactibase preferred_prefix: bactibase uri_format: http://bactibase.hammamilab.org/$1 bams: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: 'BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions.' homepage: https://bams1.org name: Brain Architecture Knowledge Management System Neuroanatomical Ontology preferred_prefix: bams references: - https://www.frontiersin.org/articles/10.3389/neuro.11.002.2008/full bao: contact: email: sschurer@med.miami.edu github: null name: Stephan Schurer orcid: null description: The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. download_owl: http://www.bioassayontology.org/bao/bao_complete.owl example: 0002989 homepage: http://bioassayontology.org mappings: aberowl: BAO biocontext: BAO bioportal: BAO fairsharing: FAIRsharing.mye76w miriam: bao n2t: bao ols: bao ontobee: BAO name: BioAssay Ontology pattern: ^\d{7}$ preferred_prefix: bao publications: - doi: 10.1186/2041-1480-5-s1-s5 pmc: PMC4108877 pubmed: '25093074' title: 'Evolving BioAssay Ontology (BAO): modularization, integration and applications.' year: 2014 - doi: 10.1371/journal.pone.0049198 pmc: PMC3498356 pubmed: '23155465' title: Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO). year: 2012 - doi: 10.1186/1471-2105-12-257 pmc: PMC3149580 pubmed: '21702939' title: 'BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results.' year: 2011 - doi: 10:1371/journal.pone.0049198 pmc: null pubmed: '10' title: Digitoxin metabolism by rat liver microsomes. year: 1975 synonyms: - BAO uri_format: http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1 version: 2.7.2 bbkg: description: Blue Brain Project's published data as knowledge graphs and Web Studios. example: topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a homepage: https://portal.bluebrain.epfl.ch mappings: miriam: bbkg name: Blue Brain Project Knowledge Graph pattern: ^[-\w]+(?:\/[-\w]+)(?:\/\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b)$ preferred_prefix: bbkg uri_format: https://bbp.epfl.ch/nexus/web/studios/public/$1 bbtp: description: Input data and analysis results for the paper "Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 ). example: f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a homepage: https://portal.bluebrain.epfl.ch mappings: miriam: bbtp name: Blue Brain Project Topological sampling Knowledge Graph pattern: ^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$ preferred_prefix: bbtp uri_format: https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1 bcgo: contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 deprecated: true description: An application ontology built for beta cell genomics studies. download_owl: https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl example: '0000015' homepage: https://github.com/obi-bcgo/bcgo license: CC BY 3.0 mappings: aberowl: BCGO biocontext: BCGO bioportal: BCGO cellosaurus: BCGO obofoundry: bcgo ontobee: BCGO name: Beta Cell Genomics Ontology pattern: ^\d{7}$ preferred_prefix: BCGO repository: https://github.com/obi-bcgo/bcgo uri_format: http://purl.obolibrary.org/obo/BCGO_$1 bcio: contact: email: srodriguez@pet.cs.nctu.edu.tw github: null name: Sergio José Rodríguez Méndez orcid: null description: The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation. download_owl: http://humanbehaviourchange.org/ontology/bcio.owl example: '040000' homepage: https://www.humanbehaviourchange.org/ mappings: aberowl: BCI-O bioportal: BCI-O ols: bcio name: The Behaviour Change Intervention Ontology pattern: ^\d{6}$ preferred_prefix: bcio uri_format: https://w3id.org/BCI-ontology#$1 bco: appears_in: - fovt contact: email: rlwalls2008@gmail.com github: ramonawalls name: Ramona Walls orcid: 0000-0001-8815-0078 description: An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. download_owl: http://purl.obolibrary.org/obo/bco.owl example: 0000081 homepage: https://github.com/BiodiversityOntologies/bco license: CC0 1.0 mappings: aberowl: BCO agroportal: BCO biocontext: BCO bioportal: BCO ecoportal: BCO fairsharing: FAIRsharing.8ktkqy obofoundry: bco ols: bco ontobee: BCO name: Biological Collections Ontology pattern: ^\d{7}$ preferred_prefix: BCO publications: - doi: 10.1371/journal.pone.0089606 pmc: PMC3940615 pubmed: '24595056' title: 'Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.' year: 2014 repository: https://github.com/BiodiversityOntologies/bco uri_format: http://purl.obolibrary.org/obo/BCO_$1 version: '2021-11-14' bcrc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Cell line collections example: '60316' homepage: https://catalog.bcrc.firdi.org.tw mappings: cellosaurus: BCRC name: BCRC Strain Collection Catalog pattern: ^\d+$ preferred_prefix: bcrc uri_format: https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1 bcrj: description: Cell line collections example: 0278 homepage: http://bcrj.org.br/celula/bcrj mappings: cellosaurus: BCRJ name: Banco de Celulas do Rio de Janeiro pattern: ^\d{4}$ preferred_prefix: bcrj uri_format: http://bcrj.org.br/celula/$1 bdgp.est: description: The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI). example: EY223054.1 has_canonical: dbest homepage: https://www.ncbi.nlm.nih.gov/dbEST/index.html mappings: biocontext: BDGP.EST miriam: bdgp.est n2t: bdgp.est ncbi: BDGP_EST prefixcommons: flybase.est name: Berkeley Drosophila Genome Project EST database pattern: ^\w+(\.)?(\d+)?$ preferred_prefix: bdgp.est uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1 bdgp.insertion: description: BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element. example: KG09531 homepage: http://flypush.imgen.bcm.tmc.edu/pscreen/ mappings: biocontext: BDGP.INSERTION miriam: bdgp.insertion n2t: bdgp.insertion prefixcommons: bdgp name: BDGP insertion DB pattern: ^\w+$ preferred_prefix: bdgp.insertion publications: - doi: 10.1534/genetics.104.026427 pmc: PMC1470905 pubmed: '15238527' title: 'The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes.' year: 2004 uri_format: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1 bdsc: description: The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research. example: '33607' homepage: https://bdsc.indiana.edu/about/mission.html mappings: miriam: bdsc n2t: bdsc name: Bloomington Drosophila Stock Center pattern: ^\d+$ preferred_prefix: bdsc uri_format: https://bdsc.indiana.edu/stocks/$1 beetlebase: description: BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications. example: TC010103 homepage: http://beetlebase.org/ mappings: biocontext: BEETLEBASE fairsharing: FAIRsharing.h5f091 miriam: beetlebase n2t: beetlebase ncbi: BEETLEBASE prefixcommons: beetlebase re3data: r3d100010921 name: Tribolium Genome Database -- Insertion pattern: ^TC\d+$ preferred_prefix: beetlebase publications: - doi: 10.1093/nar/gkp807 pmc: PMC2808946 pubmed: '19820115' title: 'BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum.' year: 2009 uri_format: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1 begdb: description: The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods. example: '4214' homepage: http://www.begdb.com mappings: biocontext: BEGDB fairsharing: FAIRsharing.nbe4fq miriam: begdb n2t: begdb name: Benchmark Energy & Geometry Database pattern: ^[0-9]+$ preferred_prefix: begdb 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 mappings: cellosaurus: BEI_Resources name: BEI Resources preferred_prefix: beiresources synonyms: - BEI_Resources uri_format: https://www.beiresources.org/Catalog/cellBanks/$1.aspx bel: comment: INDRA uses bel as a catch-all for scomp/sfam contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents. example: 9-1-1 Complex homepage: https://biological-expression-language.github.io/ mappings: fairsharing: FAIRsharing.dp0jvd name: Biological Expression Language preferred_prefix: bel bfo: appears_in: - ado - agro - aism - cdno - colao - duo - ecocore - epio - foodon - fovt - hso - lepao - mco - ons - pcl - pco - psdo - rbo - xpo - zp contact: email: phismith@buffalo.edu github: phismith name: Barry Smith orcid: 0000-0003-1384-116X description: The upper level ontology upon which OBO Foundry ontologies are built. download_obo: http://purl.obolibrary.org/obo/bfo.obo download_owl: http://purl.obolibrary.org/obo/bfo.owl example: '0000001' homepage: http://ifomis.org/bfo/ license: CC BY 4.0 mappings: aberowl: BFO agroportal: BFO biocontext: BFO bioportal: BFO fairsharing: FAIRsharing.wcpd6f go: BFO obofoundry: bfo ols: bfo ontobee: BFO name: Basic Formal Ontology pattern: ^\d{7}$ 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=$1 bgee.gene: description: Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee. example: FBgn0000015 homepage: https://bgee.org/ mappings: biocontext: BGEE.GENE miriam: bgee.gene n2t: bgee.gene name: Bgee gene pattern: ^[A-Za-z]+\d+$ 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/ name: The Bibliographic Ontology preferred_prefix: bibo uri_format: http://purl.org/ontology/bibo/$1 bido: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF. example: CategorialBibliometricData homepage: http://www.sparontologies.net/ontologies/bido mappings: fairsharing: FAIRsharing.d7f0a9 name: Bibliometric Data Ontology preferred_prefix: BiDO repository: https://github.com/sparontologies/bido uri_format: http://purl.org/spar/bido/$1 bigg.compartment: description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments. example: c homepage: http://bigg.ucsd.edu/compartments/ mappings: biocontext: BIGG.COMPARTMENT miriam: bigg.compartment n2t: bigg.compartment name: BiGG Compartment pattern: ^[a-z_A-Z]+$ 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/$1 bila: contact: email: henrich@embl.de github: null name: Thorsten Heinrich orcid: null deprecated: true description: This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource. download_owl: http://purl.obolibrary.org/obo/bila.owl example: '0000000' homepage: http://4dx.embl.de/4DXpress mappings: biocontext: BILA fairsharing: FAIRsharing.eqgjeq obofoundry: bila name: Bilateria anatomy pattern: ^\d{7}$ preferred_prefix: BILA uri_format: http://purl.obolibrary.org/obo/BILA_$1 bind: deprecated: true description: Accession number of an entry from the BIND database. homepage: http://bind.ca mappings: biocontext: BIND edam: '1129' prefixcommons: bind name: BIND accession number preferred_prefix: bind publications: - doi: null pmc: null pubmed: '12519993' title: 'BIND: the Biomolecular Interaction Network Database' year: null - doi: null pmc: null pubmed: '10871269' title: BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways year: null uri_format: http://www.bind.ca/Action?identifier=bindid&idsearch=$1 bindingdb: description: BindingDB is the first public database of protein-small molecule affinity data. example: e999 homepage: https://www.bindingdb.org mappings: biocontext: BINDINGDB fairsharing: FAIRsharing.3b36hk miriam: bindingdb n2t: bindingdb prefixcommons: bindingdb re3data: r3d100012074 uniprot: BindingDB name: BindingDB pattern: ^\w\d+$ preferred_prefix: bindingdb publications: - 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/$1 biocatalogue.service: description: The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all. example: '614' homepage: https://www.biocatalogue.org/ mappings: biocontext: BIOCATALOGUE.SERVICE miriam: biocatalogue.service n2t: biocatalogue.service name: BioCatalogue Service pattern: ^\d+$ preferred_prefix: biocatalogue.service uri_format: https://www.biocatalogue.org/services/$1 biocyc: description: BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. example: ECOLI:CYT-D-UBIOX-CPLX homepage: http://biocyc.org mappings: biocontext: BIOCYC edam: '2104' go: BioCyc miriam: biocyc n2t: biocyc prefixcommons: biocyc uniprot: BioCyc name: BioCyc collection of metabolic pathway databases pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$ preferred_prefix: biocyc publications: - doi: 10.1093/nar/gki892 pmc: 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=$1 biogrid: description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. example: '31623' homepage: http://thebiogrid.org/ mappings: biocontext: BIOGRID fairsharing: FAIRsharing.9d5f5r miriam: biogrid n2t: biogrid prefixcommons: biogrid re3data: r3d100010350 uniprot: BioGRID name: BioGRID pattern: ^\d+$ preferred_prefix: biogrid publications: - doi: 10.1093/nar/gkj109 pmc: PMC1347471 pubmed: '16381927' title: 'BioGRID: a general repository for interaction datasets.' year: 2006 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/$1 biolegend: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: BioLegend is a life sciences supply vendor. example: '3403' homepage: https://www.biolegend.com name: BioLegend pattern: ^\d+$ preferred_prefix: biolegend uri_format: https://www.biolegend.com/Default.aspx?ID=6664&productid=$1 biolink: contact: email: cjmungall@lbl.gov github: null name: Chris Mungall orcid: null description: A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations. download_owl: http://aber-owl.net/media/ontologies/BIOLINK/42/biolink.owl example: Gene homepage: https://biolink.github.io/biolink-model/ mappings: aberowl: BIOLINK biolink: biolink bioportal: BIOLINK fairsharing: FAIRsharing.ad9d85 miriam: biolink name: Biolink Model pattern: ^\S+$ preferred_prefix: biolink uri_format: https://w3id.org/biolink/vocab/$1 biominder: description: Database of the dielectric properties of biological tissues. example: aef4c195-9cf9-46db-a12a-7cfd1ff3eec3 homepage: https://datalab.rwth-aachen.de/MINDER mappings: biocontext: BIOMINDER miriam: biominder n2t: biominder name: Bio-MINDER Tissue Database pattern: ^[a-z0-9\-]+$ preferred_prefix: biominder uri_format: https://datalab.rwth-aachen.de/MINDER/resource/$1 biomodels.db: description: BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. example: BIOMD0000000048 homepage: https://www.ebi.ac.uk/biomodels/ mappings: biocontext: BIOMODELS.DB go: BIOMD miriam: biomodels.db n2t: biomodels.db prefixcommons: biomodels name: BioModels Database pattern: ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ preferred_prefix: biomodels.db providers: - code: CURATOR_REVIEW description: Caltech mirror homepage: http://biomodels.caltech.edu/ name: Caltech mirror uri_format: http://biomodels.caltech.edu/$1 - code: omicsdi description: BioModels through OmicsDI homepage: https://www.omicsdi.org/ name: BioModels through OmicsDI uri_format: https://www.omicsdi.org/dataset/biomodels/$1 publications: - doi: 10.1093/nar/gkj092 pmc: PMC1347454 pubmed: '16381960' title: 'BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.' year: 2006 synonyms: - BIOMD uri_format: https://www.ebi.ac.uk/biomodels/$1 biomodels.kisao: banana: KISAO banana_peel: _ contact: email: jonrkarr@gmail.com github: jonrkarr name: Jonathan Karr orcid: 0000-0002-2605-5080 description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment. download_owl: http://purl.obolibrary.org/obo/kisao.owl example: '0000057' homepage: https://github.com/SED-ML/KiSAO license: Artistic License 2.0 mappings: aberowl: KISAO biocontext: KISAO bioportal: KISAO fairsharing: FAIRsharing.jcg19w miriam: biomodels.kisao n2t: biomodels.kisao obofoundry: kisao ols: kisao ontobee: KISAO prefixcommons: kisao name: Kinetic Simulation Algorithm Ontology namespace_in_lui: true pattern: ^\d+$ preferred_prefix: biomodels.kisao providers: - code: legacy description: This is the URI scheme used in the ontology but it does not resolve. homepage: https://www.biomodels.net name: Legacy Biomodels URL uri_format: https://www.biomodels.net/kisao/KISAO#KISAO_$1 publications: - doi: 10.1038/msb.2011.77 pmc: PMC3261705 pubmed: '22027554' title: Controlled vocabularies and semantics in systems biology. year: 2011 repository: https://github.com/SED-ML/KiSAO synonyms: - kisao uri_format: https://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=kisao:KISAO_$1 version: '2.30' biomodels.teddy: banana: TEDDY banana_peel: _ contact: email: biomodels-net-support@lists.sf.net github: null name: BioModels.net team orcid: null description: The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. download_owl: http://svn.code.sf.net/p/teddyontology/code/teddy/tags/current/teddy-inferred.owl example: '0000066' homepage: http://teddyontology.sourceforge.net/ mappings: aberowl: TEDDY biocontext: BIOMODELS.TEDDY bioportal: TEDDY fairsharing: FAIRsharing.w9jvbt miriam: biomodels.teddy n2t: biomodels.teddy ols: teddy prefixcommons: teddy name: Terminology for Description of Dynamics pattern: ^\d+$ preferred_prefix: biomodels.teddy publications: - doi: 10.1038/msb.2011.77 pmc: PMC3261705 pubmed: '22027554' title: Controlled vocabularies and semantics in systems biology. year: 2011 synonyms: - teddy uri_format: https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1 version: '2014-04-24' biomodels.vocabulary: description: Vocabulary used in the RDF representation of SBML models. example: rateRule homepage: http://biomodels.net/rdf/vocabulary.rdf mappings: biocontext: BIOMODELS.VOCABULARY miriam: biomodels.vocabulary n2t: biomodels.vocabulary name: SBML RDF Vocabulary pattern: ^[A-Za-z]+$ preferred_prefix: biomodels.vocabulary uri_format: http://biomodels.net/rdf/vocabulary.rdf#$1 bionumbers: description: BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data. example: '104674' homepage: https://bionumbers.hms.harvard.edu mappings: biocontext: BIONUMBERS edam: '2660' miriam: bionumbers n2t: bionumbers prefixcommons: bionumbers name: BioNumbers pattern: ^\d+$ preferred_prefix: bionumbers uri_format: https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1 bioportal: description: BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. example: '1046' homepage: http://bioportal.bioontology.org/ mappings: biocontext: BIOPORTAL fairsharing: FAIRsharing.4m97ah miriam: bioportal n2t: bioportal prefixcommons: bioportal re3data: r3d100012344 name: BioPortal pattern: ^\d+$ preferred_prefix: bioportal publications: - doi: 10.1093/nar/gkp440 pmc: PMC2703982 pubmed: '19483092' title: 'BioPortal: ontologies and integrated data resources at the click of a mouse.' year: 2009 uri_format: http://bioportal.bioontology.org/ontologies/$1 bioproject: description: BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories. example: PRJDB3 has_canonical: ena.embl homepage: http://trace.ddbj.nig.ac.jp/bioproject/ mappings: biocontext: BIOPROJECT fairsharing: FAIRsharing.aqhv1y miriam: bioproject n2t: bioproject re3data: r3d100013330 name: BioProject pattern: ^PRJ[DEN][A-Z]\d+$ preferred_prefix: bioproject providers: - code: ebi description: BioProject at European Nucleotide Archive (ENA) homepage: https://www.ebi.ac.uk/ena/ name: BioProject at European Nucleotide Archive (ENA) uri_format: https://www.ebi.ac.uk/ena/browser/view/$1 - code: ncbi description: BioProject at NCBI homepage: https://www.ncbi.nlm.nih.gov/bioproject name: BioProject at NCBI uri_format: https://www.ncbi.nlm.nih.gov/bioproject?term=$1 uri_format: https://www.ncbi.nlm.nih.gov/bioproject/?term=$1 bioregistry: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database. example: bioregistry homepage: https://bioregistry.io name: Bioregistry preferred_prefix: bioregistry publications: - doi: 10.1101/2022.07.08.499378 pmc: null pubmed: null title: Unifying the Identification of Biomedical Entities with the Bioregistry year: null repository: https://github.com/biopragmatics/bioregistry uri_format: https://bioregistry.io/registry/$1 bioregistry.collection: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Manually curated collections of resources stored in the bioregistry example: '0000001' homepage: https://bioregistry.io/collection name: Bioregistry Collections pattern: ^\d{7}$ preferred_prefix: bioregistry.collection uri_format: https://bioregistry.io/collection/$1 bioregistry.registry: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Bioregistry's meta-registry example: miriam homepage: https://bioregistry.io/metaregistry/ name: Bioregistry Metaregistry preferred_prefix: bioregistry.registry uri_format: https://bioregistry.io/metaregistry/$1 bioregistry.schema: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Schema for the export of the Bioregistry as RDF example: '0000001' homepage: https://bioregistry.io/schema name: Bioregistry Schema pattern: ^\d{7}$ preferred_prefix: bioregistry.schema uri_format: https://bioregistry.io/schema/#$1 biorxiv: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The bioRxiv is a preprint server for biology example: 2022.07.08.499378 example_extras: - 000091 - 000091v1 - 2022.07.08.499378v2 homepage: https://biorxiv.org mappings: go: bioRxiv name: bioRxiv pattern: ^(\d{4}\.\d{2}\.\d{2}\.)?\d{6,8}(v\d{1,3})?$ preferred_prefix: biorxiv providers: - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/biorxiv/$1 uri_format: https://www.biorxiv.org/content/10.1101/$1 biosample: description: The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation. example: SAMEA2397676 homepage: https://www.ebi.ac.uk/biosamples/ mappings: biocontext: BIOSAMPLE cellosaurus: BioSamples fairsharing: FAIRsharing.qr6pqk miriam: biosample n2t: biosample re3data: r3d100012828 name: BioSample pattern: ^SAM[NED](\w)?\d+$ preferred_prefix: biosample providers: - code: CURATOR_REVIEW description: BioSample at DNA Data Bank of Japan homepage: http://trace.ddbj.nig.ac.jp/biosample/ name: BioSample at DNA Data Bank of Japan uri_format: http://trace.ddbj.nig.ac.jp/BSSearch/biosample?acc=$1 - code: ncbi description: BioSample at NCBI homepage: http://www.ncbi.nlm.nih.gov/biosample name: BioSample at NCBI uri_format: http://www.ncbi.nlm.nih.gov/biosample?term=$1 synonyms: - biosamples uri_format: https://www.ebi.ac.uk/biosamples/sample/$1 biosimulations: description: BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools. example: Yeast-cell-cycle-Irons-J-Theor-Biol-2009 homepage: https://icahn.mssm.edu/ mappings: miriam: biosimulations re3data: r3d100013361 name: biosimulations pattern: ^[a-zA-Z0-9_-]{3,}$ preferred_prefix: biosimulations uri_format: https://biosimulations.org/projects/$1 biosimulators: description: BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML). example: vcell homepage: https://biosimulators.org/ mappings: fairsharing: FAIRsharing.pwEima miriam: biosimulators re3data: r3d100013432 name: BioSimulators pattern: ^[a-zA-Z0-9-_]+$ preferred_prefix: biosimulators uri_format: https://biosimulators.org/simulators/$1 biostudies: description: The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication. example: S-EPMC6266652 homepage: https://www.ebi.ac.uk/biostudies/ mappings: fairsharing: FAIRsharing.mtjvme miriam: biostudies n2t: biostudies re3data: r3d100012627 name: BioStudies database pattern: ^S-[A-Z]{4}[A-Z\d\-]+$ preferred_prefix: biostudies uri_format: https://www.ebi.ac.uk/biostudies/studies/$1 biosystems: description: The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. example: '001' homepage: https://www.ncbi.nlm.nih.gov/biosystems/ mappings: biocontext: BIOSYSTEMS fairsharing: FAIRsharing.w2eeqr miriam: biosystems n2t: biosystems prefixcommons: biosystems name: BioSystems pattern: ^\d+$ preferred_prefix: biosystems publications: - doi: 10.1093/nar/gkp858 pmc: PMC2808896 pubmed: '19854944' title: The NCBI BioSystems database. year: 2009 uri_format: https://www.ncbi.nlm.nih.gov/biosystems/$1 biotools: description: BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research. example: bioregistry homepage: https://bio.tools/ mappings: biocontext: BIOTOOLS fairsharing: FAIRsharing.63520c miriam: biotools n2t: biotools re3data: r3d100013668 name: BioTools pattern: ^[-A-Za-z0-9\_]*$ preferred_prefix: biotools uri_format: https://bio.tools/$1 biozil: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Redistributor of bilogics and biomedical supplies example: ls-c35719-120 homepage: https://www.biozol.de/en name: BIOZIL preferred_prefix: biozil uri_format: https://www.biozol.de/en/product/$1 birnlex: comment: Part of the NeuroLex namespace now contact: email: wbug@ncmir.ucsd.edu github: null name: William Bug orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. download_owl: http://aber-owl.net/media/ontologies/BIRNLEX/1/birnlex.owl example: '2023' homepage: https://bioportal.bioontology.org/ontologies/BIRNLEX mappings: aberowl: BIRNLEX bioportal: BIRNLEX fairsharing: FAIRsharing.jedbbt name: Biomedical Informatics Research Network Lexicon pattern: ^\d+$ preferred_prefix: birnlex uri_format: http://uri.neuinfo.org/nif/nifstd/birnlex_$1 biro: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively. example: BibliographicRecord homepage: http://www.sparontologies.net/ontologies/biro mappings: fairsharing: FAIRsharing.99da5f name: Bibliographic Reference Ontology preferred_prefix: BiRO repository: https://github.com/sparontologies/biro uri_format: http://purl.org/spar/biro/$1 bitbucket: description: Bitbucket is a Git-based source code repository hosting service owned by Atlassian. example: andreadega/systems-biology-compiler homepage: https://www.atlassian.com/ mappings: fairsharing: FAIRsharing.fc3431 miriam: bitbucket re3data: r3d100013478 name: Bitbucket pattern: ^[0-9A-Za-z-_\.]+/[0-9A-Za-z-_\.]+$ preferred_prefix: bitbucket uri_format: https://bitbucket.org/$1 bitterdb.cpd: description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds. example: '46' homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php mappings: biocontext: BITTERDB.CPD miriam: bitterdb.cpd n2t: bitterdb.cpd name: BitterDB Compound pattern: ^\d+$ preferred_prefix: bitterdb.cpd uri_format: http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1 bitterdb.rec: description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors. example: '1' homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php mappings: biocontext: BITTERDB.REC miriam: bitterdb.rec n2t: bitterdb.rec name: BitterDB Receptor pattern: ^\d+$ preferred_prefix: bitterdb.rec uri_format: http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1 bko: comment: This resource also uses SBO terms and resolves them, e.g., http://www.sbgnbricks.org/BKO/full/entry/all/SBO:0000177/. contact: email: adrienrougny@gmail.com github: adrienrougny name: Adrien Rougny orcid: 0000-0002-2118-035X contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way. download_owl: http://aber-owl.net/media/ontologies/BKO/1/bko.owl example: '0000204' github_request_issue: 283 homepage: http://www.sbgnbricks.org/ mappings: aberowl: BKO bioportal: BKO name: SBGN Bricks data and ontology pattern: ^\d+$ preferred_prefix: bko reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1 bmrb: description: BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy. example: '15000' homepage: http://www.bmrb.wisc.edu/ mappings: fairsharing: FAIRsharing.p06nme miriam: bmrb uniprot: BMRB name: Biological Magnetic Resonance Data Bank pattern: ^(bmr|bmse|bmst)?[0-9]{1,6}$ preferred_prefix: bmrb uri_format: http://rest.bmrb.wisc.edu/bmrb/$1/html bmrb.restraint: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively. example: '28789' homepage: https://restraintsgrid.bmrb.io/NRG/MRGridServlet name: NMR Restraints Grid pattern: ^\d+$ preferred_prefix: bmrb.restraint uri_format: https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1 bold.taxonomy: description: The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information. example: '27267' homepage: http://www.boldsystems.org/ mappings: biocontext: BOLD.TAXONOMY miriam: bold.taxonomy n2t: bold.taxonomy ncbi: BOLD prefixcommons: bold name: Barcode of Life database pattern: ^\d+$ preferred_prefix: bold.taxonomy publications: - doi: 10.1111/j.1471-8286.2007.01678.x pmc: PMC1890991 pubmed: '18784790' title: 'bold: The Barcode of Life Data System (http://www.barcodinglife.org).' year: 2007 uri_format: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1 bootstrep: contact: email: vlee@ebi.ac.uk github: null name: Vivian Lee orcid: null deprecated: true homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html mappings: biocontext: BOOTSTREP obofoundry: bootstrep name: Gene Regulation Ontology preferred_prefix: BOOTSTREP uri_format: http://purl.obolibrary.org/obo/BOOTSTREP_$1 bpdb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Database of biopesticides maintained by the University of Hertfordshire ' example: '2404' homepage: https://sitem.herts.ac.uk/aeru/bpdb/index.htm name: Bio-Pesticides DataBase pattern: ^\d+$ preferred_prefix: bpdb uri_format: https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm brenda: description: BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. example: 1.1.1.1 homepage: https://www.brenda-enzymes.org/ mappings: biocontext: BRENDA fairsharing: FAIRsharing.etp533 go: BRENDA miriam: brenda n2t: brenda prefixcommons: brenda re3data: r3d100010616 uniprot: BRENDA name: BRENDA, The Comprehensive Enzyme Information System pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ preferred_prefix: brenda publications: - doi: 10.1093/nar/gkn820 pmc: PMC2686525 pubmed: '18984617' title: 'BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009.' year: 2008 uri_format: https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1 brenda.ligand: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Information for ligands in the BRENDA database. example: '278' homepage: https://www.brenda-enzymes.de/ligand.php name: BRENDA Ligand pattern: ^\d+$ preferred_prefix: brenda.ligand uri_format: https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1 brenda.ligandgroup: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Information for ligand groups (chemical classes). example: '18030' homepage: https://www.brenda-enzymes.de/ligand.php name: BRENDA Ligand Group pattern: ^\d+$ preferred_prefix: brenda.ligandgroup uri_format: https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1 broad: description: Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae. example: S7000002168151102 homepage: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/ mappings: biocontext: BROAD miriam: broad n2t: broad name: Broad Fungal Genome Initiative pattern: ^S\d+$ preferred_prefix: broad uri_format: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1 bs: comment: An alernative vocabulary that has been aligned and integrated in Sequence Ontology (SO). contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library. download_obo: https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/subsets/biosapiens.obo example: '00042' homepage: https://github.com/The-Sequence-Ontology/SO-Ontologies name: Biosapiens Protein Feature Ontology pattern: ^\d+$ preferred_prefix: bs repository: https://github.com/The-Sequence-Ontology/SO-Ontologies uri_format: https://biopragmatics.github.io/providers/bs/$1 bspo: appears_in: - aism - colao - fovt - lepao - zp contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. download_json: http://purl.obolibrary.org/obo/bspo.json download_obo: https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo download_owl: http://purl.obolibrary.org/obo/bspo.owl example: 0000029 homepage: https://github.com/obophenotype/biological-spatial-ontology license: CC BY 3.0 mappings: aberowl: BSPO biocontext: BSPO bioportal: BSPO fairsharing: FAIRsharing.newa3z obofoundry: bspo ols: bspo ontobee: BSPO name: Biological Spatial Ontology pattern: ^\d{7}$ preferred_prefix: BSPO publications: - doi: 10.1186/2041-1480-5-34 pmc: PMC4137724 pubmed: '25140222' title: 'Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.' year: 2014 repository: https://github.com/obophenotype/biological-spatial-ontology uri_format: http://purl.obolibrary.org/obo/BSPO_$1 version: '2022-06-28' bto: banana: BTO contact: email: c.dudek@tu-braunschweig.de github: chdudek name: Christian-Alexander Dudek orcid: 0000-0001-9117-7909 description: The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. download_json: http://purl.obolibrary.org/obo/bto.json download_obo: http://purl.obolibrary.org/obo/bto.obo download_owl: http://purl.obolibrary.org/obo/bto.owl example: 0000590 homepage: http://www.brenda-enzymes.org license: CC BY 4.0 mappings: aberowl: BTO biocontext: BTO bioportal: BTO cellosaurus: BTO fairsharing: FAIRsharing.1414v8 go: BTO miriam: bto n2t: bto obofoundry: bto ols: bto ontobee: BTO prefixcommons: bto wikidata: P5501 name: BRENDA tissue / enzyme source namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: BTO publications: - doi: 10.1093/nar/gky1048 pmc: PMC6323942 pubmed: '30395242' title: 'BRENDA in 2019: a European ELIXIR core data resource.' year: 2019 - doi: 10.1093/nar/gku1068 pmc: PMC4383907 pubmed: '25378310' title: 'BRENDA in 2015: exciting developments in its 25th year of existence.' year: 2014 - doi: 10.1093/nar/gks1049 pmc: PMC3531171 pubmed: '23203881' title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.' year: 2012 - doi: 10.1093/nar/gkq968 pmc: PMC3013802 pubmed: '21030441' title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources.' year: 2010 - doi: 10.1093/nar/gkh081 pmc: PMC308815 pubmed: '14681450' title: 'BRENDA, the enzyme database: updates and major new developments.' year: 2004 repository: https://github.com/BRENDA-Enzymes/BTO synonyms: - BTO uri_format: https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=BTO:$1 version: '2021-10-26' bugbase.expt: description: BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments. example: '288' homepage: http://bugs.sgul.ac.uk/E-BUGS mappings: biocontext: BUGBASE.EXPT miriam: bugbase.expt n2t: bugbase.expt name: BugBase Expt pattern: ^\d+$ preferred_prefix: bugbase.expt uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view bugbase.protocol: description: BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols. example: '67' homepage: http://bugs.sgul.ac.uk/E-BUGS mappings: biocontext: BUGBASE.PROTOCOL miriam: bugbase.protocol n2t: bugbase.protocol name: BugBase Protocol pattern: ^\d+$ preferred_prefix: bugbase.protocol uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$1&action=view bykdb: description: The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information. example: A0A009E7X8 homepage: https://bykdb.ibcp.fr/BYKdb/ mappings: biocontext: BYKDB fairsharing: FAIRsharing.jr30xc miriam: bykdb n2t: bykdb prefixcommons: bykdb name: Bacterial Tyrosine Kinase Database pattern: ^[A-Z0-9]+$ preferred_prefix: bykdb provides: uniprot publications: - doi: 10.1093/nar/gkr915 pmc: PMC3245071 pubmed: '22080550' title: 'BYKdb: the Bacterial protein tYrosine Kinase database.' year: 2011 uri_format: https://bykdb.ibcp.fr/data/html/annotated/$1.html c4o: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date. example: InTextReferencePointer homepage: http://www.sparontologies.net/ontologies/c4o mappings: fairsharing: FAIRsharing.beb855 name: Citation Counting and Context Characterisation Ontology preferred_prefix: C4O repository: https://github.com/sparontologies/c4o uri_format: http://purl.org/spar/c4o/$1 cabri: description: CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it. example: dsmz_mutz-id:ACC 291 homepage: http://www.cabri.org/ mappings: biocontext: CABRI edam: '2380' fairsharing: FAIRsharing.qx2rvz miriam: cabri n2t: cabri ncbi: CABRI name: Common Access to Biological Resources and Information Project pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$ preferred_prefix: cabri providers: - code: CURATOR_REVIEW description: CABRI Cell Lines catalogue in Brussels (SRS) homepage: http://www.be.cabri.org/ name: CABRI Cell Lines catalogue in Brussels (SRS) uri_format: http://www.be.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1] uri_format: http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1] cadsr: description: The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR. example: '3771992' homepage: https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki mappings: miriam: cadsr n2t: cadsr name: Cancer Data Standards Registry and Repository pattern: ^[0-9]*$ preferred_prefix: cadsr uri_format: https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1] caloha: banana: TS banana_peel: '-' contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins. download_obo: https://download.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo example: '0001' homepage: https://github.com/calipho-sib/controlled-vocabulary name: CALIPHO Group Ontology of Human Anatomy pattern: ^\d+$ preferred_prefix: caloha references: - https://twitter.com/neXtProt_news/status/1350105997633867781 repository: https://github.com/calipho-sib/controlled-vocabulary twitter: neXtProt_news uri_format: https://biopragmatics.github.io/providers/caloha/$1 cameo: description: The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB. example: 2019-08-03_00000089_1 homepage: https://cameo3d.org mappings: biocontext: CAMEO fairsharing: FAIRsharing.dq34p2 miriam: cameo n2t: cameo name: Continuous Automated Model Evaluation pattern: ^[0-9\-_]+$ preferred_prefix: cameo uri_format: https://www.cameo3d.org/sp/targets/target/$1 caps: description: CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. example: '434' homepage: http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home mappings: biocontext: CAPS miriam: caps n2t: caps name: CAPS-DB pattern: ^\d+$ preferred_prefix: caps uri_format: http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1 caro: appears_in: - aism - colao - ehdaa2 - lepao - pco contact: email: haendel@ohsu.edu github: mellybelly name: Melissa Haendel orcid: 0000-0001-9114-8737 description: None download_json: http://purl.obolibrary.org/obo/caro.json download_obo: http://purl.obolibrary.org/obo/caro.obo download_owl: http://purl.obolibrary.org/obo/caro.owl example: '0000000' homepage: https://github.com/obophenotype/caro/ license: CC BY 3.0 mappings: aberowl: CARO biocontext: CARO bioportal: CARO fairsharing: FAIRsharing.3kcgmr go: CARO obofoundry: caro ols: caro ontobee: CARO name: Common Anatomy Reference Ontology pattern: ^\d{7}$ preferred_prefix: CARO providers: - code: obo.1 description: This incorrect encoding was found inside IDO-COVID-19 homepage: http://purl.obolibrary.org name: Nonstandard OBO PURL uri_format: http://purl.obolibrary.org/obo/ido.owl/CARO_$1 publications: - doi: 10.1007/978-1-84628-885-2_16 pmc: null pubmed: null title: CARO – The Common Anatomy Reference Ontology year: null repository: https://github.com/obophenotype/caro uri_format: http://purl.obolibrary.org/obo/CARO_$1 version: '2022-02-18' cas: description: CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information. example: 50-00-0 homepage: https://commonchemistry.cas.org/ mappings: biocontext: CAS cheminf: '000446' edam: '1002' fairsharing: FAIRsharing.r7Kwy7 go: CAS hl7: 2.16.840.1.113883.6.61 miriam: cas n2t: cas prefixcommons: cas wikidata: P231 name: CAS Chemical Registry pattern: ^\d{1,7}\-\d{2}\-\d$ preferred_prefix: cas providers: - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/cas/$1 synonyms: - CASID - CAS_RN - SECONDARY_CAS_RN - cas_id uri_format: https://commonchemistry.cas.org/detail?ref=$1 casspc: comment: Jim Balhoff said that Catalog of Fishes does not publish their data in a machine readable format, but a long time ago they sent a CSV dump to help in the development of TTO and VTO. These ontologies are effectively retired and CASSPC terms are only also used in Phenoscape. contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 contributor_extras: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true example: '5359' homepage: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp mappings: go: CASSPC name: Eschmeyer's Catalog of Fishes pattern: ^\d+$ preferred_prefix: casspc uri_format: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1 cath: description: CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence. example: 1.10.8.10 homepage: http://www.cathdb.info mappings: biocontext: CATH edam: '2700' fairsharing: FAIRsharing.xgcyyn miriam: cath n2t: cath prefixcommons: cath re3data: r3d100012629 name: CATH Protein Structural Domain Superfamily pattern: ^[1-6]\.[0-9]+\.[0-9]+\.[0-9]+$ preferred_prefix: cath publications: - doi: 10.1016/s0969-2126(97)00260-8 pmc: null pubmed: '9309224' title: CATH--a hierarchic classification of protein domain structures. year: 1997 uri_format: http://www.cathdb.info/cathnode/$1 cath.domain: description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains. example: 1cukA01 homepage: http://www.cathdb.info/ mappings: biocontext: CATH.DOMAIN edam: '1040' miriam: cath.domain n2t: cath.domain name: CATH domain pattern: ^\w+$ preferred_prefix: cath.domain uri_format: http://www.cathdb.info/domain/$1 cath.superfamily: description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification. example: 1.10.10.200 homepage: http://www.cathdb.info/ mappings: biocontext: CATH.SUPERFAMILY miriam: cath.superfamily n2t: cath.superfamily name: CATH superfamily part_of: cath pattern: ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$ preferred_prefix: cath.superfamily uri_format: http://www.cathdb.info/cathnode/$1 cattleqtldb: description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs. example: '4685' homepage: https://www.animalgenome.org/QTLdb mappings: biocontext: CATTLEQTLDB miriam: cattleqtldb n2t: cattleqtldb prefixcommons: cattleqtldb name: Animal Genome Cattle QTL part_of: qtldb pattern: ^\d+$ preferred_prefix: cattleqtldb uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 cazy: description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features. example: GT10 homepage: http://www.cazy.org/ mappings: biocontext: CAZY fairsharing: FAIRsharing.ntyq70 go: CAZY miriam: cazy n2t: cazy prefixcommons: cazy uniprot: CAZy name: Carbohydrate Active EnZYmes pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$ preferred_prefix: cazy publications: - doi: 10.1093/nar/gkn663 pmc: PMC2686590 pubmed: '18838391' title: 'The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics.' year: 2008 uri_format: http://www.cazy.org/$1.html cba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE.' example: '375364' homepage: http://www.cba.ac.cn name: Chinese Biological Abstracts pattern: ^\d+$ preferred_prefix: cba uri_format: https://europepmc.org/article/CBA/$1 cbioportal: description: The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. example: laml_tcga_pub homepage: http://www.cbioportal.org mappings: fairsharing: FAIRsharing.6L6MjA miriam: cbioportal n2t: cbioportal name: The cBioPortal for Cancer Genomics pattern: ^[a-z0-9\_]+$ preferred_prefix: cbioportal uri_format: https://www.cbioportal.org/study/summary?id=$1 ccdc: description: The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC. example: '1829126' homepage: https://www.ccdc.cam.ac.uk/ mappings: miriam: ccdc name: CCDC Number pattern: ^\d{6,7}$ preferred_prefix: ccdc uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG ccds: description: The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations. example: CCDS13573.1 homepage: http://www.ncbi.nlm.nih.gov/CCDS/ mappings: biocontext: CCDS fairsharing: FAIRsharing.46s4nt miriam: ccds n2t: ccds prefixcommons: ccds uniprot: CCDS name: Consensus CDS pattern: ^CCDS\d+\.\d+$ preferred_prefix: ccds publications: - doi: 10.1101/gr.080531.108 pmc: PMC2704439 pubmed: '19498102' title: 'The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.' year: 2009 uri_format: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1 ccle: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Datasets around different cancer cell lines generated by the Broad Institute and Novartis example: BT20_BREAST homepage: https://www.cbioportal.org/study/summary?id=ccle_broad_2019 mappings: cellosaurus: CCLE name: Cancer Cell Line Encyclopedia Cells preferred_prefix: ccle synonyms: - ccle.cell uri_format: https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1 cco: banana: CCO contact: email: vladimir.n.mironov@gmail.com github: null name: Vladimir Mironov orcid: null description: The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process. download_obo: https://www.bio.ntnu.no/ontology/CCO/cco.obo download_owl: https://www.bio.ntnu.no/ontology/CCO/cco.owl example: '0000003' homepage: http://www.semantic-systems-biology.org/apo mappings: aberowl: CCO biocontext: CCO bioportal: CCO fairsharing: FAIRsharing.xhwrnr miriam: cco n2t: cco ols: cco prefixcommons: cco name: Cell Cycle Ontology namespace_in_lui: true pattern: ^\w+$ preferred_prefix: cco publications: - doi: 10.1186/gb-2009-10-5-r58 pmc: PMC2718524 pubmed: '19480664' title: 'The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process.' year: 2009 uri_format: https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1 version: '2016-03-23' ccrid: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Cell line databases/resources example: 4201PAT-CCTCC00348 homepage: http://www.cellresource.cn mappings: cellosaurus: CCRID name: National Experimental Cell Resource Sharing Platform preferred_prefix: ccrid uri_format: http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1 cdao: contact: email: balhoff@renci.org github: balhoff name: Jim Balhoff orcid: 0000-0002-8688-6599 description: The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character. download_owl: http://purl.obolibrary.org/obo/cdao.owl example: '0000072' homepage: https://github.com/evoinfo/cdao license: CC0 1.0 mappings: aberowl: CDAO agroportal: CDAO biocontext: CDAO bioportal: CDAO fairsharing: FAIRsharing.kay31r obofoundry: cdao ols: cdao ontobee: CDAO name: Comparative Data Analysis Ontology pattern: ^\d{7}$ preferred_prefix: CDAO publications: - doi: 10.4137/ebo.s2320 pmc: PMC2747124 pubmed: '19812726' title: Initial implementation of a comparative data analysis ontology. year: 2009 repository: https://github.com/evoinfo/cdao uri_format: http://purl.obolibrary.org/obo/CDAO_$1 version: '2019-06-26' cdd: description: The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. example: cd00400 homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd mappings: biocontext: CDD edam: '2666' fairsharing: FAIRsharing.ea287c go: CDD miriam: cdd n2t: cdd ncbi: CDD prefixcommons: cdd uniprot: CDD name: Conserved Domain Database at NCBI pattern: ^(cd)?\d{5}$ preferred_prefix: cdd publications: - doi: 10.1093/nar/gkn845 pmc: PMC2686570 pubmed: '18984618' title: 'CDD: specific functional annotation with the Conserved Domain Database.' year: 2008 uri_format: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 cdno: contact: email: l.andres.hernandez.18@student.scu.edu.au github: LilyAndres name: Liliana Andres Hernandez orcid: 0000-0002-7696-731X depends_on: - bfo - chebi - envo - pato - ro description: None download_obo: http://purl.obolibrary.org/obo/cdno.obo download_owl: http://purl.obolibrary.org/obo/cdno.owl example: '0000013' homepage: https://cdno.info/ license: CC BY 3.0 mappings: aberowl: CDNO bioportal: CDNO obofoundry: cdno ols: cdno ontobee: CDNO name: Compositional Dietary Nutrition Ontology pattern: ^\d{7}$ preferred_prefix: CDNO publications: - doi: 10.1002/csc2.20092 pmc: null pubmed: null title: Knowledge representation and data sharing to unlock crop variation for nutritional food security year: null repository: https://github.com/Southern-Cross-Plant-Science/cdno uri_format: http://purl.obolibrary.org/obo/CDNO_$1 version: '2022-06-23' cdpd: description: The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN). example: '63250' homepage: http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp mappings: biocontext: CDPD miriam: cdpd n2t: cdpd name: Canadian Drug Product Database pattern: ^\d+$ preferred_prefix: cdpd uri_format: http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1 cdt: appears_in: - ohd contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment. download_owl: https://github.com/oral-health-and-disease-ontologies/ohd-ontology/blob/master/src/ontology/older/CDTCodes%20as%20Classes_pruned.owl example: '1000001' homepage: https://www.ada.org/publications/CDT mappings: hl7: 2.16.840.1.113883.6.116 name: Current Dental Terminology pattern: ^\d{7}$ preferred_prefix: cdt cell_biolabs: description: Cell line collections example: AKR-270 homepage: https://www.cellbiolabs.com mappings: cellosaurus: Cell_Biolabs name: Cell Biolabs cell line products preferred_prefix: cell_biolabs uri_format: https://www.cellbiolabs.com/search?keywords=$1 cell_model_passport: description: Cell line databases/resources example: SIDM01262 homepage: https://cellmodelpassports.sanger.ac.uk/ mappings: cellosaurus: Cell_Model_Passport name: Sanger Cell Model Passports preferred_prefix: cell_model_passport uri_format: https://cellmodelpassports.sanger.ac.uk/passports/$1 cellbank.australia: description: CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world. example: ab-1-ha homepage: http://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/ mappings: cellosaurus: CBA name: CellBank Australia preferred_prefix: cellbank.australia uri_format: https://www.cellbankaustralia.com/$1.html cellimage: description: 'The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.' example: '24801' homepage: http://cellimagelibrary.org/ mappings: biocontext: CELLIMAGE fairsharing: FAIRsharing.8t18te miriam: cellimage n2t: cellimage prefixcommons: cellimage name: Cell Image Library pattern: ^\d+$ preferred_prefix: cellimage uri_format: http://cellimagelibrary.org/images/$1 cellopub: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Cellosaurus identifeirs for publications, like Pubmed example: CLPUB00496 homepage: https://web.expasy.org/cellosaurus/ mappings: cellosaurus: CelloPub name: Cellosaurus Publication pattern: ^CLPUB\d+$ preferred_prefix: cellopub uri_format: https://web.expasy.org/cellosaurus/cellopub/$1 cellosaurus: banana: CVCL banana_peel: _ contact: email: Amos.Bairoch@sib.swiss github: AmosBairoch name: Amos Bairoch orcid: 0000-0003-2826-6444 description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.' download_obo: https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo example: '0440' homepage: https://cellosaurus.org mappings: biocontext: CELLOSAURUS cellosaurus: Cellosaurus fairsharing: FAIRsharing.hkk309 miriam: cellosaurus n2t: cellosaurus re3data: r3d100013293 wikidata: P3289 name: Cellosaurus pattern: ^[A-Z0-9]{4}$ preferred_prefix: cellosaurus providers: - code: legacy description: The legacy URI for the Cellosaurus website, updated on August 30, 2022 [ref](https://twitter.com/Cellosaurus/status/1564658792691810305). homepage: https://web.expasy.org/cellosaurus name: Legacy Endpoint uri_format: https://web.expasy.org/cellosaurus/CVCL_$1 synonyms: - CVCL twitter: cellosaurus uri_format: https://www.cellosaurus.org/CVCL_$1 cellosaurus.resource: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The set of prefixes used in the Cellosaurus resource example: 4DN homepage: https://web.expasy.org/cellosaurus/ name: Cellosaurus Registry preferred_prefix: cellosaurus.resource uri_format: https://bioregistry.io/metaregistry/cellosaurus/$1 cellrepo: description: The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines example: '82' homepage: https://cellrepo.ico2s.org/ mappings: miriam: cellrepo name: Cell Version Control Repository pattern: ^[0-9]+$ preferred_prefix: cellrepo uri_format: https://cellrepo.ico2s.org/repositories/$1 cemo: contact: email: n.queralt_rosinach@lumc.nl github: NuriaQueralt name: Núria Queralt Rosinach orcid: 0000-0003-0169-8159 contributor: email: null github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The covid-19 epidemiology and monitoring ontology (cemo) provides a common ontological model to make epidemiological quantitative data for monitoring the covid-19 outbreak machine-readable and interoperable to facilitate its exchange, integration and analysis, to eventually support evidence-based rapid response. download_owl: https://raw.githubusercontent.com/NuriaQueralt/covid19-epidemiology-ontology/main/owl/cemo.owl example: length_of_intensive_care_unit_(icu)_stay github_request_issue: 593 homepage: https://github.com/NuriaQueralt/covid19-epidemiology-ontology license: CC0 1.0 name: The COVID-19 epidemiology and monitoring ontology pattern: ^[()0-9a-z_-]+$ preferred_prefix: cemo repository: https://github.com/NuriaQueralt/covid19-epidemiology-ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://purl.obolibrary.org/obo/cemo.owl#$1 ceph: contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 deprecated: true description: An anatomical and developmental ontology for cephalopods download_obo: https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo download_owl: http://purl.obolibrary.org/obo/ceph.owl example: 0000109 homepage: https://github.com/obophenotype/cephalopod-ontology license: CC BY 3.0 mappings: aberowl: CEPH biocontext: CEPH bioportal: CEPH fairsharing: FAIRsharing.p58bm4 obofoundry: ceph ols: ceph ontobee: CEPH name: Cephalopod Ontology pattern: ^\d{7}$ preferred_prefix: CEPH repository: https://github.com/obophenotype/cephalopod-ontology uri_format: http://purl.obolibrary.org/obo/CEPH_$1 version: '2016-01-12' cgd: description: The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products. example: CAL0003079 homepage: http://www.candidagenome.org/ mappings: biocontext: CGD fairsharing: FAIRsharing.j7j53 go: CGD miriam: cgd n2t: cgd ncbi: CGD prefixcommons: cgd uniprot: CGD name: Candida Genome Database pattern: ^CAL\d{7}$ preferred_prefix: cgd publications: - doi: 10.1093/nar/gki003 pmc: PMC539957 pubmed: '15608216' title: The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information. year: 2005 uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 cghdb: description: Cell line databases/resources example: 300165/p13898_2106T homepage: http://www.cghtmd.jp/CGHDatabase/index_e.jsp mappings: cellosaurus: CGH-DB name: CGH Data Base preferred_prefix: cghdb uri_format: http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en cgnc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans) example: '10087' homepage: http://birdgenenames.org/cgnc/ mappings: prefixcommons: cgnc re3data: r3d100012429 name: Chicken Gene Nomenclature Consortium pattern: ^\d+$ preferred_prefix: cgnc publications: - doi: 10.1186/1471-2164-10-s2-s5 pmc: PMC2966335 pubmed: '19607656' title: The Chicken Gene Nomenclature Committee report. year: 2009 synonyms: - BirdBase - CGNC uri_format: http://birdgenenames.org/cgnc/GeneReport?id=$1 cgsc: description: The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. example: '74' homepage: http://cgsc.biology.yale.edu/index.php mappings: biocontext: CGSC fairsharing: FAIRsharing.1tbrdz go: CGSC miriam: cgsc n2t: cgsc prefixcommons: cgsc name: Coli Genetic Stock Center pattern: ^\d+$ preferred_prefix: cgsc uri_format: http://cgsc.biology.yale.edu/Site.php?ID=$1 charprot: description: CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession. example: CH_001923 homepage: http://www.jcvi.org/charprotdb mappings: biocontext: CHARPROT miriam: charprot n2t: charprot name: CharProt pattern: ^CH_\d+$ preferred_prefix: charprot uri_format: http://www.jcvi.org/charprotdb/index.cgi/view/$1 chebi: appears_in: - cdno - chiro - cl - ecocore - ecto - envo - fobi - foodon - genepio - maxo - mco - ons - pcl - proco - scdo - uberon - xpo banana: CHEBI contact: email: amalik@ebi.ac.uk github: amalik01 name: Adnan Malik orcid: 0000-0001-8123-5351 description: Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. download_obo: http://purl.obolibrary.org/obo/chebi.obo download_owl: http://purl.obolibrary.org/obo/chebi.owl example: '24867' homepage: http://www.ebi.ac.uk/chebi license: CC BY 4.0 mappings: aberowl: CHEBI biocontext: CHEBI bioportal: CHEBI cellosaurus: ChEBI cheminf: '000407' edam: '1174' fairsharing: FAIRsharing.62qk8w go: CHEBI miriam: chebi n2t: chebi obofoundry: chebi ols: chebi ontobee: CHEBI prefixcommons: chebi re3data: r3d100012626 wikidata: P683 name: Chemical Entities of Biological Interest namespace_in_lui: true pattern: ^\d+$ 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:$1 version: '211' chembl: description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. example: CHEMBL4303805 homepage: https://www.ebi.ac.uk/chembl mappings: cheminf: '000412' fairsharing: FAIRsharing.m3jtpg miriam: chembl prefixcommons: chembl re3data: r3d100010539 uniprot: ChEMBL name: ChEMBL pattern: ^CHEMBL\d+$ preferred_prefix: chembl synonyms: - ChEMBL - ChEMBL_ID - 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 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/$1 chemdb: description: ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. example: '3966782' homepage: http://cdb.ics.uci.edu/ mappings: biocontext: CHEMDB fairsharing: FAIRsharing.dstf7h miriam: chemdb n2t: chemdb prefixcommons: chemdb name: ChemDB pattern: ^\d+$ preferred_prefix: chemdb publications: - doi: 10.1093/bioinformatics/btm341 pmc: null pubmed: '17599932' title: ChemDB update--full-text search and virtual chemical space. year: 2007 uri_format: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1 chemidplus: description: ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. example: 57-27-2 homepage: https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp mappings: biocontext: CHEMIDPLUS edam: '2658' fairsharing: FAIRsharing.5949vn miriam: chemidplus n2t: chemidplus prefixcommons: chemidplus name: ChemIDplus pattern: ^\d+\-\d+\-\d+$ preferred_prefix: chemidplus synonyms: - ChemIDplus uri_format: https://chem.nlm.nih.gov/chemidplus/rn/$1 cheminf: appears_in: - proco contact: email: egon.willighagen@gmail.com github: egonw name: Egon Willighagen orcid: 0000-0001-7542-0286 description: Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. download_owl: https://github.com/semanticchemistry/semanticchemistry/raw/master/ontology/cheminf.owl example: '000410' homepage: https://github.com/semanticchemistry/semanticchemistry license: CC0 1.0 mappings: aberowl: CHEMINF biocontext: CHEMINF bioportal: CHEMINF fairsharing: FAIRsharing.sjhvyy obofoundry: cheminf ols: cheminf ontobee: CHEMINF name: Chemical Information Ontology pattern: ^\d{6}$ 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/ mappings: aberowl: CHEMROF bioportal: CHEMROF name: Chemical Entity Materials and Reactions Ontological Framework preferred_prefix: ChEMROF uri_format: https://chemkg.github.io/chemrof/$1 chemspider: description: ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources. example: '56586' homepage: http://www.chemspider.com/ mappings: biocontext: CHEMSPIDER cheminf: '000405' edam: '1173' fairsharing: FAIRsharing.96f3gm miriam: chemspider n2t: chemspider prefixcommons: chemspider re3data: r3d100010205 wikidata: P661 name: ChemSpider pattern: ^\d+$ preferred_prefix: chemspider synonyms: - ChemSpiderID - Chemspider uri_format: http://www.chemspider.com/Chemical-Structure.$1.html chickenqtldb: description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs. example: '14362' homepage: https://www.animalgenome.org/QTLdb mappings: biocontext: CHICKENQTLDB miriam: chickenqtldb n2t: chickenqtldb prefixcommons: chickenqtldb name: Animal Genome Chicken QTL part_of: qtldb pattern: ^\d+$ preferred_prefix: chickenqtldb uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 chiro: contact: email: vasilevs@ohsu.edu github: nicolevasilevsky name: Nicole Vasilevsky orcid: 0000-0001-5208-3432 depends_on: - chebi - go - hp - mp - ncbitaxon - pr - uberon description: CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes. download_obo: http://purl.obolibrary.org/obo/chiro.obo download_owl: http://purl.obolibrary.org/obo/chiro.owl homepage: https://github.com/obophenotype/chiro license: CC0 1.0 mappings: aberowl: CHIRO bioportal: CHIRO obofoundry: chiro ols: chiro ontobee: CHIRO name: ChEBI Integrated Role Ontology no_own_terms: true preferred_prefix: CHIRO publications: - doi: 10.26434/chemrxiv.12591221 pmc: null pubmed: null title: Extension of Roles in the ChEBI Ontology year: null repository: https://github.com/obophenotype/chiro uri_format: http://purl.obolibrary.org/obo/CHIRO_$1 version: '2015-11-23' chmo: appears_in: - rbo - scdo contact: email: batchelorc@rsc.org github: batchelorc name: Colin Batchelor orcid: 0000-0001-5985-7429 description: CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI). download_obo: http://purl.obolibrary.org/obo/chmo.obo download_owl: http://purl.obolibrary.org/obo/chmo.owl example: 0002902 homepage: https://github.com/rsc-ontologies/rsc-cmo license: CC BY 4.0 mappings: aberowl: CHMO biocontext: CHMO bioportal: CHMO fairsharing: FAIRsharing.9j4wh2 obofoundry: chmo ols: chmo ontobee: CHMO name: Chemical Methods Ontology pattern: ^\d{7}$ preferred_prefix: CHMO repository: https://github.com/rsc-ontologies/rsc-cmo uri_format: http://purl.obolibrary.org/obo/CHMO_$1 version: '2022-04-19' cido: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment. download_owl: https://github.com/CIDO-ontology/cido/raw/master/cido.owl example: '0000005' homepage: https://github.com/cido-ontology/cido license: CC BY 4.0 mappings: aberowl: CIDO bioportal: CIDO fairsharing: FAIRsharing.aVmpKl obofoundry: cido ols: cido ontobee: CIDO name: Coronavirus Infectious Disease Ontology pattern: ^\d{7}$ preferred_prefix: CIDO publications: - doi: 10.1038/s41597-020-0523-6 pmc: PMC7293349 pubmed: '32533075' title: CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. year: 2020 repository: https://github.com/cido-ontology/cido uri_format: http://purl.obolibrary.org/obo/CIDO_$1 version: 1.0.326 cio: contact: email: frederic.bastian@unil.ch github: fbastian name: Frédéric Bastian orcid: 0000-0002-9415-5104 description: An ontology to capture confidence information about annotations. download_obo: http://purl.obolibrary.org/obo/cio.obo download_owl: http://purl.obolibrary.org/obo/cio.owl example: '0000040' homepage: https://github.com/BgeeDB/confidence-information-ontology license: CC0 1.0 mappings: aberowl: CIO biocontext: CIO bioportal: CIO fairsharing: FAIRsharing.e3t0yw obofoundry: cio ols: cio ontobee: CIO name: Confidence Information Ontology pattern: ^\d{7}$ preferred_prefix: CIO publications: - doi: 10.1093/database/bav043 pmc: PMC4425939 pubmed: '25957950' title: 'The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.' year: 2015 repository: https://github.com/BgeeDB/confidence-information-ontology uri_format: http://purl.obolibrary.org/obo/CIO_$1 version: '2015-03-10' citexplore: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes. example: C6155 homepage: https://www.ebi.ac.uk/citexplore/ mappings: fairsharing: FAIRsharing.619eqr prefixcommons: citexplore name: CiteXplore preferred_prefix: citexplore publications: - doi: 10.1097/mol.0b013e328362df13 pmc: null pubmed: '23759795' title: Cerebrotendinous xanthomatosis. year: 2013 references: - https://www.embl.de/aboutus/communication_outreach/media_relations/2006/061127_hinxton/ synonyms: - CTX uri_format: https://europepmc.org/article/CTX/$1 cito: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology that enables characterization of the nature or type of citations, both factually and rhetorically. example: sharesAuthorInstitutionWith homepage: http://www.sparontologies.net/ontologies/cito mappings: fairsharing: FAIRsharing.b220d4 name: Citation Typing Ontology preferred_prefix: CiTO publications: - doi: 10.1016/j.websem.2012.08.001 pmc: null pubmed: null title: 'FaBiO and CiTO: Ontologies for describing bibliographic resources and citations' year: null repository: https://github.com/sparontologies/cito uri_format: http://purl.org/spar/cito/$1 civic.aid: description: 'A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC.' example: '3' homepage: https://civicdb.org/ mappings: miriam: civic.aid name: CIViC Assertion pattern: ^[0-9]+$ preferred_prefix: civic.aid uri_format: https://civicdb.org/links/assertions/$1 civic.did: description: Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement. example: '46' homepage: https://civicdb.org/ mappings: miriam: civic.did name: CIViC Disease pattern: ^[0-9]+$ preferred_prefix: civic.did uri_format: https://civicdb.org/links/diseases/$1 civic.eid: description: Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract). example: '1199' homepage: https://civicdb.org/ mappings: miriam: civic.eid name: CIViC Evidence pattern: ^[0-9]+$ preferred_prefix: civic.eid uri_format: https://civicdb.org/links/evidence/$1 civic.gid: description: A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus on emphasizing the clinical relevance from a molecular perspective rather than describing the biological function of the gene unless necessary to contextualize its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes, specific treatments for the gene’s associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis example: '272' homepage: https://civicdb.org/ mappings: miriam: civic.gid name: CIViC Gene pattern: ^[0-9]+$ preferred_prefix: civic.gid uri_format: https://civicdb.org/links/gene/$1 civic.sid: description: In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source. example: '62' homepage: https://civicdb.org/ mappings: miriam: civic.sid name: CIViC Source pattern: ^[0-9]+$ preferred_prefix: civic.sid uri_format: https://civicdb.org/links/sources/$1 civic.tid: description: Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant. example: '14' homepage: https://civicdb.org/ mappings: miriam: civic.tid name: CIViC Therapy pattern: ^[0-9]+$ preferred_prefix: civic.tid uri_format: https://civicdb.org/links/drugs/$1 civic.vid: description: CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making. example: '12' homepage: https://civicdb.org/ mappings: miriam: civic.vid name: CIViC Variant pattern: ^[0-9]+$ preferred_prefix: civic.vid uri_format: https://civicdb.org/links/variant/$1 cl: appears_in: - clo - ecao - ehdaa2 - go - mco - pcl - uberon - xpo banana: CL contact: email: addiehl@buffalo.edu github: addiehl name: Alexander Diehl orcid: 0000-0001-9990-8331 depends_on: - chebi - go - ncbitaxon - pato - pr - ro - uberon description: The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi. download_obo: https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-full.obo download_owl: http://purl.obolibrary.org/obo/cl.owl example: '0000062' homepage: https://obophenotype.github.io/cell-ontology/ license: CC BY 4.0 mappings: aberowl: CL agroportal: CL biocontext: CL bioportal: CL cellosaurus: CL fairsharing: FAIRsharing.j9y503 go: CL miriam: cl n2t: cl obofoundry: cl ols: cl ontobee: CL prefixcommons: cl wikidata: P7963 name: Cell Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: CL publications: - doi: 10.1186/s13326-016-0088-7 pmc: PMC4932724 pubmed: '27377652' title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.' year: 2016 - doi: 10.1186/1471-2105-12-6 pmc: PMC3024222 pubmed: '21208450' title: Logical development of the cell ontology. year: 2011 repository: https://github.com/obophenotype/cell-ontology uri_format: https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:$1 version: '2022-08-16' clao: contact: email: lagonzalezmo@unal.edu.co github: luis-gonzalez-m name: Luis González-Montaña orcid: 0000-0002-9136-9932 depends_on: - ro description: 'CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).' download_obo: http://purl.obolibrary.org/obo/clao.obo download_owl: http://purl.obolibrary.org/obo/clao.owl example: 0000088 homepage: https://github.com/luis-gonzalez-m/Collembola license: CC0 1.0 mappings: aberowl: CLAO bioportal: CLAO obofoundry: clao ols: clao ontobee: CLAO name: Collembola Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: CLAO repository: https://github.com/luis-gonzalez-m/Collembola uri_format: http://purl.obolibrary.org/obo/CLAO_$1 version: '2021-09-27' classyfire: banana: C comment: There's a mismatch between the MIRIAM URI format string, which has a C prefix in front of class identifiers and the ontology which does not use them. description: ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API. download_obo: http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip example: 0004828 homepage: http://classyfire.wishartlab.com/ mappings: miriam: classyfire name: ClassyFire pattern: ^\d{7}$ preferred_prefix: classyfire synonyms: - CHEMONTID uri_format: http://classyfire.wishartlab.com/tax_nodes/C$1 cldb: description: The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories. example: cl3603 homepage: http://bioinformatics.hsanmartino.it/hypercldb/indexes.html mappings: biocontext: CLDB cellosaurus: CLDB miriam: cldb n2t: cldb name: Cell Line Database pattern: ^(cl|tum)\d+$ preferred_prefix: cldb uri_format: http://bioinformatics.hsanmartino.it/hypercldb/$1.html clingene: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The allele registry provides and maintains identifiers for genetic variants example: CA981206459 homepage: https://reg.clinicalgenome.org mappings: biolink: CAID name: ClinGen Allele Registry preferred_prefix: clingene uri_format: https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1 clinicaltrials: description: ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries example: NCT00222573 homepage: https://clinicaltrials.gov/ mappings: biocontext: CLINICALTRIALS miriam: clinicaltrials n2t: clinicaltrials prefixcommons: clinicaltrials name: ClinicalTrials.gov pattern: ^NCT\d{8}$ preferred_prefix: clinicaltrials providers: - code: smartpatients description: Smart Patients is an online community for patients and their families. Join us to talk with other patients about the latest research for your condition. homepage: https://www.smartpatients.com name: Smart Patients uri_format: https://www.smartpatients.com/trials/$1 uri_format: https://clinicaltrials.gov/ct2/show/$1 clinvar: description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier. example: '12345' homepage: http://www.ncbi.nlm.nih.gov/clinvar/ mappings: biocontext: ClinVar biolink: CLINVAR cellosaurus: ClinVar fairsharing: FAIRsharing.wx5r6f hl7: clinVar-V miriam: clinvar n2t: clinvar re3data: r3d100013331 wikidata: P1929 name: ClinVar Variation pattern: ^\d+$ preferred_prefix: clinvar uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1 clinvar.record: description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession. example: RCV000033555.3 homepage: http://www.ncbi.nlm.nih.gov/clinvar/ mappings: biocontext: CLINVAR.RECORD miriam: clinvar.record n2t: clinvar.record name: ClinVar Record part_of: clinvar pattern: ^RCV\d+(\.\d+)?$ preferred_prefix: clinvar.record uri_format: http://www.ncbi.nlm.nih.gov/clinvar/$1 clinvar.submission: description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession. example: SCV000151292 homepage: http://www.ncbi.nlm.nih.gov/clinvar/ mappings: biocontext: CLINVAR.SUBMISSION miriam: clinvar.submission n2t: clinvar.submission name: ClinVar Submission pattern: ^SCV\d+(\.\d+)?$ preferred_prefix: clinvar.submission uri_format: http://www.ncbi.nlm.nih.gov/clinvar?term=$1 clinvar.submitter: description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs). example: '26957' homepage: https://www.ncbi.nlm.nih.gov/clinvar/ mappings: miriam: clinvar.submitter name: ClinVar Submitter pattern: ^\d+$ preferred_prefix: clinvar.submitter uri_format: https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1 clo: appears_in: - mco contact: email: siiraa@umich.edu github: siiraa name: Sirarat Sarntivijai orcid: 0000-0002-2548-641X depends_on: - cl - doid - ncbitaxon - uberon description: The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns. download_owl: http://purl.obolibrary.org/obo/clo.owl example: 0000091 homepage: http://www.clo-ontology.org license: CC BY 3.0 mappings: aberowl: CLO biocontext: CLO bioportal: CLO cellosaurus: CLO fairsharing: FAIRsharing.4dvtcz obofoundry: clo ols: clo ontobee: CLO prefixcommons: clo wikidata: P2158 name: Cell Line Ontology pattern: ^\d{7}$ preferred_prefix: CLO publications: - doi: 10.1186/2041-1480-5-37 pmc: PMC4387853 pubmed: '25852852' title: 'CLO: The cell line ontology.' year: 2014 - doi: 10.1186/gb-2005-6-2-r21 pmc: PMC551541 pubmed: '15693950' title: An ontology for cell types. year: 2005 repository: https://github.com/CLO-Ontology/CLO synonyms: - CLO uri_format: http://purl.obolibrary.org/obo/CLO_$1 version: 2.1.178 cls: description: Cell line collections example: 300108/p3934_A-172 homepage: https://cls.shop/ mappings: cellosaurus: CLS name: Cell Lines Service preferred_prefix: cls uri_format: https://cls.shop/$1 clyh: contact: email: lucas.leclere@obs-vlfr.fr github: L-Leclere name: Lucas Leclere orcid: 0000-0002-7440-0467 depends_on: - iao - ro - uberon description: Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica. download_obo: http://purl.obolibrary.org/obo/clyh.obo download_owl: http://purl.obolibrary.org/obo/clyh.owl example: '1000100' homepage: https://github.com/EBISPOT/clyh_ontology license: CC BY 3.0 mappings: aberowl: CLYH bioportal: CLYH obofoundry: clyh ols: clyh ontobee: CLYH name: Clytia hemisphaerica Development and Anatomy Ontology pattern: ^\d+$ preferred_prefix: CLYH repository: https://github.com/EBISPOT/clyh_ontology uri_format: http://purl.obolibrary.org/obo/CLYH_$1 version: '2020-05-29' cmecs: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard. example: '595' homepage: https://cmecscatalog.org/cmecs name: Costal and Marine Ecological Classification Standard pattern: ^\d+$ preferred_prefix: cmecs references: - http://www.natureserve.org/sites/default/files/publications/files/cmecs_version_06-2012_final.pdf uri_format: https://cmecscatalog.org/cmecs/classification/unit/$1.html cmf: contact: email: engelsta@ohsu.edu github: null name: Mark Engelstad orcid: 0000-0001-5889-4463 deprecated: true description: This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain homepage: https://code.google.com/p/craniomaxillofacial-ontology/ mappings: aberowl: CMF biocontext: CMF obofoundry: cmf ontobee: CMF name: CranioMaxilloFacial ontology preferred_prefix: CMF uri_format: http://purl.obolibrary.org/obo/CMF_$1 cmo: appears_in: - scdo contact: email: jrsmith@mcw.edu github: jrsjrs name: Jennifer Smith orcid: 0000-0002-6443-9376 description: Morphological and physiological measurement records generated from clinical and model organism research and health programs. download_obo: http://purl.obolibrary.org/obo/cmo.obo download_owl: http://purl.obolibrary.org/obo/cmo.owl example: '0001350' homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html license: CC0 1.0 mappings: aberowl: CMO biocontext: CMO bioportal: CMO fairsharing: FAIRsharing.dq78pn obofoundry: cmo ols: cmo ontobee: CMO name: Clinical measurement ontology pattern: ^\d{7}$ preferred_prefix: CMO publications: - doi: 10.1186/2041-1480-4-26 pmc: PMC3882879 pubmed: '24103152' title: 'The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.' year: 2013 - doi: 10.3389/fgene.2012.00087 pmc: PMC3361058 pubmed: '22654893' title: Three ontologies to define phenotype measurement data. year: 2012 repository: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology twitter: ratgenome uri_format: http://purl.obolibrary.org/obo/CMO_$1 version: '2019-02-19' cmpo: contact: email: jupp@ebi.ac.uk github: null name: Simon Jupp orcid: null description: CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. download_owl: http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl example: '0000435' homepage: http://www.ebi.ac.uk/cmpo mappings: aberowl: CMPO bioportal: CMPO fairsharing: FAIRsharing.knp11s ols: cmpo name: Cellular Microscopy Phenotype Ontology pattern: ^\d{7}$ preferred_prefix: cmpo publications: - doi: 10.1186/s13326-016-0074-0 pmc: PMC4870745 pubmed: '27195102' title: The cellular microscopy phenotype ontology. year: 2016 repository: https://github.com/EBISPOT/CMPO twitter: EBIOLS uri_format: http://www.ebi.ac.uk/cmpo/CMPO_$1 version: '2017-12-19' co_320: description: Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables download_owl: https://cropontology.org/ontology/CO_320/Rice/owl example: 0000618 homepage: https://cropontology.org/ontology/CO_320/Rice mappings: agroportal: CO_320 cropoct: CO_320 fairsharing: FAIRsharing.2jkxp5 ols: co_320 name: Rice ontology pattern: ^\d{7}$ preferred_prefix: co_320 uri_format: https://www.cropontology.org/rdf/CO_320:$1 version: '2019-10-09' co_321: description: July 2018 download_owl: https://cropontology.org/ontology/CO_321/Wheat/owl example: 0000449 homepage: https://cropontology.org/ontology/CO_321/Wheat mappings: agroportal: CO_321 cropoct: CO_321 fairsharing: FAIRsharing.czzmpg ols: co_321 name: Wheat ontology pattern: ^\d{7}$ preferred_prefix: co_321 publications: - doi: 10.1093/aobpla/plq008 pmc: PMC3000699 pubmed: '22476066' title: 'Multifunctional crop trait ontology for breeders'' data: field book, annotation, data discovery and semantic enrichment of the literature.' year: 2010 uri_format: https://www.cropontology.org/rdf/CO_321:$1 version: '2019-10-09' co_322: description: Maize Trait Dictionary in template 5 - CIMMYT- September 2016 download_owl: https://cropontology.org/ontology/CO_322/Maize/owl example: '0000773' homepage: https://cropontology.org/ontology/CO_322/Maize mappings: agroportal: CO_322 cropoct: CO_322 fairsharing: FAIRsharing.eeyne8 ols: co_322 name: Maize ontology pattern: ^\d{7}$ preferred_prefix: co_322 uri_format: https://www.cropontology.org/rdf/CO_322:$1 version: '2019-10-09' co_323: description: ICARDA - TDv5 - Sept 2018 download_owl: https://cropontology.org/ontology/CO_323/Barley/owl example: '0000252' homepage: https://cropontology.org/ontology/CO_323/Barley mappings: agroportal: CO_323 cropoct: CO_323 fairsharing: FAIRsharing.f69084 ols: co_323 name: Barley ontology pattern: ^\d{7}$ preferred_prefix: co_323 uri_format: https://www.cropontology.org/rdf/CO_323:$1 version: '2019-11-20' co_324: description: Sorghum TDv5 - Oct 2019 download_owl: https://cropontology.org/ontology/CO_324/Sorghum/owl example: '0000111' homepage: https://cropontology.org/ontology/CO_324/Sorghum mappings: agroportal: CO_324 cropoct: CO_324 fairsharing: FAIRsharing.dxx0c ols: co_324 name: Sorghum ontology pattern: ^\d{7}$ preferred_prefix: co_324 uri_format: https://www.cropontology.org/rdf/CO_324:$1 version: '2019-10-09' co_325: description: Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019 download_owl: https://cropontology.org/ontology/CO_325/Banana/owl example: 0000519 homepage: https://cropontology.org/ontology/CO_325/Banana mappings: agroportal: CO_325 cropoct: CO_325 fairsharing: FAIRsharing.gdszhh ols: co_325 name: Banana ontology pattern: ^\d{7}$ preferred_prefix: co_325 uri_format: https://www.cropontology.org/rdf/CO_325:$1 version: '2019-10-09' co_326: description: Draft version download_owl: https://cropontology.org/ontology/CO_326/Coconut/owl example: '0000254' homepage: https://cropontology.org/ontology/CO_326/Coconut mappings: cropoct: CO_326 ols: co_326 name: Coconut ontology pattern: ^\d{7}$ preferred_prefix: co_326 uri_format: https://www.cropontology.org/rdf/CO_326:$1 co_327: description: Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016 download_owl: http://www.cropontology.org/ontology/CO_327/Pearl%20millet/owl example: 0000095 homepage: http://www.cropontology.org/ontology/CO_327/Pearl%20millet mappings: agroportal: CO_327 cropoct: CO_327 fairsharing: FAIRsharing.4e3qh9 ols: co_327 name: Pearl millet ontology pattern: ^\d{7}$ preferred_prefix: co_327 uri_format: https://www.cropontology.org/rdf/CO_327:$1 co_330: description: CIP - potato ontology - december 2018 download_owl: https://cropontology.org/ontology/CO_330/Potato/owl example: '0000106' homepage: https://cropontology.org/ontology/CO_330/Potato mappings: agroportal: CO_330 cropoct: CO_330 fairsharing: FAIRsharing.4fa657 ols: co_330 name: Potato ontology pattern: ^\d{7}$ preferred_prefix: co_330 uri_format: https://www.cropontology.org/rdf/CO_330:$1 version: '2019-10-09' co_331: description: Sweet Potato Trait Dictionary in template v5 - CIP - November 2019 download_owl: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato/owl example: 0000088 homepage: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato mappings: agroportal: CO_331 cropoct: CO_331 fairsharing: FAIRsharing.4g5qcw ols: co_331 name: Sweet Potato ontology pattern: ^\d{7}$ preferred_prefix: co_331 uri_format: https://www.cropontology.org/rdf/CO_331:$1 co_333: description: 'This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017.' download_owl: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology/owl example: '3000045' homepage: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology mappings: agroportal: CO_333 cropoct: CO_333 fairsharing: FAIRsharing.af5655 ols: co_333 name: Beet Ontology ontology pattern: ^\d+$ preferred_prefix: co_333 uri_format: https://www.cropontology.org/rdf/CO_333:$1 co_334: description: Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016 download_owl: https://cropontology.org/ontology/CO_334/Cassava/owl example: '0000070' homepage: https://cropontology.org/ontology/CO_334/Cassava mappings: agroportal: CO_334 cropoct: CO_334 fairsharing: FAIRsharing.v06c4q ols: co_334 name: Cassava ontology pattern: ^\d{7}$ preferred_prefix: co_334 uri_format: https://www.cropontology.org/rdf/CO_334:$1 version: '2019-10-09' co_335: description: CIAT Common bean trait dictionary - version August 2014 download_owl: http://www.cropontology.org/ontology/CO_335/Common%20Bean/owl example: 0000189 homepage: http://www.cropontology.org/ontology/CO_335/Common%20Bean mappings: agroportal: CO_335 cropoct: CO_335 fairsharing: FAIRsharing.a14123 ols: co_335 name: Common Bean ontology pattern: ^\d{7}$ preferred_prefix: co_335 uri_format: https://www.cropontology.org/rdf/CO_335:$1 co_336: description: Soybean Trait Dictionary in template v5 - IITA - July 2015 download_owl: https://cropontology.org/ontology/CO_336/Soybean/owl example: 0000339 homepage: https://cropontology.org/ontology/CO_336/Soybean mappings: agroportal: CO_336 cropoct: CO_336 fairsharing: FAIRsharing.j75srj ols: co_336 name: Soybean ontology pattern: ^\d{7}$ preferred_prefix: co_336 uri_format: https://www.cropontology.org/rdf/CO_336:$1 co_337: description: Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015 download_owl: https://cropontology.org/ontology/CO_337/Groundnut/owl example: '0000054' homepage: https://cropontology.org/ontology/CO_337/Groundnut mappings: agroportal: CO_337 cropoct: CO_337 fairsharing: FAIRsharing.ge8y23 ols: co_337 name: Groundnut ontology pattern: ^\d{7}$ preferred_prefix: co_337 uri_format: https://www.cropontology.org/rdf/CO_337:$1 version: '2019-10-09' co_338: description: Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015 download_owl: https://cropontology.org/ontology/CO_338/Chickpea/owl example: 0000138 homepage: https://cropontology.org/ontology/CO_338/Chickpea mappings: agroportal: CO_338 cropoct: CO_338 fairsharing: FAIRsharing.js20q3 ols: co_338 name: Chickpea ontology pattern: ^\d{7}$ preferred_prefix: co_338 uri_format: https://www.cropontology.org/rdf/CO_338:$1 version: '2019-10-09' co_339: description: Lentil Trait Dictionary in template v5 - ICARDA - July 2015 download_owl: https://cropontology.org/ontology/CO_339/Lentil/owl example: '0000032' homepage: https://cropontology.org/ontology/CO_339/Lentil mappings: agroportal: CO_339 cropoct: CO_339 fairsharing: FAIRsharing.ry1ezg ols: co_339 name: Lentil ontology pattern: ^\d{7}$ preferred_prefix: co_339 uri_format: https://www.cropontology.org/rdf/CO_339:$1 version: '2019-10-09' co_340: description: Cowpea Trait Dictionary in template v5 - IITA - August 2015 download_owl: https://cropontology.org/ontology/CO_340/Cowpea/owl example: 0000639 homepage: https://cropontology.org/ontology/CO_340/Cowpea mappings: agroportal: CO_340 cropoct: CO_340 fairsharing: FAIRsharing.31apg2 ols: co_340 name: Cowpea ontology pattern: ^\d{7}$ preferred_prefix: co_340 publications: - doi: 10.3389/fphys.2012.00326 pmc: PMC3429094 pubmed: '22934074' title: Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice. year: 2012 uri_format: https://www.cropontology.org/rdf/CO_340:$1 version: '2019-10-09' co_341: description: Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015 download_owl: https://cropontology.org/ontology/CO_341/Pigeonpea/owl example: '0000140' homepage: https://cropontology.org/ontology/CO_341/Pigeonpea mappings: agroportal: CO_341 cropoct: CO_341 fairsharing: FAIRsharing.ehe3yp ols: co_341 name: Pigeonpea ontology pattern: ^\d{7}$ preferred_prefix: co_341 uri_format: https://www.cropontology.org/rdf/CO_341:$1 version: '2019-11-18' co_343: description: version 2019 - pvs download_owl: https://cropontology.org/ontology/CO_343/Yam/owl example: '0100010' homepage: https://cropontology.org/ontology/CO_343/Yam mappings: agroportal: CO_343 cropoct: CO_343 fairsharing: FAIRsharing.7e9cff ols: co_343 name: Yam ontology pattern: ^\d{7}$ preferred_prefix: co_343 uri_format: https://www.cropontology.org/rdf/CO_343:$1 version: '2019-10-09' co_345: description: Brachiaria (forages) ontology TD v5 - Version Oct 2016 download_owl: https://cropontology.org/ontology/CO_345/Brachiaria/owl example: '0000127' homepage: https://cropontology.org/ontology/CO_345/Brachiaria mappings: agroportal: CO_345 cropoct: CO_345 fairsharing: FAIRsharing.9e9683 ols: co_345 name: Brachiaria ontology pattern: ^\d{7}$ preferred_prefix: co_345 uri_format: https://www.cropontology.org/rdf/CO_345:$1 version: '2019-10-09' co_346: description: oct 2016 download_owl: https://cropontology.org/ontology/CO_346/Mungbean/owl example: 0000199 homepage: https://cropontology.org/ontology/CO_346/Mungbean mappings: agroportal: CO_346 cropoct: CO_346 fairsharing: FAIRsharing.fgd5gq ols: co_346 name: Mungbean ontology pattern: ^\d{7}$ preferred_prefix: co_346 uri_format: https://www.cropontology.org/rdf/CO_346:$1 version: '2019-10-09' co_347: description: 'March 2017 version ' download_owl: http://www.cropontology.org/ontology/CO_347/Castor%20bean/owl example: 0000108 homepage: http://www.cropontology.org/ontology/CO_347/Castor%20bean mappings: agroportal: CO_347 cropoct: CO_347 fairsharing: FAIRsharing.qrrvyk ols: co_347 name: Castor bean ontology pattern: ^\d{7}$ preferred_prefix: co_347 uri_format: https://www.cropontology.org/rdf/CO_347:$1 co_348: description: Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France). download_owl: https://cropontology.org/ontology/CO_348/Brassica/owl example: '1100107' homepage: https://cropontology.org/ontology/CO_348/Brassica mappings: agroportal: CO_348 cropoct: CO_348 fairsharing: FAIRsharing.af7a2d ols: co_348 name: Brassica ontology pattern: ^\d+$ preferred_prefix: co_348 uri_format: https://www.cropontology.org/rdf/CO_348:$1 version: '2019-11-29' co_350: description: Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo download_owl: https://cropontology.org/ontology/CO_350/Oat/owl example: '0000215' homepage: https://cropontology.org/ontology/CO_350/Oat mappings: agroportal: CO_350 cropoct: CO_350 fairsharing: FAIRsharing.35e1c3 ols: co_350 name: Oat ontology pattern: ^\d{7}$ preferred_prefix: co_350 uri_format: https://www.cropontology.org/rdf/CO_350:$1 version: '2019-10-09' co_356: description: Grape Ontology including OIV and bioversity descriptors. INRA July 2017 download_owl: https://cropontology.org/ontology/CO_356/Vitis/owl example: '4000027' homepage: https://cropontology.org/ontology/CO_356/Vitis mappings: agroportal: CO_356 cropoct: CO_356 fairsharing: FAIRsharing.c7f4d7 ols: co_356 name: Vitis ontology pattern: ^\d+$ preferred_prefix: co_356 uri_format: https://www.cropontology.org/rdf/CO_356:$1 version: '2019-11-29' co_357: description: 'This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE.' download_owl: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology/owl example: '1000290' homepage: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology mappings: agroportal: CO_357 cropoct: CO_357 fairsharing: FAIRsharing.2b04ae ols: co_357 name: Woody Plant Ontology ontology pattern: ^\d+$ preferred_prefix: co_357 uri_format: https://www.cropontology.org/rdf/CO_357:$1 co_358: description: Cotton ontology from CottonGen database - June 2019 download_owl: https://cropontology.org/ontology/CO_358/Cotton/owl example: 0000139 homepage: https://cropontology.org/ontology/CO_358/Cotton mappings: agroportal: CO_358 cropoct: CO_358 ols: co_358 name: Cotton ontology pattern: ^\d{7}$ preferred_prefix: co_358 uri_format: https://www.cropontology.org/rdf/CO_358:$1 version: '2020-01-03' co_359: description: December 2019 download_owl: https://cropontology.org/ontology/CO_359/Sunflower/owl example: 0000947 homepage: https://cropontology.org/ontology/CO_359/Sunflower mappings: agroportal: CO_359 cropoct: CO_359 ols: co_359 name: Sunflower ontology pattern: ^\d{7}$ preferred_prefix: co_359 uri_format: https://www.cropontology.org/rdf/CO_359:$1 co_360: description: Sugar Kelp trait ontology download_owl: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait/owl example: '0000071' homepage: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait mappings: agroportal: CO_360 cropoct: CO_360 fairsharing: FAIRsharing.1c1738 ols: co_360 name: Sugar Kelp trait ontology pattern: ^\d{7}$ preferred_prefix: co_360 uri_format: https://www.cropontology.org/rdf/CO_360:$1 co_365: description: developed by ICARDA - Dec 2018 download_owl: https://cropontology.org/ontology/CO_365/Fababean/owl example: '0000205' homepage: https://cropontology.org/ontology/CO_365/Fababean mappings: agroportal: CO_365 cropoct: CO_365 ols: co_365 name: Fababean ontology pattern: ^\d{7}$ preferred_prefix: co_365 uri_format: https://www.cropontology.org/rdf/CO_365:$1 version: '2019-10-15' co_366: description: version Dec 2019 download_owl: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut/owl example: '0000072' homepage: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut mappings: agroportal: CO_366 cropoct: CO_366 ols: co_366 name: Bambara groundnut ontology pattern: ^\d{7}$ preferred_prefix: co_366 uri_format: https://www.cropontology.org/rdf/CO_366:$1 co_367: description: 'Curator name: Clara S. Stanschewski; Curator Affiliation: King Abdullah University of Science and Technology; Contributing Scientists or Crop expert group: The Salt Lab and the Quinoa Phenotyping Consortium Creation Date: 23.05.2021' example: '0000004' homepage: https://cropontology.org/term/CO_367:ROOT mappings: cropoct: CO_367 name: Quinoa Ontology ontology pattern: ^\d{7}$ preferred_prefix: co_367 co_370: description: Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales. example: 0000890 homepage: https://cropontology.org/term/CO_370:ROOT mappings: cropoct: CO_370 name: Apple ontology pattern: ^\d{7}$ preferred_prefix: co_370 cob: contact: email: bpeters@lji.org github: bpeters42 name: Bjoern Peters orcid: 0000-0002-8457-6693 description: COB brings together key terms from a wide range of OBO projects to improve interoperability. download_owl: http://purl.obolibrary.org/obo/cob.owl example: 0000080 homepage: https://obofoundry.org/COB/ license: CC0 1.0 mappings: aberowl: COB bioportal: COB obofoundry: cob ols: cob ontobee: COB name: Core Ontology for Biology and Biomedicine pattern: ^\d{7}$ preferred_prefix: COB repository: https://github.com/OBOFoundry/COB uri_format: http://purl.obolibrary.org/obo/COB_$1 version: '2022-05-02' coconut: comment: '@mSorok is the dev of the resource, hope I got it right!' contributor: email: adriano.rutz@ik.me github: adafede name: Adriano Rutz orcid: 0000-0003-0443-9902 description: COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a "flat" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties. example: CNP0171505 github_request_issue: 221 homepage: https://coconut.naturalproducts.net name: COlleCtion of Open Natural ProdUcTs pattern: ^CNP\d{7}$ preferred_prefix: coconut reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://coconut.naturalproducts.net/compound/coconut_id/$1 codelink: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release).' example: GE86325 homepage: https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt name: GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray pattern: ^GE\d+$ preferred_prefix: codelink references: - https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-8060/A-GEOD-8060.adf.txt - https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt cog: contact: email: cogs@ncbi.nlm.nih.gov github: null name: Michael Y Galperin orcid: 0000-0002-2265-5572 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems.' example: COG0001 homepage: https://www.ncbi.nlm.nih.gov/research/cog/ mappings: biolink: COG fairsharing: FAIRsharing.djsbw2 go: COG_Cluster prefixcommons: cog name: Cluster of orthologous genes pattern: ^COG\d+$ preferred_prefix: cog synonyms: - COG_Cluster uri_format: https://www.ncbi.nlm.nih.gov/research/cog/cog/$1 cog.category: contact: email: cogs@ncbi.nlm.nih.gov github: null name: Michael Y Galperin orcid: 0000-0002-2265-5572 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Higher-level classifications of COG Pathways example: K homepage: https://www.ncbi.nlm.nih.gov/research/cog/ name: COG Categories part_of: cog preferred_prefix: cog.category uri_format: https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1 cog.pathway: contact: email: cogs@ncbi.nlm.nih.gov github: null name: Michael Y Galperin orcid: 0000-0002-2265-5572 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. example: NAD%20biosynthesis homepage: https://www.ncbi.nlm.nih.gov/research/cog/pathways mappings: go: COG_Pathway name: COG Pathways part_of: cog preferred_prefix: cog.pathway uri_format: https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1 cohd: comment: not really sure where the source is. this also links to a system called athena. I was not able to figure out what COHD stands for. contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012 homepage: https://github.com/MIT-LCP/mimic-omop name: MIMIC III Database no_own_terms: true preferred_prefix: cohd repository: https://github.com/MIT-LCP/mimic-omop col.taiwan: contributor: email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 description: Identifier (name code) for a taxon in the catalogue of life in taiwan example: '431472' github_request_issue: 466 homepage: http://taibnet.sinica.edu.tw/home.php mappings: wikidata: P3088 name: Catalogue of Life in Taiwan pattern: ^[1-9]\d{5}$ preferred_prefix: col.taiwan reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1 colao: contact: email: entiminae@gmail.com github: JCGiron name: Jennifer C. Giron orcid: 0000-0002-0851-6883 depends_on: - aism - bfo - bspo - caro - pato - ro - uberon description: The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. download_obo: http://purl.obolibrary.org/obo/colao.obo download_owl: http://purl.obolibrary.org/obo/colao.owl example: '0000000' homepage: https://github.com/insect-morphology/colao license: CC BY 4.0 mappings: aberowl: COLAO bioportal: COLAO obofoundry: colao ols: colao ontobee: COLAO name: Coleoptera Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: COLAO repository: https://github.com/insect-morphology/colao uri_format: http://purl.obolibrary.org/obo/COLAO_$1 version: '2022-06-18' colonatlas: description: Cell line databases/resources example: ALA homepage: http://www.coloncanceratlas.org mappings: cellosaurus: ColonAtlas name: Colorectal Cancer Atlas preferred_prefix: colonatlas uri_format: http://www.coloncanceratlas.org/search_cell_line?cell_line=$1 combine.specifications: description: The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network. example: sbgn.er.level-1.version-1.2 homepage: https://co.mbine.org/standards/ mappings: biocontext: COMBINE.SPECIFICATIONS miriam: combine.specifications n2t: combine.specifications name: COMBINE specifications pattern: ^\w+(\-|\.|\w)*$ preferred_prefix: combine.specifications uri_format: https://co.mbine.org/specifications/$1 come: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif. example: MOL000160 homepage: https://www.flymine.org/come mappings: prefixcommons: come name: The Bioinorganic Motif Database preferred_prefix: come uri_format: https://www.flymine.org/come/entry?gn=$1 commoncoreontology: contact: email: mpjensen@buffalo.edu github: mark-jensen name: Mark Jensen orcid: 0000-0001-9228-8838 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The Common Core Ontologies (CCO) comprise twelve ontologies that are designed to represent and integrate taxonomies of generic classes and relations across all domains of interest. CCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained by the BFO framework, from which it inherits much of its basic semantic relationships.' example: DirectiveInformationContentEntity homepage: http://www.ontologyrepository.com license: CC BY 4.0 name: Common Core Ontologies preferred_prefix: commoncoreontology repository: https://github.com/CommonCoreOntology/CommonCoreOntologies uri_format: http://www.ontologyrepository.com/CommonCoreOntologies/$1 complexportal: description: A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases. example: CPX-263 homepage: https://www.ebi.ac.uk/complexportal mappings: biocontext: COMPLEXPORTAL go: ComplexPortal miriam: complexportal n2t: complexportal re3data: r3d100013295 uniprot: ComplexPortal wikidata: P7718 name: Complex Portal pattern: ^CPX-[0-9]+$ preferred_prefix: complexportal synonyms: - ComplexPortal uri_format: https://www.ebi.ac.uk/complexportal/complex/$1 comptox: description: The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks. example: DTXSID2021028 homepage: https://comptox.epa.gov/dashboard mappings: biocontext: COMPTOX miriam: comptox n2t: comptox wikidata: P3117 name: CompTox Chemistry Dashboard pattern: ^DTXSID\d+$ preferred_prefix: comptox uri_format: https://comptox.epa.gov/dashboard/$1 compulyeast: description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record. example: O08709 homepage: http://compluyeast2dpage.dacya.ucm.es/ mappings: biocontext: COMPULYEAST fairsharing: FAIRsharing.rbjs3e miriam: compulyeast n2t: compulyeast name: Compluyeast-2D-DB pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ preferred_prefix: compulyeast provides: uniprot uri_format: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1 confident.event: contact: email: Philip.Stroemert@tib.eu github: StroemPhi name: Philip Strömert orcid: 0000-0002-1595-3213 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating. example: 37af84f2-bfd7-4653-b608-eaff44febba6 github_request_issue: 519 homepage: https://www.confident-conference.org/index.php/Category:Event name: ConfIDent Event pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$ preferred_prefix: confident.event uri_format: https://www.confident-conference.org/index.php/Event:$1 confident.series: contact: email: Philip.Stroemert@tib.eu github: StroemPhi name: Philip Strömert orcid: 0000-0002-1595-3213 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating. example: AAC github_request_issue: 519 homepage: https://www.confident-conference.org/index.php/Category:Event_Series name: ConfIDent Event Series preferred_prefix: confident.series uri_format: https://www.confident-conference.org/index.php/Event_Series:$1 conoserver: description: ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails. example: '2639' homepage: http://www.conoserver.org/ mappings: biocontext: CONOSERVER fairsharing: FAIRsharing.y00hz4 miriam: conoserver n2t: conoserver uniprot: ConoServer name: ConoServer pattern: ^\d+$ preferred_prefix: conoserver uri_format: http://www.conoserver.org/?page=card&table=protein&id=$1 conso: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases. example: CONSO00010 homepage: https://pharmacome.github.io/conso/ name: Curation of Neurodegeneration Supporting Ontology pattern: ^CONSO\d{5}$ preferred_prefix: conso uri_format: https://pharmacome.github.io/conso/$1 cordis.article: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020). example: '436605' homepage: https://cordis.europa.eu/ name: CORDIS Article pattern: ^\d+$ preferred_prefix: cordis.article uri_format: https://cordis.europa.eu/article/id/$1 cordis.project: contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020). example: '817732' github_request_issue: 450 homepage: https://cordis.europa.eu/ name: CORDIS Project pattern: ^\d+$ preferred_prefix: cordis.project reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://cordis.europa.eu/project/id/$1 coriell: description: The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world. example: GM17027 homepage: http://ccr.coriell.org/ mappings: biocontext: Coriell cellosaurus: Coriell go: CORIELL miriam: coriell n2t: coriell name: Coriell Institute for Medical Research pattern: ^[A-Z]{2}\d+$ preferred_prefix: coriell uri_format: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1 corrdb: description: A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies. example: '37232' homepage: https://www.animalgenome.org mappings: fairsharing: FAIRsharing.IziuCK miriam: corrdb re3data: r3d100011496 name: CorrDB pattern: ^[0-9]+$ preferred_prefix: corrdb uri_format: https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1 corum: description: The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded. example: '100' homepage: https://mips.helmholtz-muenchen.de/genre/proj/corum/ mappings: biocontext: CORUM fairsharing: FAIRsharing.ohbpNw go: CORUM miriam: corum n2t: corum prefixcommons: corum uniprot: CORUM name: Comprehensive Resource of Mammalian protein complexes pattern: ^\d+$ preferred_prefix: corum uri_format: https://mips.helmholtz-muenchen.de/corum/?id=$1 cosmic: description: COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes. example: BRAF homepage: http://cancer.sanger.ac.uk/cosmic/ mappings: biocontext: COSMIC cellosaurus: Cosmic edam: '3264' fairsharing: FAIRsharing.s5zmbp miriam: cosmic n2t: cosmic name: COSMIC Gene pattern: ^[A-Z0-9]+$ preferred_prefix: cosmic uri_format: http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1 cosmic.cell: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer example: '906801' homepage: https://cancer.sanger.ac.uk/cell_lines/ mappings: cellosaurus: Cosmic-CLP name: COSMIC Cell Lines pattern: ^\d+$ preferred_prefix: cosmic.cell uri_format: https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1 covid19: contact: email: dylan.mcgagh@magd.ox.ac.uk github: null name: Dylan McGagh orcid: null description: Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease. download_owl: http://aber-owl.net/media/ontologies/COVID19/3/covid19.owl example: SFB_COVID19_MW286762 homepage: https://covid19.sfb.uit.no mappings: aberowl: COVID19 bioportal: COVID19 miriam: covid19 name: COVID-19 Surveillance Ontology pattern: ^\w+_COVID19_[-\w]+$ preferred_prefix: covid19 uri_format: https://covid19.sfb.uit.no/api/records/$1 covoc: contact: email: zmp@ebi.ac.uk github: zoependlington name: Zoë May Pendlington orcid: 0000-0002-4071-8397 description: The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more. download_owl: http://purl.obolibrary.org/obo/covoc/releases/2020-08-28/covoc.owl example: '0010034' homepage: https://github.com/EBISPOT/covoc mappings: ols: covoc name: CoVoc Coronavirus Vocabulary pattern: ^\d{7}$ preferred_prefix: covoc repository: https://github.com/EBISPOT/covoc uri_format: http://purl.obolibrary.org/obo/COVOC_$1 version: '2020-08-28' cp: appears_in: - cl comment: Part of cell ontology but deprecated, see https://github.com/obophenotype/cell-ontology/issues/572 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: Cellular Phenotypes preferred_prefix: cp cpc: description: The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013. example: A01M1/026 homepage: https://worldwide.espacenet.com/classification mappings: biocontext: CPC fairsharing: FAIRsharing.e08886 miriam: cpc n2t: cpc name: Cooperative Patent Classification pattern: ^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H, Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$ preferred_prefix: cpc uri_format: https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1 cpga: contact: email: po-discuss@plantontology.org github: null name: Plant Ontology Administrators orcid: null deprecated: true description: A structured controlled vocabulary for the anatomy of Graminae. Please note that this ontology has now been superseded by the Plant Ontology. homepage: http://www.gramene.org/plant_ontology/ mappings: biocontext: gro.cpga bioportal: GRO-CPGA obofoundry: gro name: Cereal Plant Gross Anatomy preferred_prefix: GRO uri_format: http://purl.obolibrary.org/obo/GRO_$1 cpt: contact: email: Intellectual.PropertyServices@ama-assn.org github: null name: American Medical Association orcid: null contributor: email: null github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 contributor_extras: - email: null github: colleenXu name: Colleen Xu orcid: 0000-0003-2975-882X description: Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)] example: '00103' github_request_issue: 357 homepage: https://www.aapc.com mappings: aberowl: CPT biolink: CPT bioportal: CPT fairsharing: FAIRsharing.wpxab1 name: Current Procedural Terminology pattern: ^\d+$ preferred_prefix: cpt publications: - doi: 10.1136/neurintsurg-2014-011156 pmc: null pubmed: '24589819' title: Current procedural terminology; a primer. year: 2014 - doi: 10.1016/j.jacr.2007.10.004 pmc: null pubmed: '18359442' title: 'CPT: an open system that describes all that you do.' year: 2008 references: - https://github.com/biopragmatics/bioregistry/pull/358 - https://github.com/biolink/biolink-model/pull/993 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - ama-cpt uri_format: https://www.aapc.com/codes/cpt-codes/$1 credit: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output. example: Software homepage: https://casrai.org/credit/ mappings: fairsharing: FAIRsharing.fe4816 name: CASRAI Contributor Roles Taxonomy preferred_prefix: credit publications: - doi: 10.3789/ansi.niso.z39.104-2022 pmc: null pubmed: null title: ANSI/NISO Z39.104-2022, CRediT, Contributor Roles Taxonomy year: null - doi: 10.1087/20150211 pmc: null pubmed: null title: 'Beyond authorship: attribution, contribution, collaboration, and credit' year: null - doi: 10.1038/d41586-019-01715-4 pmc: null pubmed: null title: Credit data generators for data reuse year: null - doi: 10.1038/508312a pmc: null pubmed: null title: 'Publishing: Credit where credit is due' year: null - doi: 10.1002/leap.1210 pmc: null pubmed: null title: How can we ensure visibility and diversity in research contributions? How the Contributor Role Taxonomy (CRediT) is helping the shift from authorship to contributorship year: null crisprdb: description: Repeated CRISPR ("clustered regularly interspaced short palindromic repeats") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data. example: '551115' homepage: http://crispr.i2bc.paris-saclay.fr/ mappings: biocontext: CRISPRDB fairsharing: FAIRsharing.7sfedh miriam: crisprdb n2t: crisprdb name: CRISPRdb pattern: ^[0-9]+$ preferred_prefix: crisprdb uri_format: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1 cro: contact: email: whimar@ohsu.edu github: marijane name: Marijane White orcid: 0000-0001-5059-4132 description: A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. download_obo: https://raw.githubusercontent.com/data2health/contributor-role-ontology/master/cro.obo download_owl: http://purl.obolibrary.org/obo/cro.owl example: 0000038 homepage: https://github.com/data2health/contributor-role-ontology license: CC BY 2.0 mappings: aberowl: CRO biocontext: CRO bioportal: CRO obofoundry: cro ols: cro ontobee: CRO name: Contributor Role Ontology pattern: ^\d{7}$ preferred_prefix: CRO repository: https://github.com/data2health/contributor-role-ontology uri_format: http://purl.obolibrary.org/obo/CRO_$1 version: '2019-12-11' crop2ml: description: CropMRespository is a database of soil and crop biophysical process models. example: '000000001' homepage: http://www.crop2ml.org mappings: miriam: crop2ml name: CropMRepository pattern: ^[0-9]{9}$ preferred_prefix: crop2ml uri_format: http://www.crop2ml.org/cropmdb/$1 cryoem: contact: email: isanchez@cnb.csic.es github: null name: Carlos Oscar Sorzano orcid: null description: Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles download_owl: http://scipion.i2pc.es/ontology/cryoem/releases/2021-03-09/cryoem.owl example: '0000052' homepage: http://scipion.i2pc.es/ontology/cryoem mappings: aberowl: CRYOEM bioportal: CRYOEM fairsharing: FAIRsharing.q47I0t ols: cryoem name: Cryo Electron Microscopy ontology pattern: ^\d{7}$ preferred_prefix: cryoem uri_format: http://scipion.i2pc.es/ontology/CRYOEM_$1 version: '2021-03-09' cryptodb: description: CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: cgd7_230 homepage: https://cryptodb.org/cryptodb/ mappings: biocontext: CRYPTODB fairsharing: FAIRsharing.t3nprm miriam: cryptodb n2t: cryptodb prefixcommons: cryptodb re3data: r3d100012265 name: CryptoDB pattern: ^\w+$ preferred_prefix: cryptodb publications: - doi: 10.1093/nar/gkj078 pmc: PMC1347441 pubmed: '16381902' title: 'CryptoDB: a Cryptosporidium bioinformatics resource update.' year: 2006 uri_format: https://cryptodb.org/cryptodb/app/record/gene/$1 csa: description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme. example: 1a05 homepage: https://www.ebi.ac.uk/thornton-srv/databases/CSA/ mappings: biocontext: CSA fairsharing: FAIRsharing.2ajtcf miriam: csa n2t: csa prefixcommons: csa name: Catalytic Site Atlas pattern: ^[0-9][A-Za-z0-9]{3}$ preferred_prefix: csa publications: - doi: 10.1093/nar/gkh028 pmc: PMC308762 pubmed: '14681376' title: 'The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.' year: 2004 uri_format: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1 csd: description: The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode. example: PELNAW homepage: https://www.ccdc.cam.ac.uk/ mappings: fairsharing: FAIRsharing.vs7865 miriam: csd name: Cambridge Structural Database pattern: ^[A-Z]{6}(\d{2})?$ preferred_prefix: csd uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG csp: contact: email: af8d@nih.gov github: null name: Anita Ghebeles orcid: null deprecated: true description: Computer Retrieval of Information on Scientific Projects (CRISP) example: 2004-2820 homepage: https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm mappings: aberowl: CRISP bioportal: CRISP hl7: 2.16.840.1.113883.6.120 name: Computer Retrieval of Information on Science Projects Thesaurus preferred_prefix: csp synonyms: - CRISP - CRISP Thesaurus - CRISP Thesaurus, 2006 - CSP2005 uri_format: http://purl.bioontology.org/ontology/CSP/$1 cst: description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways. example: Akt_PKB homepage: http://www.cellsignal.com/pathways/index.html mappings: biocontext: CST fairsharing: FAIRsharing.n8pxvx hl7: 2.16.840.1.113883.6.62 miriam: cst n2t: cst name: Cell Signaling Technology Pathways pattern: ^[A-Za-z0-9_-]+$ preferred_prefix: cst uri_format: http://www.cellsignal.com/reference/pathway/$1.html cst.ab: description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products. example: '3305' homepage: http://www.cellsignal.com/catalog/index.html mappings: biocontext: CST.AB miriam: cst.ab n2t: cst.ab prefixcommons: cst name: Cell Signaling Technology Antibody pattern: ^\d+$ preferred_prefix: cst.ab uri_format: http://www.cellsignal.com/products/$1.html ctcae: appears_in: - oae contact: email: ncictcaehelp@mail.nih.gov github: null name: CTCAE Help orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: The Common Terminology Criteria for Adverse Events (CTCAE),[1] formerly called the Common Toxicity Criteria (CTC or NCI-CTC), are a set of criteria for the standardized classification of adverse effects of drugs used in cancer therapy. The CTCAE system is a product of the US National Cancer Institute (NCI). download_owl: http://aber-owl.net/media/ontologies/CTCAE/2/ctcae.owl example: E12768 homepage: https://evs.nci.nih.gov/ftp1/CTCAE/About.html mappings: aberowl: CTCAE bioportal: CTCAE name: Common Terminology Criteria for Adverse Events pattern: ^E\d+$ preferred_prefix: ctcae publications: - doi: null pmc: PMC5977606 pubmed: '29854250' title: 'Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs.' year: 2018 references: - https://github.com/OAE-ontology/OAE/issues/8 - https://en.wikipedia.org/wiki/Common_Terminology_Criteria_for_Adverse_Events synonyms: - CTCAE ctd.chemical: description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. example: D001151 homepage: http://ctdbase.org/ mappings: biocontext: CTD.CHEMICAL biolink: CTD.CHEMICAL miriam: ctd.chemical n2t: ctd.chemical name: CTD Chemical part_of: ctd pattern: ^[CD]\d+$ preferred_prefix: ctd.chemical provides: mesh uri_format: http://ctdbase.org/detail.go?type=chem&acc=$1 ctd.disease: description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. example: D053716 homepage: http://ctdbase.org/ mappings: biocontext: CTD.DISEASE biolink: CTD.DISEASE miriam: ctd.disease n2t: ctd.disease name: CTD Disease part_of: ctd pattern: ^D\d+$ preferred_prefix: ctd.disease provides: mesh uri_format: http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1 ctd.gene: description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. example: '101' homepage: http://ctdbase.org/ mappings: biocontext: CTD.GENE biolink: CTD.GENE miriam: ctd.gene n2t: ctd.gene name: CTD Gene part_of: ctd pattern: ^\d+$ preferred_prefix: ctd.gene provides: ncbigene uri_format: http://ctdbase.org/detail.go?type=gene&acc=$1 cteno: contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 depends_on: - ro - uberon description: An anatomical and developmental ontology for ctenophores (Comb Jellies) download_obo: https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo download_owl: http://purl.obolibrary.org/obo/cteno.owl example: '0000047' homepage: https://github.com/obophenotype/ctenophore-ontology license: CC BY 3.0 mappings: aberowl: CTENO biocontext: CTENO bioportal: CTENO fairsharing: FAIRsharing.mgxgza obofoundry: cteno ols: cteno ontobee: CTENO name: Ctenophore Ontology pattern: ^\d{7}$ preferred_prefix: CTENO repository: https://github.com/obophenotype/ctenophore-ontology uri_format: http://purl.obolibrary.org/obo/CTENO_$1 version: '2016-10-19' cto: contact: email: alpha.tom.kodamullil@scai.fraunhofer.de github: akodamullil name: Dr. Alpha Tom Kodamullil orcid: 0000-0001-9896-3531 description: The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials. download_owl: http://purl.obolibrary.org/obo/cto.owl example: '0000022' homepage: https://github.com/ClinicalTrialOntology/CTO/ license: CC BY 4.0 mappings: aberowl: CTO bioportal: CTO fairsharing: FAIRsharing.qp211a obofoundry: cto ols: cto ontobee: CTO name: Clinical Trials Ontology pattern: ^\d{7}$ preferred_prefix: CTO repository: https://github.com/ClinicalTrialOntology/CTO uri_format: http://purl.obolibrary.org/obo/CTO_$1 version: 1.0.0 cubedb: comment: website down as of 2021-10-04 deprecated: true description: Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available. example: AKR homepage: http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html mappings: biocontext: CUBEDB miriam: cubedb n2t: cubedb name: Cube db pattern: ^[A-Za-z_0-9]+$ preferred_prefix: cubedb uri_format: http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/ cvdo: contact: email: paul.fabry@usherbrooke.ca github: pfabry name: Paul Fabry orcid: 0000-0002-3336-2476 description: An ontology to describe entities related to cardiovascular diseases download_owl: http://purl.obolibrary.org/obo/cvdo.owl example: '0000546' homepage: https://github.com/OpenLHS/CVDO license: CC BY 4.0 mappings: aberowl: CVDO biocontext: CVDO bioportal: CVDO fairsharing: FAIRsharing.2basyz obofoundry: cvdo ols: cvdo ontobee: CVDO name: Cardiovascular Disease Ontology pattern: ^\d{7}$ preferred_prefix: CVDO repository: https://github.com/OpenLHS/CVDO uri_format: http://purl.obolibrary.org/obo/CVDO_$1 version: '2020-03-05' cvx: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The CDC's National Center of Immunization and Respiratory Diseases (NCIRD) developed and maintains the CVX (vaccine administered) code set. The table below has the most up to date values. It includes both active and inactive vaccines available in the US. CVX codes for inactive vaccines allow transmission of historical immunization records. example: '54' homepage: https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx mappings: hl7: 2.16.840.1.113883.6.59 name: Vaccine administered code set pattern: ^\d+$ preferred_prefix: cvx d1id: description: DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences. example: 00030692-0FE1-4A1B-955E-A2E55D659267 homepage: https://www.dataone.org mappings: biocontext: D1ID miriam: d1id n2t: d1id name: DataONE pattern: ^\S+$ preferred_prefix: d1id uri_format: https://cn.dataone.org/cn/v2/resolve/{$1} dailymed: description: DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read. example: 973a9333-fec7-46dd-8eb5-25738f06ee54 homepage: https://dailymed.nlm.nih.gov/dailymed/ mappings: biocontext: DAILYMED miriam: dailymed n2t: dailymed prefixcommons: dailymed name: DailyMed pattern: ^[A-Za-z0-9-]+$ preferred_prefix: dailymed uri_format: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1 dandi: description: 'DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable). DANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data. These data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.' example: '000017' homepage: https://dandiarchive.org/ mappings: miriam: dandi re3data: r3d100013638 name: Distributed Archives for Neurophysiology Data Integration pattern: ^\d{6}(\/\d+\.\d+\.\d+)?$ preferred_prefix: dandi uri_format: https://dandiarchive.org/dandiset/$1 darc: description: DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors. example: '1250' homepage: http://darcsite.genzentrum.lmu.de/darc/index.php mappings: biocontext: DARC fairsharing: FAIRsharing.evfe2s miriam: darc n2t: darc name: Database of Aligned Ribosomal Complexes pattern: ^\d+$ preferred_prefix: darc uri_format: http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1 dashr: description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records. example: hsa-mir-200a homepage: http://lisanwanglab.org/DASHR/ mappings: biocontext: DASHR fairsharing: FAIRsharing.ztvs34 miriam: dashr n2t: dashr name: Database of small human noncoding RNAs pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ preferred_prefix: dashr uri_format: http://lisanwanglab.org/DASHR/entry/$1 dashr.expression: description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression. example: hsa-mir-200a homepage: https://dashr1.lisanwanglab.org/show-expression-table.php?start=0 mappings: biocontext: DASHR.EXPRESSION miriam: dashr.expression n2t: dashr.expression name: DASHR expression pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ preferred_prefix: dashr.expression uri_format: https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable datacite: contact: email: p.vanschayck@maastrichtuniversity.nl github: null name: Paul van Schayck orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF. download_owl: http://aber-owl.net/media/ontologies/DATACITE/2/datacite.owl example: AgentIdentifierScheme homepage: http://www.sparontologies.net/ontologies/datacite mappings: aberowl: DATACITE bioportal: DATACITE fairsharing: FAIRsharing.c06f1e name: DataCite Ontology preferred_prefix: DataCite repository: https://github.com/sparontologies/datacite uri_format: http://purl.org/spar/datacite/$1 datanator.gene: description: Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. example: K00973 homepage: https://datanator.info/ mappings: miriam: datanator.gene name: Datanator Gene part_of: datanator pattern: ^K[0-9]+$ preferred_prefix: datanator.gene uri_format: https://www.datanator.info/gene/$1 datanator.metabolite: description: Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. example: OUYCCCASQSFEME-MRVPVSSYSA-N homepage: https://datanator.info/ mappings: miriam: datanator.metabolite name: Datanator Metabolite part_of: datanator pattern: ^[A-Z\-]+$ preferred_prefix: datanator.metabolite uri_format: https://www.datanator.info/metabolite/$1 datanator.reaction: description: "\tDatanator is an integrated database of genomic and biochemical data\ \ designed to help investigators find data about specific molecules and reactions\ \ in specific organisms and specific environments for meta-analyses and mechanistic\ \ models. Datanator currently includes metabolite concentrations, RNA modifications\ \ and half-lives, protein abundances and modifications, and reaction kinetics\ \ integrated from several databases and numerous publications. The Datanator website\ \ and REST API provide tools for extracting clouds of data about specific molecules\ \ and reactions in specific organisms and specific environments, as well as data\ \ about similar molecules and reactions in taxonomically similar organisms." example: XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N homepage: https://icahn.mssm.edu/ mappings: miriam: datanator.reaction name: Datanator Reaction pattern: ^.*?--%3E.*?$ preferred_prefix: datanator.reaction uri_format: https://datanator.info/reaction/$1 datf: deprecated: true description: DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals. example: AT1G01030.1 homepage: http://datf.cbi.pku.edu.cn/ mappings: biocontext: DATF miriam: datf n2t: datf prefixcommons: datf name: Database of Arabidopsis Transcription Factors pattern: ^AT[1-5]G\d{5}(\.\d+)?$ preferred_prefix: datf uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1 dbd: description: The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins. example: '0045310' homepage: http://www.transcriptionfactor.org/ mappings: biocontext: DBD edam: '2716' miriam: dbd n2t: dbd prefixcommons: dbd name: Transcription Factor Database pattern: ^\d+$ preferred_prefix: dbd uri_format: http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD dbest: description: The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. example: BP100000 homepage: https://www.ncbi.nlm.nih.gov/nucest mappings: biocontext: DBEST edam: '1105' fairsharing: FAIRsharing.v9fya8 miriam: dbest n2t: dbest ncbi: dbEST prefixcommons: dbest name: EST database maintained at the NCBI. pattern: ^([A-Z]+)?\d+(\.\d+)?$ preferred_prefix: dbest providers: - code: CURATOR_REVIEW description: dbEST through DNA Data Bank of Japan (DDBJ) homepage: http://www.ddbj.nig.ac.jp/ name: dbEST through DNA Data Bank of Japan (DDBJ) uri_format: http://getentry.ddbj.nig.ac.jp/getentry/na/$1 - code: ebi description: dbEST through European Nucleotide Archive (ENA) homepage: https://www.ebi.ac.uk/ena name: dbEST through European Nucleotide Archive (ENA) uri_format: https://www.ebi.ac.uk/ena/data/view/$1 uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1 dbg2introns: description: The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. example: Cu.me.I1 homepage: http://webapps2.ucalgary.ca/~groupii/ mappings: biocontext: DBG2INTRONS miriam: dbg2introns n2t: dbg2introns prefixcommons: mgiid name: DBG2 Introns pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$ preferred_prefix: dbg2introns publications: - doi: 10.1093/nar/gkr1043 pmc: PMC3245105 pubmed: '22080509' title: Database for bacterial group II introns. year: 2011 uri_format: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1 dbgap: description: The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. example: phs000768.v2.p1 homepage: https://www.ncbi.nlm.nih.gov/projects/gap mappings: biocontext: DBGAP fairsharing: FAIRsharing.88v2k0 miriam: dbgap n2t: dbgap name: Database of Genotypes and Phenotypes pattern: ^phs[0-9]{6}(.v\d+.p\d+)?$ preferred_prefix: dbgap uri_format: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1 dbmhc: appears_in: - cellosaurus deprecated: true description: Cell line databases/resources example: '48439' homepage: https://www.ncbi.nlm.nih.gov/gv/mhc/ mappings: cellosaurus: dbMHC name: Database of human Major Histocompatibility Complex pattern: ^\d+$ preferred_prefix: dbmhc dbo: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki. example: careerPrizeMoney github_request_issue: 515 homepage: https://dbpedia.org/ontology name: DBPedia Ontology preferred_prefix: dbo uri_format: https://dbpedia.org/ontology/$1 dbprobe: description: The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities. example: '1000000' homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe mappings: biocontext: DBPROBE edam: '2719' miriam: dbprobe n2t: dbprobe ncbi: dbProbe prefixcommons: dbprobe name: NCBI Probe database Public registry of nucleic acid reagents pattern: ^\d+$ preferred_prefix: dbprobe uri_format: https://www.ncbi.nlm.nih.gov/probe/?term=$1 dbsnp: description: The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. example: rs121909098 homepage: https://www.ncbi.nlm.nih.gov/snp/ mappings: biocontext: dbSNP cellosaurus: dbSNP edam: '1106' fairsharing: FAIRsharing.edxb58 go: dbSNP hl7: 2.16.840.1.113883.6.284 miriam: dbsnp n2t: dbsnp ncbi: dbSNP prefixcommons: dbsnp re3data: r3d100010652 uniprot: dbSNP name: NCBI dbSNP pattern: ^rs\d+$ preferred_prefix: dbsnp providers: - code: sib description: SNP2TFBS homepage: https://ccg.epfl.ch/snp2tfbs/ name: SNP2TFBS uri_format: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1 publications: - doi: 10.1093/nar/29.1.308 pmc: PMC29783 pubmed: '11125122' title: 'dbSNP: the NCBI database of genetic variation.' year: 2001 uri_format: https://www.ncbi.nlm.nih.gov/snp/$1 dbvar.study: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Studies in dbVar. example: nstd102 homepage: https://www.ncbi.nlm.nih.gov/dbvar name: Database of Genomic Structural Variation - Study preferred_prefix: dbvar.study synonyms: - dbvar.studies uri_format: https://www.ncbi.nlm.nih.gov/dbvar/studies/$1 dbvar.variant: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Variants in dbVar. example: nsv3875336 homepage: https://www.ncbi.nlm.nih.gov/dbvar name: Database of Genomic Structural Variation - Variant preferred_prefix: dbvar.variant synonyms: - dbvar.variants uri_format: https://www.ncbi.nlm.nih.gov/dbvar/variants/$1 dc: contact: email: kdurante@stanford.edu github: null name: Kim Durante orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. download_owl: http://aber-owl.net/media/ontologies/DC/3/dc.owl example: contributor homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ mappings: aberowl: DC biocontext: dc bioportal: DC fairsharing: FAIRsharing.3nx7t name: Dublin Core preferred_prefix: dc synonyms: - dc11 uri_format: http://purl.org/dc/elements/1.1/$1 dc_cl: contact: email: Lindsay.Cowell@utsouthwestern.edu github: null name: Lindsay Cowell orcid: 0000-0003-1617-8244 deprecated: true example: '0000003' homepage: http://www.dukeontologygroup.org/Projects.html mappings: biocontext: DC_CL obofoundry: dc_cl name: Dendritic cell pattern: ^\d{7}$ preferred_prefix: DC_CL uri_format: http://purl.obolibrary.org/obo/DC_CL_$1 dcat: contact: email: kdurante@stanford.edu github: null name: kdurante orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web download_owl: http://aber-owl.net/media/ontologies/DCAT/2/dcat.owl example: Dataset homepage: https://www.w3.org/ns/dcat mappings: aberowl: DCAT biocontext: dcat biolink: dcat bioportal: DCAT fairsharing: FAIRsharing.h4j3qm name: Data Catalog preferred_prefix: dcat uri_format: http://www.w3.org/ns/dcat#$1 dcterms: contact: email: futo@stanford.edu github: null name: Michelle Futornick orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. download_owl: http://aber-owl.net/media/ontologies/dcterms/1/dcterms.owl example: title homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ mappings: aberowl: dcterms biocontext: dcterms biolink: dct bioportal: DCTERMS fairsharing: FAIRsharing.9vtwjs name: Dublin Core Metadata Vocabulary preferred_prefix: dcterms synonyms: - dc.terms - dct uri_format: http://purl.org/dc/terms/$1 dctypes: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. example: Collection homepage: https://dublincore.org/specifications/dublin-core/dcmi-terms/ mappings: biocontext: dctypes name: Dublin Core Types preferred_prefix: dctypes uri_format: http://purl.org/dc/dcmitype/$1 ddanat: contact: email: pfey@northwestern.edu github: pfey03 name: Petra Fey orcid: 0000-0002-4532-2703 description: A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum download_obo: http://purl.obolibrary.org/obo/ddanat.obo download_owl: http://purl.obolibrary.org/obo/ddanat.owl example: '0000006' homepage: http://dictybase.org/ license: CC0 1.0 mappings: aberowl: DDANAT biocontext: DDANAT bioportal: DDANAT fairsharing: FAIRsharing.z656ab go: DDANAT obofoundry: ddanat ols: ddanat ontobee: DDANAT prefixcommons: ddanat name: Dictyostelium discoideum anatomy pattern: ^\d{7}$ preferred_prefix: DDANAT publications: - doi: 10.1186/1471-2164-9-130 pmc: PMC2323390 pubmed: '18366659' title: An anatomy ontology to represent biological knowledge in Dictyostelium discoideum. year: 2008 repository: https://github.com/dictyBase/migration-data twitter: dictybase uri_format: http://purl.obolibrary.org/obo/DDANAT_$1 version: '2020-04-13' ddinter.drug: contact: email: oriental-cds@163.com github: null name: Dongsheng Cao orcid: 0000-0003-3604-3785 contributor: email: null github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 description: Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety. example: DDInter20 github_request_issue: 492 homepage: http://ddinter.scbdd.com license: CC-BY-NC-SA-4.0 name: Curated Drug-Drug Interactions Database - Drug pattern: ^DDInter\d+$ 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/$1 ddinter.interaction: contact: email: oriental-cds@163.com github: null name: Dongsheng Cao orcid: 0000-0003-3604-3785 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety. example: '1122888' github_request_issue: 492 homepage: http://ddinter.scbdd.com license: CC-BY-NC-SA-4.0 name: Curated Drug-Drug Interactions Database - Interaction pattern: ^\d+$ preferred_prefix: ddinter.interaction uri_format: http://ddinter.scbdd.com/ddinter/interact/$1 ddpheno: contact: email: pfey@northwestern.edu github: pfey03 name: Petra Fey orcid: 0000-0002-4532-2703 description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. download_json: http://purl.obolibrary.org/obo/ddpheno.json download_obo: https://raw.githubusercontent.com/obophenotype/dicty-phenotype-ontology/master/ddpheno.obo download_owl: http://purl.obolibrary.org/obo/ddpheno.owl example: '0001417' homepage: http://dictybase.org/ license: CC0 1.0 mappings: aberowl: DDPHENO biocontext: DDPHENO bioportal: DDPHENO fairsharing: FAIRsharing.9c1p18 obofoundry: ddpheno ols: ddpheno ontobee: DDPHENO name: Dictyostelium discoideum phenotype ontology pattern: ^\d{7}$ 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_$1 version: '2020-06-19' debio: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON. download_json: https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.json download_obo: https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.obo download_owl: https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.owl example: '0000001' homepage: https://biopragmatics.github.io/debio name: Decentralized Biomedical Ontology pattern: ^\d{7}$ 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/$1 decipher: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms example: '1' homepage: https://www.deciphergenomics.org/ mappings: biocontext: DECIPHER fairsharing: FAIRsharing.l8Sf5x name: DECIPHER CNV Syndromes pattern: ^\d+$ preferred_prefix: decipher publications: - doi: 10.1016/j.ajhg.2009.03.010 pmc: null pubmed: null title: 'DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources' year: null 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: 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 mappings: fairsharing: FAIRsharing.39fd58 name: Discourse Elements Ontology preferred_prefix: DEO publications: - doi: https://doi.org/10.3233/sw-150177 pmc: null pubmed: null title: The Document Components Ontology (DoCO) year: null repository: https://github.com/sparontologies/deo 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/$1 depod: description: The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources. example: PTPN1 homepage: http://www.depod.bioss.uni-freiburg.de mappings: biocontext: DEPOD fairsharing: FAIRsharing.q9j2e3 miriam: depod n2t: depod re3data: r3d100011936 uniprot: DEPOD name: Human Dephosphorylation Database pattern: ^[A-Z0-9]+$ preferred_prefix: depod provides: hgnc.symbol uri_format: http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1 dermo: contact: email: pns12@cam.ac.uk github: null name: Paul Schofield orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders download_obo: http://aber-owl.net/media/ontologies/DERMO/10/dermo.obo example: '0000000' homepage: https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x mappings: aberowl: DERMO bioportal: DERMO fairsharing: FAIRsharing.k008w7 name: Human Dermatological Disease Ontology pattern: ^\d{7}$ preferred_prefix: dermo uri_format: http://purl.obolibrary.org/obo/DERMO_$1 dev.ga4ghdos: description: Assists in resolving data across cloud resources. example: 23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00 homepage: http://github.com/ga4gh/data-object-service-schemas mappings: biocontext: DEV.GA4GHDOS miriam: dev.ga4ghdos n2t: dev.ga4ghdos name: Development Data Object Service pattern: ^[a-zA-Z0-9\-:#\.]+$ preferred_prefix: dev.ga4ghdos uri_format: https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1 dg.4503: description: Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org example: 0000ffeb-36e0-4a29-b21d-84423bda979d homepage: https://gen3.biodatacatalyst.nhlbi.nih.gov mappings: miriam: dg.4503 name: BioData Catalyst pattern: ^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$ preferred_prefix: dg.4503 uri_format: https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/$1 dg.4dfc: description: DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org example: 81944ba1-81d0-436e-8552-33d77a27834b homepage: https://nci-crdc.datacommons.io/ mappings: miriam: dg.4dfc name: NCI Data Commons Framework Services pattern: ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$ preferred_prefix: dg.4dfc uri_format: https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1 dg.6vts: description: Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org example: 2afacf00-9a1d-4d80-8c32-69d3923d3913 homepage: https://jcoin.datacommons.io mappings: miriam: dg.6vts name: JCOIN pattern: ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$ preferred_prefix: dg.6vts uri_format: https://jcoin.datacommons.io/ga4gh/drs/v1/objects/$1 dg.anv0: description: DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org example: 00077f1c-c45a-47ba-8e6c-1bf6b6b43fce homepage: https://gen3.theanvil.io mappings: miriam: dg.anv0 name: Anvil pattern: ^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$ preferred_prefix: dg.anv0 uri_format: https://gen3.theanvil.io/ga4gh/drs/v1/objects/$1 dg.f82a1a: description: Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org example: 00026f50-858a-446b-8ed9-b0e3ecd7b20e homepage: https://kidsfirstdrc.org mappings: miriam: dg.f82a1a name: Kids First pattern: ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$ preferred_prefix: dg.f82a1a uri_format: https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/$1 dg5b0d: description: The Blood Profiling Atlas in Cancer (BloodPAC) supports the management, analysis and sharing of liquid biopsy data for the oncology research community and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for cancer treatment and prevention. The data commons supports cross-project analyses by harmonizing data from different projects through the collaborative development of a data dictionary, providing an API for data queries and download, and providing a cloud-based analysis workspace with rich tools and resources. example: 00000d53-99bc-4d3e-8ed7-6dc358baccb7 homepage: https://data.bloodpac.org/. mappings: miriam: dg.5b0d name: BloodPAC pattern: ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$ preferred_prefix: dg5b0d uri_format: https://data.bloodpac.org/ga4gh/drs/v1/objects/$1 dgrc: description: Cell line collections example: '215' homepage: https://dgrc.bio.indiana.edu/cells/Catalog mappings: cellosaurus: DGRC name: Drosophila Genomics Resource Center pattern: ^\d+$ preferred_prefix: dgrc uri_format: https://dgrc.bio.indiana.edu/product/View?product=$1 dhba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A controlled vocabulary to support the study of transcription in the developing human brain download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dhba.obo example: '10153' homepage: https://www.brainspan.org/ name: Developing Human Brain Atlas pattern: ^\d+$ preferred_prefix: DHBA uri_format: https://biopragmatics.github.io/providers/dhba/$1 dicom: contact: email: dclunie@dclunie.com github: null name: David Clunie orcid: null description: DICOM Controlled Terminology download_owl: ftp://medical.nema.org/MEDICAL/Dicom/Resources/Ontology/DCM/dcm.owl example: '109082' homepage: http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html mappings: bioportal: DCM fairsharing: FAIRsharing.b7z8by hl7: DCM ols: dicom name: DICOM Controlled Terminology pattern: ^\d+$ preferred_prefix: dicom 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 mappings: biocontext: dictyBase fairsharing: FAIRsharing.4shj9c go: dictyBase ncbi: dictyBase prefixcommons: dictybase re3data: r3d100010586 uniprot: dictyBase name: dictyBase preferred_prefix: dictybase synonyms: - dictyBase uri_format: http://dictybase.org/gene/$1 dictybase.est: description: The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information. example: DDB0016567 homepage: http://dictybase.org/ mappings: biocontext: DICTYBASE.EST miriam: dictybase.est n2t: dictybase.est name: dictyBase Expressed Sequence Tag part_of: dictybase pattern: ^DDB\d+$ preferred_prefix: dictybase.est uri_format: http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1 dictybase.gene: description: The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information. example: DDB_G0267522 homepage: http://dictybase.org/ mappings: biocontext: DICTYBASE.GENE miriam: dictybase.gene n2t: dictybase.gene name: Dictybase Gene part_of: dictybase pattern: ^DDB_G\d+$ preferred_prefix: dictybase.gene uri_format: http://dictybase.org/gene/$1 did: banana: did description: DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary. example: sov:WRfXPg8dantKVubE3HX8pw homepage: https://w3c-ccg.github.io/did-spec/ mappings: miriam: did n2t: did name: Decentralized Identifier namespace_in_lui: true pattern: ^[a-z0-9]+:[A-Za-z0-9.\-:]+$ preferred_prefix: did uri_format: https://uniresolver.io/#did:$1 dideo: contact: email: mbrochhausen@gmail.com github: mbrochhausen name: Mathias Brochhausen orcid: 0000-0003-1834-3856 description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology download_owl: http://purl.obolibrary.org/obo/dideo.owl example: 00000180 homepage: https://github.com/DIDEO/DIDEO license: CC BY 4.0 mappings: aberowl: DIDEO biocontext: DIDEO bioportal: DIDEO fairsharing: FAIRsharing.9y8f0n obofoundry: dideo ols: dideo ontobee: DIDEO name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology pattern: ^\d{8}$ preferred_prefix: DIDEO publications: - doi: 10.1186/s13326-018-0183-z pmc: PMC5944177 pubmed: '29743102' title: Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse. year: 2018 - doi: null pmc: PMC5765984 pubmed: '29295242' title: Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies to Improve Evidence Base Curation. year: 2017 - doi: 10.1016/j.knosys.2016.10.006 pmc: null pubmed: null title: 'Conceptual models of drug-drug interactions : A summary of recent efforts' year: null repository: https://github.com/DIDEO/DIDEO uri_format: http://purl.obolibrary.org/obo/DIDEO_$1 version: '2022-06-14' dinto: contact: email: maria.herrero@kcl.ac.uk github: null name: Maria Herrero orcid: null 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 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: - doi: 10.1021/acs.jcim.5b00119 pmc: null pubmed: '26147071' title: 'DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug-Drug Interactions and Their Mechanisms.' year: 2015 repository: https://github.com/labda/DINTO uri_format: http://purl.obolibrary.org/obo/DINTO_$1 dip: description: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions example: DIP-743N homepage: https://dip.doe-mbi.ucla.edu/ mappings: biocontext: DIP edam: '2616' fairsharing: FAIRsharing.qje0v8 miriam: dip n2t: dip prefixcommons: dip uniprot: DIP name: Database of Interacting Proteins pattern: ^DIP(\:)?\-\d{1,}[ENXS]$ preferred_prefix: dip publications: - doi: 10.1093/nar/gkh086 pmc: PMC308820 pubmed: '14681454' title: 'The Database of Interacting Proteins: 2004 update.' year: 2004 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=$1&searchmode=exact disdriv: contact: email: lynn.schriml@gmail.com github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 description: Drivers of human diseases including environmental, maternal and social exposures. download_owl: http://purl.obolibrary.org/obo/disdriv.owl example: '0000000' homepage: http://www.disease-ontology.org license: CC0 1.0 mappings: aberowl: DISDRIV bioportal: DISDRIV obofoundry: disdriv ols: disdriv name: Disease Drivers Ontology pattern: ^\d+$ preferred_prefix: DISDRIV repository: https://github.com/DiseaseOntology/DiseaseDriversOntology twitter: diseaseontology uri_format: http://purl.obolibrary.org/obo/DISDRIV_$1 diseaseclass: appears_in: - efo contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: Legacy disease classes that later became MONDO download_obo: https://github.com/obophenotype/human-disease-ontology/raw/master/src/experimental/missing-omc.obo example: 0000598 name: Disease Class pattern: ^\d{7}$ 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$1.htm disprot: description: DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature. example: DP00003 homepage: https://disprot.org/ mappings: biocontext: DISPROT edam: '2723' fairsharing: FAIRsharing.dt9z89 miriam: disprot n2t: disprot prefixcommons: disprot re3data: r3d100010561 uniprot: DisProt name: DisProt pattern: ^DP\d{5}$ preferred_prefix: disprot publications: - doi: 10.1093/nar/gkl893 pmc: PMC1751543 pubmed: '17145717' title: 'DisProt: the Database of Disordered Proteins.' year: 2006 uri_format: https://disprot.org/$1 disprot.region: description: DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature. example: DP00086r013 homepage: https://www.disprot.org mappings: miriam: disprot.region name: DisProt region pattern: ^DP\d{5}r\d{3}$ 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/$1 dmba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A controlled vocabulary to support the study of transcription in the developing mouse brain download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dmba.obo example: '15567' homepage: https://developingmouse.brain-map.org/ name: Developing Mouse Brain Atlas pattern: ^\d+$ 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 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: 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 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: null repository: https://github.com/sparontologies/doco uri_format: http://purl.org/spar/doco/$1 doi: banana: doi comment: 'The [DOI resolution factsheet](https://www.doi.org/factsheets/DOIProxy.html) specifies that `https://doi.org/DOI` is the preferred format: > Users may resolve DOI names that are structured to use the DOI system Proxy Server (https://doi.org (preferred)). The resolution of the DOI name in this case depends on the use of URL syntax: the example DOI name doi:10.10.123/456 would be resolved from the address: "https://doi.org/10.123/456". Any standard browser encountering a DOI name in this form will be able to resolve it. The proxy service (both doi.org and the **earlier but no longer preferred** dx.doi.org) is accessible over IPv6, and supports DNSSEC. The proxy servers respond to HTTPS (**preferred**) as well as HTTP requests.' contributor_extras: - email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 - email: null github: dhimmel name: Daniel Himmelstein orcid: 0000-0002-3012-7446 description: The Digital Object Identifier System is for identifying content objects in the digital environment. example: 10.1101/2022.07.08.499378 example_extras: - 10.21/FQSQT4T3 - 10.1333/s00897980202a - 10.1139/z02-135 - 10.1016/j.foodchem.2008.11.065 - 10.1093/acprof:oso/9780195159561.001.1 homepage: https://www.doi.org/ mappings: biocontext: DOI biolink: doi cellosaurus: DOI edam: '1188' fairsharing: FAIRsharing.hFLKCn go: DOI miriam: doi n2t: doi prefixcommons: doi name: Digital Object Identifier pattern: ^10.\d{2,9}/.*$ 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/$1 doid: appears_in: - clo - scdo banana: DOID contact: email: lynn.schriml@gmail.com github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. download_json: http://purl.obolibrary.org/obo/doid.json download_obo: https://github.com/DiseaseOntology/HumanDiseaseOntology/raw/main/src/ontology/doid.obo download_owl: http://purl.obolibrary.org/obo/doid.owl example: 0110974 homepage: http://www.disease-ontology.org license: CC0 1.0 mappings: aberowl: DOID biocontext: DOID bioportal: DOID fairsharing: FAIRsharing.8b6wfq miriam: doid n2t: doid obofoundry: doid ols: doid ontobee: DOID prefixcommons: do wikidata: P699 name: Human Disease Ontology namespace_in_lui: true pattern: ^\d+$ 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:$1 version: '2022-06-07' dommino: description: DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides. example: 2GC4 homepage: http://korkinlab.org/dommino mappings: biocontext: DOMMINO miriam: dommino n2t: dommino name: Database of Macromolecular Interactions pattern: ^[0-9][A-Za-z0-9]{3}$ preferred_prefix: dommino uri_format: http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1 door: description: DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes. example: '1398574' homepage: http://csbl.bmb.uga.edu/DOOR/operon.php mappings: biocontext: DOOR miriam: door n2t: door prefixcommons: door name: Database for Prokaryotic Operons pattern: ^\d+$ preferred_prefix: door uri_format: http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1 doqcs.model: description: The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models. example: '57' homepage: http://doqcs.ncbs.res.in/ mappings: biocontext: DOQCS.MODEL miriam: doqcs.model n2t: doqcs.model prefixcommons: doqcs.model name: 'Database of Quantitative Cellular Signaling: Model' part_of: doqcs pattern: ^\d+$ 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=$1 doqcs.pathway: description: The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways. example: '131' homepage: http://doqcs.ncbs.res.in/ mappings: biocontext: DOQCS.PATHWAY miriam: doqcs.pathway n2t: doqcs.pathway prefixcommons: doqcs.pathway name: 'Database of Quantitative Cellular Signaling: Pathway' part_of: doqcs pattern: ^\d+$ 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 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_$1 version: '2022-08-11' dpv: description: Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. example: '100' homepage: http://www.dpvweb.net/ mappings: biocontext: DPV miriam: dpv n2t: dpv name: Description of Plant Viruses pattern: ^\d+$ preferred_prefix: dpv uri_format: http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1 dragondb.allele: comment: Deprecated because the website is dead deprecated: true description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information. example: cho homepage: http://www.antirrhinum.net/ mappings: biocontext: DRAGONDB.ALLELE miriam: dragondb.allele n2t: dragondb.allele name: DragonDB Allele part_of: dragondb pattern: ^\w+$ preferred_prefix: dragondb.allele uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele dragondb.dna: comment: Deprecated because the website is dead deprecated: true description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information. example: 3hB06 homepage: http://www.antirrhinum.net/ mappings: biocontext: DRAGONDB.DNA miriam: dragondb.dna n2t: dragondb.dna name: DragonDB DNA part_of: dragondb pattern: ^\d\w+$ preferred_prefix: dragondb.dna uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA dragondb.locus: comment: Deprecated because the website is dead deprecated: true description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information. example: DEF homepage: http://www.antirrhinum.net/ mappings: biocontext: DRAGONDB.LOCUS miriam: dragondb.locus n2t: dragondb.locus name: DragonDB Locus part_of: dragondb pattern: ^\w+$ preferred_prefix: dragondb.locus uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus dragondb.protein: comment: Deprecated because the website is dead deprecated: true description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information. example: AMDEFA homepage: http://www.antirrhinum.net/ mappings: biocontext: DRAGONDB.PROTEIN miriam: dragondb.protein n2t: dragondb.protein name: DragonDB Protein part_of: dragondb pattern: ^\w+$ preferred_prefix: dragondb.protein uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide dron: appears_in: - scdo contact: email: hoganwr@gmail.com github: hoganwr name: William Hogan orcid: 0000-0002-9881-1017 description: We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive). download_json: http://purl.obolibrary.org/obo/dron.json download_obo: http://purl.obolibrary.org/obo/dron.obo download_owl: http://purl.obolibrary.org/obo/dron.owl example: '00023232' homepage: https://github.com/ufbmi/dron license: CC BY 3.0 mappings: aberowl: DRON biocontext: DRON bioportal: DRON fairsharing: FAIRsharing.w5ntfd obofoundry: dron ols: dron ontobee: DRON name: The Drug Ontology pattern: ^\d{8}$ preferred_prefix: DRON publications: - doi: 10.1186/s13326-017-0121-5 pmc: PMC5335794 pubmed: '28253937' title: 'Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request.' year: 2017 - doi: 10.1186/s13326-016-0048-2 pmc: PMC4836073 pubmed: '27096073' title: An accurate and precise representation of drug ingredients. year: 2016 - doi: 10.1186/2041-1480-4-44 pmc: PMC3931349 pubmed: '24345026' title: Building a drug ontology based on RxNorm and other sources. year: 2013 repository: https://github.com/ufbmi/dron uri_format: http://purl.obolibrary.org/obo/DRON_$1 version: '2022-04-22' drsc: description: The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene. example: DRSC05221 homepage: http://flyrnai.org/ mappings: biocontext: DRSC miriam: drsc n2t: drsc name: Drosophila RNAi Screening Center pattern: ^DRSC\d+$ preferred_prefix: drsc uri_format: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1 drugbank: description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information. example: DB14938 homepage: http://www.drugbank.ca mappings: biocontext: DrugBank cellosaurus: DrugBank cheminf: '000406' edam: '2326' fairsharing: FAIRsharing.353yat miriam: drugbank n2t: drugbank prefixcommons: drugbank re3data: r3d100010544 uniprot: DrugBank wikidata: P715 name: DrugBank pattern: ^DB\d{5}$ preferred_prefix: drugbank publications: - doi: 10.1093/nar/gkt1068 pmc: PMC3965102 pubmed: '24203711' title: 'DrugBank 4.0: shedding new light on drug metabolism.' year: 2013 - doi: 10.1093/nar/gkq1126 pmc: PMC3013709 pubmed: '21059682' title: 'DrugBank 3.0: a comprehensive resource for ''omics'' research on drugs.' year: 2010 - doi: 10.1093/nar/gkm958 pmc: PMC2238889 pubmed: '18048412' title: 'DrugBank: a knowledgebase for drugs, drug actions and drug targets.' year: 2007 - doi: 10.1093/nar/gkj067 pmc: PMC1347430 pubmed: '16381955' title: 'DrugBank: a comprehensive resource for in silico drug discovery and exploration.' year: 2006 synonyms: - DRUGBANK_ID - DrugBank uri_format: http://www.drugbank.ca/drugs/$1 drugbank.category: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Close to 5K Categorizations for drugs, similar to ATCC. example: DBCAT000600 homepage: https://go.drugbank.com/categories name: DrugBank Drug Category part_of: drugbank pattern: ^DBCAT\d+$ preferred_prefix: drugbank.category uri_format: https://www.drugbank.ca/categories/$1 drugbank.salt: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets. example: DBSALT001211 homepage: http://www.drugbank.ca mappings: biocontext: DRUGBANK.TARGET name: DrugBank Salts part_of: drugbank pattern: ^DBSALT\d{6}$ preferred_prefix: drugbank.salt synonyms: - drugbank.target uri_format: https://go.drugbank.com/salts/$1 drugbankv4.target: description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database. example: BE0000048 homepage: http://www.drugbank.ca/targets mappings: biocontext: DRUGBANKV4.TARGET miriam: drugbankv4.target n2t: drugbankv4.target name: DrugBank Target v4 part_of: drugbank pattern: ^BE\d{7}$ preferred_prefix: drugbankv4.target uri_format: http://www.drugbank.ca/biodb/bio_entities/$1 drugcentral: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action. example: '307' homepage: http://drugcentral.org mappings: biolink: DrugCentral fairsharing: FAIRsharing.3me82d uniprot: DrugCentral name: Drug Central pattern: ^\d+$ preferred_prefix: drugcentral synonyms: - Drug_Central uri_format: http://drugcentral.org/drugcard/$1 dsm4: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia] example: '315.1' example_extras: - '291.89' homepage: https://en.wikipedia.org/wiki/Diagnostic_and_Statistical_Manual_of_Mental_Disorders#DSM-IV-TR_(2000) mappings: hl7: 2.16.840.1.113883.6.126 wikidata: P663 name: Diagnostic and Statistical Manual of Mental Disorders (4th Edition) pattern: ^\d+\.\d+$ preferred_prefix: dsm4 synonyms: - dsm-iv dsm5: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia] example: '312.33' homepage: https://en.wikipedia.org/wiki/DSM-5 mappings: hl7: 2.16.840.1.113883.6.344 wikidata: P1930 name: Diagnostic and Statistical Manual of Mental Disorders (5th Edition) pattern: ^\d{3}\.\d{2}$ preferred_prefix: dsm5 references: - https://archive.org/details/diagnosticstatis0005unse synonyms: - dsm-v dsmz: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). example: ACC-1 homepage: https://www.dsmz.de mappings: cellosaurus: DSMZ re3data: r3d100010219 name: Deutsche Sammlung von Mikroorganismen und Zellkulturen preferred_prefix: dsmz uri_format: https://www.dsmz.de/collection/catalogue/details/culture/$1 dso: contact: email: evan@epatters.org github: epatters name: Evan Patterson orcid: 0000-0002-8600-949X contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Data Science Ontology is a research project of IBM Research AI and Stanford University Statistics. Its long-term objective is to improve the efficiency and transparency of collaborative, data-driven science. example: classification-model homepage: https://www.datascienceontology.org/ name: Data Science Ontology preferred_prefix: dso repository: https://github.com/IBM/datascienceontology uri_format: https://www.datascienceontology.org/concept/$1 dto: appears_in: - pr contact: email: sschurer@med.miami.edu github: null name: Stephan Schurer orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.' download_owl: http://aber-owl.net/media/ontologies/DTO/4/dto.owl example: '90000018' homepage: https://github.com/DrugTargetOntology/DTO mappings: aberowl: DTO bioportal: DTO fairsharing: FAIRsharing.tke3y2 name: Drug Target Ontology pattern: ^\d+$ 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_$1 duo: appears_in: - scdo contact: email: mcourtot@gmail.com github: mcourtot name: Melanie Courtot orcid: 0000-0002-9551-6370 depends_on: - bfo - iao description: DUO is an ontology which represent data use conditions. download_owl: http://purl.obolibrary.org/obo/duo.owl example: '0000046' homepage: https://github.com/EBISPOT/DUO license: CC BY 4.0 mappings: aberowl: DUO biocontext: DUO bioportal: DUO fairsharing: FAIRsharing.5dnjs2 obofoundry: duo ols: duo ontobee: DUO name: Data Use Ontology pattern: ^\d{7}$ preferred_prefix: DUO 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/ name: EasyChair Call for Paper preferred_prefix: easychair.cfp uri_format: https://easychair.org/cfp/$1 easychair.topic: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Call for paper topics in EasyChair example: '27106865' homepage: https://easychair.org/cfp/ name: EasyChair Topic pattern: ^\d+$ 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=$1 ecao: contact: email: ettensohn@cmu.edu github: ettensohn name: Charles Ettensohn orcid: 0000-0002-3625-0955 depends_on: - cl - ro - uberon description: None download_obo: http://purl.obolibrary.org/obo/ecao.obo download_owl: http://purl.obolibrary.org/obo/ecao.owl example: 0107180 homepage: https://github.com/echinoderm-ontology/ecao_ontology license: CC BY 3.0 mappings: aberowl: ECAO bioportal: ECAO obofoundry: ecao ols: ecao ontobee: ECAO name: The Echinoderm Anatomy and Development Ontology pattern: ^\d{7}$ preferred_prefix: ECAO repository: https://github.com/echinoderm-ontology/ecao_ontology uri_format: http://purl.obolibrary.org/obo/ECAO_$1 version: '2020-05-22' eccode: description: The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions. example: 1.1.1.1 example_decoys: - '100' - '2.' - 2.n1 - 2.3. - 2.3.n1 - 2.3.1. - 2.3.1.n - 2.3.4.1. example_extras: - '2' - '2.3' - 2.3.1 - 2.3.1.n12 - 3.1.26.n2 homepage: https://www.ebi.ac.uk/intenz/ mappings: biocontext: EC-CODE edam: '1011' fairsharing: FAIRsharing.q1fdkc go: EC miriam: ec-code n2t: ec-code prefixcommons: intenz wikidata: P591 name: Enzyme Commission Code pattern: ^\d{1,2}(((\.\d{1,3}){1,3})|(\.\d+){2}\.n\d{1,3})?$ preferred_prefix: eccode providers: - code: CURATOR_REVIEW description: KEGG Ligand Database for Enzyme Nomenclature homepage: https://www.genome.jp/dbget-bin/www_bfind?enzyme name: KEGG Ligand Database for Enzyme Nomenclature uri_format: https://www.genome.jp/dbget-bin/www_bget?ec:$1 - code: enzymeportal description: Enzyme Portal through EMBL-EBI homepage: https://www.ebi.ac.uk/enzymeportal name: Enzyme Portal through EMBL-EBI uri_format: https://www.ebi.ac.uk/enzymeportal/ec/$1 - code: expasy description: Enzyme nomenclature database, ExPASy (Expert Protein Analysis System) homepage: https://enzyme.expasy.org/ name: Enzyme nomenclature database, ExPASy (Expert Protein Analysis System) uri_format: https://enzyme.expasy.org/EC/$1 - code: expenz description: ExploreEnz at Trinity College homepage: http://www.enzyme-database.org/ name: ExploreEnz at Trinity College uri_format: http://www.enzyme-database.org/query.php?ec=$1 synonyms: - EC - EC number - EC-CODE - ECCODE - EC_CODE - ec-code - intenz uri_format: https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1 ecg: contact: email: rwinslow@jhu.edu github: null name: Raimond L. Winslow, PhD & Stephen Granite orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms. download_owl: http://aber-owl.net/media/ontologies/ECG/12/ecg.owl example: 000000159 homepage: https://bioportal.bioontology.org/ontologies/ECG mappings: aberowl: ECG bioportal: ECG fairsharing: FAIRsharing.azr389 name: Electrocardiogram Ontology pattern: ^\d+$ preferred_prefix: ecg publications: - doi: 10.1016/j.jbi.2010.08.007 pmc: null pubmed: '20800107' title: Using an ECG reference ontology for semantic interoperability of ECG data. year: 2010 synonyms: - ECGOntology uri_format: http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_$1 echobase: description: EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products. example: EB0170 homepage: http://www.york.ac.uk/ mappings: biocontext: ECHOBASE go: EchoBASE miriam: echobase n2t: echobase prefixcommons: echobase re3data: r3d100011646 uniprot: EchoBASE name: EchoBASE post-genomic database for Escherichia coli pattern: ^EB\d+$ preferred_prefix: echobase publications: - doi: 10.1093/nar/gki028 pmc: PMC539982 pubmed: '15608209' title: 'EchoBASE: an integrated post-genomic database for Escherichia coli.' year: 2005 uri_format: http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1 ecmdb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes. example: ECMDB00005 homepage: https://ecmdb.ca name: E. coli Metabolite Database pattern: ^ECMDB\d+$ preferred_prefix: ecmdb synonyms: - ECMDB uri_format: http://ecmdb.ca/compounds/$1 ecn: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A seven-digit identifier for chemical substances for regulatory purposes within the European Union. example: 200-003-9 homepage: https://echa.europa.eu/information-on-chemicals mappings: cheminf: '000447' name: European Community number pattern: ^\d{3}-\d{3}-\d$ preferred_prefix: ecn references: - https://github.com/biopragmatics/bioregistry/issues/257 - https://en.wikipedia.org/wiki/European_Community_number eco: banana: ECO contact: email: mgiglio@som.umaryland.edu github: mgiglio99 name: Michelle Giglio orcid: 0000-0001-7628-5565 description: Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity. download_obo: http://purl.obolibrary.org/obo/eco.obo download_owl: http://purl.obolibrary.org/obo/eco.owl example: 0007807 homepage: https://www.evidenceontology.org license: CC0 1.0 mappings: aberowl: ECO biocontext: ECO bioportal: ECO fairsharing: FAIRsharing.wvpgwn go: ECO miriam: eco n2t: eco obofoundry: eco ols: eco ontobee: ECO prefixcommons: eco name: Evidence ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: ECO publications: - doi: 10.1093/nar/gky1036 pmc: PMC6323956 pubmed: '30407590' title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence information.' year: 2019 - doi: 10.1007/978-1-4939-3743-1_18 pmc: PMC6377151 pubmed: '27812948' title: 'The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.' year: 2017 - doi: 10.1093/database/bau075 pmc: PMC4105709 pubmed: '25052702' title: Standardized description of scientific evidence using the Evidence Ontology (ECO). year: 2014 - doi: 10.1142/9789812704856_0019 pmc: null pubmed: '14992503' title: An evidence ontology for use in pathway/genome databases. year: 2004 repository: https://github.com/evidenceontology/evidenceontology uri_format: https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1 version: '2022-08-05' ecocore: contact: email: p.buttigieg@gmail.com github: pbuttigieg name: Pier Luigi Buttigieg orcid: 0000-0002-4366-3088 depends_on: - bfo - chebi - envo - go - iao - pato - pco - po - ro - uberon description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. download_obo: http://purl.obolibrary.org/obo/ecocore.obo download_owl: http://purl.obolibrary.org/obo/ecocore.owl example: '00000001' homepage: https://github.com/EcologicalSemantics/ecocore license: CC BY 3.0 mappings: aberowl: ECOCORE biocontext: ECOCORE bioportal: ECOCORE obofoundry: ecocore ols: ecocore ontobee: ECOCORE name: An ontology of core ecological entities pattern: ^\d+$ preferred_prefix: ECOCORE repository: https://github.com/EcologicalSemantics/ecocore uri_format: http://purl.obolibrary.org/obo/ECOCORE_$1 version: '2022-03-09' ecocyc: description: EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways. example: AICARTRANSIMPCYCLO-CPLX homepage: http://ecocyc.org/ mappings: fairsharing: FAIRsharing.65dmtr go: EcoCyc ncbi: ECOCYC name: EcoCyc preferred_prefix: ecocyc uri_format: https://biocyc.org/gene?id=$1 ecogene: description: The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. example: EG10173 homepage: http://ecogene.org/ mappings: biocontext: EcoGene fairsharing: FAIRsharing.3q3kvn miriam: ecogene n2t: ecogene ncbi: EcoGene prefixcommons: ecogene re3data: r3d100010546 name: Database of Escherichia coli Sequence and Function pattern: ^EG\d+$ preferred_prefix: ecogene publications: - doi: 10.1093/nar/28.1.60 pmc: PMC102481 pubmed: '10592181' title: 'EcoGene: a genome sequence database for Escherichia coli K-12.' year: 2000 uri_format: http://www.ecogene.org/gene/$1 ecolexicon: comment: No resolution - everything is in a single page app contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology. example: canal homepage: http://ecolexicon.ugr.es/en/index.htm name: EcoLexicon preferred_prefix: ecolexicon ecoliwiki: description: EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes. example: aaeA homepage: http://ecoliwiki.net/colipedia/ mappings: biocontext: ECOLIWIKI fairsharing: FAIRsharing.tx95wa go: EcoliWiki miriam: ecoliwiki n2t: ecoliwiki name: EcoliWiki from EcoliHub pattern: ^[A-Za-z0-9-]+$ preferred_prefix: ecoliwiki uri_format: http://ecoliwiki.net/colipedia/index.php/$1:Gene ecto: contact: email: annethessen@gmail.com github: diatomsRcool name: Anne Thessen orcid: 0000-0002-2908-3327 depends_on: - chebi - envo - exo - go - iao - maxo - nbo - ncbitaxon - ncit - pato - ro - uberon - xco description: ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology). download_json: http://purl.obolibrary.org/obo/ecto.json download_obo: http://purl.obolibrary.org/obo/ecto.obo download_owl: http://purl.obolibrary.org/obo/ecto.owl example: '0000001' homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology license: CC0 1.0 mappings: aberowl: ECTO biolink: ECTO bioportal: ECTO obofoundry: ecto ols: ecto ontobee: ECTO name: Environmental conditions, treatments and exposures ontology pattern: ^\d{7}$ preferred_prefix: ECTO repository: https://github.com/EnvironmentOntology/environmental-exposure-ontology uri_format: http://purl.obolibrary.org/obo/ECTO_$1 version: '2022-08-12' ecyano.entity: description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities. example: '23' homepage: http://www.e-cyanobacterium.org/bcs/entity/ mappings: biocontext: ECYANO.ENTITY miriam: ecyano.entity n2t: ecyano.entity name: E-cyanobacterium entity part_of: ecyano pattern: ^\d+$ preferred_prefix: ecyano.entity uri_format: https://www.e-cyanobacterium.org/bcs/entity/$1 ecyano.experiment: description: E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments. example: '18' homepage: https://www.e-cyanobacterium.org/experiments-repository/ mappings: miriam: ecyano.experiment name: E-cyanobacterium Experimental Data part_of: ecyano pattern: ^\d+$ preferred_prefix: ecyano.experiment uri_format: https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1 ecyano.model: description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models. example: '26' homepage: http://e-cyanobacterium.org/models/ mappings: biocontext: ECYANO.MODEL miriam: ecyano.model n2t: ecyano.model name: E-cyanobacterium model pattern: ^\d+$ preferred_prefix: ecyano.model uri_format: https://e-cyanobacterium.org/models/model/$1 ecyano.rule: description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules. example: '56' homepage: http://www.e-cyanobacterium.org/bcs/rule/ mappings: biocontext: ECYANO.RULE miriam: ecyano.rule n2t: ecyano.rule name: E-cyanobacterium rule part_of: ecyano pattern: ^\d+$ preferred_prefix: ecyano.rule uri_format: https://e-cyanobacterium.org/bcs/rule/$1 edam: contact: email: matus.kalas@uib.no github: matuskalas name: Matúš Kalaš orcid: 0000-0002-1509-4981 description: 'EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).' download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo download_owl: https://raw.githubusercontent.com/edamontology/edamontology/master/releases/EDAM.owl example: data_1664 homepage: http://edamontology.org mappings: aberowl: EDAM agroportal: EDAM biocontext: EDAM bioportal: EDAM fairsharing: FAIRsharing.a6r7zs miriam: edam n2t: edam ols: edam ontobee: EDAM prefixcommons: edam name: Bioinformatics operations, data types, formats, identifiers and topics pattern: ^(data|topic|operation|format)\_\d{4}$ preferred_prefix: edam publications: - doi: 10.1093/bioinformatics/btt113 pmc: PMC3654706 pubmed: '23479348' title: 'EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.' year: 2013 repository: https://github.com/edamontology/edamontology twitter: edamontology uri_format: https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1 version: '2019-07-17' edam.data: contact: email: matus.kalas@uib.no github: matuskalas name: Matúš Kalaš orcid: 0000-0002-1509-4981 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output. download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo example: '1664' homepage: http://edamontology.org mappings: biolink: EDAM-DATA name: EDAM Data part_of: edam pattern: ^\d+$ preferred_prefix: edam.data repository: https://github.com/edamontology/edamontology twitter: edamontology uri_format: http://edamontology.org/data_$1 edam.format: contact: email: matus.kalas@uib.no github: matuskalas name: Matúš Kalaš orcid: 0000-0002-1509-4981 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data. download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo example: '1915' homepage: http://edamontology.org mappings: biolink: EDAM-FORMAT name: EDAM Format part_of: edam pattern: ^\d+$ preferred_prefix: edam.format repository: https://github.com/edamontology/edamontology twitter: edamontology uri_format: http://edamontology.org/format_$1 edam.operation: contact: email: matus.kalas@uib.no github: matuskalas name: Matúš Kalaš orcid: 0000-0002-1509-4981 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.' download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo example: '0004' homepage: http://edamontology.org mappings: biolink: EDAM-OPERATION name: EDAM Operation part_of: edam pattern: ^\d+$ preferred_prefix: edam.operation repository: https://github.com/edamontology/edamontology twitter: edamontology uri_format: http://edamontology.org/operation_$1 edam.topic: contact: email: matus.kalas@uib.no github: matuskalas name: Matúš Kalaš orcid: 0000-0002-1509-4981 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other. download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo example: '0003' homepage: http://edamontology.org mappings: biolink: EDAM-TOPIC name: EDAM Topic part_of: edam pattern: ^\d+$ preferred_prefix: edam.topic repository: https://github.com/edamontology/edamontology twitter: edamontology uri_format: http://edamontology.org/topic_$1 edda: contact: email: tanja.bekhuis@tcbinfosci.com github: null name: Tanja Bekhuis orcid: null description: Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries. download_owl: http://aber-owl.net/media/ontologies/EDDA/11/edda.owl example: health_care_quality_assessment homepage: https://bioportal.bioontology.org/ontologies/EDDA mappings: aberowl: EDDA bioportal: EDDA fairsharing: FAIRsharing.2ffmsb name: EDDA Study Designs Taxonomy preferred_prefix: edda uri_format: http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1 efo: contact: email: plwhetzel@gmail.com github: twhetzel name: Trish Whetzel orcid: 0000-0002-3458-4839 description: The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team. download_obo: http://www.ebi.ac.uk/efo/efo.obo download_owl: http://www.ebi.ac.uk/efo/releases/v3.45.0/efo.owl example: '0005147' homepage: http://www.ebi.ac.uk/efo mappings: aberowl: EFO agroportal: EFO biocontext: EFO biolink: EFO bioportal: EFO cellosaurus: EFO fairsharing: FAIRsharing.1gr4tz miriam: efo n2t: efo ols: efo ontobee: EFO name: Experimental Factor Ontology pattern: ^\d{7}$ preferred_prefix: EFO providers: - code: ebi description: EFO through Functional Genomics Group (EBI) homepage: https://www.ebi.ac.uk/efo/ name: EFO through Functional Genomics Group (EBI) uri_format: https://www.ebi.ac.uk/efo/EFO_$1 publications: - doi: 10.1093/bioinformatics/btq099 pmc: PMC2853691 pubmed: '20200009' title: Modeling sample variables with an Experimental Factor Ontology. year: 2010 repository: https://github.com/EBISPOT/efo/ uri_format: http://www.ebi.ac.uk/efo/EFO_$1 version: 3.45.0 ega.dataset: description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'. example: EGAD00000000001 homepage: https://ega-archive.org/ mappings: biocontext: EGA.DATASET fairsharing: FAIRsharing.mya1ff miriam: ega.dataset n2t: ega.dataset name: European Genome-phenome Archive Dataset pattern: ^EGAD\d{11}$ preferred_prefix: ega.dataset providers: - code: omicsdi description: EGA Dataset through OmicsDI homepage: https://www.omicsdi.org/ name: EGA Dataset through OmicsDI uri_format: https://www.omicsdi.org/dataset/ega/$1 uri_format: https://www.ebi.ac.uk/ega/datasets/$1 ega.study: description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets. example: EGAS00000000001 homepage: https://www.ebi.ac.uk/ega/studies mappings: biocontext: EGA.STUDY miriam: ega.study n2t: ega.study name: European Genome-phenome Archive Study pattern: ^EGAS\d{11}$ preferred_prefix: ega.study uri_format: https://www.ebi.ac.uk/ega/studies/$1 eggnog: description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).' example: veNOG12876 homepage: http://eggnog.embl.de/version_3.0/ mappings: biocontext: EGGNOG fairsharing: FAIRsharing.j1wj7d miriam: eggnog n2t: eggnog prefixcommons: eggnog uniprot: eggNOG name: eggNOG pattern: ^\w+$ preferred_prefix: eggnog publications: - doi: 10.1093/nar/gkp951 pmc: PMC2808932 pubmed: '19900971' title: 'eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.' year: 2009 uri_format: http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1 ehda: contact: email: J.Bard@ed.ac.uk github: null name: Jonathan Bard orcid: null deprecated: true description: A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once. download_obo: http://aber-owl.net/media/ontologies/EHDA/6/ehda.obo example: '1' homepage: http://genex.hgu.mrc.ac.uk/ mappings: aberowl: EHDA biocontext: EHDA bioportal: EHDA obofoundry: ehda prefixcommons: ehda name: Human developmental anatomy, timed version pattern: ^\d+$ preferred_prefix: EHDA uri_format: http://purl.obolibrary.org/obo/EHDA_$1 ehdaa: contact: email: J.Bard@ed.ac.uk github: null name: Jonathan Bard orcid: null deprecated: true description: A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release. download_obo: http://aber-owl.net/media/ontologies/EHDAA/6/ehdaa.obo example: '1' homepage: http://obofoundry.org/ontology/ehdaa.html mappings: aberowl: EHDAA biocontext: EHDAA bioportal: EHDAA obofoundry: ehdaa prefixcommons: ehdaa name: Human developmental anatomy, abstract version pattern: ^\d+$ preferred_prefix: EHDAA uri_format: http://purl.obolibrary.org/obo/EHDAA_$1 ehdaa2: contact: email: J.Bard@ed.ac.uk github: null name: Jonathan Bard orcid: null depends_on: - aeo - caro - cl deprecated: true description: A structured controlled vocabulary of stage-specific anatomical structures of the developing human. download_obo: http://purl.obolibrary.org/obo/ehdaa2.obo download_owl: http://purl.obolibrary.org/obo/ehdaa2.owl example: '0000000' homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology license: CC BY 4.0 mappings: aberowl: EHDAA2 biocontext: EHDAA2 bioportal: EHDAA2 fairsharing: FAIRsharing.7zxrs6 obofoundry: ehdaa2 ols: ehdaa2 ontobee: EHDAA2 name: Human developmental anatomy, abstract pattern: ^\d{7}$ 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_$1 version: '2013-07-04' elm: description: Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances. example: CLV_MEL_PAP_1 homepage: http://elm.eu.org/ mappings: biocontext: ELM fairsharing: FAIRsharing.rj3kj5 miriam: elm n2t: elm uniprot: ELM name: Eukaryotic Linear Motif Resource pattern: ^[A-Za-z_0-9]+$ preferred_prefix: elm uri_format: http://elm.eu.org/elms/elmPages/$1.html emap: contact: email: Terry.Hayamizu@jax.org github: tfhayamizu name: Terry Hayamizu orcid: 0000-0002-0956-8634 deprecated: true description: A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). download_owl: http://purl.obolibrary.org/obo/emap.owl example: '1' homepage: http://emouseatlas.org mappings: biocontext: EMAP bioportal: EMAP obofoundry: emap name: Mouse gross anatomy and development, timed pattern: ^\d+$ preferred_prefix: EMAP uri_format: http://purl.obolibrary.org/obo/EMAP_$1 emapa: contact: email: Terry.Hayamizu@jax.org github: tfhayamizu name: Terry Hayamizu orcid: 0000-0002-0956-8634 description: An ontology for mouse anatomy covering embryonic development and postnatal stages. download_obo: http://purl.obolibrary.org/obo/emapa.obo download_owl: http://purl.obolibrary.org/obo/emapa.owl example: '26753' homepage: http://www.informatics.jax.org/expression.shtml license: CC BY 4.0 mappings: aberowl: EMAPA biocontext: EMAPA bioportal: EMAPA fairsharing: FAIRsharing.j0fa1d go: EMAPA obofoundry: emapa ols: emapa ontobee: EMAPA name: Mouse Developmental Anatomy Ontology pattern: ^\d+$ preferred_prefix: EMAPA repository: https://github.com/obophenotype/mouse-anatomy-ontology synonyms: - EMAPA_RETIRED uri_format: http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:$1 version: '2022-07-14' emdb: description: The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community. example: EMD-1001 homepage: https://www.ebi.ac.uk/pdbe/emdb/ mappings: biocontext: EMDB edam: '1146' fairsharing: FAIRsharing.651n9j miriam: emdb n2t: emdb name: Electron Microscopy Data Bank pattern: ^EMD-\d{4}$ preferred_prefix: emdb uri_format: https://www.ebi.ac.uk/pdbe/entry/emdb/$1 emolecules: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Catalog of purchasable reagents and building blocks example: '491187' homepage: https://reaxys.emolecules.com name: Reaxys eMolecules pattern: ^\d+$ preferred_prefix: emolecules uri_format: https://reaxys.emolecules.com/cgi-bin/more?vid=$1 empiar: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure example: '10595' homepage: https://www.ebi.ac.uk/pdbe/emdb mappings: fairsharing: FAIRsharing.dff3ef name: Electron Microscopy Public Image Archive pattern: ^\d+$ preferred_prefix: empiar uri_format: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1 ena.embl: description: The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers. example: BN000065 homepage: https://www.ebi.ac.uk/ena/ mappings: biocontext: ENA.EMBL fairsharing: FAIRsharing.dj8nt8 go: ENA miriam: ena.embl n2t: ena.embl prefixcommons: ena name: European Nucleotide Archive pattern: ^[A-Z]+[0-9]+(\.\d+)?$ 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 synonyms: - ena uri_format: https://www.ebi.ac.uk/ena/browser/view/$1 encode: description: The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. example: ENCSR163RYW homepage: https://www.encodeproject.org mappings: biocontext: ENCODE cellosaurus: ENCODE fairsharing: FAIRsharing.v0hbjs miriam: encode n2t: encode re3data: r3d100013051 name: Encyclopedia of DNA Elements pattern: ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$ preferred_prefix: encode uri_format: https://www.encodeproject.org/$1 enm: contact: email: hsarimv@central.ntua.gr github: null name: Haralambos Sarimveis orcid: null description: 'The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. > This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. ' download_owl: http://enanomapper.github.io/ontologies/enanomapper.owl example: '8000221' homepage: http://www.enanomapper.net/ mappings: aberowl: ENM bioportal: ENM fairsharing: FAIRsharing.2gpf81 ols: enm name: eNanoMapper Ontology pattern: ^\d+$ preferred_prefix: enm publications: - doi: 10.1186/s13326-015-0005-5 pmc: PMC4374589 pubmed: '25815161' title: 'eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment.' year: 2015 uri_format: http://purl.enanomapper.org/onto/ENM_$1 version: '7.4' ensembl: description: Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms. example: ENSG00000139618 example_extras: - ENSG00000049246.14 - ENSG00000109819.9 - ENSG00000132326.12 - ENSG00000179094.16 - ENST00000264867.7 homepage: https://www.ensembl.org/ mappings: biocontext: ENSEMBL edam: '2610' fairsharing: FAIRsharing.fx0mw7 go: ENSEMBL miriam: ensembl n2t: ensembl ncbi: ENSEMBL prefixcommons: ensembl re3data: r3d100010228 uniprot: Ensembl wikidata: P594 name: Ensembl Gene pattern: ^((ENS[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$ preferred_prefix: ensembl providers: - code: CURATOR_REVIEW description: Ensembl US West mirror homepage: http://uswest.ensembl.org/ name: Ensembl US West mirror uri_format: http://uswest.ensembl.org/id/$1 - code: CURATOR_REVIEW description: Ensembl US East mirror homepage: http://useast.ensembl.org/ name: Ensembl US East mirror uri_format: http://useast.ensembl.org/id/$1 - code: CURATOR_REVIEW description: Ensembl Asia mirror homepage: http://asia.ensembl.org/ name: Ensembl Asia mirror uri_format: http://asia.ensembl.org/id/$1 - code: bgee description: Gene expression in various tissues homepage: https://bgee.org name: Bgee uri_format: https://bgee.org/?page=gene&gene_id=$1 - code: gnomad 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. homepage: https://gnomad.broadinstitute.org name: Genome Aggregation database uri_format: https://gnomad.broadinstitute.org/gene/$1 - code: opentargets.genetics description: Open Targets Genetics is a comprehensive tool highlighting variant-centric statistical evidence to allow both prioritisation of candidate causal variants at trait-associated loci and identification of potential drug targets. homepage: https://genetics.opentargets.org name: OpenTargets Genetics uri_format: https://genetics.opentargets.org/gene/$1 publications: - doi: 10.1093/nar/gkj133 pmc: PMC1347495 pubmed: '16381931' title: Ensembl 2006. year: 2006 synonyms: - Ensembl uri_format: https://www.ensembl.org/id/$1 ensembl.bacteria: description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes. example: MU9_3181 homepage: https://bacteria.ensembl.org/ mappings: biocontext: ENSEMBL.BACTERIA fairsharing: FAIRsharing.zsgmvd miriam: ensembl.bacteria n2t: ensembl.bacteria prefixcommons: ensembl.bacteria re3data: r3d100011195 uniprot: EnsemblBacteria name: Ensembl Bacteria pattern: ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$ preferred_prefix: ensembl.bacteria publications: - doi: 10.1093/nar/gkp871 pmc: PMC2808935 pubmed: '19884133' title: 'Ensembl Genomes: extending Ensembl across the taxonomic space.' year: 2009 uri_format: https://bacteria.ensembl.org/id/$1 ensembl.fungi: description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes. example: CADAFLAT00006211 homepage: https://fungi.ensembl.org/ mappings: biocontext: ENSEMBL.FUNGI fairsharing: FAIRsharing.bg5xqs go: EnsemblFungi miriam: ensembl.fungi n2t: ensembl.fungi prefixcommons: ensembl.fungi re3data: r3d100011196 uniprot: EnsemblFungi name: Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi. pattern: ^[A-Z-a-z0-9]+$ preferred_prefix: ensembl.fungi uri_format: https://fungi.ensembl.org/id/$1 ensembl.metazoa: description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes. example: FBtr0084214 homepage: https://metazoa.ensembl.org/ mappings: biocontext: ENSEMBL.METAZOA fairsharing: FAIRsharing.c23cqq go: EnsemblMetazoa miriam: ensembl.metazoa n2t: ensembl.metazoa prefixcommons: ensembl.metazoa re3data: r3d100011198 uniprot: EnsemblMetazoa name: Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa. pattern: ^\w+(\.)?\d+$ preferred_prefix: ensembl.metazoa uri_format: https://metazoa.ensembl.org/id/$1 ensembl.plant: description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes. example: AT1G73965 homepage: https://plants.ensembl.org/ mappings: biocontext: ENSEMBL.PLANT miriam: ensembl.plant n2t: ensembl.plant prefixcommons: ensembl.plant name: Ensembl Plants pattern: ^\w+(\.\d+)?(\.\d+)?$ preferred_prefix: ensembl.plant uri_format: https://plants.ensembl.org/id/$1 ensembl.protist: description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes. example: PF3D7_1328700 homepage: https://protists.ensembl.org mappings: biocontext: ENSEMBL.PROTIST miriam: ensembl.protist n2t: ensembl.protist prefixcommons: ensembl.protist name: Ensembl Protists pattern: ^\w+$ preferred_prefix: ensembl.protist uri_format: https://protists.ensembl.org/id/$1 ensemblglossary: description: The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used. download_owl: http://ensembl.org/glossary/ensembl-glossary/releases/2022-08-31/ensembl-glossary.owl example: 0000198 homepage: http://ensembl.org/glossary mappings: ols: ensemblglossary name: Ensembl Glossary pattern: ^\d{7}$ preferred_prefix: ensemblglossary uri_format: http://ensembl.org/glossary/ENSGLOSSARY_$1 version: '2022-08-31' envipath: description: enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products. example: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea homepage: https://envipath.org/ mappings: fairsharing: FAIRsharing.g0c5qn miriam: envipath re3data: r3d100012715 name: enviPath pattern: ^[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}\/[\w-]+\/[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}$ preferred_prefix: envipath uri_format: https://envipath.org/package/$1 envo: appears_in: - agro - cdno - ecocore - ecto - foodon - ons - pco - rbo - scdo banana: ENVO contact: email: pier.buttigieg@awi.de github: pbuttigieg name: Pier Luigi Buttigieg orcid: 0000-0002-4366-3088 depends_on: - chebi - foodon - go - ncbitaxon - pco - po - ro - uberon description: The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. download_json: http://purl.obolibrary.org/obo/envo.json download_obo: http://purl.obolibrary.org/obo/envo.obo download_owl: http://purl.obolibrary.org/obo/envo.owl example: 09200010 homepage: http://environmentontology.org/ license: CC0 1.0 mappings: aberowl: ENVO agroportal: ENVO biocontext: ENVO bioportal: ENVO fairsharing: FAIRsharing.azqskx miriam: envo n2t: envo obofoundry: envo ols: envo ontobee: ENVO name: Environment Ontology namespace_in_lui: true pattern: ^\d{7,8}$ 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 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 name: Enzo Life Sciences preferred_prefix: enzo synonyms: - Enzo Life Sciences uri_format: https://www.enzolifesciences.com/$1 eo: appears_in: - foodon banana: EO contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp name: Pankaj Jaiswal orcid: 0000-0002-1005-8383 deprecated: true description: The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. download_obo: http://purl.obolibrary.org/obo/eo.obo download_owl: http://purl.obolibrary.org/obo/eo.owl example: '0007404' homepage: http://planteome.org/ license: CC BY 4.0 mappings: aberowl: EO agroportal: EO biocontext: EO miriam: eo n2t: eo obofoundry: eo prefixcommons: eo name: Plant Environment Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: EO 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:$1 eol: contact: email: pylebail@rennes.inra.fr github: null name: LeBail Pierre-Yves orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems. download_owl: http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=eol.owl example: 0001927 homepage: http://www.atol-ontology.com mappings: aberowl: EOL agroportal: EOL bioportal: EOL fairsharing: FAIRsharing.w7bw2y ols: eol re3data: r3d100011663 name: Environment Ontology for Livestock pattern: ^\d{7}$ preferred_prefix: eol uri_format: http://purl.org/obo/owlEOL_$1 version: '2018-09-13' eolife: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A collaborative project intended to create an encyclopedia documenting all living species known to science example: '1044544' homepage: https://eol.org mappings: fairsharing: FAIRsharing.3J6NYn wikidata: P830 name: Encyclopedia of Life pattern: ^\d+$ preferred_prefix: eolife uri_format: https://eol.org/pages/$1 epcc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Collection of European paediatric cardiac coding files homepage: https://www.aepc.org/european-paediatric-cardiac-coding name: European Paediatric Cardiac Codes preferred_prefix: epcc proprietary: true references: - https://www.cambridge.org/core/journals/cardiology-in-the-young/article/abs/european-paediatric-cardiac-codes-the-long-list-with-icd9-icd10-crossmapping-and-crossmap-to-epcc-short-list/FCA4DFCCB661298294A3D113FC79D5BE epd: description: The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. example: TA_H3 homepage: http://epd.vital-it.ch/ mappings: biocontext: EPD edam: '2386' fairsharing: FAIRsharing.sym4ne miriam: epd n2t: epd ncbi: EPD uniprot: EPD name: Eukaryotic Promoter Database pattern: ^[A-Z-_0-9]+$ preferred_prefix: epd uri_format: http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1 epio: contact: email: alpha.tom.kodamullil@scai.fraunhofer.de github: akodamullil name: Alpha Tom Kodamullil orcid: 0000-0001-9896-3531 depends_on: - bfo description: A application driven Epilepsy Ontology with official terms from the ILAE. download_owl: http://purl.obolibrary.org/obo/epio.owl example: '0000011' homepage: https://github.com/SCAI-BIO/EpilepsyOntology license: CC BY 4.0 mappings: aberowl: EPIO bioportal: EPIO obofoundry: epio ontobee: EPIO name: Epilepsy Ontology pattern: ^\d{7}$ preferred_prefix: EPIO repository: https://github.com/SCAI-BIO/EpilepsyOntology uri_format: http://purl.obolibrary.org/obo/EPIO_$1 epo: contact: email: ferdinand.dhombres@inserm.fr github: null name: Ferdinand Dhombres orcid: null deprecated: true description: An ontology designed to support the semantic annotation of epidemiology resources download_owl: https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/epidemiology-ontology/epo.owl homepage: https://code.google.com/p/epidemiology-ontology/ mappings: aberowl: EPO biocontext: EPO bioportal: EPO obofoundry: epo ontobee: EPO name: Epidemiology Ontology preferred_prefix: EPO uri_format: http://purl.obolibrary.org/obo/EPO_$1 epso: contact: email: satyasahoo@ieee.org github: null name: Satya Sahoo orcid: null description: 'The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. ' download_owl: http://aber-owl.net/media/ontologies/EPSO/3/epso.owl example: '0000400' homepage: http://prism.case.edu/prism/index.php/EpilepsyOntology mappings: aberowl: EPSO bioportal: EPSO fairsharing: FAIRsharing.ttprgy ontobee: EPSO name: Epilepsy and Seizure Ontology pattern: ^\d{7}$ preferred_prefix: epso publications: - doi: 10.1136/amiajnl-2013-001696 pmc: null pubmed: null title: 'Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care' year: null uri_format: http://www.case.edu/EpilepsyOntology.owl#$1 erm: contact: email: egon.willighagen@gmail.com github: egonw name: Egon Willighagen orcid: 0000-0001-7542-0286 description: The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project. download_rdf: https://nanocommons.github.io/identifiers/registry example: ERM00000044 homepage: https://nanocommons.github.io/identifiers/ mappings: cheminf: 000569 miriam: erm n2t: erm name: European Registry of Materials pattern: ^ERM[0-9]{8}$ preferred_prefix: erm publications: - doi: 10.1186/s13321-022-00614-7 pmc: null pubmed: null title: 'European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials' year: null twitter: nanocommons uri_format: https://nanocommons.github.io/identifiers/registry#$1 ero: contact: email: Marc_Ciriello@hms.harvard.edu github: null name: Marc Ciriello orcid: null deprecated: true description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. download_owl: http://purl.obolibrary.org/obo/ero.owl example: '0001655' homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology license: CC BY 2.0 mappings: aberowl: ERO biocontext: ERO bioportal: ERO fairsharing: FAIRsharing.nwgynk obofoundry: ero ols: ero ontobee: ERO name: eagle-i resource ontology pattern: ^\d{7}$ preferred_prefix: ERO publications: - doi: 10.1109/jcdl.2017.7991571 pmc: PMC5868434 pubmed: '29599662' title: 'Automating data citation: the eagle-i experience.' year: 2017 - doi: 10.1093/database/bar067 pmc: PMC3308157 pubmed: '22434835' title: 'Research resources: curating the new eagle-i discovery system.' year: 2012 uri_format: http://purl.obolibrary.org/obo/ERO_$1 version: '2016-07-27' erv: description: Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features. example: THE1B homepage: https://herv.img.cas.cz/ mappings: biocontext: ERV miriam: erv n2t: erv name: Human Endogenous Retrovirus Database pattern: ^[A-Za-z0-9\-\_]+$ preferred_prefix: erv uri_format: https://herv.img.cas.cz/s/$1 estdab: comment: Website is dead deprecated: true description: Cell line databases/resources example: '046' homepage: https://www.ebi.ac.uk/ipd/estdab/ mappings: cellosaurus: ESTDAB name: European Searchable Tumour Line Database pattern: ^\d{3}$ preferred_prefix: estdab uri_format: https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1 eu89h: description: The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union. example: jrc-eurl-ecvam-chemagora homepage: http://data.jrc.ec.europa.eu/ mappings: biocontext: EU89H miriam: eu89h n2t: eu89h name: JRC Data Catalogue pattern: ^[a-z0-9\-_]+$ preferred_prefix: eu89h uri_format: http://data.europa.eu/89h/$1 euclinicaltrials: description: "The EU Clinical Trials Register contains information on clinical trials\ \ conducted in the European Union (EU), or the European Economic Area (EEA) which\ \ started after 1 May 2004.\r\nIt also includes trials conducted outside these\ \ areas if they form part of a paediatric investigation plan (PIP), or are sponsored\ \ by a marketing authorisation holder, and involve the use of a medicine in the\ \ paediatric population." example: 2008-005144-16 homepage: https://www.clinicaltrialsregister.eu/ mappings: biocontext: EUCLINICALTRIALS miriam: euclinicaltrials n2t: euclinicaltrials name: EU Clinical Trials pattern: ^\d{4}\-\d{6}\-\d{2}$ preferred_prefix: euclinicaltrials uri_format: https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1 eupath: appears_in: - scdo contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 description: The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available. download_owl: http://purl.obolibrary.org/obo/eupath.owl example: '0010316' homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology license: CC BY 4.0 mappings: aberowl: EUPATH biocontext: EUPATH bioportal: EUPATH fairsharing: FAIRsharing.9rhr9j obofoundry: eupath ols: eupath ontobee: EUPATH name: VEuPathDB ontology pattern: ^\d{7}$ preferred_prefix: EUPATH publications: - doi: 10.5281/zenodo.6685957 pmc: null pubmed: null title: Malaria study data integration and information retrieval based on OBO Foundry ontologies. year: null repository: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology uri_format: http://purl.obolibrary.org/obo/EUPATH_$1 version: '2022-06-08' eurofir: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries. homepage: https://www.eurofir.org name: European Food Information Resource Network preferred_prefix: eurofir proprietary: true ev: appears_in: - cl contact: email: evoc@sanbi.ac.za github: null name: eVOC mailing list orcid: null deprecated: true homepage: http://www.evocontology.org/ mappings: biocontext: EV obofoundry: ev prefixcommons: evoc name: eVOC (Expressed Sequence Annotation for Humans) preferred_prefix: EV references: - https://twitter.com/Bgeedb/status/1350124337815281664 uri_format: http://purl.obolibrary.org/obo/EV_$1 evm: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: eVOC mouse development stage preferred_prefix: evm references: - https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r229 exac.gene: description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information. example: ENSG00000169174 homepage: http://exac.broadinstitute.org/ mappings: biocontext: EXAC.GENE miriam: exac.gene n2t: exac.gene name: ExAC Gene pattern: ^ENSG\d{11}$ preferred_prefix: exac.gene uri_format: http://exac.broadinstitute.org/gene/$1 exac.transcript: description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information. example: ENST00000407236 homepage: http://exac.broadinstitute.org/ mappings: biocontext: EXAC.TRANSCRIPT miriam: exac.transcript n2t: exac.transcript name: ExAC Transcript pattern: ^ENST\d{11}$ preferred_prefix: exac.transcript uri_format: http://exac.broadinstitute.org/transcript/$1 exac.variant: description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information. example: 22-46615880-T-C homepage: http://exac.broadinstitute.org/ mappings: biocontext: EXAC.VARIANT miriam: exac.variant n2t: exac.variant name: ExAC Variant pattern: ^\d{1,2}\-\d+\-[GATC]\-[GATC]$ preferred_prefix: exac.variant uri_format: http://exac.broadinstitute.org/variant/$1 exo: appears_in: - ecto - scdo contact: email: annethessen@gmail.com github: diatomsRcool name: Anne Thessen orcid: 0000-0002-2908-3327 description: ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics. download_obo: http://purl.obolibrary.org/obo/exo.obo download_owl: http://purl.obolibrary.org/obo/exo.owl example: 0000078 homepage: https://github.com/CTDbase/exposure-ontology license: CC BY 4.0 mappings: aberowl: EXO biocontext: EXO biolink: ExO bioportal: EXO fairsharing: FAIRsharing.6hna78 obofoundry: exo ols: exo ontobee: ExO name: Exposure ontology pattern: ^\d{7}$ preferred_prefix: ExO publications: - doi: 10.1021/es2033857 pmc: PMC3314380 pubmed: '22324457' title: 'Providing the missing link: the exposure science ontology ExO.' year: 2012 repository: https://github.com/CTDbase/exposure-ontology synonyms: - ExO uri_format: http://purl.obolibrary.org/obo/EXO_$1 version: '2022-06-29' fabio: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references. download_owl: http://aber-owl.net/media/ontologies/FaBiO/1/fabio.owl example: d4e2515 homepage: https://github.com/sparontologies/fabio mappings: aberowl: FaBiO biolink: fabio fairsharing: FAIRsharing.2f3180 name: FaBiO, the FRBR-aligned Bibliographic Ontology preferred_prefix: fabio providers: - code: rdf description: A persistent URL for FaBiO homepage: https://github.com/sparontologies/fabio name: FABIO PURL uri_format: http://purl.org/spar/fabio/$1 publications: - doi: 10.1016/j.websem.2012.08.001 pmc: null pubmed: null title: 'FaBiO and CiTO: Ontologies for describing bibliographic resources and citations' year: null repository: https://github.com/sparontologies/fabio uri_format: https://sparontologies.github.io/fabio/current/fabio.html#$1 facebase: description: FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects. example: FB00000917 homepage: https://www.facebase.org mappings: biocontext: FACEBASE fairsharing: FAIRsharing.mqvqde miriam: facebase n2t: facebase re3data: r3d100013263 name: FaceBase Data Repository pattern: ^FB\d{8}$ preferred_prefix: facebase uri_format: https://www.facebase.org/data/record/#1/isa:dataset/accession=$1 fairsharing: description: The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies. example: bsg-000052 homepage: https://fairsharing.org/ mappings: biocontext: FAIRSHARING fairsharing: FAIRsharing.2abjs5 miriam: fairsharing n2t: fairsharing re3data: r3d100010142 name: FAIRsharing pattern: ^bsg-[dscp]?\d{6}$ preferred_prefix: fairsharing uri_format: https://fairsharing.org/$1 faldo: contact: email: faldo@googlegroups.com github: null name: FALDO group orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources download_owl: http://aber-owl.net/media/ontologies/FALDO/1/faldo.owl example: ForwardStrandPosition homepage: http://biohackathon.org/resource/faldo mappings: aberowl: FALDO agroportal: FALDO biocontext: faldo bioportal: FALDO fairsharing: FAIRsharing.haxp7g name: 'Feature Annotation Location Description Ontology ' preferred_prefix: faldo publications: - doi: 10.1186/s13326-016-0067-z pmc: PMC4907002 pubmed: '27296299' title: 'FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.' year: 2016 uri_format: http://biohackathon.org/resource/faldo#$1 fao: contact: email: vw253@cam.ac.uk github: ValWood name: Val Wood orcid: 0000-0001-6330-7526 description: A structured controlled vocabulary for the anatomy of fungi. download_obo: http://purl.obolibrary.org/obo/fao.obo download_owl: http://purl.obolibrary.org/obo/fao.owl example: '0000001' homepage: https://github.com/obophenotype/fungal-anatomy-ontology/ license: CC0 1.0 mappings: aberowl: FAO biocontext: FAO bioportal: FAO fairsharing: FAIRsharing.xs6t67 obofoundry: fao ols: fao ontobee: FAO prefixcommons: fao name: Fungal gross anatomy pattern: ^\d{7}$ preferred_prefix: FAO repository: https://github.com/obophenotype/fungal-anatomy-ontology uri_format: http://purl.obolibrary.org/obo/FAO_$1 version: '2020-05-07' fbbi: contact: email: wawong@gmail.com github: wawong name: Willy Wong orcid: 0000-0002-8841-5870 description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. download_obo: http://aber-owl.net/media/ontologies/FBbi/14/fbbi.obo download_owl: http://purl.obolibrary.org/obo/fbbi.owl example: 00000268 homepage: http://cellimagelibrary.org/ license: CC BY 4.0 mappings: aberowl: FBbi biocontext: FBbi bioportal: FBbi fairsharing: FAIRsharing.ny3z9j obofoundry: fbbi ols: fbbi ontobee: FBBI prefixcommons: fbbi name: Biological Imaging Methods Ontology pattern: ^\d+$ preferred_prefix: FBbi repository: https://github.com/CRBS/Biological_Imaging_Methods_Ontology synonyms: - FBbi uri_format: http://purl.obolibrary.org/obo/FBbi_$1 version: '2020-11-06' fbbt: contact: email: cp390@cam.ac.uk github: Clare72 name: Clare Pilgrim orcid: 0000-0002-1373-1705 description: An ontology of Drosophila melanogaster anatomy. download_json: http://purl.obolibrary.org/obo/fbbt.json download_obo: http://purl.obolibrary.org/obo/fbbt.obo download_owl: http://purl.obolibrary.org/obo/fbbt.owl example: 00007294 homepage: http://purl.obolibrary.org/obo/fbbt license: CC BY 4.0 mappings: aberowl: FBBT biocontext: FBbt bioportal: FB-BT fairsharing: FAIRsharing.y2qkst go: FBbt obofoundry: fbbt ols: fbbt ontobee: FBBT prefixcommons: fbbt name: Drosophila gross anatomy part_of: flybase pattern: ^\d{8}$ preferred_prefix: FBbt publications: - doi: 10.1186/2041-1480-4-32 pmc: PMC4015547 pubmed: '24139062' title: The Drosophila anatomy ontology. year: 2013 - doi: 10.1093/bioinformatics/bts113 pmc: null pubmed: '22402613' title: A strategy for building neuroanatomy ontologies. year: 2012 - doi: 10.1093/bioinformatics/btr677 pmc: null pubmed: '22180411' title: The Virtual Fly Brain browser and query interface. year: 2011 - doi: 10.1093/nar/gkj068 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:$1 version: '2022-06-09' fbcv: appears_in: - ontoavida contact: email: cp390@cam.ac.uk github: Clare72 name: Clare Pilgrim orcid: 0000-0002-1373-1705 description: A miscellaneous ontology of terms used for curation in FlyBase, including the DPO. download_json: http://purl.obolibrary.org/obo/fbcv.json download_obo: https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/fbcv.obo download_owl: http://purl.obolibrary.org/obo/fbcv.owl example: 0000586 homepage: http://purl.obolibrary.org/obo/fbcv license: CC BY 4.0 mappings: aberowl: FBCV biocontext: FBcv bioportal: FB-CV fairsharing: FAIRsharing.6tgyxf obofoundry: fbcv ols: fbcv ontobee: FBCV prefixcommons: fbcv name: FlyBase Controlled Vocabulary part_of: flybase pattern: ^\d{7}$ 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_$1 version: '2022-06-09' fbdv: contact: email: cp390@cam.ac.uk github: Clare72 name: Clare Pilgrim orcid: 0000-0002-1373-1705 description: An ontology of Drosophila melanogaster developmental stages. download_json: http://purl.obolibrary.org/obo/fbdv.json download_obo: http://purl.obolibrary.org/obo/fbdv.obo download_owl: http://purl.obolibrary.org/obo/fbdv.owl example: '00000000' homepage: http://purl.obolibrary.org/obo/fbdv license: CC BY 4.0 mappings: aberowl: FBDV biocontext: FBdv bioportal: FB-DV fairsharing: FAIRsharing.p52pzj obofoundry: fbdv ols: fbdv ontobee: FBdv prefixcommons: fbdv name: Drosophila development pattern: ^\d{8}$ preferred_prefix: FBdv repository: https://github.com/FlyBase/drosophila-developmental-ontology synonyms: - FBdv 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$1 fbsp: contact: email: cp390@cam.ac.uk github: Clare72 name: Clare Pilgrim orcid: 0000-0002-1373-1705 deprecated: true description: The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. download_obo: http://aber-owl.net/media/ontologies/FB-SP/7/fb-sp.obo download_owl: http://purl.obolibrary.org/obo/fbsp.owl example: '00000000' homepage: http://www.flybase.org/ mappings: aberowl: FB-SP biocontext: FBSP bioportal: FB-SP obofoundry: fbsp name: Fly taxonomy part_of: flybase pattern: ^\d{8}$ preferred_prefix: FBSP uri_format: http://purl.obolibrary.org/obo/FBSP_$1 fbtc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The cell line vocabulary inside FlyBase example: 0000190 homepage: https://flybase.org name: Flybase Cell Line part_of: flybase pattern: ^\d{7}$ preferred_prefix: fbtc uri_format: https://flybase.org/reports/FBtc$1 fcb: description: 'Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR). ' example: FCB005 homepage: https://w3id.org mappings: miriam: fcb name: the FAIR Cookbook pattern: ^FCB\d{3}$ preferred_prefix: fcb uri_format: https://w3id.org/faircookbook/$1 fcsfree: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Cell line databases/resources example: 240-17-488-3-4-12 homepage: https://fcs-free.org mappings: cellosaurus: FCS-free name: Fetal Calf Serum-Free Database preferred_prefix: fcsfree uri_format: https://fcs-free.org/fcs-database?$1 fhir.implementation: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A set of guides on implementing various processes within hospitals or healthcare systems. example: immds homepage: https://hl7.org/fhir/us/ name: FHIR United States Implementation Guides preferred_prefix: fhir.implementation uri_format: https://hl7.org/fhir/us/$1 fideo: contact: email: georgeta.bordea@u-bordeaux.fr github: getbordea name: Georgeta Bordea orcid: 0000-0001-9921-8234 description: The Food Interactions with Drugs Evidence Ontology (FIDEO) represents Food-Drug Interactions and underlying interaction mechanisms described in scientific publications, drug and adverse effects databases, and drug interactions compendia. The ontology builds on previous efforts from the FoodOn, DRON, ChEBI, and DIDEO ontologies as well as the Thériaque database. This ontology is maintained at https://gitub.u-bordeaux.fr/erias/fideo, and requests for changes or additions should be filed at the issue tracker there. download_owl: http://purl.obolibrary.org/obo/fideo.owl example: '00000021' homepage: https://gitub.u-bordeaux.fr/erias/fideo license: CC0 1.0 mappings: aberowl: FIDEO bioportal: FIDEO obofoundry: fideo ols: fideo ontobee: FIDEO name: Food Interactions with Drugs Evidence Ontology pattern: ^\d{8}$ preferred_prefix: FIDEO repository: https://github.com/getbordea/fideo uri_format: http://purl.obolibrary.org/obo/FIDEO_$1 fishbase.species: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years.' example: '6472' homepage: http://fishbase.org mappings: re3data: r3d100010912 wikidata: P938 name: FishBase pattern: ^\d+$ preferred_prefix: fishbase.species synonyms: - fishbase uri_format: https://www.fishbase.ca/summary/$1 fivestars: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata. example: hasOpenAccessRating homepage: http://www.sparontologies.net/ontologies/fivestars mappings: fairsharing: FAIRsharing.6dfe9b name: Five Stars of Online Research Articles Ontology preferred_prefix: FiveStars publications: - doi: 10.1045/january2012-shotton pmc: null pubmed: null title: The Five Stars of Online Journal Articles - a Framework for Article Evaluation year: null repository: https://github.com/sparontologies/fivestars fix: contact: email: chebi-help@ebi.ac.uk github: null name: chEBI orcid: null deprecated: true description: An ontology of physico-chemical methods and properties. download_obo: http://purl.obolibrary.org/obo/fix.obo download_owl: http://purl.obolibrary.org/obo/fix.owl example: 0000390 homepage: https://www.ebi.ac.uk/chebi/ mappings: aberowl: FIX biocontext: FIX bioportal: FIX fairsharing: FAIRsharing.wwy1ns obofoundry: fix ols: fix ontobee: FIX prefixcommons: fix name: Physico-chemical methods and properties part_of: chebi pattern: ^\d{7}$ preferred_prefix: FIX uri_format: http://purl.obolibrary.org/obo/FIX_$1 version: '2020-04-13' flopo: contact: email: robert.hoehndorf@kaust.edu.sa github: leechuck name: Robert Hoehndorf orcid: 0000-0001-8149-5890 description: Traits and phenotypes of flowering plants occurring in digitized Floras download_owl: http://purl.obolibrary.org/obo/flopo.owl example: '0005250' homepage: https://github.com/flora-phenotype-ontology/flopoontology license: CC0 1.0 mappings: aberowl: FLOPO agroportal: FLOPO biocontext: FLOPO bioportal: FLOPO fairsharing: FAIRsharing.ny9vnm obofoundry: flopo ols: flopo ontobee: FLOPO name: Flora Phenotype Ontology pattern: ^\d{7}$ preferred_prefix: FLOPO publications: - doi: 10.1186/s13326-016-0107-8 pmc: PMC5109718 pubmed: '27842607' title: 'The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.' year: 2016 - doi: 10.3897/bdj.2.e1125 pmc: PMC4092319 pubmed: '25057255' title: Enriched biodiversity data as a resource and service. year: 2014 repository: https://github.com/flora-phenotype-ontology/flopoontology uri_format: http://purl.obolibrary.org/obo/FLOPO_$1 version: '2019-09-09' flowrepository: description: FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field. example: FR-FCM-ZYGW homepage: https://flowrepository.org/ mappings: fairsharing: FAIRsharing.veg2d6 miriam: flowrepository n2t: flowrepository re3data: r3d100011280 name: FlowRepository pattern: ^FR\-FCM\-\w{4}$ preferred_prefix: flowrepository uri_format: https://flowrepository.org/id/$1 flu: contact: email: burkesquires@gmail.com github: null name: Burke Squires orcid: null deprecated: true description: Starting in the fall of 2007, a collaborative group of influenza researchers have established an influenza ontology. The influenza ontology is an application ontology. Consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS) download_owl: http://purl.obolibrary.org/obo/flu.owl example: '0000404' homepage: http://purl.obolibrary.org/obo/flu/ mappings: aberowl: FLU biocontext: FLU bioportal: FLU obofoundry: flu name: Influenza Ontology pattern: ^\d{7}$ preferred_prefix: FLU uri_format: http://purl.obolibrary.org/obo/FLU_$1 flybase: description: FlyBase is the database of the Drosophila Genome Projects and of associated literature. example: FBgn0011293 homepage: http://flybase.org/ mappings: biocontext: FlyBase cellosaurus: FlyBase edam: '1089' fairsharing: FAIRsharing.wrvze3 go: FB miriam: fb n2t: fb ncbi: FLYBASE prefixcommons: flybase re3data: r3d100010591 uniprot: FlyBase wikidata: P3852 name: FlyBase Gene pattern: ^FB\w{2}\d{7}$ preferred_prefix: FlyBase providers: - code: agr description: FlyBase through the Alliance of Genome Resources homepage: https://www.alliancegenome.org name: FlyBase through the Alliance of Genome Resources uri_format: https://www.alliancegenome.org/gene/FB:$1 - code: bioentitylink description: FlyBase through BioEntity Link homepage: https://bioentity.link/ name: FlyBase through BioEntity Link uri_format: https://bioentity.link/#/lexicon/public/$1 synonyms: - FB - FlyBase uri_format: https://flybase.org/reports/$1 flybrain.ndb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A database of fly neurons and pathways with an associated 3D viewer. example: '10531' homepage: https://flybrain-ndb.virtualflybrain.org name: FlyBrain Neuron Database pattern: ^\d+$ preferred_prefix: flybrain.ndb uri_format: https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html fma: banana: FMA contact: email: mejino@u.washington.edu github: null name: Onard Mejino orcid: null deprecated: true description: The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. download_owl: http://purl.obolibrary.org/obo/fma.owl example: '63189' homepage: http://si.washington.edu/projects/fma license: CC BY 3.0 mappings: aberowl: FMA biocontext: FMA bioportal: FMA edam: '1182' fairsharing: FAIRsharing.x56jsy go: FMA hl7: 2.16.840.1.113883.6.119 miriam: fma n2t: fma obofoundry: fma ols: fma ontobee: FMA prefixcommons: fma name: Foundational Model of Anatomy namespace_in_lui: true pattern: ^\d+$ preferred_prefix: FMA publications: - doi: 10.1016/j.artmed.2016.04.003 pmc: PMC4915823 pubmed: '27235801' title: 'From frames to OWL2: Converting the Foundational Model of Anatomy.' year: 2016 - doi: 10.1016/j.websem.2007.12.001 pmc: PMC2500209 pubmed: '18688289' title: Translating the Foundational Model of Anatomy into OWL. year: 2008 - doi: 10.1016/j.websem.2006.05.007 pmc: PMC2270940 pubmed: '18360535' title: 'The foundational model of anatomy in OWL: Experience and perspectives.' year: 2006 - doi: 10.1109/iembs.2004.1404513 pmc: null pubmed: '17271570' title: 'The foundational model of anatomy: a template for the symbolic representation of multi-scale physiological functions.' year: null - doi: null pmc: PMC1560487 pubmed: '16779026' title: 'Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study.' year: 2005 - doi: 10.1016/j.jbi.2003.11.007 pmc: null pubmed: '14759820' title: 'A reference ontology for biomedical informatics: the Foundational Model of Anatomy.' year: 2003 repository: https://bitbucket.org/uwsig/fma synonyms: - FMAID - FMA_RETIRED uri_format: https://www.ebi.ac.uk/ols/ontologies/fma/terms?obo_id=FMA:$1 version: '2020-04-13' foaf: contact: email: rafael.goncalves@stanford.edu github: null name: Rafael Gonçalves orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people''s heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world.' download_owl: http://aber-owl.net/media/ontologies/foaf/1/foaf.owl example: familyName homepage: http://xmlns.com/foaf/spec/ mappings: aberowl: foaf biocontext: foaf biolink: foaf bioportal: FOAF name: Friend of a Friend preferred_prefix: foaf uri_format: http://xmlns.com/foaf/0.1/$1 fobi: contact: email: polcaes@gmail.com github: pcastellanoescuder name: Pol Castellano Escuder orcid: 0000-0001-6466-877X depends_on: - chebi - foodon description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data download_owl: http://purl.obolibrary.org/obo/fobi.owl example: 030719 example_extras: - '0142' - '07504' homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology license: CC BY 3.0 mappings: aberowl: FOBI agroportal: FOBI bioportal: FOBI obofoundry: fobi ols: fobi ontobee: FOBI name: Food-Biomarker Ontology pattern: ^\d{4,6}$ preferred_prefix: FOBI publications: - doi: 10.1093/bioinformatics/btab626 pmc: null pubmed: '34601570' title: 'The fobitools framework: the first steps towards food enrichment analysis.' year: 2021 - doi: 10.1093/databa/baaa033 pmc: PMC7298227 pubmed: '32556148' title: 'FOBI: an ontology to represent food intake data and associate it with metabolomic data.' year: 2020 repository: https://github.com/pcastellanoescuder/FoodBiomarkerOntology uri_format: http://purl.obolibrary.org/obo/FOBI_$1 foodb.compound: description: FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds. example: FDB002100 homepage: https://foodb.ca/ mappings: biocontext: FOODB.COMPOUND biolink: foodb.compound miriam: foodb.compound n2t: foodb.compound re3data: r3d100012152 name: FooDB Compound pattern: ^FDB\d+$ preferred_prefix: foodb.compound synonyms: - foodb uri_format: http://foodb.ca/compounds/$1 foodb.food: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Foods in FooDB example: FOOD00020 homepage: https://foodb.ca/foods mappings: biolink: foodb.food name: FooDB Food pattern: ^FOOD\d+$ preferred_prefix: foodb.food uri_format: https://foodb.ca/foods/$1 foodex2: description: FoodEx2 is a comprehensive food classification and description system aimed at covering the need to describe food in data collections across different food safety domains. example: A0TMC homepage: http://www.efsa.europa.eu/ mappings: agroportal: FOODEX2 name: Food classification and description system preferred_prefix: foodex2 uri_format: http://data.food.gov.uk/codes/foodtype/id/$1 foodon: appears_in: - agro - envo - fobi - maxo - one - ons banana: FOODON contact: email: damion_dooley@sfu.ca github: ddooley name: Damion Dooley orcid: 0000-0002-8844-9165 depends_on: - bfo - chebi - envo - eo - ncbitaxon - obi - ro - uberon description: FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies. download_obo: http://purl.obolibrary.org/obo/foodon.obo download_owl: http://purl.obolibrary.org/obo/foodon.owl example: 03307879 homepage: https://foodon.org/ license: CC BY 3.0 mappings: aberowl: FOODON agroportal: FOODON biocontext: FOODON bioportal: FOODON fairsharing: FAIRsharing.dzxae miriam: foodon n2t: foodon obofoundry: foodon ols: foodon ontobee: FOODON name: The Food Ontology namespace_in_lui: true pattern: ^[0-9]{8}$ preferred_prefix: FOODON publications: - doi: 10.1038/s41538-018-0032-6 pmc: PMC6550238 pubmed: '31304272' title: 'FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration.' year: 2018 - doi: 10.3389/fmicb.2017.01068 pmc: PMC5483436 pubmed: '28694792' title: 'Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance.' year: 2017 repository: https://github.com/FoodOntology/foodon uri_format: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1 version: '2022-02-01' fossilworks.journal: contributor: email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 description: Identifier for a journal article in the fossilworks website example: '61467' github_request_issue: 468 homepage: http://fossilworks.org mappings: wikidata: P7720 name: Fossilworks Journal part_of: fossilworks pattern: ^\d+$ preferred_prefix: fossilworks.journal reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://fossilworks.org/?a=referenceInfo&reference_no=$1 fossilworks.taxon: contributor: email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 description: Identifier for an animal, plant, or microorganism from the fossilworks website example: '40565' github_request_issue: 469 homepage: http://www.fossilworks.org mappings: wikidata: P842 name: Fossilworks Taxon part_of: fossilworks pattern: ^[1-9]\d{0,5}$ preferred_prefix: fossilworks.taxon reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1 fovt: contact: email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 depends_on: - bco - bfo - bspo - iao - oba - pato - ro - uberon description: None download_obo: http://purl.obolibrary.org/obo/fovt.obo download_owl: http://purl.obolibrary.org/obo/fovt.owl example: 0000009 homepage: https://github.com/futres/fovt license: CC0 1.0 mappings: aberowl: FOVT bioportal: FOVT obofoundry: fovt ols: fovt ontobee: FOVT name: FuTRES Ontology of Vertebrate Traits pattern: ^\d{7}$ preferred_prefix: FOVT repository: https://github.com/futres/fovt uri_format: http://purl.obolibrary.org/obo/FOVT_$1 version: '2021-11-10' fplx: contact: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships. example: GPIb_IX_V homepage: https://sorgerlab.github.io/famplex/ mappings: aberowl: FPLX biocontext: FPLX bioportal: FPLX miriam: fplx n2t: fplx name: FamPlex pattern: ^[a-zA-Z0-9][A-Za-z0-9_]+$ preferred_prefix: fplx publications: - doi: 10.1186/s12859-018-2211-5 pmc: PMC6022344 pubmed: '29954318' title: 'FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining' year: 2018 synonyms: - famplex uri_format: https://sorgerlab.github.io/famplex/$1 fr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology that enables the description of reviews of scientific articles and other scholarly resources. example: ReviewVersion homepage: http://www.sparontologies.net/ontologies/fr mappings: fairsharing: FAIRsharing.e7e609 name: FAIR* Reviews Ontology preferred_prefix: FR repository: https://github.com/sparontologies/fr frapo: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc. example: Grant homepage: http://www.sparontologies.net/ontologies/frapo mappings: aberowl: FRAPO fairsharing: FAIRsharing.0a2576 name: Funding, Research Administration and Projects Ontology preferred_prefix: FRAPO repository: https://github.com/sparontologies/frapo uri_format: http://purl.org/cerif/frapo/$1 frbr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO. example: Expression homepage: http://www.sparontologies.net/ontologies/frbr mappings: fairsharing: FAIRsharing.b34b43 name: Functional Requirements for Bibliographic Records preferred_prefix: FRBR repository: https://github.com/sparontologies/frbr uri_format: http://purl.org/vocab/frbr/core#$1 fsnp: description: The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification. example: rs17852708 homepage: http://compbio.cs.queensu.ca/F-SNP/ mappings: biocontext: FSNP miriam: fsnp n2t: fsnp prefixcommons: fsnp name: F-SNP pattern: ^rs\d+$ preferred_prefix: fsnp uri_format: http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1 ftt: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific. example: '273' homepage: https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3 name: Feature Type Thesaurus pattern: ^\d+$ preferred_prefix: ftt references: - https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200 - https://github.com/EnvironmentOntology/envo/issues/1130 uri_format: https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1 funcbase.fly: description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data. example: '10194' homepage: http://func.mshri.on.ca/fly mappings: biocontext: FUNCBASE.FLY miriam: funcbase.fly n2t: funcbase.fly name: FuncBase Fly pattern: ^\d+$ preferred_prefix: funcbase.fly uri_format: http://func.mshri.on.ca/fly/genes/list_functional_scores/$1 funcbase.human: description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data. example: '119514' homepage: http://func.mshri.on.ca/human/ mappings: biocontext: FUNCBASE.HUMAN miriam: funcbase.human n2t: funcbase.human name: FuncBase Human pattern: ^\d+$ preferred_prefix: funcbase.human uri_format: http://func.mshri.on.ca/human/genes/list_functional_scores/$1 funcbase.mouse: description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse. example: '1351341' homepage: http://func.mshri.on.ca/mouse/ mappings: biocontext: FUNCBASE.MOUSE miriam: funcbase.mouse n2t: funcbase.mouse name: FuncBase Mouse pattern: ^\d+$ preferred_prefix: funcbase.mouse uri_format: http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1 funcbase.yeast: description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast. example: '2701' homepage: http://func.mshri.on.ca/yeast mappings: biocontext: FUNCBASE.YEAST miriam: funcbase.yeast n2t: funcbase.yeast name: FuncBase Yeast pattern: ^\d+$ preferred_prefix: funcbase.yeast uri_format: http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1 funderregistry: description: The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world. example: '100000001' homepage: https://www.crossref.org/ mappings: miriam: funderregistry name: FunderRegistry pattern: ^\d{9,9}$ preferred_prefix: funderregistry uri_format: http://data.crossref.org/fundingdata/funder/10.13039/$1 fungidb: description: FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina. example: CNBG_0001 homepage: https://fungidb.org/fungidb mappings: biocontext: FUNGIDB fairsharing: FAIRsharing.xf30yc miriam: fungidb n2t: fungidb re3data: r3d100011906 name: FungiDB pattern: ^[A-Za-z_0-9]+$ preferred_prefix: fungidb uri_format: https://fungidb.org/fungidb/app/record/gene/$1 fungorum: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier for a fungus taxon in Index Fungorum example: '154022' homepage: http://www.indexfungorum.org mappings: ncbi: Fungorum wikidata: P1391 name: Index Fungorum pattern: ^[1-9]\d{0,5}$ preferred_prefix: fungorum uri_format: http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1 fyeco: comment: Rather than admitting FYECO to the OBO foundry, we secure the prefix here at bioregistry. The FYECO namespace shows up in a lot of ingests (basically anywhere you ingest PomBase gene-phenotype data). Future work includes mapping FYECO to other OBO ontologies, but this is way ahead in the future. contact: email: vw253@cam.ac.uk github: ValWood name: Val Wood orcid: 0000-0001-6330-7526 contributor: email: vw253@cam.ac.uk github: ValWood name: Val Wood orcid: 0000-0001-6330-7526 description: PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase. example: '0000003' github_request_issue: 268 homepage: https://github.com/pombase/fypo mappings: biolink: FYECO name: Fission Yeast Experimental Conditions Ontology pattern: ^\d{7}$ preferred_prefix: FYECO repository: https://github.com/pombase/fypo reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 fyler: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'A hierarchical classification of congenital heart disease ' example: '4447' homepage: https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906 name: Fyler pattern: ^\d+$ preferred_prefix: fyler references: - https://github.com/obophenotype/human-phenotype-ontology/issues/2568 - https://github.com/obophenotype/human-phenotype-ontology/issues/2511 fypo: contact: email: vw253@cam.ac.uk github: ValWood name: Val Wood orcid: 0000-0001-6330-7526 description: A formal ontology of phenotypes observed in fission yeast. download_json: http://purl.obolibrary.org/obo/fypo.json download_obo: http://purl.obolibrary.org/obo/fypo.obo download_owl: http://purl.obolibrary.org/obo/fypo.owl example: '0001707' homepage: https://github.com/pombase/fypo license: CC BY 4.0 mappings: aberowl: FYPO biocontext: FYPO biolink: FYPO bioportal: FYPO fairsharing: FAIRsharing.4vr0ys go: FYPO obofoundry: fypo ols: fypo ontobee: FYPO name: Fission Yeast Phenotype Ontology pattern: ^\d{7}$ preferred_prefix: FYPO publications: - doi: 10.1093/bioinformatics/btt266 pmc: PMC3694669 pubmed: '23658422' title: 'FYPO: the fission yeast phenotype ontology.' year: 2013 repository: https://github.com/pombase/fypo uri_format: http://purl.obolibrary.org/obo/FYPO_$1 version: '2022-07-14' ga4ghdos: description: Assists in resolving data across cloud resources. example: dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d homepage: http://github.com/ga4gh/data-object-service-schemas mappings: biocontext: GA4GHDOS miriam: ga4ghdos n2t: ga4ghdos name: Data Object Service pattern: ^[a-zA-Z0-9\-:#/\.]+$ preferred_prefix: ga4ghdos uri_format: https://dataguids.org/ga4gh/dos/v1/dataobjects/$1 gabi: description: GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'. example: '2679240' homepage: http://www.gabipd.org/ mappings: biocontext: GABI miriam: gabi n2t: gabi ncbi: GABI prefixcommons: gabi name: Network of Different Plant Genomic Research Projects pattern: ^\w+$ preferred_prefix: gabi publications: - doi: 10.1093/nar/gkn611 pmc: PMC2686513 pubmed: '18812395' title: 'GabiPD: the GABI primary database--a plant integrative ''omics'' database.' year: 2008 uri_format: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject galen: comment: I really tried, but could not figure out what GALEN stands for contact: email: j@deltaflow.com github: null name: Julian Seidenberg orcid: null deprecated: true description: A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic. download_owl: http://aber-owl.net/media/ontologies/GALEN/1/galen.owl example: MagnitudeValueType homepage: https://www.opengalen.org mappings: aberowl: GALEN bioportal: GALEN name: GALEN preferred_prefix: galen uri_format: http://www.co-ode.org/ontologies/galen#$1 gard: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease. example: '6038' homepage: https://rarediseases.info.nih.gov/diseases mappings: wikidata: P4317 name: Genetic and Rare Diseases Information Center pattern: ^\d+$ preferred_prefix: gard synonyms: - GARD - Genetic and Rare Diseases Information Center uri_format: https://rarediseases.info.nih.gov/diseases/$1/index gateway: description: The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access. example: fd8d0743-344a-4758-bb97-f8ad84a37357 homepage: https://www.hdruk.ac.uk mappings: miriam: gateway name: Health Data Research Innovation Gateway pattern: ^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$ preferred_prefix: gateway uri_format: https://web.www.healthdatagateway.org/dataset/$1 gaz: appears_in: - scdo contact: email: lschriml@som.umaryland.edu github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 deprecated: true description: A gazetteer constructed on ontological principles download_obo: http://purl.obolibrary.org/obo/gaz.obo download_owl: http://purl.obolibrary.org/obo/gaz.owl example: '00620027' homepage: http://environmentontology.github.io/gaz/ license: CC0 1.0 mappings: aberowl: GAZ biocontext: GAZ bioportal: GAZ fairsharing: FAIRsharing.wkdjpb obofoundry: gaz ols: gaz ontobee: GAZ wikidata: P6778 name: Gazetteer pattern: ^\d{8}$ preferred_prefix: GAZ repository: https://github.com/EnvironmentOntology/gaz uri_format: http://purl.obolibrary.org/obo/GAZ_$1 gbif: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity\ \ Information Facility—is international network and data infrastructure funded\ \ by the world's governments and aimed at providing anyone, anywhere, open access\ \ to data about all types of life on Earth." example: '4238' homepage: https://www.gbif.org/species mappings: fairsharing: FAIRsharing.zv11j3 wikidata: P846 name: Global Biodiversity Information Facility pattern: ^\d+$ preferred_prefix: gbif twitter: GBIF uri_format: https://www.gbif.org/species/$1 gc: comment: 'see comment here: https://github.com/obophenotype/ncbitaxon/issues/47' contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries. example: '11' homepage: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html name: Genetic Code pattern: ^\d+$ preferred_prefix: gc references: - https://github.com/obophenotype/ncbitaxon/issues/47 synonyms: - gc_id uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1 gcst: description: The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide. example: GCST000035 homepage: https://www.ebi.ac.uk mappings: miriam: gcst n2t: gcst name: GWAS Catalog pattern: ^GCST\d{6}\d*$ preferred_prefix: gcst uri_format: https://www.ebi.ac.uk/gwas/studies/$1 gdc: description: The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis. example: ae8c77fe-e6c8-44d5-8265-4a38c637bbef homepage: https://gdc.cancer.gov mappings: biocontext: GDC miriam: gdc n2t: gdc name: Genomic Data Commons Data Portal pattern: ^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$ preferred_prefix: gdc uri_format: https://portal.gdc.cancer.gov/cases/$1 gdsc: description: The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies. example: '1242' homepage: https://www.cancerrxgene.org mappings: cellosaurus: GDSC miriam: gdsc n2t: gdsc name: Genomics of Drug Sensitivity in Cancer pattern: ^[0-9]+$ preferred_prefix: gdsc uri_format: https://www.cancerrxgene.org/translation/Drug/$1 gecko: contact: email: rbca.jackson@gmail.com github: beckyjackson name: Rebecca Jackson orcid: 0000-0003-4871-5569 description: An ontology to represent genomics cohort attributes. download_owl: http://purl.obolibrary.org/obo/gecko.owl example: '0000044' homepage: https://github.com/IHCC-cohorts/GECKO license: CC BY 4.0 mappings: aberowl: GECKO bioportal: GECKO fairsharing: FAIRsharing.3da56b obofoundry: gecko ols: gecko ontobee: GECKO name: Genomics Cohorts Knowledge Ontology pattern: ^\d{7}$ preferred_prefix: GECKO repository: https://github.com/IHCC-cohorts/GECKO uri_format: http://purl.obolibrary.org/obo/GECKO_$1 version: '2021-01-18' gemet: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts. example: '627' homepage: https://www.eionet.europa.eu/gemet/en/themes/ mappings: agroportal: GEMET name: General Multilingual Environmental Thesaurus pattern: ^\d+$ preferred_prefix: gemet uri_format: https://www.eionet.europa.eu/gemet/en/concept/$1 genatlas: description: GenAtlas is a database containing information on human genes, markers and phenotypes. example: HBB homepage: http://genatlas.medecine.univ-paris5.fr/ mappings: biocontext: GENATLAS fairsharing: FAIRsharing.pmg2vd miriam: genatlas n2t: genatlas prefixcommons: genatlas uniprot: GenAtlas name: Genatlas pattern: ^\w+$ preferred_prefix: genatlas publications: - doi: 10.1016/s0764-4469(99)80021-3 pmc: null pubmed: '9835018' title: Genatlas database, genes and development defects. year: 1998 uri_format: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1 genbank: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). example: U49845 homepage: https://www.ncbi.nlm.nih.gov/genbank/ mappings: biocontext: GenBank cheminf: '000304' edam: '2292' fairsharing: FAIRsharing.9kahy4 go: GenBank prefixcommons: genbank re3data: r3d100010528 uniprot: GenBank name: GenBank preferred_prefix: genbank uri_format: https://www.ncbi.nlm.nih.gov/nucleotide/$1 genecards: description: The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene. example: ABL1 homepage: http://www.genecards.org/ mappings: biocontext: GENECARDS fairsharing: FAIRsharing.g7jbvn miriam: genecards n2t: genecards prefixcommons: genecards re3data: r3d100012015 uniprot: GeneCards name: GeneCards pattern: ^[A-Za-z-0-9_]+(\@)?$ preferred_prefix: genecards publications: - doi: 10.1093/database/baq020 pmc: PMC2938269 pubmed: '20689021' title: 'GeneCards Version 3: the human gene integrator.' year: 2010 uri_format: https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1 genedb: deprecated: true description: GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed. example: LinJ.20.0070 homepage: https://www.genedb.org/ mappings: biocontext: GENEDB edam: '1035' fairsharing: FAIRsharing.j7esqq go: GeneDB miriam: genedb n2t: genedb ncbi: GeneDB prefixcommons: genedb re3data: r3d100010626 uniprot: GeneDB wikidata: P3382 name: GeneDB pattern: ^[\w\d\.-]*$ preferred_prefix: genedb publications: - doi: 10.1093/nar/gkh007 pmc: PMC308742 pubmed: '14681429' title: 'GeneDB: a resource for prokaryotic and eukaryotic organisms.' year: 2004 uri_format: https://www.genedb.org/gene/$1 genefarm: description: GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products. example: '4892' homepage: http://urgi.versailles.inra.fr/Genefarm/ mappings: biocontext: GENEFARM fairsharing: FAIRsharing.2mayq0 miriam: genefarm n2t: genefarm prefixcommons: genefarm name: GeneFarm pattern: ^\d+$ preferred_prefix: genefarm publications: - doi: 10.1093/nar/gki115 pmc: PMC540069 pubmed: '15608279' title: GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. year: 2005 uri_format: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1 genepio: contact: email: damion_dooley@sfu.ca github: ddooley name: Damion Dooley orcid: 0000-0002-8844-9165 depends_on: - chebi - ncbitaxon - po - ro - uberon description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. download_owl: http://purl.obolibrary.org/obo/genepio.owl example: 0001885 homepage: http://genepio.org/ license: CC BY 3.0 mappings: aberowl: GENEPIO biocontext: GENEPIO fairsharing: FAIRsharing.y1mmbv obofoundry: genepio ols: genepio ontobee: GENEPIO name: Genomic Epidemiology Ontology pattern: ^\d{7}$ preferred_prefix: GENEPIO repository: https://github.com/GenEpiO/genepio uri_format: http://purl.obolibrary.org/obo/GENEPIO_$1 version: '2022-02-06' genetree: description: Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl. example: ENSGT00550000074763 homepage: http://www.ensembl.org/ mappings: biocontext: GENETREE miriam: genetree n2t: genetree prefixcommons: genetree uniprot: GeneTree name: GeneTree pattern: ^ENSGT\d+$ preferred_prefix: genetree publications: - doi: 10.1093/nar/gkj133 pmc: PMC1347495 pubmed: '16381931' title: Ensembl 2006. year: 2006 uri_format: http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1 genewiki: description: The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI. example: '1017' homepage: http://en.wikipedia.org/wiki/Gene_Wiki mappings: biocontext: GENEWIKI fairsharing: FAIRsharing.t3snf miriam: genewiki n2t: genewiki uniprot: GeneWiki name: Gene Wiki pattern: ^\d+$ preferred_prefix: genewiki uri_format: http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1 geno: contact: email: mhb120@gmail.com github: mbrush name: Matthew Brush orcid: 0000-0002-1048-5019 description: "GENO is an OWL model of genotypes, their more fundamental sequence\ \ components, and links to related biological and experimental entities. At present\ \ many parts of the model are exploratory and set to undergo refactoring. In\ \ addition, many classes and properties have GENO URIs but are place holders for\ \ classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI,\ \ etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype\ \ associations. This will support description of asserted and inferred relationships\ \ between a genotypes, phenotypes, and environments, and the evidence/provenance\ \ behind these associations. \n\nDocumentation is under development as well, and\ \ for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" download_json: http://purl.obolibrary.org/obo/geno.json download_obo: https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/develop/geno-full.obo download_owl: http://purl.obolibrary.org/obo/geno.owl example: '0000632' homepage: https://github.com/monarch-initiative/GENO-ontology/ license: CC BY 4.0 mappings: aberowl: GENO biocontext: GENO bioportal: GENO fairsharing: FAIRsharing.kpbna7 obofoundry: geno ols: geno ontobee: GENO name: Genotype Ontology pattern: ^\d{7}$ preferred_prefix: GENO repository: https://github.com/monarch-initiative/GENO-ontology uri_format: http://purl.obolibrary.org/obo/GENO_$1 version: '2022-03-05' genpept: description: The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank. example: CAA71118.1 homepage: https://www.ncbi.nlm.nih.gov/protein mappings: biocontext: GENPEPT miriam: genpept n2t: genpept name: GenPept pattern: ^\w{3}\d{5}(\.\d+)?$ preferred_prefix: genpept uri_format: https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept genprop: description: Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome. example: GenProp0699 homepage: https://www.ebi.ac.uk/interpro/genomeproperties/ mappings: biocontext: GENPROP miriam: genprop n2t: genprop prefixcommons: jcvi.genprop name: Genome Properties pattern: ^GenProp\d+$ preferred_prefix: genprop uri_format: https://www.ebi.ac.uk/interpro/genomeproperties/#$1 geo: banana_peel: _ description: The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval. download_owl: http://aber-owl.net/media/ontologies/GEO/4/geo.owl example: GDS1234 homepage: https://www.ncbi.nlm.nih.gov/geo/ mappings: aberowl: GEO biocontext: GEO cellosaurus: GEO edam: '1147' fairsharing: FAIRsharing.27rndz go: GEO miriam: geo n2t: geo prefixcommons: geo name: NCBI Gene Expression Omnibus pattern: ^G(PL|SM|SE|DS)\d+$ preferred_prefix: geo publications: - doi: 10.1093/nar/30.1.207 pmc: PMC99122 pubmed: '11752295' title: 'Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.' year: 2002 uri_format: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1 geogeo: banana: GEO banana_peel: _ contact: email: hoganwr@gmail.com github: hoganwr name: Bill Hogan orcid: 0000-0002-9881-1017 description: An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in "The US declared war on Germany" vs. the US in "The plane entered US airspace". download_owl: http://purl.obolibrary.org/obo/geo.owl example: '000000021' homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki license: CC BY 4.0 mappings: biocontext: GEO bioportal: GEO miriam: geogeo obofoundry: geo ols: geo ontobee: GEO name: Geographical Entity Ontology namespace_in_lui: true pattern: ^\d{9}$ preferred_prefix: GEOGEO repository: https://github.com/ufbmi/geographical-entity-ontology uri_format: http://purl.obolibrary.org/obo/GEO_$1 version: '2016-03-26' geonames: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge. example: '3532759' homepage: https://www.geonames.org mappings: fairsharing: FAIRsharing.6dba71 re3data: r3d100010245 name: GeoNames pattern: ^\d+$ preferred_prefix: geonames synonyms: - Geomames - Geonamaes uri_format: https://www.geonames.org/$1 geonames.feature: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes. example: ADM1 homepage: https://www.geonames.org/export/codes.html name: GeoNames Feature Code preferred_prefix: geonames.feature uri_format: https://www.geonames.org/recent-changes/featurecode/$1/ gexo: contact: email: vladimir.n.mironov@gmail.com github: null name: Vladimir Mironov orcid: null description: Gene Expression Ontology download_obo: https://www.bio.ntnu.no/ontology/GeXO/gexo.obo download_owl: https://www.bio.ntnu.no/ontology/GeXO/gexo.owl homepage: http://www.semantic-systems-biology.org/apo mappings: aberowl: GEXO bioportal: GEXO fairsharing: FAIRsharing.3e0sn4 ols: gexo name: Gene Expression Ontology no_own_terms: true preferred_prefix: gexo publications: - doi: 10.1186/s12859-014-0386-y pmc: PMC4279962 pubmed: '25490885' title: Finding gene regulatory network candidates using the gene expression knowledge base. year: 2014 version: '2019-09-18' gfo: contact: email: heinrich.herre@imise.uni-leipzig.de github: null name: Heinrich Herre orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The General Formal Ontology is a top-level ontology for conceptual modeling, which is being constantly further developed by Onto-Med. It includes elaborations of categories like objects, processes, time and space, properties, relations, roles, functions, facts, and situations. Moreover, we are working on an integration with the notion of levels of reality in order to more appropriately capture entities in the material, mental, and social areas. download_owl: http://www.onto-med.de/ontologies/gfo.owl example: projects_to homepage: https://www.onto-med.de/ontologies/gfo mappings: aberowl: GFO bioportal: GFO fairsharing: FAIRsharing.175hsz name: General Formal Ontology preferred_prefix: gfo uri_format: http://www.onto-med.de/ontologies/gfo.owl#$1 ghr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA). example: saddan homepage: https://medlineplus.gov/genetics/condition name: Genetics Home Reference preferred_prefix: ghr uri_format: https://medlineplus.gov/genetics/condition/$1 giardiadb: description: GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: GL50803_102438 homepage: https://giardiadb.org/giardiadb/ mappings: biocontext: GIARDIADB fairsharing: FAIRsharing.e7skwg miriam: giardiadb n2t: giardiadb prefixcommons: giardiadb re3data: r3d100012458 name: GiardiaDB pattern: ^\w+$ preferred_prefix: giardiadb publications: - doi: 10.1093/nar/gkn631 pmc: PMC2686445 pubmed: '18824479' title: 'GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.' year: 2008 uri_format: https://giardiadb.org/giardiadb/app/record/gene/$1 github: description: GitHub is an online host of Git source code repositories. example: biopragmatics/bioregistry example_extras: - biopragmatics - cthoyt homepage: https://github.com/ mappings: fairsharing: FAIRsharing.c55d5e miriam: github re3data: r3d100010375 name: github pattern: ^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$ preferred_prefix: github uri_format: https://github.com/$1 github.issue: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An issue in any public repository on GitHub. example: biopragmatics/bioregistry/424 homepage: https://github.com/ name: GitHub Issue preferred_prefix: github.issue uri_format: https://bioregistry.io/resolve/github/issue/$1 github.pull: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A pull request in any public repository on GitHub. example: biopragmatics/bioregistry/416 homepage: https://github.com/ name: GitHub Pull Request preferred_prefix: github.pull uri_format: https://bioregistry.io/resolve/github/pull/$1 gitlab: description: GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance. With GitLab, every team in your organization can collaboratively plan, build, secure, and deploy software to drive business outcomes faster with complete transparency, consistency and traceability. example: morpheus.lab/morpheus homepage: https://gitlab.com/ mappings: fairsharing: FAIRsharing.530e61 miriam: gitlab name: GitLab pattern: ^.*/.*$ preferred_prefix: gitlab uri_format: https://gitlab.com/$1 glida.gpcr: description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors. example: ACM1_HUMAN homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ mappings: biocontext: GLIDA.GPCR miriam: glida.gpcr n2t: glida.gpcr name: GLIDA GPCR pattern: ^[A-Z-_0-9]+$ preferred_prefix: glida.gpcr uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1 glida.ligand: description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands. example: L000001 homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ mappings: biocontext: GLIDA.LIGAND miriam: glida.ligand n2t: glida.ligand name: GLIDA Ligand pattern: ^L\d+$ preferred_prefix: glida.ligand uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1 glycoepitope: description: GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes. example: EP0311 homepage: https://www.glycoepitope.jp/epitopes/ mappings: biocontext: GLYCOEPITOPE miriam: glycoepitope n2t: glycoepitope name: GlycoEpitope pattern: ^EP\d{4}$ preferred_prefix: glycoepitope uri_format: https://www.glycoepitope.jp/epitopes/$1 glycomedb: comment: this is exactly the same as glytoucan. Idk why there are two different ones description: GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links. example: G77500AY has_canonical: glytoucan homepage: https://glytoucan.org/ mappings: biocontext: GLYCOMEDB edam: '2664' fairsharing: FAIRsharing.k5k0yh miriam: glycomedb n2t: glycomedb prefixcommons: glycomedb re3data: r3d100011527 name: GlycomeDB pattern: ^\w+$ preferred_prefix: glycomedb publications: - doi: 10.1093/glycob/cwp137 pmc: null pubmed: '19759275' title: 'Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences.' year: 2009 uri_format: https://glytoucan.org/Structures/Glycans/$1 glyconavi: description: GlycoNAVI is a website for carbohydrate research. It consists of the "GlycoNAVI Database" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the "GlycoNAVI tools" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools. example: GN_G03681DA example_extras: - GN_GlyTouCan_G03681DA homepage: https://www.noguchi.or.jp/ mappings: fairsharing: FAIRsharing.wvp1t7 miriam: glyconavi name: GlycoNAVI pattern: ^GN_[A-Za-z0-9_:]+$ preferred_prefix: glyconavi uri_format: https://glyconavi.org/hub/?id=$1 glycopost: description: GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their "raw/processed" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines. example: GPST000024 homepage: https://glycopost.glycosmos.org mappings: fairsharing: FAIRsharing.2y1KMt miriam: glycopost name: GlycoPOST pattern: ^GPST[0-9]{6}$ preferred_prefix: glycopost uri_format: https://glycopost.glycosmos.org/entry/$1 glycosciencesdb: contact: email: thomas@luetteke-online.de github: glycosciences name: Thomas Lütteke orcid: 0000-0002-7140-9933 contributor: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: A database to support glycobiology and glycomics research. Its main focus is on 3D structures, including 3D structure models as well as references to PDB entries that feature carbohydrates. example: '1' github_request_issue: 537 homepage: http://www.glycosciences.de/database/ name: Glycosciences.DB pattern: ^\d+$ preferred_prefix: glycosciencesdb publications: - doi: 10.1093/nar/gky994 pmc: null pubmed: null title: 'Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update)' year: null reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - glycosciences.db uri_format: http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=$1 glygen: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data. example: G24361QY homepage: https://glygen.org/glycan/ mappings: fairsharing: FAIRsharing.aI1J5W uniprot: GlyGen name: Computational and Informatics Resources for Glycoscience preferred_prefix: glygen uri_format: https://glygen.org/glycan/$1 glytoucan: description: GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data. example: G00054MO homepage: https://glytoucan.org mappings: biocontext: GLYTOUCAN miriam: glytoucan n2t: glytoucan re3data: r3d100012388 name: GlyTouCan pattern: ^G[0-9]{5}[A-Z]{2}$ preferred_prefix: glytoucan uri_format: https://glytoucan.org/Structures/Glycans/$1 gmd: description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena. example: 68513255-fc44-4041-bc4b-4fd2fae7541d homepage: http://gmd.mpimp-golm.mpg.de/ mappings: biocontext: GMD fairsharing: FAIRsharing.jykmkw miriam: gmd n2t: gmd name: Golm Metabolome Database pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ preferred_prefix: gmd uri_format: http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx gmd.analyte: description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes. example: 4f0fa9b6-514f-4ff4-98cc-0009bc08eb80 homepage: http://gmd.mpimp-golm.mpg.de/ mappings: biocontext: GMD.ANALYTE miriam: gmd.analyte n2t: gmd.analyte name: Golm Metabolome Database Analyte pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ preferred_prefix: gmd.analyte uri_format: http://gmd.mpimp-golm.mpg.de/Analytes/$1 gmd.gcms: description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra. example: 53d583d8-40c6-40e1-9296-23f821cd77a5 homepage: http://gmd.mpimp-golm.mpg.de/ mappings: biocontext: GMD.GCMS miriam: gmd.gcms n2t: gmd.gcms name: Golm Metabolome Database GC-MS spectra pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ preferred_prefix: gmd.gcms uri_format: http://gmd.mpimp-golm.mpg.de/Spectrums/$1 gmd.profile: description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues. example: 10b38aaf-b977-4950-85b8-f4775f66658d homepage: http://gmd.mpimp-golm.mpg.de/ mappings: biocontext: GMD.PROFILE miriam: gmd.profile n2t: gmd.profile name: Golm Metabolome Database Profile pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ preferred_prefix: gmd.profile uri_format: http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1 gmd.ref: description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances. example: 8cf84adb-b4db-4807-ac98-0004247c35df homepage: http://gmd.mpimp-golm.mpg.de/ mappings: biocontext: GMD.REF miriam: gmd.ref n2t: gmd.ref name: Golm Metabolome Database Reference Substance pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ preferred_prefix: gmd.ref uri_format: http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1 gmelin: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s. example: '1466' homepage: https://link.springer.com/bookseries/562 mappings: edam: '1004' wikidata: P1578 name: Gmelins Handbuch der anorganischen Chemie pattern: ^[1-9][0-9]{3,6}$ preferred_prefix: gmelin proprietary: true references: - https://en.wikipedia.org/wiki/Gmelin_database gno: contact: email: nje5@georgetown.edu github: edwardsnj name: Nathan Edwards orcid: 0000-0001-5168-3196 description: An ontology for glycans based on GlyTouCan, but organized by subsumption. download_json: http://purl.obolibrary.org/obo/gno.json download_obo: http://purl.obolibrary.org/obo/gno.obo download_owl: http://purl.obolibrary.org/obo/gno.owl example: '10004892' example_extras: - G99373GG homepage: https://gnome.glyomics.org/ license: CC BY 4.0 mappings: aberowl: GNO bioportal: GNO obofoundry: gno ols: gno ontobee: GNO name: Glycan Naming and Subsumption Ontology pattern: ^(\d{8}|(\w+\d+\w+))$ preferred_prefix: GNO providers: - code: gno.composition description: GNOme composition browser homepage: https://gnome.glyomics.org/CompositionBrowser.html name: GNOme Composition Browser uri_format: https://gnome.glyomics.org/CompositionBrowser.html?focus=$1 - code: gno.structure description: GNOme structure browser homepage: https://gnome.glyomics.org/StructureBrowser.html name: GNOme Structure Viewer uri_format: https://gnome.glyomics.org/StructureBrowser.html?focus=$1 publications: - doi: 10.5281/zenodo.6678278 pmc: null pubmed: null title: GNOme - Glycan Naming and Subsumption Ontology year: null repository: https://github.com/glygen-glycan-data/GNOme synonyms: - gnome uri_format: http://purl.obolibrary.org/obo/GNO_$1 version: 1.10.0 gnpis: description: GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. example: AY109603 homepage: https://urgi.versailles.inra.fr/gnpis/ mappings: biocontext: GNPIS fairsharing: FAIRsharing.dw22y3 miriam: gnpis n2t: gnpis re3data: r3d100012647 name: GnpIS pattern: ^[A-Za-z0-9]+$ preferred_prefix: gnpis uri_format: https://urgi.versailles.inra.fr/gnpis/#result/term=$1 go: appears_in: - agro - chiro - cl - ecocore - ecto - envo - maxo - pcl - pco - planp - uberon - xpo - zp banana: GO contact: email: suzia@stanford.edu github: suzialeksander name: Suzi Aleksander orcid: 0000-0001-6787-2901 depends_on: - cl - ncbitaxon - ro - uberon description: The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. download_json: http://purl.obolibrary.org/obo/go.json download_obo: http://purl.obolibrary.org/obo/go.obo download_owl: http://purl.obolibrary.org/obo/go.owl example: '0032571' homepage: http://geneontology.org/ license: CC BY 4.0 mappings: aberowl: GO agroportal: GO biocontext: GO bioportal: GO edam: '1176' fairsharing: FAIRsharing.6xq0ee go: GO hl7: 2.16.840.1.113883.6.128 miriam: go n2t: go ncbi: GO obofoundry: go ols: go ontobee: GO prefixcommons: go uniprot: GO wikidata: P686 name: Gene Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: GO providers: - code: CURATOR_REVIEW description: GO Browser homepage: http://www.informatics.jax.org/searches/GO_form.shtml name: GO Browser uri_format: http://www.informatics.jax.org/searches/GO.cgi?id=GO:$1 - code: CURATOR_REVIEW description: GO through PANTHER homepage: http://www.pantherdb.org/ name: GO through PANTHER uri_format: http://www.pantherdb.org/panther/category.do?categoryAcc=GO:$1 - code: jax description: The JAX endpoint for exploring GO homepage: http://www.informatics.jax.org name: Jackson Laboratories uri_format: http://www.informatics.jax.org/vocab/gene_ontology/GO:$1 - code: quickgo description: QuickGO (Gene Ontology browser) homepage: https://www.ebi.ac.uk/QuickGO/ name: QuickGO (Gene Ontology browser) uri_format: https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:$1 publications: - doi: 10.1093/nar/gkaa1113 pmc: PMC7779012 pubmed: '33290552' title: 'The Gene Ontology resource: enriching a GOld mine.' year: 2021 - doi: 10.1093/nar/gky1055 pmc: PMC6323945 pubmed: '30395331' title: 'The Gene Ontology Resource: 20 years and still GOing strong.' year: 2019 - doi: 10.1093/nar/gku1179 pmc: PMC4383973 pubmed: '25428369' title: 'Gene Ontology Consortium: going forward.' year: 2014 - doi: 10.1186/1471-2164-14-513 pmc: PMC3733925 pubmed: '23895341' title: 'Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.' year: 2013 - doi: 10.1093/nar/gks1050 pmc: PMC3531070 pubmed: '23161678' title: Gene Ontology annotations and resources. year: 2012 - doi: 10.1093/nar/gkr1028 pmc: PMC3245151 pubmed: '22102568' title: 'The Gene Ontology: enhancements for 2011.' year: 2011 - doi: 10.1093/nar/gkp1018 pmc: PMC2808930 pubmed: '19920128' title: 'The Gene Ontology in 2010: extensions and refinements.' year: 2009 - doi: 10.1093/nar/gkh036 pmc: PMC308770 pubmed: '14681407' title: The Gene Ontology (GO) database and informatics resource. year: 2004 - doi: 10.1038/75556 pmc: PMC3037419 pubmed: '10802651' title: 'Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.' year: 2000 repository: https://github.com/geneontology/go-ontology synonyms: - gobp - gobpid - gocc - goccid - gomf - gomfid twitter: news4go uri_format: http://amigo.geneontology.org/amigo/term/GO:$1 version: '2022-07-01' go.model: description: GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform. example: 5fce9b7300001250 homepage: http://www.geneontology.org/gocam mappings: go: gomodel name: Gene Ontology Causal Assembly Model preferred_prefix: go.model uri_format: http://noctua.geneontology.org/editor/graph/gomodel:$1 go.ref: banana: GO_REF description: The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of "GO content" meetings at which substantial changes in the ontologies are discussed and made. example: '0000041' homepage: http://www.geneontology.org/cgi-bin/references.cgi mappings: biocontext: GO_REF go: GO_REF miriam: go_ref n2t: go.ref name: Gene Ontology Database references namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: go.ref uri_format: https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-$1.md go.resource: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A database-specific registry supporting curation in the Gene Ontology example: CHEBI homepage: http://geneontology.org/ name: Gene Ontology Registry preferred_prefix: go.resource uri_format: https://bioregistry.io/metaregistry/go/$1 goa: description: The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. example: P12345 homepage: https://www.ebi.ac.uk/GOA/ mappings: biocontext: GOA fairsharing: FAIRsharing.7zffgc miriam: goa n2t: goa ncbi: GOA prefixcommons: goa name: Gene Ontology Annotation Database pattern: ^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$ preferred_prefix: goa provides: uniprot publications: - doi: 10.1093/nar/gkn803 pmc: PMC2686469 pubmed: '18957448' title: The GOA database in 2009--an integrated Gene Ontology Annotation resource. year: 2008 uri_format: https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1 goche: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Represent chemical entities having particular CHEBI roles download_owl: https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl example: '25512' homepage: https://github.com/geneontology/go-ontology name: GO Chemicals pattern: ^\d+$ preferred_prefix: GOCHE references: - https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638472847049400 - https://github.com/geneontology/go-ontology/issues/19535 repository: https://github.com/geneontology/go-ontology synonyms: - go.chebi - go.chemical - go.chemicals uri_format: https://biopragmatics.github.io/providers/goche/$1 goeco: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported. example: IPI homepage: http://geneontology.org/docs/guide-go-evidence-codes/ name: GO Evidence Code preferred_prefix: goeco gold: description: 'The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.' example: Gs0000008 homepage: https://gold.jgi.doe.gov/ mappings: fairsharing: FAIRsharing.5q1p14 miriam: gold prefixcommons: gold name: Genomes Online Database pattern: ^[A-Z][a-z][0-9]+$ preferred_prefix: gold uri_format: https://gold.jgi.doe.gov/resolver?id=$1 gold.genome: description: '- DEPRECATION NOTE - Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. The GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes.' example: Gi07796 homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi mappings: biocontext: GOLD.GENOME miriam: gold.genome n2t: gold.genome name: GOLD genome pattern: ^(Gi|Gc)\d+$ 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. Terminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC''s Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry.' example: G02681 homepage: https://goldbook.iupac.org license: CC BY 4.0-NC-ND name: IUPAC Gold Book Compendium of Chemical Terminology preferred_prefix: goldbook uri_format: https://goldbook.iupac.org/terms/view/$1 google.book: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Search the world's most comprehensive index of full-text books. example: qafeQTWIWmcC github_request_issue: 511 homepage: https://books.google.com mappings: wikidata: P675 name: Google Books preferred_prefix: google.book uri_format: https://books.google.com/books?id=$1 google.patent: contributor_extras: - email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date. example: US4145692 example_extras: - USRE38117E1 homepage: https://www.google.com/patents/ mappings: biocontext: GOOGLE.PATENT cellosaurus: Patent miriam: google.patent n2t: google.patent name: Google Patents pattern: ^[A-Z]{2,4}\d+([A-Z])?([0-9])?$ preferred_prefix: google.patent synonyms: - patent uri_format: https://www.google.com/patents/$1 google.scholar: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.' example: PjrpzUIAAAAJ homepage: https://scholar.google.com/ mappings: biolink: GSID name: Google Scholar Researcher preferred_prefix: google.scholar gorel: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO. download_owl: ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl example: '0002005' homepage: http://geneontology.org/docs/ontology-relations/ mappings: biolink: GOREL go: GOREL name: GO Relations pattern: ^\d{7}$ preferred_prefix: gorel providers: - code: obo.legacy description: Legacy OBO PURLs homepage: http://purl.obolibrary.org/obo/gorel.owl name: Legacy OBO uri_format: http://purl.obolibrary.org/obo/GOREL_$1 gpcrdb: description: The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models. example: RL3R1_HUMAN homepage: http://www.gpcrdb.org/ mappings: biocontext: GPCRDB fairsharing: FAIRsharing.e4n3an miriam: gpcrdb n2t: gpcrdb prefixcommons: gpcrdb uniprot: GPCRDB name: G protein-coupled receptor database pattern: ^\w+$ preferred_prefix: gpcrdb publications: - doi: 10.1093/nar/gkq1009 pmc: PMC3013641 pubmed: '21045054' title: 'GPCRDB: information system for G protein-coupled receptors.' year: 2010 uri_format: https://gpcrdb.org/protein/$1 gpmdb: description: The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. example: GPM32310002988 homepage: http://gpmdb.thegpm.org/ mappings: biocontext: GPMDB fairsharing: FAIRsharing.fhcmwq miriam: gpmdb n2t: gpmdb name: Global Proteome Machine Database pattern: ^GPM\d+$ preferred_prefix: gpmdb providers: - code: omicsdi description: GPMDB through OmicsDI homepage: https://www.omicsdi.org/ name: GPMDB through OmicsDI uri_format: https://www.omicsdi.org/dataset/gpmdb/$1 uri_format: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1 graingenes.reference: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A database for Triticeae and Avena references. example: WGS-95-1333 homepage: http://wheat.pw.usda.gov name: GrainGenes preferred_prefix: graingenes.reference uri_format: https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1 graingenes.symbol: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A database for Triticeae and Avena gene symbols. example: 1-FEH+w3 homepage: http://wheat.pw.usda.gov name: GrainGenes preferred_prefix: graingenes.symbol uri_format: http://wheat.pw.usda.gov/report?class=gene;name=$1 gramene.gene: description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene. example: GR:0080039 homepage: http://www.gramene.org/ mappings: biocontext: GRAMENE.GENE go: GR_GENE miriam: gramene.gene n2t: gramene.gene name: Gramene Gene pattern: ^GR\:\d+$ preferred_prefix: gramene.gene synonyms: - GR_GENE uri_format: http://www.gramene.org/db/genes/search_gene?acc=$1 gramene.growthstage: banana: GRO description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene. example: '0007133' homepage: http://www.gramene.org/ mappings: biocontext: GRAMENE.GROWTHSTAGE miriam: gramene.growthstage n2t: gramene.growthstage name: Gramene Growth Stage Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: gramene.growthstage uri_format: http://www.gramene.org/db/ontology/search?id=GRO:$1 gramene.protein: description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene. example: '78073' homepage: http://www.gramene.org/ mappings: biocontext: GRAMENE.PROTEIN go: GR_PROTEIN miriam: gramene.protein n2t: gramene.protein name: Gramene protein pattern: ^\d+$ preferred_prefix: gramene.protein synonyms: - GR_PROTEIN uri_format: http://www.gramene.org/db/protein/protein_search?protein_id=$1 gramene.qtl: description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene. example: CQG5 homepage: http://www.gramene.org/ mappings: biocontext: GRAMENE.QTL go: GR_QTL miriam: gramene.qtl n2t: gramene.qtl name: Gramene QTL pattern: ^\w+$ preferred_prefix: gramene.qtl synonyms: - GR_QTL uri_format: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1 gramene.reference: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Literature references in Gramene example: '6200' homepage: http://www.gramene.org name: Gramene Reference pattern: ^\d+$ preferred_prefix: gramene.reference synonyms: - gramene.ref uri_format: http://www.gramene.org/db/literature/pub_search?ref_id=$1 gramene.taxonomy: description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene. example: GR_tax:013681 homepage: http://www.gramene.org/ mappings: biocontext: GRAMENE.TAXONOMY miriam: gramene.taxonomy n2t: gramene.taxonomy name: Gramene Taxonomy pattern: ^GR\_tax\:\d+$ preferred_prefix: gramene.taxonomy uri_format: http://www.gramene.org/db/ontology/search?id=$1 grassbase: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species. example: imp10873 github_request_issue: 218 homepage: https://www.kew.org/data/grasses-syn/index.htm mappings: wikidata: P1832 name: GrassBase pattern: ^(imp|gen)\d{5}$ preferred_prefix: grassbase uri_format: https://www.kew.org/data/grasses-db/www/$1 greengenes: description: A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. example: '100000' homepage: http://greengenes.lbl.gov/ mappings: biocontext: GREENGENES fairsharing: FAIRsharing.bpxgb6 miriam: greengenes n2t: greengenes ncbi: Greengenes prefixcommons: greengenes re3data: r3d100010549 name: 16S rRNA gene database pattern: ^\d+$ preferred_prefix: greengenes publications: - doi: 10.1128/aem.03006-05 pmc: PMC1489311 pubmed: '16820507' title: Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. year: 2006 uri_format: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1 grid: description: International coverage of the world's leading research organisations, indexing 92% of funding allocated globally. example: grid.225360.0 homepage: https://www.grid.ac/ mappings: biocontext: GRID fairsharing: FAIRsharing.0pUMYW miriam: grid n2t: grid name: Global Research Identifier Database pattern: ^grid\.[0-9]+\.[a-f0-9]{1,2}$ preferred_prefix: grid uri_format: https://www.grid.ac/institutes/$1 grin.taxonomy: description: GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact. example: '19333' homepage: http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en mappings: biocontext: GRIN.TAXONOMY go: GRIN miriam: grin.taxonomy n2t: grin.taxonomy ncbi: GRIN name: Germplasm Resources Information Network pattern: ^\d+$ preferred_prefix: grin.taxonomy uri_format: http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1 gro: contact: email: vlee@ebi.ac.uk github: null name: Vivian Lee orcid: null deprecated: true description: The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. download_owl: http://aber-owl.net/media/ontologies/GRO/5/gro.owl example: Lipid homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html mappings: aberowl: GRO bioportal: GRO name: Gene Regulation Ontology preferred_prefix: gro uri_format: http://www.bootstrep.eu/ontology/GRO#$1 grsdb: description: GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank. example: '10142' homepage: http://bioinformatics.ramapo.edu/GRSDB2/ mappings: biocontext: GRSDB miriam: grsdb n2t: grsdb prefixcommons: grsdb name: G-Rich Sequences Database pattern: ^\d+$ preferred_prefix: grsdb uri_format: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1 gsfa: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The "Codex General Standard for Food Additives" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database. example: '174' homepage: http://www.fao.org/gsfaonline name: General Standard for Food Additives Online Database pattern: ^\d+$ preferred_prefix: gsfa synonyms: - FAO/WHO_standards uri_format: http://www.fao.org/gsfaonline/additives/details.html?id=$1 gsso: appears_in: - ontoavida - scdo banana: GSSO contact: email: kronkcj@mail.uc.edu github: Superraptor name: Clair Kronk orcid: 0000-0001-8397-8810 description: The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology. download_json: http://purl.obolibrary.org/obo/gsso.json download_obo: http://purl.obolibrary.org/obo/gsso.obo download_owl: http://purl.obolibrary.org/obo/gsso.owl example: 002368 homepage: https://gsso.research.cchmc.org/ license: Apache 2.0 License mappings: aberowl: GSSO bioportal: GSSO miriam: gsso obofoundry: gsso ols: gsso ontobee: GSSO name: Gender, Sex, and Sexual Orientation Ontology namespace_in_lui: true pattern: ^\d{6}$ preferred_prefix: GSSO repository: https://github.com/Superraptor/GSSO uri_format: http://purl.obolibrary.org/obo/GSSO_$1 version: 2.0.5 gtex: description: The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. example: BRIP1 homepage: https://www.gtexportal.org mappings: biocontext: GTEX biolink: GTEx miriam: gtex n2t: gtex name: Genotype-Tissue Expression pattern: ^\w.+$ preferred_prefix: gtex uri_format: https://www.gtexportal.org/home/gene/$1 gtr: appears_in: - mondo comment: Identifiers appearing in MONDO don't match any of the resources apparent endpoints contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease example: AN0097748 homepage: https://www.ncbi.nlm.nih.gov/gtr/ name: Genetic Testing Registry preferred_prefix: gtr synonyms: - medgen.gtr uri_format: https://www.ncbi.nlm.nih.gov/gtr/conditions/$1 gudmap: description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract. example: Q-2958 homepage: http://www.gudmap.org/ mappings: biocontext: GUDMAP fairsharing: FAIRsharing.910c39 miriam: gudmap n2t: gudmap re3data: r3d100012193 name: Genitourinary Development Molecular Anatomy Project pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$ preferred_prefix: gudmap uri_format: https://gudmap.org/id/$1 gwascentral.marker: description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker. example: HGVM15354 homepage: https://www.gwascentral.org/markers mappings: biocontext: GWASCENTRAL.MARKER miriam: gwascentral.marker n2t: gwascentral.marker name: GWAS Central Marker pattern: ^HGVM\d+$ preferred_prefix: gwascentral.marker uri_format: https://www.gwascentral.org/marker/$1 gwascentral.phenotype: description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype. example: HGVPM623 homepage: https://www.gwascentral.org/phenotypes mappings: biocontext: GWASCENTRAL.PHENOTYPE miriam: gwascentral.phenotype n2t: gwascentral.phenotype name: GWAS Central Phenotype pattern: ^HGVPM\d+$ preferred_prefix: gwascentral.phenotype uri_format: https://www.gwascentral.org/phenotype/$1 gwascentral.study: description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study. example: HGVST1828 homepage: https://www.gwascentral.org/studies mappings: biocontext: GWASCENTRAL.STUDY miriam: gwascentral.study n2t: gwascentral.study name: GWAS Central Study pattern: ^HGVST\d+$ preferred_prefix: gwascentral.study uri_format: https://www.gwascentral.org/study/$1 gxa.expt: description: The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments. example: E-MTAB-2037 homepage: https://www.ebi.ac.uk/gxa/ mappings: biocontext: GXA.EXPT miriam: gxa.expt n2t: gxa.expt name: GXA Expt pattern: ^[AEP]-\w{4}-\d+$ preferred_prefix: gxa.expt providers: - code: omicsdi description: GXA Expt through OmicsDI homepage: https://www.omicsdi.org/ name: GXA Expt through OmicsDI uri_format: https://www.omicsdi.org/dataset/atlas-experiments/$1 uri_format: https://www.ebi.ac.uk/gxa/experiments/$1 gxa.gene: description: The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes. example: AT4G01080 homepage: https://www.ebi.ac.uk/gxa/ mappings: biocontext: GXA.GENE miriam: gxa.gene n2t: gxa.gene name: GXA Gene pattern: ^\w+$ preferred_prefix: gxa.gene uri_format: https://www.ebi.ac.uk/gxa/genes/$1 habronattus: contact: email: peteremidford@yahoo.com github: null name: Peter Midford orcid: 0000-0001-6512-3296 deprecated: true homepage: http://www.mesquiteproject.org/ontology/Habronattus/index.html mappings: biocontext: HABRONATTUS obofoundry: habronattus name: Habronattus courtship preferred_prefix: HABRONATTUS uri_format: http://purl.obolibrary.org/obo/HABRONATTUS_$1 hamap: description: HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries. example: MF_01400 homepage: https://hamap.expasy.org/ mappings: biocontext: HAMAP edam: '2766' fairsharing: FAIRsharing.63m4ss go: HAMAP miriam: hamap n2t: hamap prefixcommons: hamap uniprot: HAMAP name: High-quality Automated and Manual Annotation of microbial Proteomes pattern: ^MF_\d+$ preferred_prefix: hamap uri_format: https://hamap.expasy.org/unirule/$1 hancestro: contact: email: danielle.welter@uni.lu github: daniwelter name: Danielle Welter orcid: 0000-0003-1058-2668 description: Human ancestry ontology for the NHGRI GWAS Catalog download_owl: http://purl.obolibrary.org/obo/hancestro.owl example: 0290 homepage: https://github.com/EBISPOT/ancestro license: CC BY 4.0 mappings: aberowl: HANCESTRO biolink: HANCESTRO bioportal: HANCESTRO fairsharing: FAIRsharing.rja8qp obofoundry: hancestro ols: hancestro ontobee: HANCESTRO name: Human Ancestry Ontology pattern: ^\d{4}$ preferred_prefix: HANCESTRO publications: - doi: 10.1186/s13059-018-1396-2 pmc: PMC5815218 pubmed: '29448949' title: A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog. year: 2018 repository: https://github.com/EBISPOT/ancestro uri_format: http://purl.obolibrary.org/obo/HANCESTRO_$1 version: '2.6' hao: contact: email: diapriid@gmail.com github: mjy name: Matt Yoder orcid: 0000-0002-5640-5491 description: A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) download_obo: http://purl.obolibrary.org/obo/hao.obo download_owl: http://purl.obolibrary.org/obo/hao.owl example: 0000187 homepage: http://hymao.org license: CC0 1.0 mappings: aberowl: HAO biocontext: HAO bioportal: HAO fairsharing: FAIRsharing.kj3m5n obofoundry: hao ols: hao ontobee: HAO name: Hymenoptera Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: HAO publications: - doi: 10.1371/journal.pone.0015991 pmc: PMC3012123 pubmed: '21209921' title: A gross anatomy ontology for hymenoptera. year: 2010 repository: https://github.com/hymao/hao uri_format: http://purl.obolibrary.org/obo/HAO_$1 version: '2021-03-05' hathitrust: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world. example: 008893080 github_request_issue: 510 homepage: https://www.hathitrust.org name: Hathi Trust Digital Library pattern: ^\d+$ preferred_prefix: hathitrust uri_format: https://catalog.hathitrust.org/Record/$1 hba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A controlled vocabulary to support the study of transcription in the human brain download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-hba.obo example: '4005' example_extras: - '265504410' homepage: https://human.brain-map.org name: Human Brain Atlas pattern: ^\d+$ preferred_prefix: HBA uri_format: https://biopragmatics.github.io/providers/hba/$1 hc.din: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A Drug Identification Number (DIN) is a computer-generated eight digit number assigned by Health Canada to a drug product prior to being marketed in Canada. It uniquely identifies all drug products sold in a dosage form in Canada and is located on the label of prescription and over-the-counter drug products that have been evaluated and authorized for sale in Canada. example: 02069237 homepage: https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/fact-sheets/drug-identification-number.html mappings: hl7: 2.16.840.1.113883.5.1105 name: Health Canada Drug Identification Number pattern: ^\d{8}$ preferred_prefix: hc.din references: - http://www.hc-sc.gc.ca/dhp-mps/prodpharma/databasdon/index-eng.php hc.npn: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Licensed Natural Health Products Database contains information about natural health products that have been issued a product licence by Health Canada. example: '18125' homepage: http://webprod.hc-sc.gc.ca/nhpid-bdipsn/search-rechercheReq.do?lang=eng mappings: hl7: 2.16.840.1.113883.5.1107 name: Health Canada Natural Product Number pattern: ^\d+$ preferred_prefix: hc.npn references: - https://www.canada.ca/en/health-canada/services/drugs-health-products/natural-non-prescription/applications-submissions/product-licensing/licensed-natural-health-products-database.html uri_format: http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id=$1 hcao: description: Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas. download_owl: http://ontology.data.humancellatlas.org/ontologies/hcao/releases/2022-06-22/hcao.owl homepage: https://www.humancellatlas.org mappings: ols: hcao name: Human Cell Atlas Ontology no_own_terms: true preferred_prefix: hcao version: '2022-06-22' hcpcs: contact: email: Cynthia.Hake@cms.hhs.gov github: null name: Cynthia Hake orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers. example: G8944 homepage: https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo mappings: aberowl: HCPCS biolink: HCPCS bioportal: HCPCS fairsharing: FAIRsharing.x81wz8 name: Healthcare Common Procedure Coding System preferred_prefix: hcpcs uri_format: http://purl.bioontology.org/ontology/HCPCS/$1 hcvdb: description: the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses. example: M58335 homepage: http://euhcvdb.ibcp.fr mappings: biocontext: HCVDB miriam: hcvdb n2t: hcvdb prefixcommons: euhcvdb name: Hepatitis C Virus Database pattern: ^M\d{5}$ preferred_prefix: hcvdb publications: - doi: 10.1093/nar/gkl970 pmc: PMC1669729 pubmed: '17142229' title: 'euHCVdb: the European hepatitis C virus database.' year: 2006 uri_format: https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1 hdr: description: The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders. example: '63' homepage: http://research.nhgri.nih.gov/apps/homeodomain/web/ mappings: biocontext: HDR miriam: hdr n2t: hdr prefixcommons: hdr name: Homeodomain Research pattern: ^\d+$ preferred_prefix: hdr uri_format: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1 hgmd: description: The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases. example: CALM1 homepage: http://www.hgmd.cf.ac.uk/ac/index.php mappings: biocontext: HGMD edam: '3265' miriam: hgmd n2t: hgmd name: Human Gene Mutation Database pattern: ^[A-Z_0-9]+$ preferred_prefix: hgmd uri_format: http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1 hgnc: contact: email: hgnc@genenames.org github: null name: Dr. Elspeth Bruford orcid: null description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database. download_owl: http://aber-owl.net/media/ontologies/HGNC/1/hgnc.owl example: '16793' homepage: http://www.genenames.org mappings: aberowl: HGNC biocontext: HGNC bioportal: HGNC cellosaurus: HGNC edam: '2298' fairsharing: FAIRsharing.amcv1e go: HGNC hl7: 2.16.840.1.113883.6.281 miriam: hgnc n2t: hgnc ncbi: HGNC prefixcommons: hgnc uniprot: HGNC wikidata: P354 name: HUGO Gene Nomenclature Committee pattern: ^\d{1,5}$ preferred_prefix: hgnc providers: - code: gencc description: The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases. Curated gene-disease relationships are submitted by GenCC member organizations. The GenCC comprises organizations that currently provide online resources (e.g. ClinGen, DECIPHER, Genomics England PanelApp, OMIM, Orphanet, PanelApp Australia, TGMI’s G2P), as well as diagnostic laboratories that have committed to sharing their internal curated gene-level knowledge (e.g. Ambry, Illumina, Invitae, Myriad Women’s Health, Mass General Brigham Laboratory for Molecular Medicine). homepage: https://thegencc.org name: The Gene Curation Coalition uri_format: https://search.thegencc.org/genes/HGNC:$1 - code: indra description: A large scale database of biomedical statements. homepage: https://db.indra.bio name: INDRA Database uri_format: https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@HGNC publications: - doi: 10.1093/nar/gky930 pmc: PMC6324057 pubmed: '30304474' title: 'Genenames.org: the HGNC and VGNC resources in 2019.' year: 2019 - doi: 10.1159/000131404 pmc: null pubmed: '295268' title: International system for human gene nomenclature (1979) ISGN (1979). year: 1979 uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1 hgnc.genefamily: description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families. example: '2029' has_canonical: hgnc.genegroup homepage: http://www.genenames.org mappings: biocontext: HGNC.GENEFAMILY miriam: hgnc.genefamily n2t: hgnc.genefamily name: HGNC gene family pattern: ^\d+$ preferred_prefix: hgnc.genefamily synonyms: - GFAM - HGNC_GROUP - hgnc.family uri_format: https://www.genenames.org/cgi-bin/genefamilies/set/$1 hgnc.genegroup: description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families. example: '141' homepage: https://www.genenames.org mappings: miriam: hgnc.genegroup name: HGNC Gene Group pattern: ^\d+$ preferred_prefix: hgnc.genegroup uri_format: https://www.genenames.org/cgi-bin/genefamilies/set/$1 hgnc.symbol: description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol. example: DAPK1 homepage: https://www.genenames.org/ mappings: biocontext: HGNC.SYMBOL miriam: hgnc.symbol n2t: hgnc.symbol name: HGNC Symbol pattern: ^[A-Za-z-0-9_]+(\@)?$ preferred_prefix: hgnc.symbol providers: - code: depmap description: DepMap summary of the given gene homepage: https://depmap.org name: DepMap Gene Summary uri_format: https://depmap.org/portal/gene/$1 - code: oncomx description: Mutation profiles for a gene homepage: https://oncomx.org name: OncoMX uri_format: https://oncomx.org/searchview/?gene=$1 - code: pathwaycommons description: Interactions between a given gene and other molecular entities homepage: https://www.pathwaycommons.org/ name: Pathway Commons Gene Interations uri_format: https://apps.pathwaycommons.org/interactions?source=$1 uri_format: https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1 hinv.locus: description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view. example: HIX0004394 homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp mappings: biocontext: HINV.LOCUS miriam: hinv.locus n2t: hinv.locus name: H-InvDb Locus pattern: ^HIX\d{7}(\.\d+)?$ preferred_prefix: hinv.locus uri_format: http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1 hinv.protein: description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view. example: HIP000030660 homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp mappings: biocontext: HINV.PROTEIN miriam: hinv.protein n2t: hinv.protein name: H-InvDb Protein pattern: ^HIP\d{9}(\.\d+)?$ preferred_prefix: hinv.protein uri_format: http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1 hinv.transcript: description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view. example: HIT000195363 homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp mappings: biocontext: HINV.TRANSCRIPT miriam: hinv.transcript n2t: hinv.transcript name: H-InvDb Transcript pattern: ^HIT\d{9}(\.\d+)?$ preferred_prefix: hinv.transcript uri_format: http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1 hipsci: description: Cell line databases/resources example: HPSI0114i-bezi_1 homepage: http://www.hipsci.org mappings: cellosaurus: HipSci name: Human Induced Pluripotent Stem Cells Initiative preferred_prefix: hipsci uri_format: http://www.hipsci.org/lines/#/lines/$1 hivreagentprogram: description: Cell line collections example: ARP-1513 homepage: https://www.hivreagentprogram.org/ mappings: cellosaurus: HIVReagentProgram name: NIH HIV Reagent Program preferred_prefix: hivreagentprogram uri_format: https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx hl7.v2codesystem: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR. example: 0778 homepage: https://terminology.hl7.org/codesystems-v2.html name: HL7 V2 Code Systems pattern: ^\d+$ preferred_prefix: hl7.v2codesystem uri_format: http://terminology.hl7.org/CodeSystem/v2-$1 hl7.v3codesystem: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR. example: AcknowledgementCondition homepage: https://terminology.hl7.org/codesystems-v2.html name: HL7 V2 Code Systems pattern: ^\w+$ preferred_prefix: hl7.v3codesystem uri_format: https://terminology.hl7.org/CodeSystem-v3-$1 hmdb: description: The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data. example: HMDB00001 homepage: http://www.hmdb.ca/ mappings: biocontext: HMDB cheminf: 000408 edam: '2622' fairsharing: FAIRsharing.sye5js miriam: hmdb n2t: hmdb prefixcommons: hmdb wikidata: P2057 name: Human Metabolome Database pattern: ^HMDB\d+$ preferred_prefix: hmdb publications: - doi: 10.1093/nar/gkl923 pmc: PMC1899095 pubmed: '17202168' title: 'HMDB: the Human Metabolome Database.' year: 2007 synonyms: - HMDB uri_format: http://www.hmdb.ca/metabolites/$1 hms.lincs.compound: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols. example: 10001-101 homepage: https://lincs.hms.harvard.edu/db/sm/ name: HMS LINCS Compound preferred_prefix: hms.lincs.compound synonyms: - HMS-LINCS - hmsl_id uri_format: https://lincs.hms.harvard.edu/db/sm/$1 hog: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc. download_obo: ftp://ftp.bgee.org/general/ontologies/HOG.obo example: '0000255' homepage: https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships name: Homologous Organ Groups pattern: ^\d{7}$ preferred_prefix: hog uri_format: https://biopragmatics.github.io/providers/hog/$1 hogenom: description: HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier. example: HBG284870 homepage: http://pbil.univ-lyon1.fr/databases/hogenom/ mappings: biocontext: HOGENOM fairsharing: FAIRsharing.qe8tz8 miriam: hogenom n2t: hogenom prefixcommons: hogenom uniprot: HOGENOM name: Database of Complete Genome Homologous Genes Families pattern: ^\w+$ preferred_prefix: hogenom publications: - doi: 10.1186/1471-2105-10-s6-s3 pmc: PMC2697650 pubmed: '19534752' title: Databases of homologous gene families for comparative genomics. year: 2009 uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1 hom: contact: email: bgee@sib.swiss github: fbastian name: Frederic Bastian orcid: 0000-0002-9415-5104 description: This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. download_owl: http://purl.obolibrary.org/obo/hom.owl example: 0000049 homepage: https://github.com/BgeeDB/homology-ontology license: CC0 1.0 mappings: aberowl: HOM biocontext: HOM bioportal: HOM fairsharing: FAIRsharing.efv7gw obofoundry: hom ols: hom ontobee: HOM name: Homology Ontology pattern: ^\d{7}$ preferred_prefix: HOM publications: - doi: 10.1016/j.tig.2009.12.012 pmc: null pubmed: '20116127' title: An ontology to clarify homology-related concepts. year: 2010 repository: https://github.com/BgeeDB/homology-ontology uri_format: http://purl.obolibrary.org/obo/HOM_$1 version: '2015-01-07' homd.seq: description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information. example: SEQF1003 homepage: http://www.homd.org/index.php mappings: biocontext: HOMD.SEQ miriam: homd.seq n2t: homd.seq prefixcommons: homd.seq name: HOMD Sequence Metainformation pattern: ^SEQF\d+$ preferred_prefix: homd.seq publications: - doi: 10.1093/database/baq013 pmc: PMC2911848 pubmed: '20624719' title: 'The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.' year: 2010 uri_format: http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1 homd.taxon: description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information. example: '811' homepage: http://www.homd.org/index.php mappings: biocontext: HOMD.TAXON miriam: homd.taxon n2t: homd.taxon prefixcommons: homd.taxon name: HOMD Taxonomy pattern: ^\d+$ preferred_prefix: homd.taxon publications: - doi: 10.1093/database/baq013 pmc: PMC2911848 pubmed: '20624719' title: 'The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.' year: 2010 uri_format: http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1 homologene: description: HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. example: '1000' homepage: https://www.ncbi.nlm.nih.gov/homologene/ mappings: biocontext: HOMOLOGENE fairsharing: FAIRsharing.mzc066 miriam: homologene n2t: homologene prefixcommons: homologene wikidata: P593 name: HomoloGene pattern: ^\d+$ preferred_prefix: homologene providers: - code: CURATOR_REVIEW description: Bio2RDF homepage: http://homologene.bio2rdf.org/fct name: Bio2RDF uri_format: http://homologene.bio2rdf.org/describe/?url=http://bio2rdf.org/homologene:$1 publications: - doi: 10.1093/nar/gkq1172 pmc: PMC3013733 pubmed: '21097890' title: Database resources of the National Center for Biotechnology Information. year: 2010 uri_format: https://www.ncbi.nlm.nih.gov/homologene/$1 horizon_discovery: description: Cell line collections example: HD+118-001 homepage: https://horizondiscovery.com/ mappings: cellosaurus: Horizon_Discovery name: Horizon Discovery cell line collection preferred_prefix: horizon_discovery uri_format: https://horizondiscovery.com/en/search?searchterm=$1 hovergen: description: HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees. example: HBG004341 homepage: https://pbil.univ-lyon1.fr/databases/hovergen.php mappings: biocontext: HOVERGEN fairsharing: FAIRsharing.dg1f0e miriam: hovergen n2t: hovergen prefixcommons: hovergen name: Homologous Vertebrate Genes Database pattern: ^HBG\d+$ preferred_prefix: hovergen publications: - doi: 10.1093/bioinformatics/bti325 pmc: null pubmed: '15713731' title: 'Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.' year: 2005 uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN hp: appears_in: - chiro - scdo banana: HP contact: email: dr.sebastian.koehler@gmail.com github: drseb name: Sebastian Koehler orcid: 0000-0002-5316-1399 description: The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. download_json: http://purl.obolibrary.org/obo/hp.json download_obo: http://purl.obolibrary.org/obo/hp.obo download_owl: http://purl.obolibrary.org/obo/hp.owl example: '0011140' homepage: http://www.human-phenotype-ontology.org/ license: hpo mappings: aberowl: HP_O biocontext: HPO bioportal: HP_O fairsharing: FAIRsharing.kbtt7f hl7: 2.16.840.1.113883.6.339 miriam: hp n2t: hp obofoundry: hp ols: hp ontobee: HP wikidata: P3841 name: Human Phenotype Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: HP publications: - doi: 10.1093/nar/gky1105 pmc: PMC6324074 pubmed: '30476213' title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. year: 2019 - doi: https://doi.org/10.1093/nar/gkw1039 pmc: PMC5210535 pubmed: '27899602' title: The Human Phenotype Ontology in 2017. year: null - doi: 10.1093/nar/gkw1039 pmc: PMC5210535 pubmed: '27899602' title: The Human Phenotype Ontology in 2017. year: 2016 - doi: 10.1016/j.ajhg.2015.05.020 pmc: PMC4572507 pubmed: '26119816' title: 'The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.' year: 2015 - doi: 10.1093/nar/gkt1026 pmc: PMC3965098 pubmed: '24217912' title: 'The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.' year: 2013 - doi: 10.1111/j.1399-0004.2010.01436.x pmc: null pubmed: '20412080' title: The human phenotype ontology. year: 2010 - doi: 10.1016/j.ajhg.2008.09.017 pmc: PMC2668030 pubmed: '18950739' title: 'The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.' year: 2008 repository: https://github.com/obophenotype/human-phenotype-ontology synonyms: - hpo twitter: hp_ontology uri_format: https://hpo.jax.org/app/browse/term/HP:$1 version: '2022-06-11' hpa: description: The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers. example: ENSG00000026508 homepage: http://www.proteinatlas.org/ mappings: biocontext: HPA fairsharing: FAIRsharing.j0t0pe go: HPA miriam: hpa n2t: hpa prefixcommons: hpa uniprot: HPA name: Human Protein Atlas tissue profile information pattern: ^ENSG\d{11}$ preferred_prefix: hpa publications: - doi: 10.1074/mcp.r800013-mcp200 pmc: null pubmed: '18669619' title: A genecentric Human Protein Atlas for expression profiles based on antibodies. year: 2008 uri_format: http://www.proteinatlas.org/$1 hpath: description: An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species. download_owl: https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo example: '2000191' homepage: https://github.com/Novartis/hpath mappings: ols: hpath name: Histopathology Ontology pattern: ^\d+$ preferred_prefix: hpath repository: https://github.com/Novartis/hpath synonyms: - MC uri_format: http://purl.obolibrary.org/obo/MC_$1 version: '2019-07-05' hpm.peptide: description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra. example: '9606117' homepage: http://www.humanproteomemap.org/index.php mappings: biocontext: HPM.PEPTIDE miriam: hpm.peptide n2t: hpm.peptide name: Human Proteome Map Peptide pattern: ^\d+$ preferred_prefix: hpm.peptide uri_format: http://www.humanproteomemap.org/spectrum.php?pep_id=$1 hpm.protein: description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins. example: '1968' homepage: http://www.humanproteomemap.org/index.php mappings: biocontext: HPM.PROTEIN miriam: hpm.protein n2t: hpm.protein name: Human Proteome Map Protein pattern: ^\d+$ preferred_prefix: hpm.protein uri_format: http://www.humanproteomemap.org/protein.php?hpm_id=$1 hprd: description: The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. example: '00001' homepage: http://www.hprd.org/ mappings: biocontext: HPRD fairsharing: FAIRsharing.y2qws7 miriam: hprd n2t: hprd prefixcommons: hprd name: Human Protein Reference Database pattern: ^\d+$ preferred_prefix: hprd publications: - doi: 10.1093/nar/gkn892 pmc: PMC2686490 pubmed: '18988627' title: Human Protein Reference Database--2009 update. year: 2008 uri_format: http://www.hprd.org/protein/$1 hpscreg: description: hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines). example: BCRTi001-A homepage: https://hpscreg.eu/ mappings: cellosaurus: hPSCreg fairsharing: FAIRsharing.7C0aVE miriam: hpscreg n2t: hpscreg re3data: r3d100012863 name: Human Pluripotent Stem Cell Registry pattern: ^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$ preferred_prefix: hpscreg uri_format: https://hpscreg.eu/cell-line/$1 hsapdv: appears_in: - scdo contact: email: frederic.bastian@unil.ch github: fbastian name: Frédéric Bastian orcid: 0000-0002-9415-5104 description: Life cycle stages for Human download_obo: http://purl.obolibrary.org/obo/hsapdv.obo download_owl: http://purl.obolibrary.org/obo/hsapdv.owl example: 0000194 homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv license: CC BY 3.0 mappings: aberowl: HSAPDV biocontext: HSAPDV biolink: HsapDv bioportal: HSAPDV fairsharing: FAIRsharing.c6vhm3 obofoundry: hsapdv ols: hsapdv ontobee: HSAPDV name: Human Developmental Stages pattern: ^\d{7}$ preferred_prefix: HsapDv repository: https://github.com/obophenotype/developmental-stage-ontologies synonyms: - HsapDv uri_format: http://purl.obolibrary.org/obo/HSAPDV_$1 version: '2020-03-10' hsdb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. example: '5621' homepage: https://pubchem.ncbi.nlm.nih.gov/source/hsdb mappings: wikidata: P2062 name: Hazardous Substances Data Bank pattern: ^\d+$ preferred_prefix: hsdb uri_format: https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1 hso: contact: email: fernanda.dorea@sva.se github: nandadorea name: Fernanda Dorea orcid: 0000-0001-8638-8525 depends_on: - bfo - ncbitaxon - obi - ro - uberon description: The health Surveillance Ontology (HSO) focuses on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance. download_owl: http://purl.obolibrary.org/obo/hso.owl example: '0000062' homepage: https://w3id.org/hso license: CC BY 3.0 mappings: aberowl: HSO bioportal: HSO obofoundry: hso ols: hso ontobee: HSO name: Health Surveillance Ontology pattern: ^\d{7}$ preferred_prefix: HSO repository: https://github.com/SVA-SE/HSO uri_format: http://purl.obolibrary.org/obo/HSO_$1 version: '2021-12-13' hssp: description: HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein. example: 102l homepage: http://swift.cmbi.kun.nl/swift/hssp/ mappings: biocontext: HSSP miriam: hssp n2t: hssp ncbi: HSSP prefixcommons: hssp name: Database of homology-derived secondary structure of proteins pattern: ^\w{4}$ preferred_prefix: hssp providers: - code: CURATOR_REVIEW description: HSSP at CMBI homepage: ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/ name: HSSP at CMBI uri_format: ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$1.hssp.bz2 publications: - doi: 10.1093/nar/24.1.201 pmc: PMC145595 pubmed: '8594579' title: The HSSP database of protein structure-sequence alignments. year: 1996 - doi: null pmc: PMC308328 pubmed: '7937066' title: The HSSP database of protein structure-sequence alignments. year: 1994 uri_format: ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2 htn: contact: email: aellenhicks@gmail.com github: aellenhicks name: Amanda Hicks orcid: 0000-0002-1795-5570 description: An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines download_owl: http://purl.obolibrary.org/obo/htn.owl example: '00000014' homepage: https://github.com/aellenhicks/htn_owl license: CC BY 4.0 mappings: aberowl: HTN bioportal: HTN obofoundry: htn ols: htn ontobee: HTN name: Hypertension Ontology pattern: ^\d{8}$ preferred_prefix: HTN repository: https://github.com/aellenhicks/htn_owl uri_format: http://purl.obolibrary.org/obo/HTN_$1 version: '2019-06-10' huge: description: The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. example: KIAA0001 homepage: http://www.kazusa.or.jp/huge/ mappings: biocontext: HUGE fairsharing: FAIRsharing.zx2ztd miriam: huge n2t: huge prefixcommons: huge uniprot: HUGE name: Human Unidentified Gene-Encoded pattern: ^KIAA\d{4}$ preferred_prefix: huge publications: - doi: 10.1093/nar/gkh035 pmc: PMC308769 pubmed: '14681467' title: 'HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE.' year: 2004 uri_format: https://www.kazusa.or.jp/huge/gfpage/$1 iao: appears_in: - agro - clyh - duo - ecocore - ecto - fovt - labo - maxo - pco - psdo - xpo contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 description: An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch. download_obo: http://purl.obolibrary.org/obo/iao.obo download_owl: http://purl.obolibrary.org/obo/iao.owl example: '0000030' homepage: https://github.com/information-artifact-ontology/IAO/ license: CC BY 4.0 mappings: aberowl: IAO biocontext: IAO bioportal: IAO fairsharing: FAIRsharing.gq1xtx go: IAO miriam: iao n2t: iao obofoundry: iao ols: iao ontobee: IAO name: Information Artifact Ontology pattern: ^\d{7}$ preferred_prefix: IAO publications: - doi: 10.3233/978-1-61499-101-4-68 pmc: null pubmed: '22874154' title: An information artifact ontology perspective on data collections and associated representational artifacts. year: 2012 repository: https://github.com/information-artifact-ontology/IAO uri_format: http://purl.obolibrary.org/obo/IAO_$1 version: '2020-12-09' icd10: contact: email: info@who.int github: null name: World Health Organization orcid: null contributor_extras: - email: null github: joeflack4 name: Joe Flack orcid: 0000-0002-2906-7319 - email: null github: matentzn name: Nico Matentzoglu orcid: 0000-0002-7356-1779 - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The 10th revision of the International Classification of Diseases (ICD) issued by the World Health Organization (WHO). ICD is formally named ''The International Statistical Classification of Diseases and Related Health Problems''. It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases. Note that the WHO version of ICD-10 is distinct from the ICD-10-CM (Clinical Modification) issued by the U.S. National Center for Health Statistics for use in the United States.' example: C34 example_decoys: - G00X - C34.90 - C4A.8 - C91.Z - C91.Z0 example_extras: - V20 - G00 - A01.1 - XVIII - R25-R29 - R25 - R25.3 homepage: https://icd.who.int/browse10 mappings: aberowl: ICD10 biocontext: ICD biolink: ICD10 bioportal: ICD10 edam: '2611' fairsharing: FAIRsharing.nj16g hl7: 2.16.840.1.113883.6.3 miriam: icd n2t: icd prefixcommons: icd wikidata: P494 name: International Classification of Diseases, 10th Revision pattern: ^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\.[0-9]))?))$ preferred_prefix: icd10 providers: - code: icd10_2008 description: The 2008 revision of ICD-10 homepage: https://icd.who.int/browse10/2008/en# name: ICD-10 Version 2008 uri_format: https://icd.who.int/browse10/2008/en#/$1 - code: icd10_2010 description: The 2010 revision of ICD-10 homepage: https://icd.who.int/browse10/2010/en# name: ICD-10 Version 2010 uri_format: https://icd.who.int/browse10/2010/en#/$1 - code: icd10_2014 description: The 2014 revision of ICD-10 homepage: https://icd.who.int/browse10/2014/en# name: ICD-10 Version 2014 uri_format: https://icd.who.int/browse10/2014/en#/$1 - code: icd10_2015 description: The 2015 revision of ICD-10 homepage: https://icd.who.int/browse10/2015/en# name: ICD-10 Version 2015 uri_format: https://icd.who.int/browse10/2015/en#/$1 - code: icd10_2016 description: The 2016 revision of ICD-10 homepage: https://icd.who.int/browse10/2016/en# name: ICD-10 Version 2016 uri_format: https://icd.who.int/browse10/2016/en#/$1 - code: icdcodelookup description: This site is dedicated exclusively to helping you look up ICD-10 codes, quickly access the codes you use most, and become more comfortable with the new code set in general. homepage: https://icdcodelookup.com/icd-10/codes name: ICD Code Lookup uri_format: https://icdcodelookup.com/icd-10/codes/$1 synonyms: - ICD - ICD-10 - ICD10 - ICD10WHO uri_format: https://icd.who.int/browse10/2019/en#/$1 icd10cm: contact: email: pbrooks@hcfa.gov github: null name: Patricia Brooks orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States issued by the National Center for Health Statistics (NCHS) and Centers for Medicare & Medicaid Services (CMS). example: F45.21 example_decoys: - C000 - c00 - C00-D499 - C00-99 - C34.90000 example_extras: - C00-D49 - U49 - C34 - C34.90 - C4A.8 - C91.Z - C91.Z0 - T37.0X1A homepage: https://www.icd10data.com/ICD10CM mappings: aberowl: ICD10CM bioportal: ICD10CM fairsharing: FAIRsharing.hpvbxb hl7: 2.16.840.1.113883.6.90 wikidata: P4229 name: International Classification of Diseases, 10th Revision, Clinical Modification pattern: ^([A-Z][0-9][0-9AB]((-[A-Z][0-9][0-9AB])|(\.[0-9A-KXZ]([0-9A-EXYZ]([0-9A-HX][0-59A-HJKMNP-S]?)?)?)?))$ preferred_prefix: icd10cm synonyms: - ICD10CM uri_format: https://icd.codes/icd10cm/$1 icd10pcs: contact: email: patricia.brooks2@cms.hhs.gov github: null name: Pat Brooks orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis. ICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records.' example: 01N50ZZ homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10PCS mappings: aberowl: ICD10PCS bioportal: ICD10PCS fairsharing: FAIRsharing.85k1jm hl7: 2.16.840.1.113883.6.4 wikidata: P1690 name: International Classification of Diseases, 10th Revision, Procedure Coding System preferred_prefix: icd10pcs uri_format: https://www.findacode.com/code.php?set=ICD10PCS&c=$1 icd11: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Diagnostic tool for epidemiology, health management and clinical purposes, maintained by the World Health Organization (WHO). It provides a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease. example: RA01.0 homepage: https://icd.who.int/ mappings: fairsharing: FAIRsharing.97805c hl7: 2.16.840.1.113883.6.347 wikidata: P7807 name: International Classification of Diseases, 11th Revision preferred_prefix: icd11 synonyms: - ICD-11 uri_format: https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1 icd9: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics. example: '277.9' homepage: https://www.cdc.gov/nchs/icd/icd9.htm mappings: biolink: ICD9 hl7: 2.16.840.1.113883.6.42 wikidata: P493 name: International Classification of Diseases, 9th Revision preferred_prefix: icd9 synonyms: - ICD9 - ICD9_2005 - MTHICD9_2006 uri_format: http://www.icd9data.com/getICD9Code.ashx?icd9=$1 icd9cm: contact: email: pbrooks@hcfa.gov github: null name: Patricia Brooks orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States. example: '784' homepage: https://www.cdc.gov/nchs/icd/icd9cm.htm mappings: aberowl: ICD9CM bioportal: ICD9CM fairsharing: FAIRsharing.10zsxb hl7: 2.16.840.1.113883.6.2 wikidata: P1692 name: International Classification of Diseases, 9th Revision, Clinical Modification pattern: ^([\dA-Z]\d{2}(\.\d{1,3}|))|(\d{2}(\.\d{1,2}|))$ preferred_prefix: icd9cm synonyms: - IC9CM - ICD9CM - ICD9CM_2005 - ICD9CM_2006 - ICDCM_2005 uri_format: http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1 icdc: description: The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer. example: 000009 homepage: https://caninecommons.cancer.gov/#/ mappings: fairsharing: FAIRsharing.d95034 miriam: icdc name: Integrated Canine Data Commons pattern: ^\d{6}$ preferred_prefix: icdc uri_format: https://caninecommons.cancer.gov/#/study/$1 icdo: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases download_owl: http://aber-owl.net/media/ontologies/ICDO/10/icdo.owl example: 9861/3 homepage: https://www.who.int/classifications/icd/adaptations/oncology/en/ mappings: aberowl: ICDO hl7: 2.16.840.1.113883.6.43 prefixcommons: icdo wikidata: P563 name: International Classification of Diseases for Oncology pattern: ^[8-9]\d{3}(/[0-3])?$ preferred_prefix: icdo synonyms: - ICD-O - ICDO uri_format: http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1 iceberg.element: description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements. example: '100' homepage: http://db-mml.sjtu.edu.cn/ICEberg/ mappings: biocontext: ICEBERG.ELEMENT miriam: iceberg.element n2t: iceberg.element name: ICEberg element pattern: ^\d+$ preferred_prefix: iceberg.element uri_format: http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1 iceberg.family: description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families. example: '1' homepage: http://db-mml.sjtu.edu.cn/ICEberg/ mappings: biocontext: ICEBERG.FAMILY miriam: iceberg.family n2t: iceberg.family name: ICEberg family pattern: ^\d+$ preferred_prefix: iceberg.family uri_format: http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$1 iceo: contact: email: liumeng94@sjtu.edu.cn github: Lemon-Liu name: Meng LIU orcid: 0000-0003-3781-6962 description: A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning. download_owl: http://purl.obolibrary.org/obo/iceo.owl example: '0000712_1' example_extras: - '0000712' homepage: https://github.com/ontoice/ICEO license: CC BY 4.0 mappings: aberowl: ICEO bioportal: ICEO obofoundry: iceo ols: iceo ontobee: ICEO name: Integrative and Conjugative Element Ontology pattern: ^\d{7}(_\d)?$ preferred_prefix: ICEO repository: https://github.com/ontoice/ICEO uri_format: http://purl.obolibrary.org/obo/ICEO_$1 version: '2.1' icepo: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. ' download_obo: https://download.nextprot.org/pub/current_release/controlled_vocabularies/icepo.obo example: '0000002' homepage: https://download.nextprot.org/pub/current_release/controlled_vocabularies/ name: Ion Channel Electrophysiology Ontology pattern: ^\d{7}$ preferred_prefix: icepo publications: - doi: null pmc: PMC4823818 pubmed: null title: 'ICEPO: the ion channel electrophysiology ontology' year: null twitter: neXtProt_news uri_format: https://biopragmatics.github.io/providers/icepo/$1 icf: comment: This might be possible to roll directly into ICD11 contact: email: info@who.int github: null name: The World Health Organization orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. As the functioning and disability of an individual occurs in a context, ICF also includes a list of environmental factors. ICF is the WHO framework for measuring health and disability at both individual and population levels. download_owl: http://aber-owl.net/media/ontologies/ICF/3/icf.owl example: '326705068' homepage: https://icd.who.int/dev11/l-icf/en mappings: aberowl: ICF bioportal: ICF fairsharing: FAIRsharing.7rngj0 hl7: 2.16.840.1.113883.6.254 name: International Classification of Functioning, Disability and Health pattern: ^\d+$ preferred_prefix: icf uri_format: http://id.who.int/icd/entity/$1 iclc: description: Cell line collections example: ATL98012 homepage: http://www.iclc.it mappings: cellosaurus: ICLC name: Interlab Cell Line Collection preferred_prefix: iclc uri_format: http://www.iclc.it/details/det_list.php?line_id=$1 ico: appears_in: - scdo contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field. download_owl: http://purl.obolibrary.org/obo/ico.owl example: '0000066' homepage: https://github.com/ICO-ontology/ICO license: CC BY 3.0 mappings: aberowl: ICO biocontext: ICO bioportal: ICO fairsharing: FAIRsharing.b9znd5 obofoundry: ico ols: ico ontobee: ICO name: Informed Consent Ontology pattern: ^\d{7}$ preferred_prefix: ICO repository: https://github.com/ICO-ontology/ICO uri_format: http://purl.obolibrary.org/obo/ICO_$1 version: 1.0.187 ideal: description: IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. example: IID00001 homepage: https://www.ideal-db.org mappings: biocontext: IDEAL fairsharing: FAIRsharing.h3y42f miriam: ideal n2t: ideal uniprot: IDEAL name: Intrinsically Disordered proteins with Extensive Annotations and Literature pattern: ^IID\d+$ preferred_prefix: ideal uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1 ido: appears_in: - scdo contact: email: Lindsay.Cowell@utsouthwestern.edu github: lgcowell name: Lindsay Cowell orcid: 0000-0003-1617-8244 description: Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases. download_owl: http://purl.obolibrary.org/obo/ido.owl example: '0000504' homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology license: CC BY 3.0 mappings: aberowl: IDO biocontext: IDO bioportal: IDO fairsharing: FAIRsharing.aae3v6 miriam: ido n2t: ido obofoundry: ido ols: ido ontobee: IDO name: Infectious Disease Ontology pattern: ^[0-9]+$ preferred_prefix: IDO providers: - code: obo.1 description: This incorrect encoding was found inside IDO-COVID-19 homepage: http://purl.obolibrary.org name: Nonstandard OBO PURL uri_format: http://purl.obolibrary.org/obo/ido.owl/IDO_$1 repository: https://github.com/infectious-disease-ontology/infectious-disease-ontology uri_format: https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1 version: '2017-11-03' idocovid19: contact: email: johnbeverley2021@u.northwestern.edu github: johnbeve name: John Beverly orcid: 0000-0002-1118-1738 description: The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease. download_owl: https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19 example: 0001191 homepage: https://github.com/infectious-disease-ontology-extensions/ido-covid-19 mappings: aberowl: IDO-COVID-19 bioportal: IDO-COVID-19 ols: idocovid19 name: The COVID-19 Infectious Disease Ontology pattern: ^\d{7}$ preferred_prefix: idocovid19 providers: - code: obo1 description: This variation uses incorrect usage of dashes instead of underscores homepage: http://purl.obolibrary.org name: Incorrect OBO PURL variation 1 uri_format: http://purl.obolibrary.org/obo/IDO-COVID-19_$1 repository: https://github.com/infectious-disease-ontology-extensions/ido-covid-19 uri_format: http://purl.obolibrary.org/obo/COVIDO_$1 version: '2020-07-21' idoden: contact: email: elvira@imbb.forth.gr github: null name: Elvira Mitraka orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology for dengue fever. download_owl: http://aber-owl.net/media/ontologies/IDODEN/6/idoden.owl example: '0003463' homepage: https://bioportal.bioontology.org/ontologies/IDODEN mappings: aberowl: IDODEN bioportal: IDODEN fairsharing: FAIRsharing.askzq4 name: Dengue Fever Ontology pattern: ^\d{7}$ preferred_prefix: idoden references: - https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003479 uri_format: http://purl.bioontology.org/ontology/IDODEN_$1 idomal: appears_in: - scdo contact: email: topalis@imbb.forth.gr github: null name: Pantelis Topalis orcid: null deprecated: true description: An application ontology to cover all aspects of malaria as well as the intervention attempts to control it. download_obo: http://purl.obolibrary.org/obo/idomal.obo download_owl: http://purl.obolibrary.org/obo/idomal.owl example: '0002350' example_extras: - '50000015' homepage: https://www.vectorbase.org/ontology-browser license: CC0 1.0 mappings: aberowl: IDOMAL biocontext: IDOMAL bioportal: IDOMAL fairsharing: FAIRsharing.2q8c28 obofoundry: idomal ols: idomal ontobee: IDOMAL name: Malaria Ontology pattern: ^(5?)\d{7}$ preferred_prefix: IDOMAL publications: - doi: 10.1186/2041-1480-4-16 pmc: PMC3848731 pubmed: '24034841' title: 'IDOMAL: the malaria ontology revisited.' year: 2013 - doi: 10.1186/1475-2875-9-230 pmc: PMC2925367 pubmed: '20698959' title: 'IDOMAL: an ontology for malaria.' year: 2010 repository: https://github.com/VEuPathDB-ontology/IDOMAL uri_format: http://purl.obolibrary.org/obo/IDOMAL_$1 version: '2015-03-16' idoo: description: Identifiers.org Ontology example: DataCollection homepage: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology mappings: miriam: idoo n2t: idoo name: Identifiers.org Ontology pattern: ^[0-9a-zA-Z]+$ preferred_prefix: idoo uri_format: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1 idot: description: Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets. example: identifierPattern homepage: http://biomodels.net/vocab/idot.rdf mappings: biocontext: idot miriam: idot n2t: idot name: Identifiers.org Terms pattern: ^[A-Za-z]+$ preferred_prefix: idot uri_format: https://biomodels.net/vocab/idot.rdf#$1 idpo: contact: email: f.quaglia@ibiom.cnr.it github: federicaquaglia name: Federica Quaglia orcid: 0000-0002-0341-4888 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR. example: '00056' homepage: https://www.disprot.org/ontology name: Intrinsically Disordered Proteins Ontology pattern: ^\d{5}$ preferred_prefix: idpo uri_format: https://www.disprot.org/idpo/IDPO:$1 idr: description: Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools. example: '0001' homepage: https://idr.openmicroscopy.org mappings: fairsharing: FAIRsharing.6wf1zw miriam: idr name: Image Data Resource pattern: ^[0-9]{4}$ preferred_prefix: idr uri_format: https://idr.openmicroscopy.org/search/?query=Name:idr$1 iedb: description: The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes. example: '1038233' homepage: https://www.lji.org/ mappings: fairsharing: FAIRsharing.c886cd miriam: iedb name: Immune Epitope Database pattern: ^[0-9]+$ preferred_prefix: iedb uri_format: https://www.iedb.org/reference/$1 ietf.language: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Shorthand representations of languages and their subtypes example: en-GB example_extras: - en - ar-SA - aaf homepage: http://www.iana.org/assignments/language-subtag-registry/language-subtag-registry mappings: wikidata: P305 name: Internet Engineering Task Force Language Tag pattern: ^\w{2,3}(-\w+)?$ preferred_prefix: ietf.language synonyms: - bcp47 iev: deprecated: true example: '0000000' homepage: http://www.inoh.org mappings: biocontext: IEV obofoundry: iev prefixcommons: iev name: Event (INOH pathway ontology) pattern: ^\d{7}$ preferred_prefix: IEV uri_format: http://purl.obolibrary.org/obo/IEV_$1 igrhcellid: description: Cell line databases/resources example: ACHN homepage: http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi mappings: cellosaurus: IGRhCellID name: Integrated Genomic Resources of human Cell Lines for Identification preferred_prefix: igrhcellid uri_format: http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1 igsn: description: IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents. example: AU124 homepage: http://www.geosamples.org/ mappings: fairsharing: FAIRsharing.Yvc76F miriam: igsn n2t: igsn name: International Geo Sample Number pattern: ^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$ preferred_prefix: igsn uri_format: http://igsn.org/$1 igsr: description: 'The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project.' example: NA06985 homepage: https://www.internationalgenome.org/ mappings: cellosaurus: IGSR fairsharing: FAIRsharing.4Vs9VM name: International Genome Sample Resource preferred_prefix: igsr uri_format: https://www.internationalgenome.org/data-portal/sample/$1 ihw: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics. example: IHW09326 homepage: https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html mappings: cellosaurus: IHW name: International Histocompatibility Workshop cell lines pattern: ^IHW\d+$ preferred_prefix: ihw illumina.probe: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip. example: ILMN_129894 homepage: https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6790/A-GEOD-6790.adf.txt name: Illumina Probe Identifier pattern: ^ILMN_\d+$ preferred_prefix: illumina.probe references: - https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-9184/A-GEOD-9184_comments.txt imanis: description: Cell line collections example: CL070 homepage: https://www.imanislife.com/collections/cell-lines/ mappings: cellosaurus: Imanis name: Imanis Life Sciences cell line products preferred_prefix: imanis uri_format: https://www.imanislife.com/?s=$1 imdrf: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence. homepage: http://www.imdrf.org/ name: International Medical Device Regulators Forum no_own_terms: true preferred_prefix: imdrf references: - https://www.fda.gov/medical-devices/mandatory-reporting-requirements-manufacturers-importers-and-device-user-facilities/mdr-adverse-event-codes imex: banana: IM banana_peel: '-' description: The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources. example: 19210-3 example_extras: - '19210' homepage: https://www.imexconsortium.org/ mappings: biocontext: IMEX miriam: imex n2t: imex prefixcommons: imex re3data: r3d100010669 name: International Molecular Exchange pattern: ^\d+(-\d+)?$ preferred_prefix: imex providers: - code: CURATOR_REVIEW description: IMEx Consortium though Intact homepage: https://www.ebi.ac.uk/intact/ name: IMEx Consortium though Intact uri_format: https://imexcentral.org/icentral/imex/rec/$1 - code: intact.search description: Search page on IntAct homepage: https://www.ebi.ac.uk/intact name: IntAct Search uri_format: https://www.ebi.ac.uk/intact/search?query=IM-$1 publications: - doi: 10.1002/pmic.200700286 pmc: null pubmed: '17893861' title: 'Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition.' year: 2007 uri_format: https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-$1 img.gene: description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information. example: '638309541' homepage: http://img.jgi.doe.gov/ mappings: biocontext: IMG.GENE miriam: img.gene n2t: img.gene prefixcommons: img.gene name: Integrated Microbial Genomes Gene pattern: ^\d+$ preferred_prefix: img.gene publications: - doi: 10.1093/nar/gkm846 pmc: PMC2238897 pubmed: '17933782' title: 'The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.' year: 2007 uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1 img.taxon: description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information. example: '648028003' homepage: http://img.jgi.doe.gov/ mappings: biocontext: IMG.TAXON miriam: img.taxon n2t: img.taxon prefixcommons: img.taxon name: Integrated Microbial Genomes Taxon pattern: ^\d+$ preferred_prefix: img.taxon publications: - doi: 10.1093/nar/gkm846 pmc: PMC2238897 pubmed: '17933782' title: 'The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.' year: 2007 uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1 imgt.hla: description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature. example: A*01:01:01:01 homepage: https://www.ebi.ac.uk/imgt/hla/allele.html mappings: biocontext: IMGT.HLA cellosaurus: IPD-IMGT/HLA edam: '2773' fairsharing: FAIRsharing.e28v7g go: IMGT_HLA miriam: imgt.hla n2t: imgt.hla ncbi: IMGT/HLA prefixcommons: imgthla name: IMGT/HLA human major histocompatibility complex sequence database pattern: ^[A-Z0-9*:]+$ preferred_prefix: imgt.hla publications: - doi: 10.1093/nar/gkj088 pmc: PMC1347451 pubmed: '16381979' title: IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences. year: 2006 synonyms: - IPD-IMGT/HLA uri_format: https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1 imgt.ligm: description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates. example: M94112 homepage: http://www.imgt.org/ mappings: biocontext: IMGT.LIGM go: IMGT_LIGM miriam: imgt.ligm n2t: imgt.ligm ncbi: IMGT/LIGM prefixcommons: imgt.ligm name: ImMunoGeneTics database covering immunoglobulins and T-cell receptors pattern: ^M\d+$ preferred_prefix: imgt.ligm providers: - code: CURATOR_REVIEW description: IMGT LIGM through DKFZ (SRS) homepage: http://genius.embnet.dkfz-heidelberg.de/ name: IMGT LIGM through DKFZ (SRS) uri_format: http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-id+4ktAl1fNMTA+-e+[IMGT:'$1'] publications: - doi: 10.1093/nar/gkj088 pmc: PMC1347451 pubmed: '16381979' title: IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences. year: 2006 uri_format: http://www.imgt.org/ligmdb/view?id=$1 imr: contact: email: curator@inoh.org github: null name: INOH curators orcid: null deprecated: true example: '0000001' homepage: http://www.inoh.org mappings: biocontext: IMR obofoundry: imr prefixcommons: imr name: Molecule role (INOH Protein name/family name ontology) pattern: ^\d{7}$ preferred_prefix: IMR uri_format: http://purl.obolibrary.org/obo/IMR_$1 inaturalist.observation: contributor: email: null github: oolonek name: Pierre-Marie Allard orcid: 0000-0003-3389-2191 description: The identifier for an observation in iNaturalist example: '36010371' github_request_issue: 517 homepage: https://www.inaturalist.org/observations mappings: wikidata: P5683 name: iNaturalist Observation pattern: ^[1-9]\d*$ preferred_prefix: inaturalist.observation reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.inaturalist.org/observations/$1 inaturalist.place: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Identifier for a place in iNaturalist example: '7207' homepage: https://www.inaturalist.org/places mappings: wikidata: P7471 name: iNaturalist Place pattern: ^[1-9]\d*$ preferred_prefix: inaturalist.place uri_format: https://www.inaturalist.org/places/$1 inaturalist.taxon: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Identifier for a species in iNaturalist example: '21723' homepage: https://www.inaturalist.org/taxa mappings: wikidata: P3151 name: iNaturalist Taxonomy pattern: ^[1-9]\d{0,6}$ preferred_prefix: inaturalist.taxon uri_format: https://www.inaturalist.org/taxa/$1 inaturalist.user: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Identifier for a user in iNaturalist example: '1426686' homepage: https://www.inaturalist.org/users name: iNaturalist User pattern: ^[1-9]\d*$ preferred_prefix: inaturalist.user uri_format: https://www.inaturalist.org/users/$1 inchi: description: The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier. example: InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 homepage: http://www.chemspider.com/ mappings: biocontext: INCHI fairsharing: FAIRsharing.ddk9t9 miriam: inchi n2t: inchi wikidata: P234 name: InChI pattern: ^InChI\=1S?\/[A-Za-z0-9\.]+(\+[0-9]+)?(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,\/\?\;\.]+)*$ preferred_prefix: inchi providers: - code: CURATOR_REVIEW description: InChI through NIST homepage: http://webbook.nist.gov/chemistry name: InChI through NIST uri_format: http://webbook.nist.gov/cgi/cbook.cgi?$1 - code: ebi description: InChI through ChEBI homepage: https://www.ebi.ac.uk/chebi/ name: InChI through ChEBI uri_format: https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=$1 - code: um description: InChI through RDF Open Molecules homepage: http://rdf.openmolecules.net/ name: InChI through RDF Open Molecules uri_format: http://rdf.openmolecules.net/?$1 uri_format: http://www.chemspider.com/$1 inchikey: description: The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI. example: RYYVLZVUVIJVGH-UHFFFAOYSA-N homepage: http://www.chemspider.com/ mappings: biocontext: INCHIKEY miriam: inchikey n2t: inchikey wikidata: P235 name: InChIKey pattern: ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])$ preferred_prefix: inchikey providers: - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/inchikey/$1 uri_format: http://www.chemspider.com/inchikey=$1 inhand: comment: This nomenclature is available via email. Truly a disgrace. contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The standard reference for nomenclature and diagnostic criteria in toxicologic pathology. homepage: https://www.goreni.org/gr3_nomenclature.php mappings: fairsharing: FAIRsharing.9gqfpm name: The International Harmonization of Nomenclature and Diagnostic criteria preferred_prefix: inhand proprietary: true publications: - doi: 10.1177/0192623309353423 pmc: null pubmed: '20032296' title: Proliferative and nonproliferative lesions of the rat and mouse respiratory tract. year: 2009 inn: comment: can not find a place to resolve to contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO. example: fluticasone homepage: https://www.who.int/teams/health-product-and-policy-standards/inn mappings: wikidata: P2275 name: International Nonproprietary Names preferred_prefix: inn synonyms: - INN_ID uri_format: https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1 ino: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles. download_owl: http://purl.obolibrary.org/obo/ino.owl example: '0000003' homepage: https://github.com/INO-ontology/ino license: CC BY 3.0 mappings: aberowl: INO biolink: INO bioportal: INO fairsharing: FAIRsharing.mm72as obofoundry: ino ols: ino ontobee: INO name: Interaction Network Ontology pattern: ^\d{7}$ preferred_prefix: INO publications: - doi: 10.1186/s13040-016-0118-0 pmc: PMC5168857 pubmed: '28031747' title: The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature. year: 2016 - doi: 10.1186/2041-1480-6-2 pmc: PMC4362819 pubmed: '25785184' title: Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. year: 2015 - doi: 10.1186/2041-1480-2-s2-s8 pmc: PMC3102897 pubmed: '21624163' title: Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. year: 2011 repository: https://github.com/INO-ontology/ino uri_format: http://purl.obolibrary.org/obo/INO_$1 version: 1.1.13 insdc: description: The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. example: X58356 homepage: https://www.ncbi.nlm.nih.gov/Genbank/ mappings: biocontext: INSDC miriam: insdc n2t: insdc prefixcommons: insdc name: Nucleotide Sequence Database pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ preferred_prefix: insdc providers: - code: CURATOR_REVIEW description: INSDC through DDBJ homepage: http://www.ddbj.nig.ac.jp/ name: INSDC through DDBJ uri_format: http://getentry.ddbj.nig.ac.jp/getentry?database=ddbj&accession_number=$1 - code: ebi description: INSDC through European Nucleotide Archive (ENA) homepage: https://www.ebi.ac.uk/ena/ name: INSDC through European Nucleotide Archive (ENA) uri_format: https://www.ebi.ac.uk/ena/data/view/$1 - code: ncbi description: INSDC through Nucleotide database at NCBI homepage: https://www.ncbi.nlm.nih.gov/nuccore/ name: INSDC through Nucleotide database at NCBI uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 publications: - doi: 10.1093/nar/18.6.1517 pmc: PMC330520 pubmed: '2326192' title: Recent changes in the GenBank On-line Service. year: 1990 - doi: 10.1093/nar/gkl986 pmc: PMC1781245 pubmed: '17202161' title: GenBank. year: 2007 - doi: 10.1093/nar/gkl913 pmc: PMC1897316 pubmed: '17148479' title: EMBL Nucleotide Sequence Database in 2006. year: 2006 - doi: 10.1126/science.298.5597.1333b pmc: null pubmed: '12436968' title: Nucleotide sequence database policies. year: 2002 uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 insdc.cds: description: The coding sequence or protein identifiers as maintained in INSDC. example: AAA35559 has_canonical: ncbiprotein homepage: http://getentry.ddbj.nig.ac.jp mappings: biocontext: INSDC.CDS miriam: insdc.cds n2t: insdc.cds name: INSDC CDS pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ preferred_prefix: insdc.cds providers: - code: CURATOR_REVIEW description: INSDC CDS through ENA homepage: https://www.ebi.ac.uk/ena name: INSDC CDS through ENA uri_format: https://www.ebi.ac.uk/ena/data/view/$1 - code: CURATOR_REVIEW description: INSDC CDS through NCBI homepage: https://www.ncbi.nlm.nih.gov/protein/ name: INSDC CDS through NCBI uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 uri_format: http://getentry.ddbj.nig.ac.jp/getentry/dad/$1 insdc.gca: description: The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage. example: GCA_000155495.1 has_canonical: ncbi.assembly homepage: https://www.ebi.ac.uk/ena/browse/genome-assembly-database mappings: biocontext: INSDC.GCA miriam: insdc.gca n2t: insdc.gca name: Genome assembly database pattern: ^GC[AF]_[0-9]{9}\.[0-9]+$ preferred_prefix: insdc.gca providers: - code: ncbi description: Genome assembly database NCBI homepage: https://www.ncbi.nlm.nih.gov/assembly/ name: Genome assembly database NCBI uri_format: https://www.ncbi.nlm.nih.gov/assembly/$1 uri_format: https://www.ebi.ac.uk/ena/data/view/$1 insdc.run: comment: 'https://www.insdc.org/ is the authoritative source for INSDC. However, confusingly, they don''t mention runs in this table. I think we should ask them to include. ENA is a partner and they have documentation here: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html Runs | (E\|D\|S)RR[0-9]{6,} | ERR123456 -- | -- | --' contributor: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: An experimental run, served thrugh the ENA example: ERR436051 github_request_issue: 131 has_canonical: ena.embl homepage: https://www.insdc.org/ name: International Nucleotide Sequence Database Collaboration (INSDC) Run pattern: ^(E|D|S)RR[0-9]{6,}$ preferred_prefix: insdc.run reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.ebi.ac.uk/ena/browser/view/$1 insdc.sra: description: 'The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.' example: SRX000007 homepage: https://www.ncbi.nlm.nih.gov/sra mappings: biocontext: INSDC.SRA fairsharing: FAIRsharing.g7t2hv miriam: insdc.sra n2t: insdc.sra name: Sequence Read Archive pattern: ^[SED]R[APRSXZ]\d+$ preferred_prefix: insdc.sra providers: - code: ddbj description: DDBJ Sequence Read Archive (DRA) homepage: http://trace.ddbj.nig.ac.jp/dra/ name: DDBJ Sequence Read Archive (DRA) uri_format: http://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc=$1 - code: ebi description: European Nucleotide Archive (ENA) homepage: https://www.ebi.ac.uk/ena name: European Nucleotide Archive (ENA) uri_format: https://www.ebi.ac.uk/ena/data/view/$1 uri_format: https://www.ncbi.nlm.nih.gov/sra/$1 intact: description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. example: EBI-2307691 homepage: https://www.ebi.ac.uk/intact/ mappings: biocontext: INTACT fairsharing: FAIRsharing.d05nwx go: IntAct miriam: intact n2t: intact prefixcommons: intact re3data: r3d100010671 uniprot: IntAct name: IntAct protein interaction database pattern: ^EBI\-[0-9]+$ preferred_prefix: intact publications: - doi: 10.1093/nar/gkh052 pmc: PMC308786 pubmed: '14681455' title: 'IntAct: an open source molecular interaction database.' year: 2004 uri_format: https://www.ebi.ac.uk/intact/interaction/$1 intact.molecule: description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules. example: EBI-366083 homepage: https://www.ebi.ac.uk/intact/ mappings: biocontext: INTACT.MOLECULE miriam: intact.molecule n2t: intact.molecule name: IntAct Molecule pattern: ^EBI\-[0-9]+$ preferred_prefix: intact.molecule uri_format: https://www.ebi.ac.uk/intact/search?query=$1 interlex: description: 'InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. ' example: 0101963 homepage: https://www.fdilab.org mappings: fairsharing: FAIRsharing.67sssf miriam: ilx name: InterLex pattern: ^[0-9]+$ preferred_prefix: interlex publications: - doi: 10.3389/fninf.2013.00018 pmc: PMC3757470 pubmed: '24009581' title: 'NeuroLex.org: an online framework for neuroscience knowledge.' year: 2013 references: - https://github.com/AllenInstitute/nomenclature synonyms: - ILX uri_format: https://scicrunch.org/scicrunch/interlex/view/ilx_$1 interpro: contact: email: interhelp@ebi.ac.uk github: null name: InterPro Help orcid: null description: InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. example: IPR016380 homepage: http://www.ebi.ac.uk/interpro/index.html mappings: biocontext: IPR biolink: interpro edam: '1133' fairsharing: FAIRsharing.pda11d go: InterPro miriam: interpro n2t: interpro ncbi: InterPro obofoundry: ipr prefixcommons: interpro re3data: r3d100010798 uniprot: InterPro wikidata: P2926 name: InterPro pattern: ^IPR\d{6}$ preferred_prefix: interpro providers: - code: CURATOR_REVIEW description: Bio2RDF homepage: http://interpro.bio2rdf.org/fct/ name: Bio2RDF uri_format: http://interpro.bio2rdf.org/describe/?url=http://bio2rdf.org/interpro:$1 publications: - doi: 10.1093/nar/gki106 pmc: PMC540060 pubmed: '15608177' title: InterPro, progress and status in 2005. year: 2005 synonyms: - IP - IPR - InterPro uri_format: https://www.ebi.ac.uk/interpro/entry/$1 ird.segment: description: Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s). example: CY077097 homepage: http://www.fludb.org/ mappings: biocontext: IRD.SEGMENT miriam: ird.segment n2t: ird.segment prefixcommons: ird.segment name: IRD Segment Sequence pattern: ^\w+(\_)?\d+(\.\d+)?$ preferred_prefix: ird.segment publications: - doi: 10.1093/nar/gkm905 pmc: PMC2238987 pubmed: '17965094' title: 'BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence.' year: 2007 uri_format: http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1 irefweb: description: 'iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.' example: '617102' homepage: http://wodaklab.org/iRefWeb/ mappings: biocontext: IREFWEB fairsharing: FAIRsharing.t31wcb miriam: irefweb n2t: irefweb prefixcommons: irefweb re3data: r3d100012725 name: iRefWeb pattern: ^\d+$ preferred_prefix: irefweb uri_format: http://wodaklab.org/iRefWeb/interaction/show/$1 iro: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true example: 0000008 name: Insect Resistance Ontology pattern: ^\d{7}$ preferred_prefix: iro uri_format: https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1 isbn: description: The International Standard Book Number (ISBN) is for identifying printed books. example: '9781584885658' homepage: http://isbndb.com/ mappings: biocontext: ISBN-13 biolink: isbn edam: '2634' go: ISBN miriam: isbn n2t: isbn prefixcommons: isbn name: International Standard Book Number pattern: ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ preferred_prefix: isbn providers: - code: CURATOR_REVIEW description: ISBN database at WorldCat homepage: http://www.worldcat.org/ name: ISBN database at WorldCat uri_format: http://www.worldcat.org/isbn/$1 synonyms: - ISBN-10 - ISBN-13 uri_format: http://isbndb.com/search-all.html?kw=$1 isfinder: description: ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available. example: ISA1083-2 homepage: http://www-is.biotoul.fr/i mappings: biocontext: ISFINDER fairsharing: FAIRsharing.xhpc3h miriam: isfinder n2t: isfinder ncbi: ISFinder prefixcommons: isfinder name: Insertion sequence elements database pattern: ^IS\w+(\-\d)?$ 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/$1 iso.3166: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An identifier for a country in numeric format per ISO 3166-1 example: '554' homepage: https://www.iso.org/iso-3166-country-codes.html mappings: wikidata: P299 name: ISO 3166-1 Country Code pattern: ^\d+$ preferred_prefix: iso.3166 issn: description: The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books. example: 0745-4570 homepage: https://portal.issn.org mappings: biocontext: ISSN biolink: issn go: ISSN miriam: issn n2t: issn name: International Standard Serial Number pattern: ^\d{4}-\d{3}[\dX]$ preferred_prefix: issn providers: - code: CURATOR_REVIEW description: ISSN at Library of Congress homepage: http://catalog.loc.gov/webvoy.htm name: ISSN at Library of Congress uri_format: https://catalog.loc.gov/vwebv/search?searchCode=STNO&searchArg=$1&searchType=1&recCount=25 uri_format: https://portal.issn.org/resource/ISSN/$1 itis: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world. example: '589462' homepage: https://www.itis.gov/ mappings: fairsharing: FAIRsharing.t19hpa re3data: r3d100011213 wikidata: P815 name: Integrated Taxonomic Information System pattern: ^\d+$ preferred_prefix: itis uri_format: https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1 ito: description: The Intelligence Task Ontology (ITO) provides a comprehensive map of machine intelligence tasks, as well as broader human intelligence or hybrid human/machine intelligence tasks. download_owl: http://aber-owl.net/media/ontologies/ITO/17/ito.owl example: ITO_01625 homepage: https://bioportal.bioontology.org/ mappings: aberowl: ITO bioportal: ITO miriam: ito name: Intelligence Task Ontology pattern: ^.+$ preferred_prefix: ito uri_format: https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https%3A%2F%2Fai-strategies.org%2Fontology%2F$1 iuphar.family: description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits. example: '78' homepage: http://www.guidetopharmacology.org/ mappings: biocontext: IUPHAR.FAMILY miriam: iuphar.family n2t: iuphar.family prefixcommons: iuphar.family name: IUPHAR family pattern: ^\d+$ preferred_prefix: iuphar.family synonyms: - IUPHARfam uri_format: http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1 iuphar.ligand: description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands. example: '1755' homepage: http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all mappings: biocontext: IUPHAR.LIGAND biolink: GTOPDB miriam: iuphar.ligand n2t: iuphar.ligand wikidata: P595 name: Guide to Pharmacology Ligand pattern: ^\d+$ preferred_prefix: iuphar.ligand synonyms: - IUPHAR_LIGAND - IUPHAR_LIGAND_ID uri_format: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1 iuphar.receptor: description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits. example: '101' homepage: http://www.guidetopharmacology.org/targets.jsp mappings: biocontext: IUPHAR.RECEPTOR go: IUPHAR_RECEPTOR miriam: iuphar.receptor n2t: iuphar.receptor wikidata: P5458 name: Guide to Pharmacology Target pattern: ^\d+$ preferred_prefix: iuphar.receptor synonyms: - IUPHAR_GPCR - IUPHARobj uri_format: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1 jax: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Information about the C57BL/6J. Includes genetic background and disease data. example: '004435' homepage: https://www.jax.org/strain mappings: biocontext: JAX fairsharing: FAIRsharing.5701h1 name: Jackson Laboratories Strain pattern: ^\d{6}$ preferred_prefix: jax uri_format: https://www.jax.org/strain/$1 jaxmice: description: JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory. example: '005012' homepage: http://jaxmice.jax.org/ mappings: biocontext: JAXMICE miriam: jaxmice n2t: jaxmice name: JAX Mice pattern: ^\d+$ preferred_prefix: jaxmice uri_format: http://jaxmice.jax.org/strain/$1.html jcggdb: description: JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc. example: JCGG-STR008690 homepage: http://jcggdb.jp/index_en.html mappings: biocontext: JCGGDB miriam: jcggdb n2t: jcggdb name: Japan Consortium for Glycobiology and Glycotechnology Database pattern: ^JCGG-STR\d{6}$ preferred_prefix: jcggdb uri_format: http://jcggdb.jp/idb/jcggdb/$1 jcm: description: The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2. example: '17254' homepage: http://www.jcm.riken.go.jp/ mappings: biocontext: JCM fairsharing: FAIRsharing.h2wrt2 miriam: jcm n2t: jcm ncbi: JCM prefixcommons: jcm name: Japan Collection of Microorganisms pattern: ^\d+$ preferred_prefix: jcm uri_format: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1 jcrb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Cell line collections example: JCRB1355 homepage: https://cellbank.nibiohn.go.jp mappings: cellosaurus: JCRB name: JRBC Cell Bank preferred_prefix: jcrb uri_format: https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1 jcsd: description: The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST). example: J55.713G homepage: http://jglobal.jst.go.jp/en/ mappings: biocontext: JCSD miriam: jcsd n2t: jcsd prefixcommons: jcsd name: Japan Chemical Substance Dictionary pattern: ^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$ preferred_prefix: jcsd uri_format: http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1 jstor: description: JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration. example: '3075966' homepage: http://www.jstor.org/ mappings: biocontext: JSTOR go: JSTOR miriam: jstor n2t: jstor name: Digital archive of scholarly articles pattern: ^\d+$ preferred_prefix: jstor uri_format: http://www.jstor.org/stable/$1 jws: description: JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser. example: achcar11 homepage: http://jjj.biochem.sun.ac.za/models/ mappings: biocontext: JWS miriam: jws n2t: jws prefixcommons: jws name: JWS Online pattern: ^\w+$ preferred_prefix: jws providers: - code: CURATOR_REVIEW description: JWS Online Model Repository at Manchester homepage: http://jjj.mib.ac.uk/index.html name: JWS Online Model Repository at Manchester uri_format: http://jjj.mib.ac.uk/models/$1 - 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/$1 kaggle: description: Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions. example: nasa/kepler-exoplanet-search-results homepage: https://kaggle.com mappings: miriam: kaggle n2t: kaggle re3data: r3d100012705 name: Kaggle pattern: ^[0-9a-zA-Z\-]+\/[0-9a-zA-Z\-]+$ preferred_prefix: kaggle uri_format: https://www.kaggle.com/$1 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 preferred_prefix: kclb uri_format: https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1 kegg: comment: KEGG prefix has been split into several others deprecated: true description: Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies. example: hsa00190 homepage: http://www.kegg.jp/ mappings: biocontext: KEGG cheminf: 000409 go: KEGG miriam: kegg n2t: kegg uniprot: KEGG name: Kyoto Encyclopedia of Genes and Genomes pattern: ^([CHDEGTMKR]\d+)|(\w+:[\w\d\.-]*)|([a-z]{3,5})|(\w{2,4}\d{5})$ preferred_prefix: kegg synonyms: - KEGG uri_format: http://www.kegg.jp/entry/$1 kegg.compound: description: KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life. example: C12345 homepage: https://www.genome.jp/kegg/ligand.html mappings: biocontext: KEGG.COMPOUND edam: '2605' miriam: kegg.compound n2t: kegg.compound prefixcommons: kegg.compound wikidata: P665 name: KEGG Compound part_of: kegg pattern: ^C\d+$ preferred_prefix: kegg.compound publications: - doi: 10.1002/0471250953.bi0112s38 pmc: null pubmed: '22700311' title: Using the KEGG database resource. year: 2012 synonyms: - KEGG COMPOUND - KEGG.COMPOUND uri_format: https://www.kegg.jp/entry/$1 kegg.dgroup: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: " KEGG DGROUP contains structurally and functionally related groups\ \ of D number entries in KEGG DRUG. There are five types of drug groups.\n\n \ \ Chemical - grouped as identical chemical structures with minor variations\ \ of salts, hydration states, etc.\n Structure - grouped as similar chemical\ \ structures having the same skeleton, etc.\n Target - grouped by drug targets\n\ \ Class - drug classes often representing similar mechanisms of action\n \ \ Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing\ \ enzymes and transporters\n\nChemical groups are often used for identifying essentially\ \ the same active ingredients of drugs in different countries." example: DG00301 homepage: http://www.genome.jp/kegg/reaction/ mappings: biolink: KEGG.DGROUP name: KEGG Drug Group part_of: kegg pattern: ^DG\d+$ 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/ 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/$1 kegg.drug: description: KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules. example: D00123 homepage: https://www.genome.jp/kegg/drug/ mappings: biocontext: KEGG.DRUG edam: '2609' miriam: kegg.drug n2t: kegg.drug prefixcommons: kegg.drug wikidata: P665 name: KEGG Drug part_of: kegg pattern: ^D\d+$ 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:$1 kegg.genes: description: KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources. example: bsu:BSU01340 homepage: http://www.genome.jp/kegg/genes.html mappings: biocontext: KEGG.GENES biolink: KEGG.GENE miriam: kegg.genes n2t: kegg.genes prefixcommons: kegg.gene wikidata: P665 name: KEGG Genes part_of: kegg pattern: ^\w+:[\w\d\.-]*$ 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/$1 kegg.glycan: description: KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways. example: G00123 homepage: https://www.genome.jp/kegg/glycan/ mappings: biocontext: KEGG.GLYCAN edam: '2613' miriam: kegg.glycan n2t: kegg.glycan prefixcommons: kegg.glycan name: KEGG Glycan part_of: kegg pattern: ^G\d+$ 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:$1 kegg.metagenome: description: The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species. example: T30002 homepage: http://www.genome.jp/kegg/catalog/org_list3.html mappings: biocontext: KEGG.METAGENOME miriam: kegg.metagenome n2t: kegg.metagenome prefixcommons: kegg.metagenome name: KEGG Metagenome part_of: kegg pattern: ^T3\d+$ preferred_prefix: kegg.metagenome publications: - doi: 10.1093/nar/gkr988 pmc: PMC3245020 pubmed: '22080510' title: KEGG for integration and interpretation of large-scale molecular data sets. year: 2011 uri_format: http://www.kegg.jp/entry/$1 kegg.module: description: KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules. example: M00002 homepage: http://www.kegg.jp/kegg/module.html mappings: biocontext: KEGG.MODULE miriam: kegg.module n2t: kegg.module name: KEGG Module part_of: kegg pattern: ^([a-z]{3,5}_)?M\d{5}$ preferred_prefix: kegg.module uri_format: http://www.kegg.jp/entry/$1 kegg.orthology: description: KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms. example: K00001 homepage: http://www.genome.jp/kegg/ko.html mappings: biocontext: KEGG.ORTHOLOGY miriam: kegg.orthology n2t: kegg.orthology prefixcommons: kegg.orthology name: KEGG Orthology part_of: kegg pattern: ^K\d+$ preferred_prefix: kegg.orthology uri_format: http://www.kegg.jp/entry/$1 kegg.pathway: description: KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks. example: rsk00410 homepage: https://www.genome.jp/kegg/pathway.html mappings: biocontext: KEGG.PATHWAY biolink: KEGG.PATHWAY edam: '2343' go: KEGG_PATHWAY miriam: kegg.pathway n2t: kegg.pathway prefixcommons: kegg.pathway wikidata: P665 name: KEGG Pathways Database part_of: kegg pattern: ^\w{2,4}\d{5}$ preferred_prefix: kegg.pathway publications: - doi: 10.1002/0471250953.bi0112s38 pmc: null pubmed: '22700311' title: Using the KEGG database resource. year: 2012 synonyms: - KEGG-path - KEGG_PATHWAY uri_format: https://www.kegg.jp/entry/$1 kegg.rclass: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns. example: RC00001 homepage: http://www.genome.jp/kegg/reaction/ mappings: biolink: KEGG.RCLASS name: KEGG Reaction Class part_of: kegg pattern: ^RC\d+$ preferred_prefix: kegg.rclass references: - https://github.com/prefixcommons/prefixes/pull/2 synonyms: - KEGG_RCLASS - KEGG_REACTION_CLASS kegg.reaction: description: KEGG reaction contains our knowledge on the universe of reactions that are relevant to life. example: R00100 homepage: https://www.genome.jp/kegg/reaction/ mappings: biocontext: KEGG.REACTION edam: '2608' go: KEGG_REACTION miriam: kegg.reaction n2t: kegg.reaction prefixcommons: kegg.reaction wikidata: P665 name: KEGG Reaction part_of: kegg pattern: ^R\d+$ preferred_prefix: kegg.reaction publications: - doi: 10.1002/0471250953.bi0112s38 pmc: null pubmed: '22700311' title: Using the KEGG database resource. year: 2012 synonyms: - KEGG_REACTION uri_format: https://www.kegg.jp/entry/$1 kerafast: description: Cell line collections example: EJH014 homepage: https://www.kerafast.com/ mappings: cellosaurus: Kerafast name: Kerafast cell lines preferred_prefix: kerafast uri_format: https://www.kerafast.com/Search?SearchTerm="$1" knapsack: description: 'KNApSAcK provides information on metabolites and the taxonomic class with which they are associated.' example: C00000001 homepage: http://www.knapsackfamily.com/KNApSAcK/ mappings: biocontext: KNAPSACK miriam: knapsack n2t: knapsack wikidata: P2064 name: KNApSAcK pattern: ^C\d{8}$ preferred_prefix: knapsack uri_format: http://www.knapsackfamily.com/knapsack_core/information.php?word=$1 kupo: appears_in: - cl comment: Website is down, now it redirects to something else that is not related contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true example: 0001009 homepage: http://www.kupkb.org/ name: Kidney and Urinary Pathway Ontology pattern: ^\d{7}$ preferred_prefix: kupo references: - https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-2-S2-S7 kyinno: description: Cell line collections example: KC-0979 homepage: https://www.kyinno.com/ mappings: cellosaurus: KYinno name: KYinno cell lines preferred_prefix: kyinno uri_format: https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf labo: contact: email: paul.fabry@usherbrooke.ca github: pfabry name: Paul Fabry orcid: 0000-0002-3336-2476 depends_on: - iao - obi - ogms - omiabis - omrse - opmi description: LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents. download_owl: http://purl.obolibrary.org/obo/labo.owl example: '0000124' homepage: https://github.com/OpenLHS/LABO license: CC BY 4.0 mappings: aberowl: LABO bioportal: LABO obofoundry: labo ols: labo ontobee: LABO name: clinical LABoratory Ontology pattern: ^\d{7}$ preferred_prefix: LABO publications: - doi: 10.5281/zenodo.6522019 pmc: null pubmed: null title: 'LABO: An Ontology for Laboratory Test Prescription and Reporting' year: null repository: https://github.com/OpenLHS/LABO uri_format: http://purl.obolibrary.org/obo/LABO_$1 version: '2021-06-08' langual: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Langual stands for "langua alimentaria" or "language of food". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970''s by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases' example: B2067 github_request_issue: 507 homepage: https://www.langual.org name: Langua aLimentaria Thesaurus pattern: ^B\d+$ preferred_prefix: langual uri_format: https://www.langual.org/langual_thesaurus.asp?termid=$1 lbo: contact: email: caripark@iastate.edu github: caripark name: Carissa Park orcid: 0000-0002-2346-5201 description: A vocabulary for cattle, chicken, horse, pig, and sheep breeds. download_obo: https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.obo download_owl: https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.owl example: 0000487 homepage: http://bioportal.bioontology.org/ontologies/LBO mappings: aberowl: LBO agroportal: LBO bioportal: LBO fairsharing: FAIRsharing.309v57 ols: lbo name: Livestock Breed Ontology pattern: ^\d{7}$ preferred_prefix: lbo repository: https://github.com/AnimalGenome/livestock-breed-ontology uri_format: http://purl.obolibrary.org/obo/LBO_$1 lei: description: Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland. example: HWUPKR0MPOU8FGXBT394 homepage: https://www.gleif.org/ mappings: miriam: lei n2t: lei name: Global LEI Index pattern: ^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$ preferred_prefix: lei uri_format: https://www.gleif.org/lei/$1 lepao: contact: email: lagonzalezmo@unal.edu.co github: luis-gonzalez-m name: Luis A. Gonzalez-Montana orcid: 0000-0002-9136-9932 depends_on: - aism - bfo - bspo - caro - pato - ro - uberon description: The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. download_obo: http://purl.obolibrary.org/obo/lepao.obo download_owl: http://purl.obolibrary.org/obo/lepao.owl example: '0000005' homepage: https://github.com/insect-morphology/lepao license: CC BY 4.0 mappings: aberowl: LEPAO bioportal: LEPAO obofoundry: lepao ols: lepao name: Lepidoptera Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: LEPAO repository: https://github.com/insect-morphology/lepao uri_format: http://purl.obolibrary.org/obo/LEPAO_$1 version: '2021-11-20' lgai.cede: description: LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR). example: LGCEDe-S-000002244 homepage: https://www.lgresearch.ai mappings: miriam: lgai.cede name: LG Chemical Entity Detection Dataset (LGCEDe) pattern: ^LGCEDe-S-\d{9}$ preferred_prefix: lgai.cede uri_format: https://s3.us-east-2.amazonaws.com/lg.cede/$1 lgic: comment: Website is gone deprecated: true description: The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available. example: 5HT3Arano homepage: https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php mappings: biocontext: LGIC miriam: lgic n2t: lgic prefixcommons: lgicdb name: Ligand-Gated Ion Channel database pattern: ^\w+$ preferred_prefix: lgic publications: - doi: 10.1093/nar/27.1.340 pmc: PMC148177 pubmed: '9847222' title: The Ligand Gated Ion Channel Database. year: 1999 uri_format: https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php licebase: description: Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects. example: EMLSAT00000003403 homepage: https://licebase.org mappings: biocontext: LICEBASE fairsharing: FAIRsharing.c7w81a miriam: licebase n2t: licebase re3data: r3d100013547 name: LiceBase pattern: ^[A-Za-z0-9\-\/]+$ preferred_prefix: licebase uri_format: https://licebase.org/?q=$1 ligandbook: description: Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community. example: '785' homepage: https://ligandbook.org/ mappings: miriam: ligandbook n2t: ligandbook name: LigandBook pattern: ^[0-9]+$ preferred_prefix: ligandbook uri_format: https://ligandbook.org/package/$1 ligandbox: description: LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. example: D00001 homepage: http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en mappings: biocontext: LIGANDBOX miriam: ligandbox n2t: ligandbox name: LigandBox pattern: ^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$ preferred_prefix: ligandbox uri_format: http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1 ligandexpo: description: Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. example: ABC homepage: http://ligand-depot.rutgers.edu/index.html mappings: biocontext: LIGANDEXPO fairsharing: FAIRsharing.2ma4gq miriam: ligandexpo n2t: ligandexpo prefixcommons: ligandexpo name: Ligand Expo pattern: ^(\w){3}$ preferred_prefix: ligandexpo providers: - code: CURATOR_REVIEW description: Ligand Expo at Rutgers homepage: http://ligand-expo.rcsb.org/ name: Ligand Expo at Rutgers uri_format: http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid publications: - doi: 10.1093/bioinformatics/bth214 pmc: null pubmed: '15059838' title: 'Ligand Depot: a data warehouse for ligands bound to macromolecules.' year: 2004 uri_format: http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid ligea: comment: This might just be a provider for CCLE description: Polymorphism and mutation databases example: CCLE_867 homepage: http://hpc-bioinformatics.cineca.it/fusion/main mappings: cellosaurus: LiGeA name: Cancer cell LInes GEne fusions portAl preferred_prefix: ligea uri_format: http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1 limore: description: Cell line databases/resources example: Li7 homepage: https://www.picb.ac.cn/limore/home mappings: cellosaurus: LIMORE name: Liver Cancer Model Repository preferred_prefix: limore uri_format: https://www.picb.ac.cn/limore/cellLines/single?para=$1 lincs.cell: description: 'The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.' example: LCL-2085 homepage: http://lincsportal.ccs.miami.edu/cells/ mappings: biocontext: LINCS.CELL cellosaurus: LINCS_LDP miriam: lincs.cell n2t: lincs.cell name: LINCS Cell pattern: ^(LCL|LDC|ES|LSC|LPC)-\d+$ preferred_prefix: lincs.cell synonyms: - LINCS_LDP uri_format: http://lincsportal.ccs.miami.edu/cells/#/view/$1 lincs.data: description: The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level). example: LDS-1110 homepage: http://lincsportal.ccs.miami.edu/datasets/ mappings: biocontext: LINCS.DATA miriam: lincs.data n2t: lincs.data name: LINCS Data pattern: ^[EL]D[SG]-\d+$ preferred_prefix: lincs.data providers: - code: omicsdi description: Lincs through OmicsDI homepage: https://www.omicsdi.org/ name: Lincs through OmicsDI uri_format: https://www.omicsdi.org/dataset/lincs/$1 uri_format: http://lincsportal.ccs.miami.edu/datasets/#/view/$1 lincs.protein: description: The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins. example: '200282' homepage: http://lincs.hms.harvard.edu/db/proteins/ mappings: biocontext: LINCS.PROTEIN miriam: lincs.protein n2t: lincs.protein name: LINCS Protein pattern: ^\d+$ preferred_prefix: lincs.protein uri_format: https://lincs.hms.harvard.edu/db/proteins/$1 lincs.smallmolecule: description: The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC). example: LSM-6306 homepage: http://lincsportal.ccs.miami.edu/SmallMolecules/ mappings: biocontext: LINCS.SMALLMOLECULE miriam: lincs.smallmolecule n2t: lincs.smallmolecule name: LINCS Small Molecule pattern: ^LSM-\d+$ preferred_prefix: lincs.smallmolecule synonyms: - lincs uri_format: http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1 linguist: description: Registry of programming languages for the Linguist program for detecting and highlighting programming languages. example: Python homepage: https://github.com/github/linguist mappings: miriam: linguist name: Linguist pattern: ^[a-zA-Z0-9 +#'*]+$ preferred_prefix: linguist repository: https://github.com/github/linguist uri_format: https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1 linkml: comment: 'Closes #508' contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks. example: SchemaDefinition github_request_issue: 512 homepage: https://linkml.io/linkml-model/docs/SchemaDefinition/ mappings: biolink: linkml name: LinkML preferred_prefix: linkml uri_format: https://w3id.org/linkml/$1 lipidbank: description: LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. example: BBA0001 homepage: http://lipidbank.jp/index.html mappings: biocontext: LIPIDBANK edam: '2665' fairsharing: FAIRsharing.bdn9br miriam: lipidbank n2t: lipidbank prefixcommons: lipidbank name: LipidBank pattern: ^\w+\d+$ preferred_prefix: lipidbank publications: - doi: null pmc: null pubmed: '12058481' title: '[LIPIDBANK for Web, the newly developed lipid database].' year: 2002 uri_format: http://lipidbank.jp/cgi-bin/detail.cgi?id=$1 lipidmaps: description: The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy. example: LMPR0102010012 homepage: http://www.lipidmaps.org mappings: biocontext: LIPIDMAPS cheminf: '000564' edam: '2625' fairsharing: FAIRsharing.cpneh8 miriam: lipidmaps n2t: lipidmaps prefixcommons: lipidmaps wikidata: P2063 name: LIPID MAPS pattern: ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$ preferred_prefix: lipidmaps providers: - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/lipidmaps/$1 publications: - doi: 10.1093/nar/gkl838 pmc: PMC1669719 pubmed: '17098933' title: 'LMSD: LIPID MAPS structure database.' year: 2006 - doi: 10.1194/jlr.e400004-jlr200 pmc: null pubmed: '15722563' title: A comprehensive classification system for lipids. year: 2005 synonyms: - LIPID MAPS - LIPID_MAPS_class - LIPID_MAPS_instance uri_format: http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1 lipro: contact: email: bakerc@unb.ca github: null name: Christipher Baker orcid: null deprecated: true description: An ontology representation of the LIPIDMAPS nomenclature classification. download_owl: http://aber-owl.net/media/ontologies/LIPRO/4/lipro.owl mappings: aberowl: LIPRO biocontext: LIPRO bioportal: LIPRO obofoundry: lipro name: Lipid Ontology preferred_prefix: LIPRO uri_format: http://purl.obolibrary.org/obo/LIPRO_$1 lncipedia: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A comprehensive compendium of human long non-coding RNAs example: SNHG3 homepage: https://lncipedia.org mappings: fairsharing: FAIRsharing.84c1a7 name: LNCipedia preferred_prefix: lncipedia loggerhead: contact: email: peteremidford@yahoo.com github: null name: Peter Midford orcid: 0000-0001-6512-3296 deprecated: true homepage: http://www.mesquiteproject.org/ontology/Loggerhead/index.html mappings: biocontext: LOGGERHEAD obofoundry: loggerhead name: Loggerhead nesting preferred_prefix: LOGGERHEAD uri_format: http://purl.obolibrary.org/obo/LOGGERHEAD_$1 loinc: contact: email: loinc@regenstrief.org github: null name: LOINC Support orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The international standard for identifying health measurements, observations, and documents. example: LL379-9 homepage: https://loinc.org/ mappings: aberowl: LOINC biolink: LOINC bioportal: LOINC fairsharing: FAIRsharing.2mk2zb hl7: 2.16.840.1.113883.6.1 name: Logical Observation Identifiers Names and Codes preferred_prefix: loinc publications: - doi: 10.1016/s1386-5056(98)00089-6 pmc: null pubmed: '9749897' title: Combining laboratory data sets from multiple institutions using the logical observation identifier names and codes (LOINC). year: 1998 - doi: 10.1093/jamia/ocu012 pmc: PMC5566197 pubmed: '25656513' title: Supporting interoperability of genetic data with LOINC. year: 2015 - doi: 10.1016/j.jbi.2012.01.005 pmc: PMC3376691 pubmed: '22285984' title: Enabling international adoption of LOINC through translation. year: 2012 synonyms: - LNC uri_format: https://loinc.org/$1 lonza: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Contains information about cells and data sheets related to transfection. example: '968' homepage: https://knowledge.lonza.com mappings: cellosaurus: Lonza name: Lonza pattern: ^\d+$ preferred_prefix: lonza uri_format: https://knowledge.lonza.com/cell?id=$1 lotus: comment: IDs are actually leading to the structural part of LOTUS only, which might change in the future. Will adapt the regexp in case. contact: email: adriano.rutz@ik.me github: adafede name: Adriano Rutz orcid: 0000-0003-0443-9902 contributor: email: adriano.rutz@ik.me github: adafede name: Adriano Rutz orcid: 0000-0003-0443-9902 description: LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry. example: LTS0004651 github_request_issue: 222 homepage: https://lotus.naturalproducts.net name: LOTUS Initiative for Open Natural Products Research pattern: ^LTS\d{7}$ preferred_prefix: lotus reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://lotus.naturalproducts.net/compound/lotus_id/$1 lpt: contact: email: caripark@iastate.edu github: caripark name: Carissa Park orcid: 0000-0002-2346-5201 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit. download_obo: https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.obo download_owl: https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.owl example: '0000001' homepage: https://github.com/AnimalGenome/livestock-product-trait-ontology mappings: aberowl: LPT agroportal: LPT biocontext: LPT bioportal: LPT fairsharing: FAIRsharing.g78mbm name: Livestock Product Trait Ontology pattern: ^\d+$ preferred_prefix: lpt repository: https://github.com/AnimalGenome/livestock-product-trait-ontology uri_format: http://purl.obolibrary.org/obo/LPT_$1 lrg: banana: LRG banana_peel: _ description: A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI. example: '1' homepage: http://www.lrg-sequence.org/ mappings: biocontext: LRG hl7: 2.16.840.1.113883.6.283 miriam: lrg n2t: lrg name: Locus Reference Genomic pattern: ^\d+$ preferred_prefix: lrg providers: - code: CURATOR_REVIEW description: Locus Reference Genomic through Ensembl homepage: http://www.ensembl.org/ name: Locus Reference Genomic through Ensembl uri_format: http://www.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1 - code: CURATOR_REVIEW description: Locus Reference Genomic through Ensembl mirror (asia) homepage: http://asia.ensembl.org/ name: Locus Reference Genomic through Ensembl mirror (asia) uri_format: http://asia.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1 - code: CURATOR_REVIEW description: Locus Reference Genomic through Ensembl mirror (US west) homepage: http://uswest.ensembl.org/ name: Locus Reference Genomic through Ensembl mirror (US west) uri_format: http://uswest.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1 - code: CURATOR_REVIEW description: Locus Reference Genomic through Ensembl mirror (US east) homepage: http://useast.ensembl.org/ name: Locus Reference Genomic through Ensembl mirror (US east) uri_format: http://useast.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1 uri_format: ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml lspci: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions) example: '1' homepage: https://labsyspharm.github.io/lspci/ name: Laboratory of Systems Pharmacology Compound pattern: ^\d+$ preferred_prefix: lspci uri_format: https://labsyspharm.github.io/lspci/$1 lter: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Ecological terms example: '182' homepage: https://vocab.lternet.edu/vocab/vocab/index.php name: Long Term Ecological Research Controlled Vocabulary pattern: ^\d+$ preferred_prefix: lter uri_format: https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1 ma: banana: MA contact: email: Terry.Hayamizu@jax.org github: tfhayamizu name: Terry Hayamizu orcid: 0000-0002-0956-8634 description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus) download_obo: http://purl.obolibrary.org/obo/ma.obo download_owl: http://purl.obolibrary.org/obo/ma.owl example: '0002502' homepage: https://github.com/obophenotype/mouse-anatomy-ontology license: CC BY 4.0 mappings: aberowl: MA biocontext: MA bioportal: MA fairsharing: FAIRsharing.pdwqcr go: MA miriam: ma n2t: ma obofoundry: ma ols: ma ontobee: MA prefixcommons: ma name: Mouse adult gross anatomy namespace_in_lui: true pattern: ^\d+$ preferred_prefix: MA publications: - doi: 10.1186/gb-2005-6-3-r29 pmc: PMC1088948 pubmed: '15774030' title: 'The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data.' year: 2005 repository: https://github.com/obophenotype/mouse-anatomy-ontology uri_format: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1 version: '2017-02-07' macie: description: MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved. example: M0001 homepage: https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html mappings: biocontext: MACIE edam: '2641' fairsharing: FAIRsharing.7xkx69 miriam: macie n2t: macie prefixcommons: macie name: Mechanism, Annotation and Classification in Enzymes pattern: ^M\d{4}$ preferred_prefix: macie publications: - doi: 10.1093/nar/gkl774 pmc: PMC1634735 pubmed: '17082206' title: 'MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.' year: 2006 uri_format: https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1 maizegdb.locus: description: MaizeGDB is the maize research community's central repository for genetics and genomics information. example: '25011' homepage: http://www.maizegdb.org/ mappings: biocontext: MAIZEGDB.LOCUS fairsharing: FAIRsharing.aq280w go: MaizeGDB_Locus miriam: maizegdb.locus n2t: maizegdb.locus ncbi: MaizeGDB prefixcommons: maizegdb re3data: r3d100010795 uniprot: MaizeGDB name: MaizeGDB Locus pattern: ^\d+$ preferred_prefix: maizegdb.locus publications: - doi: 10.1155/2008/496957 pmc: PMC2518694 pubmed: '18769488' title: 'MaizeGDB: The maize model organism database for basic, translational, and applied research.' year: 2008 synonyms: - MaizeGDB uri_format: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1 mamo: banana: MAMO banana_peel: _ contact: email: mamo-ontology-discuss@lists.sourceforge.net github: null name: mamo-ontology-discuss orcid: null deprecated: true description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. download_owl: http://purl.obolibrary.org/obo/mamo.owl example: '0000026' homepage: http://sourceforge.net/p/mamo-ontology/wiki/Home/ license: Artistic License 2.0 mappings: aberowl: MAMO biocontext: MAMO bioportal: MAMO fairsharing: FAIRsharing.kbz5jh miriam: mamo n2t: mamo obofoundry: mamo ols: mamo ontobee: MAMO name: Mathematical modeling ontology pattern: ^\d{7}$ preferred_prefix: MAMO repository: http://sourceforge.net/p/mamo-ontology uri_format: http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1 version: '2020-08-24' mao: contact: email: julie@igbmc.u-strasbg.fr github: null name: Julie Thompson orcid: null deprecated: true homepage: http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html mappings: biocontext: MAO obofoundry: mao prefixcommons: mao name: Multiple alignment preferred_prefix: MAO uri_format: http://purl.obolibrary.org/obo/MAO_$1 massbank: description: MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da). example: PB000166 homepage: http://www.massbank.jp mappings: biocontext: MASSBANK fairsharing: FAIRsharing.dk451a miriam: massbank n2t: massbank wikidata: P6689 name: MassBank pattern: ^[A-Z]{2}[A-Z0-9][0-9]{5}$ preferred_prefix: massbank providers: - code: CURATOR_REVIEW description: MassBank in Europe homepage: https://massbank.eu/ name: MassBank in Europe uri_format: https://massbank.eu/MassBank/RecordDisplay?id=$1 uri_format: http://www.massbank.jp/RecordDisplay?id=$1 massive: description: MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. example: MSV000082131 homepage: https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp mappings: biocontext: MASSIVE fairsharing: FAIRsharing.LYsiMd miriam: massive n2t: massive uniprot: MassIVE name: MassIVE pattern: ^MSV\d+$ preferred_prefix: massive providers: - code: omicsdi description: MassIVE through OmicsDI homepage: https://www.omicsdi.org/ name: MassIVE through OmicsDI uri_format: https://www.omicsdi.org/dataset/massive/$1 uri_format: https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1 mat: contact: email: j.bard@ed.ac.uk github: null name: Jonathan Bard orcid: null deprecated: true description: Minimal set of terms for anatomy download_obo: http://aber-owl.net/media/ontologies/MAT/3/mat.obo example: '0000000' mappings: aberowl: MAT biocontext: MAT bioportal: MAT obofoundry: mat name: Minimal Anatomical Terminology pattern: ^\d{7}$ preferred_prefix: MAT uri_format: http://purl.obolibrary.org/obo/MAT_$1 matrixdb: appears_in: - complexportal contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides example: MULT_4_VAR1_bovine homepage: http://matrixdb.univ-lyon1.fr/ mappings: fairsharing: FAIRsharing.91yrz6 prefixcommons: matrixdb re3data: r3d100010672 name: MatrixDB preferred_prefix: matrixdb publications: - doi: 10.1093/bioinformatics/btp025 pmc: PMC2647840 pubmed: '19147664' title: MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. year: 2009 uri_format: http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1 matrixdb.association: description: MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations. example: P00747__P07355 homepage: http://matrixdb.univ-lyon1.fr/ mappings: biocontext: MATRIXDB.ASSOCIATION miriam: matrixdb.association n2t: matrixdb.association name: MatrixDB Association pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$ preferred_prefix: matrixdb.association uri_format: http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association maxo: appears_in: - ecto contact: email: Leigh.Carmody@jax.org github: LCCarmody name: Leigh Carmody orcid: 0000-0001-7941-2961 depends_on: - chebi - foodon - go - iao - ro - uberon description: An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations. download_json: http://purl.obolibrary.org/obo/maxo.json download_obo: http://purl.obolibrary.org/obo/maxo.obo download_owl: http://purl.obolibrary.org/obo/maxo.owl example: 0000008 homepage: https://github.com/monarch-initiative/MAxO license: CC BY 3.0 mappings: aberowl: MAXO biolink: MAXO bioportal: MAXO obofoundry: maxo ols: maxo ontobee: MAXO name: Medical Action Ontology pattern: ^\d{7}$ preferred_prefix: MAXO repository: https://github.com/monarch-initiative/MAxO twitter: MonarchInit uri_format: http://purl.obolibrary.org/obo/MAXO_$1 version: '2022-06-23' mba: contact: email: chinhda@alleninstitute.org github: null name: Allen Institute for Brain Science orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A controlled vocabulary to support the study of transcription in the mouse brain download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-mba.obo example: '688' homepage: https://mouse.brain-map.org mappings: bioportal: ABA-AMB name: Mouse Brain Atlas pattern: ^\d+$ preferred_prefix: MBA uri_format: https://biopragmatics.github.io/providers/mba/$1 mcc: contact: email: usha@molecularconnections.com github: null name: Usha Mahadevan orcid: null deprecated: true description: Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive of machine-interpretable definitions of basic concepts in the domain and relations among them. The need for ontologies that provide a systematic arrangement of available data and allow cross talk across various related domains is gaining momentum. In this backdrop, we have developed a comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format. example: ThoracicArtery homepage: http://www.molecularconnections.com mappings: bioportal: MCCL name: Cell Line Ontology [derivative] preferred_prefix: mcc uri_format: http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#$1 mco: contact: email: citlalli.mejiaalmonte@gmail.com github: citmejia name: Citlalli Mejía-Almonte orcid: 0000-0002-0142-5591 depends_on: - bfo - chebi - cl - clo - micro - ncbitaxon - ncit - obi - omit - omp - pato - peco - uberon - zeco description: Microbial Conditions Ontology is an ontology... download_obo: http://purl.obolibrary.org/obo/mco.obo download_owl: http://purl.obolibrary.org/obo/mco.owl example: 0000858 homepage: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology license: CC BY 3.0 mappings: aberowl: MCO bioportal: MCO obofoundry: mco ols: mco ontobee: MCO name: Microbial Conditions Ontology pattern: ^\d+$ preferred_prefix: MCO repository: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology uri_format: http://purl.obolibrary.org/obo/MCO_$1 version: '2019-05-15' mdm: contact: email: bernd.mueller@zbmed.de github: null name: Bernd Müller orcid: null description: The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems. download_owl: http://aber-owl.net/media/ontologies/MDM/4/mdm.owl example: '4776' homepage: https://medical-data-models.org/ mappings: aberowl: MDM biocontext: MDM bioportal: MDM fairsharing: FAIRsharing.wnk2eq miriam: mdm n2t: mdm name: Medical Data Models pattern: ^\d+$ preferred_prefix: mdm uri_format: https://medical-data-models.org/forms/$1 meddra: contact: email: mssohelp@meddra.org github: null name: MedDRA MSSO orcid: null description: The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT). example: '10015919' homepage: http://bioportal.bioontology.org/ontologies/MEDDRA mappings: aberowl: MEDDRA biocontext: MEDDRA bioportal: MEDDRA fairsharing: FAIRsharing.ad3137 hl7: mdr miriam: meddra n2t: meddra wikidata: P3201 name: Medical Dictionary for Regulatory Activities Terminology pattern: ^\d+$ preferred_prefix: meddra publications: - doi: 10.1016/s1386-5056(00)00062-9 pmc: null pubmed: '10961570' title: The use of a medical dictionary for regulatory activities terminology (MedDRA) in prescription-event monitoring in Japan (J-PEM). year: 2000 - doi: 10.2165/00002018-199920020-00002 pmc: null pubmed: '10082069' title: The medical dictionary for regulatory activities (MedDRA). year: 1999 synonyms: - MEDRA - MeDRA - MedDRA - Medical Dictionary for Regulatory Activities uri_format: http://purl.bioontology.org/ontology/MEDDRA/$1 medgen: description: MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder. example: '760050' homepage: https://www.ncbi.nlm.nih.gov/medgen/ mappings: biocontext: MedGen biolink: medgen miriam: medgen n2t: medgen ncbi: MedGen name: Human Medical Genetics pattern: ^[CN]*\d{4,7}$ preferred_prefix: medgen uri_format: https://www.ncbi.nlm.nih.gov/medgen/$1 medlineplus: contact: email: custserv@nlm.nih.gov github: null name: NLM Customer Service orcid: null description: MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language. example: 002804 homepage: http://www.nlm.nih.gov/medlineplus/ mappings: aberowl: MEDLINEPLUS biocontext: MEDLINEPLUS bioportal: MEDLINEPLUS fairsharing: FAIRsharing.bf8dsb hl7: 2.16.840.1.113883.6.173 miriam: medlineplus n2t: medlineplus name: MedlinePlus Health Topics pattern: ^\d+$ preferred_prefix: medlineplus providers: - code: medlineplus.fp description: First-party version of medline plus. homepage: https://medlineplus.gov name: MedLine Plus home page uri_format: https://medlineplus.gov/ency/article/$1.htm uri_format: http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm merops.clan: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. example: IA homepage: https://www.ebi.ac.uk/merops name: MEROPS Clan part_of: merops preferred_prefix: merops.clan publications: - doi: 10.1093/nar/gkx1134 pmc: PMC5753285 pubmed: '29145643' title: The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. year: 2018 references: - https://github.com/biopragmatics/bioregistry/issues/439 uri_format: https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=$1 merops.entry: description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors. example: I31.952 example_extras: - S01.001 homepage: http://merops.sanger.ac.uk/index.htm mappings: biocontext: MEROPS.INHIBITOR edam: '2629' fairsharing: FAIRsharing.2s4n8r go: MEROPS miriam: merops.inhibitor n2t: merops.inhibitor prefixcommons: merops uniprot: MEROPS name: MEROPS Entry pattern: ^[SCTAGMNUI]\d{2}\.([AB]\d{2}|\d{3})$ preferred_prefix: merops.entry publications: - doi: 10.1093/nar/gkx1134 pmc: PMC5753285 pubmed: '29145643' title: The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. year: 2018 - doi: 10.1093/nar/gkm954 pmc: PMC2238837 pubmed: '17991683' title: 'MEROPS: the peptidase database.' year: 2007 references: - https://github.com/biopragmatics/bioregistry/issues/439 synonyms: - merops.inhibitor uri_format: https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1 merops.family: description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families. example: S1 homepage: http://merops.sanger.ac.uk/index.htm mappings: biocontext: MEROPS.FAMILY miriam: merops.family n2t: merops.family name: MEROPS Family part_of: merops pattern: ^[SCTAGMNU]\d+$ preferred_prefix: merops.family publications: - doi: 10.1093/nar/gkx1134 pmc: PMC5753285 pubmed: '29145643' title: The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. year: 2018 references: - https://github.com/biopragmatics/bioregistry/issues/439 uri_format: https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1 mesh: contact: email: custserv@nlm.nih.gov github: null name: NLM Customer Service orcid: null description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc. example: C063233 example_extras: - D000001 homepage: http://id.nlm.nih.gov/mesh/ license: CC0 1.0 mappings: aberowl: MESH biocontext: MESH biolink: MESH bioportal: MESH cellosaurus: MeSH edam: '1177' fairsharing: FAIRsharing.qnkw45 go: MeSH hl7: 2.16.840.1.113883.6.177 miriam: mesh n2t: mesh prefixcommons: mesh wikidata: P486 name: Medical Subject Headings pattern: ^(C|D)\d{6,9}$ preferred_prefix: mesh publications: - doi: null pmc: PMC197951 pubmed: '13982385' title: Medical subject headings. year: 1963 synonyms: - MESH - MESHA - MESHC - MESHCS - MESHD - MESHPP - MESH_DESCRIPTOR_UI - MESH_SUPPLEMENTAL_RECORD_UI - MSH - MSH2010_2010_02_22 uri_format: https://meshb.nlm.nih.gov/record/ui?ui=$1 mesh.2012: description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012. example: '17186' homepage: http://www.nlm.nih.gov/mesh/ mappings: biocontext: MESH.2012 miriam: mesh.2012 n2t: mesh.2012 name: MeSH 2012 pattern: ^[A-Za-z0-9]+$ preferred_prefix: mesh.2012 uri_format: http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded mesh.2013: description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013. example: '17165' homepage: http://www.nlm.nih.gov/mesh/ mappings: biocontext: MESH.2013 miriam: mesh.2013 n2t: mesh.2013 name: MeSH 2013 pattern: ^[A-Za-z0-9]+$ preferred_prefix: mesh.2013 uri_format: http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded metabolights: description: MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies. example: MTBLS1 homepage: https://www.ebi.ac.uk/metabolights/ mappings: biocontext: METABOLIGHTS cellosaurus: MetaboLights miriam: metabolights n2t: metabolights re3data: r3d100011556 wikidata: P3890 name: MetaboLights Compound pattern: ^MTBLS\d+$ preferred_prefix: metabolights providers: - code: omicsdi description: MataboLights through OmicsDI homepage: https://www.omicsdi.org/ name: MataboLights through OmicsDI uri_format: https://www.omicsdi.org/dataset/metabolights_dataset/$1 uri_format: https://www.ebi.ac.uk/metabolights/$1 metacyc.compound: description: MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. example: CPD-10330 homepage: https://metacyc.org mappings: biocontext: METACYC.COMPOUND biolink: MetaCyc fairsharing: FAIRsharing.yytevr go: MetaCyc miriam: metacyc.compound n2t: metacyc.compound re3data: r3d100011294 name: Metabolic Encyclopedia of metabolic and other pathways pattern: ^[A-Za-z0-9+_.%-:]+$ preferred_prefix: metacyc.compound synonyms: - MetaCyc uri_format: https://metacyc.org/compound?orgid=META&id=$1 metacyc.reaction: description: MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. example: RXN-14904 homepage: https://metacyc.org mappings: biocontext: METACYC.REACTION biolink: metacyc.reaction miriam: metacyc.reaction n2t: metacyc.reaction name: MetaCyc Reaction pattern: ^[A-Za-z0-9+_.%-:]+$ preferred_prefix: metacyc.reaction uri_format: https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1 metanetx.chemical: description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components. example: MNXM1723 homepage: https://www.metanetx.org/ mappings: biocontext: METANETX.CHEMICAL miriam: metanetx.chemical n2t: metanetx.chemical name: MetaNetX chemical pattern: ^(MNXM\d+|BIOMASS|WATER)$ preferred_prefix: metanetx.chemical uri_format: https://www.metanetx.org/chem_info/$1 metanetx.compartment: description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments. example: MNXC15 homepage: https://www.metanetx.org/ mappings: biocontext: METANETX.COMPARTMENT miriam: metanetx.compartment n2t: metanetx.compartment name: MetaNetX compartment pattern: ^(MNX[CD]\d+|BOUNDARY|IN|OUT)$ preferred_prefix: metanetx.compartment uri_format: https://www.metanetx.org/comp_info/$1 metanetx.reaction: description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions. example: MNXR101574 homepage: https://www.metanetx.org/ mappings: biocontext: METANETX.REACTION biolink: METANETX.REACTION miriam: metanetx.reaction n2t: metanetx.reaction name: MetaNetX reaction pattern: ^(MNXR\d+|EMPTY)$ preferred_prefix: metanetx.reaction uri_format: https://www.metanetx.org/equa_info/$1 metatlas: contact: email: mihail.anton@chalmers.se github: mihai-sysbio name: Mihail Anton orcid: 0000-0002-7753-9042 contributor: email: mihail.anton@chalmers.se github: mihai-sysbio name: Mihail Anton orcid: 0000-0002-7753-9042 description: A resource for exploring metabolism, starting with a set of of community-curated genome-scale metabolic models of human and model organisms, enriched with pathway maps and other tools for easy browsing and analysis. example: MAM01234c example_decoys: - MAR11851c example_extras: - MAR11851 github_request_issue: 495 homepage: https://metabolicatlas.org mappings: miriam: metatlas name: Metabolic Atlas pattern: ^(MAM\d{5}\w)|(MAR\d{5})$ preferred_prefix: metatlas reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://metabolicatlas.org/identifier/MetabolicAtlas/$1 metatlas.metabolite: contact: email: mihail.anton@chalmers.se github: mihai-sysbio name: Mihail Anton orcid: 0000-0002-7753-9042 contributor: email: mihail.anton@chalmers.se github: mihai-sysbio name: Mihail Anton orcid: 0000-0002-7753-9042 description: A subspace of Metabolic Atlas for compartment-specific records for metabolites. example: MAM01234c github_request_issue: 495 homepage: https://metabolicatlas.org name: Metabolic Atlas Metabolite part_of: metatlas pattern: ^MAM\d{5}\w$ preferred_prefix: metatlas.metabolite reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://metabolicatlas.org/identifier/MetabolicAtlas/$1 metatlas.reaction: contact: email: mihail.anton@chalmers.se github: mihai-sysbio name: Mihail Anton orcid: 0000-0002-7753-9042 contributor: email: mihail.anton@chalmers.se github: mihai-sysbio name: Mihail Anton orcid: 0000-0002-7753-9042 description: A subspace of Metabolic Atlas for reactions. example: MAR11851 github_request_issue: 495 homepage: https://metabolicatlas.org name: Metabolic Atlas Reaction part_of: metatlas pattern: ^MAR\d{5}$ preferred_prefix: metatlas.reaction reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://metabolicatlas.org/identifier/MetabolicAtlas/$1 metlin: description: The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry. example: '1455' homepage: http://masspec.scripps.edu/ mappings: biocontext: METLIN miriam: metlin n2t: metlin re3data: r3d100012311 name: Metabolite and Tandem Mass Spectrometry Database pattern: ^\d{4}$ preferred_prefix: metlin uri_format: http://metlin.scripps.edu/metabo_info.php?molid=$1 mex: description: A public place to process, interpret and share GC/MS metabolomics datasets. example: '36' homepage: https://www.metabolome-express.org/ mappings: biocontext: MEX miriam: mex n2t: mex name: Metabolome Express pattern: ^\d+$ preferred_prefix: mex providers: - code: omicsdi description: Metabolome Express through OmicsDI homepage: https://www.omicsdi.org/ name: Metabolome Express through OmicsDI uri_format: https://www.omicsdi.org/dataset/metabolome_express/MEX$1 uri_format: https://www.metabolome-express.org/datasetview.php?datasetid=$1 mf: contact: email: janna.hastings@gmail.com github: jannahastings name: Janna Hastings orcid: 0000-0002-3469-4923 description: The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning. download_owl: http://purl.obolibrary.org/obo/mf.owl example: 0000091 homepage: https://github.com/jannahastings/mental-functioning-ontology license: CC BY 3.0 mappings: aberowl: MF biocontext: MF bioportal: MF fairsharing: FAIRsharing.4gm9gt obofoundry: mf ols: mf ontobee: MF name: Mental Functioning Ontology pattern: ^\d{7}$ preferred_prefix: MF repository: https://github.com/jannahastings/mental-functioning-ontology uri_format: http://purl.obolibrary.org/obo/MF_$1 version: '2021-11-17' mfmo: contact: email: druzinsk@uic.edu github: RDruzinsky name: Robert Druzinsky orcid: 0000-0002-1572-1316 depends_on: - uberon description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors. download_owl: http://purl.obolibrary.org/obo/mfmo.owl example: 0000208 homepage: https://github.com/rdruzinsky/feedontology license: CC BY 3.0 mappings: aberowl: MFMO biocontext: MFMO bioportal: MFMO fairsharing: FAIRsharing.669cnk obofoundry: mfmo ols: mfmo ontobee: MFMO name: Mammalian Feeding Muscle Ontology pattern: ^\d{7}$ preferred_prefix: MFMO repository: https://github.com/RDruzinsky/feedontology uri_format: http://purl.obolibrary.org/obo/MFMO_$1 version: '2013-11-16' mfo: contact: email: Thorsten.Henrich@embl-heidelberg.de github: null name: Thorsten Henrich orcid: null deprecated: true description: A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes. download_obo: http://aber-owl.net/media/ontologies/MFO/14/mfo.obo download_owl: http://purl.obolibrary.org/obo/mfo.owl mappings: aberowl: MFO biocontext: MFO bioportal: MFO obofoundry: mfo prefixcommons: mfo name: Medaka fish anatomy and development preferred_prefix: MFO uri_format: http://purl.obolibrary.org/obo/MFO_$1 mfoem: contact: email: janna.hastings@gmail.com github: jannahastings name: Janna Hastings orcid: 0000-0002-3469-4923 description: An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings. download_owl: http://purl.obolibrary.org/obo/mfoem.owl example: '000204' homepage: https://github.com/jannahastings/emotion-ontology license: CC BY 3.0 mappings: aberowl: MFOEM biocontext: MFOEM bioportal: MFOEM fairsharing: FAIRsharing.dx30m8 obofoundry: mfoem ols: mfoem ontobee: MFOEM name: Emotion Ontology pattern: ^\d{6}$ preferred_prefix: MFOEM publications: - doi: 10.1186/2041-1480-5-38 pmc: PMC4417517 pubmed: '25937879' title: Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference. year: 2014 repository: https://github.com/jannahastings/emotion-ontology uri_format: http://purl.obolibrary.org/obo/MFOEM_$1 version: '2021-11-17' mfomd: contact: email: janna.hastings@gmail.com github: jannahastings name: Janna Hastings orcid: 0000-0002-3469-4923 description: The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF). download_owl: http://purl.obolibrary.org/obo/mfomd.owl example: '0000046' homepage: https://github.com/jannahastings/mental-functioning-ontology license: CC BY 3.0 mappings: aberowl: MFOMD biocontext: MFOMD bioportal: MFOMD fairsharing: FAIRsharing.q053vb obofoundry: mfomd ols: mfomd ontobee: MFOMD name: Mental Disease Ontology pattern: ^\d{7}$ preferred_prefix: MFOMD repository: https://github.com/jannahastings/mental-functioning-ontology uri_format: http://purl.obolibrary.org/obo/MFOMD_$1 version: '2020-04-26' mge: banana: mge description: ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. example: '2' homepage: http://aclame.ulb.ac.be/ mappings: biocontext: ACLAME edam: '2631' miriam: mge n2t: mge prefixcommons: aclame name: Aclame namespace_in_lui: true pattern: ^\d+$ preferred_prefix: mge publications: - doi: 10.1093/nar/gkh084 pmc: PMC308818 pubmed: '14681355' title: 'ACLAME: a CLAssification of Mobile genetic Elements.' year: 2004 synonyms: - aclame uri_format: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1 mgi: banana: MGI description: The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data. example: '6017782' homepage: http://www.informatics.jax.org/ mappings: biocontext: MGI cellosaurus: MGI edam: '3274' fairsharing: FAIRsharing.fcwyhz go: MGI miriam: mgi n2t: mgi ncbi: MGI prefixcommons: mgi uniprot: MGI wikidata: P671 name: Mouse Genome Informatics namespace_in_lui: true pattern: ^\d+$ preferred_prefix: MGI providers: - code: agr description: MGI through the Alliance of Genome Resources homepage: https://www.alliancegenome.org name: MGI through the Alliance of Genome Resources uri_format: https://www.alliancegenome.org/gene/MGI:$1 - code: bioentitylink description: MGD through BioEntity Link homepage: https://bioentity.link/ name: MGD through BioEntity Link uri_format: https://bioentity.link/#/lexicon/public/MGI:$1 - code: mgi.marker description: MGI Marker homepage: http://www.informatics.jax.org/marker name: MGI Marker uri_format: http://www.informatics.jax.org/marker/MGI:$1 publications: - doi: 10.1093/nar/gki113 pmc: PMC540067 pubmed: '15608240' title: 'The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology.' year: 2005 synonyms: - MGD - MGI uri_format: http://www.informatics.jax.org/accession/MGI:$1 mgnify.analysis: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Analyses of microbiome data within MGnify example: MGYA00002270 homepage: https://www.ebi.ac.uk/metagenomics/ name: MGnify Analysis pattern: ^MGYA\d+$ preferred_prefix: mgnify.analysis uri_format: https://www.ebi.ac.uk/metagenomics/analyses/$1 mgnify.proj: description: MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis. example: ERP004492 homepage: https://www.ebi.ac.uk/metagenomics mappings: miriam: mgnify.proj n2t: mgnify.proj name: MGnify Project pattern: ^[A-Z]+[0-9]+$ preferred_prefix: mgnify.proj uri_format: https://www.ebi.ac.uk/metagenomics/projects/$1 mgnify.samp: description: The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples. example: SRS086444 homepage: https://www.ebi.ac.uk/metagenomics mappings: miriam: mgnify.samp n2t: mgnify.samp name: MGnify Sample pattern: ^[A-Z]+[0-9]+$ preferred_prefix: mgnify.samp uri_format: https://www.ebi.ac.uk/metagenomics/samples/$1 mi: banana: MI contact: email: pporras@ebi.ac.uk github: pporrasebi name: Pablo Porras Millán orcid: 0000-0002-8429-8793 description: The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative. download_obo: http://purl.obolibrary.org/obo/mi.obo download_owl: http://purl.obolibrary.org/obo/mi.owl example: 0058 homepage: https://github.com/HUPO-PSI/psi-mi-CV license: CC BY 4.0 mappings: aberowl: MI biocontext: PSIMI biolink: MI bioportal: MI fairsharing: FAIRsharing.8qzmtr go: PSI-MI miriam: mi n2t: psimi obofoundry: mi ols: mi ontobee: MI prefixcommons: psi.mi name: Molecular Interactions Controlled Vocabulary namespace_in_lui: true pattern: ^\d{4}$ preferred_prefix: MI publications: - doi: 10.1038/nbt926 pmc: null pubmed: '14755292' title: The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. year: 2004 repository: https://github.com/HUPO-PSI/psi-mi-CV synonyms: - PSI-MI uri_format: https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1 miaa: comment: same as MAT contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: Minimal Information About Anatomy ontology preferred_prefix: miaa references: - https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/rols/inst/doc/rols.pdf miapa: contact: email: hilmar.lapp@duke.edu github: hlapp name: Hilmar Lapp orcid: 0000-0001-9107-0714 description: 'The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies. This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project''s main page at http://evoio.org/wiki/MIAPA.' download_owl: http://purl.obolibrary.org/obo/miapa.owl example: '0000010' homepage: http://www.evoio.org/wiki/MIAPA license: CC0 1.0 mappings: aberowl: MIAPA biocontext: MIAPA bioportal: MIAPA fairsharing: FAIRsharing.ca48xs obofoundry: miapa ols: miapa ontobee: MIAPA name: Minimum Anformation About a Phylogenetic Analysis Ontology pattern: ^\d{7}$ preferred_prefix: MIAPA publications: - doi: 10.1089/omi.2006.10.231 pmc: null pubmed: null title: 'Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)' year: null repository: https://github.com/evoinfo/miapa uri_format: http://purl.obolibrary.org/obo/MIAPA_$1 version: '2017-05-09' micro: appears_in: - mco contact: email: carrine.blank@umontana.edu github: carrineblank name: Carrine Blank orcid: 0000-0002-2100-6351 description: An ontology of prokaryotic phenotypic and metabolic characters download_owl: http://purl.obolibrary.org/obo/micro.owl example: 0002999 homepage: https://github.com/carrineblank/MicrO license: CC BY 2.0 mappings: aberowl: MICRO biocontext: MICRO fairsharing: FAIRsharing.brhpb0 obofoundry: micro ols: micro ontobee: MicrO name: Ontology of Prokaryotic Phenotypic and Metabolic Characters pattern: ^\d{7}$ preferred_prefix: MICRO publications: - doi: 10.1186/s13326-016-0060-6 pmc: PMC4830071 pubmed: '27076900' title: 'MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.' year: 2016 repository: https://github.com/carrineblank/MicrO uri_format: http://purl.obolibrary.org/obo/MICRO_$1 version: 1.5.1 microscope: description: MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. example: '5601141' homepage: http://www.genoscope.cns.fr/agc/microscope mappings: biocontext: MICROSCOPE fairsharing: FAIRsharing.3t5qc3 miriam: microscope n2t: microscope re3data: r3d100012928 name: MicroScope pattern: ^\d+$ preferred_prefix: microscope uri_format: http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1 microsporidia: description: MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: ECU03_0820i homepage: http://microsporidiadb.org/micro/ mappings: biocontext: MICROSPORIDIA miriam: microsporidia n2t: microsporidia prefixcommons: microsporidia name: MicrosporidiaDB pattern: ^\w+$ preferred_prefix: microsporidia publications: - doi: 10.1093/nar/gkp941 pmc: PMC2808945 pubmed: '19914931' title: 'EuPathDB: a portal to eukaryotic pathogen databases.' year: 2009 uri_format: http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 millipore: description: Cell line collections example: SCC111 homepage: https://www.merckmillipore.com/ mappings: cellosaurus: Millipore name: Merck Millipore (EMD Millipore) preferred_prefix: millipore uri_format: https://www.merckmillipore.com/catalogue/item/$1 mimodb: description: MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank. example: '1' homepage: http://immunet.cn/bdb/ mappings: biocontext: MIMODB fairsharing: FAIRsharing.bv0zjz miriam: mimodb n2t: mimodb prefixcommons: mimodb name: MimoDB pattern: ^\d+$ preferred_prefix: mimodb publications: - doi: 10.1093/nar/gkr922 pmc: PMC3245166 pubmed: '22053087' title: 'MimoDB 2.0: a mimotope database and beyond.' year: 2011 uri_format: http://immunet.cn/bdb/index.php/mimoset/$1 minid: description: Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. example: b97957 homepage: https://fair-research.org mappings: biocontext: MINID miriam: minid n2t: minid name: Minimal Viable Identifier pattern: ^[A-Za-z0-9]+$ preferred_prefix: minid uri_format: https://hdl.handle.net/hdl:20.500.12582/$1 minid.test: description: 'Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. ' example: 3SBPLMKKVEVR homepage: https://fair-research.org mappings: miriam: minid.test name: MINID Test pattern: ^[A-Za-z0-9]+$ preferred_prefix: minid.test uri_format: https://hdl.handle.net/hdl:20.500.12633/$1 mint: banana: MINT banana_peel: '-' description: The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals. example: '6978836' homepage: https://mint.bio.uniroma2.it mappings: biocontext: MINT edam: '2615' fairsharing: FAIRsharing.2bdvmk miriam: mint n2t: mint prefixcommons: mint uniprot: MINT name: Molecular Interaction Database pattern: ^\d{1,7}$ preferred_prefix: mint providers: - code: ebi description: MINT subset through IntAct homepage: https://www.ebi.ac.uk/intact/ name: MINT subset through IntAct uri_format: https://www.ebi.ac.uk/intact/query/interaction_id:$1 publications: - doi: 10.1093/nar/gkl950 pmc: PMC1751541 pubmed: '17135203' title: 'MINT: the Molecular INTeraction database.' year: 2006 uri_format: https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-$1 mipmod: description: MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures. example: HOSAPI0399 homepage: http://bioinfo.iitk.ac.in/MIPModDB mappings: biocontext: MIPMOD miriam: mipmod n2t: mipmod prefixcommons: mipmod name: MIPModDB pattern: ^\w+$ preferred_prefix: mipmod publications: - doi: 10.1093/nar/gkr914 pmc: PMC3245135 pubmed: '22080560' title: 'MIPModDB: a central resource for the superfamily of major intrinsic proteins.' year: 2011 uri_format: http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1 mir: banana: MIR description: The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or "PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources. example: '00100037' homepage: https://registry.identifiers.org/registry mappings: biocontext: MIR miriam: mir n2t: mir name: Identifiers.org Registry namespace_in_lui: true pattern: ^\d{8}$ preferred_prefix: mir uri_format: https://registry.identifiers.org/registry?query="MIR:$1" mirbase: description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). example: MI0026471 homepage: http://www.mirbase.org/ mappings: biocontext: MIRBASE biolink: mirbase edam: '2642' fairsharing: FAIRsharing.hmgte8 miriam: mirbase n2t: mirbase ncbi: miRBase prefixcommons: mirbase re3data: r3d100010566 wikidata: P2870 name: miRBase pre-miRNA pattern: ^MI\d{7}$ preferred_prefix: mirbase publications: - doi: 10.1093/nar/gkh023 pmc: PMC308757 pubmed: '14681370' title: The microRNA Registry. year: 2004 uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1 mirbase.family: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download. example: MIPF0000002 homepage: http://www.mirbase.org/ name: miRBase Families preferred_prefix: mirbase.family synonyms: - MIRBASE_FAMILY uri_format: http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1 mirbase.mature: description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence. example: MIMAT0046872 homepage: http://www.mirbase.org/ mappings: biocontext: MIRBASE.MATURE miriam: mirbase.mature n2t: mirbase.mature prefixcommons: mirbase.mature wikidata: P2871 name: miRBase mature miRNA pattern: ^MIMAT\d{7}$ preferred_prefix: mirbase.mature synonyms: - MIRBASEM uri_format: http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1 mirex: description: mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages. example: 165a homepage: http://comgen.pl/mirex/?page=home mappings: biocontext: MIREX fairsharing: FAIRsharing.q3b39v miriam: mirex n2t: mirex name: mirEX pattern: ^\d+(\w+)?$ preferred_prefix: mirex uri_format: http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes miriam: description: Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain. example: pubmed homepage: https://www.ebi.ac.uk mappings: edam: '1162' fairsharing: FAIRsharing.ap169a miriam: identifiers.namespace name: Identifiers.org namespace pattern: ^[a-z_\.]+$ preferred_prefix: miriam synonyms: - identifiers.namespace uri_format: https://registry.identifiers.org/registry/$1 miriam.collection: banana: MIR deprecated: true description: MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections. example: 00000008 homepage: https://www.ebi.ac.uk/miriam/ mappings: biocontext: MIRIAM.COLLECTION miriam: miriam.collection n2t: miriam.collection name: MIRIAM Registry collection part_of: miriam pattern: ^000\d{5}$ preferred_prefix: miriam.collection uri_format: https://www.ebi.ac.uk/miriam/main/$1 miriam.resource: banana: MIR deprecated: true description: MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases. example: '00100005' homepage: https://www.ebi.ac.uk/miriam/ mappings: biocontext: MIRIAM.RESOURCE miriam: miriam.resource n2t: miriam.resource prefixcommons: miriam.resource name: MIRIAM Legacy Registry Identifier part_of: miriam pattern: ^001\d{5}$ preferred_prefix: miriam.resource publications: - doi: 10.1186/1752-0509-1-58 pmc: PMC2259379 pubmed: '18078503' title: 'MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology.' year: 2007 uri_format: https://www.ebi.ac.uk/miriam/main/resources/$1 mirnao: contact: email: topalis@imbb.forth.gr github: null name: Pantelis Topalis orcid: null deprecated: true description: An application ontology for use with miRNA databases. download_owl: http://purl.obolibrary.org/obo/mirnao.owl homepage: http://code.google.com/p/mirna-ontology/ license: CC0 1.0 mappings: aberowl: MIRNAO biocontext: MIRNAO bioportal: MIRNAO obofoundry: mirnao ontobee: miRNAO name: microRNA Ontology preferred_prefix: MIRNAO uri_format: http://purl.obolibrary.org/obo/MIRNAO_$1 mirnest: description: miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species. example: MNEST029358 homepage: http://rhesus.amu.edu.pl/mirnest/copy/ mappings: biocontext: MIRNEST fairsharing: FAIRsharing.5pfx4r miriam: mirnest n2t: mirnest prefixcommons: mirnest name: miRNEST pattern: ^MNEST\d+$ preferred_prefix: mirnest publications: - doi: 10.1093/nar/gkr1159 pmc: PMC3245016 pubmed: '22135287' title: 'miRNEST database: an integrative approach in microRNA search and annotation.' year: 2011 uri_format: http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1 miro: contact: email: louis@imbb.forth.gr github: null name: Christos (Kitsos) Louis orcid: null deprecated: true description: Application ontology for entities related to insecticide resistance in mosquitos download_obo: http://purl.obolibrary.org/obo/miro.obo download_owl: http://purl.obolibrary.org/obo/miro.owl example: '40000617' homepage: https://github.com/VEuPathDB-ontology/MIRO mappings: aberowl: MIRO biocontext: MIRO bioportal: MIRO fairsharing: FAIRsharing.sjf113 obofoundry: miro ols: miro ontobee: MIRO name: Mosquito insecticide resistance pattern: ^\d{8}$ preferred_prefix: MIRO publications: - doi: 10.1371/journal.pntd.0000465 pmc: PMC2694272 pubmed: '19547750' title: 'MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide resistance in mosquito disease vectors.' year: 2009 repository: https://github.com/VEuPathDB-ontology/MIRO uri_format: http://purl.obolibrary.org/obo/MIRO_$1 version: '2014-05-14' mirtarbase: description: miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. example: MIRT000002 homepage: http://mirtarbase.mbc.nctu.edu.tw/ mappings: biocontext: MIRTARBASE fairsharing: FAIRsharing.f0bxfg miriam: mirtarbase n2t: mirtarbase name: miRTarBase pattern: ^MIRT\d{6}$ preferred_prefix: mirtarbase uri_format: http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1 mirte: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs example: miR-1 homepage: http://www.russelllab.org/miRNAs/ name: miRNA Target Prediction at EMBL preferred_prefix: mirte mlc: description: MLCommons Association artifacts, including benchmark results, datasets, and saved models. example: 0.7-123 homepage: https://mlcommons.org/en/ mappings: miriam: mlc name: MLCommons Association pattern: ^[0-9a-zA-Z\.\-\_]+$ preferred_prefix: mlc uri_format: https://www.mlcommons.org/mlc-id/$1 mmdb: description: The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites. example: '50885' homepage: http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure mappings: biocontext: MMDB edam: '2667' miriam: mmdb n2t: mmdb prefixcommons: mmdb name: Molecular Modeling Database pattern: ^\d{1,5}$ preferred_prefix: mmdb publications: - doi: 10.1093/nar/gkl952 pmc: PMC1751549 pubmed: '17135201' title: 'MMDB: annotating protein sequences with Entrez''s 3D-structure database.' year: 2006 uri_format: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1 mmmp.biomaps: description: A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma. example: '37' homepage: http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp mappings: biocontext: MMMP:BIOMAPS biolink: mmmp.biomaps miriam: mmmp:biomaps n2t: biomaps name: Melanoma Molecular Map Project Biomaps pattern: ^\d+$ preferred_prefix: mmmp.biomaps synonyms: - mmmp:biomaps uri_format: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1 mmo: contact: email: jrsmith@mcw.edu github: jrsjrs name: Jennifer Smith orcid: 0000-0002-6443-9376 description: 'A representation of the variety of methods used to make clinical and phenotype measurements. ' download_obo: http://purl.obolibrary.org/obo/mmo.obo download_owl: http://purl.obolibrary.org/obo/mmo.owl example: '0000574' homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 license: CC0 1.0 mappings: aberowl: MMO biocontext: MMO bioportal: MMO fairsharing: FAIRsharing.bgkyd7 obofoundry: mmo ols: mmo ontobee: MMO name: Measurement method ontology pattern: ^\d{7}$ preferred_prefix: MMO publications: - doi: 10.1186/2041-1480-4-26 pmc: PMC3882879 pubmed: '24103152' title: 'The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.' year: 2013 - doi: 10.3389/fgene.2012.00087 pmc: PMC3361058 pubmed: '22654893' title: Three ontologies to define phenotype measurement data. year: 2012 repository: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology twitter: ratgenome uri_format: http://purl.obolibrary.org/obo/MMO_$1 version: '2019-03-27' mmp.cat: description: MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples. example: MMP743597.11 homepage: https://mmp.sfb.uit.no/databases/marcat/ mappings: biocontext: MMP.CAT miriam: mmp.cat n2t: mmp.cat name: MarCat pattern: ^MMP\d+.\d+$ preferred_prefix: mmp.cat uri_format: https://mmp.sfb.uit.no/databases/marcat/#/records/$1 mmp.db: description: MarDB includes all sequenced marine microbial genomes regardless of level of completeness. example: MMP02954345.1 homepage: https://mmp.sfb.uit.no/databases/mardb/ mappings: biocontext: MMP.DB miriam: mmp.db n2t: mmp.db name: MarDB pattern: ^MMP\d+.\d+$ preferred_prefix: mmp.db uri_format: https://mmp.sfb.uit.no/databases/mardb/#/records/$1 mmp.fun: description: MarFun is manually curated database for marine fungi which is a part of the MAR databases. example: MMP3888430 homepage: https://mmp.sfb.uit.no/databases/marfun mappings: miriam: mmp.fun name: MarFun pattern: ^MMP\d+.\d+$ preferred_prefix: mmp.fun uri_format: https://mmp.sfb.uit.no/databases/marfun/#/records/$1 mmp.ref: description: MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes. example: MMP3312982.2 homepage: https://mmp.sfb.uit.no/databases/marref/ mappings: biocontext: MMP.REF miriam: mmp.ref n2t: mmp.ref name: MarRef pattern: ^MMP\d+.\d+$ preferred_prefix: mmp.ref uri_format: https://mmp.sfb.uit.no/databases/marref/#/records/$1 mmrrc: description: The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections. example: '70' homepage: https://www.mmrrc.org mappings: biocontext: MMRRC cellosaurus: MMRRC fairsharing: FAIRsharing.9dpd18 miriam: mmrrc n2t: mmrrc name: Mutant Mouse Resource and Research Centers pattern: ^\d+$ preferred_prefix: mmrrc uri_format: http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1 mmsl: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included. example: '3355' homepage: https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html mappings: hl7: 2.16.840.1.113883.6.175 name: Multum MediSource Lexicon pattern: ^\d+$ preferred_prefix: mmsl synonyms: - MMSL_CODE mmusdv: contact: email: frederic.bastian@unil.ch github: fbastian name: Frédéric Bastian orcid: 0000-0002-9415-5104 description: Life cycle stages for Mus Musculus download_obo: http://purl.obolibrary.org/obo/mmusdv.obo download_owl: http://purl.obolibrary.org/obo/mmusdv.owl example: '0000066' homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv license: CC BY 3.0 mappings: aberowl: MMUSDV biocontext: MMUSDV biolink: MmusDv bioportal: MMUSDV fairsharing: FAIRsharing.zchb68 obofoundry: mmusdv ols: mmusdv ontobee: MMUSDV name: Mouse Developmental Stages pattern: ^\d{7}$ preferred_prefix: MmusDv repository: https://github.com/obophenotype/developmental-stage-ontologies synonyms: - MmusDv uri_format: http://purl.obolibrary.org/obo/MMUSDV_$1 version: '2020-03-10' mo: contact: email: stoeckrt@pcbi.upenn.edu github: null name: Chris Stoeckert orcid: 0000-0002-5714-991X deprecated: true description: The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. download_owl: http://purl.obolibrary.org/obo/mo.owl example: ArrayGroup homepage: http://mged.sourceforge.net/ontologies/MGEDontology.php mappings: aberowl: MO biocontext: MO bioportal: MO miriam: mo n2t: mo obofoundry: mo name: Microarray experimental conditions pattern: ^\w+$ preferred_prefix: MO providers: - code: ebi description: MGED Ontology at SourceForge homepage: https://mged.sourceforge.net/ontologies/MGEDontology.php name: MGED Ontology at SourceForge uri_format: https://mged.sourceforge.net/ontologies/MGEDontology.php#$1 uri_format: http://purl.obolibrary.org/obo/MO_$1 mobidb: description: MobiDB is a database of protein disorder and mobility annotations. example: P10636 homepage: http://mobidb.bio.unipd.it mappings: biocontext: MOBIDB fairsharing: FAIRsharing.jwra3e miriam: mobidb n2t: mobidb uniprot: MobiDB name: MobiDB pattern: ^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$ preferred_prefix: mobidb provides: uniprot uri_format: https://mobidb.org/$1 mod: banana: MOD contact: email: pierre-alain.binz@chuv.ch github: pabinz name: Pierre-Alain Binz orcid: 0000-0002-0045-7698 description: The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications. download_obo: http://purl.obolibrary.org/obo/mod.obo download_owl: http://purl.obolibrary.org/obo/mod.owl example: '01467' homepage: http://www.psidev.info/MOD license: CC BY 4.0 mappings: aberowl: PSIMOD biocontext: MOD bioportal: PSIMOD fairsharing: FAIRsharing.2m4ms9 go: PSI-MOD miriam: mod n2t: mod obofoundry: mod ols: mod ontobee: MOD prefixcommons: psi.mod name: Protein modification namespace_in_lui: true pattern: ^\d{5}$ preferred_prefix: MOD publications: - doi: 10.1038/nbt0808-864 pmc: null pubmed: '18688235' title: The PSI-MOD community standard for representation of protein modification data. year: 2008 repository: https://github.com/HUPO-PSI/psi-mod-CV synonyms: - PSI-MOD uri_format: https://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=MOD:$1 modeldb: description: ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment. example: '45539' homepage: http://senselab.med.yale.edu/ModelDB/ mappings: biocontext: MODELDB edam: '2669' fairsharing: FAIRsharing.5rb3fk miriam: modeldb n2t: modeldb prefixcommons: modeldb re3data: r3d100011330 name: ModelDB pattern: ^\d+$ preferred_prefix: modeldb publications: - doi: 10.1385/ni:1:1:135 pmc: PMC3728921 pubmed: '15055399' title: 'ModelDB: making models publicly accessible to support computational neuroscience.' year: 2003 uri_format: http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1 modeldb.concept: description: Concept used by ModelDB, an accessible location for storing and efficiently retrieving computational neuroscience models. example: '3639' homepage: https://www.yale.edu mappings: miriam: modeldb.concept name: ModelDB concept pattern: ^\d+$ preferred_prefix: modeldb.concept uri_format: https://senselab.med.yale.edu/ModelDB/ModelList?id=$1 molbase: description: Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier. example: 128796-39-4 homepage: http://www.molbase.com/ mappings: biocontext: MOLBASE miriam: molbase n2t: molbase name: Molbase pattern: ^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$ preferred_prefix: molbase uri_format: http://www.molbase.com/en/index.php?app=search&search_keyword=$1 molbase.sheffield: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students. example: '1868' homepage: https://winter.group.shef.ac.uk/molbase/ name: MolBase pattern: ^\d+$ preferred_prefix: molbase.sheffield molmedb: contact: email: karel.berka@upol.cz github: KarelBerka name: Karel Berka orcid: 0000-0001-9472-2589 contributor_extras: - email: dominik.martinat@gmail.com github: DominikMartinat name: Dominik Martinat orcid: 0000-0001-6611-7883 description: 'MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations. ' example: MM00040 homepage: http://www.upol.cz/en/ mappings: fairsharing: FAIRsharing.CWzk3C miriam: molmedb name: MolMeDB pattern: ^[m,M]{2}[0-9]{5}[0-9]*$ preferred_prefix: molmedb uri_format: https://molmedb.upol.cz/mol/$1 mondo: contact: email: nicole@tislab.org github: nicolevasilevsky name: Nicole Vasilevsky orcid: 0000-0001-5208-3432 description: A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. download_json: http://purl.obolibrary.org/obo/mondo.json download_obo: http://purl.obolibrary.org/obo/mondo.obo download_owl: http://purl.obolibrary.org/obo/mondo.owl example: '0000001' homepage: https://monarch-initiative.github.io/mondo license: CC BY 4.0 mappings: aberowl: MONDO biocontext: MONDO bioportal: MONDO fairsharing: FAIRsharing.b2979t obofoundry: mondo ols: mondo ontobee: MONDO wikidata: P5270 name: Monarch Disease Ontology pattern: ^\d{7}$ preferred_prefix: MONDO publications: - doi: 10.1101/2022.04.13.22273750 pmc: null pubmed: null title: 'Mondo: Unifying diseases for the world, by the world' year: null repository: https://github.com/monarch-initiative/mondo twitter: MonarchInit uri_format: http://purl.obolibrary.org/obo/MONDO_$1 version: '2022-08-01' mop: contact: email: batchelorc@rsc.org github: batchelorc name: Colin Batchelor orcid: 0000-0001-5985-7429 description: MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation. download_obo: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.obo download_owl: http://purl.obolibrary.org/obo/mop.owl example: 0000079 homepage: https://github.com/rsc-ontologies/rxno license: CC BY 4.0 mappings: aberowl: MOP biocontext: MOP bioportal: MOP fairsharing: FAIRsharing.mct09a obofoundry: mop ols: mop ontobee: MOP name: Molecular Process Ontology pattern: ^\d{7}$ preferred_prefix: MOP repository: https://github.com/rsc-ontologies/rxno uri_format: http://purl.obolibrary.org/obo/MOP_$1 version: '2022-02-01' morpheus: description: 'The Morpheus model repository is an open-access data resource to store, search and retrieve unpublished and published computational models of spatio-temporal and multicellular biological systems, encoded in the MorpheusML language and readily executable with the Morpheus software. ' example: M0001 homepage: https://morpheus.gitlab.io/ mappings: miriam: morpheus name: Morpheus model repository pattern: ^M[0-9]{4,}$ preferred_prefix: morpheus uri_format: https://morpheus.gitlab.io/models/$1 mp: appears_in: - chiro - scdo banana: MP contact: email: drsbello@gmail.com github: sbello name: Sue Bello orcid: 0000-0003-4606-0597 description: The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways. download_json: http://purl.obolibrary.org/obo/mp.json download_obo: http://purl.obolibrary.org/obo/mp.obo download_owl: http://purl.obolibrary.org/obo/mp.owl example: '0005452' homepage: http://www.informatics.jax.org/searches/MP_form.shtml license: CC BY 4.0 mappings: aberowl: MP biocontext: MP bioportal: MP fairsharing: FAIRsharing.kg1x4z miriam: mp n2t: mp obofoundry: mp ols: mp ontobee: MP prefixcommons: mp name: Mammalian Phenotype Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: MP publications: - doi: 10.1186/s13326-015-0009-1 pmc: PMC4378007 pubmed: '25825651' title: Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens. year: 2015 - doi: 10.1007/s00335-012-9421-3 pmc: PMC3463787 pubmed: '22961259' title: The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. year: 2012 - doi: 10.1002/wsbm.44 pmc: PMC2801442 pubmed: '20052305' title: 'The mammalian phenotype ontology: enabling robust annotation and comparative analysis.' year: null - doi: 10.1186/gb-2004-6-1-r7 pmc: PMC549068 pubmed: '15642099' title: The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. year: 2004 repository: https://github.com/mgijax/mammalian-phenotype-ontology uri_format: http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1 mpath: contact: email: pns12@hermes.cam.ac.uk github: PaulNSchofield name: Paul Schofield orcid: 0000-0002-5111-7263 description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes download_obo: https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo download_owl: http://purl.obolibrary.org/obo/mpath.owl example: '728' homepage: http://www.pathbase.net license: CC BY 3.0 mappings: aberowl: MPATH biocontext: MPATH bioportal: MPATH fairsharing: FAIRsharing.3wbgm0 obofoundry: mpath ols: mpath ontobee: MPATH prefixcommons: mpath name: Mouse pathology ontology pattern: ^\d+$ preferred_prefix: MPATH publications: - doi: 10.1177/0300985810374845 pmc: PMC3038412 pubmed: '20587689' title: Pathbase and the MPATH ontology. Community resources for mouse histopathology. year: 2010 repository: https://github.com/PaulNSchofield/mpath synonyms: - MPATH uri_format: http://purl.obolibrary.org/obo/MPATH_$1 version: '2020-05-19' mpid: description: The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts. example: '172' homepage: http://www.jcvi.org/mpidb/about.php mappings: biocontext: MPID fairsharing: FAIRsharing.eyjkws miriam: mpid n2t: mpid prefixcommons: mpi name: Microbial Protein Interaction Database pattern: ^\d+$ preferred_prefix: mpid providers: - code: ebi description: Microbial Protein Interaction Database subset through IntAct homepage: https://www.ebi.ac.uk/intact/ name: Microbial Protein Interaction Database subset through IntAct uri_format: https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$1 publications: - doi: 10.1093/bioinformatics/btn285 pmc: PMC2638870 pubmed: '18556668' title: 'MPIDB: the microbial protein interaction database.' year: 2008 synonyms: - mpidb uri_format: http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1 mpio: contact: email: mbrochhausen@uams.edu github: mbrochhausen name: Mathias Brochhausen orcid: 0000-0003-1834-3856 description: An ontology of minimum information regarding potential drug-drug interaction information. download_owl: http://purl.obolibrary.org/obo/mpio.owl example: '0000004' homepage: https://github.com/MPIO-Developers/MPIO license: CC BY 4.0 mappings: aberowl: MPIO biocontext: MPIO bioportal: MPIO obofoundry: mpio ols: mpio ontobee: MPIO name: Minimum PDDI Information Ontology pattern: ^\d{7}$ preferred_prefix: MPIO repository: https://github.com/MPIO-Developers/MPIO uri_format: http://purl.obolibrary.org/obo/MPIO_$1 version: '2019-01-30' mro: contact: email: bpeters@lji.org github: bpeters42 name: Bjoern Peters orcid: 0000-0002-8457-6693 description: The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions. download_owl: http://purl.obolibrary.org/obo/mro.owl example: '0000634' homepage: https://github.com/IEDB/MRO license: CC BY 3.0 mappings: aberowl: MRO biocontext: MRO bioportal: MRO fairsharing: FAIRsharing.k893xa obofoundry: mro ols: mro ontobee: MRO name: MHC Restriction Ontology pattern: ^\d{7}$ preferred_prefix: MRO publications: - doi: 10.1186/s13326-016-0045-5 pmc: PMC4709943 pubmed: '26759709' title: An ontology for major histocompatibility restriction. year: 2016 repository: https://github.com/IEDB/MRO uri_format: http://purl.obolibrary.org/obo/MRO_$1 version: '2022-06-17' ms: banana: MS contact: email: gerhard.mayer@rub.de github: germa name: Gerhard Mayer orcid: 0000-0002-1767-2343 depends_on: - pato - uo description: The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. download_obo: http://purl.obolibrary.org/obo/ms.obo download_owl: http://purl.obolibrary.org/obo/ms.owl example: '1000560' homepage: http://www.psidev.info/groups/controlled-vocabularies license: CC BY 3.0 mappings: aberowl: MS biocontext: MS bioportal: MS miriam: ms n2t: ms obofoundry: ms ols: ms ontobee: MS name: Mass spectrometry ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: MS publications: - doi: 10.1093/database/bat009 pmc: PMC3594986 pubmed: '23482073' title: The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. year: 2013 repository: https://github.com/HUPO-PSI/psi-ms-CV uri_format: https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:$1 msigdb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can example: M1 homepage: https://www.gsea-msigdb.org mappings: biolink: MSigDB name: Molecular Signatures Database pattern: ^M\d+$ preferred_prefix: msigdb synonyms: - msig uri_format: https://biopragmatics.github.io/providers/msigdb/$1 msio: description: an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies. download_owl: https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl example: '0000111' homepage: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO mappings: ols: msio name: Metabolomics Standards Initiative Ontology pattern: ^\d{7}$ preferred_prefix: msio repository: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO uri_format: http://purl.obolibrary.org/obo/MSIO_$1 version: 1.0.1 multicellds: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata. example: MCDS_S_0000000001 homepage: http://multicellds.org/MultiCellDB.php mappings: fairsharing: FAIRsharing.pqzyd5 name: MultiCellDS preferred_prefix: multicellds uri_format: http://multicellds.org/MultiCellDB/$1 multicellds.cell_line: description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata. example: MCDS_L_0000000001 homepage: http://multicellds.org/MultiCellDB.php mappings: biocontext: MULTICELLDS.CELL_LINE miriam: multicellds.cell_line n2t: multicellds.cell_line name: MultiCellDS Digital Cell Line part_of: multicellds pattern: ^MCDS_L_[a-zA-Z0-9]{1,10}$ preferred_prefix: multicellds.cell_line uri_format: http://multicellds.org/MultiCellDB/$1 multicellds.collection: description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections). example: MCDS_C_0000000001 homepage: http://multicellds.org/MultiCellDB.php mappings: biocontext: MULTICELLDS.COLLECTION miriam: multicellds.collection n2t: multicellds.collection name: MultiCellDS collection part_of: multicellds pattern: ^MCDS_C_[a-zA-Z0-9]{1,10}$ preferred_prefix: multicellds.collection uri_format: http://multicellds.org/MultiCellDB/$1 multicellds.snapshot: description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data. example: MCDS_S_0000000001 homepage: http://multicellds.org/MultiCellDB.php mappings: biocontext: MULTICELLDS.SNAPSHOT miriam: multicellds.snapshot n2t: multicellds.snapshot name: MultiCellDS Digital snapshot part_of: multicellds pattern: ^MCDS_S_[a-zA-Z0-9]{1,10}$ preferred_prefix: multicellds.snapshot uri_format: http://multicellds.org/MultiCellDB/$1 mw.project: description: Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC). example: PR000001 homepage: http://www.metabolomicsworkbench.org/ mappings: biocontext: MW.PROJECT miriam: mw.project n2t: mw.project name: Metabolomics Workbench Project pattern: ^PR[0-9]{6}$ preferred_prefix: mw.project uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1 mw.study: description: Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC). example: ST000900 homepage: http://www.metabolomicsworkbench.org/ mappings: biocontext: MW.STUDY miriam: mw.study n2t: mw.study name: Metabolomics Workbench Study pattern: ^ST[0-9]{6}$ preferred_prefix: mw.study providers: - code: omicsdi description: Metabolomics Workbench Study through OmicsDI homepage: https://www.omicsdi.org/ name: Metabolomics Workbench Study through OmicsDI uri_format: https://www.omicsdi.org/dataset/metabolomics_workbench/$1 uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1 myco.lepra: description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information. example: ML0224 homepage: http://mycobrowser.epfl.ch/leprosy.html mappings: biocontext: MYCO.LEPRA miriam: myco.lepra n2t: myco.lepra prefixcommons: myco.lepra name: MycoBrowser leprae pattern: ^ML\w+$ preferred_prefix: myco.lepra uri_format: http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1 myco.marinum: description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information. example: MMAR_2462 homepage: http://mycobrowser.epfl.ch/marinolist.html mappings: biocontext: MYCO.MARINUM miriam: myco.marinum n2t: myco.marinum prefixcommons: myco.marinum name: MycoBrowser marinum pattern: ^MMAR\_\d+$ preferred_prefix: myco.marinum uri_format: http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1 myco.smeg: description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information. example: MSMEG_3769 homepage: http://mycobrowser.epfl.ch/smegmalist.html mappings: biocontext: MYCO.SMEG miriam: myco.smeg n2t: myco.smeg prefixcommons: myco.smeg name: MycoBrowser smegmatis pattern: ^MSMEG\w+$ preferred_prefix: myco.smeg uri_format: http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1 myco.tuber: description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information. example: Rv1908c homepage: http://tuberculist.epfl.ch/ mappings: biocontext: MYCO.TUBER miriam: myco.tuber n2t: myco.tuber ncbi: TubercuList prefixcommons: tuberculist uniprot: TubercuList name: TubercuList knowledge base pattern: ^Rv\d{4}(A|B|c)?$ preferred_prefix: myco.tuber synonyms: - TubercuList uri_format: http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1 mycobank: description: MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations. example: '349124' homepage: http://www.mycobank.org/ mappings: biocontext: MYCOBANK fairsharing: FAIRsharing.v8se8r miriam: mycobank n2t: mycobank ncbi: MycoBank prefixcommons: mycobank re3data: r3d100011222 name: Fungal Nomenclature and Species Bank pattern: ^\d+$ preferred_prefix: mycobank uri_format: http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1 mzspec: banana: mzspec description: The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it. example: PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2 homepage: http://proteomecentral.proteomexchange.org/ mappings: biocontext: MZSPEC miriam: mzspec n2t: mzspec name: Universal Spectrum Identifier namespace_in_lui: true pattern: ^.+$ preferred_prefix: mzspec providers: - code: CURATOR_REVIEW description: Universal Spectrum Identifier through Peptide Atlas homepage: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum name: Universal Spectrum Identifier through Peptide Atlas uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum?usi=mzspec:$1 uri_format: http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1 n2t: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ARK resolver as well as resolver built with common prefixes as in Identifiers.org example: chebi homepage: https://n2t.net name: Name-to-Thing preferred_prefix: n2t uri_format: 'https://n2t.net/$1:' namerxn: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO). example: 4.2.78 homepage: https://www.nextmovesoftware.com/namerxn.html name: NameRXN preferred_prefix: namerxn proprietary: true publications: - doi: 10.1038/s42256-020-00284-w pmc: null pubmed: null title: Mapping the space of chemical reactions using attention-based neural networks year: null - doi: 10.1021/acs.jmedchem.6b00153 pmc: null pubmed: null title: 'Big Data from Pharmaceutical Patents: A Computational Analysis of Medicinal Chemists’ Bread and Butter' year: null references: - https://www.nextmovesoftware.com/products/HazELNutPoster.pdf - https://twitter.com/cthoyt/status/1443929184745758723 napdi: description: The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs). example: '28' homepage: https://repo.napdi.org/ mappings: biocontext: NAPDI fairsharing: FAIRsharing.y9x8wk miriam: napdi n2t: napdi name: Natural Product-Drug Interaction Research Data Repository pattern: ^[0-9]+$ preferred_prefix: napdi uri_format: https://repo.napdi.org/study/$1 napp: description: NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters. example: '351' homepage: http://napp.u-psud.fr/ mappings: biocontext: NAPP fairsharing: FAIRsharing.vr52p3 miriam: napp n2t: napp prefixcommons: napp name: Nucleic Acids Phylogenetic Profiling pattern: ^\d+$ preferred_prefix: napp uri_format: http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1 narcis: description: NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases. example: oai:cwi.nl:4725 homepage: http://www.narcis.nl mappings: biocontext: NARCIS fairsharing: FAIRsharing.f63h4k miriam: narcis n2t: narcis name: National Academic Research and Collaborations Information System pattern: ^oai\:cwi\.nl\:\d+$ preferred_prefix: narcis uri_format: http://www.narcis.nl/publication/RecordID/$1 nasc: description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. example: N1899 homepage: http://arabidopsis.info/ mappings: biocontext: NASC fairsharing: FAIRsharing.2sqcxs miriam: nasc n2t: nasc prefixcommons: nasc re3data: r3d100010906 name: NASC code pattern: ^(\w+)?\d+$ preferred_prefix: nasc uri_format: http://arabidopsis.info/StockInfo?NASC_id=$1 nbn: description: The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier. example: urn:nbn:fi:tkk-004781 homepage: http://nbn-resolving.org/resolve_urn.htm mappings: biocontext: NBN miriam: nbn n2t: nbn name: National Bibliography Number pattern: ^urn\:nbn\:[A-Za-z_0-9]+\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$ preferred_prefix: nbn uri_format: http://nbn-resolving.org/resolver?identifier=$1&verb=redirect nbo: appears_in: - ecto - pcl - scdo contact: email: g.gkoutos@bham.ac.uk github: gkoutos name: George Gkoutos orcid: 0000-0002-2061-091X description: An ontology of human and animal behaviours and behavioural phenotypes download_obo: https://github.com/obo-behavior/behavior-ontology/raw/master/nbo.obo download_owl: http://purl.obolibrary.org/obo/nbo.owl example: '0000564' homepage: https://github.com/obo-behavior/behavior-ontology/ license: CC BY 3.0 mappings: aberowl: NBO biocontext: NBO bioportal: NBO fairsharing: FAIRsharing.pktgc6 obofoundry: nbo ols: nbo ontobee: NBO name: Neuro Behavior Ontology pattern: ^\d{7}$ preferred_prefix: NBO publications: - doi: 10.1007/s00335-013-9481-z pmc: null pubmed: '24177753' title: Analyzing gene expression data in mice with the Neuro Behavior Ontology. year: 2013 - doi: 10.1016/b978-0-12-388408-4.00004-6 pmc: null pubmed: '23195121' title: 'The neurobehavior ontology: an ontology for annotation and integration of behavior and behavioral phenotypes.' year: 2012 repository: https://github.com/obo-behavior/behavior-ontology uri_format: http://purl.obolibrary.org/obo/NBO_$1 version: '2021-02-15' nbrc: description: NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information. example: '00001234' homepage: http://www.nbrc.nite.go.jp/e/index.html mappings: biocontext: NBRC fairsharing: FAIRsharing.ftamrc miriam: nbrc n2t: nbrc ncbi: NBRC prefixcommons: nbrc name: NITE Biological Resource Center pattern: ^\d+$ preferred_prefix: nbrc uri_format: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1 ncats.bioplanet: contact: email: ruili.huang@nih.gov github: null name: Ruili Huang orcid: 0000-0001-8886-8311 contributor: email: null github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 description: The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays. example: '3' github_request_issue: 445 homepage: https://tripod.nih.gov/bioplanet/ mappings: biolink: ncats.bioplanet name: National Center for Advancing Translation Sciences BioPlanet pattern: ^\d+$ preferred_prefix: ncats.bioplanet publications: - doi: 10.3389/fphar.2019.00445 pmc: null pubmed: null title: The NCATS BioPlanet – An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics year: null reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 twitter: ncats_nih_gov uri_format: https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1 ncats.drug: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 - email: null github: vdancik name: Vlado Dancik orcid: 0000-0002-5970-6660 - email: null github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 description: 'The National Center for Advancing Translational Sciences](http://www.ncats.nih.gov/) (NCATS) has developed Inxight Drugs as a comprehensive portal for drug development information. NCATS Inxight Drugs contains information on ingredients in medicinal products, including: - US Approved Drugs - Marketed Drugs - Investigational Drugs - Other Substances' example: '44259' example_extras: - 1IJV77EI07 homepage: https://drugs.ncats.io/ mappings: biolink: ncats.drug name: NCATS Drugs preferred_prefix: ncats.drug synonyms: - inxight - inxight-drugs uri_format: https://drugs.ncats.io/drug/$1 ncbi.assembly: description: A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. example: GCF_000005845.2 homepage: https://www.ncbi.nlm.nih.gov/ mappings: biocontext: NCBIAssembly miriam: assembly re3data: r3d100012688 name: Assembly pattern: ^[a-zA-Z0-9_\.]+$ preferred_prefix: ncbi.assembly uri_format: https://www.ncbi.nlm.nih.gov/assembly/$1 ncbi.genome: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations. example: '51' homepage: https://www.ncbi.nlm.nih.gov/genome mappings: biocontext: NCBIGenome edam: '2787' re3data: r3d100010785 name: NCBI Genome pattern: ^\d+$ preferred_prefix: ncbi.genome uri_format: https://www.ncbi.nlm.nih.gov/genome/$1 ncbi.resource: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources example: ECOCYC homepage: https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/ name: NCBI Registry preferred_prefix: ncbi.resource uri_format: https://bioregistry.io/metaregistry/ncbi/$1 ncbibook: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. ' example: NBK331 homepage: https://www.ncbi.nlm.nih.gov/books name: NCBI Bookshelf pattern: ^NBK\d+$ preferred_prefix: ncbibook uri_format: https://www.ncbi.nlm.nih.gov/books/$1 ncbigene: description: Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis. example: '100010' homepage: https://www.ncbi.nlm.nih.gov/gene mappings: biocontext: NCBIGene biolink: NCBIGene edam: '1027' fairsharing: FAIRsharing.5h3maw go: NCBIGene hl7: geneCodeNCBI miriam: ncbigene n2t: ncbigene ncbi: GeneID prefixcommons: ncbigene re3data: r3d100010650 wikidata: P351 name: Entrez Gene pattern: ^\d+$ preferred_prefix: NCBIGene providers: - code: CURATOR_REVIEW description: Bio2RDF homepage: http://ncbigene.bio2rdf.org/fct name: Bio2RDF uri_format: http://ncbigene.bio2rdf.org/describe/?url=http://bio2rdf.org/ncbigene:$1 - code: marrvel description: Helps browse potential orthologs in model organisms for a given gene homepage: http://marrvel.org name: Model organism Aggregated Resources for Rare Variant ExpLoration uri_format: http://marrvel.org/model/gene/$1 - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/ncbi-gene/$1 publications: - doi: 10.1093/nar/gki031 pmc: PMC539985 pubmed: '15608257' title: 'Entrez Gene: gene-centered information at NCBI.' year: 2005 synonyms: - EGID - EntrezGene - NCBIGene - NCBI_GeneID - entrez - entrez gene/locuslink uri_format: https://www.ncbi.nlm.nih.gov/gene/$1 ncbigi: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A GI number (for GenInfo Identifier, sometimes written in lower case, _gi_) is a simple series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Version number of the sequence record. Each time a sequence record is changed, it is assigned a new GI number. example: '568815597' homepage: https://www.ncbi.nlm.nih.gov/genbank/sequenceids/ mappings: biocontext: NCBIGI go: NCBI_gi name: GenInfo Identifier pattern: ^\d+$ preferred_prefix: ncbigi references: - https://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html - https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/Format/exercises/qa_accession_vs_gi.html synonyms: - NCBI_gi - ncbi.gi uri_format: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$1 ncbiprotein: description: The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. example: CAA71118.1 homepage: https://www.ncbi.nlm.nih.gov/protein mappings: biocontext: NCBIProtein go: NCBI_NP miriam: ncbiprotein n2t: ncbiprotein prefixcommons: ncbi.protein re3data: r3d100010776 name: NCBI Protein pattern: ^(\w+\d+(\.\d+)?)|(NP_\d+)$ preferred_prefix: NCBIProtein uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 ncbitaxon: appears_in: - agro - chiro - cl - clo - ecto - envo - foodon - genepio - go - hso - mco - ons - pcl - pco - vbo contact: email: frederic.bastian@unil.ch github: fbastian name: Frederic Bastian orcid: 0000-0002-9415-5104 description: The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined. download_json: http://purl.obolibrary.org/obo/ncbitaxon.json download_obo: http://purl.obolibrary.org/obo/ncbitaxon.obo download_owl: http://purl.obolibrary.org/obo/ncbitaxon.owl example: '2170610' homepage: https://github.com/obophenotype/ncbitaxon license: CC0 1.0 mappings: aberowl: NCBITAXON agroportal: NCBITAXON biocontext: TAXONOMY bioportal: NCBITAXON cellosaurus: NCBI_TaxID edam: '1179' fairsharing: FAIRsharing.fj07xj go: taxon hl7: NCBI miriam: taxonomy n2t: taxonomy ncbi: taxon obofoundry: ncbitaxon ols: ncbitaxon ontobee: NCBITaxon prefixcommons: uniprot.taxonomy re3data: r3d100010415 wikidata: P685 name: NCBI Taxonomy pattern: ^\d+$ preferred_prefix: NCBITaxon providers: - code: CURATOR_REVIEW description: Taxonomy through UniProt PURL homepage: https://www.uniprot.org/taxonomy/ name: Taxonomy through UniProt PURL uri_format: https://purl.uniprot.org/taxonomy/$1 - code: CURATOR_REVIEW description: Bio2RDF homepage: https://bio2rdf.org/ name: Bio2RDF uri_format: https://bio2rdf.org/taxonomy:$1 - code: ebi description: European Nucleotide Archive (ENA) homepage: https://www.ebi.ac.uk/ena/ name: European Nucleotide Archive (ENA) uri_format: https://www.ebi.ac.uk/ena/data/view/Taxon:$1 - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/ncbi-taxon/$1 publications: - doi: 10.1093/database/baaa062 pmc: PMC7408187 pubmed: '32761142' title: 'NCBI Taxonomy: a comprehensive update on curation, resources and tools.' year: 2020 - doi: 10.1093/nar/gkx1094 pmc: PMC5753231 pubmed: '29140468' title: GenBank. year: 2018 - doi: 10.1093/nar/gkr1178 pmc: PMC3245000 pubmed: '22139910' title: The NCBI Taxonomy database. year: 2011 repository: https://github.com/obophenotype/ncbitaxon synonyms: - NCBI Taxonomy - NCBITaxon - NCBI_Taxon_ID - NCBI_taxid - TAX - TaxonomyID - taxid - taxon - taxonomy - uniprot.taxonomy uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1 version: '2022-08-18' ncim: description: NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical. example: C0026339 homepage: http://ncim.nci.nih.gov/ mappings: biocontext: NCIM miriam: ncim n2t: ncim name: NCI Metathesaurus pattern: ^C\d+$ preferred_prefix: ncim uri_format: http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1 ncit: appears_in: - ecto - mco - ontoavida - scdo contact: email: haendel@ohsu.edu github: mellybelly name: Melissa Haendel orcid: 0000-0001-9114-8737 description: NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code. download_obo: http://purl.obolibrary.org/obo/ncit.obo download_owl: http://purl.obolibrary.org/obo/ncit.owl example: C138986 homepage: https://github.com/NCI-Thesaurus/thesaurus-obo-edition license: CC BY 4.0 mappings: aberowl: NCIT biocontext: NCIT bioportal: NCIT cellosaurus: NCIt fairsharing: FAIRsharing.4cvwxa hl7: 2.16.840.1.113883.6.206 miriam: ncit n2t: ncit obofoundry: ncit ols: ncit ontobee: NCIT prefixcommons: ncit wikidata: P1748 name: NCI Thesaurus pattern: ^C\d+$ preferred_prefix: NCIT providers: - code: evs description: Links to a no-longer existing OWL file homepage: https://ncit.nci.nih.gov/ncitbrowser/ name: Legacy NCBI OWL uri_format: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#$1 publications: - doi: 10.3233/ao-2008-0051 pmc: PMC2753293 pubmed: '19789731' title: 'Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages.' year: 2008 - doi: 10.3233/978-1-60750-949-3-33 pmc: null pubmed: '15360769' title: 'NCI Thesaurus: using science-based terminology to integrate cancer research results.' year: 2004 repository: https://github.com/NCI-Thesaurus/thesaurus-obo-edition synonyms: - NCI - NCI2004_11_17 - NCIT - NCIT_Thesaurus - NCITm - NCITt - NCI_Thesaurus - NCIt - NCit - ncithesaurus uri_format: http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1 version: 22.07d ncro: contact: email: huang@southalabama.edu github: Huang-OMIT name: Jingshan Huang orcid: 0000-0003-2408-2883 description: An ontology for non-coding RNA, both of biological origin, and engineered. download_obo: https://raw.githubusercontent.com/OmniSearch/ncro/master/src/ontology/ncro.obo download_owl: http://purl.obolibrary.org/obo/ncro.owl example: 0002927 homepage: http://omnisearch.soc.southalabama.edu/w/index.php/Ontology license: CC BY 4.0 mappings: aberowl: NCRO biocontext: NCRO bioportal: NCRO fairsharing: FAIRsharing.vppyga obofoundry: ncro ols: ncro ontobee: NCRO name: Non-Coding RNA Ontology pattern: ^\d{7}$ preferred_prefix: NCRO repository: https://github.com/OmniSearch/ncro uri_format: http://purl.obolibrary.org/obo/NCRO_$1 version: '2015-12-10' ndc: description: The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily. example: 0002-1975-61 homepage: http://www.accessdata.fda.gov/scripts/cder/ndc/ mappings: biocontext: NDC hl7: 2.16.840.1.113883.6.69 miriam: ndc n2t: ndc name: National Drug Code pattern: ^\d+\-\d+\-\d+$ preferred_prefix: ndc providers: - code: CURATOR_REVIEW description: Bio2RDF homepage: http://ndc.bio2rdf.org/fct name: Bio2RDF uri_format: http://ndc.bio2rdf.org/describe/?url=http://bio2rdf.org/ndc:$1 uri_format: http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1 nddf: contact: email: cs@firstdatabank.com github: null name: First DataBank Customer Support orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: FDB MedKnowledge encompasses medications approved by the U.S. Food and Drug Administration, and information on commonly-used over-the-counter and alternative therapy agents such as herbals, nutraceuticals and dietary supplements. example: 002678 homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDDF mappings: aberowl: NDDF biolink: NDDF bioportal: NDDF fairsharing: FAIRsharing.8qcbs0 hl7: 2.16.840.1.113883.6.208 name: National Drug Data File pattern: ^\d{6}$ preferred_prefix: nddf uri_format: http://purl.bioontology.org/ontology/NDDF/$1 ndex: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge. example: aa78a43f-9c4d-11eb-9e72-0ac135e8bacf homepage: https://www.ndexbio.org mappings: fairsharing: FAIRsharing.8nq9t6 name: Network Data Exchange preferred_prefix: ndex uri_format: https://www.ndexbio.org/viewer/networks/$1 ndfrt: contact: email: michael.lincoln@va.gov github: null name: Michael J. Lincoln MD orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction].' example: N0000001662 homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDFRT mappings: aberowl: NDFRT bioportal: NDFRT fairsharing: FAIRsharing.901nkj hl7: 2.16.840.1.113883.6.209 ontobee: NDF-RT prefixcommons: ndfrt wikidata: P2115 name: National Drug File - Reference Terminology preferred_prefix: ndfrt publications: - doi: null pmc: PMC1480331 pubmed: '14728237' title: Adequacy of representation of the National Drug File Reference Terminology Physiologic Effects reference hierarchy for commonly prescribed medications. year: 2003 synonyms: - NUI - ndf-rt uri_format: https://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#$1 nemo: contact: email: gfrishkoff@gsu.edu github: null name: Gwen Frishkoff orcid: null description: This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects. download_owl: http://aber-owl.net/media/ontologies/NEMO/24/nemo.owl example: smp-m3w9hbe homepage: https://www.nemoarchive.org mappings: aberowl: NEMO bioportal: NEMO fairsharing: FAIRsharing.n66krd miriam: nemo name: Neural ElectroMagnetic Ontology pattern: ^[a-z]{3}-[a-km-z0-9]{7}$ preferred_prefix: nemo publications: - doi: 10.4056/sigs.2025347 pmc: PMC3235514 pubmed: '22180824' title: 'Minimal Information for Neural Electromagnetic Ontologies (MINEMO): A standards-compliant method for analysis and integration of event-related potentials (ERP) data.' year: 2011 - doi: 10.1038/npre.2009.3458.1 pmc: null pubmed: null title: 'Development of Neural Electromagnetic Ontologies (NEMO): Ontology-based Tools for Representation and Integration of Event-related Brain Potentials' year: null uri_format: https://assets.nemoarchive.org/$1 neurolex: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4802 description: The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex). example: '4' homepage: https://github.com/SciCrunch/NIF-Ontology license: CC BY-4.0 mappings: biocontext: NEUROLEX miriam: neurolex n2t: neurolex prefixcommons: neurolex name: 'NIF Standard Ontology: Neurolex' part_of: nif pattern: ^\d+$ preferred_prefix: neurolex publications: - doi: 10.1007/s12021-008-9032-z pmc: PMC2743139 pubmed: '18975148' title: 'The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.' year: 2008 repository: https://github.com/SciCrunch/NIF-Ontology synonyms: - NLX - nlx twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_$1 neuromorpho: description: NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons. example: Rosa2 homepage: http://neuromorpho.org/index.jsp mappings: biocontext: NEUROMORPHO edam: '2657' miriam: neuromorpho n2t: neuromorpho prefixcommons: neuromorpho name: NeuroMorpho pattern: ^\w+$ preferred_prefix: neuromorpho publications: - doi: 10.1038/nrn1885 pmc: null pubmed: '16552417' title: 'Mobilizing the base of neuroscience data: the case of neuronal morphologies.' year: 2006 uri_format: http://neuromorpho.org/neuron_info.jsp?neuron_name=$1 neuronames: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it. example: '268' homepage: http://braininfo.rprc.washington.edu/ mappings: wikidata: P4394 name: NeuroNames pattern: ^\d+$ preferred_prefix: neuronames references: - https://en.wikipedia.org/wiki/NeuroNames synonyms: - neuroname uri_format: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1 neurondb: description: 'NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.' example: '265' homepage: http://senselab.med.yale.edu/NeuronDB/ mappings: biocontext: NEURONDB edam: '2656' fairsharing: FAIRsharing.45a10e miriam: neurondb n2t: neurondb prefixcommons: neurondb name: NeuronDB pattern: ^\d+$ preferred_prefix: neurondb uri_format: http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1 neurovault.collection: description: Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images. example: '3304' homepage: http://neurovault.org mappings: biocontext: NEUROVAULT.COLLECTION miriam: neurovault.collection n2t: neurovault.collection name: NeuroVault Collection pattern: ^[1-9][0-9]*$ preferred_prefix: neurovault.collection uri_format: https://neurovault.org/collections/$1 neurovault.image: description: Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images. example: '58788' homepage: http://neurovault.org mappings: biocontext: NEUROVAULT.IMAGE miriam: neurovault.image n2t: neurovault.image name: NeuroVault Image pattern: ^[1-9][0-9]*$ preferred_prefix: neurovault.image uri_format: https://neurovault.org/images/$1 nextdb: description: NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones. example: 6b1 homepage: http://nematode.lab.nig.ac.jp/ mappings: biocontext: NEXTDB fairsharing: FAIRsharing.xz5m1a miriam: nextdb n2t: nextdb ncbi: NextDB prefixcommons: nextdb name: Nematode Expression Pattern DataBase pattern: ^[A-Za-z0-9]+$ preferred_prefix: nextdb uri_format: http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1 nextprot: description: neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases. example: NX_O00165 homepage: https://www.nextprot.org/ mappings: biocontext: NEXTPROT fairsharing: FAIRsharing.62evqh miriam: nextprot n2t: nextprot uniprot: neXtProt name: nextProt pattern: ^NX_\w+$ preferred_prefix: nextprot synonyms: - NXP twitter: neXtProt_news uri_format: https://www.nextprot.org/db/entry/$1 nextprot.family: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: "NeXtProt is a comprehensive human-centric discovery platform, offering\ \ its users a seamless integration of and navigation through protein-related data.\ \ \n(Developed by the SIB Swiss Institute of Bioinformatics)" example: '01406' homepage: https://www.nextprot.org/ name: neXtProt family pattern: ^\d+$ preferred_prefix: nextprot.family synonyms: - NXPFA twitter: neXtProt_news uri_format: https://www.nextprot.org/term/FA-$1 ngl: description: NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA. example: GLDS-141 homepage: https://genelab-data.ndc.nasa.gov/genelab/ mappings: biocontext: NGL miriam: ngl n2t: ngl name: NASA GeneLab pattern: ^GLDS-\d+$ preferred_prefix: ngl uri_format: https://genelab-data.ndc.nasa.gov/genelab/accession/$1 nhcdr: description: Cell line collections example: ND50028 homepage: https://stemcells.nindsgenetics.org mappings: cellosaurus: NHCDR name: NINDS Human Cell and Data Repository preferred_prefix: nhcdr uri_format: https://stemcells.nindsgenetics.org?line=$1 niaest: description: A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones. example: J0705A10 homepage: http://lgsun.grc.nia.nih.gov/cDNA/ mappings: biocontext: NIAEST fairsharing: FAIRsharing.xwqg9h miriam: niaest n2t: niaest ncbi: niaEST prefixcommons: niaest name: NIA Mouse cDNA Project pattern: ^\w\d{4}\w\d{2}(\-[35])?$ preferred_prefix: niaest uri_format: http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1 nif.cell: contact: email: smtifahim@gmail.com github: null name: Fahim Imam orcid: null deprecated: true description: Neuronal cell types download_owl: http://aber-owl.net/media/ontologies/NIFCELL/15/nifcell.owl homepage: http://neuinfo.org/ mappings: aberowl: NIFCELL biocontext: NIF_CELL bioportal: NIFCELL obofoundry: nif_cell name: NIF Cell part_of: nif preferred_prefix: NIF_CELL uri_format: http://purl.obolibrary.org/obo/NIF_CELL_$1 nif.dysfunction: contact: email: smtifahim@gmail.com github: null name: Fahim Imam orcid: null deprecated: true homepage: http://neuinfo.org/ mappings: biocontext: NIF_DYSFUNCTION obofoundry: nif_dysfunction name: NIF Dysfunction part_of: nif preferred_prefix: NIF_DYSFUNCTION uri_format: http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1 nif.ext: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: NIFEXT covers IRIs that were "external" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed. example: '7123' homepage: https://github.com/SciCrunch/NIF-Ontology license: CC BY-4.0 name: 'NIF Standard Ontology: External' part_of: nif pattern: ^\d+$ preferred_prefix: nif.ext repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NIFEXT twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nifext_$1 nif.grossanatomy: contact: email: smtifahim@gmail.com github: null name: Fahim Imam orcid: null deprecated: true homepage: http://neuinfo.org/ mappings: biocontext: NIF_GROSSANATOMY obofoundry: nif_grossanatomy name: NIF Gross Anatomy part_of: nif preferred_prefix: NIF_GROSSANATOMY uri_format: http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1 nif.std: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing. download_owl: http://aber-owl.net/media/ontologies/NIFSTD/23/nifstd.owl example: BAMSC981 homepage: https://github.com/SciCrunch/NIF-Ontology license: CC BY-4.0 mappings: aberowl: NIFSTD bioportal: NIFSTD fairsharing: FAIRsharing.vgw1m6 name: NIF Standard Ontology part_of: nif pattern: ^BAMSC\d+$ preferred_prefix: nif.std publications: - doi: 10.1007/s12021-008-9032-z pmc: PMC2743139 pubmed: '18975148' title: 'The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.' year: 2008 repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NIFSTD twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/$1 nihreporter.project: contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding. example: '10343835' github_request_issue: 400 homepage: https://reporter.nih.gov/ name: NIH RePORTER pattern: ^\d+$ preferred_prefix: nihreporter.project reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://reporter.nih.gov/project-details/$1 nist: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species. homepage: https://webbook.nist.gov/chemistry/ name: NIST Chemistry WebBook no_own_terms: true preferred_prefix: nist synonyms: - NIST - NIST Chemistry WebBook nlm: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings. example: '101775319' homepage: https://www.ncbi.nlm.nih.gov/nlmcatalog mappings: biolink: NLMID name: National Library of Medicine Catalog pattern: ^\d+$ preferred_prefix: nlm uri_format: https://www.ncbi.nlm.nih.gov/nlmcatalog/$1 nlx.anat: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4804 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: NLXANAT covers anatomy terms. Almost all terms are also in Uberon. example: 090201 homepage: https://scicrunch.org/scicrunch/interlex/dashboard name: NeuroLex Anatomy part_of: nif pattern: ^\d+$ preferred_prefix: nlx.anat reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1 nlx.br: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4804 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4804 description: NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999). example: '145' homepage: https://github.com/SciCrunch/NIF-Ontology license: CC BY-4.0 name: 'NIF Standard Ontology: Brain Regions' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.br repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXBR twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_br_$1 nlx.cell: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4805 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4805 description: NLXCELL conatins cell types with a focus on neuron types. example: '91005' homepage: https://github.com/SciCrunch/NIF-Ontology license: CC BY-4.0 name: 'NIF Standard Ontology: Cell Types' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.cell repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXCELL twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1 nlx.chem: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4806 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4806 description: NLXCHEM covers chemicals. Most classes are also in ChEBI. example: '90801' homepage: https://github.com/SciCrunch/NIF-Ontology license: CC BY-4.0 name: 'NIF Standard Ontology: Chemical' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.chem repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXCHEM twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1 nlx.dys: appears_in: - mondo contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4804 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc. example: '20090303' homepage: https://scicrunch.org/scicrunch/interlex/dashboard name: NeuroLex Dysfunction part_of: nif pattern: ^\d+$ preferred_prefix: nlx.dys reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1 nlx.func: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4808 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4808 description: NLXFUNC covers terms for cognitive function. example: '90801' homepage: https://github.com/SciCrunch/NIF-Ontology license: CC BY-4.0 name: 'NIF Standard Ontology: Cognitive Function' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.func repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXFUNC twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_func_$1 nlx.inv: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4809 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4809 description: NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis. example: '90901' homepage: https://github.com/SciCrunch/NIF-Ontology license: CC BY-4.0 name: 'NIF Standard Ontology: Investigations' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.inv repository: https://github.com/SciCrunch/NIF-Ontology synonyms: - NLXINV twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1 nlx.mol: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4810 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4810 description: NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system. example: '90806' homepage: https://github.com/SciCrunch/NIF-Ontology license: CC BY-4.0 name: 'NIF Standard Ontology: Molecules' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.mol repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXMOL twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1 nlx.oen: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4811 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4811 description: NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results). example: '0001000' homepage: https://github.com/SciCrunch/NIF-Ontology license: CC BY-4.0 name: 'NIF Standard Ontology: OEN Terms in Neurolex' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.oen repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXOEN twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/oen_$1 nlx.org: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4812 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4812 description: NLXORG covers organisms. example: 090701 homepage: https://github.com/SciCrunch/NIF-Ontology license: CC BY-4.0 name: 'NIF Standard Ontology: Organisms' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.org repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXORG twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1 nlx.qual: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4813 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4813 description: NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO). example: '100810' homepage: https://github.com/SciCrunch/NIF-Ontology license: CC BY-4.0 name: 'NIF Standard Ontology: Qualities' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.qual repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXQUAL twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1 nlx.res: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4814 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4814 description: NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites example: 090924 homepage: https://github.com/SciCrunch/NIF-Ontology license: CC BY-4.0 name: 'NIF Standard Ontology: Digital Resources' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.res repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXRES twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_res_$1 nlx.sub: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4815 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4815 description: NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO). example: 090803 homepage: https://github.com/SciCrunch/NIF-Ontology license: CC BY-4.0 mappings: go: NIF_Subcellular name: 'NIF Standard Ontology: Subcellular Entities' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.sub repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXSUB - nif_subcellular twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1 nmdc: contact: email: donny@polyneme.xyz github: dwinston name: Donny Winston orcid: 0000-0002-8424-0604 contributor: email: donny@polyneme.xyz github: dwinston name: Donny Winston orcid: 0000-0002-8424-0604 description: An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem. example: y3ax-8bq3-60 homepage: https://microbiomedata.org/ mappings: miriam: nmdc name: National Microbiome Data Collaborative pattern: ^[\w\-.]{3,}$ preferred_prefix: nmdc reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://drs.microbiomedata.org/objects/$1 nmr: banana: NMR contact: email: schober@imbi.uni-freiburg.de github: null name: Schober Daniel orcid: null deprecated: true description: nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi. download_owl: https://nmrml.org/cv/stable/nmrCV.owl example: '1000003' homepage: http://msi-ontology.sourceforge.net/ mappings: aberowl: NMR biocontext: NMR bioportal: NMR miriam: nmr n2t: nmr obofoundry: nmr ols: nmrcv prefixcommons: nmr name: NMR-instrument specific component of metabolomics investigations namespace_in_lui: true pattern: ^\d+$ preferred_prefix: NMR synonyms: - nmrcv uri_format: https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1 version: 1.1.0 nmrshiftdb2: description: NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. example: '234' homepage: https://nmrshiftdb.nmr.uni-koeln.de mappings: fairsharing: FAIRsharing.nYaZ1N miriam: nmrshiftdb2 name: NMR Shift Database pattern: ^[0-9]+$ preferred_prefix: nmrshiftdb2 uri_format: https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1 noaa: contributor: email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 description: Identifier for a species on the noaa fisheries website example: long-finned-pilot-whale github_request_issue: 456 homepage: https://www.fisheries.noaa.gov/species-directory mappings: wikidata: P6049 name: NOAA Fisheries Species Directory pattern: ^[a-z]+(\-[a-z]+)*$ preferred_prefix: noaa reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.fisheries.noaa.gov/species/$1 nomen: contact: email: diapriid@gmail.com github: mjy name: Matt Yoder orcid: 0000-0002-5640-5491 description: NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature. download_owl: http://purl.obolibrary.org/obo/nomen.owl example: 0000295 homepage: https://github.com/SpeciesFileGroup/nomen license: CC0 1.0 mappings: aberowl: NOMEN bioportal: NOMEN obofoundry: nomen ols: nomen ontobee: NOMEN name: A nomenclatural ontology for biological names pattern: ^\d{7}$ preferred_prefix: NOMEN repository: https://github.com/SpeciesFileGroup/nomen uri_format: http://purl.obolibrary.org/obo/NOMEN_$1 noncodev3: description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4. example: '377550' homepage: http://www.noncode.org/ mappings: biocontext: NONCODEV3 miriam: noncodev3 n2t: noncodev3 name: NONCODE v3 pattern: ^\d+$ preferred_prefix: noncodev3 uri_format: http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1 noncodev4.gene: description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions. example: NONHSAG00001 homepage: http://www.bioinfo.org/NONCODEv4/ mappings: biocontext: NONCODEV4.GENE miriam: noncodev4.gene n2t: noncodev4.gene name: NONCODE v4 Gene pattern: ^NONHSAG\d{5}$ preferred_prefix: noncodev4.gene uri_format: http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1 noncodev4.rna: description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts. example: NONHSAT000001 homepage: http://www.bioinfo.org/NONCODEv4/ mappings: biocontext: NONCODEV4.RNA miriam: noncodev4.rna n2t: noncodev4.rna name: NONCODE v4 Transcript pattern: ^NONHSAT\d{6}$ preferred_prefix: noncodev4.rna uri_format: http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1 norine: description: Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings. example: NOR00681 homepage: http://bioinfo.lifl.fr/norine/ mappings: biocontext: NORINE fairsharing: FAIRsharing.gf8yhy miriam: norine n2t: norine prefixcommons: norine name: Nonribosomal Peptides Database pattern: ^NOR\d+$ preferred_prefix: norine uri_format: http://bioinfo.lifl.fr/norine/result.jsp?ID=$1 novus: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A vendor of antibodies and other biologics example: nb100-56351 homepage: https://www.novusbio.com name: Novus Biologicals preferred_prefix: novus uri_format: https://www.novusbio.com/products/$1 npass: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data. ' example: NPC139585 homepage: http://bidd.group/NPASS/ name: Natural Product Activity and Species Source Database pattern: ^NPC\d+$ preferred_prefix: npass npo: contact: email: nathan.baker@pnnl.gov github: sobolevnrm name: Nathan Baker orcid: 0000-0002-5892-6506 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy. download_owl: http://aber-owl.net/media/ontologies/NPO/31/npo.owl example: '1731' homepage: https://bioportal.bioontology.org/ontologies/NPO mappings: aberowl: NPO bioportal: NPO fairsharing: FAIRsharing.vy0p71 name: NanoParticle Ontology pattern: ^\d+$ preferred_prefix: npo publications: - doi: 10.1016/j.jbi.2010.03.001 pmc: PMC3042056 pubmed: '20211274' title: NanoParticle Ontology for cancer nanotechnology research. year: 2010 repository: https://github.com/sobolevnrm/npo uri_format: http://purl.bioontology.org/ontology/npo#NPO_$1 nsc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Identifier used by the Cancer Chemotherapy National Service Center. example: '27223' homepage: https://wiki.nci.nih.gov/display/NCIDTPdata/Chemical+Data mappings: cheminf: '000565' name: USA National Service Center Number pattern: ^\d+$ preferred_prefix: nsc references: - https://pubchem.ncbi.nlm.nih.gov/source/DTP/NCI uri_format: https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist=$1 nsf.award: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Information about research projects that NSF has funded since 1989 can be found by searching the Award Abstracts database. The information includes abstracts that describe the research, and names of principal investigators and their institutions. The database includes both completed and in-process research. example: '1458400' homepage: https://www.nsf.gov/awards/about.jsp name: National Science Foundation Award pattern: ^\d+$ preferred_prefix: nsf.award uri_format: https://www.nsf.gov/awardsearch/showAward?AWD_ID=$1 nucc.characteristic: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Provider Characteristics code set is for use with health care provider information for enrollment and credentialing transactions and their corresponding responses. It is intended to provide codified responses to questions presented to a health care provider applying to or registering with an entity and to report the outcome of such application or registration. It may also be used for responses to inquiries regarding provider participation or registration in a program or plan. example: 2A example_extras: - '11' - '10' homepage: https://nucc.org/index.php/code-sets-mainmenu-41/provider-characteristics-mainmenu-39 name: National Uniform Claim Committee Characteristic pattern: ^\d(\d|\w)$ preferred_prefix: nucc.characteristic nucc.taxonomy: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: "The Health Care Provider Taxonomy code set is an external, nonmedical\ \ data code set designed for use in an electronic environment, specifically within\ \ the ASC X12N Health Care transactions. This includes the transactions mandated\ \ under HIPAA.\n\nThe taxonomy code is a unique alphanumeric code, ten characters\ \ in length. The code set is structured into three distinct \"Levels\" including\ \ Provider Grouping, Classification, and Area of Specialization.\n\n - **Level\ \ I, Provider Grouping** A major grouping of service(s) or occupation(s) of health\ \ care providers. For example: Allopathic & Osteopathic Physicians, Dental Providers,\ \ Hospitals, etc.\n - **Level II, Classification** A more specific service or\ \ occupation related to the Provider Grouping. For example, the Classification\ \ for Allopathic & Osteopathic Physicians is based upon the General Specialty\ \ Certificates as issued by the appropriate national boards. The following boards\ \ will however, have their general certificates appear as Level III areas of specialization\ \ strictly due to display limitations of the code set for Boards that have multiple\ \ general certificates: Medical Genetics, Preventive Medicine, Psychiatry & Neurology,\ \ Radiology, Surgery, Otolaryngology, Pathology.\n - **Level III, Area of Specialization**\ \ A more specialized area of the Classification in which a provider chooses to\ \ practice or make services available. For example, the Area of Specialization\ \ for provider grouping Allopathic & Osteopathic Physicians is based upon the\ \ Subspecialty Certificates as issued by the appropriate national boards." example: 207LH0002X homepage: https://taxonomy.nucc.org name: National Uniform Claim Committee Taxonomy pattern: ^\d{3}\w(\w|\d_)\d{4}X$ preferred_prefix: nucc.taxonomy references: - https://www.nucc.org/images/stories/CSV/nucc_taxonomy_221.csv - https://www.nucc.org nuclearbd: description: NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs. example: prgr_human homepage: http://www.receptors.org/nucleardb/ mappings: biocontext: NUCLEARBD miriam: nuclearbd n2t: nuclearbd name: NucleaRDB pattern: ^\w+\_\w+$ preferred_prefix: nuclearbd uri_format: http://www.receptors.org/nucleardb/proteins/$1 nucleotide: description: The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery. example: '880798137' has_canonical: insdc homepage: https://www.ncbi.nlm.nih.gov/ mappings: miriam: nucleotide name: Nucleotide pattern: ^[a-zA-Z0-9_\.]+$ preferred_prefix: nucleotide uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 oa: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture. download_owl: http://aber-owl.net/media/ontologies/OA/4/oa.owl example: sourceDateStart homepage: http://www.w3.org/ns/oa mappings: aberowl: OA biocontext: oa bioportal: OA name: Web Annotation Ontology preferred_prefix: oa uri_format: http://www.w3.org/ns/oa#$1 oae: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqunh He orcid: 0000-0001-9189-9661 description: The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc. download_owl: http://purl.obolibrary.org/obo/oae.owl example: 0002959 homepage: https://github.com/OAE-ontology/OAE/ license: CC BY 3.0 mappings: aberowl: OAE biocontext: OAE bioportal: OAE fairsharing: FAIRsharing.tw4q8x obofoundry: oae ols: oae ontobee: OAE name: Ontology of Adverse Events pattern: ^\d{7}$ preferred_prefix: OAE publications: - doi: 10.1186/2041-1480-5-29 pmc: PMC4120740 pubmed: '25093068' title: 'OAE: The Ontology of Adverse Events.' year: 2014 repository: https://github.com/OAE-ontology/OAE uri_format: http://purl.obolibrary.org/obo/OAE_$1 version: 1.2.44 oarcs: contact: email: mjyoder@illinois.edu github: mjy name: Matt Yoder orcid: 0000-0002-5640-5491 description: OArCS is an ontology describing the Arthropod ciruclatory system. download_owl: http://purl.obolibrary.org/obo/oarcs.owl example: 0000029 homepage: https://github.com/aszool/oarcs license: CC BY 3.0 mappings: aberowl: OARCS biocontext: OARCS bioportal: OARCS fairsharing: FAIRsharing.yqn857 obofoundry: oarcs ols: oarcs ontobee: OARCS name: Ontology of Arthropod Circulatory Systems pattern: ^\d{7}$ preferred_prefix: OARCS publications: - doi: 10.1093/sysbio/syw108 pmc: null pubmed: null title: The first organ-based free ontology for arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its integration into a novel formalization scheme for morphological descriptions year: null repository: https://github.com/aszool/oarcs uri_format: http://purl.obolibrary.org/obo/OARCS_$1 version: '2019-04-18' oba: appears_in: - fovt contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO. download_json: http://purl.obolibrary.org/obo/oba.json download_obo: http://purl.obolibrary.org/obo/oba.obo download_owl: http://purl.obolibrary.org/obo/oba.owl example: '0000001' example_extras: - VT0003769 homepage: https://github.com/obophenotype/bio-attribute-ontology license: CC0 1.0 mappings: aberowl: OBA biocontext: OBA bioportal: OBA fairsharing: FAIRsharing.mp0rwf obofoundry: oba ols: oba ontobee: OBA name: Ontology of Biological Attributes pattern: ^(VT)?\d{7}$ preferred_prefix: OBA repository: https://github.com/obophenotype/bio-attribute-ontology uri_format: http://purl.obolibrary.org/obo/OBA_$1 version: '2022-08-03' obcs: contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 description: 'OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. ' download_owl: http://purl.obolibrary.org/obo/obcs.owl example: '0000121' homepage: https://github.com/obcs/obcs license: CC BY 3.0 mappings: aberowl: OBCS biocontext: OBCS bioportal: OBCS fairsharing: FAIRsharing.5p12xh obofoundry: obcs ols: obcs ontobee: OBCS name: Ontology of Biological and Clinical Statistics pattern: ^\d{7}$ preferred_prefix: OBCS publications: - doi: 10.1186/s13326-016-0100-2 pmc: PMC5024438 pubmed: '27627881' title: The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. year: 2016 repository: https://github.com/obcs/obcs uri_format: http://purl.obolibrary.org/obo/OBCS_$1 version: '101' obi: appears_in: - agro - foodon - hso - labo - mco - one - ons - proco - rbo - scdo banana: OBI banana_peel: ':' contact: email: bpeters@lji.org github: bpeters42 name: Bjoern Peters orcid: 0000-0002-8457-6693 description: The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO). download_obo: https://github.com/obi-ontology/obi/raw/master/views/obi.obo download_owl: http://purl.obolibrary.org/obo/obi.owl example: 0400109 homepage: http://obi-ontology.org license: CC BY 4.0 mappings: aberowl: OBI biocontext: OBI bioportal: OBI fairsharing: FAIRsharing.284e1z go: OBI miriam: obi n2t: obi obofoundry: obi ols: obi ontobee: OBI prefixcommons: obi name: Ontology for Biomedical Investigations namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: OBI publications: - doi: 10.1371/journal.pone.0154556 pmc: PMC4851331 pubmed: '27128319' title: The Ontology for Biomedical Investigations. year: 2016 - doi: 10.1093/database/bau132 pmc: PMC4309925 pubmed: '25632945' title: 'Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach.' year: 2015 - doi: 10.1186/2041-1480-4-s1-s6 pmc: PMC3633001 pubmed: '23734660' title: 'Query enhancement through the practical application of ontology: the IEDB and OBI.' year: 2013 - doi: 10.4056/sigs.1994602 pmc: PMC3235517 pubmed: '22180825' title: Minimum Information about a Genotyping Experiment (MIGEN). year: 2011 - doi: 10.1186/2041-1480-1-s1-s7 pmc: PMC2903726 pubmed: '20626927' title: Modeling biomedical experimental processes with OBI. year: 2010 repository: https://github.com/obi-ontology/obi uri_format: http://purl.obolibrary.org/obo/OBI_$1 version: '2022-07-11' obib: contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 description: The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology. download_owl: http://purl.obolibrary.org/obo/obib.owl example: 0000389 homepage: https://github.com/biobanking/biobanking license: CC BY 4.0 mappings: aberowl: OBIB biocontext: OBIB bioportal: OBIB fairsharing: FAIRsharing.bxc508 obofoundry: obib ols: obib ontobee: OBIB name: Ontology for Biobanking pattern: ^\d{7}$ preferred_prefix: OBIB publications: - doi: 10.1186/s13326-016-0068-y pmc: null pubmed: null title: OBIB-a novel ontology for biobanking year: null repository: https://github.com/biobanking/biobanking uri_format: http://purl.obolibrary.org/obo/OBIB_$1 version: '2021-11-12' obo: description: The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies. homepage: http://www.obofoundry.org/ mappings: biocontext: OBO fairsharing: FAIRsharing.847069 name: Open Biological and Biomedical Ontologies preferred_prefix: obo uri_format: http://purl.obolibrary.org/obo/$1 oboinowl: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties download_obo: https://github.com/geneontology/go-ontology/raw/master/contrib/oboInOwl.obo download_owl: https://github.com/geneontology/go-ontology/raw/master/contrib/oboInOwl.owl example: hasDbXref homepage: https://github.com/geneontology/go-ontology/tree/master/contrib mappings: biocontext: oboInOwl biolink: oboformat name: OBO in OWL preferred_prefix: oboInOwl repository: https://github.com/geneontology/go-ontology synonyms: - oboformat - oio uri_format: http://www.geneontology.org/formats/oboInOwl#$1 occ: description: The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law. example: br/1 homepage: https://w3id.org/oc/corpus mappings: miriam: occ n2t: occ name: OpenCitations Corpus pattern: ^[a-z][a-z]/[0-9]+$ preferred_prefix: occ uri_format: https://w3id.org/oc/corpus/$1 oci: description: "Each OCI (Open Citation Identifier) has a simple structure: oci:number-number,\ \ where “oci:” is the identifier prefix, and is used to identify a citation as\ \ a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/\ \ for additional information.\r\n\r\nOCIs for citations stored within the OpenCitations\ \ Corpus are constructed by combining the OpenCitations Corpus local identifiers\ \ for the citing and cited bibliographic resources, separating them with a dash.\ \ For example, oci:2544384-7295288 is a valid OCI for the citation between two\ \ papers stored within the OpenCitations Corpus.\r\n\r\nOCIs can also be created\ \ for bibliographic resources described in an external bibliographic database,\ \ if they are similarly identified there by identifiers having a unique numerical\ \ part. For example, the OCI for the citation that exists between Wikidata resources\ \ Q27931310 and Q22252312 is oci:01027931310–01022252312.\r\n\r\nOCIs can also\ \ be created for bibliographic resources described in external bibliographic database\ \ such as Crossref or DataCite where they are identified by alphanumeric Digital\ \ Object Identifiers (DOIs), rather than purely numerical strings." example: 1-18 homepage: http://opencitations.net mappings: biocontext: OCI miriam: oci n2t: oci name: Open Citation Identifier pattern: ^[0-9]+-[0-9]+$ preferred_prefix: oci uri_format: https://w3id.org/oc/oci/$1 ocid: banana: ocid description: '''ocid'' stands for "Ontology Concept Identifiers" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology.' example: '190000021540' homepage: https://ontochem.com/ mappings: miriam: ocid name: Ontology Concept Identifiers namespace_in_lui: true pattern: ^[0-9]{12}$ preferred_prefix: ocid uri_format: https://ocid.ontochem.com/prefname?ocid=$1 oclc: description: The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information. example: '634515043' homepage: https://www.oclc.org/en/about.html mappings: biocontext: OCLC miriam: oclc n2t: oclc name: Online Computer Library Center WorldCat pattern: ^[0-9]+$ preferred_prefix: oclc uri_format: https://www.worldcat.org/oclc/$1 odam: description: Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed. example: frim1 homepage: https://metabolome.cgfb.u-bordeaux.fr/ mappings: miriam: odam name: Open Data for Access and Mining pattern: ^[A-Za-z0-9]+$ preferred_prefix: odam uri_format: http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1 odc.sci: description: The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data. example: '602' homepage: https://odc-sci.org mappings: fairsharing: FAIRsharing.M6Ruz3 miriam: odc.sci name: Open Data Commons for Spinal Cord Injury pattern: ^[0-9]*$ preferred_prefix: odc.sci uri_format: https://odc-sci.org/data/$1 odc.tbi: description: The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data. example: '408' homepage: https://odc-tbi.org mappings: miriam: odc.tbi name: Open Data Commons for Traumatic Brain Injury pattern: ^[0-9]*$ preferred_prefix: odc.tbi uri_format: https://odc-tbi.org/data/$1 odor: description: OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors example: '74' homepage: http://senselab.med.yale.edu/OdorDB mappings: biocontext: ODOR miriam: odor n2t: odor name: Odor Molecules DataBase pattern: ^\d+$ preferred_prefix: odor uri_format: http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5 ogg: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: 'OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. ' download_owl: http://purl.obolibrary.org/obo/ogg.owl example: '3000887619' homepage: https://bitbucket.org/hegroup/ogg license: CC BY 3.0 mappings: aberowl: OGG biocontext: OGG bioportal: OGG fairsharing: FAIRsharing.zmx7nn obofoundry: ogg ols: ogg ontobee: OGG name: The Ontology of Genes and Genomes pattern: ^\d+$ preferred_prefix: OGG repository: https://bitbucket.org/hegroup/ogg uri_format: http://purl.obolibrary.org/obo/OGG_$1 version: 1.0.59 ogi: contact: email: linikujp@gmail.com github: linikujp name: Asiyah Yu Lin orcid: 0000-0002-5379-5359 deprecated: true description: "OGI formalized the genomic element by defining an upper class 'genetic\ \ interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous\ \ physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.)\ \ between and including two points (Nucleic Acid Base Residue) on a chromosome\ \ or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated\ \ paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology”\ \ Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary\ \ Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\n\ Yu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI)\ \ to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding\ \ of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam,\ \ Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons\ \ (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology\ \ Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th-\ \ Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n" download_owl: http://purl.obolibrary.org/obo/ogi.owl example: 0000019 homepage: https://code.google.com/archive/p/ontology-for-genetic-interval/ mappings: aberowl: OGI biocontext: OGI bioportal: OGI obofoundry: ogi ols: ogi ontobee: OGI name: Ontology for genetic interval pattern: ^\d{7}$ preferred_prefix: OGI synonyms: - OGI.owl uri_format: http://purl.obolibrary.org/obo/OGI_$1 version: '2.0' ogms: appears_in: - labo - scdo contact: email: baeverma@jcvi.org github: BAevermann name: Brian Aevermann orcid: 0000-0003-1346-1327 description: 'The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: ''disease'', ''disorder'', ''disease course'', ''diagnosis'', ''patient'', and ''healthcare provider''. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.' download_obo: http://purl.obolibrary.org/obo/ogms.obo download_owl: http://purl.obolibrary.org/obo/ogms.owl example: '0000031' homepage: https://github.com/OGMS/ogms license: CC BY 4.0 mappings: aberowl: OGMS biocontext: OGMS bioportal: OGMS fairsharing: FAIRsharing.rvz0m9 obofoundry: ogms ols: ogms ontobee: OGMS name: Ontology for General Medical Science pattern: ^\d{7}$ preferred_prefix: OGMS publications: - doi: 10.1186/2041-1480-4-42 pmc: PMC4028878 pubmed: '24314207' title: The neurological disease ontology. year: 2013 repository: https://github.com/OGMS/ogms synonyms: - ogms/OMRE uri_format: http://purl.obolibrary.org/obo/OGMS_$1 version: '2021-08-19' ogsf: contact: email: linikujp@gmail.com github: linikujp name: Asiyah Yu Lin orcid: 0000-0002-5379-5359 description: An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process. download_owl: http://purl.obolibrary.org/obo/ogsf.owl example: '0000025' homepage: https://github.com/linikujp/OGSF license: CC BY 3.0 mappings: aberowl: OGSF biocontext: OGSF bioportal: OGSF fairsharing: FAIRsharing.egv2cz obofoundry: ogsf ols: ogsf ontobee: OGSF name: Ontology of Genetic Susceptibility Factor pattern: ^\d{7}$ preferred_prefix: OGSF publications: - doi: 10.1186/2041-1480-5-19 pmc: PMC4068904 pubmed: '24963371' title: The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events. year: 2014 - doi: null pmc: null pubmed: '20847592' title: Ontology driven modeling for the knowledge of genetic susceptibility to disease. year: 2009 repository: https://github.com/linikujp/OGSF uri_format: http://purl.obolibrary.org/obo/OGSF_$1 version: '2.0' ohd: contact: email: wdduncan@gmail.com github: wdduncan name: Bill Duncan orcid: 0000-0001-9625-1899 description: The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records. download_owl: http://purl.obolibrary.org/obo/ohd.owl example: '0000006' homepage: https://purl.obolibrary.org/obo/ohd/home license: CC BY 4.0 mappings: aberowl: OHD biocontext: OHD bioportal: OHD fairsharing: FAIRsharing.bg7bb6 obofoundry: ohd ols: ohd ontobee: OHD name: Oral Health and Disease Ontology pattern: ^\d{7}$ preferred_prefix: OHD publications: - doi: null pmc: null pubmed: '32819435' title: Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology year: null repository: https://github.com/oral-health-and-disease-ontologies/ohd-ontology uri_format: http://purl.obolibrary.org/obo/OHD_$1 version: '2016-06-27' ohmi: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions. download_owl: http://purl.obolibrary.org/obo/ohmi.owl example: '0000460' homepage: https://github.com/ohmi-ontology/ohmi license: CC BY 4.0 mappings: aberowl: OHMI biocontext: OHMI bioportal: OHMI fairsharing: FAIRsharing.cz9cnp obofoundry: ohmi ols: ohmi ontobee: OHMI name: Ontology of Host-Microbiome Interactions pattern: ^\d{7}$ preferred_prefix: OHMI repository: https://github.com/ohmi-ontology/ohmi uri_format: http://purl.obolibrary.org/obo/OHMI_$1 version: '2019-09-17' ohpi: contact: email: edong@umich.edu github: e4ong1031 name: Edison Ong orcid: 0000-0002-5159-414X description: OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration). download_owl: http://purl.obolibrary.org/obo/ohpi.owl example: '9001411' homepage: https://github.com/OHPI/ohpi license: CC BY 4.0 mappings: aberowl: OHPI bioportal: OHPI fairsharing: FAIRsharing.vxpUJ6 obofoundry: ohpi ols: ohpi ontobee: OHPI name: Ontology of Host Pathogen Interactions pattern: ^\d+$ preferred_prefix: OHPI publications: - doi: 10.1093/nar/gky999 pmc: PMC6324020 pubmed: '30365026' title: 'Victors: a web-based knowledge base of virulence factors in human and animal pathogens.' year: 2019 repository: https://github.com/OHPI/ohpi uri_format: http://purl.obolibrary.org/obo/OHPI_$1 version: '2019-10-02' oid: contributor_extras: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes. example: 2.16.840 example_extras: - '2' - '2.16' - 2.16.840.1 - 2.16.840.1.113883 - 2.16.840.1.113883.6 - 2.16.840.1.113883.6.88 homepage: http://www.oid-info.com/introduction.htm mappings: miriam: oid n2t: oid name: ISO Object Identifier pattern: ^[\d.]+$ preferred_prefix: oid providers: - code: orange description: Mirror of OID site from Orange homepage: https://oid-rep.orange-labs.fr name: Mirror of OID site from Orange uri_format: https://oid-rep.orange-labs.fr/get/$1 references: - https://en.wikipedia.org/wiki/Object_identifier uri_format: http://oid-info.com/get/$1 olatdv: contact: email: frederic.bastian@unil.ch github: fbastian name: Frédéric Bastian orcid: 0000-0002-9415-5104 description: Life cycle stages for Medaka download_obo: http://purl.obolibrary.org/obo/olatdv.obo download_owl: http://purl.obolibrary.org/obo/olatdv.owl example: '0000210' homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv license: CC BY 3.0 mappings: aberowl: OLATDV biocontext: OLATDV bioportal: OLATDV fairsharing: FAIRsharing.c86z66 obofoundry: olatdv ols: olatdv ontobee: OLATDV name: Medaka Developmental Stages pattern: ^\d{7}$ preferred_prefix: OlatDv repository: https://github.com/obophenotype/developmental-stage-ontologies uri_format: http://purl.obolibrary.org/obo/OLATDV_$1 version: '2020-03-10' om: contact: email: hajo.rijgersberg@wur.nl github: null name: Hajo Rijgersberg orcid: null description: 'The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units meter and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant: km/s/Mpc, or the quantity vaselife. OM defines the complete set of concepts in the domain as distinguished in the textual standards. As a result the ontology can answer a wider range of competency questions than the existing approaches do. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology; Typography; Shipping; Food engineering; Post-harvest; technology; Dynamics of texture and taste; Packaging' download_owl: https://raw.githubusercontent.com/HajoRijgersberg/OM/master/om-2.0.rdf example: Dimension homepage: https://github.com/HajoRijgersberg/OM mappings: aberowl: OM agroportal: OM bioportal: OM ols: om name: Ontology of units of Measure preferred_prefix: om repository: https://github.com/HajoRijgersberg/OM uri_format: http://www.ontology-of-units-of-measure.org/resource/om-2/$1 version: 2.0.38 oma.grp: description: OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs. example: LCSCCPN homepage: https://omabrowser.org/cgi-bin/gateway.pl mappings: biocontext: OMA.GRP miriam: oma.grp n2t: oma.grp name: OMA Group pattern: ^[A-Z]+$ preferred_prefix: oma.grp uri_format: https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1 oma.hog: banana: HOG description: 'Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. ' example: 0459895 homepage: https://omabrowser.org mappings: miriam: oma.hog name: OMA HOGs namespace_in_lui: true pattern: ^[0-9]{7}(\.[0-9a-z.]+)?(_[0-9]+)?$ preferred_prefix: oma.hog uri_format: https://omabrowser.org/oma/hog/HOG:$1 oma.protein: description: OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records. example: HUMAN16963 homepage: https://omabrowser.org/cgi-bin/gateway.pl mappings: biocontext: OMA.PROTEIN miriam: oma.protein n2t: oma.protein name: OMA Protein pattern: ^[A-Z0-9]{5}\d+$ preferred_prefix: oma.protein uri_format: https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1 omia: comment: website is down as of 2021-10-04 deprecated: true description: Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse). example: '1000' homepage: http://omia.angis.org.au/ mappings: biocontext: OMIA miriam: omia n2t: omia prefixcommons: omia name: Online Mendelian Inheritance in Animals pattern: ^\d+$ preferred_prefix: omia uri_format: http://omia.angis.org.au/$1/ omiabis: appears_in: - labo contact: email: mbrochhausen@gmail.com github: null name: Mathias Brochhausen orcid: 0000-0003-1834-3856 deprecated: true description: An ontological version of MIABIS (Minimum Information About BIobank data Sharing) download_owl: http://purl.obolibrary.org/obo/omiabis.owl example: 0001079 homepage: https://github.com/OMIABIS/omiabis-dev license: CC BY 3.0 mappings: aberowl: OMIABIS biocontext: OMIABIS bioportal: OMIABIS obofoundry: omiabis ols: omiabis ontobee: OMIABIS name: Ontologized MIABIS pattern: ^\d{7}$ preferred_prefix: OMIABIS repository: https://github.com/OMIABIS/omiabis-dev uri_format: http://purl.obolibrary.org/obo/OMIABIS_$1 version: '2014-05-28' omim: contact: email: ahamosh@jhmi.edu github: ahamosh name: Ada Hamosh orcid: 0000-0002-1780-5230 description: Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. example: '603903' homepage: https://omim.org/ mappings: aberowl: OMIM biocontext: OMIM bioportal: OMIM edam: '1153' fairsharing: FAIRsharing.b084yh go: OMIM hl7: 2.16.840.1.113883.6.174 miriam: mim n2t: mim ncbi: MIM prefixcommons: omim uniprot: MIM wikidata: P492 name: Online Mendelian Inheritance in Man pattern: ^\d+$ preferred_prefix: omim providers: - code: CURATOR_REVIEW description: OMIM mirror at John Hopkins homepage: http://mirror.omim.org/ name: OMIM mirror at John Hopkins uri_format: http://mirror.omim.org/entry/$1 publications: - doi: 10.1093/nar/gku1205 pmc: null pubmed: '25428349' title: 'OMIM.org: Online Mendelian Inheritance in Man (OMIM(R)), an online catalog of human genes and genetic disorders.' year: null - doi: 10.1093/nar/gki033 pmc: PMC539987 pubmed: '15608251' title: Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. year: 2005 synonyms: - OMIM - mim uri_format: https://omim.org/entry/$1 omim.ps: contact: email: ahamosh@jhmi.edu github: ahamosh name: Ada Hamosh orcid: 0000-0002-1780-5230 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - email: null github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 description: A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome. example: PS214100 homepage: https://www.omim.org/phenotypicSeriesTitles/all mappings: biolink: OMIM.PS name: OMIM Phenotypic Series part_of: omim pattern: ^PS\d+$ preferred_prefix: omim.ps synonyms: - MIMPS - OMIMPS - PS - mim.ps uri_format: https://omim.org/phenotypicSeries/$1 omit: appears_in: - mco contact: email: huang@southalabama.edu github: Huang-OMIT name: Jingshan Huang orcid: 0000-0003-2408-2883 description: The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). download_obo: https://raw.githubusercontent.com/OmniSearch/omit/master/src/ontology/omit.obo download_owl: http://purl.obolibrary.org/obo/omit.owl example: 0000069 homepage: http://omit.cis.usouthal.edu/ license: CC BY 3.0 mappings: aberowl: OMIT biocontext: OMIT bioportal: OMIT fairsharing: FAIRsharing.mf91p5 miriam: omit n2t: omit obofoundry: omit ols: omit ontobee: OMIT name: Ontology for MicroRNA Target pattern: ^\d{7}$ preferred_prefix: OMIT publications: - doi: 10.1186/s13326-016-0064-2 pmc: PMC4863347 pubmed: '27175225' title: 'OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.' year: 2016 - doi: 10.1371/journal.pone.0100855 pmc: PMC4099014 pubmed: '25025130' title: 'OMIT: dynamic, semi-automated ontology development for the microRNA domain.' year: 2014 - doi: 10.1007/s11095-011-0573-8 pmc: null pubmed: '21879385' title: 'OMIT: a domain-specific knowledge base for microRNA target prediction.' year: 2011 repository: https://github.com/OmniSearch/omit synonyms: - OMIT uri_format: https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$1 version: '2019-06-07' omo: appears_in: - pcl contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO). download_owl: http://purl.obolibrary.org/obo/omo.owl homepage: https://github.com/information-artifact-ontology/ontology-metadata license: CC0 1.0 mappings: aberowl: OMO bioportal: OMO obofoundry: omo ols: omo ontobee: OMO name: OBO Metadata Ontology no_own_terms: true preferred_prefix: OMO repository: https://github.com/information-artifact-ontology/ontology-metadata uri_format: http://purl.obolibrary.org/obo/OMO_$1 version: '2022-04-27' omop: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format. homepage: https://www.ohdsi.org/data-standardization/the-common-data-model/ name: Observational Medical Outcomes Partnership no_own_terms: true preferred_prefix: omop references: - https://github.com/callahantiff/OMOP2OBO omp: appears_in: - mco contact: email: jimhu@tamu.edu github: jimhu-tamu name: James C. Hu orcid: 0000-0001-9016-2684 description: An ontology of phenotypes covering microbes download_obo: http://purl.obolibrary.org/obo/omp.obo download_owl: http://purl.obolibrary.org/obo/omp.owl example: '0005067' homepage: http://microbialphenotypes.org license: CC BY 3.0 mappings: aberowl: OMP biocontext: OMP bioportal: OMP fairsharing: FAIRsharing.cc3f2x obofoundry: omp ols: omp ontobee: OMP name: Ontology of Microbial Phenotypes pattern: ^\d{7}$ preferred_prefix: OMP publications: - doi: 10.1186/s12866-014-0294-3 pmc: PMC4287307 pubmed: '25433798' title: An ontology for microbial phenotypes. year: 2014 repository: https://github.com/microbialphenotypes/OMP-ontology uri_format: http://purl.obolibrary.org/obo/OMP_$1 version: '2022-08-05' omrse: appears_in: - labo contact: email: hoganwr@gmail.com github: hoganwr name: Bill Hogan orcid: 0000-0002-9881-1017 description: This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations. download_json: http://purl.obolibrary.org/obo/omrse.json download_obo: https://github.com/ufbmi/OMRSE/raw/master/omrse-full.obo download_owl: http://purl.obolibrary.org/obo/omrse.owl example: '00000022' homepage: https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview license: CC BY 4.0 mappings: aberowl: OMRSE biocontext: OMRSE bioportal: OMRSE fairsharing: FAIRsharing.z0p37e obofoundry: omrse ols: omrse ontobee: OMRSE name: Ontology of Medically Related Social Entities pattern: ^\d{8}$ preferred_prefix: OMRSE publications: - doi: 10.1186/s13326-016-0087-8 pmc: PMC4942889 pubmed: '27406187' title: 'The ontology of medically related social entities: recent developments.' year: 2016 repository: https://github.com/ufbmi/OMRSE uri_format: http://purl.obolibrary.org/obo/OMRSE_$1 version: '2022-04-06' oncotree: appears_in: - efo contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research. example: BLL homepage: http://oncotree.mskcc.org name: OncoTree preferred_prefix: oncotree uri_format: http://oncotree.mskcc.org/api/tumorTypes/search/code/$1 one: contact: email: chenyangnutrition@gmail.com github: cyang0128 name: Chen Yang orcid: 0000-0001-9202-5309 depends_on: - foodon - obi - ons description: An ontology to standardize research output of nutritional epidemiologic studies. download_owl: http://purl.obolibrary.org/obo/one.owl example: '0001021' homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies license: CC BY 4.0 mappings: aberowl: ONE bioportal: ONE fairsharing: FAIRsharing.USxx0K obofoundry: one ols: one ontobee: ONE name: Ontology for Nutritional Epidemiology pattern: ^\d{7}$ preferred_prefix: ONE publications: - doi: e1300 pmc: PMC6628051 pubmed: '31181762' title: 'An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content.' year: null - doi: 10.3390/nu11061300 pmc: PMC6628051 pubmed: '31181762' title: 'An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content.' year: 2019 repository: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies uri_format: http://purl.obolibrary.org/obo/ONE_$1 ons: appears_in: - one contact: email: francesco.vitali@ibba.cnr.it github: FrancescoVit name: Francesco Vitali orcid: 0000-0001-9125-4337 depends_on: - bfo - chebi - envo - foodon - ncbitaxon - obi - ro - uberon description: The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies. download_owl: http://purl.obolibrary.org/obo/ons.owl example: '0000060' homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies license: CC BY 4.0 mappings: aberowl: ONS bioportal: ONS fairsharing: FAIRsharing.rfec93 obofoundry: ons ols: ons ontobee: ONS name: Ontology for Nutritional Studies pattern: ^\d{7}$ preferred_prefix: ONS publications: - doi: 10.1186/s12263-018-0601-y pmc: PMC5928560 pubmed: '29736190' title: 'ONS: an ontology for a standardized description of interventions and observational studies in nutrition.' year: 2018 repository: https://github.com/enpadasi/Ontology-for-Nutritional-Studies uri_format: http://purl.obolibrary.org/obo/ONS_$1 version: Release version 1.2.3 ontoavida: contact: email: fortuna@ebd.csic.es github: miguelfortuna name: Miguel A. Fortuna orcid: 0000-0002-8374-1941 depends_on: - fbcv - gsso - ncit - ro - stato description: 'The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of the most widely used computational approach for performing experimental evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment). The lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight. OntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA). More information can be found at https://obofoundry.org/ontology/ontoavida.html' download_obo: http://purl.obolibrary.org/obo/ontoavida.obo download_owl: http://purl.obolibrary.org/obo/ontoavida.owl example: '00000001' homepage: https://gitlab.com/fortunalab/ontoavida license: CC BY 4.0 mappings: aberowl: ONTOAVIDA bioportal: ONTOAVIDA obofoundry: ontoavida ols: ontoavida ontobee: ONTOAVIDA name: Ontology for Avida digital evolution platform pattern: ^\d{8}$ preferred_prefix: ONTOAVIDA repository: https://gitlab.com/fortunalab/ontoavida uri_format: http://purl.obolibrary.org/obo/ONTOAVIDA_$1 version: '2022-03-15' ontoneo: contact: email: fernanda.farinelli@gmail.com github: FernandaFarinelli name: Fernanda Farinelli orcid: 0000-0003-2338-8872 description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby. download_owl: http://purl.obolibrary.org/obo/ontoneo.owl example: 00000098 homepage: http://ontoneo.com license: CC BY 3.0 mappings: aberowl: ONTONEO biocontext: ONTONEO bioportal: ONTONEO fairsharing: FAIRsharing.5a4y1y obofoundry: ontoneo ols: ontoneo ontobee: ONTONEO name: Obstetric and Neonatal Ontology pattern: ^\d{8}$ preferred_prefix: ONTONEO repository: https://github.com/ontoneo-project/Ontoneo uri_format: http://purl.obolibrary.org/obo/ONTONEO_$1 version: v1.6 oostt: contact: email: mbrochhausen@gmail.com github: mbrochhausen name: Mathias Brochhausen orcid: 0000-0003-1834-3856 description: An ontology built for representating the organizational components of trauma centers and trauma systems. download_owl: http://purl.obolibrary.org/obo/oostt.owl example: 00000099 homepage: https://github.com/OOSTT/OOSTT license: CC BY 4.0 mappings: aberowl: OOSTT biocontext: OOSTT bioportal: OOSTT fairsharing: FAIRsharing.b4sa0w obofoundry: oostt ols: oostt ontobee: OOSTT name: Ontology of Organizational Structures of Trauma centers and Trauma systems pattern: ^\d{8}$ preferred_prefix: OOSTT repository: https://github.com/OOSTT/OOSTT uri_format: http://purl.obolibrary.org/obo/OOSTT_$1 version: '2021-01-11' opb: banana: OPB banana_peel: _ contact: email: maxneal@gmail.com github: null name: Max Neal orcid: null description: The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms. download_owl: http://aber-owl.net/media/ontologies/OPB/13/opb.owl example: '00573' homepage: http://bioportal.bioontology.org/ontologies/OPB mappings: aberowl: OPB biocontext: OPB bioportal: OPB fairsharing: FAIRsharing.qcceez miriam: opb n2t: opb prefixcommons: opb name: Ontology of Physics for Biology pattern: ^\d+$ preferred_prefix: opb publications: - doi: 10.1186/2041-1480-4-41 pmc: PMC3904761 pubmed: '24295137' title: 'Ontology of physics for biology: representing physical dependencies as a basis for biological processes.' year: 2013 - doi: 10.1371/journal.pone.0028708 pmc: PMC3246444 pubmed: '22216106' title: 'Physical properties of biological entities: an introduction to the ontology of physics for biology.' year: 2011 uri_format: http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1 openalex: contact: email: hpiwowar@gmail.com github: hpiwowar name: Heather Piwowar orcid: 0000-0003-1613-5981 contributor: email: null github: dhimmel name: Daniel Himmelstein orcid: 0000-0002-3012-7446 description: OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other. example: W2741809807 github_request_issue: 280 homepage: https://openalex.org/ name: OpenAlex pattern: ^[WAICV]\d{2,}$ preferred_prefix: openalex reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://openalex.org/$1 opl: contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 description: The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium. download_owl: http://purl.obolibrary.org/obo/opl.owl example: 0000319 homepage: https://github.com/OPL-ontology/OPL license: CC BY 4.0 mappings: aberowl: OPL biocontext: OPL bioportal: OPL fairsharing: FAIRsharing.ez2nhb obofoundry: opl ols: opl ontobee: OPL name: Ontology for Parasite LifeCycle pattern: ^\d{7}$ preferred_prefix: OPL publications: - doi: 10.1186/2041-1480-3-5 pmc: PMC3488002 pubmed: '22621763' title: 'The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms.' year: 2012 repository: https://github.com/OPL-ontology/OPL uri_format: http://purl.obolibrary.org/obo/OPL_$1 version: '2021-01-28' opm: description: The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization. example: 1h68 homepage: http://opm.phar.umich.edu/ mappings: biocontext: OPM fairsharing: FAIRsharing.7c683b miriam: opm n2t: opm name: Orientations of Proteins in Membranes Database pattern: ^[0-9][A-Za-z0-9]{3}$ preferred_prefix: opm uri_format: http://opm.phar.umich.edu/protein.php?pdbid=$1 opmi: appears_in: - labo - scdo contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles. download_owl: http://purl.obolibrary.org/obo/opmi.owl example: '0000101' homepage: https://github.com/OPMI/opmi license: CC BY 4.0 mappings: aberowl: OPMI bioportal: OPMI obofoundry: opmi ols: opmi ontobee: OPMI name: Ontology of Precision Medicine and Investigation pattern: ^\d{7}$ preferred_prefix: OPMI repository: https://github.com/OPMI/opmi uri_format: http://purl.obolibrary.org/obo/OPMI_$1 version: 1.0.158 orcid: description: ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities. example: 0000-0002-5355-2576 homepage: https://orcid.org mappings: biocontext: ORCID biolink: ORCID miriam: orcid n2t: orcid wikidata: P496 name: Open Researcher and Contributor pattern: ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$ preferred_prefix: orcid providers: - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/orcid/$1 synonyms: - ORCID - ORCiD uri_format: https://orcid.org/$1 ordb: description: The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs). example: '8497' homepage: http://senselab.med.yale.edu/OrDB/ mappings: biocontext: ORDB fairsharing: FAIRsharing.6375zh miriam: ordb n2t: ordb prefixcommons: ordb name: Olfactory Receptor Database pattern: ^\d+$ preferred_prefix: ordb uri_format: http://senselab.med.yale.edu/ORDB/Data/$1 oridb.sacch: description: OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae. example: '1' homepage: http://cerevisiae.oridb.org/index.php mappings: biocontext: ORIDB.SACCH miriam: oridb.sacch n2t: oridb.sacch name: OriDB Saccharomyces pattern: ^\d+$ preferred_prefix: oridb.sacch uri_format: http://cerevisiae.oridb.org/details.php?id=$1 oridb.schizo: description: OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe. example: '1' homepage: http://pombe.oridb.org/index.php mappings: biocontext: ORIDB.SCHIZO miriam: oridb.schizo n2t: oridb.schizo name: OriDB Schizosaccharomyces pattern: ^\d+$ preferred_prefix: oridb.schizo uri_format: http://pombe.oridb.org/details.php?id=$1 ornaseq: contact: email: safisher@upenn.edu github: safisher name: Stephen Fisher orcid: 0000-0001-8034-7685 description: An application ontology designed to annotate next-generation sequencing experiments performed on RNA. download_obo: http://purl.obolibrary.org/obo/ornaseq.obo download_owl: http://purl.obolibrary.org/obo/ornaseq.owl example: '0000010' homepage: http://kim.bio.upenn.edu/software/ornaseq.shtml license: CC BY 4.0 mappings: aberowl: ORNASEQ bioportal: ORNASEQ obofoundry: ornaseq ols: ornaseq ontobee: ORNASEQ name: Ontology of RNA Sequencing pattern: ^\d{7}$ preferred_prefix: ORNASEQ repository: https://github.com/safisher/ornaseq uri_format: http://purl.obolibrary.org/obo/ORNASEQ_$1 version: '2019-07-08' orphanet: description: Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases. example: '85163' homepage: http://www.orpha.net/consor/ mappings: biocontext: Orphanet fairsharing: FAIRsharing.6bd5k6 miriam: orphanet n2t: orphanet prefixcommons: orphanet uniprot: Orphanet wikidata: P1550 name: Orphanet pattern: ^\d+$ preferred_prefix: orphanet providers: - code: CURATOR_REVIEW description: Bio2RDF homepage: http://orphanet.bio2rdf.org/fct name: Bio2RDF uri_format: http://orphanet.bio2rdf.org/describe/?url=http://bio2rdf.org/orphanet:$1 publications: - doi: null pmc: null pubmed: '19058507' title: '[Orphanet and the Dutch Steering Committee Orphan Drugs. A European and Dutch databank of information on rare diseases].' year: 2008 synonyms: - ORPHA uri_format: http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1 orphanet.ordo: banana: Orphanet banana_peel: _ contact: email: ordo.orphanet@inserm.fr github: null name: Ana Rath orcid: null description: "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary\ \ for rare diseases, capturing relationships between diseases, genes and other\ \ relevant features which will form a useful resource for the computational analysis\ \ of rare diseases.\r\nIt integrates a nosology (classification of rare diseases),\ \ relationships (gene-disease relations, epiemological data) and connections with\ \ other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC,\ \ ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10)." download_owl: http://www.orphadata.org/data/ORDO/ordo_orphanet.owl example: C023 example_extras: - '478' homepage: https://www.ebi.ac.uk/ols/ontologies/ordo mappings: aberowl: ordo biocontext: ORPHANET.ORDO biolink: ORPHA bioportal: ORDO cellosaurus: ORDO fairsharing: FAIRsharing.pbbnwa miriam: orphanet.ordo n2t: orphanet.ordo ols: ordo name: Orphanet Rare Disease Ontology pattern: ^C?\d+$ preferred_prefix: orphanet.ordo publications: - doi: null pmc: null pubmed: '22874158' title: 'Rare diseases knowledge management: the contribution of proximity measurements in OntoOrpha and OMIM.' year: 2012 synonyms: - ordo uri_format: http://www.orpha.net/ORDO/Orphanet_$1 version: '4.1' orth: contact: email: jfernand@um.es github: jesualdotomasfernandezbreis name: Jesualdo Tomás Fernández-Breis orcid: 0000-0002-7558-2880 description: 'The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way.' download_owl: https://github.com/qfo/OrthologyOntology/raw/master/orthOntology_RC_v2_A.owl example: HomologyRelation homepage: https://github.com/qfo/OrthologyOntology mappings: aberowl: ORTH bioportal: ORTH fairsharing: FAIRsharing.4877h0 ols: orth name: Orthology Ontology preferred_prefix: orth publications: - doi: 10.1186/s13326-016-0077-x pmc: null pubmed: null title: 'The Orthology Ontology: development and applications' year: null repository: https://github.com/qfo/OrthologyOntology uri_format: http://purl.org/net/orth#$1 version: 'This ontology is the second version of the orthology ontology first published in 2015 and available at http://purl.bioontology.org/ontology/ORTH . @authors T.M. de Farias, H. Chiba, J.T. Fernandez-Breis, E. Antezana, D. Kuznetsov, C. Dessimoz and F. Villiers.' orthodb: description: OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups example: Q9P0K8 homepage: https://www.orthodb.org mappings: biocontext: ORTHODB fairsharing: FAIRsharing.x989d5 miriam: orthodb n2t: orthodb prefixcommons: orthodb uniprot: OrthoDB name: OrthoDB pattern: ^\w+$ preferred_prefix: orthodb provides: uniprot publications: - doi: 10.1093/nar/gkq930 pmc: PMC3013786 pubmed: '20972218' title: 'OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011.' year: 2010 uri_format: http://cegg.unige.ch/orthodb/results?searchtext=$1 oryzabase.gene: description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information. example: '117' homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ mappings: biocontext: ORYZABASE.GENE miriam: oryzabase.gene n2t: oryzabase.gene name: Oryzabase Gene pattern: ^\d+$ preferred_prefix: oryzabase.gene uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1 oryzabase.mutant: description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information. example: '21393' homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ mappings: biocontext: ORYZABASE.MUTANT miriam: oryzabase.mutant n2t: oryzabase.mutant name: Oryzabase Mutant pattern: ^\d+$ preferred_prefix: oryzabase.mutant uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1 oryzabase.reference: description: The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan. example: '42840' homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ mappings: miriam: oryzabase.reference n2t: oryzabase.reference name: Oryzabase Reference pattern: ^\d+$ preferred_prefix: oryzabase.reference uri_format: https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1 oryzabase.stage: description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information. example: '34' homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ mappings: biocontext: ORYZABASE.STAGE miriam: oryzabase.stage n2t: oryzabase.stage name: Oryzabase Stage pattern: ^\d+$ preferred_prefix: oryzabase.stage uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1 oryzabase.strain: description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information. example: '1' homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ mappings: biocontext: ORYZABASE.STRAIN miriam: oryzabase.strain n2t: oryzabase.strain name: Oryzabase Strain pattern: ^\d+$ preferred_prefix: oryzabase.strain uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1 oslc: contact: email: jamsden@us.ibm.com github: null name: Jim Amsden orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains. example: Property homepage: http://open-services.net/ns/core name: OASIS Open Services for Lifecycle Collaboration Core Vocabulary preferred_prefix: oslc uri_format: http://open-services.net/ns/core#$1 otl: description: Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information. example: AADB12 homepage: http://oryzatagline.cirad.fr/ mappings: biocontext: OTL fairsharing: FAIRsharing.61c2x6 miriam: otl n2t: otl prefixcommons: otl name: Oryza Tag Line pattern: ^A[A-Z]+\d+$ preferred_prefix: otl uri_format: http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1 otol: contributor: email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 description: Identifier for an entity in open tree of life example: '3905431' github_request_issue: 470 homepage: https://tree.opentreeoflife.org mappings: wikidata: P9157 name: Open Tree of Life pattern: ^[1-9]\d*$ preferred_prefix: otol reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://tree.opentreeoflife.org/taxonomy/browse?id=$1 ovae: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqunh He orcid: 0000-0001-9189-9661 description: 'OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). ' download_owl: http://purl.obolibrary.org/obo/ovae.owl example: 0000609 homepage: http://www.violinet.org/ovae/ license: CC BY 3.0 mappings: aberowl: OVAE biocontext: OVAE bioportal: OVAE fairsharing: FAIRsharing.w4x6n4 obofoundry: ovae ols: ovae ontobee: OVAE name: Ontology of Vaccine Adverse Events pattern: ^\d{7}$ preferred_prefix: OVAE publications: - doi: 10.1186/2041-1480-4-40 pmc: PMC4177204 pubmed: '24279920' title: The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines. year: 2013 repository: https://github.com/OVAE-Ontology/ovae uri_format: http://purl.obolibrary.org/obo/OVAE_$1 version: 1.0.34 owl: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. ' download_owl: https://triplydb.com/w3c/owl/download.trig.gz example: Ontology homepage: https://www.w3.org/TR/owl-features/ mappings: biocontext: owl fairsharing: FAIRsharing.atygwy name: Web Ontology Language preferred_prefix: owl uri_format: http://www.w3.org/2002/07/owl#$1 p3db.protein: description: Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites. example: '70' homepage: http://www.p3db.org/ mappings: biocontext: P3DB.PROTEIN miriam: p3db.protein n2t: p3db.protein name: P3DB Protein pattern: ^\d+$ preferred_prefix: p3db.protein uri_format: http://www.p3db.org/protein.php?id=$1&ref=0 p3db.site: description: Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins. example: '65' homepage: http://www.p3db.org/ mappings: biocontext: P3DB.SITE miriam: p3db.site n2t: p3db.site name: P3DB Site pattern: ^\d+$ preferred_prefix: p3db.site uri_format: http://www.p3db.org/phosphosite.php?id=$1&ref=0 paleodb: description: The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data. example: '83088' homepage: http://paleodb.org/ mappings: biocontext: PALEODB miriam: paleodb n2t: paleodb prefixcommons: paleodb name: Paleobiology Database pattern: ^\d+$ preferred_prefix: paleodb uri_format: http://fossilworks.org/?a=taxonInfo&taxon_no=$1 panorama: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow. It makes links to the Proteomics Exchange when possible. example: FxnI151FMs homepage: https://panoramaweb.org mappings: fairsharing: FAIRsharing.uBpQ1q name: Panorama Public preferred_prefix: panorama uri_format: https://panoramaweb.org/$1.url panther.family: description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families. example: PTHR12345 homepage: http://www.pantherdb.org/ mappings: biocontext: PANTHER.FAMILY biolink: PANTHER.FAMILY go: PANTHER miriam: panther.family n2t: panther.family name: Protein ANalysis THrough Evolutionary Relationships Classification System part_of: panther pattern: ^PTHR\d{5}(\:SF\d{1,3})?$ preferred_prefix: panther.family uri_format: http://www.pantherdb.org/panther/family.do?clsAccession=$1 panther.node: description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes. example: PTN000000026 homepage: http://pantree.org/ mappings: biocontext: PANTHER.NODE miriam: panther.node n2t: panther.node name: PANTHER Node part_of: panther pattern: ^PTN\d{9}$ preferred_prefix: panther.node uri_format: http://www.pantree.org/node/annotationNode.jsp?id=$1 panther.pathway: description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components. example: P00024 homepage: http://www.pantherdb.org/ mappings: biocontext: PANTHER.PATHWAY edam: '1161' miriam: panther.pathway n2t: panther.pathway name: PANTHER Pathway part_of: panther pattern: ^P\d{5}$ preferred_prefix: panther.pathway uri_format: http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1 panther.pthcmp: description: "The PANTHER (Protein ANalysis THrough Evolutionary Relationships)\ \ Classification System is a resource that classifies genes by their functions,\ \ using published scientific experimental evidence and evolutionary relationships\ \ to predict function even in the absence of direct experimental evidence. The\ \ PANTHER Pathway Component collection references specific classes of molecules\ \ that play the same mechanistic role within a pathway, across species. Pathway\r\ \ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified\ \ component is a protein, DNA, or transcribed RNA, it is associated with protein\ \ sequences in the PANTHER protein family trees through manual curation." example: P00266 homepage: http://www.pantherdb.org/ mappings: biocontext: PANTHER.PTHCMP miriam: panther.pthcmp n2t: panther.pthcmp name: PANTHER Pathway Component part_of: panther pattern: ^(G|P|U|C|S)\d{5}$ preferred_prefix: panther.pthcmp uri_format: http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1 pao: contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp name: Pankaj Jaiswal orcid: 0000-0002-1005-8383 deprecated: true homepage: http://www.plantontology.org mappings: biocontext: PAO obofoundry: pao name: Plant Anatomy Ontology preferred_prefix: PAO uri_format: http://purl.obolibrary.org/obo/PAO_$1 pass2: deprecated: true description: The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity. example: '46977' homepage: http://caps.ncbs.res.in/pass2 mappings: biocontext: PASS2 miriam: pass2 n2t: pass2 prefixcommons: pass2 name: Protein Alignment organised as Structural Superfamily pattern: ^\d+$ preferred_prefix: pass2 uri_format: http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1 pathbank: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. example: SMP0000219 homepage: https://pathbank.org mappings: fairsharing: FAIRsharing.3xwMon name: PathBank pattern: ^(SMP|PW)\d+$ preferred_prefix: pathbank uri_format: https://pathbank.org/view/$1 pathwaycommons: description: Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language. example: '485991' homepage: http://www.pathwaycommons.org/pc/ mappings: biocontext: PATHWAYCOMMONS miriam: pathwaycommons n2t: pathwaycommons prefixcommons: pathwaycommons re3data: r3d100012731 uniprot: PathwayCommons name: Pathway Commons pattern: ^\d+$ preferred_prefix: pathwaycommons uri_format: http://www.pathwaycommons.org/pc/record2.do?id=$1 pato: appears_in: - agro - aism - cdno - cl - colao - ecocore - ecto - fovt - lepao - mco - ms - pcl - pco - phipo - planp - proco - rbo - xpo - zp banana: PATO contact: email: g.gkoutos@gmail.com github: gkoutos name: George Gkoutos orcid: 0000-0002-2061-091X description: PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. download_json: http://purl.obolibrary.org/obo/pato.json download_obo: http://purl.obolibrary.org/obo/pato.obo download_owl: http://purl.obolibrary.org/obo/pato.owl example: 0001998 homepage: https://github.com/pato-ontology/pato/ license: CC BY 3.0 mappings: aberowl: PATO agroportal: PATO biocontext: PATO bioportal: PATO fairsharing: FAIRsharing.ezwdhz go: PATO miriam: pato n2t: pato obofoundry: pato ols: pato ontobee: PATO prefixcommons: pato name: Phenotype And Trait Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: PATO providers: - code: purl description: Legacy PURLs found in OAE homepage: http://purl.org/obo/owl/ name: Legacy PURL uri_format: http://purl.org/obo/owl/PATO#PATO_$1 publications: - doi: 10.1093/bib/bbx035 pmc: PMC6169674 pubmed: '28387809' title: 'The anatomy of phenotype ontologies: principles, properties and applications.' year: 2018 - doi: 10.1186/gb-2010-11-1-r2 pmc: PMC2847714 pubmed: '20064205' title: Integrating phenotype ontologies across multiple species. year: 2010 - doi: 10.1186/gb-2004-6-1-r8 pmc: PMC549069 pubmed: '15642100' title: Using ontologies to describe mouse phenotypes. year: 2004 repository: https://github.com/pato-ontology/pato uri_format: https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=PATO:$1 version: '2022-08-31' pav: contact: email: stian@soiland-reyes.com github: null name: Stian Soiland-Reyes orcid: null contributor: email: null github: matentzn name: Nico Matentzoglu orcid: 0000-0002-7356-1779 contributor_extras: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources. download_owl: http://aber-owl.net/media/ontologies/PAV/3/pav.owl example: authoredBy github_request_issue: 186 homepage: https://pav-ontology.github.io/pav/ mappings: aberowl: PAV biocontext: pav biolink: pav bioportal: PAV fairsharing: FAIRsharing.nbfwwv name: Provenance, Authoring, and Versioning Vocabulary pattern: ^[a-z][a-zA-Z]+$ preferred_prefix: pav publications: - doi: 10.1186/2041-1480-4-37 pmc: PMC4177195 pubmed: '24267948' title: 'PAV ontology: provenance, authoring and versioning.' year: 2013 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://purl.org/pav/$1 paxdb.organism: description: PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species. example: '9606' homepage: http://pax-db.org/ mappings: biocontext: PAXDB.ORGANISM miriam: paxdb.organism n2t: paxdb.organism name: PaxDb Organism pattern: ^\d+$ preferred_prefix: paxdb.organism uri_format: http://pax-db.org/#!species/$1 paxdb.protein: description: PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels. example: '977869' homepage: http://pax-db.org/ mappings: biocontext: PAXDB.PROTEIN miriam: paxdb.protein n2t: paxdb.protein name: PaxDb Protein pattern: ^\d+$ preferred_prefix: paxdb.protein uri_format: http://pax-db.org/#!protein/$1 pazar: description: The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors. example: TF0001053 homepage: http://www.pazar.info/ mappings: biocontext: PAZAR fairsharing: FAIRsharing.33yggg miriam: pazar n2t: pazar prefixcommons: pazar name: Pazar Transcription Factor pattern: ^TF\w+$ preferred_prefix: pazar uri_format: http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1 pba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A controlled vocabulary to support the study of transcription in the primate brain download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-pba.obo example: '128011350' homepage: https://www.blueprintnhpatlas.org/ name: Primate Brain Atlas pattern: ^\d+$ preferred_prefix: PBA uri_format: https://biopragmatics.github.io/providers/pba/$1 pcl: contact: email: davidos@ebi.ac.uk github: dosumis name: David Osumi-Sutherland orcid: 0000-0002-7073-9172 depends_on: - bfo - chebi - cl - go - nbo - ncbitaxon - omo - pato - pr - ro - so - uberon description: Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties. download_json: http://purl.obolibrary.org/obo/pcl.json download_obo: http://purl.obolibrary.org/obo/pcl.obo download_owl: http://purl.obolibrary.org/obo/pcl.owl example: '0011124' homepage: https://github.com/obophenotype/provisional_cell_ontology license: CC BY 4.0 mappings: aberowl: PCL bioportal: PCL fairsharing: FAIRsharing.bfcfd0 obofoundry: pcl ols: pcl ontobee: PCL name: Provisional Cell Ontology pattern: ^\d{7}$ preferred_prefix: PCL publications: - doi: 10.1101/2021.10.10.463703 pmc: null pubmed: null title: 'Brain Data Standards Ontology: A data-driven ontology of transcriptomically defined cell types in the primary motor cortex' year: null repository: https://github.com/obophenotype/provisional_cell_ontology uri_format: http://purl.obolibrary.org/obo/PCL_$1 version: '2022-04-27' pco: appears_in: - ecocore - envo contact: email: rlwalls2008@gmail.com github: ramonawalls name: Ramona Walls orcid: 0000-0001-8815-0078 depends_on: - bfo - caro - envo - go - iao - ncbitaxon - pato - ro description: The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. download_obo: http://purl.obolibrary.org/obo/pco.obo download_owl: http://purl.obolibrary.org/obo/pco.owl example: '0000021' homepage: https://github.com/PopulationAndCommunityOntology/pco license: CC0 1.0 mappings: aberowl: PCO agroportal: PCO biocontext: PCO bioportal: PCO ecoportal: PCO fairsharing: FAIRsharing.vq28qp obofoundry: pco ols: pco ontobee: PCO name: Population and Community Ontology pattern: ^\d{7}$ preferred_prefix: PCO repository: https://github.com/PopulationAndCommunityOntology/pco uri_format: http://purl.obolibrary.org/obo/PCO_$1 version: '2021-05-03' pd_st: contact: email: henrich@embl.de github: null name: Thorsten Heinrich orcid: null deprecated: true homepage: http://4dx.embl.de/platy mappings: biocontext: PD_ST obofoundry: pd_st name: Platynereis stage ontology preferred_prefix: PD_ST uri_format: http://purl.obolibrary.org/obo/PD_ST_$1 pdb: description: The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. example: 2gc4 homepage: https://www.wwpdb.org/ mappings: biocontext: PDB edam: '1127' fairsharing: FAIRsharing.mckkb4 go: PDB miriam: pdb n2t: pdb ncbi: PDB prefixcommons: pdbj re3data: r3d100010910 uniprot: RCSB-PDB wikidata: P638 name: PDB Structure pattern: ^[0-9][A-Za-z0-9]{3}$ preferred_prefix: pdb providers: - code: CURATOR_REVIEW description: Proteopedia homepage: http://www.proteopedia.org/ name: Proteopedia uri_format: http://proteopedia.org/wiki/index.php/$1 - code: ebi description: Protein Databank through PDBsum homepage: https://www.ebi.ac.uk/pdbsum/ name: Protein Databank through PDBsum uri_format: https://www.ebi.ac.uk/pdbsum/$1 - code: pdbe description: Protein Databank in Europe (PDBe) homepage: http://www.pdbe.org/ name: Protein Databank in Europe (PDBe) uri_format: https://www.ebi.ac.uk/pdbe/entry/pdb/$1 - code: pdbj description: Protein Data Bank Japan (PDBj) homepage: http://www.pdbj.org/ name: Protein Data Bank Japan (PDBj) uri_format: https://pdbj.org/mine/summary/$1 - code: rcsb description: RCSB PDB homepage: https://www.rcsb.org/ name: RCSB PDB uri_format: https://www.rcsb.org/structure/$1 synonyms: - RCSB_PDB - pdbe - pdbj - wwpdb uri_format: https://www.wwpdb.org/pdb?id=$1 pdb-ccd: comment: might be same as pdb.ligand, not sure though contributor_extras: - email: bmeldal@ebi.ac.uk github: bmeldal-eg name: Birgit Meldal orcid: 0000-0003-4062-6158 description: The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names. example: AB0 example_extras: - A - PI has_canonical: pdb.ligand homepage: https://www.ebi.ac.uk/pdbe-srv/pdbechem/ mappings: biocontext: PDB-CCD miriam: pdb-ccd n2t: pdb-ccd prefixcommons: ccd name: Chemical Component Dictionary pattern: ^\w{1,3}$ preferred_prefix: pdb-ccd publications: - doi: 10.1038/nsb1203-980 pmc: null pubmed: '14634627' title: Announcing the worldwide Protein Data Bank. year: 2003 synonyms: - pdbechem uri_format: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1 pdb.ligand: description: The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands. example: TRQ homepage: http://www.pdb.org/ mappings: biocontext: PDB.LIGAND miriam: pdb.ligand n2t: pdb.ligand prefixcommons: pdbligand wikidata: P3636 name: Protein Data Bank Ligand pattern: ^[A-Za-z0-9]+$ preferred_prefix: pdb.ligand providers: - code: CURATOR_REVIEW description: PDB Ligand at Protein Databank in Europe (PDBe) homepage: https://www.pdbe.org/ name: PDB Ligand at Protein Databank in Europe (PDBe) uri_format: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1 synonyms: - PDB_CHEM_ID uri_format: http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$1 pdc.study: contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The National Cancer Institute's Proteomic Data Commons (PDC) makes cancer-related proteomic datasets easily accessible to the public. example: PDC000351 github_request_issue: 430 homepage: https://pdc.cancer.gov/pdc name: Proteomic Data Commons pattern: ^PDC\d+$ preferred_prefix: pdc.study reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://pdc.cancer.gov/pdc/study/$1 pdro: contact: email: paul.fabry@usherbrooke.ca github: pfabry name: Paul Fabry orcid: 0000-0002-3336-2476 description: An ontology to describe entities related to prescription of drugs download_owl: http://purl.obolibrary.org/obo/pdro.owl example: 0010039 homepage: https://github.com/OpenLHS/PDRO license: CC BY 4.0 mappings: aberowl: PDRO biocontext: PDRO bioportal: PDRO fairsharing: FAIRsharing.9te3ev obofoundry: pdro ols: pdro ontobee: PDRO name: The Prescription of Drugs Ontology pattern: ^\d{7}$ preferred_prefix: PDRO publications: - doi: 10.3390/ijerph182212025 pmc: PMC8619589 pubmed: '34831777' title: 'The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its Parts.' year: 2021 repository: https://github.com/OpenLHS/PDRO uri_format: http://purl.obolibrary.org/obo/PDRO_$1 version: '2021-06-08' pdumdv: contact: email: frederic.bastian@unil.ch github: fbastian name: Frédéric Bastian orcid: 0000-0002-9415-5104 description: Life cycle stages for Platynereis dumerilii download_obo: http://purl.obolibrary.org/obo/pdumdv.obo download_owl: http://purl.obolibrary.org/obo/pdumdv.owl example: '0001410' homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv license: CC BY 3.0 mappings: aberowl: PDUMDV biocontext: PDUMDV bioportal: PDUMDV fairsharing: FAIRsharing.493qns obofoundry: pdumdv ols: pdumdv ontobee: PDUMDV name: Platynereis Developmental Stages pattern: ^\d{7}$ preferred_prefix: PdumDv repository: https://github.com/obophenotype/developmental-stage-ontologies synonyms: - PdumDv uri_format: http://purl.obolibrary.org/obo/PDUMDV_$1 version: '2020-03-10' peco: appears_in: - agro - mco contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp name: Pankaj Jaiswal orcid: 0000-0002-1005-8383 description: A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. download_obo: https://raw.githubusercontent.com/Planteome/plant-experimental-conditions-ontology/master/peco.obo download_owl: http://purl.obolibrary.org/obo/peco.owl example: '0007114' homepage: http://planteome.org/ license: CC BY 4.0 mappings: aberowl: PECO agroportal: PECO biocontext: PECO bioportal: PECO fairsharing: FAIRsharing.6yNXYK obofoundry: peco ols: peco ontobee: PECO name: Plant Experimental Conditions Ontology pattern: ^\d{7}$ preferred_prefix: PECO publications: - doi: 10.1093/nar/gkx1152 pmc: PMC5753347 pubmed: '29186578' title: 'The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.' year: 2018 repository: https://github.com/Planteome/plant-experimental-conditions-ontology uri_format: http://purl.obolibrary.org/obo/PECO_$1 version: '2020-08-21' ped: description: The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins. example: PED00037 homepage: https://proteinensemble.org/ mappings: fairsharing: FAIRsharing.31385c miriam: ped name: Protein Ensemble Database pattern: ^PED\d{5}$ preferred_prefix: ped uri_format: https://proteinensemble.org/$1 ped.ensemble: description: The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins. example: PED00017e001 homepage: https://proteinensemble.org/ mappings: miriam: ped.ensemble name: Protein Ensemble Database ensemble part_of: ped pattern: ^PED\d{5}e\d{3}$ preferred_prefix: ped.ensemble uri_format: https://proteinensemble.org/$1 peff: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true download_obo: https://github.com/HUPO-PSI/PEFF/raw/master/CV/psi-peff-OBSOLETE-DO_NOT_USE.obo example: '0001011' homepage: https://www.psidev.info/peff name: PSI Extended File Format pattern: ^\d{7}$ preferred_prefix: peff uri_format: https://biopragmatics.github.io/providers/peff/$1 pennsieve: description: 'Pennsieve is a publicly accessible Scientific Data Management and publication platform. The platform supports data curation, sharing and publishing complex scientific datasets with a focus on integration between graph-based metadata and file-archival. The platform provides a "peer"-reviewed publication mechanism and public datasets are available through its Discover Web Application and APIs. ' example: N:package:e3243db3-7986-488e-9a10-c7a0bfdcfe8a homepage: https://discover.pennsieve.io mappings: miriam: ps name: Pennsieve pattern: ^N:package:[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$ preferred_prefix: pennsieve uri_format: https://discover.pennsieve.io/package/$1 peptideatlas: description: The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools. example: PAp00000009 homepage: http://www.peptideatlas.org/ mappings: biocontext: PEPTIDEATLAS edam: '2626' fairsharing: FAIRsharing.dvyrsz miriam: peptideatlas n2t: peptideatlas prefixcommons: peptideatlas re3data: r3d100010889 uniprot: PeptideAtlas name: PeptideAtlas pattern: ^PAp[0-9]{8}$ preferred_prefix: peptideatlas publications: - doi: 10.1038/embor.2008.56 pmc: PMC2373374 pubmed: '18451766' title: 'PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows.' year: 2008 uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1 peptideatlas.dataset: description: Experiment details about PeptideAtlas entries. Each PASS entry provides direct access to the data files submitted to PeptideAtlas. example: PASS01237 homepage: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_Summary mappings: miriam: peptideatlas.dataset n2t: peptideatlas.dataset name: PeptideAtlas Dataset pattern: ^PASS\d{5}$ preferred_prefix: peptideatlas.dataset uri_format: http://www.peptideatlas.org/PASS/$1 perkinelmer: description: Cell line collections example: SCC111 homepage: https://www.perkinelmer.com/ mappings: cellosaurus: PerkinElmer name: PerkinElmer cell line collection preferred_prefix: perkinelmer uri_format: https://www.perkinelmer.com/searchresult?searchName=$1 peroxibase: description: Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences. example: '5282' homepage: http://peroxibase.toulouse.inra.fr/ mappings: biocontext: PEROXIBASE fairsharing: FAIRsharing.z1czxj miriam: peroxibase n2t: peroxibase prefixcommons: peroxibase uniprot: PeroxiBase name: Peroxibase pattern: ^\d+$ preferred_prefix: peroxibase publications: - doi: 10.1093/jxb/ern317 pmc: null pubmed: '19112168' title: 'PeroxiBase: a powerful tool to collect and analyse peroxidase sequences from Viridiplantae.' year: 2008 uri_format: http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1 pesticides: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients. example: derivatives%2Fthiocyclam%20hydrochloride homepage: http://www.alanwood.net/pesticides name: Alan Wood's Pesticides preferred_prefix: pesticides uri_format: http://www.alanwood.net/pesticides/$1.html pfam: description: The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored. example: PF11779 homepage: https://pfam.xfam.org/ mappings: biocontext: PFAM edam: '1138' fairsharing: FAIRsharing.y3scf6 go: Pfam miriam: pfam n2t: pfam ncbi: PFAM prefixcommons: pfam uniprot: Pfam wikidata: P3519 name: Pfam pattern: ^PF\d{5}$ preferred_prefix: pfam providers: - code: sanger description: The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored. homepage: http://pfam.sanger.ac.uk/ name: Sanger Pfam Mirror uri_format: http://pfam.sanger.ac.uk/family?entry=$1 - code: xfam description: Pfam's familes in their old home in the xfam.org homepage: https://pfam.xfam.org name: Xfam uri_format: https://pfam.xfam.org/family?acc=$1 publications: - doi: 10.1093/nar/27.1.260 pmc: PMC148151 pubmed: '9847196' title: 'Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.' year: 1999 - doi: 10.1093/nar/26.1.320 pmc: PMC147209 pubmed: '9399864' title: 'Pfam: multiple sequence alignments and HMM-profiles of protein domains.' year: 1998 - doi: 10.1002/(sici)1097-0134(199707)28:3<405::aid-prot10>3.0.co;2-l pmc: null pubmed: '9223186' title: 'Pfam: a comprehensive database of protein domain families based on seed alignments.' year: 1997 - doi: 10.1093/nar/gkh121 pmc: PMC308855 pubmed: '14681378' title: The Pfam protein families database. year: 2004 - doi: 10.1093/nar/30.1.276 pmc: PMC99071 pubmed: '11752314' title: The Pfam protein families database. year: 2002 - doi: 10.1093/nar/28.1.263 pmc: PMC102420 pubmed: '10592242' title: The Pfam protein families database. year: 2000 references: - https://twitter.com/PfamDB/status/1555149527228813314 synonyms: - PF uri_format: https://www.ebi.ac.uk/interpro/entry/pfam/$1 pfam.clan: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Higher order grouping of Pfam families example: CL0192 homepage: https://pfam.xfam.org mappings: edam: '2758' name: Pfam Clans pattern: ^CL\d+$ preferred_prefix: pfam.clan providers: - code: xfam description: Pfam's clans in their old home in the xfam.org homepage: https://pfam.xfam.org name: Xfam uri_format: https://pfam.xfam.org/clan/$1 references: - https://twitter.com/PfamDB/status/1555149527228813314 uri_format: https://www.ebi.ac.uk/interpro/set/pfam/$1 pfr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets. example: '1001' homepage: http://repository.topdownproteomics.org/proteoforms mappings: fairsharing: FAIRsharing.wqsxtg name: Proteoform Atlas pattern: ^\d+$ preferred_prefix: pfr synonyms: - TDR uri_format: http://repository.topdownproteomics.org/proteoforms/$1 pgdso: contact: email: po-discuss@plantontology.org github: null name: Plant Ontology Administrators orcid: null deprecated: true homepage: http://www.plantontology.org mappings: biocontext: PGDSO obofoundry: pgdso name: Plant Growth and Development Stage preferred_prefix: PGDSO uri_format: http://purl.obolibrary.org/obo/PGDSO_$1 pgs: description: The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation. example: PGS000018 homepage: http://pgscatalog.org mappings: miriam: pgs name: Polygenic Score Catalog pattern: ^PGS[0-9]{6}$ preferred_prefix: pgs uri_format: https://www.pgscatalog.org/pgs/$1 pgx: description: The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt "neoplasm" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs. example: pgxbs-kftva5zv homepage: https://progenetix.org/ mappings: biocontext: PGX cellosaurus: Progenetix fairsharing: FAIRsharing.65tdnz miriam: pgx n2t: pgx re3data: r3d100012820 name: Progenetix pattern: ^\w{3,15}[-_]\w[\w.-]{3,128}$ preferred_prefix: pgx synonyms: - Progenetix uri_format: https://progenetix.org/services/ids/$1 pharmacodb.cell: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by cell line. example: 22RV1_12_2019 homepage: https://pharmacodb.ca/cell_lines mappings: cellosaurus: PharmacoDB name: PharmacoDB Cells preferred_prefix: pharmacodb.cell uri_format: https://pharmacodb.ca/cell_lines/$1 pharmacodb.dataset: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by dataset. example: '1' homepage: https://pharmacodb.ca/datasets name: PharmacoDB Datasets pattern: ^\d+$ preferred_prefix: pharmacodb.dataset uri_format: https://pharmacodb.ca/datasets/$1 pharmacodb.tissue: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by tissue. example: '13' homepage: https://pharmacodb.ca/tissues name: PharmacoDB Tissues pattern: ^\d+$ preferred_prefix: pharmacodb.tissue uri_format: https://pharmacodb.ca/tissues/$1 pharmgkb.disease: description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. example: PA447218 homepage: http://www.pharmgkb.org/ mappings: biocontext: PHARMGKB.DISEASE edam: '2651' miriam: pharmgkb.disease n2t: pharmgkb.disease prefixcommons: pharmgkb.disease wikidata: P7001 name: PharmGKB Disease pattern: ^PA\d+$ preferred_prefix: pharmgkb.disease publications: - doi: 10.2217/bmm.11.94 pmc: PMC3339046 pubmed: '22103613' title: 'From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource.' year: 2011 - doi: 10.1038/sj.tpj.6500035 pmc: null pubmed: '11908751' title: 'Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base.' year: 2001 uri_format: http://www.pharmgkb.org/disease/$1 pharmgkb.drug: description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. example: PA448710 homepage: http://www.pharmgkb.org/ mappings: biocontext: PHARMGKB.DRUG edam: '2652' miriam: pharmgkb.drug n2t: pharmgkb.drug prefixcommons: pharmgkb.drug wikidata: P7001 name: PharmGKB Drug pattern: ^PA\d+$ preferred_prefix: pharmgkb.drug publications: - doi: 10.2217/bmm.11.94 pmc: PMC3339046 pubmed: '22103613' title: 'From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource.' year: 2011 - doi: 10.1038/sj.tpj.6500035 pmc: null pubmed: '11908751' title: 'Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base.' year: 2001 uri_format: http://www.pharmgkb.org/drug/$1 pharmgkb.gene: description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. example: PA131 homepage: http://www.pharmgkb.org/ mappings: biocontext: PHARMGKB.GENE bioportal: PHARMGKB go: PharmGKB miriam: pharmgkb.gene n2t: pharmgkb.gene prefixcommons: pharmgkb.gene wikidata: P7001 name: Pharmacogenetics and Pharmacogenomics Knowledge Base pattern: ^PA\w+$ preferred_prefix: pharmgkb.gene publications: - doi: 10.2217/bmm.11.94 pmc: PMC3339046 pubmed: '22103613' title: 'From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource.' year: 2011 uri_format: http://www.pharmgkb.org/gene/$1 pharmgkb.pathways: description: "The PharmGKB database is a central repository for genetic, genomic,\ \ molecular and cellular phenotype data and clinical information about people\ \ who have participated in pharmacogenomics research studies. The data includes,\ \ but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic\ \ research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter\ \ domains. \r\nPharmGKB Pathways are drug centric, gene based, interactive pathways\ \ which focus on candidate genes and gene groups and associated genotype and phenotype\ \ data of relevance for pharmacogenetic and pharmacogenomic studies." example: PA146123006 homepage: http://www.pharmgkb.org/ mappings: biocontext: PHARMGKB.PATHWAYS edam: '2650' miriam: pharmgkb.pathways n2t: pharmgkb.pathways prefixcommons: pharmgkb.pathways wikidata: P7001 name: PharmGKB pattern: ^PA\d+$ preferred_prefix: pharmgkb.pathways publications: - doi: 10.2217/bmm.11.94 pmc: PMC3339046 pubmed: '22103613' title: 'From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource.' year: 2011 - doi: 10.1038/sj.tpj.6500035 pmc: null pubmed: '11908751' title: 'Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base.' year: 2001 uri_format: http://www.pharmgkb.org/pathway/$1 phenolexplorer: description: Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis. example: '75' homepage: http://www.phenol-explorer.eu/foods/ mappings: biocontext: PHENOLEXPLORER miriam: phenolexplorer n2t: phenolexplorer re3data: r3d100012197 name: Phenol-Explorer pattern: ^\d+$ preferred_prefix: phenolexplorer uri_format: http://phenol-explorer.eu/foods/$1 phenx: contact: email: yingqin@rti.org github: null name: PhenX Admin orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants. download_owl: http://aber-owl.net/media/ontologies/PHENX/16/phenx.owl example: '130502' github_request_issue: 503 homepage: https://www.phenxtoolkit.org/ mappings: aberowl: PHENX bioportal: PHENX fairsharing: FAIRsharing.y5jcwa name: PhenX Toolkit pattern: ^\d+$ preferred_prefix: phenx publications: - doi: 10.1038/gim.2016.199 pmc: PMC5507752 pubmed: '28079902' title: PhenX measures for phenotyping rare genetic conditions. year: 2017 - doi: 10.1093/aje/kwr193 pmc: PMC3141081 pubmed: '21749974' title: 'The PhenX Toolkit: get the most from your measures.' year: 2011 - doi: 10.1097/mol.0b013e3283377395 pmc: PMC8038872 pubmed: '20154612' title: 'PhenX: a toolkit for interdisciplinary genetics research.' year: 2010 synonyms: - phenxtoolkit uri_format: https://www.phenxtoolkit.org/protocols/view/$1 phipo: contact: email: alayne.cuzick@rothamsted.ac.uk github: CuzickA name: Alayne Cuzick orcid: 0000-0001-8941-3984 depends_on: - pato description: Ontology of species-neutral phenotypes observed in pathogen-host interactions. download_obo: http://purl.obolibrary.org/obo/phipo.obo download_owl: http://purl.obolibrary.org/obo/phipo.owl example: '0000001' homepage: https://github.com/PHI-base/phipo license: CC BY 3.0 mappings: aberowl: PHIPO bioportal: PHIPO obofoundry: phipo ols: phipo ontobee: PHIPO name: Pathogen Host Interaction Phenotype Ontology pattern: ^\d{7}$ preferred_prefix: PHIPO publications: - doi: 10.1093/nar/gkab1037 pmc: PMC8728202 pubmed: '34788826' title: 'PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions.' year: 2022 repository: https://github.com/PHI-base/phipo uri_format: http://purl.obolibrary.org/obo/PHIPO_$1 version: '2021-07-14' phosphopoint.kinase: description: PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information. example: AURKA homepage: http://kinase.bioinformatics.tw/ mappings: biocontext: PHOSPHOPOINT.KINASE miriam: phosphopoint.kinase n2t: phosphopoint.kinase name: PhosphoPoint Kinase pattern: ^\w+$ preferred_prefix: phosphopoint.kinase uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1 phosphopoint.protein: description: PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information. example: AURKA homepage: http://kinase.bioinformatics.tw/ mappings: biocontext: PHOSPHOPOINT.PROTEIN miriam: phosphopoint.protein n2t: phosphopoint.protein name: PhosphoPoint Phosphoprotein pattern: ^\w+$ preferred_prefix: phosphopoint.protein uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0 phosphosite.protein: description: PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database. example: '12300' homepage: http://www.phosphosite.org/homeAction.do mappings: biocontext: PHOSPHOSITE.PROTEIN miriam: phosphosite.protein n2t: phosphosite.protein name: PhosphoSite Protein pattern: ^\d{5}$ preferred_prefix: phosphosite.protein uri_format: http://www.phosphosite.org/proteinAction.do?id=$1 phosphosite.residue: description: PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence. example: '2842' homepage: http://www.phosphosite.org/homeAction.do mappings: biocontext: PHOSPHOSITE.RESIDUE miriam: phosphosite.residue n2t: phosphosite.residue name: PhosphoSite Residue pattern: ^\d+$ preferred_prefix: phosphosite.residue uri_format: http://www.phosphosite.org/siteAction.do?id=$1 phosphosite.sitegroup: comment: Potentially could use a URI format like https://www.phosphosite.org/siteGroupAction.action?protOrg=1156&id=$1, but it's not obvious what the protOrg does. contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur. example: '447860' homepage: https://www.phosphosite.org name: PhosphoSite Site Group pattern: ^\d+$ preferred_prefix: phosphosite.sitegroup reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 phylomedb: description: PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins. example: Phy000CLXM_RAT homepage: http://phylomedb.org/ mappings: biocontext: PHYLOMEDB fairsharing: FAIRsharing.7hxxc4 miriam: phylomedb n2t: phylomedb prefixcommons: phylomedb uniprot: PhylomeDB name: PhylomeDB pattern: ^\w+$ preferred_prefix: phylomedb publications: - doi: 10.1093/nar/gkm899 pmc: PMC2238872 pubmed: '17962297' title: 'PhylomeDB: a database for genome-wide collections of gene phylogenies.' year: 2007 uri_format: http://phylomedb.org/?seqid=$1 phytozome.locus: description: Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information. example: Glyma0021s00410 homepage: http://www.phytozome.net/ mappings: biocontext: PHYTOZOME.LOCUS miriam: phytozome.locus n2t: phytozome.locus ncbi: Phytozome name: Plant Genome Network pattern: ^[A-Za-z0-9]+$ preferred_prefix: phytozome.locus synonyms: - JGI Phytozome uri_format: http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1 pictar: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true example: hsa-let-7a homepage: https://pictar.mdc-berlin.de/ name: PicTar preferred_prefix: pictar synonyms: - pictar-vert pid.pathway: description: The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information. example: eff796f3-6195-11e5-8ac5-06603eb7f303 homepage: http://pid.nci.nih.gov/ mappings: biocontext: PID.PATHWAY edam: '2344' fairsharing: FAIRsharing.ncgh1j miriam: pid.pathway n2t: pid.pathway prefixcommons: pid name: 'NCI Pathway Interaction Database: Pathway' pattern: ^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$ preferred_prefix: pid.pathway publications: - doi: 10.1093/nar/gkn653 pmc: PMC2686461 pubmed: '18832364' title: 'PID: the Pathway Interaction Database.' year: 2008 synonyms: - pid uri_format: http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1 pigqtldb: description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs. example: '14' homepage: https://www.animalgenome.org/QTLdb mappings: biocontext: PIGQTLDB miriam: pigqtldb n2t: pigqtldb prefixcommons: pigqtldb name: Animal Genome Pig QTL part_of: qtldb pattern: ^\d+$ preferred_prefix: pigqtldb uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 pina: description: Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. example: Q13485 homepage: http://cbg.garvan.unsw.edu.au/pina/ mappings: biocontext: PINA fairsharing: FAIRsharing.7q4gsz miriam: pina n2t: pina name: Protein Interaction Network Analysis pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ preferred_prefix: pina provides: uniprot uri_format: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1 piroplasma: description: PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: TA14985 homepage: http://piroplasmadb.org/ mappings: biocontext: PIROPLASMA miriam: piroplasma n2t: piroplasma name: PiroplasmaDB pattern: ^TA\d+$ preferred_prefix: piroplasma uri_format: http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 pirsf: description: The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. example: PIRSF000100 homepage: https://pir.georgetown.edu/ mappings: biocontext: PIRSF edam: '1136' fairsharing: FAIRsharing.vssch2 go: PIRSF miriam: pirsf n2t: pirsf prefixcommons: pirsf uniprot: PIRSF name: PIR Superfamily Classification System pattern: ^PIRSF\d{6}$ preferred_prefix: pirsf publications: - doi: 10.1093/nar/gkh097 pmc: PMC308831 pubmed: '14681371' title: 'PIRSF: family classification system at the Protein Information Resource.' year: 2004 uri_format: https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1 pkdb: description: 'PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. ' example: PKDB00198 homepage: https://www.hu-berlin.de/?set_language=en&cl=en mappings: fairsharing: FAIRsharing.AYegqK miriam: pkdb name: PK-DB pattern: ^PKDB[0-9]{5}$ preferred_prefix: pkdb uri_format: https://pk-db.com/data/$1 plana: appears_in: - planp contact: email: smr@stowers.org github: srobb1 name: Sofia Robb orcid: 0000-0002-3528-5267 depends_on: - ro - uberon description: PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea. download_obo: http://purl.obolibrary.org/obo/plana.obo download_owl: http://purl.obolibrary.org/obo/plana.owl example: '0000001' homepage: https://github.com/obophenotype/planaria-ontology license: CC BY 3.0 mappings: aberowl: PLANA biocontext: PLANA bioportal: PLANA fairsharing: FAIRsharing.g1qrqs obofoundry: plana ols: plana ontobee: PLANA name: Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology pattern: ^\d{7}$ preferred_prefix: PLANA publications: - doi: 10.1242/dev.196097 pmc: PMC8353266 pubmed: '34318308' title: 'Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms.' year: 2021 repository: https://github.com/obophenotype/planaria-ontology uri_format: http://purl.obolibrary.org/obo/PLANA_$1 version: '2022-03-02' planp: contact: email: smr@stowers.org github: srobb1 name: Sofia Robb orcid: 0000-0002-3528-5267 depends_on: - go - pato - plana - ro description: Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea. download_obo: http://purl.obolibrary.org/obo/planp.obo download_owl: http://purl.obolibrary.org/obo/planp.owl example: '0000001' homepage: https://github.com/obophenotype/planarian-phenotype-ontology license: CC BY 3.0 mappings: aberowl: PLANP bioportal: PLANP obofoundry: planp ols: planp ontobee: PLANP name: Planarian Phenotype Ontology pattern: ^\d+$ preferred_prefix: PLANP repository: https://github.com/obophenotype/planarian-phenotype-ontology uri_format: http://purl.obolibrary.org/obo/PLANP_$1 version: '2020-03-28' planttfdb: description: The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors. example: Ath_AT1G01030.1 homepage: http://planttfdb.cbi.pku.edu.cn mappings: biocontext: PLANTTFDB fairsharing: FAIRsharing.ex3fqk miriam: planttfdb n2t: planttfdb prefixcommons: planttfdb name: Plant Transcription Factor Database pattern: ^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\._\-#]*)$ preferred_prefix: planttfdb uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1 plasmodb: description: AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: PF11_0344 homepage: http://plasmodb.org/plasmo/ mappings: biocontext: PLASMODB fairsharing: FAIRsharing.g4n8sw go: PlasmoDB miriam: plasmodb n2t: plasmodb ncbi: ApiDB_PlasmoDB prefixcommons: plasmodb re3data: r3d100011569 name: PlasmoDB pattern: ^\w+$ preferred_prefix: plasmodb publications: - doi: 10.1093/nar/gkn814 pmc: PMC2686598 pubmed: '18957442' title: 'PlasmoDB: a functional genomic database for malaria parasites.' year: 2008 synonyms: - ApiDB_PlasmoDB uri_format: http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 plo: contact: email: mb4@sanger.ac.uk github: null name: Matt Berriman orcid: null deprecated: true homepage: http://www.sanger.ac.uk/Users/mb4/PLO/ mappings: biocontext: PLO obofoundry: plo name: Plasmodium Life Cycle preferred_prefix: PLO uri_format: http://purl.obolibrary.org/obo/PLO_$1 pmap.cutdb: description: The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites). example: '25782' homepage: http://cutdb.burnham.org mappings: biocontext: PMAP.CUTDB miriam: pmap.cutdb n2t: pmap.cutdb prefixcommons: pmap.cutdb name: CutDB pattern: ^\d+$ preferred_prefix: pmap.cutdb publications: - doi: 10.1093/nar/gkl813 pmc: PMC1669773 pubmed: '17142225' title: 'CutDB: a proteolytic event database.' year: 2006 uri_format: http://cutdb.burnham.org/relation/show/$1 pmap.substratedb: description: The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates. example: '1915' homepage: http://substrate.burnham.org/ mappings: biocontext: PMAP.SUBSTRATEDB miriam: pmap.substratedb n2t: pmap.substratedb prefixcommons: pmap.substratedb name: SubstrateDB pattern: ^\d+$ preferred_prefix: pmap.substratedb publications: - doi: 10.1093/nar/gkn683 pmc: PMC2686432 pubmed: '18842634' title: 'PMAP: databases for analyzing proteolytic events and pathways.' year: 2008 uri_format: http://substrate.burnham.org/protein/annotation/$1/html pmc: description: PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature. example: PMC3084216 homepage: http://europepmc.org/ mappings: biocontext: PMCID fairsharing: FAIRsharing.wpt5mp go: PMCID miriam: pmc n2t: pmc prefixcommons: pmc wikidata: P932 name: Pubmed Central pattern: ^PMC\d+$ preferred_prefix: pmc providers: - code: ncbi description: PubMed Central homepage: https://www.ncbi.nlm.nih.gov/pmc/ name: PubMed Central uri_format: https://www.ncbi.nlm.nih.gov/pmc/articles/$1/?tool=pubmed synonyms: - PMC - PMCID uri_format: http://europepmc.org/articles/$1 pmdb: description: The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques. example: PM0012345 homepage: https://bioinformatics.cineca.it/PMDB/ mappings: biocontext: PMDB fairsharing: FAIRsharing.wkaakq miriam: pmdb n2t: pmdb prefixcommons: pmdb name: Protein Model Database pattern: ^PM\d{7}$ preferred_prefix: pmdb uri_format: https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1 pmp: description: The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers. example: Q0VCA6 homepage: http://www.proteinmodelportal.org/ mappings: biocontext: PMP miriam: pmp n2t: pmp prefixcommons: pmp name: Protein Model Portal pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ preferred_prefix: pmp provides: uniprot publications: - doi: 10.1007/s10969-008-9048-5 pmc: PMC2704613 pubmed: '19037750' title: The Protein Model Portal. year: 2008 uri_format: http://www.proteinmodelportal.org/query/uniprot/$1 pmr: contact: email: laia.subirats@gmail.com github: null name: Laia Subirats orcid: null description: Resource for the community to store, retrieve, search, reference, and reuse CellML models. download_owl: http://aber-owl.net/media/ontologies/PMR/4/pmr.owl example: ebf69ca24298b28b2361e7d43eb52d6c homepage: https://www.auckland.ac.nz/en.html mappings: aberowl: PMR bioportal: PMR fairsharing: FAIRsharing.bcjrnq miriam: pmr name: Physical Medicine and Rehabilitation pattern: ^[a-z0-9]{32,32}$ preferred_prefix: pmr uri_format: https://models.physiomeproject.org/exposure/$1 pmr.workspace: description: Workspace (Git repository) for modeling projects managed by the Physiome Model Repository example: modularmassactionprimer homepage: https://www.auckland.ac.nz/en.html mappings: miriam: pmr.workspace name: Physiome Model Repository workspace pattern: ^[a-zA-Z0-9_\-]+(/.*?)?$ preferred_prefix: pmr.workspace uri_format: https://models.physiomeproject.org/workspace/$1 po: appears_in: - agro - ecocore - envo - genepio banana: PO contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp name: Pankaj Jaiswal orcid: 0000-0002-1005-8383 description: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. download_obo: http://purl.obolibrary.org/obo/po.obo download_owl: http://purl.obolibrary.org/obo/po.owl example: 0009089 homepage: http://browser.planteome.org/amigo license: CC BY 4.0 mappings: aberowl: PO agroportal: PO biocontext: PO bioportal: PO edam: '1180' fairsharing: FAIRsharing.3ngg40 go: PO miriam: po n2t: po obofoundry: po ols: po ontobee: PO prefixcommons: po name: Plant Ontology namespace_in_lui: true pattern: ^\d+$ preferred_prefix: PO publications: - doi: 10.1093/nar/gkx1152 pmc: PMC5753347 pubmed: '29186578' title: 'The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.' year: 2018 - doi: 10.1007/978-1-4939-3167-5_5 pmc: null pubmed: '26519402' title: 'The Plant Ontology: A Tool for Plant Genomics.' year: 2016 - doi: 10.1371/journal.pbio.1002033 pmc: PMC4285398 pubmed: '25562316' title: Finding our way through phenotypes. year: 2015 - doi: 10.1093/pcp/pcs163 pmc: PMC3583023 pubmed: '23220694' title: The plant ontology as a tool for comparative plant anatomy and genomic analyses. year: 2012 - doi: 10.1002/cfg.496 pmc: PMC2447502 pubmed: '18629207' title: 'Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages.' year: 2005 - doi: 10.1002/cfg.154 pmc: PMC2447263 pubmed: '18628842' title: The Plant Ontology Consortium and plant ontologies. year: 2002 - doi: 10.1093/nar/gkm908 pmc: PMC2238838 pubmed: '18194960' title: 'The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.' year: 2008 repository: https://github.com/Planteome/plant-ontology twitter: planteome uri_format: http://www.plantontology.org/amigo/go.cgi?view=details&query=PO:$1 version: '2021-08-13' pocketome: description: Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries. example: 1433C_TOBAC_1_252 homepage: http://www.pocketome.org/sfSearch.cgi?act=browseall mappings: biocontext: POCKETOME fairsharing: FAIRsharing.tc6df8 miriam: pocketome n2t: pocketome name: Pocketome pattern: ^[A-Za-z_0-9]+$ preferred_prefix: pocketome uri_format: http://www.pocketome.org/files/$1.html polbase: description: Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity. example: 19-T4 homepage: http://polbase.neb.com/ mappings: biocontext: POLBASE fairsharing: FAIRsharing.s9ztmd miriam: polbase n2t: polbase name: PolBase pattern: ^[A-Za-z-0-9]+$ preferred_prefix: polbase uri_format: https://polbase.neb.com/polymerases/$1#sequences pombase: description: PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets. example: SPCC13B11.01 homepage: https://www.pombase.org/ mappings: biocontext: PomBase biolink: PomBase fairsharing: FAIRsharing.8jsya3 go: PomBase miriam: pombase n2t: pombase ncbi: PomBase prefixcommons: pombase re3data: r3d100011478 uniprot: PomBase wikidata: P6245 name: PomBase pattern: ^S\w+(\.)?\w+(\.)?$ preferred_prefix: pombase publications: - doi: 10.1093/nar/gkr853 pmc: PMC3245111 pubmed: '22039153' title: 'PomBase: a comprehensive online resource for fission yeast.' year: 2011 synonyms: - PomBase uri_format: https://www.pombase.org/gene/$1 poro: contact: email: robert.thacker@stonybrook.edu github: bobthacker name: Bob Thacker orcid: 0000-0002-9654-0073 depends_on: - ro - uberon description: An ontology describing the anatomical structures and characteristics of Porifera (sponges) download_obo: http://purl.obolibrary.org/obo/poro.obo download_owl: http://purl.obolibrary.org/obo/poro.owl example: '0000550' homepage: https://github.com/obophenotype/porifera-ontology license: CC BY 3.0 mappings: aberowl: PORO biocontext: PORO bioportal: PORO fairsharing: FAIRsharing.93g1th obofoundry: poro ols: poro ontobee: PORO name: Porifera Ontology pattern: ^\d{7}$ preferred_prefix: PORO publications: - doi: 10.1186/2041-1480-5-39 pmc: PMC4177528 pubmed: '25276334' title: 'The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology.' year: 2014 repository: https://github.com/obophenotype/porifera-ontology uri_format: http://purl.obolibrary.org/obo/PORO_$1 version: '2016-10-06' ppdb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties. ' example: '1484' homepage: https://sitem.herts.ac.uk/aeru/ppdb/ mappings: fairsharing: FAIRsharing.7k8zh0 name: Pesticide Properties DataBase pattern: ^\d+$ preferred_prefix: ppdb uri_format: https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm ppo: contact: email: rlwalls2008@gmail.com github: ramonawalls name: Ramona Walls orcid: 0000-0001-8815-0078 description: An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales. download_owl: http://purl.obolibrary.org/obo/ppo.owl example: 0002058 homepage: https://github.com/PlantPhenoOntology/PPO license: CC BY 3.0 mappings: aberowl: PPO agroportal: PPO biocontext: PPO bioportal: PPO fairsharing: FAIRsharing.hakg7c obofoundry: ppo ols: ppo ontobee: PPO name: Plant Phenology Ontology pattern: ^\d{7}$ preferred_prefix: PPO publications: - doi: 10.3389/fpls.2018.00517 pmc: PMC5938398 pubmed: '29765382' title: 'The Plant Phenology Ontology: A New Informatics Resource for Large-Scale Integration of Plant Phenology Data.' year: 2018 repository: https://github.com/PlantPhenoOntology/PPO uri_format: http://purl.obolibrary.org/obo/PPO_$1 version: '2018-10-26' ppr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Preprints are articles which have not been peer-reviewed from various preprint servers and open research platforms such as bioRxiv, ChemRxiv, PeerJ Preprints and F1000. example: ppr103739 homepage: https://europepmc.org name: Europe PMC Preprints preferred_prefix: ppr uri_format: https://europepmc.org/article/ppr/$1 pr: appears_in: - chiro - cl - pcl - scdo - uberon banana: PR contact: email: dan5@georgetown.edu github: nataled name: Darren Natale orcid: 0000-0001-5809-9523 description: The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies. download_obo: http://purl.obolibrary.org/obo/pr.obo download_owl: http://purl.obolibrary.org/obo/pr.owl example: '000000024' homepage: http://proconsortium.org license: CC BY 4.0 mappings: aberowl: PR agroportal: PR biocontext: PR bioportal: PR fairsharing: FAIRsharing.4ndncv go: PR miriam: pr n2t: pr obofoundry: pr ols: pr ontobee: PR prefixcommons: pr uniprot: PRO wikidata: P4926 name: Protein Ontology namespace_in_lui: true pattern: ^\d+$ preferred_prefix: PR publications: - doi: 10.1093/nar/gkw1075 pmc: PMC5210558 pubmed: '27899649' title: 'Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.' year: 2016 - doi: 10.1093/nar/gkt1173 pmc: PMC3964965 pubmed: '24270789' title: 'Protein Ontology: a controlled structured network of protein entities.' year: 2013 - doi: 10.1186/1471-2105-12-371 pmc: PMC3189193 pubmed: '21929785' title: The representation of protein complexes in the Protein Ontology (PRO). year: 2011 - doi: 10.1093/nar/gkq907 pmc: PMC3013777 pubmed: '20935045' title: 'The Protein Ontology: a structured representation of protein forms and complexes.' year: 2010 - doi: 10.1186/1471-2105-8-s9-s1 pmc: PMC2217659 pubmed: '18047702' title: Framework for a protein ontology. year: 2007 repository: https://github.com/PROconsortium/PRoteinOntology synonyms: - PR - PRO uri_format: https://proconsortium.org/app/entry/PR:$1 version: '67.0' prefixcommons: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A registry of life science prefxes example: ChEBI homepage: https://prefixcommons.org name: Prefix Commons preferred_prefix: prefixcommons uri_format: https://bioregistry.io/metaregistry/prefixcommons/$1 pride: description: The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays. download_owl: https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/pride_cv.obo example: '1' homepage: https://github.com/PRIDE-Utilities/pride-ontology mappings: aberowl: PRIDE biocontext: PRIDE cellosaurus: PRIDE fairsharing: FAIRsharing.e1byny miriam: pride n2t: pride ols: pride prefixcommons: pride uniprot: PRIDE name: PRIDE Controlled Vocabulary pattern: ^\d+$ preferred_prefix: pride publications: - doi: 10.1002/0471250953.bi1308s21 pmc: null pubmed: '18428683' title: Using the Proteomics Identifications Database (PRIDE). year: 2008 - doi: 10.1093/nar/gkm1021 pmc: PMC2238846 pubmed: '18033805' title: 'PRIDE: new developments and new datasets.' year: 2007 - doi: 10.1093/nar/gkj138 pmc: PMC1347500 pubmed: '16381953' title: 'PRIDE: a public repository of protein and peptide identifications for the proteomics community.' year: 2006 - doi: 10.1002/pmic.200401303 pmc: null pubmed: '16041671' title: 'PRIDE: the proteomics identifications database.' year: 2005 repository: https://github.com/PRIDE-Utilities/pride-ontology uri_format: https://www.ebi.ac.uk/pride/archive/assays/$1 pride.project: description: The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects. example: PXD000440 homepage: https://www.ebi.ac.uk/pride/ mappings: biocontext: PRIDE.PROJECT miriam: pride.project n2t: pride.project name: PRIDE Project pattern: ^P(X|R)D\d{6}$ preferred_prefix: pride.project providers: - code: omicsdi description: PRIDE Project through OmicsDI homepage: https://www.omicsdi.org/ name: PRIDE Project through OmicsDI uri_format: https://www.omicsdi.org/dataset/pride/$1 uri_format: https://www.ebi.ac.uk/pride/archive/projects/$1 prints: description: PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours. example: PR00001 homepage: http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/ mappings: biocontext: PRINTS fairsharing: FAIRsharing.h8r843 go: PRINTS miriam: prints n2t: prints uniprot: PRINTS name: PRINTS compendium of protein fingerprints pattern: ^PR\d{5}$ preferred_prefix: prints uri_format: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off probesanddrugs: contact: email: ctibor.skuta@img.cas.cz github: null name: Ctibor Škuta orcid: 0000-0001-5325-4934 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Probes & Drugs portal (P&D) is a hub for the integration of high-quality bioactive compound sets enabling their analysis and comparison. Its main focus is on chemical probes and drugs but it also includes additional relevant sets from specialist databases/scientific publications, and vendor sets. Upon these, established bioactive chemistry sources (such as ChEMBL, BindingDB, Guide To Pharmacology, DrugCentral or DrugBank) are utilized for compounds' biological annotation. example: PD000596 homepage: https://www.probes-drugs.org license: CC BY-SA 4.0 name: Probes and Drugs pattern: ^PD\d{6}$ preferred_prefix: probesanddrugs uri_format: https://www.probes-drugs.org/compound/$1 probonto: description: ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities. download_owl: https://raw.githubusercontent.com/probonto/ontology/master/probonto4ols.owl example: PROB_c0000005 homepage: http://probonto.org mappings: biocontext: PROBONTO fairsharing: FAIRsharing.8zqzm9 miriam: probonto n2t: probonto ols: probonto name: Probability Distribution Ontology pattern: ^PROB_c\d+$ preferred_prefix: probonto uri_format: https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=$1 version: 2.5.0 proco: contact: email: wes_schafer@merck.com github: schaferw name: Wes Schafer orcid: 0000-0002-8786-1756 depends_on: - chebi - cheminf - obi - pato - ro - sbo description: PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry. download_owl: http://purl.obolibrary.org/obo/proco.owl example: '0000001' homepage: https://github.com/proco-ontology/PROCO license: CC BY 4.0 mappings: aberowl: PROCO obofoundry: proco ols: proco ontobee: PROCO name: Process Chemistry Ontology pattern: ^\d{7}$ preferred_prefix: PROCO repository: https://github.com/proco-ontology/PROCO uri_format: http://purl.obolibrary.org/obo/PROCO_$1 version: PROCO release 20220414 prodom: description: ProDom is a database of protein domain families generated from the global comparison of all available protein sequences. example: PD10000 homepage: http://prodom.prabi.fr/prodom/current/html/home.php mappings: biocontext: PRODOM fairsharing: FAIRsharing.a8z6gz miriam: prodom n2t: prodom prefixcommons: prodom name: ProDom pattern: ^PD\d+$ preferred_prefix: prodom publications: - doi: 10.1093/nar/gki034 pmc: PMC539988 pubmed: '15608179' title: 'The ProDom database of protein domain families: more emphasis on 3D.' year: 2005 uri_format: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1 proglyc: description: ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information. example: AC119 homepage: http://www.proglycprot.org/ mappings: biocontext: PROGLYC miriam: proglyc n2t: proglyc name: ProGlycProt pattern: ^[A-Z]C\d{1,3}$ preferred_prefix: proglyc uri_format: http://www.proglycprot.org/detail.aspx?ProId=$1 propreo: contact: email: satya30@uga.edu github: null name: Satya S. Sahoo orcid: null deprecated: true description: A comprehensive proteomics data and process provenance ontology. download_owl: http://aber-owl.net/media/ontologies/PROPREO/2/propreo.owl homepage: http://lsdis.cs.uga.edu/projects/glycomics/propreo/ mappings: aberowl: PROPREO biocontext: PROPREO bioportal: PROPREO obofoundry: propreo prefixcommons: propreo name: Proteomics data and process provenance preferred_prefix: PROPREO uri_format: http://purl.obolibrary.org/obo/PROPREO_$1 prosite: description: PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. example: PS00001 homepage: https://www.expasy.org/prosite/ mappings: biocontext: PROSITE fairsharing: FAIRsharing.vwc6bd go: Prosite miriam: prosite n2t: prosite prefixcommons: prosite uniprot: PROSITE wikidata: P4355 name: PROSITE pattern: ^PS\d{5}$ preferred_prefix: prosite publications: - doi: 10.1093/nar/gkj063 pmc: PMC1347426 pubmed: '16381852' title: The PROSITE database. year: 2006 uri_format: https://prosite.expasy.org/$1 protclustdb: description: ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters. example: O80725 homepage: https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters mappings: biocontext: PROTCLUSTDB fairsharing: FAIRsharing.da493y miriam: protclustdb n2t: protclustdb prefixcommons: protclustdb name: ProtClustDB pattern: ^\w+$ preferred_prefix: protclustdb publications: - doi: 10.1093/nar/gkn734 pmc: PMC2686591 pubmed: '18940865' title: The National Center for Biotechnology Information's Protein Clusters Database. year: 2008 uri_format: https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1 proteomicsdb.peptide: comment: The fact that this has .peptide as a subspace is a bit of a misnomer. Its original registration with MIRIAM uses a subview over the protein to point to peptides, but the identifiers in this semantic space seem to be about proteins. description: ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein. example: '53504' homepage: https://www.proteomicsdb.org/#peptideSearch mappings: biocontext: PROTEOMICSDB.PEPTIDE miriam: proteomicsdb.peptide n2t: proteomicsdb.peptide name: ProteomicsDB Peptide pattern: ^\d+$ preferred_prefix: proteomicsdb.peptide uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1 proteomicsdb.protein: description: ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins. example: '53504' homepage: https://www.proteomicsdb.org/#human mappings: biocontext: PROTEOMICSDB.PROTEIN miriam: proteomicsdb.protein n2t: proteomicsdb.protein name: ProteomicsDB Protein pattern: ^\d+$ preferred_prefix: proteomicsdb.protein uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1/summary protonet.cluster: description: ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information. example: '4349895' homepage: http://www.protonet.cs.huji.ac.il/ mappings: biocontext: PROTONET.CLUSTER miriam: protonet.cluster n2t: protonet.cluster prefixcommons: protonet.cluster name: ProtoNet Cluster pattern: ^\d+$ preferred_prefix: protonet.cluster publications: - doi: 10.1110/ps.062185706 pmc: PMC2242553 pubmed: '16672244' title: 'Functional annotation prediction: all for one and one for all.' year: 2006 uri_format: http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1 protonet.proteincard: description: ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information. example: '16941567' homepage: http://www.protonet.cs.huji.ac.il/ mappings: biocontext: PROTONET.PROTEINCARD miriam: protonet.proteincard n2t: protonet.proteincard prefixcommons: protonet.proteincard name: ProtoNet ProteinCard pattern: ^\d+$ preferred_prefix: protonet.proteincard publications: - doi: 10.1110/ps.062185706 pmc: PMC2242553 pubmed: '16672244' title: 'Functional annotation prediction: all for one and one for all.' year: 2006 uri_format: http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1 prov: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web. download_owl: http://www.w3.org/ns/prov-o-20130430 example: Activity homepage: https://www.w3.org/ns/prov mappings: aberowl: PROV biocontext: prov biolink: prov ols: prov name: PROV Namespace preferred_prefix: prov uri_format: http://www.w3.org/ns/prov#$1 version: '2013-04-30' pscdb: description: The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion. example: '051' homepage: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html mappings: biocontext: PSCDB fairsharing: FAIRsharing.3d4jx0 miriam: pscdb n2t: pscdb name: Protein Structural Change Database pattern: ^\d+$ preferred_prefix: pscdb uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html psdo: contact: email: zachll@umich.edu github: zachll name: Zach Landis-Lewis orcid: 0000-0002-9117-9338 depends_on: - bfo - iao - ro - stato description: Performance Summary Display Ontology (PSDO) (pronounced "pseudo" or "sudo") is an application ontology about charts, tables, and graphs that are used to communicate performance information to employees and teams in organizations. PSDO's domain focus is on healthcare organizations that use performance summary displays in clinical dashboards and feedback interventions for healthcare professionals and teams. The displays commonly show information about the quality of care and health outcomes that has been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is not peer-reviewed. download_owl: http://purl.obolibrary.org/obo/psdo.owl example: '0000055' homepage: https://github.com/Display-Lab/psdo license: CC BY 3.0 mappings: aberowl: PSDO bioportal: PSDO obofoundry: psdo ols: psdo ontobee: PSDO name: Performance Summary Display Ontology pattern: ^\d{7}$ preferred_prefix: PSDO repository: https://github.com/Display-Lab/psdo uri_format: http://purl.obolibrary.org/obo/PSDO_$1 version: 1.0.0 pseudogene: contact: email: yhl3@gersteinlab.org github: null name: Gerstein Lab orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase. example: PGOHUM00000289843 homepage: http://www.pseudogene.org mappings: bioportal: pseudo prefixcommons: pseudogene name: PseudoGene preferred_prefix: pseudogene synonyms: - pseudogene.org uri_format: http://tables.pseudogene.org/[?species_name]/$1 pseudomonas: description: The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation. example: PSEEN0001 homepage: http://www.pseudomonas.com/ mappings: biocontext: PSEUDOMONAS miriam: pseudomonas n2t: pseudomonas name: Pseudomonas Genome Database pattern: ^P\w+$ preferred_prefix: pseudomonas uri_format: http://www.pseudomonas.com/feature/show/?locus_tag=$1 psipar: banana: PAR comment: This resource is no longer loaded on XML and the sourceforge link from the HUPO website to the psi-par.obo artifact is dead. deprecated: true description: Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms. example: '0116' homepage: https://www.psidev.info/psi-par mappings: biocontext: PSIPAR miriam: psipar n2t: psipar name: Protein Affinity Reagents pattern: ^\d+$ preferred_prefix: psipar uri_format: https://www.ebi.ac.uk/ontology-lookup/?termId=$1 pso: contact: email: cooperl@oregonstate.edu github: cooperl09 name: Laurel Cooper orcid: 0000-0002-6379-8932 depends_on: - ro description: The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter. download_obo: http://purl.obolibrary.org/obo/pso.obo download_owl: http://purl.obolibrary.org/obo/pso.owl example: '0000013' homepage: https://github.com/Planteome/plant-stress-ontology license: CC BY 3.0 mappings: aberowl: PSO bioportal: PSO fairsharing: FAIRsharing.dyj433 obofoundry: pso ols: pso ontobee: PSO name: Plant Stress Ontology pattern: ^\d{7}$ preferred_prefix: PSO publications: - doi: 10.1093/nar/gkx1152 pmc: PMC5753347 pubmed: '29186578' title: 'The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.' year: 2018 repository: https://github.com/Planteome/plant-stress-ontology uri_format: http://purl.obolibrary.org/obo/PSO_$1 version: '2020-05-19' pspub: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Documentation of the Phenoscape Curation Workflow homepage: https://wiki.phenoscape.org/wiki/Curation_workflow name: Phenoscape Publication preferred_prefix: pspub pubchem.bioassay: description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results. example: '1018' homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay mappings: biocontext: PUBCHEM.BIOASSAY edam: '2638' go: PubChem_BioAssay miriam: pubchem.bioassay n2t: pubchem.bioassay prefixcommons: pubchem.bioassay name: NCBI PubChem database of bioassay records part_of: pubchem pattern: ^\d+$ preferred_prefix: pubchem.bioassay publications: - doi: 10.1093/nar/gkl1031 pmc: PMC1781113 pubmed: '17170002' title: Database resources of the National Center for Biotechnology Information. year: 2006 twitter: pubchem uri_format: https://pubchem.ncbi.nlm.nih.gov/bioassay/$1 pubchem.cell: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Cell Lines in PubChem example: '31' homepage: https://pubchem.ncbi.nlm.nih.gov name: PubChem Cell Line part_of: pubchem pattern: ^\d+$ preferred_prefix: pubchem.cell twitter: pubchem uri_format: https://pubchem.ncbi.nlm.nih.gov/cell/$1 pubchem.classification: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The PubChem Classification Browser allows you to browse the distribution of PubChem data among nodes in the hierarchy of interest, thereby providing an aggregate view of PubChem data. It also allows you to search for PubChem records annotated with the desired hierarchy/term, providing a powerful way to quickly find the subset of PubChem records. example: '87' homepage: https://pubchem.ncbi.nlm.nih.gov/classification/ name: PubChem Classification part_of: pubchem pattern: ^\d+$ preferred_prefix: pubchem.classification twitter: pubchem uri_format: https://pubchem.ncbi.nlm.nih.gov/classification/#hid=$1 pubchem.compound: description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records. example: '100101' homepage: https://pubchem.ncbi.nlm.nih.gov/ mappings: biocontext: PUBCHEM.COMPOUND biolink: CID cellosaurus: PubChem cheminf: '000140' edam: '2639' fairsharing: FAIRsharing.g63c77 go: PubChem_Compound miriam: pubchem.compound n2t: pubchem.compound prefixcommons: pubchem.compound re3data: r3d100010129 wikidata: P662 name: PubChem CID part_of: pubchem pattern: ^\d+$ preferred_prefix: pubchem.compound 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/pubchem/$1 synonyms: - CID - DSSTox_CID - PUBCHEM_CID - PubChem_Compound_CID - Pubchem - pubchem_id twitter: pubchem uri_format: https://pubchem.ncbi.nlm.nih.gov/compound/$1 pubchem.element: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number. example: '1' homepage: https://pubchem.ncbi.nlm.nih.gov/periodic-table name: PubChem Element part_of: pubchem pattern: ^\d+$ preferred_prefix: pubchem.element twitter: pubchem uri_format: https://pubchem.ncbi.nlm.nih.gov/element/$1 pubchem.substance: description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records. example: '100101' homepage: https://pubchem.ncbi.nlm.nih.gov/ mappings: biocontext: PUBCHEM.SUBSTANCE cheminf: '000141' go: PubChem_Substance miriam: pubchem.substance n2t: pubchem.substance prefixcommons: pubchem.substance wikidata: P2153 name: PubChem Substance ID (SID) part_of: pubchem pattern: ^\d+$ preferred_prefix: pubchem.substance publications: - doi: 10.1093/nar/gkl1031 pmc: PMC1781113 pubmed: '17170002' title: Database resources of the National Center for Biotechnology Information. year: 2006 synonyms: - DSSTox_Generic_SID twitter: pubchem uri_format: https://pubchem.ncbi.nlm.nih.gov/substance/$1 publons.researcher: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Database of researchers to track publications, citation metrics, peer reviews, and journal editing work. example: '1981638' homepage: https://publons.com/researcher mappings: biolink: ResearchID name: Publons Researcher pattern: ^\d+$ preferred_prefix: publons.researcher uri_format: https://publons.com/researcher/$1 pubmed: description: PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. example: '16333295' homepage: https://www.ncbi.nlm.nih.gov/PubMed/ mappings: biocontext: PUBMED cellosaurus: PubMed cheminf: '000302' edam: '1187' fairsharing: FAIRsharing.a5sv8m go: PMID miriam: pubmed n2t: pubmed prefixcommons: pubmed wikidata: P698 name: PubMed pattern: ^\d+$ preferred_prefix: pubmed providers: - code: CURATOR_REVIEW description: PubMed through Linkedlife data homepage: http://linkedlifedata.com/ name: PubMed through Linkedlife data uri_format: http://linkedlifedata.com/resource/pubmed/id/$1 - code: epmc description: Europe PMC homepage: http://europepmc.org/ name: Europe PMC uri_format: http://europepmc.org/abstract/MED/$1 - code: hubmed description: HubMed homepage: http://www.hubmed.org/ name: HubMed uri_format: http://www.hubmed.org/display.cgi?uids=$1 - code: pubmed.new description: New-style link for pubmed homepage: https://pubmed.ncbi.nlm.nih.gov name: PubMed (new) uri_format: https://pubmed.ncbi.nlm.nih.gov/$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/pubmed/$1 - code: uniprot.citation description: UniProt mints PURLs for citations identifiers homepage: https://uniprot.org/ name: UniProt uri_format: http://purl.uniprot.org/citations/$1 - code: uniprot.pubmed description: UniProt mints PURLs for PubMed identifiers homepage: https://uniprot.org/ name: UniProt uri_format: http://purl.uniprot.org/pubmed/$1 publications: - doi: 10.1093/nar/gkj158 pmc: PMC1347520 pubmed: '16381840' title: Database resources of the National Center for Biotechnology Information. year: 2006 synonyms: - MEDLINE - PMID - PubMed - pmid uri_format: https://www.ncbi.nlm.nih.gov/pubmed/$1 puro: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology for the characterisation of the roles of agents – people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians. example: RoleInTime homepage: http://www.sparontologies.net/ontologies/pro mappings: fairsharing: FAIRsharing.3e88d6 name: Publishing Roles Ontology preferred_prefix: PuRO publications: - doi: 10.1145/2362499.2362502 pmc: null pubmed: null title: 'Scholarly publishing and Linked Data: describing roles, statuses, temporal and contextual extents' year: null repository: https://github.com/sparontologies/pro uri_format: http://purl.org/spar/pro/$1 pw: banana: PW contact: email: gthayman@mcw.edu github: gthayman name: G. Thomas Hayman orcid: 0000-0002-9553-7227 description: 'The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions.' download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo download_owl: http://purl.obolibrary.org/obo/pw.owl example: '0000423' homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html license: CC BY 4.0 mappings: aberowl: PW biocontext: PW bioportal: PW fairsharing: FAIRsharing.f73xhd miriam: pw n2t: pw obofoundry: pw ols: pw ontobee: PW prefixcommons: pw wikidata: P7333 name: Pathway ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: PW publications: - doi: 10.1186/s40246-014-0017-8 pmc: PMC4191248 pubmed: '25265995' title: 'Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease.' year: 2014 - doi: 10.1186/2041-1480-5-7 pmc: PMC3922094 pubmed: '24499703' title: The pathway ontology - updates and applications. year: 2014 - doi: 10.1093/database/bar010 pmc: PMC3072770 pubmed: '21478484' title: The Rat Genome Database pathway portal. year: 2011 repository: https://github.com/rat-genome-database/PW-Pathway-Ontology twitter: ratgenome uri_format: http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:$1 version: '2019-10-23' pwo: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity. example: Workflow homepage: http://www.sparontologies.net/ontologies/pwo mappings: fairsharing: FAIRsharing.c4e46c name: Publishing Workflow Ontology preferred_prefix: PWO publications: - doi: https://doi.org/10.3233/sw-160230 pmc: null pubmed: null title: The Publishing Workflow Ontology (PWO) year: null repository: https://github.com/sparontologies/pwo uri_format: http://purl.org/spar/pwo/$1 px: description: The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination. example: PXD000500 homepage: http://www.proteomexchange.org/ mappings: biocontext: PX miriam: px n2t: px name: ProteomeXchange pattern: ^(R)?PXD\d{6}$ preferred_prefix: px uri_format: http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1 pypi: description: The Python Package Index (PyPI) is a repository for Python packages. example: numpy homepage: https://www.python.org/psf/ mappings: miriam: pypi name: PyPI pattern: ^[a-zA-Z_][a-zA-Z0-9\-_]+$ preferred_prefix: pypi uri_format: https://pypi.org/project/$1 qb: contact: email: richard@cyganiak.de github: cygri name: Richard Cyganiak orcid: 0000-0001-9950-5209 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF. It is based on the core information model from SDMX (and thus also DDI). download_rdf: http://purl.org/linked-data/cube# example: Observation homepage: https://www.w3.org/TR/vocab-data-cube name: The data cube vocabulary pattern: ^\w+$ preferred_prefix: qb repository: UKGovLD/publishing-statistical-data uri_format: http://purl.org/linked-data/cube#$1 qtldb: description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent. example: '4685' homepage: https://www.animalgenome.org/QTLdb mappings: miriam: qtldb name: Animal Genome QTL pattern: ^\d+$ preferred_prefix: qtldb uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 qudt: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types. download_owl: http://aber-owl.net/media/ontologies/QUDT/4/qudt.owl download_rdf: http://qudt.org/schema/qudt/ example: baseDimensionEnumeration homepage: https://qudt.org mappings: aberowl: QUDT biolink: qud bioportal: QUDT fairsharing: FAIRsharing.d3pqw7 name: Quantities, Units, Dimensions, and Types Ontology preferred_prefix: qudt uri_format: http://qudt.org/schema/qudt#$1 radiomics: contact: email: alberto.traverso@maastro.nl github: null name: Alberto Traverso orcid: null description: The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual. [bioportal] example: LK99 homepage: http://www.radiomics.org/RO mappings: bioportal: RO name: Radiomics Ontology preferred_prefix: radiomics uri_format: http://www.radiomics.org/RO/$1 radlex: contact: email: radlex-feedback@lists.rsna.org github: null name: Radiological Society of North America orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'A comprehensive set of radiology terms for use in radiology reporting, decision support, data mining, data registries, education and research. RadLex provides the foundation for vital data resources used in radiology: - The LOINC/RSNA Radiology Playbook - RadElement Common Data Elements -RadReport Radiology Reporting Templates The development of RadLex has been supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the cancer Biomedical Informatics Grid (caBIG) project.' download_owl: http://aber-owl.net/media/ontologies/RADLEX/37/radlex.owl example: RID1 homepage: https://radlex.org license: http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/RadLex_License_Agreement_and_Terms_of_Use_V2_Final.pdf mappings: aberowl: RADLEX bioportal: RADLEX fairsharing: FAIRsharing.shm2f2 hl7: 2.16.840.1.113883.6.256 name: RSNA Informatics RadLex pattern: ^RID\d+$ preferred_prefix: radlex publications: - doi: 10.1016/j.jvir.2009.04.031 pmc: null pubmed: '19560008' title: 'The IR Radlex Project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology.' year: null - doi: 10.1016/j.jvir.2008.10.022 pmc: null pubmed: '19081735' title: 'The IR RadLex project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology.' year: null - doi: 10.2214/ajr.174.5.1741463 pmc: null pubmed: '10789815' title: Radiology lexicon. year: null uri_format: https://radlex.org/RID/$1 version: '4.1' rapdb.locus: description: Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB. example: Os01g0883800 homepage: https://rapdb.dna.affrc.go.jp/ mappings: miriam: rapdb.locus name: RAP-DB Locus pattern: ^Os\S+g\d{7}$ preferred_prefix: rapdb.locus synonyms: - irgsp uri_format: https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$1 rapdb.transcript: description: Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB. example: Os01t0883800-02 homepage: https://rapdb.dna.affrc.go.jp/ mappings: miriam: rapdb.transcript name: RAP-DB Transcript pattern: ^Os\S+t\d{7}-\d{2}$ preferred_prefix: rapdb.transcript uri_format: https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1 rbk: description: (Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function. example: Q-2958 homepage: https://www.rebuildingakidney.org/ mappings: biocontext: RBK fairsharing: FAIRsharing.78d3ad miriam: rbk n2t: rbk name: Rebuilding a Kidney pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$ preferred_prefix: rbk uri_format: https://www.rebuildingakidney.org/id/$1 rbo: contact: email: daniel.c.berrios@nasa.gov github: DanBerrios name: Daniel C. Berrios orcid: 0000-0003-4312-9552 depends_on: - bfo - chmo - envo - obi - pato - ro - uo description: RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. download_json: http://purl.obolibrary.org/obo/rbo.json download_obo: http://purl.obolibrary.org/obo/rbo.obo download_owl: http://purl.obolibrary.org/obo/rbo.owl example: '00000105' example_extras: - '010007' homepage: https://github.com/Radiobiology-Informatics-Consortium/RBO license: CC BY 3.0 mappings: aberowl: RBO bioportal: RBO obofoundry: rbo ols: rbo ontobee: RBO name: Radiation Biology Ontology pattern: ^\d{6,8}$ preferred_prefix: RBO repository: https://github.com/Radiobiology-Informatics-Consortium/RBO uri_format: http://purl.obolibrary.org/obo/RBO_$1 version: '2022-06-02' rcb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center. example: RCB0002 homepage: https://cell.brc.riken.jp/en/rcb mappings: cellosaurus: RCB name: RIKEN Bioresource Center Cell Bank pattern: ^RCB\d+$ preferred_prefix: rcb uri_format: https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1 rdf: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts example: RDF homepage: http://www.w3.org/1999/02/22-rdf-syntax-ns mappings: biocontext: rdf fairsharing: FAIRsharing.p77ph9 name: Resource Description Framework preferred_prefix: rdf uri_format: http://www.w3.org/1999/02/22-rdf-syntax-ns#$1 rdfs: contact: email: danbri@w3.org github: null name: Dan Brickley orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary. download_owl: https://triplydb.com/w3c/rdfs/download.trig.gz example: label homepage: https://www.w3.org/TR/rdf-schema/ mappings: aberowl: RDFS biocontext: rdfs bioportal: RDFS fairsharing: FAIRsharing.v9n3gk name: RDF Schema preferred_prefix: rdfs uri_format: http://www.w3.org/2000/01/rdf-schema#$1 rdo: contact: email: archanamca92@gmail.com github: null name: Archana Patel orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms. download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.obo download_owl: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.owl example: '9002859' homepage: https://ratmine.mcw.edu/ontology/disease/ mappings: aberowl: RDO bioportal: RDO name: RGD Disease_Ontology pattern: ^\d{7}$ preferred_prefix: rdo uri_format: http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1 re3data: description: Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines. example: r3d100010772 homepage: https://datacite.org mappings: miriam: re3data name: re3data pattern: ^r3d\d{9,9}$ preferred_prefix: re3data uri_format: https://www.re3data.org/repository/$1 reactome: description: The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology. example: R-BTA-418592 homepage: https://www.reactome.org/ mappings: biocontext: REACTOME cheminf: '000411' edam: '1155' go: Reactome miriam: reactome n2t: reactome prefixcommons: reactome re3data: r3d100010861 uniprot: Reactome wikidata: P3937 name: Reactome pattern: ^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$ preferred_prefix: reactome providers: - code: pathwaycommons description: Pathway diagram drawn with Cytoscape homepage: https://www.pathwaycommons.org name: Pathway Commons uri_format: https://apps.pathwaycommons.org/pathways?uri=http%3A%2F%2Fidentifiers.org%2Freactome%2F$1 publications: - doi: 10.1093/nar/gki072 pmc: PMC540026 pubmed: '15608231' title: 'Reactome: a knowledgebase of biological pathways.' year: 2005 synonyms: - RE - REACT uri_format: https://reactome.org/content/detail/$1 reaxys: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier. example: '1257009' homepage: https://www.reaxys.com mappings: edam: '1003' wikidata: P1579 name: Reaxys pattern: ^\d+$ preferred_prefix: reaxys synonyms: - Beilstein - Reaxys rebase: description: REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. example: '101' homepage: http://rebase.neb.com/rebase/ mappings: biocontext: REBASE edam: '2325' fairsharing: FAIRsharing.9sb9qh go: REBASE miriam: rebase n2t: rebase prefixcommons: rebase re3data: r3d100012171 uniprot: REBASE name: REBASE restriction enzyme database pattern: ^\d+$ preferred_prefix: rebase publications: - doi: 10.1093/nar/gkp874 pmc: PMC2808884 pubmed: '19846593' title: 'REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.' year: 2009 uri_format: http://rebase.neb.com/rebase/enz/$1.html receptome.family: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database. example: '5.1' homepage: http://www.receptome.org name: Human Plasma Membrane Receptome Families preferred_prefix: receptome.family uri_format: http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1 refseq: contributor_extras: - email: null github: slobentanzer name: Sebastian Lobentanzer orcid: 0000-0003-3399-6695 description: The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products. example: NP_012345 example_extras: - WP_029104145.1 has_canonical: ncbiprotein homepage: https://www.ncbi.nlm.nih.gov/projects/RefSeq/ mappings: biocontext: RefSeq edam: '1098' fairsharing: FAIRsharing.4jg0qw go: RefSeq hl7: 2.16.840.1.113883.6.280 miriam: refseq n2t: refseq prefixcommons: refseq uniprot: RefSeq name: Reference Sequence Collection pattern: ^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\d+)|(NZ_[A-Z]{2,4}\d+))(\.\d+)?$ preferred_prefix: refseq publications: - doi: 10.1093/nar/gkl842 pmc: PMC1716718 pubmed: '17130148' title: 'NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.' year: 2006 references: - https://github.com/biopragmatics/bioregistry/issues/545 synonyms: - REFSEQ_PROT uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 reo: comment: 'From James O.: It was an ontology for "reagents" developed by @Matthew Brush. Since OBI was interested in reagents, Matt developed it in coordination with OBI and had plans to submit it to OBO. I believe that REO was once included in Ontobee, and OBI even started using some REO terms. But REO was never submitted to OBO. I believe it was abandoned.' contact: email: matt@tislab.org github: mbrush name: Matthew Brush orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs. download_owl: https://github.com/tis-lab/reagent-ontology/raw/master/reo/ontology_files/reo_pre-merged_or_reasoned_files/reo_reasoned_9-6-12.owl example: 0000079 homepage: https://github.com/tis-lab/reagent-ontology mappings: ontobee: REO name: Reagent Ontology pattern: ^\d{7}$ preferred_prefix: reo references: - https://github.com/obi-ontology/obi/issues/1015 - https://code.google.com/archive/p/reagent-ontology/ - https://github.com/obi-ontology/obi/issues/1135 repository: https://github.com/tis-lab/reagent-ontology uri_format: http://purl.obolibrary.org/obo/REO_$11 repeatsdb.protein: description: RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database. example: P29894 homepage: https://repeatsdb.org/ mappings: miriam: repeatsdb.protein name: RepeatsDB Protein pattern: ^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$ preferred_prefix: repeatsdb.protein provides: uniprot uri_format: https://repeatsdb.org/protein/$1 repeatsdb.structure: description: RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database. example: 2gc4E homepage: https://repeatsdb.org/ mappings: miriam: repeatsdb.structure name: RepeatsDB Structure pattern: ^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$ preferred_prefix: repeatsdb.structure uri_format: https://repeatsdb.org/structure/$1 reproduceme: contact: email: sheeba.samuel@uni-jena.de github: null name: Sheeba Samuel orcid: null description: The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility. download_owl: https://sheeba-samuel.github.io/REPRODUCE-ME/doc/reproduce-me.xml example: MicrobeamManipulation homepage: https://w3id.org/reproduceme/research mappings: aberowl: REPRODUCE-ME bioportal: REPRODUCE-ME ols: reproduceme name: REPRODUCE-ME Ontology preferred_prefix: reproduceme uri_format: https://w3id.org/reproduceme#$1 version: '1.1' resid: contact: email: john.garavelli@ebi.ac.uk github: null name: John Garavelli orcid: null deprecated: true description: The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. example: AA0001 homepage: https://proteininformationresource.org/resid/ mappings: biocontext: RESID edam: '2619' go: RESID miriam: resid n2t: resid obofoundry: resid prefixcommons: resid name: Protein covalent bond pattern: ^AA\d{4}$ preferred_prefix: RESID publications: - doi: 10.1002/pmic.200300764 pmc: null pubmed: '15174124' title: Annotation of post-translational modifications in the Swiss-Prot knowledge base. year: 2004 uri_format: https://proteininformationresource.org/cgi-bin/resid?id=$1 reto: contact: email: vladimir.n.mironov@gmail.com github: null name: Vladimir Mironov orcid: null description: Regulation of Transcription download_obo: https://www.bio.ntnu.no/ontology/ReTO/reto.obo download_owl: https://www.bio.ntnu.no/ontology/ReTO/reto.owl homepage: http://www.semantic-systems-biology.org/apo mappings: aberowl: RETO bioportal: RETO fairsharing: FAIRsharing.4qyf0f ols: reto name: Regulation of Transcription Ontology no_own_terms: true preferred_prefix: reto version: '2019-09-17' rex: contact: email: chebi-help@ebi.ac.uk github: null name: Chebi Administrators orcid: null deprecated: true description: An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. download_owl: http://purl.obolibrary.org/obo/rex.owl example: '0000512' homepage: https://www.ebi.ac.uk/chebi/ mappings: aberowl: REX biocontext: REX bioportal: REX fairsharing: FAIRsharing.g0a7s0 obofoundry: rex ols: rex ontobee: REX prefixcommons: rex name: Physico-chemical process part_of: chebi pattern: ^\d{7}$ preferred_prefix: REX uri_format: http://purl.obolibrary.org/obo/REX_$1 version: '2017-11-19' rexo: contact: email: vladimir.n.mironov@gmail.com github: null name: Vladimir Mironov orcid: null description: Regulation of Gene Expression download_obo: https://www.bio.ntnu.no/ontology/ReXO/rexo.obo download_owl: https://www.bio.ntnu.no/ontology/ReXO/rexo.owl homepage: http://www.semantic-systems-biology.org/apo mappings: aberowl: REXO bioportal: REXO fairsharing: FAIRsharing.recas1 ols: rexo name: Regulation of Gene Expression Ontology no_own_terms: true preferred_prefix: rexo publications: - doi: 10.1186/s12859-014-0386-y pmc: PMC4279962 pubmed: '25490885' title: Finding gene regulatory network candidates using the gene expression knowledge base. year: 2014 version: '2019-04-11' rfam: description: 'The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion.' example: RF00230 homepage: https://rfam.xfam.org/ mappings: biocontext: RFAM edam: '2356' fairsharing: FAIRsharing.fex4c8 go: Rfam miriam: rfam n2t: rfam ncbi: RFAM name: Rfam database of RNA families pattern: ^RF\d{5}$ preferred_prefix: rfam uri_format: https://rfam.xfam.org/family/$1 rfc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Legacy site for IETF RFC proposals example: '5013' homepage: https://www.ietf.org/ mappings: n2t: rfc name: Internet Standard -- IETF Request for Comments pattern: ^\d+$ preferred_prefix: rfc uri_format: https://tools.ietf.org/rfc/rfc$1 rgd: description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes. example: '7499841' homepage: http://rgd.mcw.edu/ mappings: aberowl: RGD biocontext: RGD bioportal: RGD cellosaurus: RGD edam: '2620' fairsharing: FAIRsharing.pfg82t go: RGD miriam: rgd n2t: rgd ncbi: RGD prefixcommons: rgd uniprot: RGD wikidata: P3853 name: Rat Genome Database pattern: ^\d{4,}$ preferred_prefix: rgd providers: - code: agr description: RGD through the Alliance of Genome Resources homepage: https://www.alliancegenome.org name: RGD through the Alliance of Genome Resources uri_format: https://www.alliancegenome.org/gene/RGD:$1 publications: - doi: 10.1093/nar/gkl988 pmc: PMC1761441 pubmed: '17151068' title: The Rat Genome Database, update 2007--easing the path from disease to data and back again. year: 2006 synonyms: - RGD twitter: ratgenome uri_format: http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1 rgd.qtl: description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes. example: '1354581' homepage: http://rgd.mcw.edu/ mappings: biocontext: RGD.QTL miriam: rgd.qtl n2t: rgd.qtl name: Rat Genome Database qTL pattern: ^\d+$ preferred_prefix: rgd.qtl twitter: ratgenome uri_format: http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1 rgd.strain: description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology. example: '5688061' homepage: http://rgd.mcw.edu/ mappings: biocontext: RGD.STRAIN miriam: rgd.strain n2t: rgd.strain name: Rat Genome Database strain pattern: ^\d+$ preferred_prefix: rgd.strain twitter: ratgenome uri_format: http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1 rhea: description: ' Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants. Rhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB.' example: '12345' homepage: https://www.rhea-db.org/ mappings: biocontext: RHEA edam: '2644' fairsharing: FAIRsharing.pn1sr5 go: RHEA miriam: rhea n2t: rhea prefixcommons: rhea re3data: r3d100010891 name: Rhea, the Annotated Reactions Database pattern: ^\d{5}$ preferred_prefix: rhea synonyms: - RHEA uri_format: https://www.rhea-db.org/rhea/$1 ricegap: description: The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines. example: LOC_Os02g13300 homepage: http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml mappings: biocontext: RICEGAP miriam: ricegap n2t: ricegap name: Rice Genome Annotation Project pattern: ^LOC\_Os\d{1,2}g\d{5}$ preferred_prefix: ricegap uri_format: http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1 ricenetdb.compound: description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' example: OSC1416 homepage: http://bis.zju.edu.cn/ricenetdb mappings: biocontext: RICENETDB.COMPOUND miriam: ricenetdb.compound n2t: ricenetdb.compound name: RiceNetDB Compound pattern: ^OSC\d{4}$ preferred_prefix: ricenetdb.compound uri_format: http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1 ricenetdb.gene: description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' example: LOC_Os01g49190.1 homepage: http://bis.zju.edu.cn/ricenetdb/ mappings: biocontext: RICENETDB.GENE miriam: ricenetdb.gene n2t: ricenetdb.gene name: RiceNetDB Gene pattern: ^LOC\_Os\d{1,2}g\d{5}\.\d$ preferred_prefix: ricenetdb.gene uri_format: http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1 ricenetdb.mirna: description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' example: osa-miR446 homepage: http://bis.zju.edu.cn/ricenetdb mappings: biocontext: RICENETDB.MIRNA miriam: ricenetdb.mirna n2t: ricenetdb.mirna name: RiceNetDB miRNA pattern: ^osa-miR\d{3,5}[a-z]{0,1}$ preferred_prefix: ricenetdb.mirna uri_format: http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1 ricenetdb.protein: description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' example: LOC_Os01g49190 homepage: http://bis.zju.edu.cn/ricenetdb/ mappings: biocontext: RICENETDB.PROTEIN miriam: ricenetdb.protein n2t: ricenetdb.protein name: RiceNetDB Protein pattern: ^LOC\_Os\d{1,2}g\d{5}$ preferred_prefix: ricenetdb.protein uri_format: http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1 ricenetdb.reaction: description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' example: OSR0818 homepage: http://bis.zju.edu.cn/ricenetdb mappings: biocontext: RICENETDB.REACTION miriam: ricenetdb.reaction n2t: ricenetdb.reaction name: RiceNetDB Reaction pattern: ^OSR\d{4}$ preferred_prefix: ricenetdb.reaction uri_format: http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1 rism: description: RISM Online is a new service that will publish the bibliographic and authority data from the catalogue of the Répertoire International des Sources Musicales project. example: people/11035 homepage: https://rism.digital/ mappings: miriam: rism name: RISM Online pattern: ^[a-z]+/[0-9]+$ preferred_prefix: rism uri_format: https://rism.online/$1 rnacentral: description: RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases. example: URS0000759CF4 homepage: https://rnacentral.org/ mappings: biocontext: RNACENTRAL edam: '3856' fairsharing: FAIRsharing.KcCjL7 go: RNAcentral miriam: rnacentral n2t: rnacentral ncbi: RNAcentral name: RNAcentral pattern: ^URS[0-9A-F]{10}(\_\d+)?$ preferred_prefix: rnacentral synonyms: - LNCRNADB uri_format: https://rnacentral.org/rna/$1 rnamod: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A comprehensive listing of post-transcriptionally modified nucleosides from RNA - example: '051' homepage: http://rna.rega.kuleuven.be/rnamods/ name: The RNA Modification Database pattern: ^\d{3}$ preferred_prefix: rnamod uri_format: http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1 rnamods: description: The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. example: '101' homepage: http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm mappings: biocontext: RNAMODS go: RNAmods miriam: rnamods n2t: rnamods prefixcommons: rnamods name: RNA Modification Database pattern: ^\d{3}$ preferred_prefix: rnamods uri_format: http://mods.rna.albany.edu/mods/modifications/view/$1 rnao: contact: email: BatchelorC@rsc.org github: null name: Colin Batchelor orcid: 0000-0001-5985-7429 deprecated: true description: Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures. download_obo: http://purl.obolibrary.org/obo/rnao.obo download_owl: http://purl.obolibrary.org/obo/rnao.owl example: 0000128 homepage: https://github.com/bgsu-rna/rnao license: CC0 1.0 mappings: aberowl: RNAO biocontext: RNAO bioportal: RNAO fairsharing: FAIRsharing.kqt2h2 obofoundry: rnao ols: rnao ontobee: RNAO prefixcommons: rnao name: RNA ontology pattern: ^\d{7}$ preferred_prefix: RNAO publications: - doi: 10.1261/rna.2343206 pmc: PMC1421088 pubmed: '16484377' title: 'The RNA Ontology Consortium: an open invitation to the RNA community.' year: 2006 - doi: 10.3233/ao-2011-0082 pmc: null pubmed: null title: 'The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data' year: null repository: https://github.com/BGSU-RNA/rnao uri_format: http://purl.obolibrary.org/obo/RNAO_$1 version: '2019-04-15' ro: appears_in: - agro - aism - cdno - cl - clao - clyh - colao - cteno - ecao - ecocore - ecto - envo - foodon - fovt - genepio - go - hso - lepao - maxo - ons - ontoavida - pcl - pco - plana - planp - poro - proco - psdo - pso - rbo - upa - xpo - zp banana: RO banana_peel: _ contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies. download_json: http://purl.obolibrary.org/obo/ro.json download_obo: http://purl.obolibrary.org/obo/ro.obo download_owl: http://purl.obolibrary.org/obo/ro.owl example: '0002533' homepage: https://oborel.github.io/ license: CC0 1.0 mappings: aberowl: RO agroportal: RO biocontext: RO biolink: RO bioportal: OBOREL fairsharing: FAIRsharing.cp0ybc go: RO miriam: ro n2t: ro obofoundry: ro ols: ro ontobee: RO prefixcommons: ro wikidata: P3590 name: Relation Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: RO publications: - doi: 10.1186/2041-1480-5-41 pmc: PMC4177597 pubmed: '25276335' title: 'Structuring research methods and data with the research object model: genomics workflows as a case study.' year: 2014 - doi: 10.1186/gb-2005-6-5-r46 pmc: PMC1175958 pubmed: '15892874' title: Relations in biomedical ontologies. year: 2005 repository: https://github.com/oborel/obo-relations synonyms: - RO_proposed_relation - obo_rel - oborel uri_format: http://purl.obolibrary.org/obo/RO_$1 version: '2022-05-23' ror: description: 'ROR (Research Organization Registry) is a global, community-led registry of open persistent identifiers for research organizations. ROR is jointly operated by California Digital Library, Crossref, and Datacite.' example: 03yrm5c26 homepage: https://ror.org mappings: miriam: ror n2t: ror name: Research Organization Registry pattern: ^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$ preferred_prefix: ror uri_format: https://ror.org/$1 rouge: description: The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. example: mKIAA4200 homepage: http://www.kazusa.or.jp/rouge/ mappings: biocontext: ROUGE fairsharing: FAIRsharing.vdbagq miriam: rouge n2t: rouge prefixcommons: rouge uniprot: Rouge name: Rodent Unidentified Gene-Encoded Large Proteins pattern: ^m\w+$ preferred_prefix: rouge uri_format: https://www.kazusa.or.jp/rouge/gfpage/$1 rrid: banana: RRID description: "The Research Resource Identification Initiative provides RRIDs to\ \ 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases\ \ / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\r\ \nThe initiative works with participating journals to intercept manuscripts in\ \ the publication process that use these resources, and allows publication authors\ \ to incorporate RRIDs within the methods sections. It also provides resolver\ \ services that access curated data from 10 data sources: the antibody registry\ \ (a curated catalog of antibodies), the SciCrunch registry (a curated catalog\ \ of software tools and databases), and model organism nomenclature authority\ \ databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These\ \ RRIDs are aggregated and can be searched through SciCrunch." example: AB_262044 homepage: https://scicrunch.org/resolver mappings: biocontext: RRID fairsharing: FAIRsharing.ATwSZG miriam: rrid n2t: rrid name: Research Resource Identification namespace_in_lui: true pattern: ^[a-zA-Z]+.+$ preferred_prefix: rrid uri_format: https://scicrunch.org/resolver/RRID:$1 rs: contact: email: sjwang@mcw.edu github: shurjenw name: Shur-Jen Wang orcid: 0000-0001-5256-8683 description: Ontology of rat strains download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.obo download_owl: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.owl example: 0001807 homepage: http://rgd.mcw.edu/rgdweb/search/strains.html license: CC BY 4.0 mappings: aberowl: RS biocontext: RS bioportal: RS fairsharing: FAIRsharing.vajn3f obofoundry: rs ols: rs ontobee: RS prefixcommons: rs name: Rat Strain Ontology pattern: ^\d{7}$ preferred_prefix: RS publications: - doi: 10.1186/2041-1480-4-36 pmc: PMC4177145 pubmed: '24267899' title: 'Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.' year: 2013 - doi: 10.1093/database/bat015 pmc: PMC3630803 pubmed: '23603846' title: 'PhenoMiner: quantitative phenotype curation at the rat genome database.' year: 2013 repository: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology twitter: ratgenome uri_format: http://purl.obolibrary.org/obo/RS_$1 version: '2019-12-13' rtecs: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'RTECS is a compendium of data extracted from the open scientific literature. The data are recorded in the format developed by the RTECS staff and arranged in alphabetical order by prime chemical name. Six types of toxicity data are included in the file: (1) primary irritation; (2) mutagenic effects; (3) reproductive effects; (4) tumorigenic effects; (5) acute toxicity; and (6) other multiple dose toxicity. Specific numeric toxicity values such as LD50, LC50, TDLo, and TCLo are noted as well as species studied and route of administration used. For each citation, the bibliographic source is listed thereby enabling the user to access the actual studies cited. No attempt has been made to evaluate the studies cited in RTECS. The user has the responsibility of making such assessments.' example: AB1925000 homepage: https://www.cdc.gov/niosh/rtecs/ mappings: cheminf: '000566' name: Registry of Toxic Effects of Chemical Substances pattern: ^AB\d+$ preferred_prefix: rtecs proprietary: true publications: - doi: https://doi.org/10.1016/s1074-9098%2899%2900058-1 pmc: null pubmed: null title: 'An overview of the Registry of Toxic Effects of Chemical Substances (RTECS): Critical information on chemical hazards' year: null references: - https://www.cdc.gov/niosh/docs/97-119/pdfs/97-119.pdf - https://www.cdc.gov/niosh/npg/npgdrtec.html runbiosimulations: description: runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive. example: 5fde96bdc5f1aa9ff0cce18a homepage: https://icahn.mssm.edu/ mappings: miriam: runbiosimulations name: runBioSimulations pattern: ^[0-9a-z]{24,24}$ preferred_prefix: runbiosimulations uri_format: https://run.biosimulations.org/simulations/$1 rxno: contact: email: batchelorc@rsc.org github: batchelorc name: Colin Batchelor orcid: 0000-0001-5985-7429 description: RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization. download_obo: https://github.com/rsc-ontologies/rxno/raw/master/rxno.obo download_owl: http://purl.obolibrary.org/obo/rxno.owl example: '0000253' homepage: https://github.com/rsc-ontologies/rxno license: CC BY 4.0 mappings: aberowl: RXNO biocontext: RXNO bioportal: RXNO fairsharing: FAIRsharing.w4tncg obofoundry: rxno ols: rxno ontobee: RXNO wikidata: P2106 name: Name Reaction Ontology pattern: ^\d{7}$ preferred_prefix: RXNO repository: https://github.com/rsc-ontologies/rxno uri_format: http://purl.obolibrary.org/obo/RXNO_$1 version: '2021-12-16' rxnorm: contact: email: custserv@nlm.nih.gov github: null name: NLM Customer Service orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary. example: '221058' homepage: https://www.nlm.nih.gov/research/umls/rxnorm/ mappings: aberowl: RXNORM biocontext: RXCUI biolink: RXNORM bioportal: RXNORM fairsharing: FAIRsharing.36pf8q hl7: 2.16.840.1.113883.6.88 wikidata: P3345 name: RxNorm pattern: ^[0-9]{1,7}$ preferred_prefix: rxnorm providers: - code: bp description: RxNorm in BioPortal homepage: http://purl.bioontology.org/ontology/RXNORM name: BioPortal uri_format: http://purl.bioontology.org/ontology/RXNORM/$1 publications: - doi: 10.1136/amiajnl-2011-000116 pmc: PMC3128404 pubmed: '21515544' title: 'Normalized names for clinical drugs: RxNorm at 6 years.' year: 2011 - doi: null pmc: PMC2655997 pubmed: '18998891' title: RxTerms - a drug interface terminology derived from RxNorm. year: 2008 - doi: 10.1109/mitp.2005.122 pmc: null pubmed: null title: 'RxNorm: prescription for electronic drug information exchange' year: null synonyms: - RXCUI uri_format: https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1 sabiork.compound: description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information. example: '75' homepage: http://sabiork.h-its.org/ mappings: miriam: sabiork.compound n2t: sabiork.compound name: SABIO-RK Compound pattern: ^\d+$ preferred_prefix: sabiork.compound uri_format: http://sabiork.h-its.org/newSearch?q=$1 sabiork.ec: description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data. example: 2.7.1.1 homepage: http://sabiork.h-its.org/ mappings: biocontext: SABIORK.EC miriam: sabiork.ec n2t: sabiork.ec prefixcommons: sabiork.ec name: SABIO-RK EC Record pattern: ^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$ preferred_prefix: sabiork.ec provides: eccode publications: - doi: null pmc: null pubmed: '17822389' title: Storing and annotating of kinetic data. year: 2007 uri_format: http://sabiork.h-its.org/newSearch?q=ecnumber:$1 sabiork.kineticrecord: description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information. example: '5046' homepage: http://sabiork.h-its.org/ mappings: biocontext: SABIORK.KINETICRECORD go: SABIO-RK miriam: sabiork.kineticrecord n2t: sabiork.kineticrecord prefixcommons: sabiork.kinetic name: SABIO Reaction Kinetics pattern: ^\d+$ preferred_prefix: sabiork.kineticrecord publications: - doi: null pmc: null pubmed: '17822389' title: Storing and annotating of kinetic data. year: 2007 uri_format: http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1 sabiork.reaction: description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information. example: '75' homepage: http://sabiork.h-its.org/ mappings: biocontext: SABIORK.REACTION edam: '2309' fairsharing: FAIRsharing.cwx04e miriam: sabiork.reaction n2t: sabiork.reaction prefixcommons: sabiork.reaction re3data: r3d100011052 uniprot: SABIO-RK name: SABIO-RK Reaction pattern: ^\d+$ preferred_prefix: sabiork.reaction synonyms: - SABIO-RK uri_format: http://sabiork.h-its.org/reacdetails.jsp?reactid=$1 sael: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List preferred_prefix: sael publications: - doi: 10.1002/cfg.434 pmc: PMC2447422 pubmed: '18629134' title: 'The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data.' year: 2004 salk: appears_in: - efo comment: spider stuff! contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Scientific research institute for neuroscience, genetics, immunology, plant biology and more. example: '037727' homepage: https://www.salk.edu/ name: Salk Institute for Biological Studies pattern: ^\d{6}$ preferred_prefix: salk uri_format: https://abrc.osu.edu/stocks/number/SALK_$1 sao: contact: email: slarson@ncmir.ucsd.edu github: null name: Stephen Larson orcid: null deprecated: true description: SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules. download_owl: http://aber-owl.net/media/ontologies/SAO/2/sao.owl example: '5277619' homepage: http://ccdb.ucsd.edu/CCDBWebSite/sao.html mappings: aberowl: SAO biocontext: SAO bioportal: SAO obofoundry: sao prefixcommons: sao name: Subcellular Anatomy Ontology pattern: ^\d+$ preferred_prefix: SAO references: - http://www.ontobee.org/ontology/SAO uri_format: http://uri.neuinfo.org/nif/nifstd/sao$1 sasbdb: description: Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data. example: SASDAX8 homepage: http://www.sasbdb.org/ mappings: biocontext: SASBDB fairsharing: FAIRsharing.i1F3Hb miriam: sasbdb n2t: sasbdb re3data: r3d100012273 uniprot: SASBDB name: Small Angle Scattering Biological Data Bank pattern: ^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$ preferred_prefix: sasbdb uri_format: http://www.sasbdb.org/data/$1 sbo: appears_in: - proco - scdo banana: SBO contact: email: sheriff@ebi.ac.uk github: rsmsheriff name: Rahuman Sheriff orcid: 0000-0003-0705-9809 description: The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort. download_obo: http://purl.obolibrary.org/obo/sbo.obo download_owl: http://purl.obolibrary.org/obo/sbo.owl example: 0000485 homepage: http://www.ebi.ac.uk/sbo/ license: Artistic License 2.0 mappings: aberowl: SBO biocontext: SBO bioportal: SBO fairsharing: FAIRsharing.s19src miriam: sbo n2t: sbo obofoundry: sbo ols: sbo ontobee: SBO prefixcommons: sbo name: Systems Biology Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: SBO providers: - code: biomodels description: Provider for SBO at BioModels homepage: http://biomodels.net name: BioModels uri_format: http://biomodels.net/SBO/SBO_$1 publications: - doi: 10.1038/msb.2011.77 pmc: PMC3261705 pubmed: '22027554' title: Controlled vocabularies and semantics in systems biology. year: 2011 - doi: 10.1186/1471-2202-7-s1-s11 pmc: PMC1775041 pubmed: '17118155' title: Model storage, exchange and integration. year: 2006 repository: https://github.com/EBI-BioModels/SBO uri_format: https://www.ebi.ac.uk/sbo/main/SBO:$1 version: '2021-08-28' scdo: contact: email: giant.plankton@gmail.com github: JadeHotchkiss name: Jade Hotchkiss orcid: 0000-0002-2193-0704 depends_on: - apollosv - aro - chebi - chmo - cmo - doid - dron - duo - envo - eupath - exo - gaz - gsso - hp - hsapdv - ico - ido - idomal - mp - nbo - ncit - obi - ogms - opmi - pr - sbo - stato - symp - uo - vo - vt description: An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease. download_obo: http://purl.obolibrary.org/obo/scdo.obo download_owl: http://purl.obolibrary.org/obo/scdo.owl example: 0000728 homepage: https://scdontology.h3abionet.org/ license: GPL-3.0 mappings: aberowl: SCDO bioportal: SCDO fairsharing: FAIRsharing.kkq6pw obofoundry: scdo ols: scdo ontobee: SCDO name: Sickle Cell Disease Ontology pattern: ^\d{7}$ preferred_prefix: SCDO publications: - doi: 10.1093/database/baac014 pmc: PMC9216550 pubmed: '35363306' title: 'The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation.' year: 2022 - doi: 10.1089/omi.2020.0153 pmc: PMC7549008 pubmed: '33021900' title: 'The Sickle Cell Disease Ontology: Enabling Collaborative Research and Co-Designing of New Planetary Health Applications.' year: 2020 - doi: 10.1093/database/baz118 pmc: PMC6878945 pubmed: '31769834' title: 'The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation.' year: 2019 repository: https://github.com/scdodev/scdo-ontology uri_format: http://purl.obolibrary.org/obo/SCDO_$1 version: '2021-04-15' schem: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Selventa legacy chemical namespace used with the Biological Expression Language example: A0001 homepage: https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-chemical-names.txt name: Selventa Chemicals pattern: ^A\d{4}$ preferred_prefix: schem uri_format: https://biopragmatics.github.io/providers/schem/$1 schema: contact: email: johardi@stanford.edu github: null name: Josef Hardi orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond. download_owl: http://aber-owl.net/media/ontologies/SCHEMAORG/2/schemaorg.owl example: Person homepage: https://schema.org mappings: aberowl: SCHEMAORG biolink: schema bioportal: SCHEMA name: Schema.org preferred_prefix: schema synonyms: - schemaorg uri_format: https://schema.org/$1 scholia.resource: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A frontend to Wikidata example: doi homepage: https://scholia.toolforge.org/ name: Scholia Registry preferred_prefix: scholia.resource uri_format: https://bioregistry.io/metaregistry/scholia/$1 scomp: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Selventa legacy complex namespace used with the Biological Expression Language example: C0001 homepage: https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-named-complexes.txt name: Selventa Complexes pattern: ^C\d{4}$ preferred_prefix: scomp uri_format: https://biopragmatics.github.io/providers/scomp/$1 scop: description: The SCOP (Structural Classification of Protein) database is a comprehensive ordering of all proteins of known structure according to their evolutionary, functional and structural relationships. The basic classification unit is the protein domain. Domains are hierarchically classified into species, proteins, families, superfamilies, folds, and classes. example: '47419' homepage: http://scop.mrc-lmb.cam.ac.uk/scop/ mappings: biocontext: SCOP fairsharing: FAIRsharing.wjzty miriam: scop n2t: scop prefixcommons: scop name: Structural Classification of Protein pattern: ^\d+$ preferred_prefix: scop providers: - code: CURATOR_REVIEW description: SCOP at Berkeley homepage: http://scop.berkeley.edu/ name: SCOP at Berkeley uri_format: http://scop.berkeley.edu/sunid=$1 uri_format: http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=$1 scopus: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: "Scopus is the largest abstract and citation database of peer-reviewed\ \ literature: scientific journals, books and conference proceedings. \nDelivering\ \ a comprehensive overview of the world's research output in the fields of science,\ \ technology, medicine, social sciences, and arts \nand humanities, Scopus features\ \ smart tools to track, analyze and visualize research." example: '56305849200' homepage: https://www.scopus.com mappings: biolink: ScopusID fairsharing: FAIRsharing.0a674c name: Scopus Researcher pattern: ^\d+$ preferred_prefix: scopus scoro: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator). example: IntellectualContribution homepage: http://www.sparontologies.net/ontologies/scoro mappings: fairsharing: FAIRsharing.c86b48 name: Scholarly Contributions and Roles Ontology preferred_prefix: SCoRO publications: - doi: https://doi.org/10.3233/sw-150177 pmc: null pubmed: null title: The Document Components Ontology (DoCO) year: null repository: https://github.com/sparontologies/scoro uri_format: http://purl.org/spar/scoro/$1 scr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources. example: 022586 github_request_issue: 421 homepage: https://scicrunch.org/browse/resourcedashboard name: SciCrunch Registry pattern: ^\d+$ preferred_prefix: scr synonyms: - scicrunch uri_format: http://scicrunch.org/resolver/SCR_$1 scretf: description: ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor. example: RSC3 homepage: http://stormo.wustl.edu/ScerTF/ mappings: biocontext: SCRETF miriam: scretf n2t: scretf name: ScerTF pattern: ^\w+$ preferred_prefix: scretf uri_format: http://stormo.wustl.edu/ScerTF/details/$1 sdbs: description: The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds.