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 fairsharing: FAIRsharing.5ab0n7 miriam: 3dmet n2t: 3dmet prefixcommons: 3dmet wikidata: P2796 name: 3D Metabolites pattern: ^B\d{5}$ preferred_prefix: 3dmet 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 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 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: banana: 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 uri_format: http://purl.obolibrary.org/obo/AAO_$1 abcd: 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=$1 abs: description: The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. example: A0014 homepage: http://genome.crg.es/datasets/abs2005/ mappings: biocontext: ABS fairsharing: FAIRsharing.7mnebr miriam: abs n2t: abs prefixcommons: abs name: Annotated Regulatory Binding Sites pattern: ^A\d+$ preferred_prefix: abs 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 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=$1 addgene: description: Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world. example: '50943' homepage: http://addgene.org/ mappings: fairsharing: FAIRsharing.8hcczk miriam: addgene n2t: addgene prefixcommons: addgene name: Addgene Plasmid Repository pattern: ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$ preferred_prefix: addgene uri_format: http://addgene.org/$1 adw: banana: ADW contact: email: adw_geeks@umich.edu github: null name: Animal Diversity Web technical staff orcid: null deprecated: true description: Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology. example: Lycalopex_vetulus homepage: http://www.animaldiversity.org mappings: biocontext: ADW bioportal: ADW fairsharing: FAIRsharing.t9fvdn miriam: adw n2t: adw obofoundry: ADW name: Animal natural history and life history pattern: ^[A-Z_a-z]+$ preferred_prefix: ADW uri_format: https://animaldiversity.org/accounts/$1 aeo: appears_in: - ehdaa2 banana: AEO contact: email: J.Bard@ed.ac.uk github: null name: Jonathan Bard orcid: null description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology download_obo: https://raw.githubusercontent.com/obophenotype/human-developmental-anatomy-ontology/master/src/ontology/aeo.obo download_owl: http://purl.obolibrary.org/obo/aeo.owl example: '0001017' homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/ license: CC BY 4.0 mappings: biocontext: AEO bioportal: AEO fairsharing: FAIRsharing.93ee19 obofoundry: AEO ols: aeo ontobee: AEO name: Anatomical Entity Ontology pattern: ^\d{7}$ preferred_prefix: AEO repository: https://github.com/obophenotype/human-developmental-anatomy-ontology synonyms: - AEO_RETIRED uri_format: http://purl.obolibrary.org/obo/AEO_$1 version: '2014-12-05' aero: banana: AERO contact: email: mcourtot@gmail.com github: null name: Melanie Courtot orcid: 0000-0002-9551-6370 deprecated: true description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events download_owl: http://purl.obolibrary.org/obo/aero.owl example: '0000125' homepage: http://purl.obolibrary.org/obo/aero license: CC BY 3.0 mappings: biocontext: AERO bioportal: AERO fairsharing: FAIRsharing.rycy2x obofoundry: AERO name: Adverse Event Reporting Ontology pattern: ^\d{7}$ 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=$1 afo: description: Allotrope Merged Ontology Suite download_owl: http://purl.allotrope.org/voc/afo/merged-OLS/REC/2019/05/10 homepage: https://www.allotrope.org/ mappings: bioportal: AFO fairsharing: FAIRsharing.595710 ols: afo name: Allotrope Merged Ontology Suite no_own_terms: true preferred_prefix: afo version: '2019-05-10' aftol.taxonomy: description: The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species. example: '959' homepage: https://aftol.umn.edu mappings: biocontext: AFTOL.TAXONOMY miriam: aftol.taxonomy n2t: aftol.taxonomy name: Assembling the Fungal Tree of Life - Taxonomy pattern: ^\d+$ 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: 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=$1 agro: banana: AGRO contact: email: m.a.laporte@cgiar.org github: marieALaporte name: Marie-Angélique Laporte orcid: 0000-0002-8461-9745 depends_on: - bfo - envo - foodon - go - iao - ncbitaxon - obi - pato - peco - po - ro - to - uo - xco description: AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities download_obo: https://raw.githubusercontent.com/KrishnaTO/agro/master/agro.obo download_owl: http://purl.obolibrary.org/obo/agro.owl example: '00020007' homepage: https://github.com/AgriculturalSemantics/agro license: CC BY 4.0 mappings: biocontext: AGRO bioportal: AGRO fairsharing: FAIRsharing.m40bhw obofoundry: AGRO ols: agro ontobee: AGRO name: Agronomy Ontology pattern: ^\d{8}$ preferred_prefix: AGRO repository: https://github.com/AgriculturalSemantics/agro uri_format: http://purl.obolibrary.org/obo/AGRO_$1 version: '2021-11-05' agrovoc: description: AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages. example: '2842' homepage: https://data.apps.fao.org/catalog/organization/agrovoc mappings: fairsharing: FAIRsharing.anpj91 name: Agronomy Vocabulary pattern: ^[a-z0-9]+$ preferred_prefix: agrovoc 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_$1 aism: appears_in: - colao - lepao banana: AISM contact: email: entiminae@gmail.com github: JCGiron name: Jennifer C. Girón orcid: 0000-0002-0851-6883 depends_on: - bfo - bspo - caro - pato - ro - uberon description: The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research. download_json: http://purl.obolibrary.org/obo/aism.json download_obo: http://purl.obolibrary.org/obo/aism.obo download_owl: http://purl.obolibrary.org/obo/aism.owl example: '0000027' homepage: https://github.com/insect-morphology/aism license: CC BY 4.0 mappings: bioportal: AISM obofoundry: AISM ols: aism ontobee: AISM name: Ontology for the Anatomy of the Insect SkeletoMuscular system pattern: ^\d{7}$ preferred_prefix: AISM repository: https://github.com/insect-morphology/aism uri_format: http://purl.obolibrary.org/obo/AISM_$1 version: '2022-03-17' allergome: description: Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources. example: '1948' homepage: http://www.allergome.org/ mappings: biocontext: ALLERGOME fairsharing: FAIRsharing.w6cxgb miriam: allergome n2t: allergome prefixcommons: allergome uniprot: Allergome name: Allergome pattern: ^\d+$ preferred_prefix: allergome 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/$1 amoebadb: description: AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: EDI_244000 homepage: http://amoebadb.org/amoeba/ mappings: biocontext: AMOEBADB fairsharing: FAIRsharing.swbypy miriam: amoebadb n2t: amoebadb prefixcommons: amoebadb name: AmoebaDB pattern: ^EDI_\d+$ preferred_prefix: amoebadb uri_format: https://amoebadb.org/amoeba/app/record/gene/$1 amphx: banana: AMPHX contact: email: hescriva@obs-banyuls.fr github: hescriva name: Hector Escriva orcid: 0000-0001-7577-5028 depends_on: - uberon description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). download_obo: http://purl.obolibrary.org/obo/amphx.obo download_owl: http://purl.obolibrary.org/obo/amphx.owl example: '1000160' homepage: https://github.com/EBISPOT/amphx_ontology license: CC BY 3.0 mappings: bioportal: AMPHX obofoundry: AMPHX ols: amphx ontobee: AMPHX name: The Amphioxus Development and Anatomy Ontology pattern: ^\d+$ 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_$1 antweb: description: AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures. example: casent0106247 homepage: http://www.antweb.org/ mappings: biocontext: ANTWEB fairsharing: FAIRsharing.yk38tw miriam: antweb n2t: antweb ncbi: AntWeb prefixcommons: antweb name: Ant Database pattern: ^casent\d+(\-D\d+)?$ preferred_prefix: antweb 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: description: Ontology from the APA example: Abdomen homepage: https://bioportal.bioontology.org/ontologies/APAONTO mappings: bioportal: APAONTO fairsharing: FAIRsharing.gkw1w8 name: Psychology Ontology preferred_prefix: apaonto 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 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=$1 apo: banana: APO contact: email: stacia@stanford.edu github: srengel name: Stacia R Engel orcid: 0000-0001-5472-917X description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi. download_obo: http://purl.obolibrary.org/obo/apo.obo download_owl: http://purl.obolibrary.org/obo/apo.owl example: 0000184 homepage: http://www.yeastgenome.org/ license: CC BY 4.0 mappings: biocontext: YPO bioportal: APO fairsharing: FAIRsharing.dyqz3y obofoundry: APO ols: apo ontobee: APO name: Ascomycete phenotype ontology pattern: ^\d{7}$ preferred_prefix: APO repository: https://github.com/obophenotype/ascomycete-phenotype-ontology uri_format: https://www.yeastgenome.org/observable/APO:$1 version: '2022-04-19' apollosv: appears_in: - scdo banana: APOLLO_SV contact: email: hoganwr@ufl.edu github: hoganwr name: William Hogan orcid: 0000-0002-9881-1017 description: Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models download_owl: http://purl.obolibrary.org/obo/apollo_sv.owl example: '00000443' homepage: https://github.com/ApolloDev/apollo-sv license: CC BY 4.0 mappings: bioportal: APOLLO-SV fairsharing: FAIRsharing.ngv2xx obofoundry: APOLLO_SV ols: apollo_sv ontobee: APOLLO_SV name: Apollo Structured Vocabulary pattern: ^\d{8}$ preferred_prefix: APOLLO_SV repository: https://github.com/ApolloDev/apollo-sv uri_format: http://purl.obolibrary.org/obo/APOLLO_SV_$1 version: 4.1.1 arachnoserver: description: ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information. example: AS000060 homepage: http://www.arachnoserver.org/ mappings: biocontext: ARACHNOSERVER fairsharing: FAIRsharing.c54ywe miriam: arachnoserver n2t: arachnoserver prefixcommons: arachnoserver uniprot: ArachnoServer name: ArachnoServer pattern: ^AS\d{6}$ preferred_prefix: arachnoserver 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:$1 aro: appears_in: - scdo banana: ARO contact: email: mcarthua@mcmaster.ca github: agmcarthur name: Andrew G. McArthur orcid: 0000-0002-1142-3063 description: Antibiotic resistance genes and mutations download_owl: http://purl.obolibrary.org/obo/aro.owl example: '1000001' homepage: https://github.com/arpcard/aro license: CC BY 4.0 mappings: biocontext: ARO bioportal: ARO obofoundry: ARO ols: aro ontobee: ARO name: Antibiotic Resistance Ontology pattern: ^\d{7}$ preferred_prefix: ARO repository: https://github.com/arpcard/aro uri_format: http://purl.obolibrary.org/obo/ARO_$1 arrayexpress: description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations. example: E-MEXP-1712 homepage: https://www.ebi.ac.uk/arrayexpress/ mappings: biocontext: ARRAYEXPRESS cellosaurus: ArrayExpress fairsharing: FAIRsharing.6k0kwd miriam: arrayexpress n2t: arrayexpress prefixcommons: arrayexpress name: ArrayExpress pattern: ^[AEP]-\w{4}-\d+$ 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 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/$1 arraymap: description: arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome. example: icdom:8500_3 homepage: https://www.arraymap.org mappings: biocontext: ARRAYMAP fairsharing: FAIRsharing.1fbc5y miriam: arraymap n2t: arraymap name: ArrayMap pattern: ^[\w\-:,]{3,64}$ preferred_prefix: arraymap uri_format: https://www.arraymap.org/pgx:$1 arxiv: description: arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology. example: 0807.4956v1 homepage: https://arxiv.org/ mappings: biocontext: ARXIV miriam: arxiv n2t: arxiv prefixcommons: arxiv scholia: arxiv name: arXiv pattern: ^(\w+(\-\w+)?(\.\w+)?)?\d{4,7}(\.\d+(v\d+)?)?$ preferred_prefix: arxiv uri_format: https://arxiv.org/abs/$1 asap: description: ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. example: ABE-0009634 homepage: http://asap.ahabs.wisc.edu/asap/home.php mappings: biocontext: ASAP fairsharing: FAIRsharing.anpa6 go: ASAP miriam: asap n2t: asap ncbi: ASAP prefixcommons: asap name: A Systematic Annotation Package for Community Analysis of Genomes pattern: ^[A-Za-z0-9-]+$ preferred_prefix: asap 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 uri_format: http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1 atc: description: The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels. example: A10BA02 homepage: http://www.whocc.no/atc_ddd_index/ mappings: biocontext: ATC bioportal: ATC fairsharing: FAIRsharing.1a27h8 miriam: atc n2t: atc prefixcommons: atc wikidata: P267 name: Anatomical Therapeutic Chemical Classification System pattern: ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$ preferred_prefix: atc synonyms: - ATC_code - ATTC uri_format: http://www.whocc.no/atc_ddd_index/?code=$1 atcc: description: The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences. example: '11303' homepage: https://www.lgcstandards-atcc.org mappings: biocontext: ATCC cellosaurus: ATCC fairsharing: FAIRsharing.j0ezpm miriam: atcc n2t: atcc ncbi: ATCC name: American Type Culture Collection pattern: ^([A-Z]+-)?\d+$ 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=$1 ato: banana: ATO contact: email: david.c.blackburn@gmail.com github: null name: David Blackburn orcid: null deprecated: true description: Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource example: '0000000' homepage: http://www.amphibanat.org mappings: biocontext: ATO bioportal: ATO fairsharing: FAIRsharing.ayjdsm obofoundry: ATO name: Amphibian taxonomy pattern: ^\d{7}$ preferred_prefix: ATO uri_format: http://purl.obolibrary.org/obo/ATO_$1 atol: description: 'ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production.' download_owl: https://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=atol.owl example: '0002233' homepage: http://www.atol-ontology.com mappings: bioportal: ATOL fairsharing: FAIRsharing.wsfk5z ols: atol name: Animal Trait Ontology for Livestock pattern: ^\d{7}$ preferred_prefix: atol 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/$1 bacdive: description: BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. example: '131392' homepage: https://bacdive.dsmz.de/ mappings: fairsharing: FAIRsharing.aSszvY miriam: bacdive n2t: bacdive name: Bacterial Diversity Metadatabase pattern: ^[0-9]+$ 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 name: Bactibase preferred_prefix: bactibase uri_format: http://bactibase.hammamilab.org/$1 bams: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: 'BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions.' homepage: https://bams1.org name: Brain Architecture Knowledge Management System Neuroanatomical Ontology preferred_prefix: bams references: - https://www.frontiersin.org/articles/10.3389/neuro.11.002.2008/full bao: description: The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. download_owl: http://www.bioassayontology.org/bao/bao_complete.owl example: 0002989 homepage: http://bioassayontology.org mappings: biocontext: BAO bioportal: BAO fairsharing: FAIRsharing.mye76w miriam: bao n2t: bao ols: bao ontobee: BAO name: BioAssay Ontology pattern: ^\d{7}$ preferred_prefix: bao 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: banana: 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 homepage: https://github.com/obi-bcgo/bcgo license: CC BY 3.0 mappings: biocontext: BCGO bioportal: BCGO cellosaurus: BCGO obofoundry: BCGO ontobee: BCGO name: Beta Cell Genomics Ontology preferred_prefix: BCGO repository: https://github.com/obi-bcgo/bcgo uri_format: http://purl.obolibrary.org/obo/BCGO_$1 bcio: description: The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation. download_owl: http://humanbehaviourchange.org/ontology/bcio.owl example: '040000' homepage: https://www.humanbehaviourchange.org/ mappings: bioportal: BCI-O ols: bcio name: The Behaviour Change Intervention Ontology pattern: ^\d{6}$ preferred_prefix: bcio bco: appears_in: - fovt banana: BCO 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: biocontext: BCO bioportal: BCO fairsharing: FAIRsharing.8ktkqy obofoundry: BCO ols: bco ontobee: BCO name: Biological Collections Ontology pattern: ^\d{7}$ preferred_prefix: BCO 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/$1 bdgp.est: description: The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI). example: EY223054.1 has_canonical: dbest homepage: https://www.ncbi.nlm.nih.gov/dbEST/index.html mappings: biocontext: BDGP.EST miriam: bdgp.est n2t: bdgp.est ncbi: BDGP_EST name: Berkeley Drosophila Genome Project EST database pattern: ^\w+(\.)?(\d+)?$ preferred_prefix: bdgp.est uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1 bdgp.insertion: description: BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element. example: KG09531 homepage: http://flypush.imgen.bcm.tmc.edu/pscreen/ mappings: biocontext: BDGP.INSERTION miriam: bdgp.insertion n2t: bdgp.insertion name: BDGP insertion DB pattern: ^\w+$ preferred_prefix: bdgp.insertion 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/$1 beetlebase: description: BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications. example: TC010103 homepage: http://beetlebase.org/ mappings: biocontext: BEETLEBASE fairsharing: FAIRsharing.h5f091 miriam: beetlebase n2t: beetlebase ncbi: BEETLEBASE prefixcommons: beetlebase name: Tribolium Genome Database -- Insertion pattern: ^TC\d+$ preferred_prefix: beetlebase 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/$1.aspx bel: comment: INDRA uses bel as a catch-all for scomp/sfam contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents. example: 9-1-1 Complex homepage: https://biological-expression-language.github.io/ mappings: fairsharing: FAIRsharing.dp0jvd name: Biological Expression Language preferred_prefix: bel bfo: appears_in: - agro - aism - cdno - colao - duo - ecocore - epio - foodon - fovt - hso - lepao - mco - ons - pcl - pco - psdo - rbo - xpo - zp banana: BFO contact: email: phismith@buffalo.edu github: phismith name: Barry Smith orcid: 0000-0003-1384-116X description: The upper level ontology upon which OBO Foundry ontologies are built. download_obo: http://purl.obolibrary.org/obo/bfo.obo download_owl: http://purl.obolibrary.org/obo/bfo.owl example: '0000001' homepage: http://ifomis.org/bfo/ license: CC BY 4.0 mappings: biocontext: BFO bioportal: BFO fairsharing: FAIRsharing.wcpd6f go: BFO obofoundry: BFO ols: bfo ontobee: BFO name: Basic Formal Ontology pattern: ^\d{7}$ 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=$1 bigg.compartment: description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments. example: c homepage: http://bigg.ucsd.edu/compartments/ mappings: biocontext: BIGG.COMPARTMENT miriam: bigg.compartment n2t: bigg.compartment name: BiGG Compartment pattern: ^[a-z_A-Z]+$ 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: banana: BILA 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. mappings: biocontext: BILA fairsharing: FAIRsharing.eqgjeq obofoundry: BILA name: Bilateria anatomy preferred_prefix: BILA uri_format: http://purl.obolibrary.org/obo/BILA_$1 bindingdb: description: BindingDB is the first public database of protein-small molecule affinity data. example: e999 homepage: https://www.bindingdb.org mappings: biocontext: BINDINGDB fairsharing: FAIRsharing.3b36hk miriam: bindingdb n2t: bindingdb prefixcommons: bindingdb uniprot: BindingDB name: BindingDB pattern: ^\w\d+$ preferred_prefix: bindingdb 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/$1 biocyc: description: BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. example: ECOLI:CYT-D-UBIOX-CPLX homepage: http://biocyc.org mappings: biocontext: BIOCYC go: BioCyc miriam: biocyc n2t: biocyc prefixcommons: biocyc uniprot: BioCyc name: BioCyc collection of metabolic pathway databases pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$ preferred_prefix: biocyc uri_format: http://biocyc.org/getid?id=$1 biogrid: description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. example: '31623' homepage: http://thebiogrid.org/ mappings: biocontext: BIOGRID fairsharing: FAIRsharing.9d5f5r miriam: biogrid n2t: biogrid prefixcommons: biogrid uniprot: BioGRID name: BioGRID pattern: ^\d+$ preferred_prefix: biogrid uri_format: http://thebiogrid.org/$1 biogrid.interaction: contact: email: md.tyers@umontreal.ca github: null name: Mike Tyers orcid: 0000-0002-9713-9994 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. example: '2649230' homepage: https://thebiogrid.org/ name: BioGRID Interactions part_of: biogrid pattern: ^\d+$ preferred_prefix: biogrid.interaction 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=$1 biolink: description: A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations. example: Gene homepage: https://biolink.github.io/biolink-model/ mappings: biolink: biolink bioportal: BIOLINK fairsharing: FAIRsharing.ad9d85 miriam: biolink name: Biolink Model pattern: ^\S+$ 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/$1 biomodels.db: description: BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. example: BIOMD0000000048 homepage: https://www.ebi.ac.uk/biomodels/ mappings: biocontext: BIOMODELS.DB go: BIOMD miriam: biomodels.db n2t: biomodels.db name: BioModels Database pattern: ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ 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 synonyms: - BIOMD uri_format: https://www.ebi.ac.uk/biomodels/$1 biomodels.kisao: banana: KISAO contact: email: jonrkarr@gmail.com github: jonrkarr name: Jonathan Karr orcid: 0000-0002-2605-5080 description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment. download_owl: http://purl.obolibrary.org/obo/kisao.owl example: KISAO_0000057 homepage: https://github.com/SED-ML/KiSAO license: Artistic License 2.0 mappings: biocontext: KISAO bioportal: KISAO fairsharing: FAIRsharing.jcg19w miriam: biomodels.kisao n2t: biomodels.kisao obofoundry: KISAO ols: kisao ontobee: KISAO prefixcommons: kisao name: Kinetic Simulation Algorithm Ontology pattern: ^KISAO_\d+$ preferred_prefix: biomodels.kisao repository: https://github.com/SED-ML/KiSAO synonyms: - kisao uri_format: http://purl.obolibrary.org/obo/KISAO_$1 version: '2.30' biomodels.teddy: description: The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. download_owl: http://svn.code.sf.net/p/teddyontology/code/teddy/tags/current/teddy-inferred.owl example: '0000066' homepage: http://teddyontology.sourceforge.net/ mappings: biocontext: BIOMODELS.TEDDY bioportal: TEDDY fairsharing: FAIRsharing.w9jvbt miriam: biomodels.teddy n2t: biomodels.teddy ols: teddy prefixcommons: teddy name: Terminology for Description of Dynamics pattern: ^\d+$ preferred_prefix: biomodels.teddy 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#$1 bionumbers: description: BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data. example: '104674' homepage: https://bionumbers.hms.harvard.edu mappings: biocontext: BIONUMBERS miriam: bionumbers n2t: bionumbers prefixcommons: bionumbers name: BioNumbers pattern: ^\d+$ preferred_prefix: bionumbers uri_format: https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1 bioportal: description: BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. example: '1046' homepage: http://bioportal.bioontology.org/ mappings: biocontext: BIOPORTAL fairsharing: FAIRsharing.4m97ah miriam: bioportal n2t: bioportal prefixcommons: bioportal name: BioPortal pattern: ^\d+$ preferred_prefix: bioportal uri_format: http://bioportal.bioontology.org/ontologies/$1 bioproject: description: BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories. example: PRJDB3 homepage: http://trace.ddbj.nig.ac.jp/bioproject/ mappings: biocontext: BIOPROJECT fairsharing: FAIRsharing.aqhv1y miriam: bioproject n2t: bioproject name: BioProject pattern: ^PRJ[DEN][A-Z]\d+$ preferred_prefix: bioproject providers: - code: ncbi description: BioProject at NCBI homepage: https://www.ncbi.nlm.nih.gov/bioproject name: BioProject at NCBI uri_format: https://www.ncbi.nlm.nih.gov/bioproject?term=$1 - code: 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 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 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/#$1 biorxiv: description: The bioRxiv is a preprint server for biology example: 2021.07.23.453588 example_extras: - 000091 - 000091v1 - 2022.01.24.477526v1 homepage: https://biorxiv.org mappings: go: bioRxiv scholia: biorxiv name: bioRxiv pattern: ^(\d{4}\.\d{2}\.\d{2}\.)?\d{6,8}(v\d{1,3})?$ preferred_prefix: biorxiv uri_format: https://www.biorxiv.org/content/10.1101/$1 biosample: description: The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation. example: SAMEA2397676 homepage: https://www.ebi.ac.uk/biosamples/ mappings: biocontext: BIOSAMPLE cellosaurus: BioSamples fairsharing: FAIRsharing.qr6pqk miriam: biosample n2t: biosample name: BioSample pattern: ^SAM[NED](\w)?\d+$ preferred_prefix: biosample providers: - 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 - 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 synonyms: - biosamples uri_format: https://www.ebi.ac.uk/biosamples/sample/$1 biosimulations: description: BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools. example: Yeast-cell-cycle-Irons-J-Theor-Biol-2009 homepage: https://icahn.mssm.edu/ mappings: miriam: biosimulations name: biosimulations pattern: ^[a-zA-Z0-9_-]{3,}$ preferred_prefix: biosimulations uri_format: https://biosimulations.org/projects/$1 biosimulators: description: BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML). example: vcell homepage: https://biosimulators.org/ mappings: fairsharing: FAIRsharing.pwEima miriam: biosimulators name: BioSimulators pattern: ^[a-zA-Z0-9-_]+$ preferred_prefix: biosimulators uri_format: https://biosimulators.org/simulators/$1 biostudies: description: The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication. example: S-EPMC6266652 homepage: https://www.ebi.ac.uk/biostudies/ mappings: fairsharing: FAIRsharing.mtjvme miriam: biostudies n2t: biostudies name: BioStudies database pattern: ^S-[A-Z]{4}[A-Z\d\-]+$ 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 uri_format: https://www.ncbi.nlm.nih.gov/biosystems/$1 biotools: description: BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research. example: uniprotkb homepage: https://bio.tools/ mappings: biocontext: BIOTOOLS fairsharing: FAIRsharing.63520c miriam: biotools n2t: biotools name: BioTools pattern: ^[-A-Za-z0-9\_]*$ 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/$1 birnlex: comment: Part of the NeuroLex namespace now description: The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. example: birnlex_2023 homepage: https://bioportal.bioontology.org/ontologies/BIRNLEX mappings: bioportal: BIRNLEX fairsharing: FAIRsharing.jedbbt name: Biomedical Informatics Research Network Lexicon preferred_prefix: birnlex bitbucket: description: Bitbucket is a Git-based source code repository hosting service owned by Atlassian. example: andreadega/systems-biology-compiler homepage: https://www.atlassian.com/ mappings: fairsharing: FAIRsharing.fc3431 miriam: bitbucket name: Bitbucket pattern: ^[0-9A-Za-z-_\.]+/[0-9A-Za-z-_\.]+$ 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=$1 bko: comment: This resource also uses SBO terms and resolves them, e.g., http://www.sbgnbricks.org/BKO/full/entry/all/SBO:0000177/. contact: email: adrienrougny@gmail.com github: adrienrougny name: Adrien Rougny orcid: 0000-0002-2118-035X contributor: email: null github: bgyori name: Benjamin Gyori orcid: 0000-0001-9439-5346 description: SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way. example: '0000204' homepage: http://www.sbgnbricks.org/ mappings: bioportal: BKO name: SBGN Bricks data and ontology pattern: ^\d+$ 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=$1 bold.taxonomy: description: The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information. example: '27267' homepage: http://www.boldsystems.org/ mappings: biocontext: BOLD.TAXONOMY miriam: bold.taxonomy n2t: bold.taxonomy ncbi: BOLD name: Barcode of Life database pattern: ^\d+$ preferred_prefix: bold.taxonomy uri_format: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1 bootstrep: banana: 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/$1.htm brenda: description: BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. example: 1.1.1.1 homepage: https://www.brenda-enzymes.org/ mappings: biocontext: BRENDA fairsharing: FAIRsharing.etp533 go: BRENDA miriam: brenda n2t: brenda prefixcommons: brenda uniprot: BRENDA name: BRENDA, The Comprehensive Enzyme Information System pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ preferred_prefix: brenda 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 bspo: appears_in: - aism - colao - fovt - lepao - zp banana: BSPO 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_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: biocontext: BSPO bioportal: BSPO fairsharing: FAIRsharing.newa3z obofoundry: BSPO ols: bspo ontobee: BSPO name: Biological Spatial Ontology pattern: ^\d{7}$ preferred_prefix: BSPO repository: https://github.com/obophenotype/biological-spatial-ontology uri_format: http://purl.obolibrary.org/obo/BSPO_$1 version: '2021-10-13' bto: banana: BTO contact: email: c.dudek@tu-braunschweig.de github: chdudek name: Christian-Alexander Dudek orcid: 0000-0001-9117-7909 description: The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. download_json: http://purl.obolibrary.org/obo/bto.json download_obo: http://purl.obolibrary.org/obo/bto.obo download_owl: http://purl.obolibrary.org/obo/bto.owl example: 0000590 homepage: http://www.brenda-enzymes.org license: CC BY 4.0 mappings: biocontext: BTO bioportal: BTO cellosaurus: BTO fairsharing: FAIRsharing.1414v8 go: BTO miriam: bto n2t: bto obofoundry: BTO ols: bto ontobee: BTO prefixcommons: bto wikidata: P5501 name: BRENDA tissue / enzyme source namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: BTO 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 uri_format: https://bykdb.ibcp.fr/data/html/annotated/$1.html cabri: description: CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it. example: dsmz_mutz-id:ACC 291 homepage: http://www.cabri.org/ mappings: biocontext: CABRI fairsharing: FAIRsharing.qx2rvz miriam: cabri n2t: cabri ncbi: CABRI name: Common Access to Biological Resources and Information Project pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$ 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=$1] caloha: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins. download_obo: https://download.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo example: TS-0001 homepage: https://github.com/calipho-sib/controlled-vocabulary name: CALIPHO Group Ontology of Human Anatomy pattern: ^TS-\d+$ preferred_prefix: caloha references: - https://twitter.com/neXtProt_news/status/1350105997633867781 repository: https://github.com/calipho-sib/controlled-vocabulary 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=$1 caro: appears_in: - aism - colao - ehdaa2 - lepao - pco banana: CARO contact: email: haendel@ohsu.edu github: mellybelly name: Melissa Haendel orcid: 0000-0001-9114-8737 description: None download_owl: http://purl.obolibrary.org/obo/caro.owl example: '0000000' homepage: https://github.com/obophenotype/caro/ license: CC BY 3.0 mappings: biocontext: CARO bioportal: CARO fairsharing: FAIRsharing.3kcgmr go: CARO obofoundry: CARO ols: caro ontobee: CARO name: Common Anatomy Reference Ontology pattern: ^\d{7}$ preferred_prefix: CARO repository: https://github.com/obophenotype/caro uri_format: http://purl.obolibrary.org/obo/CARO_$1 version: '2022-02-18' cas: description: CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information. example: 50-00-0 homepage: https://commonchemistry.cas.org/ mappings: biocontext: CAS cheminf: '000446' fairsharing: FAIRsharing.r7Kwy7 go: CAS miriam: cas n2t: cas prefixcommons: cas scholia: cas wikidata: P231 name: CAS Chemical Registry pattern: ^\d{1,7}\-\d{2}\-\d$ 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=$1 casspc: comment: Jim Balhoff said that Catalog of Fishes does not publish their data in a machine readable format, but a long time ago they sent a CSV dump to help in the development of TTO and VTO. These ontologies are effectively retired and CASSPC terms are only also used in Phenoscape. contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 deprecated: true example: '5359' homepage: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp mappings: go: CASSPC name: Eschmeyer's Catalog of Fishes pattern: ^\d+$ preferred_prefix: casspc uri_format: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1 cath: description: CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence. example: 1.10.8.10 homepage: http://www.cathdb.info mappings: biocontext: CATH fairsharing: FAIRsharing.xgcyyn miriam: cath n2t: cath prefixcommons: cath name: CATH Protein Structural Domain Superfamily pattern: ^[1-6]\.[0-9]+\.[0-9]+\.[0-9]+$ preferred_prefix: cath uri_format: http://www.cathdb.info/cathnode/$1 cath.domain: description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains. example: 1cukA01 homepage: http://www.cathdb.info/ mappings: biocontext: CATH.DOMAIN miriam: cath.domain n2t: cath.domain name: CATH domain pattern: ^\w+$ 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 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 uri_format: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1 ccle: 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=$1 cco: banana: CCO description: The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process. download_obo: https://www.bio.ntnu.no/ontology/CCO/cco.obo download_owl: https://www.bio.ntnu.no/ontology/CCO/cco.owl example: '0000003' homepage: http://www.semantic-systems-biology.org/apo mappings: biocontext: CCO bioportal: CCO fairsharing: FAIRsharing.xhwrnr miriam: cco n2t: cco ols: cco prefixcommons: cco name: Cell Cycle Ontology namespace_in_lui: true pattern: ^\w+$ preferred_prefix: cco 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=$1 cdao: banana: CDAO contact: email: balhoff@renci.org github: balhoff name: Jim Balhoff orcid: 0000-0002-8688-6599 description: The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character. download_owl: http://purl.obolibrary.org/obo/cdao.owl example: '0000072' homepage: https://github.com/evoinfo/cdao license: CC0 1.0 mappings: biocontext: CDAO bioportal: CDAO fairsharing: FAIRsharing.kay31r obofoundry: CDAO ols: cdao ontobee: CDAO name: Comparative Data Analysis Ontology pattern: ^\d{7}$ preferred_prefix: CDAO repository: https://github.com/evoinfo/cdao uri_format: http://purl.obolibrary.org/obo/CDAO_$1 version: '2019-06-26' cdd: description: The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. example: cd00400 homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd mappings: biocontext: CDD fairsharing: FAIRsharing.ea287c go: CDD miriam: cdd n2t: cdd ncbi: CDD prefixcommons: cdd uniprot: CDD name: Conserved Domain Database at NCBI pattern: ^(cd)?\d{5}$ preferred_prefix: cdd uri_format: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 cdno: banana: CDNO contact: email: l.andres.hernandez.18@student.scu.edu.au github: LilyAndres name: Liliana Andres Hernandez orcid: 0000-0002-7696-731X depends_on: - bfo - chebi - envo - pato - ro description: None download_obo: http://purl.obolibrary.org/obo/cdno.obo download_owl: http://purl.obolibrary.org/obo/cdno.owl example: '0000013' homepage: https://cdno.info/ license: CC BY 3.0 mappings: bioportal: CDNO obofoundry: CDNO ols: cdno ontobee: CDNO name: Compositional Dietary Nutrition Ontology pattern: ^\d{7}$ preferred_prefix: CDNO repository: https://github.com/Southern-Cross-Plant-Science/cdno uri_format: http://purl.obolibrary.org/obo/CDNO_$1 version: '2022-04-06' cdpd: description: The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN). example: '63250' homepage: http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp mappings: biocontext: CDPD miriam: cdpd n2t: cdpd name: Canadian Drug Product Database pattern: ^\d+$ preferred_prefix: cdpd uri_format: http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1 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 preferred_prefix: cellopub uri_format: https://web.expasy.org/cellosaurus/cellopub/$1 cellosaurus: description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.' download_obo: https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo example: CVCL_0440 homepage: https://web.expasy.org/cellosaurus/ mappings: biocontext: CELLOSAURUS cellosaurus: Cellosaurus fairsharing: FAIRsharing.hkk309 miriam: cellosaurus n2t: cellosaurus wikidata: P3289 name: Cellosaurus pattern: ^CVCL_[A-Z0-9]{4}$ preferred_prefix: cellosaurus synonyms: - CVCL uri_format: https://web.expasy.org/cellosaurus/$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/$1 ceph: banana: CEPH contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: An anatomical and developmental ontology for cephalopods download_obo: https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo download_owl: http://purl.obolibrary.org/obo/ceph.owl example: 0000109 homepage: https://github.com/obophenotype/cephalopod-ontology license: CC BY 3.0 mappings: biocontext: CEPH bioportal: CEPH fairsharing: FAIRsharing.p58bm4 obofoundry: CEPH ols: ceph ontobee: CEPH name: Cephalopod Ontology pattern: ^\d{7}$ 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 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=$1&aid=%t&lang=en cgnc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans) example: '10087' homepage: http://birdgenenames.org/cgnc/ mappings: prefixcommons: cgnc name: Chicken Gene Nomenclature Consortium pattern: ^\d+$ preferred_prefix: cgnc 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/$1 chebi: appears_in: - cdno - chiro - cl - ecocore - ecto - envo - fobi - foodon - genepio - maxo - mco - ons - pcl - scdo - uberon - xpo banana: CHEBI contact: email: amalik@ebi.ac.uk github: amalik01 name: Adnan Malik orcid: 0000-0001-8123-5351 description: Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. download_obo: http://purl.obolibrary.org/obo/chebi.obo download_owl: http://purl.obolibrary.org/obo/chebi.owl example: '24867' homepage: http://www.ebi.ac.uk/chebi license: CC BY 4.0 mappings: biocontext: CHEBI bioportal: CHEBI cellosaurus: ChEBI cheminf: '000407' fairsharing: FAIRsharing.62qk8w go: CHEBI miriam: chebi n2t: chebi obofoundry: CHEBI ols: chebi ontobee: CHEBI prefixcommons: chebi wikidata: P683 name: Chemical Entities of Biological Interest namespace_in_lui: true pattern: ^\d+$ 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 repository: https://github.com/ebi-chebi/ChEBI synonyms: - CHEBI - CHEBIID - ChEBI uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1 version: '210' chembl: description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. example: CHEMBL4303805 homepage: https://www.ebi.ac.uk/chembl mappings: cheminf: '000412' fairsharing: FAIRsharing.m3jtpg miriam: chembl prefixcommons: chembl uniprot: ChEMBL name: ChEMBL pattern: ^CHEMBL\d+$ 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/$1 chembl.compound: description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. example: CHEMBL465070 homepage: https://www.ebi.ac.uk/chembldb/ mappings: biocontext: CHEMBL.COMPOUND miriam: chembl.compound n2t: chembl.compound wikidata: P592 name: ChEMBL part_of: chembl pattern: ^CHEMBL\d+$ 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 uri_format: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1 chemidplus: description: ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. example: 57-27-2 homepage: https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp mappings: biocontext: CHEMIDPLUS fairsharing: FAIRsharing.5949vn miriam: chemidplus n2t: chemidplus prefixcommons: chemidplus name: ChemIDplus pattern: ^\d+\-\d+\-\d+$ preferred_prefix: chemidplus synonyms: - ChemIDplus uri_format: https://chem.nlm.nih.gov/chemidplus/rn/$1 cheminf: banana: CHEMINF contact: email: egon.willighagen@gmail.com github: egonw name: Egon Willighagen orcid: 0000-0001-7542-0286 description: Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. download_owl: https://github.com/semanticchemistry/semanticchemistry/raw/master/ontology/cheminf.owl example: '000410' homepage: https://github.com/semanticchemistry/semanticchemistry license: CC BY 4.0 mappings: biocontext: CHEMINF bioportal: CHEMINF fairsharing: FAIRsharing.sjhvyy obofoundry: CHEMINF ols: cheminf ontobee: CHEMINF name: Chemical Information Ontology pattern: ^\d{6}$ preferred_prefix: CHEMINF repository: https://github.com/semanticchemistry/semanticchemistry uri_format: http://purl.obolibrary.org/obo/CHEMINF_$1 version: '2.0' chemspider: description: ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources. example: '56586' homepage: http://www.chemspider.com/ mappings: biocontext: CHEMSPIDER cheminf: '000405' fairsharing: FAIRsharing.96f3gm miriam: chemspider n2t: chemspider prefixcommons: chemspider wikidata: P661 name: ChemSpider pattern: ^\d+$ 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: banana: 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: bioportal: CHIRO obofoundry: CHIRO ols: chiro ontobee: CHIRO name: ChEBI Integrated Role Ontology no_own_terms: true preferred_prefix: CHIRO repository: https://github.com/obophenotype/chiro uri_format: http://purl.obolibrary.org/obo/CHIRO_$1 version: '2015-11-23' chmo: appears_in: - rbo - scdo banana: CHMO contact: email: batchelorc@rsc.org github: batchelorc name: Colin Batchelor orcid: 0000-0001-5985-7429 description: CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI). download_owl: http://purl.obolibrary.org/obo/chmo.owl example: 0002902 homepage: https://github.com/rsc-ontologies/rsc-cmo license: CC BY 4.0 mappings: biocontext: CHMO bioportal: CHMO fairsharing: FAIRsharing.9j4wh2 obofoundry: CHMO ols: chmo ontobee: CHMO name: Chemical Methods Ontology pattern: ^\d{7}$ preferred_prefix: CHMO repository: https://github.com/rsc-ontologies/rsc-cmo uri_format: http://purl.obolibrary.org/obo/CHMO_$1 version: '2022-04-19' cido: banana: CIDO contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment. download_owl: http://purl.obolibrary.org/obo/cido.owl example: '0000005' homepage: https://github.com/cido-ontology/cido license: CC BY 4.0 mappings: bioportal: CIDO fairsharing: FAIRsharing.aVmpKl obofoundry: CIDO ols: cido ontobee: CIDO name: Coronavirus Infectious Disease Ontology pattern: ^\d{7}$ preferred_prefix: CIDO repository: https://github.com/cido-ontology/cido uri_format: http://purl.obolibrary.org/obo/CIDO_$1 version: 1.0.326 cio: banana: CIO contact: email: frederic.bastian@unil.ch github: fbastian name: Frédéric Bastian orcid: 0000-0002-9415-5104 description: An ontology to capture confidence information about annotations. download_obo: http://purl.obolibrary.org/obo/cio.obo download_owl: http://purl.obolibrary.org/obo/cio.owl example: '0000040' homepage: https://github.com/BgeeDB/confidence-information-ontology license: CC0 1.0 mappings: biocontext: CIO bioportal: CIO fairsharing: FAIRsharing.e3t0yw obofoundry: CIO ols: cio ontobee: CIO name: Confidence Information Ontology pattern: ^\d{7}$ preferred_prefix: CIO 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 references: - https://www.embl.de/aboutus/communication_outreach/media_relations/2006/061127_hinxton/ synonyms: - CTX uri_format: https://europepmc.org/article/CTX/$1 civic.aid: description: 'A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC.' example: '3' homepage: https://civicdb.org/ mappings: miriam: civic.aid name: CIViC Assertion pattern: ^[0-9]+$ preferred_prefix: civic.aid uri_format: https://civicdb.org/links/assertions/$1 civic.eid: description: Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract). example: '1199' homepage: https://civicdb.org/ mappings: miriam: civic.eid name: CIViC Evidence pattern: ^[0-9]+$ preferred_prefix: civic.eid uri_format: https://civicdb.org/links/evidence/$1 cl: appears_in: - clo - ecao - ehdaa2 - go - mco - pcl - uberon - xpo banana: CL contact: email: addiehl@buffalo.edu github: addiehl name: Alexander Diehl orcid: 0000-0001-9990-8331 depends_on: - chebi - go - ncbitaxon - pato - pr - ro - uberon description: The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi. download_obo: https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-full.obo download_owl: http://purl.obolibrary.org/obo/cl.owl example: '0000062' homepage: https://obophenotype.github.io/cell-ontology/ license: CC BY 4.0 mappings: biocontext: CL bioportal: CL cellosaurus: CL fairsharing: FAIRsharing.j9y503 go: CL miriam: cl n2t: cl obofoundry: CL ols: cl ontobee: CL prefixcommons: cl wikidata: P7963 name: Cell Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: CL repository: https://github.com/obophenotype/cell-ontology uri_format: https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:$1 version: '2022-02-16' clao: banana: CLAO contact: email: lagonzalezmo@unal.edu.co github: luis-gonzalez-m name: Luis González-Montaña orcid: 0000-0002-9136-9932 depends_on: - ro description: 'CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).' download_obo: http://purl.obolibrary.org/obo/clao.obo download_owl: http://purl.obolibrary.org/obo/clao.owl example: 0000088 homepage: https://github.com/luis-gonzalez-m/Collembola license: CC0 1.0 mappings: bioportal: CLAO obofoundry: CLAO ols: clao ontobee: CLAO name: Collembola Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: CLAO repository: https://github.com/luis-gonzalez-m/Collembola uri_format: http://purl.obolibrary.org/obo/CLAO_$1 version: '2021-09-27' classyfire: description: ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API. example: C0004828 homepage: http://classyfire.wishartlab.com/ mappings: miriam: classyfire name: ClassyFire pattern: ^C[0-9]{7}$ preferred_prefix: classyfire uri_format: http://classyfire.wishartlab.com/tax_nodes/$1 cldb: description: The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories. example: cl3603 homepage: http://bioinformatics.hsanmartino.it/hypercldb/indexes.html mappings: biocontext: CLDB cellosaurus: CLDB miriam: cldb n2t: cldb name: Cell Line Database pattern: ^(cl|tum)\d+$ preferred_prefix: cldb uri_format: http://bioinformatics.hsanmartino.it/hypercldb/$1.html clingene: 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 uri_format: https://clinicaltrials.gov/ct2/show/$1 clinvar: description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier. example: '12345' homepage: http://www.ncbi.nlm.nih.gov/clinvar/ mappings: biocontext: ClinVar biolink: CLINVAR cellosaurus: ClinVar fairsharing: FAIRsharing.wx5r6f miriam: clinvar n2t: clinvar wikidata: P1929 name: ClinVar Variation pattern: ^\d+$ preferred_prefix: clinvar uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1 clinvar.record: description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession. example: RCV000033555.3 homepage: http://www.ncbi.nlm.nih.gov/clinvar/ mappings: biocontext: CLINVAR.RECORD miriam: clinvar.record n2t: clinvar.record name: ClinVar Record pattern: ^RCV\d+(\.\d+)?$ 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/$1 clo: appears_in: - mco banana: CLO contact: email: siiraa@umich.edu github: siiraa name: Sirarat Sarntivijai orcid: 0000-0002-2548-641X depends_on: - cl - doid - ncbitaxon - uberon description: The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns. download_owl: http://purl.obolibrary.org/obo/clo.owl example: 0000091 homepage: http://www.clo-ontology.org license: CC BY 3.0 mappings: biocontext: CLO bioportal: CLO cellosaurus: CLO fairsharing: FAIRsharing.4dvtcz obofoundry: CLO ols: clo ontobee: CLO prefixcommons: clo wikidata: P2158 name: Cell Line Ontology pattern: ^\d{7}$ preferred_prefix: CLO 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://www.clsgmbh.de/$1.html clyh: banana: CLYH contact: email: lucas.leclere@obs-vlfr.fr github: L-Leclere name: Lucas Leclere orcid: 0000-0002-7440-0467 depends_on: - iao - ro - uberon description: Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica. download_obo: http://purl.obolibrary.org/obo/clyh.obo download_owl: http://purl.obolibrary.org/obo/clyh.owl example: '1000100' homepage: https://github.com/EBISPOT/clyh_ontology license: CC BY 3.0 mappings: bioportal: CLYH obofoundry: CLYH ols: clyh ontobee: CLYH name: Clytia hemisphaerica Development and Anatomy Ontology pattern: ^\d+$ 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: banana: 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: biocontext: CMF obofoundry: CMF ontobee: CMF name: CranioMaxilloFacial ontology preferred_prefix: CMF uri_format: http://purl.obolibrary.org/obo/CMF_$1 cmo: appears_in: - scdo banana: CMO contact: email: jrsmith@mcw.edu github: jrsjrs name: Jennifer Smith orcid: 0000-0002-6443-9376 description: Morphological and physiological measurement records generated from clinical and model organism research and health programs. download_obo: http://purl.obolibrary.org/obo/cmo.obo download_owl: http://purl.obolibrary.org/obo/cmo.owl example: '0001350' homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html license: CC0 1.0 mappings: biocontext: CMO bioportal: CMO fairsharing: FAIRsharing.dq78pn obofoundry: CMO ols: cmo ontobee: CMO name: Clinical measurement ontology pattern: ^\d{7}$ preferred_prefix: CMO repository: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology uri_format: http://purl.obolibrary.org/obo/CMO_$1 version: '2019-02-19' cmpo: description: CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. download_owl: http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl example: '0000435' homepage: http://www.ebi.ac.uk/cmpo mappings: bioportal: CMPO fairsharing: FAIRsharing.knp11s ols: cmpo name: Cellular Microscopy Phenotype Ontology pattern: ^\d{7}$ preferred_prefix: cmpo 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: 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:$1 version: '2019-10-09' co_321: description: July 2018 download_owl: https://cropontology.org/ontology/CO_321/Wheat/owl example: 0000449 homepage: https://cropontology.org/ontology/CO_321/Wheat mappings: fairsharing: FAIRsharing.czzmpg ols: co_321 name: Wheat ontology pattern: ^\d{7}$ preferred_prefix: co_321 uri_format: https://www.cropontology.org/rdf/CO_321:$1 version: '2019-10-09' co_322: description: Maize Trait Dictionary in template 5 - CIMMYT- September 2016 download_owl: https://cropontology.org/ontology/CO_322/Maize/owl example: '0000773' homepage: https://cropontology.org/ontology/CO_322/Maize mappings: fairsharing: FAIRsharing.eeyne8 ols: co_322 name: Maize ontology pattern: ^\d{7}$ preferred_prefix: co_322 uri_format: https://www.cropontology.org/rdf/CO_322:$1 version: '2019-10-09' co_323: description: ICARDA - TDv5 - Sept 2018 download_owl: https://cropontology.org/ontology/CO_323/Barley/owl example: '0000252' homepage: https://cropontology.org/ontology/CO_323/Barley mappings: fairsharing: FAIRsharing.f69084 ols: co_323 name: Barley ontology pattern: ^\d{7}$ preferred_prefix: co_323 uri_format: https://www.cropontology.org/rdf/CO_323:$1 version: '2019-11-20' co_324: description: Sorghum TDv5 - Oct 2019 download_owl: https://cropontology.org/ontology/CO_324/Sorghum/owl example: '0000111' homepage: https://cropontology.org/ontology/CO_324/Sorghum mappings: fairsharing: FAIRsharing.dxx0c ols: co_324 name: Sorghum ontology pattern: ^\d{7}$ preferred_prefix: co_324 uri_format: https://www.cropontology.org/rdf/CO_324:$1 version: '2019-10-09' co_325: description: Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019 download_owl: https://cropontology.org/ontology/CO_325/Banana/owl example: 0000519 homepage: https://cropontology.org/ontology/CO_325/Banana mappings: fairsharing: FAIRsharing.gdszhh ols: co_325 name: Banana ontology pattern: ^\d{7}$ preferred_prefix: co_325 uri_format: https://www.cropontology.org/rdf/CO_325:$1 version: '2019-10-09' co_326: description: Draft version download_owl: https://cropontology.org/ontology/CO_326/Coconut/owl example: '0000254' homepage: https://cropontology.org/ontology/CO_326/Coconut mappings: ols: co_326 name: Coconut ontology pattern: ^\d{7}$ preferred_prefix: co_326 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: 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:$1 co_330: description: CIP - potato ontology - december 2018 download_owl: https://cropontology.org/ontology/CO_330/Potato/owl example: '0000106' homepage: https://cropontology.org/ontology/CO_330/Potato mappings: fairsharing: FAIRsharing.4fa657 ols: co_330 name: Potato ontology pattern: ^\d{7}$ preferred_prefix: co_330 uri_format: https://www.cropontology.org/rdf/CO_330:$1 version: '2019-10-09' co_331: description: Sweet Potato Trait Dictionary in template v5 - CIP - November 2019 download_owl: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato/owl example: 0000088 homepage: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato mappings: fairsharing: FAIRsharing.4g5qcw ols: co_331 name: Sweet Potato ontology pattern: ^\d{7}$ preferred_prefix: co_331 uri_format: https://www.cropontology.org/rdf/CO_331:$1 co_333: description: 'This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017.' download_owl: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology/owl example: '3000045' homepage: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology mappings: fairsharing: FAIRsharing.af5655 ols: co_333 name: Beet Ontology ontology pattern: ^\d+$ preferred_prefix: co_333 uri_format: https://www.cropontology.org/rdf/CO_333:$1 co_334: description: Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016 download_owl: https://cropontology.org/ontology/CO_334/Cassava/owl example: '0000070' homepage: https://cropontology.org/ontology/CO_334/Cassava mappings: fairsharing: FAIRsharing.v06c4q ols: co_334 name: Cassava ontology pattern: ^\d{7}$ preferred_prefix: co_334 uri_format: https://www.cropontology.org/rdf/CO_334:$1 version: '2019-10-09' co_335: description: CIAT Common bean trait dictionary - version August 2014 download_owl: http://www.cropontology.org/ontology/CO_335/Common%20Bean/owl example: 0000189 homepage: http://www.cropontology.org/ontology/CO_335/Common%20Bean mappings: fairsharing: FAIRsharing.a14123 ols: co_335 name: Common Bean ontology pattern: ^\d{7}$ preferred_prefix: co_335 uri_format: https://www.cropontology.org/rdf/CO_335:$1 co_336: description: Soybean Trait Dictionary in template v5 - IITA - July 2015 download_owl: https://cropontology.org/ontology/CO_336/Soybean/owl example: 0000339 homepage: https://cropontology.org/ontology/CO_336/Soybean mappings: fairsharing: FAIRsharing.j75srj ols: co_336 name: Soybean ontology pattern: ^\d{7}$ preferred_prefix: co_336 uri_format: https://www.cropontology.org/rdf/CO_336:$1 co_337: description: Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015 download_owl: https://cropontology.org/ontology/CO_337/Groundnut/owl example: '0000054' homepage: https://cropontology.org/ontology/CO_337/Groundnut mappings: fairsharing: FAIRsharing.ge8y23 ols: co_337 name: Groundnut ontology pattern: ^\d{7}$ preferred_prefix: co_337 uri_format: https://www.cropontology.org/rdf/CO_337:$1 version: '2019-10-09' co_338: description: Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015 download_owl: https://cropontology.org/ontology/CO_338/Chickpea/owl example: 0000138 homepage: https://cropontology.org/ontology/CO_338/Chickpea mappings: fairsharing: FAIRsharing.js20q3 ols: co_338 name: Chickpea ontology pattern: ^\d{7}$ preferred_prefix: co_338 uri_format: https://www.cropontology.org/rdf/CO_338:$1 version: '2019-10-09' co_339: description: Lentil Trait Dictionary in template v5 - ICARDA - July 2015 download_owl: https://cropontology.org/ontology/CO_339/Lentil/owl example: '0000032' homepage: https://cropontology.org/ontology/CO_339/Lentil mappings: fairsharing: FAIRsharing.ry1ezg ols: co_339 name: Lentil ontology pattern: ^\d{7}$ preferred_prefix: co_339 uri_format: https://www.cropontology.org/rdf/CO_339:$1 version: '2019-10-09' co_340: description: Cowpea Trait Dictionary in template v5 - IITA - August 2015 download_owl: https://cropontology.org/ontology/CO_340/Cowpea/owl example: 0000639 homepage: https://cropontology.org/ontology/CO_340/Cowpea mappings: fairsharing: FAIRsharing.31apg2 ols: co_340 name: Cowpea ontology pattern: ^\d{7}$ preferred_prefix: co_340 uri_format: https://www.cropontology.org/rdf/CO_340:$1 version: '2019-10-09' co_341: description: Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015 download_owl: https://cropontology.org/ontology/CO_341/Pigeonpea/owl example: '0000140' homepage: https://cropontology.org/ontology/CO_341/Pigeonpea mappings: fairsharing: FAIRsharing.ehe3yp ols: co_341 name: Pigeonpea ontology pattern: ^\d{7}$ preferred_prefix: co_341 uri_format: https://www.cropontology.org/rdf/CO_341:$1 version: '2019-11-18' co_343: description: version 2019 - pvs download_owl: https://cropontology.org/ontology/CO_343/Yam/owl example: '0100010' homepage: https://cropontology.org/ontology/CO_343/Yam mappings: fairsharing: FAIRsharing.7e9cff ols: co_343 name: Yam ontology pattern: ^\d{7}$ preferred_prefix: co_343 uri_format: https://www.cropontology.org/rdf/CO_343:$1 version: '2019-10-09' co_345: description: Brachiaria (forages) ontology TD v5 - Version Oct 2016 download_owl: https://cropontology.org/ontology/CO_345/Brachiaria/owl example: '0000127' homepage: https://cropontology.org/ontology/CO_345/Brachiaria mappings: fairsharing: FAIRsharing.9e9683 ols: co_345 name: Brachiaria ontology pattern: ^\d{7}$ preferred_prefix: co_345 uri_format: https://www.cropontology.org/rdf/CO_345:$1 version: '2019-10-09' co_346: description: oct 2016 download_owl: https://cropontology.org/ontology/CO_346/Mungbean/owl example: 0000199 homepage: https://cropontology.org/ontology/CO_346/Mungbean mappings: fairsharing: FAIRsharing.fgd5gq ols: co_346 name: Mungbean ontology pattern: ^\d{7}$ preferred_prefix: co_346 uri_format: https://www.cropontology.org/rdf/CO_346:$1 version: '2019-10-09' co_347: description: 'March 2017 version ' download_owl: http://www.cropontology.org/ontology/CO_347/Castor%20bean/owl example: 0000108 homepage: http://www.cropontology.org/ontology/CO_347/Castor%20bean mappings: fairsharing: FAIRsharing.qrrvyk ols: co_347 name: Castor bean ontology pattern: ^\d{7}$ preferred_prefix: co_347 uri_format: https://www.cropontology.org/rdf/CO_347:$1 co_348: description: Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France). download_owl: https://cropontology.org/ontology/CO_348/Brassica/owl example: '1100107' homepage: https://cropontology.org/ontology/CO_348/Brassica mappings: fairsharing: FAIRsharing.af7a2d ols: co_348 name: Brassica ontology pattern: ^\d+$ preferred_prefix: co_348 uri_format: https://www.cropontology.org/rdf/CO_348:$1 version: '2019-11-29' co_350: description: Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo download_owl: https://cropontology.org/ontology/CO_350/Oat/owl example: '0000215' homepage: https://cropontology.org/ontology/CO_350/Oat mappings: fairsharing: FAIRsharing.35e1c3 ols: co_350 name: Oat ontology pattern: ^\d{7}$ preferred_prefix: co_350 uri_format: https://www.cropontology.org/rdf/CO_350:$1 version: '2019-10-09' co_356: description: Grape Ontology including OIV and bioversity descriptors. INRA July 2017 download_owl: https://cropontology.org/ontology/CO_356/Vitis/owl example: '4000027' homepage: https://cropontology.org/ontology/CO_356/Vitis mappings: fairsharing: FAIRsharing.c7f4d7 ols: co_356 name: Vitis ontology pattern: ^\d+$ preferred_prefix: co_356 uri_format: https://www.cropontology.org/rdf/CO_356:$1 version: '2019-11-29' co_357: description: 'This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE.' download_owl: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology/owl example: '1000290' homepage: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology mappings: fairsharing: FAIRsharing.2b04ae ols: co_357 name: Woody Plant Ontology ontology pattern: ^\d+$ preferred_prefix: co_357 uri_format: https://www.cropontology.org/rdf/CO_357:$1 co_358: description: Cotton ontology from CottonGen database - June 2019 download_owl: https://cropontology.org/ontology/CO_358/Cotton/owl example: 0000139 homepage: https://cropontology.org/ontology/CO_358/Cotton mappings: ols: co_358 name: Cotton ontology pattern: ^\d{7}$ preferred_prefix: co_358 uri_format: https://www.cropontology.org/rdf/CO_358:$1 version: '2020-01-03' co_359: description: December 2019 download_owl: https://cropontology.org/ontology/CO_359/Sunflower/owl example: 0000947 homepage: https://cropontology.org/ontology/CO_359/Sunflower mappings: ols: co_359 name: Sunflower ontology pattern: ^\d{7}$ preferred_prefix: co_359 uri_format: https://www.cropontology.org/rdf/CO_359:$1 co_360: description: Sugar Kelp trait ontology download_owl: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait/owl example: '0000071' homepage: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait mappings: fairsharing: FAIRsharing.1c1738 ols: co_360 name: Sugar Kelp trait ontology pattern: ^\d{7}$ preferred_prefix: co_360 uri_format: https://www.cropontology.org/rdf/CO_360:$1 co_365: description: developed by ICARDA - Dec 2018 download_owl: https://cropontology.org/ontology/CO_365/Fababean/owl example: '0000205' homepage: https://cropontology.org/ontology/CO_365/Fababean mappings: ols: co_365 name: Fababean ontology pattern: ^\d{7}$ preferred_prefix: co_365 uri_format: https://www.cropontology.org/rdf/CO_365:$1 version: '2019-10-15' co_366: description: version Dec 2019 download_owl: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut/owl example: '0000072' homepage: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut mappings: ols: co_366 name: Bambara groundnut ontology pattern: ^\d{7}$ preferred_prefix: co_366 uri_format: https://www.cropontology.org/rdf/CO_366:$1 cob: banana: COB contact: email: bpeters@lji.org github: bpeters42 name: Bjoern Peters orcid: 0000-0002-8457-6693 description: COB brings together key terms from a wide range of OBO projects to improve interoperability. download_owl: http://purl.obolibrary.org/obo/cob.owl example: 0000080 homepage: https://github.com/OBOFoundry/COB license: CC0 1.0 mappings: bioportal: COB obofoundry: COB ols: cob ontobee: COB name: Core Ontology for Biology and Biomedicine pattern: ^\d{7}$ preferred_prefix: COB repository: https://github.com/OBOFoundry/COB uri_format: http://purl.obolibrary.org/obo/COB_$1 version: '2022-05-02' coconut: comment: '@mSorok is the dev of the resource, hope I got it right!' contributor: email: null github: adafede name: Adriano Rutz orcid: 0000-0003-0443-9902 description: COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a "flat" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties. example: CNP0171505 homepage: https://coconut.naturalproducts.net name: COlleCtion of Open Natural ProdUcTs pattern: ^CNP\d{7}$ 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 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 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/$1 cohd: comment: not really sure where the source is. this also links to a system called athena. I was not able to figure out what COHD stands for. contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012 homepage: https://github.com/MIT-LCP/mimic-omop name: MIMIC III Database no_own_terms: true preferred_prefix: cohd repository: https://github.com/MIT-LCP/mimic-omop colao: banana: COLAO contact: email: entiminae@gmail.com github: JCGiron name: Jennifer C. Giron orcid: 0000-0002-0851-6883 depends_on: - aism - bfo - bspo - caro - pato - ro - uberon description: The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. download_obo: http://purl.obolibrary.org/obo/colao.obo download_owl: http://purl.obolibrary.org/obo/colao.owl example: '0000000' homepage: https://github.com/insect-morphology/colao license: CC BY 4.0 mappings: bioportal: COLAO obofoundry: COLAO ols: colao ontobee: COLAO name: Coleoptera Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: COLAO repository: https://github.com/insect-morphology/colao uri_format: http://purl.obolibrary.org/obo/COLAO_$1 version: '2021-12-14' 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=$1 complexportal: description: A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases. example: CPX-263 homepage: https://www.ebi.ac.uk/complexportal mappings: biocontext: COMPLEXPORTAL go: ComplexPortal miriam: complexportal n2t: complexportal uniprot: ComplexPortal wikidata: P7718 name: Complex Portal pattern: ^CPX-[0-9]+$ 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=$1 conoserver: description: ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails. example: '2639' homepage: http://www.conoserver.org/ mappings: biocontext: CONOSERVER fairsharing: FAIRsharing.y00hz4 miriam: conoserver n2t: conoserver uniprot: ConoServer name: ConoServer pattern: ^\d+$ 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/$1 coriell: description: The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world. example: GM17027 homepage: http://ccr.coriell.org/ mappings: biocontext: Coriell cellosaurus: Coriell go: CORIELL miriam: coriell n2t: coriell name: Coriell Institute for Medical Research pattern: ^[A-Z]{2}\d+$ preferred_prefix: coriell uri_format: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1 corrdb: description: A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies. example: '37232' homepage: https://www.animalgenome.org mappings: fairsharing: FAIRsharing.IziuCK miriam: corrdb name: CorrDB pattern: ^[0-9]+$ 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=$1 cosmic: description: COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes. example: BRAF homepage: http://cancer.sanger.ac.uk/cosmic/ mappings: biocontext: COSMIC cellosaurus: Cosmic fairsharing: FAIRsharing.s5zmbp miriam: cosmic n2t: cosmic name: COSMIC Gene pattern: ^[A-Z0-9]+$ 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=$1 covid19: description: Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease. example: SFB_COVID19_MW286762 homepage: https://covid19.sfb.uit.no mappings: bioportal: COVID-19 miriam: covid19 name: COVID-19 Ontology pattern: ^\w+_COVID19_[-\w]+$ 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 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: banana: GRO contact: email: po-discuss@plantontology.org github: null name: Plant Ontology Administrators orcid: null deprecated: true 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_$1 cpt: contributor: email: null github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 description: Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)] example: '00103' homepage: https://www.aapc.com mappings: biolink: CPT bioportal: CPT fairsharing: FAIRsharing.wpxab1 name: Current Procedural Terminology pattern: ^\d+$ preferred_prefix: cpt references: - https://github.com/biopragmatics/bioregistry/issues/357 - 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 uri_format: https://www.aapc.com/codes/cpt-codes/$1 credit: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output. example: Software homepage: https://casrai.org/credit/ name: CASRAI Contributor Roles Taxonomy preferred_prefix: credit crisprdb: description: Repeated CRISPR ("clustered regularly interspaced short palindromic repeats") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data. example: '551115' homepage: http://crispr.i2bc.paris-saclay.fr/ mappings: biocontext: CRISPRDB fairsharing: FAIRsharing.7sfedh miriam: crisprdb n2t: crisprdb name: CRISPRdb pattern: ^[0-9]+$ preferred_prefix: crisprdb uri_format: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1 cro: banana: CRO contact: email: whimar@ohsu.edu github: marijane name: Marijane White orcid: 0000-0001-5059-4132 description: A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. download_obo: https://raw.githubusercontent.com/data2health/contributor-role-ontology/master/cro.obo download_owl: http://purl.obolibrary.org/obo/cro.owl example: 0000038 homepage: https://github.com/data2health/contributor-role-ontology license: CC BY 2.0 mappings: biocontext: CRO bioportal: CRO obofoundry: CRO ols: cro ontobee: CRO name: Contributor Role Ontology pattern: ^\d{7}$ preferred_prefix: CRO repository: https://github.com/data2health/contributor-role-ontology uri_format: http://purl.obolibrary.org/obo/CRO_$1 version: '2019-12-11' cryoem: description: Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles download_owl: http://scipion.i2pc.es/ontology/cryoem/releases/2021-03-09/cryoem.owl example: '0000052' homepage: http://scipion.i2pc.es/ontology/cryoem mappings: bioportal: CRYOEM ols: cryoem name: Cryo Electron Microscopy ontology pattern: ^\d{7}$ preferred_prefix: cryoem 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 name: CryptoDB pattern: ^\w+$ preferred_prefix: cryptodb 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 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:$1&sid=IDORG csp: deprecated: true example: 2004-2820 homepage: https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm mappings: bioportal: CRISP name: Computer Retrieval of Information on Science Projects Thesaurus preferred_prefix: csp synonyms: - CRISP - CRISP Thesaurus - CRISP Thesaurus, 2006 - CSP2005 cst: description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways. example: Akt_PKB homepage: http://www.cellsignal.com/pathways/index.html mappings: biocontext: CST bioportal: CST fairsharing: FAIRsharing.n8pxvx miriam: cst n2t: cst prefixcommons: cst name: Cancer Staging Terms pattern: ^[A-Za-z0-9_-]+$ preferred_prefix: cst uri_format: http://www.cellsignal.com/reference/pathway/$1.html cst.ab: description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products. example: '3305' homepage: http://www.cellsignal.com/catalog/index.html mappings: biocontext: CST.AB miriam: cst.ab n2t: cst.ab name: Cell Signaling Technology Antibody pattern: ^\d+$ preferred_prefix: cst.ab uri_format: http://www.cellsignal.com/products/$1.html ctd.chemical: description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. example: D001151 homepage: http://ctdbase.org/ mappings: biocontext: CTD.CHEMICAL biolink: CTD.CHEMICAL miriam: ctd.chemical n2t: ctd.chemical name: CTD Chemical part_of: ctd pattern: ^[CD]\d+$ 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=$1 cteno: banana: CTENO contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 depends_on: - ro - uberon description: An anatomical and developmental ontology for ctenophores (Comb Jellies) download_obo: https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo download_owl: http://purl.obolibrary.org/obo/cteno.owl example: '0000047' homepage: https://github.com/obophenotype/ctenophore-ontology license: CC BY 3.0 mappings: biocontext: CTENO bioportal: CTENO fairsharing: FAIRsharing.mgxgza obofoundry: CTENO ols: cteno ontobee: CTENO name: Ctenophore Ontology pattern: ^\d{7}$ preferred_prefix: CTENO repository: https://github.com/obophenotype/ctenophore-ontology uri_format: http://purl.obolibrary.org/obo/CTENO_$1 version: '2016-10-19' cto: banana: CTO contact: email: alpha.tom.kodamullil@scai.fraunhofer.de github: akodamullil name: Dr. Alpha Tom Kodamullil orcid: 0000-0001-9896-3531 description: The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials. download_owl: http://purl.obolibrary.org/obo/cto.owl example: '0000022' homepage: https://github.com/ClinicalTrialOntology/CTO/ license: CC BY 4.0 mappings: bioportal: CTO fairsharing: FAIRsharing.qp211a obofoundry: CTO ols: cto ontobee: CTO name: Clinical Trials Ontology pattern: ^\d{7}$ 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/$1/ cvdo: banana: CVDO contact: email: paul.fabry@usherbrooke.ca github: pfabry name: Paul Fabry orcid: 0000-0002-3336-2476 description: An ontology to describe entities related to cardiovascular diseases download_owl: http://purl.obolibrary.org/obo/cvdo.owl example: '0000546' homepage: https://github.com/OpenLHS/CVDO license: CC BY 4.0 mappings: biocontext: CVDO bioportal: CVDO fairsharing: FAIRsharing.2basyz obofoundry: CVDO ols: cvdo ontobee: CVDO name: Cardiovascular Disease Ontology pattern: ^\d{7}$ preferred_prefix: CVDO repository: https://github.com/OpenLHS/CVDO uri_format: http://purl.obolibrary.org/obo/CVDO_$1 version: '2020-03-05' d1id: description: DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences. example: 00030692-0FE1-4A1B-955E-A2E55D659267 homepage: https://www.dataone.org mappings: biocontext: D1ID miriam: d1id n2t: d1id name: DataONE pattern: ^\S+$ 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=$1 dandi: description: 'DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable). DANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data. These data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.' example: '000017' homepage: https://dandiarchive.org/ mappings: miriam: dandi name: Distributed Archives for Neurophysiology Data Integration pattern: ^\d{6}(\/\d+\.\d+\.\d+)?$ 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#$1#exprPerTissueTable datanator.gene: description: Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. example: K00973 homepage: https://datanator.info/ mappings: miriam: datanator.gene name: Datanator Gene part_of: datanator pattern: ^K[0-9]+$ 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=$1 dbd: description: The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins. example: '0045310' homepage: http://www.transcriptionfactor.org/ mappings: biocontext: DBD miriam: dbd n2t: dbd prefixcommons: dbd name: Transcription Factor Database pattern: ^\d+$ preferred_prefix: dbd uri_format: http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD dbest: description: The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. example: BP100000 homepage: https://www.ncbi.nlm.nih.gov/nucest mappings: biocontext: DBEST fairsharing: FAIRsharing.v9fya8 miriam: dbest n2t: dbest ncbi: dbEST prefixcommons: dbest name: EST database maintained at the NCBI. pattern: ^([A-Z]+)?\d+(\.\d+)?$ preferred_prefix: dbest providers: - code: 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 - 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 uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1 dbg2introns: description: The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. example: Cu.me.I1 homepage: http://webapps2.ucalgary.ca/~groupii/ mappings: biocontext: DBG2INTRONS miriam: dbg2introns n2t: dbg2introns name: DBG2 Introns pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$ preferred_prefix: dbg2introns 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 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 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=$1 dbsnp: description: The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. example: rs121909098 homepage: https://www.ncbi.nlm.nih.gov/snp/ mappings: biocontext: dbSNP cellosaurus: dbSNP fairsharing: FAIRsharing.edxb58 go: dbSNP miriam: dbsnp n2t: dbsnp ncbi: dbSNP prefixcommons: dbsnp uniprot: dbSNP name: NCBI dbSNP pattern: ^rs\d+$ 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 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: description: Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. example: contributor has_canonical: dcterms homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ mappings: biocontext: dc bioportal: DC fairsharing: FAIRsharing.3nx7t name: Dublin Core preferred_prefix: dc uri_format: http://purl.org/dc/terms/$1 dc_cl: banana: DC_CL contact: email: Lindsay.Cowell@utsouthwestern.edu github: null name: Lindsay Cowell orcid: 0000-0003-1617-8244 deprecated: true example: '0000003' homepage: http://www.dukeontologygroup.org/Projects.html mappings: biocontext: DC_CL obofoundry: DC_CL name: Dendritic cell pattern: ^\d{7}$ preferred_prefix: DC_CL uri_format: http://purl.obolibrary.org/obo/DC_CL_$1 dcat: description: DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web example: Dataset homepage: https://www.w3.org/ns/dcat mappings: 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: 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: title homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ mappings: biocontext: dcterms biolink: dct bioportal: DCTERMS fairsharing: FAIRsharing.9vtwjs name: Dublin Core Metadata Vocabulary preferred_prefix: dcterms synonyms: - dc.terms uri_format: http://purl.org/dc/terms/$1 dctypes: 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/$1 ddanat: banana: DDANAT contact: email: pfey@northwestern.edu github: pfey03 name: Petra Fey orcid: 0000-0002-4532-2703 description: A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum download_obo: http://purl.obolibrary.org/obo/ddanat.obo download_owl: http://purl.obolibrary.org/obo/ddanat.owl example: '0000006' homepage: http://dictybase.org/ license: CC0 1.0 mappings: biocontext: DDANAT bioportal: DDANAT fairsharing: FAIRsharing.z656ab go: DDANAT obofoundry: DDANAT ols: ddanat ontobee: DDANAT prefixcommons: ddanat name: Dictyostelium discoideum anatomy pattern: ^\d{7}$ preferred_prefix: DDANAT repository: https://github.com/dictyBase/migration-data uri_format: http://purl.obolibrary.org/obo/DDANAT_$1 version: '2020-04-13' ddpheno: banana: DDPHENO contact: email: pfey@northwestern.edu github: pfey03 name: Petra Fey orcid: 0000-0002-4532-2703 description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. download_obo: https://raw.githubusercontent.com/obophenotype/dicty-phenotype-ontology/master/ddpheno.obo download_owl: http://purl.obolibrary.org/obo/ddpheno.owl example: '0001417' homepage: http://dictybase.org/ license: CC0 1.0 mappings: biocontext: DDPHENO bioportal: DDPHENO fairsharing: FAIRsharing.9c1p18 obofoundry: DDPHENO ols: ddpheno ontobee: DDPHENO name: Dictyostelium discoideum phenotype ontology pattern: ^\d{7}$ preferred_prefix: DDPHENO repository: https://github.com/obophenotype/dicty-phenotype-ontology uri_format: http://purl.obolibrary.org/obo/DDPHENO_$1 version: '2020-06-19' decipher: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms example: '1' homepage: https://www.deciphergenomics.org/ mappings: biocontext: DECIPHER fairsharing: FAIRsharing.l8Sf5x name: DECIPHER CNV Syndromes pattern: ^\d+$ preferred_prefix: decipher references: - https://www.deciphergenomics.org/redirect?to=https%3A%2F%2Fdx.doi.org%2F10.1016%2Fj.ajhg.2009.03.010 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/$1 depmap: description: Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells. example: ACH-000001 homepage: https://depmap.org/portal mappings: cellosaurus: DepMap name: DepMap Cell Lines pattern: ^ACH-\d+$ preferred_prefix: depmap uri_format: https://depmap.org/portal/cell_line/$1 depod: description: The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources. example: PTPN1 homepage: http://www.depod.bioss.uni-freiburg.de mappings: biocontext: DEPOD fairsharing: FAIRsharing.q9j2e3 miriam: depod n2t: depod uniprot: DEPOD name: Human Dephosphorylation Database pattern: ^[A-Z0-9]+$ preferred_prefix: depod provides: hgnc.symbol uri_format: http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1 dermo: description: DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders example: '0000000' homepage: https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x mappings: bioportal: DERMO fairsharing: FAIRsharing.k008w7 name: Human Dermatological Disease Ontology pattern: ^\d{7}$ preferred_prefix: dermo 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 dicom: 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 ols: dicom name: DICOM Controlled Terminology pattern: ^\d+$ preferred_prefix: dicom 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 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:$1 dideo: banana: DIDEO contact: email: mbrochhausen@gmail.com github: mbrochhausen name: Mathias Brochhausen orcid: 0000-0003-1834-3856 description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology download_owl: http://purl.obolibrary.org/obo/dideo.owl example: 00000180 homepage: https://github.com/DIDEO/DIDEO license: CC BY 4.0 mappings: biocontext: DIDEO bioportal: DIDEO fairsharing: FAIRsharing.9y8f0n obofoundry: DIDEO ols: dideo ontobee: DIDEO name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology pattern: ^\d{8}$ preferred_prefix: DIDEO repository: https://github.com/DIDEO/DIDEO uri_format: http://purl.obolibrary.org/obo/DIDEO_$1 version: '2021-06-11' dinto: banana: 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: biocontext: DINTO bioportal: DINTO obofoundry: DINTO ontobee: DINTO name: The Drug-Drug Interactions Ontology preferred_prefix: DINTO repository: https://github.com/labda/DINTO uri_format: http://purl.obolibrary.org/obo/DINTO_$1 dip: description: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions example: DIP-743N homepage: https://dip.doe-mbi.ucla.edu/ mappings: biocontext: DIP fairsharing: FAIRsharing.qje0v8 miriam: dip n2t: dip prefixcommons: dip uniprot: DIP name: Database of Interacting Proteins pattern: ^DIP(\:)?\-\d{1,}[ENXS]$ preferred_prefix: dip 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=$1&searchmode=exact disdriv: banana: DISDRIV contact: email: lynn.schriml@gmail.com github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 description: Drivers of human diseases including environmental, maternal and social exposures. download_owl: http://purl.obolibrary.org/obo/disdriv.owl example: '0000000' homepage: http://www.disease-ontology.org license: CC0 1.0 mappings: bioportal: DISDRIV obofoundry: DISDRIV ols: disdriv name: Disease Drivers Ontology pattern: ^\d+$ preferred_prefix: DISDRIV repository: https://github.com/DiseaseOntology/DiseaseDriversOntology 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 diseasesdb: 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 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 fairsharing: FAIRsharing.dt9z89 miriam: disprot n2t: disprot prefixcommons: disprot uniprot: DisProt name: DisProt pattern: ^DP\d{5}$ preferred_prefix: disprot 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/$1 dmba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A controlled vocabulary to support the study of transcription in the developing mouse brain download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dmba.obo example: '688' homepage: https://developingmouse.brain-map.org/ name: Developing Mouse Brain Atlas pattern: ^\d+$ preferred_prefix: DMBA 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.' description: The Digital Object Identifier System is for identifying content objects in the digital environment. example: 10.1038/nbt1156 homepage: https://www.doi.org/ mappings: biocontext: DOI biolink: doi cellosaurus: DOI fairsharing: FAIRsharing.hFLKCn go: DOI miriam: doi n2t: doi prefixcommons: doi scholia: doi name: Digital Object Identifier pattern: ^(doi\:)?\d{2}\.\d{4}.*$ preferred_prefix: doi providers: - 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: 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: 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/$1 doid: appears_in: - clo - scdo banana: DOID contact: email: lynn.schriml@gmail.com github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. download_obo: https://github.com/DiseaseOntology/HumanDiseaseOntology/raw/main/src/ontology/doid.obo download_owl: http://purl.obolibrary.org/obo/doid.owl example: 0110974 homepage: http://www.disease-ontology.org license: CC0 1.0 mappings: biocontext: DOID bioportal: DOID fairsharing: FAIRsharing.8b6wfq miriam: doid n2t: doid obofoundry: DOID ols: doid ontobee: DOID prefixcommons: do wikidata: P699 name: Human Disease Ontology namespace_in_lui: true pattern: ^\d+$ 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 repository: https://github.com/DiseaseOntology/HumanDiseaseOntology synonyms: - do uri_format: https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:$1 version: '2022-04-28' dommino: description: DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides. example: 2GC4 homepage: http://korkinlab.org/dommino mappings: biocontext: DOMMINO miriam: dommino n2t: dommino name: Database of Macromolecular Interactions pattern: ^[0-9][A-Za-z0-9]{3}$ 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 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 uri_format: http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1 dpo: banana: FBcv 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 3.0 mappings: bioportal: DPO obofoundry: FBcv ols: dpo ontobee: DPO name: Drosophila Phenotype Ontology no_own_terms: true part_of: fbcv preferred_prefix: DPO repository: https://github.com/FlyBase/drosophila-phenotype-ontology uri_format: http://purl.obolibrary.org/obo/FBcv_$1 version: '2022-04-13' dpv: description: Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. example: '100' homepage: http://www.dpvweb.net/ mappings: biocontext: DPV miriam: dpv n2t: dpv name: Description of Plant Viruses pattern: ^\d+$ 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=$1;class=Peptide dron: appears_in: - scdo banana: DRON contact: email: hoganwr@gmail.com github: hoganwr name: William Hogan orcid: 0000-0002-9881-1017 description: We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive). download_owl: http://purl.obolibrary.org/obo/dron.owl example: '00023232' homepage: https://github.com/ufbmi/dron license: CC BY 3.0 mappings: biocontext: DRON bioportal: DRON fairsharing: FAIRsharing.w5ntfd obofoundry: DRON ols: dron ontobee: DRON name: The Drug Ontology pattern: ^\d{8}$ preferred_prefix: DRON 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=$1 drugbank: description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information. example: DB14938 homepage: http://www.drugbank.ca mappings: biocontext: DrugBank cellosaurus: DrugBank cheminf: '000406' fairsharing: FAIRsharing.353yat miriam: drugbank n2t: drugbank prefixcommons: drugbank uniprot: DrugBank wikidata: P715 name: DrugBank pattern: ^DB\d{5}$ preferred_prefix: drugbank synonyms: - DRUGBANK_ID - DrugBank uri_format: http://www.drugbank.ca/drugs/$1 drugbank.salt: description: DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets. example: DBSALT001211 homepage: http://www.drugbank.ca mappings: biocontext: DRUGBANK.TARGET name: DrugBank Salts part_of: drugbank pattern: ^DBSALT\d{6}$ 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/$1 drugcentral: description: DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action. example: '307' homepage: http://drugcentral.org mappings: biolink: DrugCentral fairsharing: FAIRsharing.3me82d uniprot: DrugCentral name: Drug Central pattern: ^\d+$ preferred_prefix: drugcentral synonyms: - Drug_Central uri_format: http://drugcentral.org/drugcard/$1 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 name: Deutsche Sammlung von Mikroorganismen und Zellkulturen preferred_prefix: dsmz uri_format: https://www.dsmz.de/collection/catalogue/details/culture/$1 dto: appears_in: - pr description: 'DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.' example: '90000018' homepage: https://github.com/DrugTargetOntology/DTO mappings: bioportal: DTO fairsharing: FAIRsharing.tke3y2 name: Drug Target Ontology pattern: ^\d+$ preferred_prefix: dto repository: https://github.com/DrugTargetOntology/DTO duo: appears_in: - scdo banana: DUO 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: 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 name: eagle-i preferred_prefix: eaglei uri_format: http://hawaii.eagle-i.net/i/$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/$1 ecacc: description: The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs). example: '90062901' homepage: https://www.phe-culturecollections.org.uk/collections/ecacc.aspx mappings: cellosaurus: ECACC name: European Collection of Authenticated Cell Culture pattern: ^\d+$ preferred_prefix: ecacc uri_format: https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1 ecao: banana: ECAO contact: email: ettensohn@cmu.edu github: ettensohn name: Charles Ettensohn orcid: 0000-0002-3625-0955 depends_on: - cl - ro - uberon description: None download_obo: http://purl.obolibrary.org/obo/ecao.obo download_owl: http://purl.obolibrary.org/obo/ecao.owl example: 0107180 homepage: https://github.com/echinoderm-ontology/ecao_ontology license: CC BY 3.0 mappings: bioportal: ECAO obofoundry: ECAO ols: ecao ontobee: ECAO name: The Echinoderm Anatomy and Development Ontology pattern: ^\d{7}$ preferred_prefix: ECAO repository: https://github.com/echinoderm-ontology/ecao_ontology uri_format: http://purl.obolibrary.org/obo/ECAO_$1 version: '2020-05-22' eccode: description: The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions. example: 1.1.1.1 example_extras: - '2' - '2.3' - 2.3.1 - 2.3.1.n12 - 3.1.26.n2 homepage: https://www.ebi.ac.uk/intenz/ mappings: biocontext: EC fairsharing: FAIRsharing.q1fdkc go: EC miriam: ec-code n2t: ec-code prefixcommons: intenz wikidata: P591 name: Enzyme Nomenclature pattern: ^\d{1,2}(((\.\d{1,3}){1,3})|(\.\d+){2}\.n\d{1,3})?$ 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: 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 - 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 synonyms: - EC - EC-CODE - ECCODE - EC_CODE - ec-code - intenz uri_format: https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1 ecg: description: The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms. example: 000000159 homepage: https://bioportal.bioontology.org/ontologies/ECG mappings: bioportal: ECG fairsharing: FAIRsharing.azr389 name: Electrocardiogram Ontology pattern: ^\d+$ preferred_prefix: ecg synonyms: - ECGOntology 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 uniprot: EchoBASE name: EchoBASE post-genomic database for Escherichia coli pattern: ^EB\d+$ preferred_prefix: echobase 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/$1 eco: banana: ECO contact: email: mgiglio@som.umaryland.edu github: mgiglio99 name: Michelle Giglio orcid: 0000-0001-7628-5565 description: Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity. download_obo: http://purl.obolibrary.org/obo/eco.obo download_owl: http://purl.obolibrary.org/obo/eco.owl example: 0007807 homepage: https://github.com/evidenceontology/evidenceontology/ license: CC0 1.0 mappings: biocontext: ECO bioportal: ECO fairsharing: FAIRsharing.wvpgwn go: ECO miriam: eco n2t: eco obofoundry: ECO ols: eco ontobee: ECO prefixcommons: eco name: Evidence ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: ECO repository: https://github.com/evidenceontology/evidenceontology uri_format: https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1 version: '2022-04-11' ecocore: banana: ECOCORE contact: email: p.buttigieg@gmail.com github: pbuttigieg name: Pier Luigi Buttigieg orcid: 0000-0002-4366-3088 depends_on: - bfo - chebi - envo - go - iao - pato - pco - po - ro - uberon description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. download_obo: http://purl.obolibrary.org/obo/ecocore.obo download_owl: http://purl.obolibrary.org/obo/ecocore.owl example: '00000001' homepage: https://github.com/EcologicalSemantics/ecocore license: CC BY 3.0 mappings: biocontext: ECOCORE bioportal: ECOCORE obofoundry: ECOCORE ols: ecocore ontobee: ECOCORE name: An ontology of core ecological entities pattern: ^\d+$ 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=$1 ecogene: description: The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. example: EG10173 homepage: http://ecogene.org/ mappings: biocontext: EcoGene fairsharing: FAIRsharing.3q3kvn miriam: ecogene n2t: ecogene ncbi: EcoGene prefixcommons: ecogene name: Database of Escherichia coli Sequence and Function pattern: ^EG\d+$ preferred_prefix: ecogene 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/$1:Gene ecto: banana: ECTO contact: email: annethessen@gmail.com github: diatomsRcool name: Anne Thessen orcid: 0000-0002-2908-3327 depends_on: - chebi - envo - exo - go - iao - maxo - nbo - ncbitaxon - ncit - pato - ro - uberon - xco description: ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology). download_json: http://purl.obolibrary.org/obo/ecto.json download_obo: http://purl.obolibrary.org/obo/ecto.obo download_owl: http://purl.obolibrary.org/obo/ecto.owl example: '0000001' homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology license: CC0 1.0 mappings: biolink: ECTO bioportal: ECTO obofoundry: ECTO ols: ecto ontobee: ECTO name: Environmental conditions, treatments and exposures ontology pattern: ^\d{7}$ preferred_prefix: ECTO repository: https://github.com/EnvironmentOntology/environmental-exposure-ontology uri_format: http://purl.obolibrary.org/obo/ECTO_$1 version: '2021-08-25' ecyano.entity: description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities. example: '23' homepage: http://www.e-cyanobacterium.org/bcs/entity/ mappings: biocontext: ECYANO.ENTITY miriam: ecyano.entity n2t: ecyano.entity name: E-cyanobacterium entity part_of: ecyano pattern: ^\d+$ 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/$1 edam: description: 'EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).' download_owl: https://raw.githubusercontent.com/edamontology/edamontology/master/releases/EDAM.owl example: data_1664 homepage: http://edamontology.org mappings: biocontext: EDAM bioportal: EDAM fairsharing: FAIRsharing.a6r7zs miriam: edam n2t: edam ols: edam ontobee: EDAM prefixcommons: edam name: Bioinformatics operations, data types, formats, identifiers and topics pattern: ^(data|topic|operation|format)\_\d{4}$ preferred_prefix: edam uri_format: https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1 version: '2019-07-17' edda: description: Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries. example: health_care_quality_assessment homepage: https://bioportal.bioontology.org/ontologies/EDDA mappings: bioportal: EDDA fairsharing: FAIRsharing.2ffmsb name: EDDA Study Designs Taxonomy preferred_prefix: edda efo: contact: email: plwhetzel@gmail.com github: twhetzel name: Trish Whetzel orcid: 0000-0002-3458-4839 description: The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team. download_obo: http://www.ebi.ac.uk/efo/efo.obo download_owl: http://www.ebi.ac.uk/efo/releases/v3.42.0/efo.owl example: '0005147' homepage: http://www.ebi.ac.uk/efo mappings: biocontext: EFO biolink: EFO bioportal: EFO cellosaurus: EFO fairsharing: FAIRsharing.1gr4tz miriam: efo n2t: efo ols: efo ontobee: EFO name: Experimental Factor Ontology pattern: ^\d{7}$ 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 repository: https://github.com/EBISPOT/efo/ uri_format: http://www.ebi.ac.uk/efo/EFO_$1 version: 3.42.0 ega.dataset: description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'. example: EGAD00000000001 homepage: https://ega-archive.org/ mappings: biocontext: EGA.DATASET fairsharing: FAIRsharing.mya1ff miriam: ega.dataset n2t: ega.dataset name: European Genome-phenome Archive Dataset pattern: ^EGAD\d{11}$ 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 providers: - code: omicsdi description: EGA Study through OmicsDI homepage: https://www.omicsdi.org/ name: EGA Study through OmicsDI uri_format: https://www.omicsdi.org/dataset/ega/$1 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 uri_format: http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1 ehda: banana: EHDA contact: email: J.Bard@ed.ac.uk github: null name: Jonathan Bard orcid: null deprecated: true example: '1' homepage: http://genex.hgu.mrc.ac.uk/ mappings: biocontext: EHDA bioportal: EHDA obofoundry: EHDA prefixcommons: ehda name: Human developmental anatomy, timed version pattern: ^\d+$ preferred_prefix: EHDA uri_format: http://purl.obolibrary.org/obo/EHDA_$1 ehdaa: banana: EHDAA contact: email: J.Bard@ed.ac.uk github: null name: Jonathan Bard orcid: null deprecated: true example: '1' mappings: biocontext: EHDAA bioportal: EHDAA obofoundry: EHDAA prefixcommons: ehdaa name: Human developmental anatomy, abstract version pattern: ^\d+$ preferred_prefix: EHDAA uri_format: http://purl.obolibrary.org/obo/EHDAA_$1 ehdaa2: banana: EHDAA2 contact: email: J.Bard@ed.ac.uk github: null name: Jonathan Bard orcid: null depends_on: - aeo - caro - cl description: A structured controlled vocabulary of stage-specific anatomical structures of the developing human. download_obo: http://purl.obolibrary.org/obo/ehdaa2.obo download_owl: http://purl.obolibrary.org/obo/ehdaa2.owl example: '0000000' homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology license: CC BY 4.0 mappings: biocontext: EHDAA2 bioportal: EHDAA2 fairsharing: FAIRsharing.7zxrs6 obofoundry: EHDAA2 ols: ehdaa2 ontobee: EHDAA2 name: Human developmental anatomy, abstract pattern: ^\d{7}$ preferred_prefix: EHDAA2 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/$1.html emap: banana: EMAP contact: email: Terry.Hayamizu@jax.org github: tfhayamizu name: Terry Hayamizu orcid: 0000-0002-0956-8634 deprecated: true description: A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). download_owl: http://purl.obolibrary.org/obo/emap.owl example: '1' homepage: http://emouseatlas.org mappings: biocontext: EMAP bioportal: EMAP obofoundry: EMAP name: Mouse gross anatomy and development, timed pattern: ^\d+$ preferred_prefix: EMAP uri_format: http://purl.obolibrary.org/obo/EMAP_$1 emapa: banana: EMAPA contact: email: Terry.Hayamizu@jax.org github: tfhayamizu name: Terry Hayamizu orcid: 0000-0002-0956-8634 description: An ontology for mouse anatomy covering embryonic development and postnatal stages. download_obo: http://purl.obolibrary.org/obo/emapa.obo download_owl: http://purl.obolibrary.org/obo/emapa.owl example: '26753' homepage: http://www.informatics.jax.org/expression.shtml license: CC BY 4.0 mappings: biocontext: EMAPA bioportal: EMAPA fairsharing: FAIRsharing.j0fa1d go: EMAPA obofoundry: EMAPA ols: emapa ontobee: EMAPA name: Mouse Developmental Anatomy Ontology pattern: ^\d+$ 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:$1 version: '2021-09-01' emdb: description: The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community. example: EMD-1001 homepage: https://www.ebi.ac.uk/pdbe/emdb/ mappings: biocontext: EMDB fairsharing: FAIRsharing.651n9j miriam: emdb n2t: emdb name: Electron Microscopy Data Bank pattern: ^EMD-\d{4}$ 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=$1 empiar: description: EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure example: '10595' homepage: https://www.ebi.ac.uk/pdbe/emdb mappings: fairsharing: FAIRsharing.dff3ef name: Electron Microscopy Public Image Archive pattern: ^\d+$ 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/$1 encode: description: The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. example: ENCSR163RYW homepage: https://www.encodeproject.org mappings: biocontext: ENCODE cellosaurus: ENCODE fairsharing: FAIRsharing.v0hbjs miriam: encode n2t: encode name: Encyclopedia of DNA Elements pattern: ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$ preferred_prefix: encode uri_format: https://www.encodeproject.org/$1 enm: description: 'The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. > This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. ' download_owl: http://enanomapper.github.io/ontologies/enanomapper.owl example: '8000221' homepage: http://www.enanomapper.net/ mappings: bioportal: ENM fairsharing: FAIRsharing.2gpf81 ols: enm name: eNanoMapper Ontology pattern: ^\d+$ preferred_prefix: enm version: '7.3' 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 fairsharing: FAIRsharing.fx0mw7 go: ENSEMBL miriam: ensembl n2t: ensembl ncbi: ENSEMBL prefixcommons: ensembl 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: 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 - 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 synonyms: - Ensembl uri_format: https://www.ensembl.org/id/$1 ensembl.bacteria: description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes. example: MU9_3181 homepage: https://bacteria.ensembl.org/ mappings: biocontext: ENSEMBL.BACTERIA fairsharing: FAIRsharing.zsgmvd miriam: ensembl.bacteria n2t: ensembl.bacteria prefixcommons: ensembl.bacteria uniprot: EnsemblBacteria name: Ensembl Bacteria pattern: ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$ preferred_prefix: ensembl.bacteria uri_format: https://bacteria.ensembl.org/id/$1 ensembl.fungi: description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes. example: CADAFLAT00006211 homepage: https://fungi.ensembl.org/ mappings: biocontext: ENSEMBL.FUNGI fairsharing: FAIRsharing.bg5xqs go: EnsemblFungi miriam: ensembl.fungi n2t: ensembl.fungi prefixcommons: ensembl.fungi uniprot: EnsemblFungi name: Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi. pattern: ^[A-Z-a-z0-9]+$ preferred_prefix: ensembl.fungi uri_format: https://fungi.ensembl.org/id/$1 ensembl.metazoa: description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes. example: FBtr0084214 homepage: https://metazoa.ensembl.org/ mappings: biocontext: ENSEMBL.METAZOA fairsharing: FAIRsharing.c23cqq go: EnsemblMetazoa miriam: ensembl.metazoa n2t: ensembl.metazoa prefixcommons: ensembl.metazoa uniprot: EnsemblMetazoa name: Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa. pattern: ^\w+(\.)?\d+$ 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/$1 ensemblglossary: description: The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used. download_owl: http://ensembl.org/glossary/ensembl-glossary/releases/2021-07-14/ensembl-glossary.owl example: 0000198 homepage: http://ensembl.org/glossary mappings: ols: ensemblglossary name: Ensembl Glossary pattern: ^\d{7}$ preferred_prefix: ensemblglossary version: '2021-07-14' 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 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/$1 envo: appears_in: - agro - cdno - ecocore - ecto - foodon - ons - pco - rbo - scdo banana: ENVO contact: email: p.buttigieg@gmail.com github: pbuttigieg name: Pier Luigi Buttigieg orcid: 0000-0002-4366-3088 depends_on: - chebi - foodon - go - ncbitaxon - pco - po - ro - uberon description: The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. download_json: http://purl.obolibrary.org/obo/envo.json download_obo: http://purl.obolibrary.org/obo/envo.obo download_owl: http://purl.obolibrary.org/obo/envo.owl example: 09200010 homepage: http://environmentontology.org/ license: CC BY 3.0 mappings: biocontext: ENVO bioportal: ENVO fairsharing: FAIRsharing.azqskx miriam: envo n2t: envo obofoundry: ENVO ols: envo ontobee: ENVO name: Environment Ontology namespace_in_lui: true pattern: ^\d{7,8}$ preferred_prefix: ENVO 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/$1 eo: appears_in: - foodon banana: EO contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp name: Pankaj Jaiswal orcid: 0000-0002-1005-8383 deprecated: true description: The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. download_obo: http://purl.obolibrary.org/obo/eo.obo download_owl: http://purl.obolibrary.org/obo/eo.owl example: '0007404' homepage: http://planteome.org/ license: CC BY 4.0 mappings: biocontext: EO miriam: eo n2t: eo obofoundry: EO prefixcommons: eo name: Plant Environment Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: EO repository: https://github.com/Planteome/plant-environment-ontology uri_format: http://archive.gramene.org/db/ontology/search?query=EO:$1 eol: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems. download_owl: https://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=eol.owl example: 0001927 homepage: http://www.atol-ontology.com mappings: bioportal: EOL fairsharing: FAIRsharing.w7bw2y ols: eol name: Environment Ontology for Livestock pattern: ^\d{7}$ preferred_prefix: eol 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/$1 epcc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Collection of European paediatric cardiac coding files homepage: https://www.aepc.org/european-paediatric-cardiac-coding name: European Paediatric Cardiac Codes preferred_prefix: epcc proprietary: true references: - https://www.cambridge.org/core/journals/cardiology-in-the-young/article/abs/european-paediatric-cardiac-codes-the-long-list-with-icd9-icd10-crossmapping-and-crossmap-to-epcc-short-list/FCA4DFCCB661298294A3D113FC79D5BE epd: description: The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. example: TA_H3 homepage: http://epd.vital-it.ch/ mappings: biocontext: EPD fairsharing: FAIRsharing.sym4ne miriam: epd n2t: epd ncbi: EPD uniprot: EPD name: Eukaryotic Promoter Database pattern: ^[A-Z-_0-9]+$ preferred_prefix: epd uri_format: http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1 epio: banana: EPIO contact: email: alpha.tom.kodamullil@scai.fraunhofer.de github: akodamullil name: Alpha Tom Kodamullil orcid: 0000-0001-9896-3531 depends_on: - bfo description: A application driven Epilepsy Ontology with official terms from the ILAE. download_owl: http://purl.obolibrary.org/obo/epio.owl example: '0000011' homepage: https://github.com/SCAI-BIO/EpilepsyOntology license: CC BY 4.0 mappings: bioportal: EPIO obofoundry: EPIO ontobee: EPIO name: Epilepsy Ontology pattern: ^\d{7}$ preferred_prefix: EPIO repository: https://github.com/SCAI-BIO/EpilepsyOntology uri_format: http://purl.obolibrary.org/obo/EPIO_$1 epo: banana: EPO 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: biocontext: EPO bioportal: EPO obofoundry: EPO ontobee: EPO name: Epidemiology Ontology preferred_prefix: EPO uri_format: http://purl.obolibrary.org/obo/EPO_$1 epso: description: 'The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. ' example: '0000400' homepage: http://prism.case.edu/prism/index.php/EpilepsyOntology mappings: bioportal: EPSO fairsharing: FAIRsharing.ttprgy ontobee: EPSO name: Epilepsy and Seizure Ontology pattern: ^\d{7}$ preferred_prefix: epso erm: 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. example: ERM00000044 homepage: https://nanocommons.github.io/identifiers/ mappings: miriam: erm n2t: erm name: European Registry of Materials pattern: ^ERM[0-9]{8}$ preferred_prefix: erm uri_format: https://nanocommons.github.io/identifiers/registry#$1 ero: banana: ERO contact: email: Marc_Ciriello@hms.harvard.edu github: null name: Marc Ciriello orcid: null deprecated: true description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. download_owl: http://purl.obolibrary.org/obo/ero.owl example: '0001655' homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology license: CC BY 2.0 mappings: biocontext: ERO bioportal: ERO fairsharing: FAIRsharing.nwgynk obofoundry: ERO ols: ero ontobee: ERO name: eagle-i resource ontology pattern: ^\d{7}$ preferred_prefix: ERO 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=$1 eupath: appears_in: - scdo banana: EUPATH contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 description: The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available. download_owl: http://purl.obolibrary.org/obo/eupath.owl example: '0010316' homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology license: CC BY 4.0 mappings: biocontext: EUPATH bioportal: EUPATH fairsharing: FAIRsharing.9rhr9j obofoundry: EUPATH ols: eupath ontobee: EUPATH name: VEuPathDB ontology pattern: ^\d{7}$ preferred_prefix: EUPATH repository: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology uri_format: http://purl.obolibrary.org/obo/EUPATH_$1 version: '2022-02-15' 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 banana: EV 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 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/$1 exo: appears_in: - ecto - scdo banana: ExO contact: email: annethessen@gmail.com github: diatomsRcool name: Anne Thessen orcid: 0000-0002-2908-3327 description: ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics. download_obo: http://purl.obolibrary.org/obo/exo.obo download_owl: http://purl.obolibrary.org/obo/exo.owl example: 0000078 homepage: https://github.com/CTDbase/exposure-ontology license: CC BY 4.0 mappings: biocontext: EXO biolink: ExO bioportal: EXO fairsharing: FAIRsharing.6hna78 obofoundry: ExO ols: exo ontobee: ExO name: Exposure ontology pattern: ^\d{7}$ preferred_prefix: ExO repository: https://github.com/CTDbase/exposure-ontology synonyms: - ExO uri_format: http://purl.obolibrary.org/obo/EXO_$1 version: '2020-03-10' 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. example: d4e2515 homepage: https://github.com/sparontologies/fabio mappings: biolink: fabio fairsharing: FAIRsharing.2f3180 name: FaBiO, the FRBR-aligned Bibliographic Ontology preferred_prefix: fabio repository: https://github.com/sparontologies/fabio uri_format: https://sparontologies.github.io/fabio/current/fabio.html#$1 facebase: description: FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects. example: FB00000917 homepage: https://www.facebase.org mappings: biocontext: FACEBASE fairsharing: FAIRsharing.mqvqde miriam: facebase n2t: facebase name: FaceBase Data Repository pattern: ^FB\d{8}$ preferred_prefix: facebase uri_format: https://www.facebase.org/data/record/#1/isa:dataset/accession=$1 fairsharing: description: The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies. example: bsg-000052 homepage: https://fairsharing.org/ mappings: biocontext: FAIRSHARING fairsharing: FAIRsharing.2abjs5 miriam: fairsharing n2t: fairsharing name: FAIRsharing pattern: ^bsg-[dscp]?\d{6}$ preferred_prefix: fairsharing uri_format: https://fairsharing.org/$1 faldo: 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 example: ForwardStrandPosition homepage: http://biohackathon.org/resource/faldo mappings: biocontext: faldo bioportal: FALDO fairsharing: FAIRsharing.haxp7g name: 'Feature Annotation Location Description Ontology ' preferred_prefix: faldo uri_format: http://biohackathon.org/resource/faldo#$1 fao: banana: FAO contact: email: vw253@cam.ac.uk github: ValWood name: Val Wood orcid: 0000-0001-6330-7526 description: A structured controlled vocabulary for the anatomy of fungi. download_obo: http://purl.obolibrary.org/obo/fao.obo download_owl: http://purl.obolibrary.org/obo/fao.owl example: '0000001' homepage: https://github.com/obophenotype/fungal-anatomy-ontology/ license: CC0 1.0 mappings: biocontext: FAO bioportal: FAO fairsharing: FAIRsharing.xs6t67 obofoundry: FAO ols: fao ontobee: FAO prefixcommons: fao name: Fungal gross anatomy pattern: ^\d{7}$ preferred_prefix: FAO repository: https://github.com/obophenotype/fungal-anatomy-ontology uri_format: http://purl.obolibrary.org/obo/FAO_$1 version: '2020-05-07' fbbi: banana: FBbi contact: email: wawong@gmail.com github: wawong name: Willy Wong orcid: 0000-0002-8841-5870 description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. download_owl: http://purl.obolibrary.org/obo/fbbi.owl example: 00000268 homepage: http://cellimagelibrary.org/ license: CC BY 4.0 mappings: biocontext: FBbi bioportal: FBbi fairsharing: FAIRsharing.ny3z9j obofoundry: FBbi ols: fbbi ontobee: FBBI prefixcommons: fbbi name: Biological Imaging Methods Ontology pattern: ^\d+$ preferred_prefix: FBbi repository: https://github.com/CRBS/Biological_Imaging_Methods_Ontology synonyms: - FBbi uri_format: http://purl.obolibrary.org/obo/FBbi_$1 version: '2020-11-06' fbbt: banana: FBbt contact: email: cp390@cam.ac.uk github: Clare72 name: Clare Pilgrim orcid: 0000-0002-1373-1705 description: An ontology of Drosophila melanogaster anatomy. download_json: http://purl.obolibrary.org/obo/fbbt.json download_obo: http://purl.obolibrary.org/obo/fbbt.obo download_owl: http://purl.obolibrary.org/obo/fbbt.owl example: 00007294 homepage: http://purl.obolibrary.org/obo/fbbt license: CC BY 3.0 mappings: biocontext: FBbt bioportal: FB-BT fairsharing: FAIRsharing.y2qkst go: FBbt obofoundry: FBbt ols: fbbt ontobee: FBBT prefixcommons: fbbt name: Drosophila gross anatomy part_of: flybase pattern: ^\d{8}$ preferred_prefix: FBbt repository: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology synonyms: - FBbt - FBbt_root uri_format: https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:$1 version: '2022-04-13' fbcv: appears_in: - ontoavida banana: FBcv contact: email: cp390@cam.ac.uk github: Clare72 name: Clare Pilgrim orcid: 0000-0002-1373-1705 description: A miscellaneous ontology of terms used for curation in FlyBase, including the DPO. download_json: http://purl.obolibrary.org/obo/fbcv.json download_obo: https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/fbcv.obo download_owl: http://purl.obolibrary.org/obo/fbcv.owl example: 0000586 homepage: http://purl.obolibrary.org/obo/fbcv license: CC BY 3.0 mappings: biocontext: FBcv bioportal: FB-CV fairsharing: FAIRsharing.6tgyxf obofoundry: FBcv ols: fbcv ontobee: FBCV prefixcommons: fbcv name: FlyBase Controlled Vocabulary part_of: flybase pattern: ^\d{7}$ preferred_prefix: FBcv repository: https://github.com/FlyBase/flybase-controlled-vocabulary synonyms: - FBcv uri_format: http://purl.obolibrary.org/obo/FBcv_$1 version: '2022-04-14' fbdv: banana: FBdv contact: email: cp390@cam.ac.uk github: Clare72 name: Clare Pilgrim orcid: 0000-0002-1373-1705 description: An ontology of Drosophila melanogaster developmental stages. download_json: http://purl.obolibrary.org/obo/fbdv.json download_obo: http://purl.obolibrary.org/obo/fbdv.obo download_owl: http://purl.obolibrary.org/obo/fbdv.owl example: '00000000' homepage: http://purl.obolibrary.org/obo/fbdv license: CC BY 3.0 mappings: biocontext: FBdv bioportal: FB-DV fairsharing: FAIRsharing.p52pzj obofoundry: FBdv ols: fbdv ontobee: FBdv prefixcommons: fbdv name: Drosophila development pattern: ^\d{8}$ preferred_prefix: FBdv repository: https://github.com/FlyBase/drosophila-developmental-ontology synonyms: - FBdv uri_format: http://purl.obolibrary.org/obo/FBdv_$1 version: '2022-04-12' fbol: comment: Website down, checked on 2021-10-07 deprecated: true description: DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms. example: '2224' homepage: http://www.fungalbarcoding.org/ mappings: biocontext: FBOL miriam: fbol n2t: fbol ncbi: FBOL name: International Fungal Working Group Fungal Barcoding. pattern: ^\d+$ 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$1 fbsp: banana: FBSP contact: email: cp390@cam.ac.uk github: Clare72 name: Clare Pilgrim orcid: 0000-0002-1373-1705 deprecated: true description: The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. download_owl: http://purl.obolibrary.org/obo/fbsp.owl example: '00000000' homepage: http://www.flybase.org/ mappings: biocontext: FBSP bioportal: FB-SP obofoundry: FBSP name: Fly taxonomy part_of: flybase pattern: ^\d{8}$ 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?$1 fideo: banana: FIDEO contact: email: georgeta.bordea@u-bordeaux.fr github: getbordea name: Georgeta Bordea orcid: 0000-0001-9921-8234 description: The Food Interactions with Drugs Evidence Ontology (FIDEO) represents Food-Drug Interactions and underlying interaction mechanisms described in scientific publications, drug and adverse effects databases, and drug interactions compendia. The ontology builds on previous efforts from the FoodOn, DRON, ChEBI, and DIDEO ontologies as well as the Thériaque database. This ontology is maintained at https://gitub.u-bordeaux.fr/erias/fideo, and requests for changes or additions should be filed at the issue tracker there. download_owl: http://purl.obolibrary.org/obo/fideo.owl example: '00000021' homepage: https://gitub.u-bordeaux.fr/erias/fideo license: CC0 1.0 mappings: bioportal: FIDEO obofoundry: FIDEO ols: fideo ontobee: FIDEO name: Food Interactions with Drugs Evidence Ontology pattern: ^\d{8}$ preferred_prefix: FIDEO repository: https://github.com/getbordea/fideo uri_format: http://purl.obolibrary.org/obo/FIDEO_$1 fishbase.species: description: 'Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years.' example: '6472' homepage: http://fishbase.org mappings: wikidata: P938 name: FishBase pattern: ^\d+$ preferred_prefix: fishbase.species synonyms: - fishbase fix: banana: FIX contact: email: null github: null name: chEBI orcid: null 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: 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_$1 version: '2020-04-13' flopo: banana: FLOPO contact: email: robert.hoehndorf@kaust.edu.sa github: leechuck name: Robert Hoehndorf orcid: 0000-0001-8149-5890 description: Traits and phenotypes of flowering plants occurring in digitized Floras download_owl: http://purl.obolibrary.org/obo/flopo.owl example: '0005250' homepage: https://github.com/flora-phenotype-ontology/flopoontology license: CC0 1.0 mappings: biocontext: FLOPO bioportal: FLOPO fairsharing: FAIRsharing.ny9vnm obofoundry: FLOPO ols: flopo ontobee: FLOPO name: Flora Phenotype Ontology pattern: ^\d{7}$ preferred_prefix: FLOPO repository: https://github.com/flora-phenotype-ontology/flopoontology uri_format: http://purl.obolibrary.org/obo/FLOPO_$1 version: '2019-09-09' flowrepository: description: FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field. example: FR-FCM-ZYGW homepage: https://flowrepository.org/ mappings: fairsharing: FAIRsharing.veg2d6 miriam: flowrepository n2t: flowrepository name: FlowRepository pattern: ^FR\-FCM\-\w{4}$ preferred_prefix: flowrepository uri_format: https://flowrepository.org/id/$1 flu: banana: FLU contact: email: burkesquires@gmail.com github: null name: Burke Squires orcid: null deprecated: true download_owl: http://purl.obolibrary.org/obo/flu.owl example: '0000404' homepage: http://purl.obolibrary.org/obo/flu/ mappings: biocontext: FLU bioportal: FLU obofoundry: FLU name: Influenza Ontology pattern: ^\d{7}$ preferred_prefix: FLU uri_format: http://purl.obolibrary.org/obo/FLU_$1 flybase: description: FlyBase is the database of the Drosophila Genome Projects and of associated literature. example: FBgn0011293 homepage: http://flybase.org/ mappings: biocontext: FlyBase cellosaurus: FlyBase fairsharing: FAIRsharing.wrvze3 go: FB miriam: fb n2t: fb ncbi: FLYBASE prefixcommons: flybase uniprot: FlyBase wikidata: P3852 name: FlyBase Gene pattern: ^FB\w{2}\d{7}$ preferred_prefix: FlyBase providers: - code: bioentitylink description: FlyBase through BioEntity Link homepage: https://bioentity.link/ name: FlyBase through BioEntity Link uri_format: https://bioentity.link/#/lexicon/public/$1 - 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 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=$1&-find=-find.html fma: banana: FMA contact: email: mejino@u.washington.edu github: null name: Onard Mejino orcid: null description: The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. download_owl: http://purl.obolibrary.org/obo/fma.owl example: '63189' homepage: http://si.washington.edu/projects/fma license: CC BY 3.0 mappings: biocontext: FMA bioportal: FMA fairsharing: FAIRsharing.x56jsy go: FMA miriam: fma n2t: fma obofoundry: FMA ols: fma ontobee: FMA prefixcommons: fma name: Foundational Model of Anatomy namespace_in_lui: true pattern: ^\d+$ preferred_prefix: FMA 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: 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.' example: familyName homepage: http://xmlns.com/foaf/spec/ mappings: biocontext: foaf biolink: foaf bioportal: FOAF name: Friend of a Friend preferred_prefix: foaf uri_format: http://xmlns.com/foaf/0.1/$1 fobi: banana: FOBI contact: email: polcaes@gmail.com github: pcastellanoescuder name: Pol Castellano Escuder orcid: 0000-0001-6466-877X depends_on: - chebi - foodon description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data download_owl: http://purl.obolibrary.org/obo/fobi.owl example: 030719 homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology license: CC BY 3.0 mappings: bioportal: FOBI obofoundry: FOBI ols: fobi ontobee: FOBI name: Food-Biomarker Ontology pattern: ^\d{6}$ preferred_prefix: FOBI repository: https://github.com/pcastellanoescuder/FoodBiomarkerOntology uri_format: http://purl.obolibrary.org/obo/FOBI_$1 foodb.compound: description: FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds. example: FDB002100 homepage: https://foodb.ca/ mappings: biocontext: FOODB.COMPOUND biolink: foodb.compound miriam: foodb.compound n2t: foodb.compound name: FooDB Compound pattern: ^FDB\d+$ preferred_prefix: foodb.compound synonyms: - foodb uri_format: http://foodb.ca/compounds/$1 foodon: appears_in: - agro - envo - fobi - maxo - one - ons banana: FOODON contact: email: damion_dooley@sfu.ca github: ddooley name: Damion Dooley orcid: 0000-0002-8844-9165 depends_on: - bfo - chebi - envo - eo - ncbitaxon - obi - ro - uberon description: FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies. download_owl: http://purl.obolibrary.org/obo/foodon.owl example: 03307879 homepage: https://foodon.org/ license: CC BY 3.0 mappings: biocontext: FOODON bioportal: FOODON fairsharing: FAIRsharing.dzxae miriam: foodon n2t: foodon obofoundry: FOODON ols: foodon ontobee: FOODON name: The Food Ontology namespace_in_lui: true pattern: ^[0-9]{8}$ preferred_prefix: FOODON repository: https://github.com/FoodOntology/foodon uri_format: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1 version: '2022-02-01' fovt: banana: FOVT contact: email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 depends_on: - bco - bfo - bspo - iao - oba - pato - ro - uberon description: None download_obo: http://purl.obolibrary.org/obo/fovt.obo download_owl: http://purl.obolibrary.org/obo/fovt.owl example: 0000009 homepage: https://github.com/futres/fovt license: CC0 1.0 mappings: bioportal: FOVT obofoundry: FOVT ols: fovt ontobee: FOVT name: FuTRES Ontology of Vertebrate Traits pattern: ^\d{7}$ preferred_prefix: FOVT repository: https://github.com/futres/fovt uri_format: http://purl.obolibrary.org/obo/FOVT_$1 version: '2021-11-10' fplx: description: FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships. example: GPIb_IX_V homepage: https://sorgerlab.github.io/famplex/ mappings: biocontext: FPLX bioportal: FPLX miriam: fplx n2t: fplx name: FamPlex pattern: ^[a-zA-Z0-9][A-Za-z0-9_]+$ preferred_prefix: fplx synonyms: - famplex uri_format: https://sorgerlab.github.io/famplex/$1 fsnp: description: The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification. example: rs17852708 homepage: http://compbio.cs.queensu.ca/F-SNP/ mappings: biocontext: FSNP miriam: fsnp n2t: fsnp prefixcommons: fsnp name: F-SNP pattern: ^rs\d+$ 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/$1 fungidb: description: FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina. example: CNBG_0001 homepage: https://fungidb.org/fungidb mappings: biocontext: FUNGIDB fairsharing: FAIRsharing.xf30yc miriam: fungidb n2t: fungidb name: FungiDB pattern: ^[A-Za-z_0-9]+$ preferred_prefix: fungidb uri_format: https://fungidb.org/fungidb/app/record/gene/$1 fyeco: comment: Rather than admitting FYECO to the OBO foundry, we secure the prefix here at bioregistry. The FYECO namespace shows up in a lot of ingests (basically anywhere you ingest PomBase gene-phenotype data). Future work includes mapping FYECO to other OBO ontologies, but this is way ahead in the future. contact: email: vw253@cam.ac.uk github: ValWood name: Val Wood orcid: 0000-0001-6330-7526 contributor: email: vw253@cam.ac.uk github: ValWood name: Val Wood orcid: 0000-0001-6330-7526 description: PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase. example: '0000003' homepage: https://github.com/pombase/fypo mappings: biolink: FYECO name: Fission Yeast Experimental Conditions Ontology pattern: ^\d{7}$ 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: banana: 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_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: 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 repository: https://github.com/pombase/fypo uri_format: http://purl.obolibrary.org/obo/FYPO_$1 version: '2022-04-28' ga4ghdos: description: Assists in resolving data across cloud resources. example: dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d homepage: http://github.com/ga4gh/data-object-service-schemas mappings: biocontext: GA4GHDOS miriam: ga4ghdos n2t: ga4ghdos name: Data Object Service pattern: ^[a-zA-Z0-9\-:#/\.]+$ 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 uri_format: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject galen: comment: I really tried, but could not figure out what GALEN stands for deprecated: true example: MagnitudeValueType homepage: https://www.opengalen.org mappings: bioportal: GALEN name: GALEN preferred_prefix: galen gard: description: Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease. example: '6038' homepage: https://rarediseases.info.nih.gov/diseases mappings: wikidata: P4317 name: Genetic and Rare Diseases Information Center pattern: ^\d+$ preferred_prefix: gard synonyms: - GARD - Genetic and Rare Diseases Information Center 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/$1 gaz: appears_in: - scdo banana: GAZ contact: email: lschriml@som.umaryland.edu github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 description: A gazetteer constructed on ontological principles download_obo: http://purl.obolibrary.org/obo/gaz.obo download_owl: http://purl.obolibrary.org/obo/gaz.owl example: '00620027' homepage: http://environmentontology.github.io/gaz/ license: CC0 1.0 mappings: biocontext: GAZ bioportal: GAZ fairsharing: FAIRsharing.wkdjpb obofoundry: GAZ ols: gaz ontobee: GAZ wikidata: P6778 name: Gazetteer pattern: ^\d{8}$ preferred_prefix: GAZ repository: https://github.com/EnvironmentOntology/gaz uri_format: http://purl.obolibrary.org/obo/GAZ_$1 gbif: description: "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity\ \ Information Facility—is international network and data infrastructure funded\ \ by the world's governments and aimed at providing anyone, anywhere, open access\ \ to data about all types of life on Earth." example: '4238' homepage: https://www.gbif.org/species mappings: fairsharing: FAIRsharing.zv11j3 wikidata: P846 name: Global Biodiversity Information Facility pattern: ^\d+$ preferred_prefix: gbif 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/$1 gecko: banana: GECKO contact: email: rbca.jackson@gmail.com github: beckyjackson name: Rebecca Jackson orcid: 0000-0003-4871-5569 description: An ontology to represent genomics cohort attributes. download_owl: http://purl.obolibrary.org/obo/gecko.owl example: '0000044' homepage: https://github.com/IHCC-cohorts/GECKO license: CC BY 4.0 mappings: bioportal: GECKO fairsharing: FAIRsharing.3da56b obofoundry: GECKO ols: gecko ontobee: GECKO name: Genomics Cohorts Knowledge Ontology pattern: ^\d{7}$ preferred_prefix: GECKO repository: https://github.com/IHCC-cohorts/GECKO uri_format: http://purl.obolibrary.org/obo/GECKO_$1 version: '2021-01-18' gemet: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts. example: '627' homepage: https://www.eionet.europa.eu/gemet/en/themes/ name: General Multilingual Environmental Thesaurus pattern: ^\d+$ 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 uri_format: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1 genbank: 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' fairsharing: FAIRsharing.9kahy4 go: GenBank prefixcommons: genbank uniprot: GenBank name: GenBank preferred_prefix: genbank uri_format: https://www.ncbi.nlm.nih.gov/nucleotide/$1 genecards: description: The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene. example: ABL1 homepage: http://www.genecards.org/ mappings: biocontext: GENECARDS fairsharing: FAIRsharing.g7jbvn miriam: genecards n2t: genecards prefixcommons: genecards uniprot: GeneCards name: GeneCards pattern: ^[A-Za-z-0-9_]+(\@)?$ preferred_prefix: genecards uri_format: https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1 genedb: deprecated: true description: GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed. example: LinJ.20.0070 homepage: https://www.genedb.org/ mappings: biocontext: GENEDB fairsharing: FAIRsharing.j7esqq go: GeneDB miriam: genedb n2t: genedb ncbi: GeneDB prefixcommons: genedb uniprot: GeneDB wikidata: P3382 name: GeneDB pattern: ^[\w\d\.-]*$ preferred_prefix: genedb 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 uri_format: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1 genepio: banana: GENEPIO contact: email: damion_dooley@sfu.ca github: ddooley name: Damion Dooley orcid: 0000-0002-8844-9165 depends_on: - chebi - ncbitaxon - po - ro - uberon description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. download_owl: http://purl.obolibrary.org/obo/genepio.owl example: 0001885 homepage: http://genepio.org/ license: CC BY 3.0 mappings: biocontext: GENEPIO fairsharing: FAIRsharing.y1mmbv obofoundry: GENEPIO ols: genepio ontobee: GENEPIO name: Genomic Epidemiology Ontology pattern: ^\d{7}$ 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 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=$1 geno: banana: GENO contact: email: mhb120@gmail.com github: mbrush name: Matthew Brush orcid: 0000-0002-1048-5019 description: "GENO is an OWL model of genotypes, their more fundamental sequence\ \ components, and links to related biological and experimental entities. At present\ \ many parts of the model are exploratory and set to undergo refactoring. In\ \ addition, many classes and properties have GENO URIs but are place holders for\ \ classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI,\ \ etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype\ \ associations. This will support description of asserted and inferred relationships\ \ between a genotypes, phenotypes, and environments, and the evidence/provenance\ \ behind these associations. \n\nDocumentation is under development as well, and\ \ for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" download_obo: https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/develop/geno-full.obo download_owl: http://purl.obolibrary.org/obo/geno.owl example: '0000632' homepage: https://github.com/monarch-initiative/GENO-ontology/ license: CC BY-SA 2.0 mappings: biocontext: GENO bioportal: GENO fairsharing: FAIRsharing.kpbna7 obofoundry: GENO ols: geno ontobee: GENO name: Genotype Ontology pattern: ^\d{7}$ 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/$1?report=genpept genprop: description: Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome. example: GenProp0699 homepage: https://www.ebi.ac.uk/interpro/genomeproperties/ mappings: biocontext: GENPROP miriam: genprop n2t: genprop name: Genome Properties pattern: ^GenProp\d+$ preferred_prefix: genprop uri_format: https://www.ebi.ac.uk/interpro/genomeproperties/#$1 geo: description: The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval. example: GDS1234 homepage: https://www.ncbi.nlm.nih.gov/geo/ mappings: biocontext: GEO cellosaurus: GEO fairsharing: FAIRsharing.27rndz go: GEO miriam: geo n2t: geo prefixcommons: geo name: NCBI Gene Expression Omnibus pattern: ^G(PL|SM|SE|DS)\d+$ preferred_prefix: geo uri_format: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1 geogeo: banana: GEO contact: email: hoganwr@gmail.com github: null name: Bill Hogan orcid: null description: An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in "The US declared war on Germany" vs. the US in "The plane entered US airspace". download_owl: http://purl.obolibrary.org/obo/geo.owl example: '000000021' homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki license: CC BY 4.0 mappings: biocontext: GEO bioportal: GEO miriam: geogeo obofoundry: GEO ols: geo ontobee: GEO name: Geographical Entity Ontology pattern: ^\d{9}$ 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: ADM1 homepage: https://www.geonames.org mappings: fairsharing: FAIRsharing.56a0Uj name: GeoNames preferred_prefix: geonames synonyms: - Geomames - Geonamaes uri_format: https://www.geonames.org/recent-changes/featurecode/$1/ gexo: 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: bioportal: GEXO fairsharing: FAIRsharing.3e0sn4 ols: gexo name: Gene Expression Ontology no_own_terms: true preferred_prefix: gexo version: '2019-09-18' 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/$1 giardiadb: description: GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: GL50803_102438 homepage: https://giardiadb.org/giardiadb/ mappings: biocontext: GIARDIADB fairsharing: FAIRsharing.e7skwg miriam: giardiadb n2t: giardiadb prefixcommons: giardiadb name: GiardiaDB pattern: ^\w+$ preferred_prefix: giardiadb uri_format: https://giardiadb.org/giardiadb/app/record/gene/$1 github: description: GitHub is an online host of Git source code repositories. example: biopragmatics/bioregistry example_extras: - biopragmatics - cthoyt homepage: https://github.com/ mappings: fairsharing: FAIRsharing.c55d5e miriam: github name: github pattern: ^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$ preferred_prefix: github uri_format: https://github.com/$1 gitlab: description: GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance. With GitLab, every team in your organization can collaboratively plan, build, secure, and deploy software to drive business outcomes faster with complete transparency, consistency and traceability. example: morpheus.lab/morpheus homepage: https://gitlab.com/ mappings: fairsharing: FAIRsharing.530e61 miriam: gitlab name: GitLab pattern: ^.*/.*$ 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/$1 glycomedb: comment: this is exactly the same as glytoucan. Idk why there are two different ones description: GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links. example: G77500AY has_canonical: glytoucan homepage: https://glytoucan.org/ mappings: biocontext: GLYCOMEDB fairsharing: FAIRsharing.k5k0yh miriam: glycomedb n2t: glycomedb prefixcommons: glycomedb name: GlycomeDB pattern: ^\w+$ preferred_prefix: glycomedb 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 glygen: 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/$1 glytoucan: description: GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data. example: G00054MO homepage: https://glytoucan.org mappings: biocontext: GLYTOUCAN miriam: glytoucan n2t: glytoucan name: GlyTouCan pattern: ^G[0-9]{5}[A-Z]{2}$ 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/$1 gmelin: description: The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s. example: '1466' homepage: https://link.springer.com/bookseries/562 mappings: wikidata: P1578 name: Gmelins Handbuch der anorganischen Chemie pattern: ^[1-9][0-9]{3,6}$ preferred_prefix: gmelin references: - https://en.wikipedia.org/wiki/Gmelin_database gno: banana: 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' homepage: https://gnome.glyomics.org/ license: CC BY 4.0 mappings: bioportal: GNO obofoundry: GNO ols: gno ontobee: GNO name: Glycan Naming and Subsumption Ontology pattern: ^\d{8}$ preferred_prefix: GNO repository: https://github.com/glygen-glycan-data/GNOme uri_format: http://purl.obolibrary.org/obo/GNO_$1 version: 1.10.0 gnpis: description: GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. example: AY109603 homepage: https://urgi.versailles.inra.fr/gnpis/ mappings: biocontext: GNPIS fairsharing: FAIRsharing.dw22y3 miriam: gnpis n2t: gnpis name: GnpIS pattern: ^[A-Za-z0-9]+$ preferred_prefix: gnpis uri_format: https://urgi.versailles.inra.fr/gnpis/#result/term=$1 go: appears_in: - agro - chiro - cl - ecocore - ecto - envo - maxo - pcl - pco - planp - uberon - xpo - zp banana: GO contact: email: suzia@stanford.edu github: suzialeksander name: Suzi Aleksander orcid: 0000-0001-6787-2901 depends_on: - cl - ncbitaxon - ro - uberon description: The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. download_json: http://purl.obolibrary.org/obo/go.json download_obo: http://purl.obolibrary.org/obo/go.obo download_owl: http://purl.obolibrary.org/obo/go.owl example: '0032571' homepage: http://geneontology.org/ license: CC BY 4.0 mappings: biocontext: GO bioportal: GO fairsharing: FAIRsharing.6xq0ee go: GO miriam: go n2t: go ncbi: GO obofoundry: GO ols: go ontobee: GO prefixcommons: go uniprot: GO wikidata: P686 name: Gene Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: GO providers: - code: 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 - 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 repository: https://github.com/geneontology/go-ontology synonyms: - gobp - gobpid - gocc - goccid - gomf - gomfid uri_format: http://amigo.geneontology.org/amigo/term/GO:$1 version: '2022-03-10' 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: 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 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 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=$1 gold.meta: description: "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has\ \ been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold,\ \ and this namespace is kept here for support to already existing citations, new\ \ ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes OnLine\ \ Database)is a resource for centralized monitoring of genome and metagenome projects\ \ worldwide. It stores information on complete and ongoing projects, along with\ \ their associated metadata. This collection references metadata associated with\ \ samples." example: Gm00047 homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi mappings: biocontext: GOLD.META miriam: gold.meta n2t: gold.meta name: GOLD metadata pattern: ^Gm\d+$ preferred_prefix: gold.meta uri_format: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1 google.patent: description: Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date. example: US4145692 homepage: https://www.google.com/patents/ mappings: biocontext: GOOGLE.PATENT cellosaurus: Patent miriam: google.patent n2t: google.patent name: Google Patents pattern: ^[A-Z]{2}\d+([A-Z])?$ preferred_prefix: google.patent synonyms: - patent uri_format: https://www.google.com/patents/$1 google.scholar: description: 'Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.' example: PjrpzUIAAAAJ homepage: https://scholar.google.com/ mappings: biolink: GSID name: Google Scholar Researcher preferred_prefix: google.scholar gorel: description: Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO. download_owl: ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl example: '0002005' homepage: http://geneontology.org/docs/ontology-relations/ mappings: biolink: GOREL go: GOREL name: GO Relations pattern: ^\d{7}$ preferred_prefix: gorel 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 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=$1 gramene.growthstage: banana: gramene.growthstage:GRO\ description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene. example: '0007133' homepage: http://www.gramene.org/ mappings: biocontext: GRAMENE.GROWTHSTAGE miriam: gramene.growthstage n2t: gramene.growthstage name: Gramene Growth Stage Ontology pattern: ^\d{7}$ 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=$1 grassbase: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species. example: imp10873 homepage: https://www.kew.org/data/grasses-syn/index.htm name: GrassBase pattern: ^(imp|gen)\d{5}$ preferred_prefix: grassbase uri_format: https://www.kew.org/data/grasses-db/www/$1 greengenes: description: A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. example: '100000' homepage: http://greengenes.lbl.gov/ mappings: biocontext: GREENGENES fairsharing: FAIRsharing.bpxgb6 miriam: greengenes n2t: greengenes ncbi: Greengenes prefixcommons: greengenes name: 16S rRNA gene database pattern: ^\d+$ preferred_prefix: greengenes 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?$1 gro: deprecated: true mappings: bioportal: GRO name: Gene Regulation Ontology preferred_prefix: gro grsdb: description: GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank. example: '10142' homepage: http://bioinformatics.ramapo.edu/GRSDB2/ mappings: biocontext: GRSDB miriam: grsdb n2t: grsdb prefixcommons: grsdb name: G-Rich Sequences Database pattern: ^\d+$ 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=$1 gsso: appears_in: - ontoavida - scdo banana: GSSO contact: email: kronkcj@mail.uc.edu github: Superraptor name: Clair Kronk orcid: 0000-0001-8397-8810 description: The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology. download_json: http://purl.obolibrary.org/obo/gsso.json download_obo: http://purl.obolibrary.org/obo/gsso.obo download_owl: http://purl.obolibrary.org/obo/gsso.owl example: 002368 homepage: https://gsso.research.cchmc.org/ license: Apache 2.0 License mappings: bioportal: GSSO miriam: gsso obofoundry: GSSO ols: gsso ontobee: GSSO name: Gender, Sex, and Sexual Orientation Ontology namespace_in_lui: true pattern: ^\d{6}$ 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/$1 gudmap: description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract. example: Q-2958 homepage: http://www.gudmap.org/ mappings: biocontext: GUDMAP fairsharing: FAIRsharing.910c39 miriam: gudmap n2t: gudmap name: Genitourinary Development Molecular Anatomy Project pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$ 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: banana: 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_$1 hamap: description: HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries. example: MF_01400 homepage: https://hamap.expasy.org/ mappings: biocontext: HAMAP fairsharing: FAIRsharing.63m4ss go: HAMAP miriam: hamap n2t: hamap prefixcommons: hamap uniprot: HAMAP name: High-quality Automated and Manual Annotation of microbial Proteomes pattern: ^MF_\d+$ preferred_prefix: hamap uri_format: https://hamap.expasy.org/unirule/$1 hancestro: banana: HANCESTRO contact: email: danielle.welter@uni.lu github: daniwelter name: Danielle Welter orcid: 0000-0003-1058-2668 description: Human ancestry ontology for the NHGRI GWAS Catalog download_owl: http://purl.obolibrary.org/obo/hancestro.owl example: 0290 homepage: https://github.com/EBISPOT/ancestro license: CC BY 4.0 mappings: biolink: HANCESTRO bioportal: HANCESTRO fairsharing: FAIRsharing.rja8qp obofoundry: HANCESTRO ols: hancestro ontobee: HANCESTRO name: Human Ancestry Ontology pattern: ^\d{4}$ preferred_prefix: HANCESTRO repository: https://github.com/EBISPOT/ancestro uri_format: http://purl.obolibrary.org/obo/HANCESTRO_$1 version: '2.5' hao: banana: HAO contact: email: diapriid@gmail.com github: mjy name: Matt Yoder orcid: 0000-0002-5640-5491 description: A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) download_obo: http://purl.obolibrary.org/obo/hao.obo download_owl: http://purl.obolibrary.org/obo/hao.owl example: 0000187 homepage: http://hymao.org license: CC0 1.0 mappings: biocontext: HAO bioportal: HAO fairsharing: FAIRsharing.kj3m5n obofoundry: HAO ols: hao ontobee: HAO name: Hymenoptera Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: HAO repository: https://github.com/hymao/hao uri_format: http://purl.obolibrary.org/obo/HAO_$1 version: '2021-03-05' hba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A controlled vocabulary to support the study of transcription in the human brain download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-hba.obo example: '4005' example_extras: - '265504410' homepage: https://human.brain-map.org name: Human Brain Atlas pattern: ^\d+$ preferred_prefix: HBA 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/2022-04-19/hcao.owl homepage: https://www.humancellatlas.org mappings: ols: hcao name: Human Cell Atlas Ontology no_own_terms: true preferred_prefix: hcao version: '2022-04-19' hcpcs: 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: biolink: HCPCS bioportal: HCPCS fairsharing: FAIRsharing.x81wz8 name: Healthcare Common Procedure Coding System preferred_prefix: hcpcs 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 name: Hepatitis C Virus Database pattern: ^M\d{5}$ preferred_prefix: hcvdb uri_format: https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1 hdr: description: The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders. example: '63' homepage: http://research.nhgri.nih.gov/apps/homeodomain/web/ mappings: biocontext: HDR miriam: hdr n2t: hdr prefixcommons: hdr name: Homeodomain Research pattern: ^\d+$ preferred_prefix: hdr uri_format: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1 hgmd: description: The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases. example: CALM1 homepage: http://www.hgmd.cf.ac.uk/ac/index.php mappings: biocontext: HGMD miriam: hgmd n2t: hgmd name: Human Gene Mutation Database pattern: ^[A-Z_0-9]+$ preferred_prefix: hgmd uri_format: http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1 hgnc: description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database. example: '16793' homepage: http://www.genenames.org mappings: biocontext: HGNC bioportal: HGNC cellosaurus: HGNC fairsharing: FAIRsharing.amcv1e go: HGNC miriam: hgnc n2t: hgnc ncbi: HGNC prefixcommons: hgnc uniprot: HGNC wikidata: P354 name: HUGO Gene Nomenclature Committee pattern: ^((HGNC|hgnc):)?\d{1,5}$ preferred_prefix: hgnc providers: - 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 - 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 uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1 hgnc.genefamily: deprecated: true description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides symbols for both structural and functional gene families. This collection refers to records using the HGNC family symbol. example: '2029' has_canonical: hgnc.genegroup homepage: http://www.genenames.org mappings: biocontext: HGNC.GENEFAMILY miriam: hgnc.family n2t: hgnc.genefamily name: HGNC Family pattern: ^[A-Z0-9-]+(#[A-Z0-9-]+)?$ 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: pathwaycommons description: Interactions between a given gene and other molecular entities homepage: https://www.pathwaycommons.org/ name: Pathway Commons Gene Interations uri_format: https://apps.pathwaycommons.org/interactions?source=$1 - code: oncomx description: Mutation profiles for a gene homepage: https://oncomx.org name: OncoMX uri_format: https://oncomx.org/searchview/?gene=$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/Home.aspx mappings: cellosaurus: HIVReagentProgram name: NIH HIV Reagent Program preferred_prefix: hivreagentprogram uri_format: https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx hmdb: description: The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data. example: HMDB00001 homepage: http://www.hmdb.ca/ mappings: biocontext: HMDB cheminf: 000408 fairsharing: FAIRsharing.sye5js miriam: hmdb n2t: hmdb prefixcommons: hmdb wikidata: P2057 name: Human Metabolome Database pattern: ^HMDB\d+$ preferred_prefix: hmdb 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 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 uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1 hom: banana: HOM contact: email: bgee@sib.swiss github: fbastian name: Frederic Bastian orcid: 0000-0002-9415-5104 description: This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. download_owl: http://purl.obolibrary.org/obo/hom.owl example: 0000049 homepage: https://github.com/BgeeDB/homology-ontology license: CC0 1.0 mappings: biocontext: HOM bioportal: HOM fairsharing: FAIRsharing.efv7gw obofoundry: HOM ols: hom ontobee: HOM name: Homology Ontology pattern: ^\d{7}$ preferred_prefix: HOM 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 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 uri_format: 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 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 uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN hp: appears_in: - chiro - scdo banana: HP contact: email: dr.sebastian.koehler@gmail.com github: drseb name: Sebastian Koehler orcid: 0000-0002-5316-1399 description: The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. download_obo: http://purl.obolibrary.org/obo/hp.obo download_owl: http://purl.obolibrary.org/obo/hp.owl example: '0011140' homepage: http://www.human-phenotype-ontology.org/ license: hpo mappings: biocontext: HPO bioportal: HP fairsharing: FAIRsharing.kbtt7f miriam: hp n2t: hp obofoundry: HP ols: hp ontobee: HP wikidata: P3841 name: Human Phenotype Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: HP repository: https://github.com/obophenotype/human-phenotype-ontology synonyms: - hpo uri_format: https://hpo.jax.org/app/browse/term/HP:$1 version: '2022-04-14' hpa: description: The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers. example: ENSG00000026508 homepage: http://www.proteinatlas.org/ mappings: biocontext: HPA fairsharing: FAIRsharing.j0t0pe go: HPA miriam: hpa n2t: hpa prefixcommons: hpa uniprot: HPA name: Human Protein Atlas tissue profile information pattern: ^ENSG\d{11}$ preferred_prefix: hpa 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 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 uri_format: http://www.hprd.org/protein/$1 hpscreg: description: hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines). example: BCRTi001-A homepage: https://hpscreg.eu/ mappings: cellosaurus: hPSCreg fairsharing: FAIRsharing.7C0aVE miriam: hpscreg n2t: hpscreg name: Human Pluripotent Stem Cell Registry pattern: ^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$ preferred_prefix: hpscreg uri_format: https://hpscreg.eu/cell-line/$1 hsapdv: appears_in: - scdo banana: HsapDv contact: email: frederic.bastian@unil.ch github: fbastian name: Frédéric Bastian orcid: 0000-0002-9415-5104 description: Life cycle stages for Human download_obo: http://purl.obolibrary.org/obo/hsapdv.obo download_owl: http://purl.obolibrary.org/obo/hsapdv.owl example: 0000194 homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv license: CC BY 3.0 mappings: biocontext: HSAPDV biolink: HsapDv bioportal: HSAPDV fairsharing: FAIRsharing.c6vhm3 obofoundry: HsapDv ols: hsapdv ontobee: HSAPDV name: Human Developmental Stages pattern: ^\d{7}$ preferred_prefix: HsapDv repository: https://github.com/obophenotype/developmental-stage-ontologies synonyms: - HsapDv uri_format: http://purl.obolibrary.org/obo/HSAPDV_$1 version: '2020-03-10' hsdb: description: The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. example: '5621' homepage: https://pubchem.ncbi.nlm.nih.gov/source/hsdb mappings: wikidata: P2062 name: Hazardous Substances Data Bank pattern: ^\d+$ preferred_prefix: hsdb uri_format: https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1 hso: banana: HSO contact: email: fernanda.dorea@sva.se github: nandadorea name: Fernanda Dorea orcid: 0000-0001-8638-8525 depends_on: - bfo - ncbitaxon - obi - ro - uberon description: The health Surveillance Ontology (HSO) focuses on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance. download_owl: http://purl.obolibrary.org/obo/hso.owl example: '0000062' homepage: https://w3id.org/hso license: CC BY 3.0 mappings: bioportal: HSO obofoundry: HSO ols: hso ontobee: HSO name: Health Surveillance Ontology pattern: ^\d{7}$ 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 uri_format: ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2 htn: banana: HTN contact: email: aellenhicks@gmail.com github: aellenhicks name: Amanda Hicks orcid: 0000-0002-1795-5570 description: An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines download_owl: http://purl.obolibrary.org/obo/htn.owl example: '00000014' homepage: https://github.com/aellenhicks/htn_owl license: CC BY 4.0 mappings: bioportal: HTN obofoundry: HTN ols: htn ontobee: HTN name: Hypertension Ontology pattern: ^\d{8}$ 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 uri_format: https://www.kazusa.or.jp/huge/gfpage/$1 iao: appears_in: - agro - clyh - duo - ecocore - ecto - fovt - labo - maxo - pco - psdo - xpo banana: IAO contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 description: An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch. download_owl: http://purl.obolibrary.org/obo/iao.owl example: '0000030' homepage: https://github.com/information-artifact-ontology/IAO/ license: CC BY 4.0 mappings: biocontext: IAO bioportal: IAO fairsharing: FAIRsharing.gq1xtx go: IAO miriam: iao n2t: iao obofoundry: IAO ols: iao ontobee: IAO name: Information Artifact Ontology pattern: ^\d{7}$ preferred_prefix: IAO repository: https://github.com/information-artifact-ontology/IAO uri_format: http://purl.obolibrary.org/obo/IAO_$1 version: '2020-12-09' icd10: description: The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes. example: C34 homepage: https://icd.who.int/browse10 mappings: biocontext: ICD biolink: ICD10 bioportal: ICD10 fairsharing: FAIRsharing.nj16g miriam: icd n2t: icd prefixcommons: icd wikidata: P494 name: International Classification of Diseases, 10th Revision pattern: ^[A-Z]\d+(\.[-\d+])?$ preferred_prefix: icd10 references: - https://icdcodelookup.com/icd-10/codes/A01.1 synonyms: - ICD - ICD-10 - ICD10 uri_format: http://apps.who.int/classifications/icd10/browse/2010/en#/$1 icd10cm: description: ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States. example: F4521 homepage: https://www.icd10data.com/ICD10CM mappings: bioportal: ICD10CM fairsharing: FAIRsharing.hpvbxb wikidata: P4229 name: International Classification of Diseases, 10th Revision, Clinical Modification preferred_prefix: icd10cm synonyms: - ICD10CM uri_format: https://icd.codes/icd10cm/$1 icd10pcs: 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: bioportal: ICD10PCS fairsharing: FAIRsharing.85k1jm 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: 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 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: 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 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=$1 icd9cm: description: ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States. example: '784' homepage: https://www.cdc.gov/nchs/icd/icd9cm.htm mappings: bioportal: ICD9CM fairsharing: FAIRsharing.10zsxb wikidata: P1692 name: International Classification of Diseases, 9th Revision, Clinical Modification pattern: ^([\dA-Z]\d{2}(\.\d{1,3}|))|(\d{2}(\.\d{1,2}|))$ 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/$1 icdo: description: The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases example: 9861/3 homepage: https://www.who.int/classifications/icd/adaptations/oncology/en/ mappings: prefixcommons: icdo wikidata: P563 name: International Classification of Diseases for Oncology pattern: ^[8-9]\d{3}(/[0-3])?$ 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=$1 iceo: banana: ICEO contact: email: liumeng94@sjtu.edu.cn github: Lemon-Liu name: Meng LIU orcid: 0000-0003-3781-6962 description: A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning. download_owl: http://purl.obolibrary.org/obo/iceo.owl example: '0000712_1' example_extras: - '0000712' homepage: https://github.com/ontoice/ICEO license: CC BY 4.0 mappings: bioportal: ICEO obofoundry: ICEO ols: iceo ontobee: ICEO name: Integrative and Conjugative Element Ontology pattern: ^\d{7}(_\d)?$ 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 references: - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4823818/ 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=$1 ico: appears_in: - scdo banana: ICO contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field. download_owl: http://purl.obolibrary.org/obo/ico.owl example: '0000066' homepage: https://github.com/ICO-ontology/ICO license: CC BY 3.0 mappings: biocontext: ICO bioportal: ICO fairsharing: FAIRsharing.b9znd5 obofoundry: ICO ols: ico ontobee: ICO name: Informed Consent Ontology pattern: ^\d{7}$ 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=$1 ido: appears_in: - scdo banana: IDO contact: email: Lindsay.Cowell@utsouthwestern.edu github: lgcowell name: Lindsay Cowell orcid: 0000-0003-1617-8244 description: Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases. download_owl: http://purl.obolibrary.org/obo/ido.owl example: '0000504' homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology license: CC BY 3.0 mappings: biocontext: IDO bioportal: IDO fairsharing: FAIRsharing.aae3v6 miriam: ido n2t: ido obofoundry: IDO ols: ido ontobee: IDO name: Infectious Disease Ontology pattern: ^[0-9]+$ preferred_prefix: IDO repository: https://github.com/infectious-disease-ontology/infectious-disease-ontology uri_format: https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1 version: '2017-11-03' idocovid19: contact: email: johnbeverley2021@u.northwestern.edu github: johnbeve name: John Beverly orcid: 0000-0002-1118-1738 description: The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease. download_owl: http://purl.obolibrary.org/obo/2020-21-07/ido-covid-19.owl example: 0001191 homepage: https://github.com/infectious-disease-ontology-extensions/ido-covid-19 mappings: bioportal: IDO-COVID-19 ols: idocovid19 name: The COVID-19 Infectious Disease Ontology pattern: ^\d{7}$ preferred_prefix: idocovid19 repository: https://github.com/infectious-disease-ontology-extensions/ido-covid-19 version: '2020-07-21' idoden: description: An ontology for dengue fever. example: '0003463' homepage: https://bioportal.bioontology.org/ontologies/IDODEN mappings: 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 idomal: appears_in: - scdo banana: IDOMAL contact: email: topalis@imbb.forth.gr github: null name: Pantelis Topalis orcid: null 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' homepage: https://www.vectorbase.org/ontology-browser license: CC0 1.0 mappings: biocontext: IDOMAL bioportal: IDOMAL fairsharing: FAIRsharing.2q8c28 obofoundry: IDOMAL ols: idomal ontobee: IDOMAL name: Malaria Ontology pattern: ^\d{7}$ preferred_prefix: IDOMAL 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/$1 iev: banana: IEV deprecated: true example: '0000000' homepage: http://www.inoh.org mappings: biocontext: IEV obofoundry: IEV prefixcommons: iev name: Event (INOH pathway ontology) pattern: ^\d{7}$ 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/$1 ihw: description: The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics. example: IHW09326 homepage: https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html mappings: cellosaurus: IHW name: International Histocompatibility Workshop cell lines pattern: ^IHW\d+$ 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=$1 imdrf: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence. homepage: http://www.imdrf.org/ name: International Medical Device Regulators Forum no_own_terms: true preferred_prefix: imdrf references: - https://www.fda.gov/medical-devices/mandatory-reporting-requirements-manufacturers-importers-and-device-user-facilities/mdr-adverse-event-codes imex: description: The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources. example: IM-19210-3 homepage: https://www.imexconsortium.org/ mappings: biocontext: IMEX miriam: imex n2t: imex prefixcommons: imex name: International Molecular Exchange pattern: ^IM-\d+(-?)(\d+?)$ 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 uri_format: https://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1 img.gene: description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information. example: '638309541' homepage: http://img.jgi.doe.gov/ mappings: biocontext: IMG.GENE miriam: img.gene n2t: img.gene prefixcommons: img.gene name: Integrated Microbial Genomes Gene pattern: ^\d+$ preferred_prefix: img.gene 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 uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1 imgt.hla: description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature. example: A*01:01:01:01 homepage: https://www.ebi.ac.uk/imgt/hla/allele.html mappings: biocontext: IMGT.HLA cellosaurus: IPD-IMGT/HLA fairsharing: FAIRsharing.e28v7g go: IMGT_HLA miriam: imgt.hla n2t: imgt.hla ncbi: IMGT/HLA prefixcommons: imgthla name: IMGT/HLA human major histocompatibility complex sequence database pattern: ^[A-Z0-9*:]+$ preferred_prefix: imgt.hla 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'] uri_format: http://www.imgt.org/ligmdb/view?id=$1 imr: banana: IMR contact: email: curator@inoh.org github: null name: INOH curators orcid: null deprecated: true example: '0000001' homepage: http://www.inoh.org mappings: biocontext: IMR obofoundry: IMR prefixcommons: imr name: Molecule role (INOH Protein name/family name ontology) pattern: ^\d{7}$ preferred_prefix: IMR uri_format: http://purl.obolibrary.org/obo/IMR_$1 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/$1 inchikey: description: The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI. example: RYYVLZVUVIJVGH-UHFFFAOYSA-N homepage: http://www.chemspider.com/ mappings: biocontext: INCHIKEY miriam: inchikey n2t: inchikey scholia: inchikey wikidata: P235 name: InChIKey pattern: ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])$ 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 inn: comment: can not find a place to resolve to 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=$1 ino: banana: INO contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles. download_owl: http://purl.obolibrary.org/obo/ino.owl example: '0000003' homepage: https://github.com/INO-ontology/ino license: CC BY 3.0 mappings: biolink: INO bioportal: INO fairsharing: FAIRsharing.mm72as obofoundry: INO ols: ino ontobee: INO name: Interaction Network Ontology pattern: ^\d{7}$ preferred_prefix: INO repository: https://github.com/INO-ontology/ino uri_format: http://purl.obolibrary.org/obo/INO_$1 version: 1.0.112 insdc: description: The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. example: X58356 homepage: https://www.ncbi.nlm.nih.gov/Genbank/ mappings: biocontext: INSDC miriam: insdc n2t: insdc prefixcommons: insdc name: Nucleotide Sequence Database pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ 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 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/$1 insdc.gca: description: The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage. example: GCA_000155495.1 homepage: https://www.ebi.ac.uk/ena/browse/genome-assembly-database mappings: biocontext: INSDC.GCA miriam: insdc.gca n2t: insdc.gca name: Genome assembly database pattern: ^GC[AF]_[0-9]{9}\.[0-9]+$ 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/$1 insdc.run: comment: 'https://www.insdc.org/ is the authoritative source for INSDC. However, confusingly, they don''t mention runs in this table. I think we should ask them to include. ENA is a partner and they have documentation here: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html Runs | (E\|D\|S)RR[0-9]{6,} | ERR123456 -- | -- | --' contributor: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: An experimental run, served thrugh the ENA example: ERR436051 has_canonical: ena.embl homepage: https://www.insdc.org/ name: International Nucleotide Sequence Database Collaboration (INSDC) Run pattern: ^(E|D|S)RR[0-9]{6,}$ 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: 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 - 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 uri_format: https://www.ncbi.nlm.nih.gov/sra/$1 intact: description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. example: EBI-2307691 homepage: https://www.ebi.ac.uk/intact/ mappings: biocontext: INTACT fairsharing: FAIRsharing.d05nwx go: IntAct miriam: intact n2t: intact prefixcommons: intact uniprot: IntAct name: IntAct protein interaction database pattern: ^EBI\-[0-9]+$ preferred_prefix: intact 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/molecule/$1 interlex: description: 'InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. ' example: 0101963 homepage: https://www.fdilab.org mappings: fairsharing: FAIRsharing.67sssf miriam: ilx name: InterLex pattern: ^[0-9]+$ preferred_prefix: interlex references: - https://github.com/AllenInstitute/nomenclature synonyms: - ILX uri_format: https://scicrunch.org/scicrunch/interlex/view/ilx_$1 interpro: contact: email: interhelp@ebi.ac.uk github: null name: InterPro Help orcid: null description: InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. example: IPR016380 homepage: http://www.ebi.ac.uk/interpro/index.html mappings: biocontext: IPR biolink: interpro fairsharing: FAIRsharing.pda11d go: InterPro miriam: interpro n2t: interpro ncbi: InterPro obofoundry: IPR prefixcommons: interpro uniprot: InterPro wikidata: P2926 name: InterPro pattern: ^IPR\d{6}$ 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 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 uri_format: http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1 irefweb: description: 'iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.' example: '617102' homepage: http://wodaklab.org/iRefWeb/ mappings: biocontext: IREFWEB fairsharing: FAIRsharing.t31wcb miriam: irefweb n2t: irefweb prefixcommons: irefweb name: iRefWeb pattern: ^\d+$ 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:$1 isbn: description: The International Standard Book Number (ISBN) is for identifying printed books. example: '9781584885658' homepage: http://isbndb.com/ mappings: biocontext: ISBN-13 biolink: isbn go: ISBN miriam: isbn n2t: isbn prefixcommons: isbn name: International Standard Book Number pattern: ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ 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 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/$1 issn: description: The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books. example: 0745-4570 homepage: https://portal.issn.org mappings: biocontext: ISSN biolink: issn go: ISSN miriam: issn n2t: issn name: International Standard Serial Number pattern: ^\d{4}-\d{3}[\dX]$ 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/$1 itis: description: Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world. example: '589462' homepage: https://www.itis.gov/ mappings: fairsharing: FAIRsharing.t19hpa wikidata: P815 name: Integrated Taxonomic Information System pattern: ^\d+$ preferred_prefix: itis uri_format: https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1 ito: description: The Intelligence Task Ontology (ITO) provides a comprehensive map of machine intelligence tasks, as well as broader human intelligence or hybrid human/machine intelligence tasks. example: ITO_01625 homepage: https://bioportal.bioontology.org/ mappings: bioportal: ITO miriam: ito name: Intelligence Task Ontology pattern: ^.+$ 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=$1 jax: description: Information about the C57BL/6J. Includes genetic background and disease data. example: '004435' homepage: https://www.jax.org/strain mappings: biocontext: JAX fairsharing: FAIRsharing.5701h1 name: Jackson Laboratories Strain pattern: ^\d{6}$ 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/ uri_format: https://jjj.bio.vu.nl/models/$1 kaggle: description: Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions. example: nasa/kepler-exoplanet-search-results homepage: https://kaggle.com mappings: miriam: kaggle n2t: kaggle name: Kaggle pattern: ^[0-9a-zA-Z\-]+\/[0-9a-zA-Z\-]+$ 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/$1 kegg.compound: description: KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life. example: C12345 homepage: https://www.genome.jp/kegg/ligand.html mappings: biocontext: KEGG.COMPOUND miriam: kegg.compound n2t: kegg.compound prefixcommons: kegg.compound wikidata: P665 name: KEGG Compound part_of: kegg pattern: ^C\d+$ preferred_prefix: kegg.compound 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/$1 kegg.drug: description: KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules. example: D00123 homepage: https://www.genome.jp/kegg/drug/ mappings: biocontext: KEGG.DRUG miriam: kegg.drug n2t: kegg.drug prefixcommons: kegg.drug wikidata: P665 name: KEGG Drug part_of: kegg pattern: ^D\d+$ preferred_prefix: kegg.drug synonyms: - KEGG DRUG - KEGG.DRUG uri_format: https://www.kegg.jp/entry/$1 kegg.environ: description: KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable. example: ev:E00032 homepage: http://www.genome.jp/kegg/drug/environ.html mappings: biocontext: KEGG.ENVIRON miriam: kegg.environ n2t: kegg.environ name: KEGG Environ part_of: kegg pattern: ^(ev\:)?E\d+$ preferred_prefix: kegg.environ 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:$1 kegg.genes: description: KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources. example: bsu:BSU01340 homepage: http://www.genome.jp/kegg/genes.html mappings: biocontext: KEGG.GENES biolink: KEGG.GENE miriam: kegg.genes n2t: kegg.genes wikidata: P665 name: KEGG Genes part_of: kegg pattern: ^\w+:[\w\d\.-]*$ preferred_prefix: kegg.genes 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 synonyms: - kegg_genome - kegg_genomes uri_format: http://www.kegg.jp/entry/$1 kegg.glycan: description: KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways. example: G00123 homepage: https://www.genome.jp/kegg/glycan/ mappings: biocontext: KEGG.GLYCAN miriam: kegg.glycan n2t: kegg.glycan prefixcommons: kegg.glycan name: KEGG Glycan part_of: kegg pattern: ^G\d+$ preferred_prefix: kegg.glycan 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 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/$1 kegg.pathway: description: KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks. example: rsk00410 homepage: https://www.genome.jp/kegg/pathway.html mappings: biocontext: KEGG-path biolink: KEGG.PATHWAY go: KEGG_PATHWAY miriam: kegg.pathway n2t: kegg.pathway prefixcommons: kegg.pathway wikidata: P665 name: KEGG Pathways Database part_of: kegg pattern: ^\w{2,4}\d{5}$ preferred_prefix: kegg.pathway 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 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 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=$1.pdf labo: banana: LABO contact: email: paul.fabry@usherbrooke.ca github: pfabry name: Paul Fabry orcid: 0000-0002-3336-2476 depends_on: - iao - obi - ogms - omiabis - omrse - opmi description: LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents. download_owl: http://purl.obolibrary.org/obo/labo.owl example: '0000124' homepage: https://github.com/OpenLHS/LABO license: CC BY 4.0 mappings: bioportal: LABO obofoundry: LABO ols: labo ontobee: LABO name: clinical LABoratory Ontology pattern: ^\d{7}$ preferred_prefix: LABO repository: https://github.com/OpenLHS/LABO uri_format: http://purl.obolibrary.org/obo/LABO_$1 version: '2021-06-08' lbo: contact: email: caripark@iastate.edu github: caripark name: Carissa Park orcid: 0000-0002-2346-5201 description: A vocabulary for cattle, chicken, horse, pig, and sheep breeds. download_obo: https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.obo download_owl: https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.owl example: 0000487 homepage: http://bioportal.bioontology.org/ontologies/LBO mappings: bioportal: LBO fairsharing: FAIRsharing.309v57 ols: lbo name: Livestock Breed Ontology pattern: ^\d{7}$ preferred_prefix: lbo repository: https://github.com/AnimalGenome/livestock-breed-ontology 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/$1 lepao: banana: LEPAO contact: email: lagonzalezmo@unal.edu.co github: luis-gonzalez-m name: Luis A. Gonzalez-Montana orcid: 0000-0002-9136-9932 depends_on: - aism - bfo - bspo - caro - pato - ro - uberon description: The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. download_obo: http://purl.obolibrary.org/obo/lepao.obo download_owl: http://purl.obolibrary.org/obo/lepao.owl example: '0000005' homepage: https://github.com/insect-morphology/lepao license: CC BY 4.0 mappings: bioportal: LEPAO obofoundry: LEPAO ols: lepao name: Lepidoptera Anatomy Ontology pattern: ^\d{7}$ 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/$1 lgic: comment: Website is gone deprecated: true description: The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available. example: 5HT3Arano homepage: https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php mappings: biocontext: LGIC miriam: lgic n2t: lgic name: Ligand-Gated Ion Channel database pattern: ^\w+$ preferred_prefix: lgic uri_format: https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php licebase: description: Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects. example: EMLSAT00000003403 homepage: https://licebase.org mappings: biocontext: LICEBASE fairsharing: FAIRsharing.c7w81a miriam: licebase n2t: licebase name: LiceBase pattern: ^[A-Za-z0-9\-\/]+$ 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 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#$1 lipidbank: description: LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. example: BBA0001 homepage: http://lipidbank.jp/index.html mappings: biocontext: LIPIDBANK fairsharing: FAIRsharing.bdn9br miriam: lipidbank n2t: lipidbank prefixcommons: lipidbank name: LipidBank pattern: ^\w+\d+$ preferred_prefix: lipidbank uri_format: http://lipidbank.jp/cgi-bin/detail.cgi?id=$1 lipidmaps: description: The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy. example: LMPR0102010012 homepage: http://www.lipidmaps.org mappings: biocontext: LIPIDMAPS cheminf: '000564' fairsharing: FAIRsharing.cpneh8 miriam: lipidmaps n2t: lipidmaps prefixcommons: lipidmaps scholia: lipidmaps wikidata: P2063 name: LIPID MAPS pattern: ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$ 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 synonyms: - LIPID MAPS - LIPID_MAPS_class - LIPID_MAPS_instance uri_format: http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1 lipro: banana: LIPRO contact: email: bakerc@unb.ca github: null name: Christipher Baker orcid: null deprecated: true description: An ontology representation of the LIPIDMAPS nomenclature classification. mappings: 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: banana: 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: description: The international standard for identifying health measurements, observations, and documents. example: LL379-9 homepage: https://loinc.org/ mappings: biolink: LOINC bioportal: LOINC fairsharing: FAIRsharing.2mk2zb name: Logical Observation Identifiers Names and Codes preferred_prefix: loinc 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=$1 lotus: comment: IDs are actually leading to the structural part of LOTUS only, which might change in the future. Will adapt the regexp in case. contact: email: adriano.rutz@ik.me github: adafede name: Adriano Rutz orcid: 0000-0003-0443-9902 contributor: email: null github: adafede name: Adriano Rutz orcid: 0000-0003-0443-9902 description: LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry. example: LTS0004651 homepage: https://lotus.naturalproducts.net name: LOTUS Initiative for Open Natural Products Research pattern: ^LTS\d{7}$ 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/$1 lpt: contact: email: caripark@iastate.edu github: caripark name: Carissa Park orcid: 0000-0002-2346-5201 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit. download_obo: https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.obo download_owl: https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.owl example: '0000001' homepage: https://github.com/AnimalGenome/livestock-product-trait-ontology mappings: biocontext: LPT bioportal: LPT fairsharing: FAIRsharing.g78mbm name: Livestock Product Trait Ontology pattern: ^\d+$ preferred_prefix: lpt repository: https://github.com/AnimalGenome/livestock-product-trait-ontology uri_format: http://purl.obolibrary.org/obo/LPT_$1 lrg: description: A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI. example: LRG_1 homepage: http://www.lrg-sequence.org/ mappings: biocontext: LRG miriam: lrg n2t: lrg name: Locus Reference Genomic pattern: ^LRG_\d+$ 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=$1 ma: banana: MA contact: email: Terry.Hayamizu@jax.org github: tfhayamizu name: Terry Hayamizu orcid: 0000-0002-0956-8634 description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus) download_obo: http://purl.obolibrary.org/obo/ma.obo download_owl: http://purl.obolibrary.org/obo/ma.owl example: '0002502' homepage: https://github.com/obophenotype/mouse-anatomy-ontology license: CC BY 4.0 mappings: biocontext: MA bioportal: MA fairsharing: FAIRsharing.pdwqcr go: MA miriam: ma n2t: ma obofoundry: MA ols: ma ontobee: MA prefixcommons: ma name: Mouse adult gross anatomy namespace_in_lui: true pattern: ^\d+$ preferred_prefix: MA repository: https://github.com/obophenotype/mouse-anatomy-ontology uri_format: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1 version: '2017-02-07' macie: description: MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved. example: M0001 homepage: https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html mappings: biocontext: MACIE fairsharing: FAIRsharing.7xkx69 miriam: macie n2t: macie prefixcommons: macie name: Mechanism, Annotation and Classification in Enzymes pattern: ^M\d{4}$ preferred_prefix: macie uri_format: https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1 maizegdb.locus: description: MaizeGDB is the maize research community's central repository for genetics and genomics information. example: '25011' homepage: http://www.maizegdb.org/ mappings: biocontext: MAIZEGDB.LOCUS fairsharing: FAIRsharing.aq280w go: MaizeGDB_Locus miriam: maizegdb.locus n2t: maizegdb.locus ncbi: MaizeGDB prefixcommons: maizegdb uniprot: MaizeGDB name: MaizeGDB Locus pattern: ^\d+$ preferred_prefix: maizegdb.locus synonyms: - MaizeGDB uri_format: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1 mamo: banana: MAMO contact: email: nicolas@ascistance.co.uk github: gambardella name: Nicolas Gambardella orcid: 0000-0002-6309-7327 description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. download_owl: http://purl.obolibrary.org/obo/mamo.owl example: '0000026' homepage: http://sourceforge.net/p/mamo-ontology/wiki/Home/ license: Artistic License 2.0 mappings: biocontext: MAMO bioportal: MAMO fairsharing: FAIRsharing.kbz5jh miriam: mamo n2t: mamo obofoundry: MAMO ols: mamo ontobee: MAMO name: Mathematical modeling ontology pattern: ^\d{7}$ 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: banana: 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=$1 mat: banana: MAT contact: email: j.bard@ed.ac.uk github: null name: Jonathan Bard orcid: null deprecated: true example: '0000000' mappings: biocontext: MAT bioportal: MAT obofoundry: MAT name: Minimal Anatomical Terminology pattern: ^\d{7}$ 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 name: MatrixDB preferred_prefix: matrixdb 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=$1&class=Association maxo: appears_in: - ecto banana: MAXO contact: email: Leigh.Carmody@jax.org github: LCCarmody name: Leigh Carmody orcid: 0000-0001-7941-2961 depends_on: - chebi - foodon - go - iao - ro - uberon description: An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations. download_json: http://purl.obolibrary.org/obo/maxo.json download_obo: http://purl.obolibrary.org/obo/maxo.obo download_owl: http://purl.obolibrary.org/obo/maxo.owl example: 0000008 homepage: https://github.com/monarch-initiative/MAxO license: CC BY 3.0 mappings: biolink: MAXO bioportal: MAXO obofoundry: MAXO ols: maxo ontobee: MAXO name: Medical Action Ontology pattern: ^\d{7}$ preferred_prefix: MAXO repository: https://github.com/monarch-initiative/MAxO uri_format: http://purl.obolibrary.org/obo/MAXO_$1 version: '2022-04-11' mba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A controlled vocabulary to support the study of transcription in the mouse brain download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-mba.obo example: '688' homepage: https://mouse.brain-map.org name: Mouse Brain Atlas pattern: ^\d+$ preferred_prefix: MBA mcc: deprecated: true mappings: bioportal: MCCL name: Cell Line Ontology [derivative] preferred_prefix: mcc mco: banana: 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: 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_$1 version: '2019-05-15' mdm: description: The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems. example: '4776' homepage: https://medical-data-models.org/ mappings: biocontext: MDM bioportal: MDM fairsharing: FAIRsharing.wnk2eq miriam: mdm n2t: mdm name: Medical Data Models pattern: ^\d+$ preferred_prefix: mdm uri_format: https://medical-data-models.org/forms/$1 meddra: description: The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT). example: '10015919' homepage: http://bioportal.bioontology.org/ontologies/MEDDRA mappings: biocontext: MEDDRA bioportal: MEDDRA fairsharing: FAIRsharing.ad3137 miriam: meddra n2t: meddra wikidata: P3201 name: Medical Dictionary for Regulatory Activities Terminology pattern: ^\d+$ preferred_prefix: meddra 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/$1 medlineplus: description: MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language. example: 002804 homepage: http://www.nlm.nih.gov/medlineplus/ mappings: biocontext: MEDLINEPLUS bioportal: MEDLINEPLUS fairsharing: FAIRsharing.bf8dsb miriam: medlineplus n2t: medlineplus name: MedlinePlus Health Topics pattern: ^\d+$ preferred_prefix: medlineplus uri_format: http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm merops: description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. example: S01.001 homepage: http://merops.sanger.ac.uk/index.htm mappings: biocontext: MEROPS fairsharing: FAIRsharing.2s4n8r go: MEROPS miriam: merops n2t: merops prefixcommons: merops uniprot: MEROPS name: MEROPS peptidase database pattern: ^[SCTAGMNU]\d{2}\.([AB]\d{2}|\d{3})$ preferred_prefix: merops uri_format: http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=$1 merops.family: description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families. example: S1 homepage: http://merops.sanger.ac.uk/index.htm mappings: biocontext: MEROPS.FAMILY miriam: merops.family n2t: merops.family name: MEROPS Family pattern: ^[SCTAGMNU]\d+$ preferred_prefix: merops.family uri_format: http://merops.sanger.ac.uk/cgi-bin/famsum?family=$1 merops.inhibitor: description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors. example: I31.952 homepage: http://merops.sanger.ac.uk/index.htm mappings: biocontext: MEROPS.INHIBITOR miriam: merops.inhibitor n2t: merops.inhibitor name: MEROPS Inhibitor pattern: ^I\d{2}\.\d{3}$ preferred_prefix: merops.inhibitor uri_format: http://merops.sanger.ac.uk/cgi-bin/pepsum?id=$1 mesh: description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc. example: C063233 example_extras: - D000001 homepage: http://id.nlm.nih.gov/mesh/ mappings: biocontext: MESH biolink: MESH bioportal: MESH cellosaurus: MeSH fairsharing: FAIRsharing.qnkw45 go: MeSH miriam: mesh n2t: mesh prefixcommons: mesh scholia: mesh wikidata: P486 name: Medical Subject Headings pattern: ^(C|D)\d{6,9}$ preferred_prefix: mesh synonyms: - MESH - MESHA - MESHC - MESHCS - MESHD - MESHPP - MESH_DESCRIPTOR_UI - MESH_SUPPLEMENTAL_RECORD_UI - MSH 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=$1&view=expanded metabolights: description: MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies. example: MTBLS1 homepage: https://www.ebi.ac.uk/metabolights/ mappings: biocontext: METABOLIGHTS cellosaurus: MetaboLights miriam: metabolights n2t: metabolights wikidata: P3890 name: MetaboLights Compound pattern: ^MTBLS\d+$ 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/$1 metacyc.compound: description: MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. example: CPD-10330 homepage: https://metacyc.org mappings: biocontext: METACYC.COMPOUND biolink: MetaCyc fairsharing: FAIRsharing.yytevr go: MetaCyc miriam: metacyc.compound n2t: metacyc.compound name: Metabolic Encyclopedia of metabolic and other pathways pattern: ^[A-Za-z0-9+_.%-:]+$ 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/$1 metlin: description: The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry. example: '1455' homepage: http://masspec.scripps.edu/ mappings: biocontext: METLIN miriam: metlin n2t: metlin name: Metabolite and Tandem Mass Spectrometry Database pattern: ^\d{4}$ 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=$1 mf: banana: MF contact: email: janna.hastings@gmail.com github: jannahastings name: Janna Hastings orcid: 0000-0002-3469-4923 description: The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning. download_owl: http://purl.obolibrary.org/obo/mf.owl example: 0000091 homepage: https://github.com/jannahastings/mental-functioning-ontology license: CC BY 3.0 mappings: biocontext: MF bioportal: MF fairsharing: FAIRsharing.4gm9gt obofoundry: MF ols: mf ontobee: MF name: Mental Functioning Ontology pattern: ^\d{7}$ preferred_prefix: MF repository: https://github.com/jannahastings/mental-functioning-ontology uri_format: http://purl.obolibrary.org/obo/MF_$1 version: '2021-11-17' mfmo: banana: MFMO contact: email: druzinsk@uic.edu github: RDruzinsky name: Robert Druzinsky orcid: 0000-0002-1572-1316 depends_on: - uberon description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors. download_owl: http://purl.obolibrary.org/obo/mfmo.owl example: 0000208 homepage: https://github.com/rdruzinsky/feedontology license: CC BY 3.0 mappings: biocontext: MFMO bioportal: MFMO fairsharing: FAIRsharing.669cnk obofoundry: MFMO ols: mfmo ontobee: MFMO name: Mammalian Feeding Muscle Ontology pattern: ^\d{7}$ preferred_prefix: MFMO repository: https://github.com/RDruzinsky/feedontology uri_format: http://purl.obolibrary.org/obo/MFMO_$1 version: '2013-11-16' mfo: banana: 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_owl: http://purl.obolibrary.org/obo/mfo.owl mappings: 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_$1 mfoem: banana: MFOEM contact: email: janna.hastings@gmail.com github: jannahastings name: Janna Hastings orcid: 0000-0002-3469-4923 description: An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings. download_owl: http://purl.obolibrary.org/obo/mfoem.owl example: '000204' homepage: https://github.com/jannahastings/emotion-ontology license: CC BY 3.0 mappings: biocontext: MFOEM bioportal: MFOEM fairsharing: FAIRsharing.dx30m8 obofoundry: MFOEM ols: mfoem ontobee: MFOEM name: Emotion Ontology pattern: ^\d{6}$ preferred_prefix: MFOEM repository: https://github.com/jannahastings/emotion-ontology uri_format: http://purl.obolibrary.org/obo/MFOEM_$1 version: '2021-11-17' mfomd: banana: MFOMD contact: email: janna.hastings@gmail.com github: jannahastings name: Janna Hastings orcid: 0000-0002-3469-4923 description: The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF). download_owl: http://purl.obolibrary.org/obo/mfomd.owl example: '0000046' homepage: https://github.com/jannahastings/mental-functioning-ontology license: CC BY 3.0 mappings: biocontext: MFOMD bioportal: MFOMD fairsharing: FAIRsharing.q053vb obofoundry: MFOMD ols: mfomd ontobee: MFOMD name: Mental Disease Ontology pattern: ^\d{7}$ preferred_prefix: MFOMD repository: https://github.com/jannahastings/mental-functioning-ontology uri_format: http://purl.obolibrary.org/obo/MFOMD_$1 version: '2020-04-26' mge: banana: mge description: ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. example: '2' homepage: http://aclame.ulb.ac.be/ mappings: miriam: mge n2t: mge name: Aclame namespace_in_lui: true pattern: ^\d+$ preferred_prefix: mge uri_format: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1 mgi: banana: MGI description: The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data. example: '6017782' homepage: http://www.informatics.jax.org/ mappings: biocontext: MGI cellosaurus: MGI fairsharing: FAIRsharing.fcwyhz go: MGI miriam: mgi n2t: mgi ncbi: MGI prefixcommons: mgi uniprot: MGI wikidata: P671 name: Mouse Genome Informatics namespace_in_lui: true pattern: ^\d+$ preferred_prefix: MGI providers: - code: 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: 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 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/$1 mi: banana: MI contact: email: pporras@ebi.ac.uk github: pporrasebi name: Pablo Porras Millán orcid: 0000-0002-8429-8793 description: The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative. download_obo: http://purl.obolibrary.org/obo/mi.obo download_owl: http://purl.obolibrary.org/obo/mi.owl example: 0058 homepage: https://github.com/HUPO-PSI/psi-mi-CV license: CC BY 4.0 mappings: biocontext: MI biolink: MI bioportal: MI go: PSI-MI miriam: mi n2t: psimi obofoundry: MI ols: mi ontobee: MI prefixcommons: psi.mi name: Molecular Interactions Controlled Vocabulary namespace_in_lui: true pattern: ^\d{4}$ preferred_prefix: MI 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:$1 miaa: comment: same as MAT contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: Minimal Information About Anatomy ontology preferred_prefix: miaa references: - https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/rols/inst/doc/rols.pdf miapa: banana: MIAPA contact: email: hilmar.lapp@duke.edu github: hlapp name: Hilmar Lapp orcid: 0000-0001-9107-0714 description: 'The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies. This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project''s main page at http://evoio.org/wiki/MIAPA.' download_owl: http://purl.obolibrary.org/obo/miapa.owl example: '0000010' homepage: http://www.evoio.org/wiki/MIAPA license: CC0 1.0 mappings: biocontext: MIAPA bioportal: MIAPA fairsharing: FAIRsharing.ca48xs obofoundry: MIAPA ols: miapa ontobee: MIAPA name: Minimum Anformation About a Phylogenetic Analysis Ontology pattern: ^\d{7}$ preferred_prefix: MIAPA repository: https://github.com/evoinfo/miapa uri_format: http://purl.obolibrary.org/obo/MIAPA_$1 version: '2017-05-09' micro: appears_in: - mco banana: MICRO contact: email: carrine.blank@umontana.edu github: carrineblank name: Carrine Blank orcid: 0000-0002-2100-6351 description: An ontology of prokaryotic phenotypic and metabolic characters download_owl: http://purl.obolibrary.org/obo/micro.owl example: 0002999 homepage: https://github.com/carrineblank/MicrO license: CC BY 2.0 mappings: biocontext: MICRO fairsharing: FAIRsharing.brhpb0 obofoundry: MICRO ols: micro ontobee: MicrO name: Ontology of Prokaryotic Phenotypic and Metabolic Characters pattern: ^\d{7}$ preferred_prefix: MICRO repository: https://github.com/carrineblank/MicrO uri_format: http://purl.obolibrary.org/obo/MICRO_$1 version: 1.5.1 microscope: description: MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. example: '5601141' homepage: http://www.genoscope.cns.fr/agc/microscope mappings: biocontext: MICROSCOPE fairsharing: FAIRsharing.3t5qc3 miriam: microscope n2t: microscope name: MicroScope pattern: ^\d+$ 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 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 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/$1 mint: description: The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals. example: MINT-10000 homepage: http://mint.bio.uniroma2.it/mint/ mappings: biocontext: MINT fairsharing: FAIRsharing.2bdvmk miriam: mint n2t: mint prefixcommons: mint uniprot: MINT name: Molecular Interaction Database pattern: ^MINT\-\d{1,7}$ 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 uri_format: http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$1 mipmod: description: MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures. example: HOSAPI0399 homepage: http://bioinfo.iitk.ac.in/MIPModDB mappings: biocontext: MIPMOD miriam: mipmod n2t: mipmod prefixcommons: mipmod name: MIPModDB pattern: ^\w+$ preferred_prefix: mipmod 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:$1" mirbase: description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). example: MI0026471 homepage: http://www.mirbase.org/ mappings: biocontext: MIRBASE biolink: mirbase fairsharing: FAIRsharing.hmgte8 miriam: mirbase n2t: mirbase ncbi: miRBase prefixcommons: mirbase wikidata: P2870 name: miRBase pre-miRNA pattern: ^MI\d{7}$ preferred_prefix: mirbase 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=$1&exref=pp2a&limit=yes miriam: description: Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain. example: pubmed homepage: https://www.ebi.ac.uk mappings: fairsharing: FAIRsharing.ap169a miriam: identifiers.namespace name: Identifiers.org namespace pattern: ^[a-z_\.]+$ preferred_prefix: miriam synonyms: - identifiers.namespace uri_format: https://registry.identifiers.org/registry/$1 miriam.collection: deprecated: true description: MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections. example: MIR:00000008 homepage: https://www.ebi.ac.uk/miriam/ mappings: biocontext: MIRIAM.COLLECTION miriam: miriam.collection n2t: miriam.collection name: MIRIAM Registry collection pattern: ^MIR:000\d{5}$ preferred_prefix: miriam.collection uri_format: https://www.ebi.ac.uk/miriam/main/$1 miriam.resource: comment: yo dawg i heard you like registries... description: MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases. example: MIR:00100005 homepage: https://www.ebi.ac.uk/miriam/ mappings: biocontext: MIRIAM.RESOURCE miriam: miriam.resource n2t: miriam.resource prefixcommons: miriam.resource name: MIRIAM Registry resource pattern: ^MIR:001\d{5}$ preferred_prefix: miriam.resource uri_format: https://www.ebi.ac.uk/miriam/main/resources/$1 mirnao: banana: 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: 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 uri_format: http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1 miro: banana: MIRO contact: email: louis@imbb.forth.gr github: null name: Christos (Kitsos) Louis orcid: null description: Application ontology for entities related to insecticide resistance in mosquitos download_obo: http://purl.obolibrary.org/obo/miro.obo download_owl: http://purl.obolibrary.org/obo/miro.owl example: '40000617' homepage: https://github.com/VEuPathDB-ontology/MIRO mappings: biocontext: MIRO bioportal: MIRO fairsharing: FAIRsharing.sjf113 obofoundry: MIRO ols: miro ontobee: MIRO name: Mosquito insecticide resistance pattern: ^\d{8}$ preferred_prefix: MIRO 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/$1 mmdb: description: The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites. example: '50885' homepage: http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure mappings: biocontext: MMDB miriam: mmdb n2t: mmdb prefixcommons: mmdb name: Molecular Modeling Database pattern: ^\d{1,5}$ preferred_prefix: mmdb 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=$1 mmo: banana: MMO contact: email: jrsmith@mcw.edu github: jrsjrs name: Jennifer Smith orcid: 0000-0002-6443-9376 description: 'A representation of the variety of methods used to make clinical and phenotype measurements. ' download_obo: http://purl.obolibrary.org/obo/mmo.obo download_owl: http://purl.obolibrary.org/obo/mmo.owl example: '0000574' homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 license: CC0 1.0 mappings: biocontext: MMO bioportal: MMO fairsharing: FAIRsharing.bgkyd7 obofoundry: MMO ols: mmo ontobee: MMO name: Measurement method ontology pattern: ^\d{7}$ preferred_prefix: MMO repository: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology 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=$1 mmsl: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included. example: '3355' homepage: https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html name: Multum MediSource Lexicon pattern: ^\d+$ preferred_prefix: mmsl synonyms: - MMSL_CODE mmusdv: banana: 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: 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_$1 version: '2020-03-10' mo: banana: MO contact: email: stoeckrt@pcbi.upenn.edu github: null name: Chris Stoeckert orcid: 0000-0002-5714-991X deprecated: true description: The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. download_owl: http://purl.obolibrary.org/obo/mo.owl example: ArrayGroup homepage: http://mged.sourceforge.net/ontologies/MGEDontology.php mappings: biocontext: MO bioportal: MO miriam: mo n2t: mo obofoundry: MO name: Microarray experimental conditions pattern: ^\w+$ 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/$1 mod: banana: MOD contact: email: pierre-alain.binz@chuv.ch github: pabinz name: Pierre-Alain Binz orcid: 0000-0002-0045-7698 description: The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications. download_obo: http://purl.obolibrary.org/obo/mod.obo download_owl: http://purl.obolibrary.org/obo/mod.owl example: '01467' homepage: http://www.psidev.info/MOD license: CC BY 4.0 mappings: biocontext: MOD bioportal: PSIMOD fairsharing: FAIRsharing.2m4ms9 go: PSI-MOD miriam: mod n2t: mod obofoundry: MOD ols: mod ontobee: MOD prefixcommons: psi.mod name: Protein modification namespace_in_lui: true pattern: ^\d{5}$ preferred_prefix: MOD 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:$1 modeldb: description: ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment. example: '45539' homepage: http://senselab.med.yale.edu/ModelDB/ mappings: biocontext: MODELDB fairsharing: FAIRsharing.5rb3fk miriam: modeldb n2t: modeldb prefixcommons: modeldb name: ModelDB pattern: ^\d+$ preferred_prefix: modeldb uri_format: http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1 molbase: description: Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier. example: 128796-39-4 homepage: http://www.molbase.com/ mappings: biocontext: MOLBASE miriam: molbase n2t: molbase name: Molbase pattern: ^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$ 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: 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/$1 mondo: banana: MONDO contact: email: nicole@tislab.org github: nicolevasilevsky name: Nicole Vasilevsky orcid: 0000-0001-5208-3432 description: A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. download_json: http://purl.obolibrary.org/obo/mondo.json download_obo: http://purl.obolibrary.org/obo/mondo.obo download_owl: http://purl.obolibrary.org/obo/mondo.owl example: '0000001' homepage: https://monarch-initiative.github.io/mondo license: CC BY 4.0 mappings: biocontext: MONDO bioportal: MONDO fairsharing: FAIRsharing.b2979t obofoundry: MONDO ols: mondo ontobee: MONDO wikidata: P5270 name: Monarch Disease Ontology pattern: ^\d{7}$ preferred_prefix: MONDO repository: https://github.com/monarch-initiative/mondo uri_format: http://purl.obolibrary.org/obo/MONDO_$1 version: '2022-05-02' mop: banana: MOP contact: email: batchelorc@rsc.org github: batchelorc name: Colin Batchelor orcid: 0000-0001-5985-7429 description: MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation. download_obo: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.obo download_owl: http://purl.obolibrary.org/obo/mop.owl example: 0000079 homepage: https://github.com/rsc-ontologies/rxno license: CC BY 4.0 mappings: biocontext: MOP bioportal: MOP fairsharing: FAIRsharing.mct09a obofoundry: MOP ols: mop ontobee: MOP name: Molecular Process Ontology pattern: ^\d{7}$ 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/$1 mp: appears_in: - chiro - scdo banana: MP contact: email: drsbello@gmail.com github: sbello name: Sue Bello orcid: 0000-0003-4606-0597 description: The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways. download_json: http://purl.obolibrary.org/obo/mp.json download_obo: http://purl.obolibrary.org/obo/mp.obo download_owl: http://purl.obolibrary.org/obo/mp.owl example: '0005452' homepage: http://www.informatics.jax.org/searches/MP_form.shtml license: CC BY 4.0 mappings: biocontext: MP bioportal: MP fairsharing: FAIRsharing.kg1x4z miriam: mp n2t: mp obofoundry: MP ols: mp ontobee: MP prefixcommons: mp name: Mammalian Phenotype Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: MP repository: https://github.com/mgijax/mammalian-phenotype-ontology uri_format: http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1 mpath: banana: MPATH contact: email: pns12@hermes.cam.ac.uk github: PaulNSchofield name: Paul Schofield orcid: 0000-0002-5111-7263 description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes download_obo: https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo download_owl: http://purl.obolibrary.org/obo/mpath.owl example: '728' homepage: http://www.pathbase.net license: CC BY 3.0 mappings: biocontext: MPATH bioportal: MPATH fairsharing: FAIRsharing.3wbgm0 obofoundry: MPATH ols: mpath ontobee: MPATH prefixcommons: mpath name: Mouse pathology ontology pattern: ^\d+$ preferred_prefix: MPATH repository: https://github.com/PaulNSchofield/mpath synonyms: - MPATH uri_format: http://purl.obolibrary.org/obo/MPATH_$1 version: '2020-05-19' mpid: description: The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts. example: '172' homepage: http://www.jcvi.org/mpidb/about.php mappings: biocontext: MPID fairsharing: FAIRsharing.eyjkws miriam: mpid n2t: mpid name: Microbial Protein Interaction Database pattern: ^\d+$ 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 synonyms: - mpidb uri_format: http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1 mpio: banana: MPIO contact: email: mbrochhausen@uams.edu github: mbrochhausen name: Mathias Brochhausen orcid: 0000-0003-1834-3856 description: An ontology of minimum information regarding potential drug-drug interaction information. download_owl: http://purl.obolibrary.org/obo/mpio.owl example: '0000004' homepage: https://github.com/MPIO-Developers/MPIO license: CC BY 4.0 mappings: biocontext: MPIO bioportal: MPIO obofoundry: MPIO ols: mpio ontobee: MPIO name: Minimum PDDI Information Ontology pattern: ^\d{7}$ preferred_prefix: MPIO repository: https://github.com/MPIO-Developers/MPIO uri_format: http://purl.obolibrary.org/obo/MPIO_$1 version: '2019-01-30' mro: banana: MRO contact: email: bpeters@lji.org github: bpeters42 name: Bjoern Peters orcid: 0000-0002-8457-6693 description: The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions. download_owl: http://purl.obolibrary.org/obo/mro.owl example: '0000634' homepage: https://github.com/IEDB/MRO license: CC BY 3.0 mappings: biocontext: MRO bioportal: MRO fairsharing: FAIRsharing.k893xa obofoundry: MRO ols: mro ontobee: MRO name: MHC Restriction Ontology pattern: ^\d{7}$ preferred_prefix: MRO repository: https://github.com/IEDB/MRO uri_format: http://purl.obolibrary.org/obo/MRO_$1 version: '2022-03-14' ms: banana: MS contact: email: gerhard.mayer@rub.de github: germa name: Gerhard Mayer orcid: 0000-0002-1767-2343 depends_on: - pato - uo description: The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. download_obo: http://purl.obolibrary.org/obo/ms.obo download_owl: http://purl.obolibrary.org/obo/ms.owl example: '1000560' homepage: http://www.psidev.info/groups/controlled-vocabularies license: CC BY 3.0 mappings: biocontext: MS bioportal: MS miriam: ms n2t: ms obofoundry: MS ols: ms ontobee: MS name: Mass spectrometry ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: MS repository: https://github.com/HUPO-PSI/psi-ms-CV uri_format: https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:$1 msigdb: description: The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can example: NADELLA_PRKAR1A_TARGETS_DN homepage: https://www.gsea-msigdb.org mappings: biolink: MSigDB name: Molecular Signatures Database preferred_prefix: msigdb synonyms: - msig msio: description: an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies. download_owl: https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl example: '0000111' homepage: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO mappings: ols: msio name: Metabolomics Standards Initiative Ontology pattern: ^\d{7}$ preferred_prefix: msio repository: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO 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=$1 mycobank: description: MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations. example: '349124' homepage: http://www.mycobank.org/ mappings: biocontext: MYCOBANK fairsharing: FAIRsharing.v8se8r miriam: mycobank n2t: mycobank ncbi: MycoBank prefixcommons: mycobank name: Fungal Nomenclature and Species Bank pattern: ^\d+$ 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/$1:' namerxn: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO). example: 4.2.78 homepage: https://www.nextmovesoftware.com/namerxn.html name: NameRXN preferred_prefix: namerxn proprietary: true references: - https://www.nextmovesoftware.com/products/HazELNutPoster.pdf - https://twitter.com/cthoyt/status/1443929184745758723 - https://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.6b00153 - https://www.nature.com/articles/s42256-020-00284-w napdi: description: The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs). example: '28' homepage: https://repo.napdi.org/ mappings: biocontext: NAPDI fairsharing: FAIRsharing.y9x8wk miriam: napdi n2t: napdi name: Natural Product-Drug Interaction Research Data Repository pattern: ^[0-9]+$ 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/$1 nasc: description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. example: N1899 homepage: http://arabidopsis.info/ mappings: biocontext: NASC fairsharing: FAIRsharing.2sqcxs miriam: nasc n2t: nasc prefixcommons: nasc name: NASC code pattern: ^(\w+)?\d+$ 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=$1&verb=redirect nbo: appears_in: - ecto - pcl - scdo banana: NBO contact: email: g.gkoutos@bham.ac.uk github: gkoutos name: George Gkoutos orcid: 0000-0002-2061-091X description: An ontology of human and animal behaviours and behavioural phenotypes download_obo: https://github.com/obo-behavior/behavior-ontology/raw/master/nbo.obo download_owl: http://purl.obolibrary.org/obo/nbo.owl example: '0000564' homepage: https://github.com/obo-behavior/behavior-ontology/ license: CC BY 3.0 mappings: biocontext: NBO bioportal: NBO fairsharing: FAIRsharing.pktgc6 obofoundry: NBO ols: nbo ontobee: NBO name: Neuro Behavior Ontology pattern: ^\d{7}$ preferred_prefix: NBO 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.drug: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The [National Center for Advancing Translational Sciences (NCATS)](https://ncats.nih.gov/) has developed Inxight: Drugs as a comprehensive portal for drug development information. NCATS Inxight: Drugs contains information on ingredients in medicinal products, including:' example: '44259' example_extras: - 1IJV77EI07 homepage: https://drugs.ncats.io/ name: NCATS Drugs preferred_prefix: ncats.drug synonyms: - inxight - inxight-drugs uri_format: https://drugs.ncats.io/drug/$1 ncbi.assembly: description: A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. example: GCF_000005845.2 homepage: https://www.ncbi.nlm.nih.gov/ mappings: biocontext: NCBIAssembly miriam: assembly name: Assembly pattern: ^[a-zA-Z0-9_\.]+$ preferred_prefix: ncbi.assembly uri_format: https://www.ncbi.nlm.nih.gov/assembly/$1 ncbi.genome: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations. example: '51' homepage: https://www.ncbi.nlm.nih.gov/genome mappings: biocontext: NCBIGenome name: NCBI Genome pattern: ^\d+$ 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/$1 ncbigene: description: Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis. example: '100010' homepage: https://www.ncbi.nlm.nih.gov/gene mappings: biocontext: NCBIGene biolink: NCBIGene fairsharing: FAIRsharing.5h3maw go: NCBIGene miriam: ncbigene n2t: ncbigene ncbi: GeneID prefixcommons: ncbigene scholia: ncbi-gene wikidata: P351 name: Entrez Gene pattern: ^\d+$ preferred_prefix: NCBIGene providers: - 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: 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 synonyms: - EGID - EntrezGene - NCBIGene - entrez - entrez gene/locuslink uri_format: https://www.ncbi.nlm.nih.gov/gene/$1 ncbiprotein: description: The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. example: CAA71118.1 homepage: https://www.ncbi.nlm.nih.gov/protein mappings: biocontext: NCBIProtein go: NCBI_NP miriam: ncbiprotein n2t: ncbiprotein prefixcommons: ncbi.protein name: NCBI Protein pattern: ^(\w+\d+(\.\d+)?)|(NP_\d+)$ preferred_prefix: NCBIProtein uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 ncbitaxon: appears_in: - agro - chiro - cl - clo - ecto - envo - foodon - genepio - go - hso - mco - ons - pcl - pco contact: email: frederic.bastian@unil.ch github: fbastian name: Frederic Bastian orcid: 0000-0002-9415-5104 description: The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined. download_json: http://purl.obolibrary.org/obo/ncbitaxon.json download_obo: http://purl.obolibrary.org/obo/ncbitaxon.obo download_owl: http://purl.obolibrary.org/obo/ncbitaxon.owl example: '2170610' homepage: https://github.com/obophenotype/ncbitaxon license: CC0 1.0 mappings: biocontext: NCBITaxon bioportal: NCBITAXON cellosaurus: NCBI_TaxID fairsharing: FAIRsharing.fj07xj go: taxon miriam: taxonomy n2t: taxonomy ncbi: taxon obofoundry: NCBITaxon ols: ncbitaxon ontobee: NCBITaxon prefixcommons: taxonomy scholia: ncbi-taxon wikidata: P685 name: NCBI Taxonomy pattern: ^\d+$ 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: 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: CURATOR_REVIEW description: Bio2RDF homepage: https://bio2rdf.org/ name: Bio2RDF uri_format: https://bio2rdf.org/taxonomy:$1 repository: https://github.com/obophenotype/ncbitaxon synonyms: - NCBITaxon - NCBI_Taxon_ID - NCBI_taxid - TAX - TaxonomyID - taxid - taxon - taxonomy uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1 version: '2021-12-14' ncim: description: NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical. example: C0026339 homepage: http://ncim.nci.nih.gov/ mappings: biocontext: NCIM miriam: ncim n2t: ncim name: NCI Metathesaurus pattern: ^C\d+$ preferred_prefix: ncim uri_format: http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1 ncit: appears_in: - ecto - mco - ontoavida - scdo contact: email: haendel@ohsu.edu github: mellybelly name: Melissa Haendel orcid: 0000-0001-9114-8737 description: NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code. download_obo: http://purl.obolibrary.org/obo/ncit.obo download_owl: http://purl.obolibrary.org/obo/ncit.owl example: C138986 homepage: https://github.com/NCI-Thesaurus/thesaurus-obo-edition license: CC BY 4.0 mappings: biocontext: NCIT bioportal: NCIT cellosaurus: NCIt fairsharing: FAIRsharing.4cvwxa miriam: ncit n2t: ncit obofoundry: NCIT ols: ncit ontobee: NCIT prefixcommons: ncit wikidata: P1748 name: NCI Thesaurus pattern: ^C\d+$ preferred_prefix: NCIT repository: https://github.com/NCI-Thesaurus/thesaurus-obo-edition synonyms: - NCI - NCI2004_11_17 - NCIT - NCIT_Thesaurus - NCITm - NCITt - NCI_Thesaurus - NCIt - ncithesaurus uri_format: http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1 version: 22.03d ncro: banana: NCRO contact: email: huang@southalabama.edu github: Huang-OMIT name: Jingshan Huang orcid: 0000-0003-2408-2883 description: An ontology for non-coding RNA, both of biological origin, and engineered. download_obo: https://raw.githubusercontent.com/OmniSearch/ncro/master/src/ontology/ncro.obo download_owl: http://purl.obolibrary.org/obo/ncro.owl example: 0002927 homepage: http://omnisearch.soc.southalabama.edu/w/index.php/Ontology license: CC BY 4.0 mappings: biocontext: NCRO bioportal: NCRO fairsharing: FAIRsharing.vppyga obofoundry: NCRO ols: ncro ontobee: NCRO name: Non-Coding RNA Ontology pattern: ^\d{7}$ preferred_prefix: NCRO repository: https://github.com/OmniSearch/ncro uri_format: http://purl.obolibrary.org/obo/NCRO_$1 version: '2015-12-10' ndc: description: The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily. example: 0002-1975-61 homepage: http://www.accessdata.fda.gov/scripts/cder/ndc/ mappings: biocontext: NDC miriam: ndc n2t: ndc name: National Drug Code pattern: ^\d+\-\d+\-\d+$ 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/$1 nddf: description: FDB MedKnowledge encompasses medications approved by the U.S. Food and Drug Administration, and information on commonly-used over-the-counter and alternative therapy agents such as herbals, nutraceuticals and dietary supplements. example: 002678 homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDDF mappings: biolink: NDDF bioportal: NDDF fairsharing: FAIRsharing.8qcbs0 name: National Drug Data File pattern: ^\d{6}$ preferred_prefix: nddf 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/$1 ndfrt: description: 'NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction].' example: N0000001662 homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDFRT mappings: bioportal: NDFRT fairsharing: FAIRsharing.901nkj ontobee: NDF-RT prefixcommons: ndfrt wikidata: P2115 name: National Drug File - Reference Terminology preferred_prefix: ndfrt synonyms: - NUI - ndf-rt nemo: description: This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects. example: smp-m3w9hbe homepage: https://www.nemoarchive.org mappings: bioportal: NEMO fairsharing: FAIRsharing.n66krd miriam: nemo name: Neural ElectroMagnetic Ontology pattern: ^[a-z]{3}-[a-km-z0-9]{7}$ preferred_prefix: nemo uri_format: https://assets.nemoarchive.org/$1 neurolex: description: The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex). example: Birnlex_721 homepage: http://www.neurolex.org/wiki/Main_Page mappings: biocontext: NEUROLEX miriam: neurolex n2t: neurolex prefixcommons: neurolex name: NeuroLex pattern: ^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO|nifext_)\d+$ preferred_prefix: neurolex uri_format: http://www.neurolex.org/wiki/$1 neuromorpho: description: NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons. example: Rosa2 homepage: http://neuromorpho.org/index.jsp mappings: biocontext: NEUROMORPHO miriam: neuromorpho n2t: neuromorpho prefixcommons: neuromorpho name: NeuroMorpho pattern: ^\w+$ preferred_prefix: neuromorpho uri_format: http://neuromorpho.org/neuron_info.jsp?neuron_name=$1 neuronames: description: BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it. example: '268' homepage: http://braininfo.rprc.washington.edu/ mappings: wikidata: P4394 name: NeuroNames pattern: ^\d+$ preferred_prefix: neuronames references: - https://en.wikipedia.org/wiki/NeuroNames synonyms: - neuroname uri_format: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1 neurondb: description: 'NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.' example: '265' homepage: http://senselab.med.yale.edu/NeuronDB/ mappings: biocontext: NEURONDB fairsharing: FAIRsharing.45a10e miriam: neurondb n2t: neurondb prefixcommons: neurondb name: NeuronDB pattern: ^\d+$ 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 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 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: banana: NIF_CELL contact: email: smtifahim@gmail.com github: null name: Fahim Imam orcid: null deprecated: true description: Neuronal cell types homepage: http://neuinfo.org/ mappings: biocontext: NIF_CELL bioportal: NIFCELL obofoundry: NIF_CELL name: NIF Cell preferred_prefix: NIF_CELL uri_format: http://purl.obolibrary.org/obo/NIF_CELL_$1 nif_dysfunction: banana: 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 preferred_prefix: NIF_DYSFUNCTION uri_format: http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1 nif_grossanatomy: banana: 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 preferred_prefix: NIF_GROSSANATOMY uri_format: http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1 nist: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species. homepage: https://webbook.nist.gov/chemistry/ name: NIST Chemistry WebBook no_own_terms: true preferred_prefix: nist synonyms: - NIST - NIST Chemistry WebBook nlm: description: Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings. example: '101775319' homepage: https://www.ncbi.nlm.nih.gov/nlmcatalog mappings: biolink: NLMID name: National Library of Medicine Catalog pattern: ^\d+$ preferred_prefix: nlm uri_format: https://www.ncbi.nlm.nih.gov/nlmcatalog/$1 nlxanat: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The InterLex project - a core component of SciCrunch and supported by projects such as the Neuroscience Information Framework project (NIF), the NIDDK Information Network (dkNET), and the Open Data Commons for Spinal Cord Injury - is a dynamic lexicon of biomedical terms. example: 090201 homepage: https://scicrunch.org/scicrunch/interlex/dashboard name: NeuroLex Anatomy part_of: neurolex pattern: ^\d{6}$ preferred_prefix: nlxanat uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1 nlxdys: appears_in: - mondo contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The InterLex project - a core component of SciCrunch and supported by projects such as the Neuroscience Information Framework project (NIF), the NIDDK Information Network (dkNET), and the Open Data Commons for Spinal Cord Injury - is a dynamic lexicon of biomedical terms. example: '20090303' homepage: https://scicrunch.org/scicrunch/interlex/dashboard name: NeuroLex Dysfunction part_of: neurolex pattern: ^\d+$ preferred_prefix: nlxdys uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1 nmdc: contact: email: donny@polyneme.xyz github: dwinston name: Donny Winston orcid: 0000-0002-8424-0604 contributor: email: donny@polyneme.xyz github: dwinston name: Donny Winston orcid: 0000-0002-8424-0604 description: An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem. example: y3ax-8bq3-60 homepage: https://microbiomedata.org/ mappings: miriam: nmdc name: National Microbiome Data Collaborative pattern: ^[\w\-.]{3,}$ 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/$1 nmr: banana: NMR contact: email: schober@imbi.uni-freiburg.de github: null name: Schober Daniel orcid: null deprecated: true description: nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi. download_owl: https://nmrml.org/cv/stable/nmrCV.owl example: '1000003' homepage: http://msi-ontology.sourceforge.net/ mappings: biocontext: NMR bioportal: NMR miriam: nmr n2t: nmr obofoundry: NMR ols: nmrcv prefixcommons: nmr name: NMR-instrument specific component of metabolomics investigations namespace_in_lui: true pattern: ^\d+$ 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/$1 nomen: banana: NOMEN contact: email: diapriid@gmail.com github: mjy name: Matt Yoder orcid: 0000-0002-5640-5491 description: NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature. download_owl: http://purl.obolibrary.org/obo/nomen.owl example: 0000295 homepage: https://github.com/SpeciesFileGroup/nomen license: CC0 1.0 mappings: bioportal: NOMEN obofoundry: NOMEN ols: nomen ontobee: NOMEN name: A nomenclatural ontology for biological names pattern: ^\d{7}$ preferred_prefix: NOMEN repository: https://github.com/SpeciesFileGroup/nomen uri_format: http://purl.obolibrary.org/obo/NOMEN_$1 version: '2019-04-17' noncodev3: description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4. example: '377550' homepage: http://www.noncode.org/ mappings: biocontext: NONCODEV3 miriam: noncodev3 n2t: noncodev3 name: NONCODE v3 pattern: ^\d+$ 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@pnl.gov github: null name: Nathan Baker orcid: null description: An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy. example: '1731' homepage: https://bioportal.bioontology.org/ontologies/NPO mappings: bioportal: NPO fairsharing: FAIRsharing.vy0p71 name: NanoParticle Ontology pattern: ^\d+$ preferred_prefix: npo 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: description: The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture. example: sourceDateStart homepage: http://www.w3.org/ns/oa mappings: biocontext: oa bioportal: OA name: Web Annotation Ontology preferred_prefix: oa uri_format: http://www.w3.org/ns/oa#$1 oae: banana: OAE contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqunh He orcid: 0000-0001-9189-9661 description: The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc. download_owl: http://purl.obolibrary.org/obo/oae.owl example: 0002959 homepage: https://github.com/OAE-ontology/OAE/ license: CC BY 3.0 mappings: biocontext: OAE bioportal: OAE fairsharing: FAIRsharing.tw4q8x obofoundry: OAE ols: oae ontobee: OAE name: Ontology of Adverse Events pattern: ^\d{7}$ preferred_prefix: OAE repository: https://github.com/OAE-ontology/OAE uri_format: http://purl.obolibrary.org/obo/OAE_$1 version: 1.2.44 oarcs: banana: OARCS contact: email: mjyoder@illinois.edu github: mjy name: Matt Yoder orcid: 0000-0002-5640-5491 description: OArCS is an ontology describing the Arthropod ciruclatory system. download_owl: http://purl.obolibrary.org/obo/oarcs.owl example: 0000029 homepage: https://github.com/aszool/oarcs license: CC BY 3.0 mappings: biocontext: OARCS bioportal: OARCS fairsharing: FAIRsharing.yqn857 obofoundry: OARCS ols: oarcs ontobee: OARCS name: Ontology of Arthropod Circulatory Systems pattern: ^\d{7}$ preferred_prefix: OARCS repository: https://github.com/aszool/oarcs uri_format: http://purl.obolibrary.org/obo/OARCS_$1 version: '2019-04-18' oba: appears_in: - fovt banana: OBA contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO. download_obo: http://purl.obolibrary.org/obo/oba.obo download_owl: http://purl.obolibrary.org/obo/oba.owl example: '0000001' homepage: https://github.com/obophenotype/bio-attribute-ontology license: CC0 1.0 mappings: biocontext: OBA bioportal: OBA fairsharing: FAIRsharing.mp0rwf obofoundry: OBA ols: oba ontobee: OBA name: Ontology of Biological Attributes pattern: ^\d{7}$ preferred_prefix: OBA repository: https://github.com/obophenotype/bio-attribute-ontology uri_format: http://purl.obolibrary.org/obo/OBA_$1 version: '2021-12-03' obcs: banana: OBCS contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 description: 'OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. ' download_owl: http://purl.obolibrary.org/obo/obcs.owl example: '0000121' homepage: https://github.com/obcs/obcs license: CC BY 3.0 mappings: biocontext: OBCS bioportal: OBCS fairsharing: FAIRsharing.5p12xh obofoundry: OBCS ols: obcs ontobee: OBCS name: Ontology of Biological and Clinical Statistics pattern: ^\d{7}$ preferred_prefix: OBCS repository: https://github.com/obcs/obcs uri_format: http://purl.obolibrary.org/obo/OBCS_$1 version: '101' obi: appears_in: - agro - foodon - hso - labo - mco - one - ons - rbo - scdo banana: OBI contact: email: bpeters@lji.org github: bpeters42 name: Bjoern Peters orcid: 0000-0002-8457-6693 description: The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO). download_obo: https://github.com/obi-ontology/obi/raw/master/views/obi.obo download_owl: http://purl.obolibrary.org/obo/obi.owl example: 0400109 homepage: http://obi-ontology.org license: CC BY 4.0 mappings: biocontext: OBI bioportal: OBI fairsharing: FAIRsharing.284e1z go: OBI miriam: obi n2t: obi obofoundry: OBI ols: obi ontobee: OBI prefixcommons: obi name: Ontology for Biomedical Investigations pattern: ^\d{7}$ preferred_prefix: OBI repository: https://github.com/obi-ontology/obi uri_format: http://purl.obolibrary.org/obo/OBI_$1 version: '2022-01-03' obib: banana: OBIB contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 description: The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology. download_owl: http://purl.obolibrary.org/obo/obib.owl example: 0000389 homepage: https://github.com/biobanking/biobanking license: CC BY 4.0 mappings: biocontext: OBIB bioportal: OBIB fairsharing: FAIRsharing.bxc508 obofoundry: OBIB ols: obib ontobee: OBIB name: Ontology for Biobanking pattern: ^\d{7}$ preferred_prefix: OBIB repository: https://github.com/biobanking/biobanking uri_format: http://purl.obolibrary.org/obo/OBIB_$1 version: '2021-11-12' obo: description: Community development of interoperable ontologies for the biological sciences homepage: http://www.obofoundry.org/ mappings: biocontext: OBO fairsharing: FAIRsharing.847069 name: Internal OBO and PyOBO Relations preferred_prefix: obo uri_format: http://purl.obolibrary.org/obo/$1 oboformat: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Related to the OBO in OWL meta-model example: alt_id homepage: https://github.com/geneontology/go-ontology/tree/master/contrib mappings: biolink: oboformat fairsharing: FAIRsharing.aa0eat name: OBO Format preferred_prefix: oboFormat repository: https://github.com/geneontology/go-ontology oboinowl: 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 example: hasDbXref homepage: https://github.com/geneontology/go-ontology/tree/master/contrib mappings: biocontext: OIO name: OBO in OWL preferred_prefix: oboInOwl repository: https://github.com/geneontology/go-ontology synonyms: - 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/$1/?db=5 ogg: banana: OGG contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: 'OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. ' download_owl: http://purl.obolibrary.org/obo/ogg.owl example: '3000887619' homepage: https://bitbucket.org/hegroup/ogg license: CC BY 3.0 mappings: biocontext: OGG bioportal: OGG fairsharing: FAIRsharing.zmx7nn obofoundry: OGG ols: ogg ontobee: OGG name: The Ontology of Genes and Genomes pattern: ^\d+$ preferred_prefix: OGG repository: https://bitbucket.org/hegroup/ogg uri_format: http://purl.obolibrary.org/obo/OGG_$1 version: 1.0.59 ogi: banana: OGI deprecated: true description: "OGI formalized the genomic element by defining an upper class 'genetic\ \ interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous\ \ physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.)\ \ between and including two points (Nucleic Acid Base Residue) on a chromosome\ \ or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated\ \ paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology”\ \ Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary\ \ Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\n\ Yu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI)\ \ to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding\ \ of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam,\ \ Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons\ \ (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology\ \ Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th-\ \ Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n" download_owl: http://purl.obolibrary.org/obo/ogi.owl example: 0000019 homepage: https://code.google.com/archive/p/ontology-for-genetic-interval/ mappings: biocontext: OGI bioportal: OGI obofoundry: OGI ols: ogi ontobee: OGI name: Ontology for genetic interval pattern: ^\d{7}$ preferred_prefix: OGI synonyms: - OGI.owl uri_format: http://purl.obolibrary.org/obo/OGI_$1 version: '2.0' ogms: appears_in: - labo - scdo banana: OGMS contact: email: baeverma@jcvi.org github: BAevermann name: Brian Aevermann orcid: 0000-0003-1346-1327 description: 'The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: ''disease'', ''disorder'', ''disease course'', ''diagnosis'', ''patient'', and ''healthcare provider''. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.' download_owl: http://purl.obolibrary.org/obo/ogms.owl example: '0000031' homepage: https://github.com/OGMS/ogms license: CC BY 4.0 mappings: biocontext: OGMS bioportal: OGMS fairsharing: FAIRsharing.rvz0m9 obofoundry: OGMS ols: ogms ontobee: OGMS name: Ontology for General Medical Science pattern: ^\d{7}$ preferred_prefix: OGMS repository: https://github.com/OGMS/ogms synonyms: - ogms/OMRE uri_format: http://purl.obolibrary.org/obo/OGMS_$1 version: '2021-08-19' ogsf: banana: OGSF contact: email: linikujp@gmail.com github: linikujp name: Asiyah Yu Lin orcid: 0000-0002-5379-5359 description: An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process. download_owl: http://purl.obolibrary.org/obo/ogsf.owl example: '0000025' homepage: https://github.com/linikujp/OGSF license: CC BY 3.0 mappings: biocontext: OGSF bioportal: OGSF fairsharing: FAIRsharing.egv2cz obofoundry: OGSF ols: ogsf ontobee: OGSF name: Ontology of Genetic Susceptibility Factor pattern: ^\d{7}$ preferred_prefix: OGSF repository: https://github.com/linikujp/OGSF uri_format: http://purl.obolibrary.org/obo/OGSF_$1 version: '2.0' ohd: banana: OHD contact: email: wdduncan@gmail.com github: wdduncan name: Bill Duncan orcid: 0000-0001-9625-1899 description: The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records. download_owl: http://purl.obolibrary.org/obo/ohd.owl example: '0000006' homepage: https://purl.obolibrary.org/obo/ohd/home license: CC BY 4.0 mappings: biocontext: OHD bioportal: OHD fairsharing: FAIRsharing.bg7bb6 obofoundry: OHD ols: ohd ontobee: OHD name: Oral Health and Disease Ontology pattern: ^\d{7}$ preferred_prefix: OHD repository: https://github.com/oral-health-and-disease-ontologies/ohd-ontology uri_format: http://purl.obolibrary.org/obo/OHD_$1 version: '2016-06-27' ohmi: banana: OHMI contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions. download_owl: http://purl.obolibrary.org/obo/ohmi.owl example: '0000460' homepage: https://github.com/ohmi-ontology/ohmi license: CC BY 4.0 mappings: biocontext: OHMI bioportal: OHMI fairsharing: FAIRsharing.cz9cnp obofoundry: OHMI ols: ohmi ontobee: OHMI name: Ontology of Host-Microbiome Interactions pattern: ^\d{7}$ preferred_prefix: OHMI repository: https://github.com/ohmi-ontology/ohmi uri_format: http://purl.obolibrary.org/obo/OHMI_$1 version: '2019-09-17' ohpi: banana: OHPI contact: email: edong@umich.edu github: e4ong1031 name: Edison Ong orcid: 0000-0002-5159-414X description: OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration). download_owl: http://purl.obolibrary.org/obo/ohpi.owl example: '9001411' homepage: https://github.com/OHPI/ohpi license: CC BY 4.0 mappings: bioportal: OHPI fairsharing: FAIRsharing.vxpUJ6 obofoundry: OHPI ols: ohpi ontobee: OHPI name: Ontology of Host Pathogen Interactions pattern: ^\d+$ preferred_prefix: OHPI repository: https://github.com/OHPI/ohpi uri_format: http://purl.obolibrary.org/obo/OHPI_$1 version: '2019-10-02' oid: description: OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes. example: 2.16.840 homepage: http://www.oid-info.com/introduction.htm mappings: miriam: oid n2t: oid name: OID Repository pattern: ^[\d.]+$ preferred_prefix: oid uri_format: http://www.oid-info.com/cgi-bin/display?oid=$1&submit=Display&action=display olatdv: banana: OlatDv contact: email: frederic.bastian@unil.ch github: fbastian name: Frédéric Bastian orcid: 0000-0002-9415-5104 description: Life cycle stages for Medaka download_obo: http://purl.obolibrary.org/obo/olatdv.obo download_owl: http://purl.obolibrary.org/obo/olatdv.owl example: '0000210' homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv license: CC BY 3.0 mappings: biocontext: OLATDV bioportal: OLATDV fairsharing: FAIRsharing.c86z66 obofoundry: OlatDv ols: olatdv ontobee: OLATDV name: Medaka Developmental Stages pattern: ^\d{7}$ 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: 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: bioportal: OM ols: om name: Ontology of units of Measure preferred_prefix: om repository: https://github.com/HajoRijgersberg/OM version: 2.0.35 oma.grp: description: OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs. example: LCSCCPN homepage: https://omabrowser.org/cgi-bin/gateway.pl mappings: biocontext: OMA.GRP miriam: oma.grp n2t: oma.grp name: OMA Group pattern: ^[A-Z]+$ preferred_prefix: oma.grp uri_format: https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1 oma.hog: banana: HOG description: 'Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. ' example: 0459895 homepage: https://omabrowser.org mappings: miriam: oma.hog name: OMA HOGs pattern: ^[0-9]{7}(\.[0-9a-z.]+)?(_[0-9]+)?$ preferred_prefix: oma.hog uri_format: https://omabrowser.org/oma/hog/HOG:$1 oma.protein: description: OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records. example: HUMAN16963 homepage: https://omabrowser.org/cgi-bin/gateway.pl mappings: biocontext: OMA.PROTEIN miriam: oma.protein n2t: oma.protein name: OMA Protein pattern: ^[A-Z0-9]{5}\d+$ 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/$1/ omiabis: appears_in: - labo banana: OMIABIS contact: email: mbrochhausen@gmail.com github: null name: Mathias Brochhausen orcid: 0000-0003-1834-3856 deprecated: true description: An ontological version of MIABIS (Minimum Information About BIobank data Sharing) download_owl: http://purl.obolibrary.org/obo/omiabis.owl example: 0001079 homepage: https://github.com/OMIABIS/omiabis-dev license: CC BY 3.0 mappings: biocontext: OMIABIS bioportal: OMIABIS obofoundry: OMIABIS ols: omiabis ontobee: OMIABIS name: Ontologized MIABIS pattern: ^\d{7}$ preferred_prefix: OMIABIS repository: https://github.com/OMIABIS/omiabis-dev uri_format: http://purl.obolibrary.org/obo/OMIABIS_$1 version: '2014-05-28' omim: contact: email: ahamosh@jhmi.edu github: ahamosh name: Ada Hamosh orcid: 0000-0002-1780-5230 description: Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. example: '603903' homepage: https://omim.org/ mappings: biocontext: OMIM bioportal: OMIM fairsharing: FAIRsharing.azq2t6 go: OMIM miriam: mim n2t: mim ncbi: MIM prefixcommons: omim uniprot: MIM wikidata: P492 name: Online Mendelian Inheritance in Man pattern: ^\d+$ 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 synonyms: - OMIM - mim uri_format: https://omim.org/entry/$1 omim.ps: contact: email: ahamosh@jhmi.edu github: ahamosh name: Ada Hamosh orcid: 0000-0002-1780-5230 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome. example: PS214100 homepage: https://www.omim.org/phenotypicSeriesTitles/all mappings: biolink: OMIM.PS name: OMIM Phenotypic Series part_of: mim pattern: ^PS\d+$ preferred_prefix: omim.ps synonyms: - MIMPS - OMIMPS - PS - mim.ps uri_format: https://omim.org/phenotypicSeries/$1 omit: appears_in: - mco banana: OMIT contact: email: huang@southalabama.edu github: Huang-OMIT name: Jingshan Huang orcid: 0000-0003-2408-2883 description: The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). download_obo: https://raw.githubusercontent.com/OmniSearch/omit/master/src/ontology/omit.obo download_owl: http://purl.obolibrary.org/obo/omit.owl example: 0000069 homepage: http://omit.cis.usouthal.edu/ license: CC BY 3.0 mappings: biocontext: OMIT bioportal: OMIT fairsharing: FAIRsharing.mf91p5 miriam: omit n2t: omit obofoundry: OMIT ols: omit ontobee: OMIT name: Ontology for MicroRNA Target pattern: ^\d{7}$ preferred_prefix: OMIT 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 banana: OMO 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: 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_$1 version: '2022-04-27' omop: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format. homepage: https://www.ohdsi.org/data-standardization/the-common-data-model/ name: Observational Medical Outcomes Partnership no_own_terms: true preferred_prefix: omop references: - https://github.com/callahantiff/OMOP2OBO omp: appears_in: - mco banana: OMP contact: email: jimhu@tamu.edu github: jimhu-tamu name: James C. Hu orcid: 0000-0001-9016-2684 description: An ontology of phenotypes covering microbes download_obo: http://purl.obolibrary.org/obo/omp.obo download_owl: http://purl.obolibrary.org/obo/omp.owl example: '0005067' homepage: http://microbialphenotypes.org license: CC BY 3.0 mappings: biocontext: OMP bioportal: OMP fairsharing: FAIRsharing.cc3f2x obofoundry: OMP ols: omp ontobee: OMP name: Ontology of Microbial Phenotypes pattern: ^\d{7}$ preferred_prefix: OMP repository: https://github.com/microbialphenotypes/OMP-ontology uri_format: http://purl.obolibrary.org/obo/OMP_$1 version: '2022-04-11' omrse: appears_in: - labo banana: OMRSE contact: email: hoganwr@gmail.com github: hoganwr name: Bill Hogan orcid: 0000-0002-9881-1017 description: This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations. download_obo: https://github.com/ufbmi/OMRSE/raw/master/omrse-full.obo download_owl: http://purl.obolibrary.org/obo/omrse.owl example: '00000022' homepage: https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview license: CC BY 4.0 mappings: biocontext: OMRSE bioportal: OMRSE fairsharing: FAIRsharing.z0p37e obofoundry: OMRSE ols: omrse ontobee: OMRSE name: Ontology of Medically Related Social Entities pattern: ^\d{8}$ preferred_prefix: OMRSE 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/$1 one: banana: ONE contact: email: chenyangnutrition@gmail.com github: cyang0128 name: Chen Yang orcid: 0000-0001-9202-5309 depends_on: - foodon - obi - ons description: An ontology to standardize research output of nutritional epidemiologic studies. download_owl: http://purl.obolibrary.org/obo/one.owl example: '0001021' homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies license: CC BY 4.0 mappings: bioportal: ONE fairsharing: FAIRsharing.USxx0K obofoundry: ONE ols: one ontobee: ONE name: Ontology for Nutritional Epidemiology pattern: ^\d{7}$ preferred_prefix: ONE repository: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies uri_format: http://purl.obolibrary.org/obo/ONE_$1 ons: appears_in: - one banana: ONS contact: email: francesco.vitali@ibba.cnr.it github: FrancescoVit name: Francesco Vitali orcid: 0000-0001-9125-4337 depends_on: - bfo - chebi - envo - foodon - ncbitaxon - obi - ro - uberon description: The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies. download_owl: http://purl.obolibrary.org/obo/ons.owl example: '0000060' homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies license: CC BY 4.0 mappings: bioportal: ONS fairsharing: FAIRsharing.rfec93 obofoundry: ONS ols: ons ontobee: ONS name: Ontology for Nutritional Studies pattern: ^\d{7}$ preferred_prefix: ONS repository: https://github.com/enpadasi/Ontology-for-Nutritional-Studies uri_format: http://purl.obolibrary.org/obo/ONS_$1 version: June 2021 release ontoavida: banana: ONTOAVIDA contact: email: fortuna@ebd.csic.es github: miguelfortuna name: Miguel A. Fortuna orcid: 0000-0002-8374-1941 depends_on: - fbcv - gsso - ncit - ro - stato description: 'The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of the most widely used computational approach for performing experimental evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment). The lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight. OntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA). More information can be found at https://obofoundry.org/ontology/ontoavida.html' download_obo: http://purl.obolibrary.org/obo/ontoavida.obo download_owl: http://purl.obolibrary.org/obo/ontoavida.owl example: '00000001' homepage: https://gitlab.com/fortunalab/ontoavida license: CC BY 4.0 mappings: bioportal: ONTOAVIDA obofoundry: ONTOAVIDA ols: ontoavida ontobee: ONTOAVIDA name: Ontology for Avida digital evolution platform pattern: ^\d{8}$ preferred_prefix: ONTOAVIDA repository: https://gitlab.com/fortunalab/ontoavida uri_format: http://purl.obolibrary.org/obo/ONTOAVIDA_$1 version: '2022-03-15' ontoneo: banana: ONTONEO contact: email: fernanda.farinelli@gmail.com github: FernandaFarinelli name: Fernanda Farinelli orcid: 0000-0003-2338-8872 description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby. download_owl: http://purl.obolibrary.org/obo/ontoneo.owl example: 00000098 homepage: http://ontoneo.com license: CC BY 3.0 mappings: biocontext: ONTONEO bioportal: ONTONEO fairsharing: FAIRsharing.5a4y1y obofoundry: ONTONEO ols: ontoneo ontobee: ONTONEO name: Obstetric and Neonatal Ontology pattern: ^\d{8}$ preferred_prefix: ONTONEO repository: https://github.com/ontoneo-project/Ontoneo uri_format: http://purl.obolibrary.org/obo/ONTONEO_$1 version: v1.6 oostt: banana: OOSTT contact: email: mbrochhausen@gmail.com github: mbrochhausen name: Mathias Brochhausen orcid: 0000-0003-1834-3856 description: An ontology built for representating the organizational components of trauma centers and trauma systems. download_owl: http://purl.obolibrary.org/obo/oostt.owl example: 00000099 homepage: https://github.com/OOSTT/OOSTT license: CC BY 4.0 mappings: biocontext: OOSTT bioportal: OOSTT fairsharing: FAIRsharing.b4sa0w obofoundry: OOSTT ols: oostt ontobee: OOSTT name: Ontology of Organizational Structures of Trauma centers and Trauma systems pattern: ^\d{8}$ preferred_prefix: OOSTT repository: https://github.com/OOSTT/OOSTT uri_format: http://purl.obolibrary.org/obo/OOSTT_$1 version: '2021-01-11' opb: description: The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms. example: '00573' homepage: http://bioportal.bioontology.org/ontologies/OPB mappings: biocontext: OPB bioportal: OPB fairsharing: FAIRsharing.qcceez miriam: opb n2t: opb prefixcommons: opb name: Ontology of Physics for Biology pattern: ^\d+$ preferred_prefix: opb uri_format: http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1 openalex: contact: email: hpiwowar@gmail.com github: hpiwowar name: Heather Piwowar orcid: 0000-0003-1613-5981 contributor: email: null github: dhimmel name: Daniel Himmelstein orcid: 0000-0002-3012-7446 description: OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other. example: W2741809807 homepage: https://openalex.org/ name: OpenAlex pattern: ^[WAICV]\d{2,}$ preferred_prefix: openalex reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://openalex.org/$1 opl: banana: OPL contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 description: The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium. download_owl: http://purl.obolibrary.org/obo/opl.owl example: 0000319 homepage: https://github.com/OPL-ontology/OPL license: CC BY 4.0 mappings: biocontext: OPL bioportal: OPL fairsharing: FAIRsharing.ez2nhb obofoundry: OPL ols: opl ontobee: OPL name: Ontology for Parasite LifeCycle pattern: ^\d{7}$ preferred_prefix: OPL 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=$1 opmi: appears_in: - labo - scdo banana: OPMI contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles. download_owl: http://purl.obolibrary.org/obo/opmi.owl example: '0000101' homepage: https://github.com/OPMI/opmi license: CC BY 4.0 mappings: bioportal: OPMI obofoundry: OPMI ols: opmi ontobee: OPMI name: Ontology of Precision Medicine and Investigation pattern: ^\d{7}$ preferred_prefix: OPMI repository: https://github.com/OPMI/opmi uri_format: http://purl.obolibrary.org/obo/OPMI_$1 version: 1.0.152 orcid: description: ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities. example: 0000-0002-5355-2576 homepage: https://orcid.org mappings: biocontext: ORCID biolink: ORCID miriam: orcid n2t: orcid scholia: orcid wikidata: P496 name: Open Researcher and Contributor pattern: ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$ preferred_prefix: orcid 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=$1 ornaseq: banana: ORNASEQ contact: email: safisher@upenn.edu github: safisher name: Stephen Fisher orcid: 0000-0001-8034-7685 description: An application ontology designed to annotate next-generation sequencing experiments performed on RNA. download_owl: http://purl.obolibrary.org/obo/ornaseq.owl example: '0000010' homepage: http://kim.bio.upenn.edu/software/ornaseq.shtml license: CC BY 4.0 mappings: bioportal: ORNASEQ obofoundry: ORNASEQ ols: ornaseq ontobee: ORNASEQ name: Ontology of RNA Sequencing pattern: ^\d{7}$ 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 synonyms: - ORPHA uri_format: http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1 orphanet.ordo: description: "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary\ \ for rare diseases, capturing relationships between diseases, genes and other\ \ relevant features which will form a useful resource for the computational analysis\ \ of rare diseases.\r\nIt integrates a nosology (classification of rare diseases),\ \ relationships (gene-disease relations, epiemological data) and connections with\ \ other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC,\ \ ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10)." download_owl: http://www.orphadata.org/data/ORDO/ordo_orphanet.owl example: C023 example_extras: - '478' homepage: https://www.ebi.ac.uk/ols/ontologies/ordo mappings: biocontext: ORPHANET.ORDO biolink: ORPHA bioportal: ORDO cellosaurus: ORDO fairsharing: FAIRsharing.pbbnwa miriam: orphanet.ordo n2t: orphanet.ordo ols: ordo name: Orphanet Rare Disease Ontology pattern: ^C?\d+$ preferred_prefix: orphanet.ordo synonyms: - ordo uri_format: http://www.orpha.net/ORDO/Orphanet_$1 version: '4.0' 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: bioportal: ORTH fairsharing: FAIRsharing.4877h0 ols: orth name: Orthology Ontology preferred_prefix: orth repository: https://github.com/qfo/OrthologyOntology 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 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/$1 otl: description: Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information. example: AADB12 homepage: http://oryzatagline.cirad.fr/ mappings: biocontext: OTL fairsharing: FAIRsharing.61c2x6 miriam: otl n2t: otl prefixcommons: otl name: Oryza Tag Line pattern: ^A[A-Z]+\d+$ preferred_prefix: otl uri_format: http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1 ovae: banana: OVAE contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqunh He orcid: 0000-0001-9189-9661 description: 'OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). ' download_owl: http://purl.obolibrary.org/obo/ovae.owl example: 0000609 homepage: http://www.violinet.org/ovae/ license: CC BY 3.0 mappings: biocontext: OVAE bioportal: OVAE fairsharing: FAIRsharing.w4x6n4 obofoundry: OVAE ols: ovae ontobee: OVAE name: Ontology of Vaccine Adverse Events pattern: ^\d{7}$ preferred_prefix: OVAE repository: https://github.com/OVAE-Ontology/ovae uri_format: http://purl.obolibrary.org/obo/OVAE_$1 version: 1.0.34 owl: description: 'Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. ' 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: 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=$1 panther.pathway: description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components. example: P00024 homepage: http://www.pantherdb.org/ mappings: biocontext: PANTHER.PATHWAY miriam: panther.pathway n2t: panther.pathway name: PANTHER Pathway part_of: panther pattern: ^P\d{5}$ 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: banana: 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/$1 pathwaycommons: description: Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language. example: '485991' homepage: http://www.pathwaycommons.org/pc/ mappings: biocontext: PATHWAYCOMMONS miriam: pathwaycommons n2t: pathwaycommons prefixcommons: pathwaycommons uniprot: PathwayCommons name: Pathway Commons pattern: ^\d+$ preferred_prefix: pathwaycommons uri_format: http://www.pathwaycommons.org/pc/record2.do?id=$1 pato: appears_in: - agro - aism - cdno - cl - colao - ecocore - ecto - fovt - lepao - mco - ms - pcl - pco - phipo - planp - rbo - xpo - zp banana: PATO contact: email: g.gkoutos@gmail.com github: gkoutos name: George Gkoutos orcid: 0000-0002-2061-091X description: PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. download_json: http://purl.obolibrary.org/obo/pato.json download_obo: http://purl.obolibrary.org/obo/pato.obo download_owl: http://purl.obolibrary.org/obo/pato.owl example: 0001998 homepage: https://github.com/pato-ontology/pato/ license: CC BY 3.0 mappings: biocontext: PATO bioportal: PATO fairsharing: FAIRsharing.ezwdhz go: PATO miriam: pato n2t: pato obofoundry: PATO ols: pato ontobee: PATO prefixcommons: pato name: Phenotype And Trait Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: PATO repository: https://github.com/pato-ontology/pato uri_format: https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=PATO:$1 version: '2022-02-20' pav: contributor: email: null github: matentzn name: Nico Matentzoglu orcid: 0000-0002-7356-1779 description: PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources. example: authoredBy homepage: https://pav-ontology.github.io/pav/ mappings: biocontext: pav biolink: pav bioportal: PAV fairsharing: FAIRsharing.nbfwwv name: Provenance, Authoring, and Versioning Vocabulary pattern: ^[a-z][a-zA-Z]+$ preferred_prefix: pav reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://purl.org/pav/$1 paxdb.organism: description: PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species. example: '9606' homepage: http://pax-db.org/ mappings: biocontext: PAXDB.ORGANISM miriam: paxdb.organism n2t: paxdb.organism name: PaxDb Organism pattern: ^\d+$ preferred_prefix: paxdb.organism uri_format: http://pax-db.org/#!species/$1 paxdb.protein: description: PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels. example: '977869' homepage: http://pax-db.org/ mappings: biocontext: PAXDB.PROTEIN miriam: paxdb.protein n2t: paxdb.protein name: PaxDb Protein pattern: ^\d+$ preferred_prefix: paxdb.protein uri_format: http://pax-db.org/#!protein/$1 pazar: description: The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors. example: TF0001053 homepage: http://www.pazar.info/ mappings: biocontext: PAZAR fairsharing: FAIRsharing.33yggg miriam: pazar n2t: pazar prefixcommons: pazar name: Pazar Transcription Factor pattern: ^TF\w+$ 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 pcl: banana: 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: bioportal: PCL obofoundry: PCL ols: pcl name: Provisional Cell Ontology pattern: ^\d{7}$ preferred_prefix: PCL repository: https://github.com/obophenotype/provisional_cell_ontology uri_format: http://purl.obolibrary.org/obo/PCL_$1 version: '2022-04-27' pco: appears_in: - ecocore - envo banana: PCO contact: email: rlwalls2008@gmail.com github: ramonawalls name: Ramona Walls orcid: 0000-0001-8815-0078 depends_on: - bfo - caro - envo - go - iao - ncbitaxon - pato - ro description: The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. download_owl: http://purl.obolibrary.org/obo/pco.owl example: '0000021' homepage: https://github.com/PopulationAndCommunityOntology/pco license: CC0 1.0 mappings: biocontext: PCO bioportal: PCO fairsharing: FAIRsharing.vq28qp obofoundry: PCO ols: pco ontobee: PCO name: Population and Community Ontology pattern: ^\d{7}$ preferred_prefix: PCO repository: https://github.com/PopulationAndCommunityOntology/pco uri_format: http://purl.obolibrary.org/obo/PCO_$1 version: '2021-05-03' pd_st: banana: 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_$1 pdb: description: The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. example: 2gc4 homepage: https://www.wwpdb.org/ mappings: biocontext: PDB fairsharing: FAIRsharing.mckkb4 go: PDB miriam: pdb n2t: pdb ncbi: PDB prefixcommons: pdbj uniprot: RCSB-PDB wikidata: P638 name: PDB Structure pattern: ^[0-9][A-Za-z0-9]{3}$ 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: rcsb description: RCSB PDB homepage: https://www.rcsb.org/ name: RCSB PDB uri_format: https://www.rcsb.org/structure/$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: 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 synonyms: - RCSB_PDB - pdbe - pdbj - wwpdb uri_format: https://www.wwpdb.org/pdb?id=$1 pdb-ccd: comment: might be same as pdb.ligand, not sure though description: The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names. example: AB0 example_extras: - A - PI has_canonical: pdb.ligand homepage: https://www.ebi.ac.uk/pdbe-srv/pdbechem/ mappings: biocontext: PDB-CCD miriam: pdb-ccd n2t: pdb-ccd name: Chemical Component Dictionary pattern: ^\w{1,3}$ preferred_prefix: pdb-ccd 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=$1 pdro: banana: PDRO contact: email: paul.fabry@usherbrooke.ca github: pfabry name: Paul Fabry orcid: 0000-0002-3336-2476 description: An ontology to describe entities related to prescription of drugs download_owl: http://purl.obolibrary.org/obo/pdro.owl example: 0010039 homepage: https://github.com/OpenLHS/PDRO license: CC BY 4.0 mappings: biocontext: PDRO bioportal: PDRO fairsharing: FAIRsharing.9te3ev obofoundry: PDRO ols: pdro ontobee: PDRO name: The Prescription of Drugs Ontology pattern: ^\d{7}$ preferred_prefix: PDRO repository: https://github.com/OpenLHS/PDRO uri_format: http://purl.obolibrary.org/obo/PDRO_$1 version: '2021-06-08' pdumdv: banana: PdumDv contact: email: frederic.bastian@unil.ch github: fbastian name: Frédéric Bastian orcid: 0000-0002-9415-5104 description: Life cycle stages for Platynereis dumerilii download_obo: http://purl.obolibrary.org/obo/pdumdv.obo download_owl: http://purl.obolibrary.org/obo/pdumdv.owl example: '0001410' homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv license: CC BY 3.0 mappings: biocontext: PDUMDV bioportal: PDUMDV fairsharing: FAIRsharing.493qns obofoundry: PdumDv ols: pdumdv ontobee: PDUMDV name: Platynereis Developmental Stages pattern: ^\d{7}$ preferred_prefix: PdumDv repository: https://github.com/obophenotype/developmental-stage-ontologies synonyms: - PdumDv uri_format: http://purl.obolibrary.org/obo/PDUMDV_$1 version: '2020-03-10' peco: appears_in: - agro - mco banana: PECO contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp name: Pankaj Jaiswal orcid: 0000-0002-1005-8383 description: A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. download_obo: https://raw.githubusercontent.com/Planteome/plant-experimental-conditions-ontology/master/peco.obo download_owl: http://purl.obolibrary.org/obo/peco.owl example: '0007114' homepage: http://planteome.org/ license: CC BY 4.0 mappings: biocontext: PECO bioportal: PECO fairsharing: FAIRsharing.6yNXYK obofoundry: PECO ols: peco ontobee: PECO name: Plant Experimental Conditions Ontology pattern: ^\d{7}$ preferred_prefix: PECO 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 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 fairsharing: FAIRsharing.dvyrsz miriam: peptideatlas n2t: peptideatlas prefixcommons: peptideatlas uniprot: PeptideAtlas name: PeptideAtlas pattern: ^PAp[0-9]{8}$ preferred_prefix: peptideatlas 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 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/$1.html pfam: description: The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored. example: PF11779 homepage: https://pfam.xfam.org/ mappings: biocontext: PFAM fairsharing: FAIRsharing.y3scf6 go: Pfam miriam: pfam n2t: pfam ncbi: PFAM prefixcommons: pfam uniprot: Pfam wikidata: P3519 name: Pfam pattern: ^PF\d{5}$ preferred_prefix: pfam synonyms: - PF uri_format: https://pfam.xfam.org/family/$1 pfam.clan: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Higher order grouping of Pfam families example: CL0192 homepage: https://pfam.xfam.org name: Pfam Clans pattern: ^CL\d+$ preferred_prefix: pfam.clan uri_format: https://pfam.xfam.org/clan/$1 pfr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets. example: '1001' homepage: http://repository.topdownproteomics.org/proteoforms mappings: fairsharing: FAIRsharing.wqsxtg name: Proteoform Atlas pattern: ^\d+$ preferred_prefix: pfr synonyms: - TDR uri_format: http://repository.topdownproteomics.org/proteoforms/$1 pgdso: banana: 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/$1 pgx: description: The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt "neoplasm" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs. example: pgxbs-kftva5zv homepage: https://progenetix.org/ mappings: biocontext: PGX cellosaurus: Progenetix fairsharing: FAIRsharing.65tdnz miriam: pgx n2t: pgx name: Progenetix pattern: ^\w{3,15}[-_]\w[\w.-]{3,128}$ preferred_prefix: pgx synonyms: - Progenetix uri_format: https://progenetix.org/services/ids/$1 pharmacodb.cell: 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/$1 pharmgkb.disease: description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. example: PA447218 homepage: http://www.pharmgkb.org/ mappings: biocontext: PHARMGKB.DISEASE miriam: pharmgkb.disease n2t: pharmgkb.disease prefixcommons: pharmgkb.disease wikidata: P7001 name: PharmGKB Disease pattern: ^PA\d+$ preferred_prefix: pharmgkb.disease uri_format: http://www.pharmgkb.org/disease/$1 pharmgkb.drug: description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. example: PA448710 homepage: http://www.pharmgkb.org/ mappings: biocontext: PHARMGKB.DRUG miriam: pharmgkb.drug n2t: pharmgkb.drug prefixcommons: pharmgkb.drug wikidata: P7001 name: PharmGKB Drug pattern: ^PA\d+$ preferred_prefix: pharmgkb.drug 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 uri_format: http://www.pharmgkb.org/gene/$1 pharmgkb.pathways: description: "The PharmGKB database is a central repository for genetic, genomic,\ \ molecular and cellular phenotype data and clinical information about people\ \ who have participated in pharmacogenomics research studies. The data includes,\ \ but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic\ \ research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter\ \ domains. \r\nPharmGKB Pathways are drug centric, gene based, interactive pathways\ \ which focus on candidate genes and gene groups and associated genotype and phenotype\ \ data of relevance for pharmacogenetic and pharmacogenomic studies." example: PA146123006 homepage: http://www.pharmgkb.org/ mappings: biocontext: PHARMGKB.PATHWAYS miriam: pharmgkb.pathways n2t: pharmgkb.pathways prefixcommons: pharmgkb.pathways wikidata: P7001 name: PharmGKB Pathways pattern: ^PA\d+$ preferred_prefix: pharmgkb.pathways uri_format: http://www.pharmgkb.org/pathway/$1 phenolexplorer: description: Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis. example: '75' homepage: http://www.phenol-explorer.eu/foods/ mappings: biocontext: PHENOLEXPLORER miriam: phenolexplorer n2t: phenolexplorer name: Phenol-Explorer pattern: ^\d+$ preferred_prefix: phenolexplorer uri_format: http://phenol-explorer.eu/foods/$1 phenx: description: A Web-based catalog of recommended measurement protocols example: '130502' homepage: https://www.phenxtoolkit.org/ mappings: bioportal: PHENX fairsharing: FAIRsharing.y5jcwa name: PhenX Toolkit pattern: ^\d+$ preferred_prefix: phenx uri_format: https://www.phenxtoolkit.org/protocols/view/$1 phipo: banana: PHIPO contact: email: alayne.cuzick@rothamsted.ac.uk github: CuzickA name: Alayne Cuzick orcid: 0000-0001-8941-3984 depends_on: - pato description: Ontology of species-neutral phenotypes observed in pathogen-host interactions. download_obo: http://purl.obolibrary.org/obo/phipo.obo download_owl: http://purl.obolibrary.org/obo/phipo.owl example: '0000001' homepage: https://github.com/PHI-base/phipo license: CC BY 3.0 mappings: bioportal: PHIPO obofoundry: PHIPO ols: phipo ontobee: PHIPO name: Pathogen Host Interaction Phenotype Ontology pattern: ^\d{7}$ preferred_prefix: PHIPO 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=$1 phylomedb: description: PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins. example: Phy000CLXM_RAT homepage: http://phylomedb.org/ mappings: biocontext: PHYLOMEDB fairsharing: FAIRsharing.7hxxc4 miriam: phylomedb n2t: phylomedb prefixcommons: phylomedb uniprot: PhylomeDB name: PhylomeDB pattern: ^\w+$ preferred_prefix: phylomedb 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:$1 pictar: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true example: hsa-let-7a homepage: https://pictar.mdc-berlin.de/ name: PicTar preferred_prefix: pictar synonyms: - pictar-vert pid.pathway: description: The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information. example: eff796f3-6195-11e5-8ac5-06603eb7f303 homepage: http://pid.nci.nih.gov/ mappings: biocontext: PID.PATHWAY fairsharing: FAIRsharing.ncgh1j miriam: pid.pathway n2t: pid.pathway prefixcommons: pid name: 'NCI Pathway Interaction Database: Pathway' pattern: ^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$ preferred_prefix: pid.pathway 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=$1 pirsf: description: The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. example: PIRSF000100 homepage: https://pir.georgetown.edu/ mappings: biocontext: PIRSF fairsharing: FAIRsharing.vssch2 go: PIRSF miriam: pirsf n2t: pirsf prefixcommons: pirsf uniprot: PIRSF name: PIR Superfamily Classification System pattern: ^PIRSF\d{6}$ preferred_prefix: pirsf 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/$1 plana: appears_in: - planp banana: PLANA contact: email: smr@stowers.org github: srobb1 name: Sofia Robb orcid: 0000-0002-3528-5267 depends_on: - ro - uberon description: PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea. download_obo: http://purl.obolibrary.org/obo/plana.obo download_owl: http://purl.obolibrary.org/obo/plana.owl example: '0000001' homepage: https://github.com/obophenotype/planaria-ontology license: CC BY 3.0 mappings: biocontext: PLANA bioportal: PLANA fairsharing: FAIRsharing.g1qrqs obofoundry: PLANA ols: plana ontobee: PLANA name: Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology pattern: ^\d{7}$ preferred_prefix: PLANA repository: https://github.com/obophenotype/planaria-ontology uri_format: http://purl.obolibrary.org/obo/PLANA_$1 version: '2022-03-02' planp: banana: PLANP contact: email: smr@stowers.org github: srobb1 name: Sofia Robb orcid: 0000-0002-3528-5267 depends_on: - go - pato - plana - ro description: Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea. download_obo: http://purl.obolibrary.org/obo/planp.obo download_owl: http://purl.obolibrary.org/obo/planp.owl example: '0000001' homepage: https://github.com/obophenotype/planarian-phenotype-ontology license: CC BY 3.0 mappings: bioportal: PLANP obofoundry: PLANP ols: planp ontobee: PLANP name: Planarian Phenotype Ontology pattern: ^\d+$ 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=$1 plasmodb: description: AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: PF11_0344 homepage: http://plasmodb.org/plasmo/ mappings: biocontext: PLASMODB fairsharing: FAIRsharing.g4n8sw go: PlasmoDB miriam: plasmodb n2t: plasmodb ncbi: ApiDB_PlasmoDB prefixcommons: plasmodb name: PlasmoDB pattern: ^\w+$ preferred_prefix: plasmodb synonyms: - ApiDB_PlasmoDB uri_format: http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 plo: banana: 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 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 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 uri_format: http://www.proteinmodelportal.org/query/uniprot/$1 pmr: description: Resource for the community to store, retrieve, search, reference, and reuse CellML models. example: ebf69ca24298b28b2361e7d43eb52d6c homepage: https://www.auckland.ac.nz/en.html mappings: bioportal: PMR fairsharing: FAIRsharing.bcjrnq miriam: pmr name: Physical Medicine and Rehabilitation pattern: ^[a-z0-9]{32,32}$ preferred_prefix: pmr uri_format: https://models.physiomeproject.org/exposure/$1 po: appears_in: - agro - ecocore - envo - genepio banana: PO contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp name: Pankaj Jaiswal orcid: 0000-0002-1005-8383 description: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. download_obo: http://purl.obolibrary.org/obo/po.obo download_owl: http://purl.obolibrary.org/obo/po.owl example: 0009089 homepage: http://browser.planteome.org/amigo license: CC BY 4.0 mappings: biocontext: PO bioportal: PO fairsharing: FAIRsharing.3ngg40 go: PO miriam: po n2t: po obofoundry: PO ols: po ontobee: PO prefixcommons: po name: Plant Ontology namespace_in_lui: true pattern: ^\d+$ preferred_prefix: PO repository: https://github.com/Planteome/plant-ontology 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/$1#sequences pombase: description: PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets. example: SPCC13B11.01 homepage: http://www.pombase.org/ mappings: biocontext: PomBase biolink: PomBase fairsharing: FAIRsharing.8jsya3 go: PomBase miriam: pombase n2t: pombase ncbi: PomBase prefixcommons: pombase uniprot: PomBase wikidata: P6245 name: PomBase pattern: ^S\w+(\.)?\w+(\.)?$ preferred_prefix: pombase synonyms: - PomBase uri_format: http://www.pombase.org/spombe/result/$1 poro: banana: PORO contact: email: robert.thacker@stonybrook.edu github: bobthacker name: Bob Thacker orcid: 0000-0002-9654-0073 depends_on: - ro - uberon description: An ontology describing the anatomical structures and characteristics of Porifera (sponges) download_obo: http://purl.obolibrary.org/obo/poro.obo download_owl: http://purl.obolibrary.org/obo/poro.owl example: '0000550' homepage: https://github.com/obophenotype/porifera-ontology license: CC BY 3.0 mappings: biocontext: PORO bioportal: PORO fairsharing: FAIRsharing.93g1th obofoundry: PORO ols: poro ontobee: PORO name: Porifera Ontology pattern: ^\d{7}$ preferred_prefix: PORO 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/$1.htm ppo: banana: PPO contact: email: rlwalls2008@gmail.com github: ramonawalls name: Ramona Walls orcid: 0000-0001-8815-0078 description: An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales. download_owl: http://purl.obolibrary.org/obo/ppo.owl example: 0002058 homepage: https://github.com/PlantPhenoOntology/PPO license: CC BY 3.0 mappings: biocontext: PPO bioportal: PPO fairsharing: FAIRsharing.hakg7c obofoundry: PPO ols: ppo ontobee: PPO name: Plant Phenology Ontology pattern: ^\d{7}$ preferred_prefix: PPO 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/$1 pr: appears_in: - chiro - cl - pcl - scdo - uberon banana: PR contact: email: dan5@georgetown.edu github: nataled name: Darren Natale orcid: 0000-0001-5809-9523 description: The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies. download_obo: http://purl.obolibrary.org/obo/pr.obo download_owl: http://purl.obolibrary.org/obo/pr.owl example: '000000024' homepage: http://proconsortium.org license: CC BY 4.0 mappings: biocontext: PR bioportal: PR fairsharing: FAIRsharing.4ndncv go: PR miriam: pr n2t: pr obofoundry: PR ols: pr ontobee: PR prefixcommons: pr uniprot: PRO wikidata: P4926 name: Protein Ontology namespace_in_lui: true pattern: ^\d+$ preferred_prefix: PR repository: https://github.com/PROconsortium/PRoteinOntology synonyms: - PR - PRO uri_format: https://proconsortium.org/app/entry/PR:$1 version: '65.0' 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/$1 pride: description: The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays. download_owl: https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/pride_cv.obo example: '1' homepage: https://github.com/PRIDE-Utilities/pride-ontology mappings: biocontext: PRIDE cellosaurus: PRIDE fairsharing: FAIRsharing.e1byny miriam: pride n2t: pride ols: pride prefixcommons: pride uniprot: PRIDE name: PRIDE Controlled Vocabulary pattern: ^\d+$ preferred_prefix: pride 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=$1&display_opts=Prints&category=None&queryform=false®expr=off probonto: description: ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities. download_owl: https://raw.githubusercontent.com/probonto/ontology/master/probonto4ols.owl example: PROB_c0000005 homepage: http://probonto.org mappings: biocontext: PROBONTO fairsharing: FAIRsharing.8zqzm9 miriam: probonto n2t: probonto ols: probonto name: Probability Distribution Ontology pattern: ^PROB_c\d+$ preferred_prefix: probonto uri_format: https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=$1 version: 2.5.0 prodom: description: ProDom is a database of protein domain families generated from the global comparison of all available protein sequences. example: PD10000 homepage: http://prodom.prabi.fr/prodom/current/html/home.php mappings: biocontext: PRODOM fairsharing: FAIRsharing.a8z6gz miriam: prodom n2t: prodom prefixcommons: prodom name: ProDom pattern: ^PD\d+$ preferred_prefix: prodom 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: banana: PROPREO contact: email: satya30@uga.edu github: null name: Satya S. Sahoo orcid: null deprecated: true homepage: http://lsdis.cs.uga.edu/projects/glycomics/propreo/ mappings: 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 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 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 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 uri_format: http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1 prov: 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: 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/$1.html psdo: banana: PSDO contact: email: zachll@umich.edu github: zachll name: Zach Landis-Lewis orcid: 0000-0002-9117-9338 depends_on: - bfo - iao - ro - stato description: Performance Summary Display Ontology (PSDO) (pronounced "pseudo" or "sudo") is an application ontology about charts, tables, and graphs that are used to communicate performance information to employees and teams in organizations. PSDO's domain focus is on healthcare organizations that use performance summary displays in clinical dashboards and feedback interventions for healthcare professionals and teams. The displays commonly show information about the quality of care and health outcomes that has been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is not peer-reviewed. download_owl: http://purl.obolibrary.org/obo/psdo.owl example: '0000055' homepage: https://github.com/Display-Lab/psdo license: CC BY 3.0 mappings: bioportal: PSDO obofoundry: PSDO ols: psdo ontobee: PSDO name: Performance Summary Display Ontology pattern: ^\d{7}$ preferred_prefix: PSDO repository: https://github.com/Display-Lab/psdo uri_format: http://purl.obolibrary.org/obo/PSDO_$1 version: 1.0.0 pseudogene: 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=$1 psipar: description: Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms. example: PAR:0116 homepage: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR mappings: biocontext: PSIPAR miriam: psipar n2t: psipar name: Protein Affinity Reagents pattern: ^PAR:\d+$ preferred_prefix: psipar uri_format: https://www.ebi.ac.uk/ontology-lookup/?termId=$1 pso: banana: PSO contact: email: cooperl@oregonstate.edu github: cooperl09 name: Laurel Cooper orcid: 0000-0002-6379-8932 depends_on: - ro description: The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter. download_obo: http://purl.obolibrary.org/obo/pso.obo download_owl: http://purl.obolibrary.org/obo/pso.owl example: '0000013' homepage: https://github.com/Planteome/plant-stress-ontology license: CC BY 3.0 mappings: bioportal: PSO fairsharing: FAIRsharing.dyj433 obofoundry: PSO ols: pso ontobee: PSO name: Plant Stress Ontology pattern: ^\d{7}$ preferred_prefix: PSO repository: https://github.com/Planteome/plant-stress-ontology uri_format: http://purl.obolibrary.org/obo/PSO_$1 version: '2020-05-19' pspub: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Documentation of the Phenoscape Curation Workflow homepage: https://wiki.phenoscape.org/wiki/Curation_workflow name: Phenoscape Publication preferred_prefix: pspub pubchem.bioassay: description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results. example: '1018' homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay mappings: biocontext: PUBCHEM.BIOASSAY go: PubChem_BioAssay miriam: pubchem.bioassay n2t: pubchem.bioassay prefixcommons: pubchem.bioassay name: NCBI PubChem database of bioassay records pattern: ^\d+$ preferred_prefix: pubchem.bioassay uri_format: https://pubchem.ncbi.nlm.nih.gov/bioassay/$1 pubchem.compound: description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records. example: '100101' homepage: https://pubchem.ncbi.nlm.nih.gov/ mappings: biocontext: CID biolink: CID cellosaurus: PubChem cheminf: '000140' fairsharing: FAIRsharing.g63c77 go: PubChem_Compound miriam: pubchem.compound n2t: pubchem.compound prefixcommons: pubchem.compound scholia: pubchem wikidata: P662 name: PubChem CID pattern: ^\d+$ 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 uri_format: https://pubchem.ncbi.nlm.nih.gov/compound/$1 pubchem.element: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number. example: '1' homepage: https://pubchem.ncbi.nlm.nih.gov/periodic-table name: PubChem Element pattern: ^\d+$ preferred_prefix: pubchem.element uri_format: https://pubchem.ncbi.nlm.nih.gov/element/$1 pubchem.substance: description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records. example: '100101' homepage: https://pubchem.ncbi.nlm.nih.gov/ mappings: biocontext: PUBCHEM.SUBSTANCE cheminf: '000141' go: PubChem_Substance miriam: pubchem.substance n2t: pubchem.substance prefixcommons: pubchem.substance wikidata: P2153 name: PubChem Substance ID (SID) pattern: ^\d+$ preferred_prefix: pubchem.substance synonyms: - DSSTox_Generic_SID uri_format: https://pubchem.ncbi.nlm.nih.gov/substance/$1 publons.researcher: description: Database of researchers to track publications, citation metrics, peer reviews, and journal editing work. example: '1981638' homepage: https://publons.com/researcher mappings: biolink: ResearchID name: Publons Researcher pattern: ^\d+$ preferred_prefix: publons.researcher uri_format: https://publons.com/researcher/$1 pubmed: description: PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. example: '16333295' homepage: https://www.ncbi.nlm.nih.gov/PubMed/ mappings: biocontext: PMID cellosaurus: PubMed cheminf: '000302' fairsharing: FAIRsharing.a5sv8m go: PMID miriam: pubmed n2t: pubmed prefixcommons: pubmed scholia: pubmed wikidata: P698 name: PubMed pattern: ^\d+$ preferred_prefix: pubmed providers: - code: hubmed description: HubMed homepage: http://www.hubmed.org/ name: HubMed uri_format: http://www.hubmed.org/display.cgi?uids=$1 - code: epmc description: Europe PMC homepage: http://europepmc.org/ name: Europe PMC uri_format: http://europepmc.org/abstract/MED/$1 - 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: 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 synonyms: - MEDLINE - PMID - pmid uri_format: https://www.ncbi.nlm.nih.gov/pubmed/$1 pw: banana: PW contact: email: gthayman@mcw.edu github: gthayman name: G. Thomas Hayman orcid: 0000-0002-9553-7227 description: 'The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions.' download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo download_owl: http://purl.obolibrary.org/obo/pw.owl example: '0000423' homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html license: CC BY 4.0 mappings: biocontext: PW bioportal: PW fairsharing: FAIRsharing.f73xhd miriam: pw n2t: pw obofoundry: PW ols: pw ontobee: PW prefixcommons: pw wikidata: P7333 name: Pathway ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: PW repository: https://github.com/rat-genome-database/PW-Pathway-Ontology uri_format: http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:$1 version: '2019-10-23' px: description: The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination. example: PXD000500 homepage: http://www.proteomexchange.org/ mappings: biocontext: PX miriam: px n2t: px name: ProteomeXchange pattern: ^(R)?PXD\d{6}$ 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/$1 qtldb: description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent. example: '4685' homepage: https://www.animalgenome.org/QTLdb mappings: miriam: qtldb name: Animal Genome QTL pattern: ^\d+$ preferred_prefix: qtldb uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 qudt: description: Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types. example: baseDimensionEnumeration homepage: https://qudt.org mappings: biolink: qud bioportal: QUDT fairsharing: FAIRsharing.d3pqw7 name: Quantities, Units, Dimensions, and Types Ontology preferred_prefix: qudt uri_format: http://qudt.org/schema/qudt#$1 radiomics: description: The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual. [bioportal] example: LK99 homepage: http://www.radiomics.org/RO mappings: bioportal: RO name: Radiomics Ontology preferred_prefix: radiomics rapdb.locus: description: Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB. example: Os01g0883800 homepage: https://rapdb.dna.affrc.go.jp/ mappings: miriam: rapdb.locus name: RAP-DB Locus pattern: ^Os\S+g\d{7}$ 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/$1 rbo: banana: RBO contact: email: daniel.c.berrios@nasa.gov github: DanBerrios name: Daniel C. Berrios orcid: 0000-0003-4312-9552 depends_on: - bfo - chmo - envo - obi - pato - ro - uo description: RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. download_json: http://purl.obolibrary.org/obo/rbo.json download_obo: http://purl.obolibrary.org/obo/rbo.obo download_owl: http://purl.obolibrary.org/obo/rbo.owl example: '00000105' homepage: https://github.com/Radiobiology-Informatics-Consortium/RBO license: CC BY 3.0 mappings: bioportal: RBO obofoundry: RBO ols: rbo ontobee: RBO name: Radiation Biology Ontology pattern: ^\d{8}$ preferred_prefix: RBO repository: https://github.com/Radiobiology-Informatics-Consortium/RBO uri_format: http://purl.obolibrary.org/obo/RBO_$1 version: '2022-04-16' rcb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center. example: RCB0002 homepage: https://cell.brc.riken.jp/en/rcb mappings: cellosaurus: RCB name: RIKEN Bioresource Center Cell Bank pattern: ^RCB\d+$ preferred_prefix: rcb uri_format: https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1 rdf: 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: description: RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary. example: label homepage: https://www.w3.org/TR/rdf-schema/ mappings: biocontext: rdfs bioportal: RDFS fairsharing: FAIRsharing.v9n3gk name: RDF Schema preferred_prefix: rdfs uri_format: http://www.w3.org/2000/01/rdf-schema#$1 rdo: description: Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms. download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.obo download_owl: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.owl example: '9002859' homepage: https://ratmine.mcw.edu/ontology/disease/ mappings: bioportal: RDO name: RGD Disease_Ontology pattern: ^\d{7}$ preferred_prefix: rdo 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/$1 reactome: description: The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology. example: R-BTA-418592 homepage: https://www.reactome.org/ mappings: biocontext: REACT cheminf: '000411' go: Reactome miriam: reactome n2t: reactome prefixcommons: reactome uniprot: Reactome wikidata: P3937 name: Reactome pattern: ^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$ 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 synonyms: - RE - REACT uri_format: https://reactome.org/content/detail/$1 reaxys: description: Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier. example: '1257009' homepage: https://www.reaxys.com mappings: wikidata: P1579 name: Reaxys pattern: ^\d+$ 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 fairsharing: FAIRsharing.9sb9qh go: REBASE miriam: rebase n2t: rebase prefixcommons: rebase uniprot: REBASE name: REBASE restriction enzyme database pattern: ^\d+$ preferred_prefix: rebase 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=$1 refseq: description: The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products. example: NP_012345 has_canonical: ncbiprotein homepage: https://www.ncbi.nlm.nih.gov/projects/RefSeq/ mappings: biocontext: RefSeq fairsharing: FAIRsharing.4jg0qw go: RefSeq miriam: refseq n2t: refseq prefixcommons: refseq uniprot: RefSeq name: Reference Sequence Collection pattern: ^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+)|(NZ\_[A-Z]{2,4}\d+))(\.\d+)?$ preferred_prefix: refseq 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 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/$1 reproduceme: description: The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility. download_owl: https://sheeba-samuel.github.io/REPRODUCE-ME/doc/reproduce-me.xml example: MicrobeamManipulation homepage: https://w3id.org/reproduceme/research mappings: bioportal: REPRODUCE-ME ols: reproduceme name: REPRODUCE-ME Ontology preferred_prefix: reproduceme version: '1.1' resid: banana: RESID contact: email: john.garavelli@ebi.ac.uk github: null name: John Garavelli orcid: null deprecated: true description: The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. example: AA0001 homepage: http://www.ebi.ac.uk/RESID/ mappings: biocontext: RESID go: RESID miriam: resid n2t: resid obofoundry: RESID prefixcommons: resid name: Protein covalent bond pattern: ^AA\d{4}$ preferred_prefix: RESID uri_format: http://pir0.georgetown.edu/cgi-bin/resid?id=$1 reto: description: Regulation of Transcription download_obo: https://www.bio.ntnu.no/ontology/ReTO/reto.obo download_owl: https://www.bio.ntnu.no/ontology/ReTO/reto.owl homepage: http://www.semantic-systems-biology.org/apo mappings: bioportal: RETO fairsharing: FAIRsharing.4qyf0f ols: reto name: Regulation of Transcription Ontology no_own_terms: true preferred_prefix: reto version: '2019-09-17' rex: banana: REX description: An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. download_owl: http://purl.obolibrary.org/obo/rex.owl example: '0000512' homepage: https://www.ebi.ac.uk/chebi/ mappings: biocontext: REX bioportal: REX fairsharing: FAIRsharing.g0a7s0 obofoundry: REX ols: rex ontobee: REX prefixcommons: rex name: Physico-chemical process part_of: chebi pattern: ^\d{7}$ preferred_prefix: REX uri_format: http://purl.obolibrary.org/obo/REX_$1 version: '2017-11-19' rexo: description: Regulation of Gene Expression download_obo: https://www.bio.ntnu.no/ontology/ReXO/rexo.obo download_owl: https://www.bio.ntnu.no/ontology/ReXO/rexo.owl homepage: http://www.semantic-systems-biology.org/apo mappings: bioportal: REXO fairsharing: FAIRsharing.recas1 ols: rexo name: Regulation of Gene Expression Ontology no_own_terms: true preferred_prefix: rexo version: '2019-04-11' rfam: description: 'The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion.' example: RF00230 homepage: https://rfam.xfam.org/ mappings: biocontext: RFAM fairsharing: FAIRsharing.fex4c8 go: Rfam miriam: rfam n2t: rfam ncbi: RFAM name: Rfam database of RNA families pattern: ^RF\d{5}$ preferred_prefix: rfam uri_format: https://rfam.xfam.org/family/$1 rgd: description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes. example: '7499841' homepage: http://rgd.mcw.edu/ mappings: biocontext: RGD bioportal: RGD cellosaurus: RGD fairsharing: FAIRsharing.pfg82t go: RGD miriam: rgd n2t: rgd ncbi: RGD prefixcommons: rgd uniprot: RGD wikidata: P3853 name: Rat Genome Database pattern: ^\d{4,}$ 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 synonyms: - RGD 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 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 uri_format: http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1 rhea: description: ' Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants. Rhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB.' example: '12345' homepage: https://www.rhea-db.org/ mappings: biocontext: RHEA fairsharing: FAIRsharing.pn1sr5 go: RHEA miriam: rhea n2t: rhea prefixcommons: rhea name: Rhea, the Annotated Reactions Database pattern: ^\d{5}$ 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=$1 rnacentral: description: RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases. example: URS0000759CF4 homepage: https://rnacentral.org/ mappings: biocontext: RNACENTRAL fairsharing: FAIRsharing.KcCjL7 go: RNAcentral miriam: rnacentral n2t: rnacentral ncbi: RNAcentral name: RNAcentral pattern: ^URS[0-9A-F]{10}(\_\d+)?$ 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/$1 rnao: banana: RNAO contact: email: BatchelorC@rsc.org github: null name: Colin Batchelor orcid: 0000-0001-5985-7429 description: Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures. download_obo: http://purl.obolibrary.org/obo/rnao.obo download_owl: http://purl.obolibrary.org/obo/rnao.owl example: 0000128 homepage: https://github.com/bgsu-rna/rnao license: CC0 1.0 mappings: biocontext: RNAO bioportal: RNAO fairsharing: FAIRsharing.kqt2h2 obofoundry: RNAO ols: rnao ontobee: RNAO prefixcommons: rnao name: RNA ontology pattern: ^\d{7}$ preferred_prefix: RNAO repository: https://github.com/BGSU-RNA/rnao uri_format: http://purl.obolibrary.org/obo/RNAO_$1 version: '2019-04-15' ro: appears_in: - agro - aism - cdno - cl - clao - clyh - colao - cteno - ecao - ecocore - ecto - envo - foodon - fovt - genepio - go - hso - lepao - maxo - ons - ontoavida - pcl - pco - plana - planp - poro - psdo - pso - rbo - upa - xpo - zp banana: RO contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies. download_json: http://purl.obolibrary.org/obo/ro.json download_obo: http://purl.obolibrary.org/obo/ro.obo download_owl: http://purl.obolibrary.org/obo/ro.owl example: '0002533' homepage: https://oborel.github.io/ license: CC0 1.0 mappings: biocontext: OBO_REL biolink: RO bioportal: OBOREL fairsharing: FAIRsharing.1vrrdh go: RO miriam: ro n2t: ro obofoundry: RO ols: ro ontobee: RO prefixcommons: ro wikidata: P3590 name: Relation Ontology pattern: ^\d{7}$ preferred_prefix: RO repository: https://github.com/oborel/obo-relations synonyms: - RO_proposed_relation - obo_rel - oborel uri_format: http://purl.obolibrary.org/obo/RO_$1 version: '2022-05-23' rouge: description: The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. example: mKIAA4200 homepage: http://www.kazusa.or.jp/rouge/ mappings: biocontext: ROUGE fairsharing: FAIRsharing.vdbagq miriam: rouge n2t: rouge prefixcommons: rouge uniprot: Rouge name: Rodent Unidentified Gene-Encoded Large Proteins pattern: ^m\w+$ 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:$1 rs: banana: RS contact: email: sjwang@mcw.edu github: shurjenw name: Shur-Jen Wang orcid: 0000-0001-5256-8683 description: Ontology of rat strains download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.obo download_owl: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.owl example: 0001807 homepage: http://rgd.mcw.edu/rgdweb/search/strains.html license: CC BY 4.0 mappings: biocontext: RS bioportal: RS fairsharing: FAIRsharing.vajn3f obofoundry: RS ols: rs ontobee: RS prefixcommons: rs name: Rat Strain Ontology pattern: ^\d{7}$ preferred_prefix: RS repository: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology uri_format: http://purl.obolibrary.org/obo/RS_$1 version: '2019-12-13' runbiosimulations: description: runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive. example: 5fde96bdc5f1aa9ff0cce18a homepage: https://icahn.mssm.edu/ mappings: miriam: runbiosimulations name: runBioSimulations pattern: ^[0-9a-z]{24,24}$ preferred_prefix: runbiosimulations uri_format: https://run.biosimulations.org/simulations/$1 rxno: banana: RXNO contact: email: batchelorc@rsc.org github: batchelorc name: Colin Batchelor orcid: 0000-0001-5985-7429 description: RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization. download_obo: https://github.com/rsc-ontologies/rxno/raw/master/rxno.obo download_owl: http://purl.obolibrary.org/obo/rxno.owl example: '0000253' homepage: https://github.com/rsc-ontologies/rxno license: CC BY 4.0 mappings: biocontext: RXNO bioportal: RXNO fairsharing: FAIRsharing.w4tncg obofoundry: RXNO ols: rxno ontobee: RXNO wikidata: P2106 name: Name Reaction Ontology pattern: ^\d{7}$ preferred_prefix: RXNO repository: https://github.com/rsc-ontologies/rxno uri_format: http://purl.obolibrary.org/obo/RXNO_$1 version: '2021-12-16' rxnorm: description: RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary. example: '221058' homepage: https://www.nlm.nih.gov/research/umls/rxnorm/ mappings: biocontext: RXCUI biolink: RXCUI bioportal: RXNORM fairsharing: FAIRsharing.36pf8q wikidata: P3345 name: RxNorm pattern: ^[0-9]{1,7}$ preferred_prefix: rxnorm 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 uri_format: http://sabiork.h-its.org/newSearch?q=ecnumber:$1 sabiork.kineticrecord: description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information. example: '5046' homepage: http://sabiork.h-its.org/ mappings: biocontext: SABIORK.KINETICRECORD go: SABIO-RK miriam: sabiork.kineticrecord n2t: sabiork.kineticrecord name: SABIO Reaction Kinetics pattern: ^\d+$ preferred_prefix: sabiork.kineticrecord uri_format: http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1 sabiork.reaction: description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information. example: '75' homepage: http://sabiork.h-its.org/ mappings: biocontext: SABIORK.REACTION fairsharing: FAIRsharing.cwx04e miriam: sabiork.reaction n2t: sabiork.reaction prefixcommons: sabiork.reaction uniprot: SABIO-RK name: SABIO-RK Reaction pattern: ^\d+$ preferred_prefix: sabiork.reaction synonyms: - SABIO-RK uri_format: http://sabiork.h-its.org/reacdetails.jsp?reactid=$1 sael: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List preferred_prefix: sael references: - https://pubmed.ncbi.nlm.nih.gov/18629134/ salk: appears_in: - efo comment: spider stuff! contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Scientific research institute for neuroscience, genetics, immunology, plant biology and more. example: '037727' homepage: https://www.salk.edu/ name: Salk Institute for Biological Studies pattern: ^\d{6}$ preferred_prefix: salk uri_format: https://abrc.osu.edu/stocks/number/SALK_$1 sao: banana: SAO contact: email: slarson@ncmir.ucsd.edu github: null name: Stephen Larson orcid: null deprecated: true homepage: http://ccdb.ucsd.edu/CCDBWebSite/sao.html mappings: biocontext: SAO bioportal: SAO obofoundry: SAO prefixcommons: sao name: Subcellular Anatomy Ontology preferred_prefix: SAO references: - http://www.ontobee.org/ontology/SAO uri_format: http://purl.obolibrary.org/obo/SAO_$1 sasbdb: description: Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data. example: SASDAX8 homepage: http://www.sasbdb.org/ mappings: biocontext: SASBDB fairsharing: FAIRsharing.i1F3Hb miriam: sasbdb n2t: sasbdb uniprot: SASBDB name: Small Angle Scattering Biological Data Bank pattern: ^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$ preferred_prefix: sasbdb uri_format: http://www.sasbdb.org/data/$1 sbo: appears_in: - scdo banana: SBO contact: email: sheriff@ebi.ac.uk github: rsmsheriff name: Rahuman Sheriff orcid: 0000-0003-0705-9809 description: The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort. download_owl: http://purl.obolibrary.org/obo/sbo.owl example: 0000485 homepage: http://www.ebi.ac.uk/sbo/ license: Artistic License 2.0 mappings: biocontext: SBO bioportal: SBO fairsharing: FAIRsharing.s19src miriam: sbo n2t: sbo obofoundry: SBO ols: sbo ontobee: SBO prefixcommons: sbo name: Systems Biology Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: SBO repository: https://github.com/EBI-BioModels/SBO uri_format: https://www.ebi.ac.uk/sbo/main/SBO:$1 version: '2021-08-28' scdo: banana: SCDO contact: email: giant.plankton@gmail.com github: JadeHotchkiss name: Jade Hotchkiss orcid: 0000-0002-2193-0704 depends_on: - apollosv - aro - chebi - chmo - cmo - doid - dron - duo - envo - eupath - exo - gaz - gsso - hp - hsapdv - ico - ido - idomal - mp - nbo - ncit - obi - ogms - opmi - pr - sbo - stato - symp - uo - vo - vt description: An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease. download_obo: http://purl.obolibrary.org/obo/scdo.obo download_owl: http://purl.obolibrary.org/obo/scdo.owl example: 0000728 homepage: https://scdontology.h3abionet.org/ license: GPL-3.0 mappings: bioportal: SCDO fairsharing: FAIRsharing.kkq6pw obofoundry: SCDO ols: scdo ontobee: SCDO name: Sickle Cell Disease Ontology pattern: ^\d{7}$ preferred_prefix: SCDO repository: https://github.com/scdodev/scdo-ontology uri_format: http://purl.obolibrary.org/obo/SCDO_$1 version: '2021-04-15' schem: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Selventa legacy chemical namespace used with the Biological Expression Language example: A0001 homepage: https://raw.githubusercontent.com/OpenBEL/resource-generator/master/datasets name: Selventa Chemicals pattern: ^A\d{4}$ preferred_prefix: schem 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/$1 scomp: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Selventa legacy complex namespace used with the Biological Expression Language example: C0001 homepage: https://raw.githubusercontent.com/OpenBEL/resource-generator/master/datasets name: Selventa Complexes pattern: ^C\d{4}$ preferred_prefix: scomp 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=$1 scopus: description: "Scopus is the largest abstract and citation database of peer-reviewed\ \ literature: scientific journals, books and conference proceedings. \nDelivering\ \ a comprehensive overview of the world's research output in the fields of science,\ \ technology, medicine, social sciences, and arts \nand humanities, Scopus features\ \ smart tools to track, analyze and visualize research." example: '56305849200' homepage: https://www.scopus.com mappings: biolink: ScopusID fairsharing: FAIRsharing.0a674c name: Scopus Researcher pattern: ^\d+$ preferred_prefix: scopus 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/$1 sdbs: description: The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra. example: '4544' homepage: http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi mappings: biocontext: SDBS miriam: sdbs n2t: sdbs name: Spectral Database for Organic Compounds pattern: ^\d+$ preferred_prefix: sdbs uri_format: http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1 sdgio: description: An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators. download_owl: https://github.com/SDG-InterfaceOntology/sdgio/raw/master/sdgio.owl example: '00020134' homepage: https://github.com/SDG-InterfaceOntology/sdgio mappings: fairsharing: FAIRsharing.d5ff6e ols: sdgio ontobee: SDGIO name: Sustainable Development Goals Interface Ontology pattern: ^\d{8}$ preferred_prefix: sdgio references: - https://github.com/SDG-InterfaceOntology/sdgio/issues/233 repository: https://github.com/SDG-InterfaceOntology/sdgio version: '2018-08-10' sdis: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Selventa legacy disease namespace used with the Biological Expression Language example: D0001 homepage: https://raw.githubusercontent.com/OpenBEL/resource-generator/master/datasets name: Selventa Diseases pattern: ^D\d{4}$ preferred_prefix: sdis sedml.format: description: Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML). example: csv homepage: http://sed-ml.org/ mappings: miriam: sedml.format name: SED-ML data format pattern: ^[a-z]+(\..*?)?$ preferred_prefix: sedml.format uri_format: https://sed-ml.org/urns.html#format:$1 sedml.language: description: Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML). example: sbml.level-3.version-2 homepage: http://sed-ml.org/ mappings: miriam: sedml.language name: SED-ML model format pattern: ^[a-z]+(\..*?)?$ preferred_prefix: sedml.language uri_format: https://sed-ml.org/urns.html#language:$1 seed: description: This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems. example: Biotin_biosynthesis homepage: http://seed-viewer.theseed.org/seedviewer.cgi mappings: biocontext: SEED go: SEED miriam: seed n2t: seed ncbi: SEED name: The SEED; pattern: ^\w+$ preferred_prefix: seed uri_format: http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1 seed.compound: description: This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems. example: cpd15380 homepage: http://modelseed.org/ mappings: biocontext: SEED.COMPOUND miriam: seed.compound n2t: seed.compound name: SEED Compound pattern: ^cpd\d+$ preferred_prefix: seed.compound uri_format: http://modelseed.org/biochem/compounds/$1 seed.reaction: description: ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions. example: rxn00001 homepage: http://modelseed.org/biochem/reactions/ mappings: biolink: SEED.REACTION miriam: seed.reaction n2t: seed.reaction name: SEED Reactions pattern: ^rxn\d+$ preferred_prefix: seed.reaction uri_format: http://modelseed.org/biochem/reactions/$1 sep: banana: SEP contact: email: psidev-gps-dev@lists.sourceforge.net github: null name: SEP developers via the PSI and MSI mailing lists orcid: null deprecated: true description: A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments. download_obo: https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo download_owl: http://purl.obolibrary.org/obo/sep.owl example: '00073' homepage: https://psidev.info/sepcv mappings: biocontext: SEP bioportal: SEP obofoundry: SEP ontobee: SEP prefixcommons: sep name: Sample processing and separation techniques pattern: ^\d{5}$ preferred_prefix: SEP uri_format: http://purl.obolibrary.org/obo/SEP_$1 sepio: banana: SEPIO contact: email: mhb120@gmail.com github: mbrush name: Matthew Brush orcid: 0000-0002-1048-5019 description: An ontology for representing the provenance of scientific claims and the evidence that supports them. download_owl: http://purl.obolibrary.org/obo/sepio.owl example: 0000048 homepage: https://github.com/monarch-initiative/SEPIO-ontology license: CC BY 3.0 mappings: biocontext: SEPIO bioportal: SEPIO obofoundry: SEPIO ols: sepio ontobee: SEPIO name: Scientific Evidence and Provenance Information Ontology pattern: ^\d{7}$ preferred_prefix: SEPIO repository: https://github.com/monarch-initiative/SEPIO-ontology uri_format: http://purl.obolibrary.org/obo/SEPIO_$1 version: $Revision$ sfam: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Selventa legacy protein family namespace used with the Biological Expression Language example: F0001 homepage: https://raw.githubusercontent.com/OpenBEL/resource-generator/master/datasets name: Selventa Families pattern: ^F\d{4}$ preferred_prefix: sfam sgd: description: The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae. example: S000002493 homepage: https://www.yeastgenome.org/ mappings: biocontext: SGD fairsharing: FAIRsharing.pzvw40 go: SGD miriam: sgd n2t: sgd ncbi: SGD prefixcommons: sgd uniprot: SGD wikidata: P3406 name: Saccharomyces Genome Database pattern: ^((S\d+$)|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?))$ preferred_prefix: sgd providers: - code: CURATOR_REVIEW description: Bio2RDF homepage: http://sgd.bio2rdf.org/fct name: Bio2RDF uri_format: http://sgd.bio2rdf.org/describe/?url=http://bio2rdf.org/sgd:$1 - code: bioentitylink description: SGD through BioEntity Link homepage: https://bioentity.link/ name: SGD through BioEntity Link uri_format: https://bioentity.link/#/lexicon/public/$1 - code: agr description: SGD through the Alliance of Genome Resources homepage: https://www.alliancegenome.org name: SGD through the Alliance of Genome Resources uri_format: https://www.alliancegenome.org/gene/SGD:$1 uri_format: https://www.yeastgenome.org/locus/$1 sgd.pathways: description: Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD). example: PWY3O-214 homepage: http://pathway.yeastgenome.org/ mappings: biocontext: SGD.PATHWAYS miriam: sgd.pathways n2t: sgd.pathways prefixcommons: sgd.pathways name: Saccharomyces genome database pathways pattern: ^PWY\w{2}\-\d{3}$ preferred_prefix: sgd.pathways uri_format: http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1 sgn: description: The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant. example: '0001' homepage: http://solgenomics.net/ mappings: biocontext: SGN fairsharing: FAIRsharing.3zqvaf go: SGN miriam: sgn n2t: sgn ncbi: SGN prefixcommons: sgn name: Sol Genomics Network pattern: ^\d+$ preferred_prefix: sgn uri_format: http://solgenomics.net/phenome/locus_display.pl?locus_id=$1 sheepqtldb: description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs. example: '19803' homepage: https://www.animalgenome.org/QTLdb mappings: biocontext: SHEEPQTLDB miriam: sheepqtldb n2t: sheepqtldb prefixcommons: sheepqtldb name: Animal Genome Sheep QTL part_of: qtldb pattern: ^\d+$ preferred_prefix: sheepqtldb uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 sibo: banana: SIBO contact: email: cjmungall@lbl.gov github: null name: Chris Mungall orcid: 0000-0002-6601-2165 description: Social Behavior in insects download_obo: http://purl.obolibrary.org/obo/sibo.obo download_owl: http://purl.obolibrary.org/obo/sibo.owl example: 0000509 homepage: https://github.com/obophenotype/sibo license: CC BY 3.0 mappings: biocontext: SIBO bioportal: SIBO fairsharing: FAIRsharing.q09hck obofoundry: SIBO ols: sibo ontobee: SIBO name: Social Insect Behavior Ontology pattern: ^\d{7}$ preferred_prefix: SIBO repository: https://github.com/obophenotype/sibo uri_format: http://purl.obolibrary.org/obo/SIBO_$1 version: '2015-06-15' sider.drug: description: SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER. example: '2244' homepage: http://sideeffects.embl.de/ mappings: biocontext: SIDER.DRUG miriam: sider.drug n2t: sider.drug name: SIDER Drug pattern: ^\d+$ preferred_prefix: sider.drug uri_format: http://sideeffects.embl.de/drugs/$1 sider.effect: description: SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER. example: C0017565 homepage: http://sideeffects.embl.de/ mappings: biocontext: SIDER.EFFECT miriam: sider.effect n2t: sider.effect name: SIDER Side Effect pattern: ^C\d+$ preferred_prefix: sider.effect provides: umls uri_format: http://sideeffects.embl.de/se/$1 sigmaaldirch: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Sigma Aldrich is a life sciences supply vendor. example: HPA000698 homepage: https://www.sigmaaldrich.com name: Sigma Aldrich preferred_prefix: sigmaaldirch uri_format: https://www.sigmaaldrich.com/US/en/product/sigma/$1 signaling-gateway: description: The Signaling Gateway provides information on mammalian proteins involved in cellular signaling. example: A001094 homepage: http://www.signaling-gateway.org/molecule mappings: biocontext: SIGNALING-GATEWAY miriam: signaling-gateway n2t: signaling-gateway prefixcommons: signaling-gateway name: Signaling Gateway pattern: ^A\d{6}$ preferred_prefix: signaling-gateway uri_format: http://www.signaling-gateway.org/molecule/query?afcsid=$1 signor: description: SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. example: SIGNOR-C41 homepage: https://signor.uniroma2.it/ mappings: fairsharing: FAIRsharing.ss78t4 miriam: signor uniprot: SIGNOR name: Signaling Network Open Resource pattern: ^SIGNOR\-[A-Z]+\d+$ preferred_prefix: signor synonyms: - SIGNOR uri_format: https://signor.uniroma2.it/relation_result.php?id=$1 signor.relation: comment: Currently, you can put a SIGNOR relation ID into the main page search box and it will resolve, but there is not currently a way to resolve them via a URL pattern contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: Identifiers for relationships between proteins and complexes, along with their type and provenance example: SIGNOR-252737 homepage: https://signor.uniroma2.it name: SIGNOR Relation part_of: signor pattern: ^SIGNOR-\d+$ preferred_prefix: signor.relation reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 sio: description: The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. download_owl: http://semanticscience.org/ontology/sio/v1.53/sio-release.owl example: 000912 homepage: https://github.com/micheldumontier/semanticscience mappings: biocontext: SIO biolink: SIO bioportal: SIO fairsharing: FAIRsharing.dpkb5f miriam: sio ols: sio ontobee: SIO name: Semanticscience Integrated Ontology pattern: ^\d{6}$ preferred_prefix: sio repository: https://github.com/micheldumontier/semanticscience uri_format: https://www.ebi.ac.uk/ols/ontologies/sio/terms?short_form=$1 version: '1.53' sisu: description: The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies. example: 17:41223048 homepage: http://www.sisuproject.fi/ mappings: biocontext: SISU fairsharing: FAIRsharing.t1a232 miriam: sisu n2t: sisu name: Sequencing Initiative Suomi pattern: ^[0-9]+:[0-9]+$ preferred_prefix: sisu uri_format: http://search.sisuproject.fi/#/variant/$1 sitex: description: SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments. example: '1000' homepage: http://www-bionet.sscc.ru/sitex/ mappings: biocontext: SITEX fairsharing: FAIRsharing.5mr9c5 miriam: sitex n2t: sitex prefixcommons: sitex name: SitEx pattern: ^\d+$ preferred_prefix: sitex uri_format: http://www-bionet.sscc.ru/sitex/index.php?siteid=$1 skip: description: SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine. example: SKIP001214 homepage: https://skip.stemcellinformatics.org/en/ mappings: cellosaurus: SKIP name: Stemcell Knowledge and Information Portal preferred_prefix: skip uri_format: https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1 skos: description: SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web example: prefLabel homepage: https://www.w3.org/2004/02/skos/ mappings: biocontext: skos name: Simple Knowledge Organization System preferred_prefix: skos uri_format: http://www.w3.org/2004/02/skos/core#$1 slkbase: description: Cell line databases/resources example: '3618' homepage: https://sumlineknowledgebase.com/ mappings: cellosaurus: SLKBase name: SUM Breast Cancer Cell Line Knowledge Base pattern: ^\d+$ preferred_prefix: slkbase uri_format: https://sumlineknowledgebase.com/?page_id=$1 smart: description: The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures. example: SM00015 homepage: http://smart.embl-heidelberg.de/ mappings: biocontext: SMART fairsharing: FAIRsharing.hsbpq3 go: SMART miriam: smart n2t: smart prefixcommons: smart uniprot: SMART name: Simple Modular Architecture Research Tool pattern: ^SM\d{5}$ preferred_prefix: smart uri_format: http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1 smid: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C. elegans and other nematodes. SMIDs aim to make life easier for describing biogenic small molecules in metabolomic and genomic applications. ' example: '137' homepage: https://smid-db.org/ name: C. elegans Small Molecule Identifier Database pattern: ^\d+$ preferred_prefix: smid synonyms: - SMID-DB uri_format: https://smid-db.org/smid/$1 smiles: description: Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions. example: COc1ccc2c(c1)OC[C@H]1[C@@H]2C2=C(OC1(C)C)C1=C(C(=O)C2=O)[C@H]2c3ccc(OC)cc3OC[C@H]2C(C)(C)O1 homepage: https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html mappings: fairsharing: FAIRsharing.qv4b3c wikidata: P233 name: Simplified molecular-input line-entry system preferred_prefix: smiles smpdb: description: The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. example: SMP0000219 homepage: https://smpdb.ca/ mappings: biocontext: SMPDB biolink: PathWhiz fairsharing: FAIRsharing.y1zyaq miriam: smpdb n2t: smpdb prefixcommons: smpdb name: Small Molecule Pathway Database pattern: ^SMP\d+$ preferred_prefix: smpdb synonyms: - SMP uri_format: https://smpdb.ca/view/$1 snap: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality. example: Quality homepage: http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf mappings: prefixcommons: snap name: Snapshot preferred_prefix: snap uri_format: http://snap.humgen.au.dk/views/geneview.cgi?gene=$1 snomedct: description: SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc. download_owl: http://snomed.info/sct/900000000000207008/version/20200131 example: '284196006' homepage: http://www.snomedbrowser.com/ mappings: biocontext: SNOMED biolink: SNOMEDCT bioportal: SNOMEDCT fairsharing: FAIRsharing.d88s6e miriam: snomedct n2t: snomedct ols: snomed prefixcommons: snomedct wikidata: P5806 name: SNOMED CT (International Edition) pattern: ^(\w+)?\d+$ preferred_prefix: snomedct synonyms: - SCTID - SCTID_2010_1_31 - SNOMECT - SNOMED - SNOMEDCT - SNOMEDCTCT - SNOMEDCTCT_2018_03_01 - SNOMEDCTCT_2019_03_01 - SNOMEDCT_2005_07_31 - SNOMEDCT_2010_1_31 - SNOMEDCT_2020_03_01 - SNOMEDCT_US - SNOMEDCT_US_2015_03_01 - SNOMEDCT_US_2016_03_01 - SNOMEDCT_US_2018_03_01 - SNOMEDCT_US_2018_09_01 - SNOMEDCT_US_2019_03_01 - SNOMEDCT_US_2019_09_01 - SNOMEDCT_US_2020_03_01 - SNOMEDCT_US_2020_09_01 - SNOMEDCT_US_2021_03_01 - SNOMEDCT_US_2021_07_31 - SNOMEDCT_US_2021_09_01 - SNOMED_CT - SNOMED_CT_US_2018_03_01 - SNOWMEDCT - SNOWMEDCT_US - SNOWMEDCT_US_2018_03_01 uri_format: http://www.snomedbrowser.com/Codes/Details/$1 version: '2020-01-31' snornabase: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'A comprehensive database of human H/ACA and C/D box snoRNAs.' example: SR0000178 homepage: https://www-snorna.biotoul.fr/ name: snoRNABase preferred_prefix: snornabase snp2tfbs: description: SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome. example: rs11603840 homepage: https://ccg.epfl.ch/snp2tfbs/ mappings: miriam: snp2tfbs name: SNP to Transcription Factor Binding Sites pattern: ^rs[0-9]+$ preferred_prefix: snp2tfbs provides: dbsnp uri_format: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1 so: appears_in: - pcl banana: SO contact: email: keilbeck@genetics.utah.edu github: keilbeck name: Karen Eilbeck orcid: 0000-0002-0831-6427 description: The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data. download_obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/master/Ontology_Files/so.obo download_owl: http://purl.obolibrary.org/obo/so.owl example: '0001157' homepage: http://www.sequenceontology.org/ license: CC BY 4.0 mappings: biocontext: SO bioportal: SO fairsharing: FAIRsharing.6bc7h9 go: SO miriam: so n2t: so obofoundry: SO ols: so ontobee: SO prefixcommons: so name: Sequence types and features ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: SO repository: https://github.com/The-Sequence-Ontology/SO-Ontologies uri_format: http://www.sequenceontology.org/miso/current_release/term/SO:$1 version: '2021-11-22' sopharm: banana: SOPHARM contact: email: Adrien.Coulet@loria.fr github: null name: Adrien Coulet orcid: null deprecated: true homepage: http://www.loria.fr/~coulet/sopharm2.0_description.php mappings: biocontext: SOPHARM bioportal: SOPHARM obofoundry: SOPHARM name: Suggested Ontology for Pharmacogenomics preferred_prefix: SOPHARM uri_format: http://purl.obolibrary.org/obo/SOPHARM_$1 soybase: description: SoyBase is a repository for curated genetics, genomics and related data resources for soybean. example: BARC-013845-01256 homepage: http://soybase.org/ mappings: biocontext: SOYBASE fairsharing: FAIRsharing.z4agsr miriam: soybase n2t: soybase ncbi: SoyBase name: Glycine max Genome Database pattern: ^\w+(\-)?\w+(\-)?\w+$ preferred_prefix: soybase uri_format: http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1 span: comment: see also snap. This ontology only exists in description in the paper and does not have an associated web resource contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality. homepage: http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf name: Span preferred_prefix: span spd: banana: SPD contact: email: ramirez@macn.gov.ar github: martinjramirez name: Martin Ramirez orcid: 0000-0002-0358-0130 description: An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). download_owl: http://purl.obolibrary.org/obo/spd.owl example: '0000001' homepage: http://research.amnh.org/atol/files/ license: CC BY 3.0 mappings: biocontext: SPD bioportal: SPD fairsharing: FAIRsharing.yecp83 obofoundry: SPD ols: spd ontobee: SPD prefixcommons: spd wikidata: P4537 name: Spider Ontology pattern: ^\d{7}$ preferred_prefix: SPD repository: https://github.com/obophenotype/spider-ontology uri_format: http://purl.obolibrary.org/obo/SPD_$1 version: '2019-02-27' spdx: description: The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception. example: CC-BY-1.0 homepage: https://spdx.org/licenses mappings: miriam: spdx n2t: spdx name: Software Package Data Exchange License pattern: ^[0-9A-Za-z\-.]+$ preferred_prefix: spdx uri_format: https://spdx.org/licenses/$1 spike.map: description: SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps. example: spike00001 homepage: http://www.cs.tau.ac.il/~spike/ mappings: biocontext: SPIKE.MAP miriam: spike.map n2t: spike.map name: SPIKE Map pattern: ^spike\d{5}$ preferred_prefix: spike.map uri_format: http://www.cs.tau.ac.il/~spike/maps/$1.html splash: description: The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance. example: splash10-0zq2000000-77302b0326a418630a84 homepage: http://mona.fiehnlab.ucdavis.edu/ mappings: biocontext: SPLASH miriam: splash n2t: splash name: Spectra Hash Code pattern: ^splash\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$ preferred_prefix: splash uri_format: http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1 spp: description: The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways. example: 10.1621/vwN2g2HaX3 homepage: https://www.signalingpathways.org/index.jsf mappings: fairsharing: FAIRsharing.WxI96O miriam: spp name: Signaling Pathways Project pattern: ^10.\w{4}/\w{10}$ preferred_prefix: spp uri_format: https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1 sprint: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: SPRINT (Search PRINTS-S) provides an interface to the PRINTS-S database. PRINTS-S is the relational cousin of the PRINTS data bank of protein family fingerprints. example: PR00001 homepage: http://130.88.97.239/dbbrowser/sprint/ mappings: prefixcommons: sprint name: Search PRINTS-S pattern: ^PR\d{5}$ preferred_prefix: sprint uri_format: 130.88.97.239/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=$1 srao: description: The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies. download_owl: https://raw.githubusercontent.com/FAIRsharing/subject-ontology/master/releases/SRAO.owl example: '0000400' homepage: https://github.com/FAIRsharing/subject-ontology mappings: fairsharing: FAIRsharing.b1xD9f ols: srao name: FAIRsharing Subject Ontology pattern: ^\d{7}$ preferred_prefix: srao repository: https://github.com/FAIRsharing/subject-ontology version: 0.3.0 ssbd.dataset: description: Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations. example: '1' homepage: https://ssbd.riken.jp mappings: fairsharing: FAIRsharing.we2r5a name: System Science of Biological Dynamics dataset pattern: ^\d+$ preferred_prefix: ssbd.dataset uri_format: https://ssbd.riken.jp/database/dataset/$1 ssbd.project: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations. example: '1' homepage: https://ssbd.riken.jp name: System Science of Biological Dynamics project pattern: ^\d+$ preferred_prefix: ssbd.project uri_format: https://ssbd.riken.jp/database/project/$1 stap: description: STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB). example: 1a24 homepage: http://psb.kobic.re.kr/STAP/refinement/ mappings: biocontext: STAP fairsharing: FAIRsharing.ja9cdq miriam: stap n2t: stap name: Statistical Torsional Angles Potentials pattern: ^[0-9][A-Za-z0-9]{3}$ preferred_prefix: stap uri_format: http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1 stato: appears_in: - ontoavida - psdo - scdo banana: STATO contact: email: alejandra.gonzalez.beltran@gmail.com github: agbeltran name: Alejandra Gonzalez-Beltran orcid: 0000-0003-3499-8262 description: STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots. download_owl: http://purl.obolibrary.org/obo/stato.owl example: 0000288 homepage: http://stato-ontology.org/ license: CC BY 3.0 mappings: biocontext: STATO bioportal: STATO fairsharing: FAIRsharing.na5xp obofoundry: STATO ols: stato ontobee: STATO name: The Statistical Methods Ontology pattern: ^\d{7}$ preferred_prefix: STATO repository: https://github.com/ISA-tools/stato uri_format: http://purl.obolibrary.org/obo/STATO_$1 version: '1.4' stitch: description: STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. example: BQJCRHHNABKAKU homepage: http://stitch.embl.de/ mappings: biocontext: STITCH fairsharing: FAIRsharing.zhwa8x miriam: stitch n2t: stitch prefixcommons: stitch name: Search Tool for Interactions of Chemicals pattern: ^\w{14}$ preferred_prefix: stitch uri_format: http://stitch.embl.de/interactions/$1 storedb: banana: STOREDB description: STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons. example: STUDY1040 homepage: https://www.storedb.org/ mappings: biocontext: STOREDB fairsharing: FAIRsharing.6h8d2r miriam: storedb n2t: storedb name: Store DB pattern: ^(STUDY|FILE|DATASET)\d+$ preferred_prefix: storedb uri_format: https://www.storedb.org/?$1 string: description: "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is\ \ a database of known and predicted protein interactions.\r\nThe interactions\ \ include direct (physical) and indirect (functional) associations; they are derived\ \ from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression,\ \ Previous Knowledge. STRING quantitatively integrates interaction data from these\ \ sources for a large number of organisms, and transfers information between these\ \ organisms where applicable." example: P53350 homepage: http://string.embl.de/ mappings: biocontext: STRING fairsharing: FAIRsharing.9b7wvk miriam: string n2t: string prefixcommons: string uniprot: STRING name: Search Tool for Retrieval of Interacting Genes/Proteins pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$ preferred_prefix: string providers: - code: CURATOR_REVIEW description: STRING Mirror at Heidelberg homepage: http://string-db.org/ name: STRING Mirror at Heidelberg uri_format: http://string-db.org/interactions/$1 provides: uniprot uri_format: http://string.embl.de/interactions/$1 sty: description: UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types. example: T039 homepage: https://lhncbc.nlm.nih.gov/semanticnetwork/ mappings: biolink: STY bioportal: STY name: Semantic Types Ontology pattern: ^T\d{3}$ preferred_prefix: sty uri_format: http://purl.bioontology.org/ontology/STY/$1 subtilist: description: "SubtiList serves to collate and integrate various aspects of the genomic\ \ information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\r\ \nSubtiList provides a complete dataset of DNA and protein sequences derived from\ \ the paradigm strain B. subtilis 168, linked to the relevant annotations and\ \ functional assignments." example: BG11523 homepage: http://genolist.pasteur.fr/SubtiList/ mappings: biocontext: SUBTILIST fairsharing: FAIRsharing.40j2vd miriam: subtilist n2t: subtilist ncbi: SubtiList prefixcommons: subtilist name: Bacillus subtilis genome sequencing project pattern: ^BG\d+$ preferred_prefix: subtilist uri_format: http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1 subtiwiki: description: "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis.\ \ It provides comprehensive information on all genes and their proteins and RNA\ \ products, as well as information related to the current investigation of the\ \ gene/protein. \r\nNote: Currently, direct access to RNA products is restricted.\ \ This is expected to be rectified soon." example: BSU29180 homepage: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page mappings: biocontext: SUBTIWIKI fairsharing: FAIRsharing.2ck3st miriam: subtiwiki n2t: subtiwiki prefixcommons: subtiwiki name: SubtiWiki pattern: ^BSU\d{5}$ preferred_prefix: subtiwiki uri_format: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1 sugarbind: description: The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands. example: lectins/172 homepage: http://sugarbind.expasy.org/ mappings: biocontext: SUGARBIND fairsharing: FAIRsharing.d064y6 miriam: sugarbind n2t: sugarbind name: SugarBind pattern: ^[A-Za-z]+\/[0-9]+$ preferred_prefix: sugarbind uri_format: http://sugarbind.expasy.org/$1 supfam: description: SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. example: SSF57615 homepage: http://supfam.org/SUPERFAMILY/ mappings: biocontext: SUPFAM miriam: supfam n2t: supfam uniprot: SUPFAM name: SUPERFAMILY pattern: ^\w+$ preferred_prefix: supfam uri_format: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1 sweetrealm: description: The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research). download_obo: https://github.com/EnvironmentOntology/envo/blob/master/src/envo/sources/sweetrealm.obo example: ANOVA homepage: https://bioportal.bioontology.org/ontologies/SWEET mappings: bioportal: SWEET name: Semantic Web for Earth and Environment Technology Ontology preferred_prefix: sweetrealm swh: banana: swh description: Software Heritage is the universal archive of software source code. example: 1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d homepage: https://archive.softwareheritage.org mappings: biocontext: SWH miriam: swh n2t: swh name: Software Heritage namespace_in_lui: true pattern: ^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\S+)*$ preferred_prefix: swh uri_format: https://archive.softwareheritage.org/browse/swh:$1 swiss-model: description: The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences. example: P23298 homepage: https://swissmodel.expasy.org mappings: biocontext: SWISS-MODEL fairsharing: FAIRsharing.vxz9pn miriam: swiss-model n2t: swiss-model prefixcommons: swissmodel name: SWISS-MODEL Repository pattern: ^\w+$ preferred_prefix: swiss-model provides: uniprot uri_format: https://swissmodel.expasy.org/repository/uniprot/$1 swisslipid: banana: SLM description: SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions. example: '000000341' homepage: http://www.swisslipids.org/#/ mappings: biocontext: SWISSLIPID fairsharing: FAIRsharing.pxr7x2 miriam: slm n2t: swisslipid uniprot: SwissLipids wikidata: P8691 name: SwissLipid namespace_in_lui: true pattern: ^\d+$ preferred_prefix: swisslipid synonyms: - slm - swisslipids uri_format: https://www.swisslipids.org/#/entity/SLM:$1 swissregulon: description: A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form. example: AHR homepage: http://swissregulon.unibas.ch mappings: biocontext: SWISSREGULON fairsharing: FAIRsharing.7fnx38 miriam: swissregulon n2t: swissregulon name: SwissRegulon pattern: ^[A-Za-z0-9]+$ preferred_prefix: swissregulon uri_format: http://swissregulon.unibas.ch/query/$1 swo: banana: SWO contact: email: allyson.lister@oerc.ox.ac.uk github: allysonlister name: Allyson Lister orcid: 0000-0002-7702-4495 description: The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community. download_owl: https://github.com/allysonlister/swo/raw/master/release/swo.owl example: '0000144' homepage: https://github.com/allysonlister/swo license: CC BY 4.0 mappings: biocontext: SWO bioportal: SWO fairsharing: FAIRsharing.sp3szt obofoundry: SWO ols: swo ontobee: SWO prefixcommons: swo name: Software ontology pattern: ^\d{7}$ preferred_prefix: SWO repository: https://github.com/allysonlister/swo uri_format: http://purl.obolibrary.org/obo/SWO_$1 version: '1.7' symp: appears_in: - scdo banana: SYMP contact: email: lynn.schriml@gmail.com github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 description: The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases. download_obo: http://purl.obolibrary.org/obo/symp.obo download_owl: http://purl.obolibrary.org/obo/symp.owl example: 0019171 homepage: http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page license: CC0 1.0 mappings: biocontext: SYMP bioportal: SYMP fairsharing: FAIRsharing.ay74mj obofoundry: SYMP ols: symp ontobee: SYMP wikidata: P8656 name: Symptom Ontology pattern: ^\d{7}$ preferred_prefix: SYMP repository: https://github.com/DiseaseOntology/SymptomOntology synonyms: - SYMP uri_format: http://purl.obolibrary.org/obo/SYMP_$1 version: '2022-04-05' syoid: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: Gemina Symptom Ontology preferred_prefix: syoid references: - https://github.com/DiseaseOntology/SymptomOntology/issues/7#event-4223716562 t3db: description: Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. example: T3D0001 homepage: http://www.t3db.org/ mappings: biocontext: T3DB fairsharing: FAIRsharing.psn0h2 miriam: t3db n2t: t3db prefixcommons: t3db name: Toxin and Toxin Target Database pattern: ^T3D\d+$ preferred_prefix: t3db uri_format: http://www.t3db.org/toxins/$1 tads: banana: TADS contact: email: dsonensh@odu.edu github: null name: Daniel Sonenshine orcid: null description: 'The anatomy of the Tick, Families: Ixodidae, Argassidae' download_obo: http://purl.obolibrary.org/obo/tads.obo download_owl: http://purl.obolibrary.org/obo/tads.owl example: '0000547' homepage: https://www.vectorbase.org/ontology-browser license: CC BY 4.0 mappings: biocontext: TADS bioportal: TADS fairsharing: FAIRsharing.8wm364 obofoundry: TADS ols: tads ontobee: TADS name: Tick Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: TADS repository: https://github.com/VEuPathDB-ontology/TADS uri_format: http://purl.obolibrary.org/obo/TADS_$1 version: '2015-08-20' tahe: banana: TAHE contact: email: pierre.sprumont@unifr.ch github: null name: Pierre Sprumont orcid: null deprecated: true mappings: biocontext: TAHE obofoundry: TAHE name: Terminology of Anatomy of Human Embryology preferred_prefix: TAHE uri_format: http://purl.obolibrary.org/obo/TAHE_$1 tahh: banana: TAHH contact: email: pierre.sprumont@unifr.ch github: null name: Pierre Sprumont orcid: null deprecated: true mappings: biocontext: TAHH obofoundry: TAHH name: Terminology of Anatomy of Human Histology preferred_prefix: TAHH uri_format: http://purl.obolibrary.org/obo/TAHH_$1 tair.gene: description: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus. example: '2200934' homepage: http://arabidopsis.org/index.jsp mappings: biocontext: TAIR.GENE miriam: tair.gene n2t: tair.gene prefixcommons: tair.gene name: TAIR Gene pattern: ^\d{7}$ preferred_prefix: tair.gene uri_format: http://arabidopsis.org/servlets/TairObject?accession=Gene:$1 tair.locus: description: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS. example: '2200950' homepage: http://arabidopsis.org/index.jsp mappings: biocontext: TAIR.LOCUS go: TAIR miriam: tair.locus n2t: tair.locus ncbi: TAIR prefixcommons: tair.locus name: The Arabidopsis Information Resource pattern: ^\d+$ preferred_prefix: tair.locus uri_format: http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1 tair.protein: description: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept example: '1009107926' homepage: http://arabidopsis.org/index.jsp mappings: biocontext: TAIR.PROTEIN miriam: tair.protein n2t: tair.protein prefixcommons: tair.protein name: TAIR Protein pattern: ^\d{10}$ preferred_prefix: tair.protein uri_format: http://arabidopsis.org/servlets/TairObject?accession=AASequence:$1 tao: banana: TAO contact: email: wasila.dahdul@usd.edu github: null name: Wasila Dahdul orcid: 0000-0003-3162-7490 deprecated: true description: Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa download_owl: http://purl.obolibrary.org/obo/tao.owl example: 0000086 homepage: http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology license: CC0 1.0 mappings: biocontext: TAO bioportal: TAO obofoundry: TAO prefixcommons: tao name: Teleost Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: TAO synonyms: - TAO_RETIRED uri_format: http://purl.obolibrary.org/obo/TAO_$1 tarbase: description: TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used. example: hsa-let-7a-2-3p homepage: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index mappings: biocontext: TARBASE fairsharing: FAIRsharing.a0k4cd miriam: tarbase n2t: tarbase name: TarBase pattern: ^[a-z]{3}\-(mir|let|lin)\-\w+(\-\w+\-\w+)$ preferred_prefix: tarbase uri_format: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1 taxrank: banana: TAXRANK contact: email: balhoff@renci.org github: balhoff name: Jim Balhoff orcid: 0000-0002-8688-6599 description: A vocabulary of taxonomic ranks (species, family, phylum, etc) download_obo: http://purl.obolibrary.org/obo/taxrank.obo download_owl: http://purl.obolibrary.org/obo/taxrank.owl example: '0000001' homepage: https://github.com/phenoscape/taxrank license: CC0 1.0 mappings: biocontext: TAXRANK bioportal: TAXRANK fairsharing: FAIRsharing.p1sejz obofoundry: TAXRANK ols: taxrank ontobee: TAXRANK prefixcommons: taxrank name: Taxonomic rank vocabulary pattern: ^\d{7}$ preferred_prefix: TAXRANK repository: https://github.com/phenoscape/taxrank uri_format: http://purl.obolibrary.org/obo/TAXRANK_$1 version: '2016-04-15' tcb: description: Cell line collections example: '2966' homepage: https://www.pirbright.ac.uk/tick-cell-lines-views-page mappings: cellosaurus: TCB name: Tick Cell Biobank pattern: ^\d+$ preferred_prefix: tcb uri_format: https://www.pirbright.ac.uk/node/$1 tcdb: description: The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally. example: 5.A.1.1.1 homepage: https://www.tcdb.org mappings: biocontext: TCDB fairsharing: FAIRsharing.p3bzqb go: TC miriam: tcdb n2t: tcdb prefixcommons: tcdb uniprot: TCDB wikidata: P7260 name: Transporter Classification Database pattern: ^\d+(\.[A-Z])?(\.\d+)?(\.\d+)?(\.\d+)?$ preferred_prefix: tcdb synonyms: - TC uri_format: http://www.tcdb.org/search/result.php?tc=$1 te: description: The Terminologia Embryologica (TE) is a standardized list of words used in the description of human embryologic and fetal structures. It was produced by the Federative International Committee on Anatomical Terminology on behalf of the International Federation of Associations of Anatomists and posted on the Internet since 2010. [wikipedia] example: E5.11.2.0.0.0.4 homepage: https://ifaa.unifr.ch/ mappings: wikidata: P1693 name: Terminologia Embryologica preferred_prefix: te references: - https://en.wikipedia.org/wiki/Terminologia_Embryologica tfclass: description: TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here.. example: 2.1.1 homepage: http://tfclass.bioinf.med.uni-goettingen.de mappings: fairsharing: FAIRsharing.XykycZ go: TFClass name: Classification of Transcription Factors in Mammalia preferred_prefix: tfclass uri_format: http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1 tgd: description: The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature. example: TTHERM_00648910 homepage: http://ciliate.org/index.php/ mappings: biocontext: TGD go: TGD miriam: tgd n2t: tgd prefixcommons: tgd name: Tetrahymena Genome Database pattern: ^TTHERM\_\d+$ preferred_prefix: tgd uri_format: http://ciliate.org/index.php/feature/details/$1 tgma: banana: TGMA contact: email: topalis@imbb.forth.gr github: null name: Pantelis Topalis orcid: null description: A structured controlled vocabulary of the anatomy of mosquitoes. download_obo: http://purl.obolibrary.org/obo/tgma.obo download_owl: http://purl.obolibrary.org/obo/tgma.owl example: 0000984 homepage: https://www.vectorbase.org/ontology-browser license: CC0 1.0 mappings: biocontext: TGMA bioportal: TGMA fairsharing: FAIRsharing.dqnfkg obofoundry: TGMA ols: tgma ontobee: TGMA prefixcommons: tgma name: Mosquito gross anatomy ontology pattern: ^\d{7}$ preferred_prefix: TGMA repository: https://github.com/VEuPathDB-ontology/TGMA uri_format: http://purl.obolibrary.org/obo/TGMA_$1 version: '2013-06-03' tgn: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true example: '1023371' homepage: https://www.getty.edu/research/tools/vocabularies/tgn/ name: Getty Thesaurus of Geographic Names pattern: ^\d+$ preferred_prefix: tgn references: - https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200 uri_format: http://vocab.getty.edu/page/tgn/$1 th: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia] example: H3.03.00.0.00007 homepage: https://ifaa.unifr.ch/ name: Terminologia Histologica preferred_prefix: th references: - https://en.wikipedia.org/wiki/Terminologia_Histologica thermofisher: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: ThermoFisher is a life sciences supply vendor. example: OSR00185W homepage: https://www.thermofisher.com name: Thermo Fisher Scientific preferred_prefix: thermofisher uri_format: https://www.thermofisher.com/antibody/product/$1 tigrfam: description: TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. example: TIGR00010 homepage: http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi mappings: biocontext: TIGRFAM miriam: tigrfam n2t: tigrfam ncbi: TIGRFAM name: TIGR protein families pattern: ^TIGR\d+$ preferred_prefix: tigrfam references: - https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/license_and_availability.txt - https://github.com/biopragmatics/bioregistry/issues/366 uri_format: https://www.ncbi.nlm.nih.gov/cdd?term=$1 tkg: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells. example: '0221' homepage: http://www2.idac.tohoku.ac.jp/dep/ccr/ mappings: cellosaurus: TKG name: Tohoku University cell line catalog pattern: ^\d+$ preferred_prefix: tkg uri_format: http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html tngb: description: Cell line collections example: '67035' homepage: http://biobanknetwork.telethon.it/ mappings: cellosaurus: TNGB name: Telethon Network of Genetic Biobanks pattern: ^\d+$ preferred_prefix: tngb uri_format: http://biobanknetwork.telethon.it/Sample/View?sampleId=$1 to: appears_in: - agro banana: TO contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp name: Pankaj Jaiswal orcid: 0000-0002-1005-8383 description: A controlled vocabulary to describe phenotypic traits in plants. download_obo: http://purl.obolibrary.org/obo/to.obo download_owl: http://purl.obolibrary.org/obo/to.owl example: '0000630' homepage: http://browser.planteome.org/amigo license: CC BY 4.0 mappings: biocontext: TO bioportal: PTO fairsharing: FAIRsharing.w69t6r obofoundry: TO ols: to ontobee: TO name: Plant Trait Ontology pattern: ^\d{7}$ preferred_prefix: TO repository: https://github.com/Planteome/plant-trait-ontology uri_format: http://purl.obolibrary.org/obo/TO_$1 version: '2022-04-13' tokue: deprecated: true description: Cell line databases/resources homepage: http://cell-lines.toku-e.com mappings: cellosaurus: TOKU-E name: TOKU-E Cell-culture Database preferred_prefix: tokue uri_format: http://cell-lines.toku-e.com/Cell-Lines_$1.html tol: description: "The Tree of Life Web Project (ToL) is a collaborative effort of biologists\ \ and nature enthusiasts from around the world. On more than 10,000 World Wide\ \ Web pages, the project provides information about biodiversity, the characteristics\ \ of different groups of organisms, and their evolutionary history (phylogeny).\ \ \r\n\r\nEach page contains information about a particular group, with pages\ \ linked one to another hierarchically, in the form of the evolutionary tree of\ \ life. Starting with the root of all Life on Earth and moving out along diverging\ \ branches to individual species, the structure of the ToL project thus illustrates\ \ the genetic connections between all living things." example: '98034' homepage: http://tolweb.org/tree/ mappings: biocontext: TOL miriam: tol n2t: tol name: Tree of Life pattern: ^\d+$ preferred_prefix: tol uri_format: http://tolweb.org/$1 topdb: description: The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases. example: AP00378 homepage: http://topdb.enzim.hu/ mappings: biocontext: TOPDB miriam: topdb n2t: topdb prefixcommons: topdb name: Topology Data Bank of Transmembrane Proteins pattern: ^[A-Z0-9]+$ preferred_prefix: topdb uri_format: http://topdb.enzim.hu/?m=show&id=$1 topfind: description: 'TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.' example: Q9UKQ2 homepage: https://topfind.clip.msl.ubc.ca mappings: biocontext: TOPFIND fairsharing: FAIRsharing.rkpmhn miriam: topfind n2t: topfind name: TopFind pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ preferred_prefix: topfind provides: uniprot uri_format: http://clipserve.clip.ubc.ca/topfind/proteins/$1 toxoplasma: description: ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: TGME49_053730 homepage: http://toxodb.org/toxo/ mappings: biocontext: TOXOPLASMA miriam: toxoplasma n2t: toxoplasma name: ToxoDB pattern: ^\w+$ preferred_prefix: toxoplasma uri_format: http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 trans: banana: TRANS contact: email: lynn.schriml@gmail.com github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 description: The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles. download_obo: http://purl.obolibrary.org/obo/trans.obo download_owl: http://purl.obolibrary.org/obo/trans.owl example: '0000024' homepage: https://github.com/DiseaseOntology/PathogenTransmissionOntology license: CC0 1.0 mappings: biocontext: TRANS bioportal: TRANS fairsharing: FAIRsharing.nygmp7 obofoundry: TRANS ols: trans ontobee: TRANS name: Pathogen Transmission Ontology pattern: ^\d{7}$ preferred_prefix: TRANS repository: https://github.com/DiseaseOntology/PathogenTransmissionOntology uri_format: http://purl.obolibrary.org/obo/TRANS_$1 version: '2020-08-04' transyt: description: The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes. example: TR0000001 homepage: https://www.bio.di.uminho.pt/ mappings: miriam: transyt name: Transport Systems Tracker pattern: ^T[A-Z]\d{7}$ preferred_prefix: transyt uri_format: https://transyt.bio.di.uminho.pt/reactions/$1 treebase: description: TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc. example: TB2:S1000 homepage: http://treebase.org/ mappings: biocontext: TREEBASE fairsharing: FAIRsharing.zcn4w4 miriam: treebase n2t: treebase prefixcommons: treebase name: TreeBASE pattern: ^TB[1,2]?:[A-Z][a-z]?\d+$ preferred_prefix: treebase uri_format: http://purl.org/phylo/treebase/phylows/study/$1?format=html treefam: description: TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. example: TF101014 homepage: http://www.treefam.org/ mappings: biocontext: TREEFAM miriam: treefam n2t: treefam prefixcommons: treefam uniprot: TreeFam name: TreeFam pattern: ^\w{1,2}\d+$ preferred_prefix: treefam uri_format: http://www.treefam.org/family/$1 trichdb: description: TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: TVAG_386080 homepage: http://trichdb.org/trichdb/ mappings: biocontext: TRICHDB fairsharing: FAIRsharing.pv0ezt miriam: trichdb n2t: trichdb name: TrichDB pattern: ^\w+$ preferred_prefix: trichdb uri_format: http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 tritrypdb: description: TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: Tb927.8.620 homepage: http://tritrypdb.org/tritrypdb/ mappings: biocontext: TRITRYPDB fairsharing: FAIRsharing.fs1z27 go: TriTrypDB miriam: tritrypdb n2t: tritrypdb name: TriTrypDB pattern: ^\w+(\.)?\w+(\.)?\w+$ preferred_prefix: tritrypdb uri_format: http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 ttd.drug: description: The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target. example: DAP000773 homepage: http://bidd.nus.edu.sg/group/ttd/ttd.asp mappings: biocontext: TTD.DRUG miriam: ttd.drug n2t: ttd.drug name: TTD Drug pattern: ^DAP\d+$ preferred_prefix: ttd.drug uri_format: http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1 ttd.target: description: The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target. example: TTDS00056 homepage: http://bidd.nus.edu.sg/group/ttd/ttd.asp mappings: biocontext: TTD.TARGET miriam: ttd.target n2t: ttd.target name: TTD Target pattern: ^TTDS\d+$ preferred_prefix: ttd.target uri_format: http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1 tto: banana: TTO contact: email: balhoff@renci.org github: balhoff name: Jim Balhoff orcid: 0000-0002-8688-6599 description: An ontology covering the taxonomy of teleosts (bony fish) download_obo: http://purl.obolibrary.org/obo/tto.obo download_owl: http://purl.obolibrary.org/obo/tto.owl example: '1058367' homepage: https://github.com/phenoscape/teleost-taxonomy-ontology license: CC0 1.0 mappings: biocontext: TTO bioportal: TTO fairsharing: FAIRsharing.1rj558 obofoundry: TTO ols: tto ontobee: TTO prefixcommons: tto name: Teleost taxonomy ontology pattern: ^\d+$ preferred_prefix: TTO repository: https://github.com/phenoscape/teleost-taxonomy-ontology uri_format: http://purl.obolibrary.org/obo/TTO_$1 version: '2018-03-26' txpo: banana: TXPO contact: email: yuki.yamagata@riken.jp github: yuki-yamagata name: Yuki Yamagata orcid: 0000-0002-9673-1283 description: 'Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity. The TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms. In applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp' download_owl: http://purl.obolibrary.org/obo/txpo.owl example: '0002066' homepage: https://toxpilot.nibiohn.go.jp/ license: CC BY 3.0 mappings: bioportal: TXPO obofoundry: TXPO ols: txpo ontobee: TXPO name: Toxic Process Ontology pattern: ^\d{7}$ preferred_prefix: TXPO repository: https://github.com/txpo-ontology/TXPO uri_format: http://purl.obolibrary.org/obo/TXPO_$1 version: '2020-07-09' uberon: appears_in: - aism - amphx - chiro - cl - clo - clyh - colao - cteno - ecao - ecocore - ecto - envo - foodon - fovt - genepio - go - hso - lepao - maxo - mco - mfmo - ons - pcl - plana - poro - zp banana: UBERON contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 depends_on: - chebi - cl - go - pr description: Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. download_obo: http://purl.obolibrary.org/obo/uberon/basic.obo download_owl: http://purl.obolibrary.org/obo/uberon.owl example: '2005080' homepage: http://uberon.org license: CC BY 3.0 mappings: biocontext: UBERON bioportal: UBERON cellosaurus: UBERON fairsharing: FAIRsharing.4c0b6b go: UBERON miriam: uberon n2t: uberon obofoundry: UBERON ols: uberon ontobee: UBERON wikidata: P1554 name: Uber Anatomy Ontology namespace_in_lui: true pattern: ^\d+$ preferred_prefix: UBERON repository: https://github.com/obophenotype/uberon synonyms: - UBERON - Uber-anatomy ontology - Uberon uri_format: http://purl.obolibrary.org/obo/UBERON_$1 version: '2022-04-18' ubio.namebank: description: NameBank is a "biological name server" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context. example: '2555646' homepage: http://www.ubio.org mappings: biocontext: UBIO.NAMEBANK miriam: ubio.namebank n2t: ubio.namebank name: uBio NameBank pattern: ^\d+$ preferred_prefix: ubio.namebank uri_format: http://www.ubio.org/browser/details.php?namebankID=$1 ubprop: comment: All of these are typedefs in uberon now contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: Uberon Property preferred_prefix: ubprop ucsc: description: The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. example: uc001rvw.5 homepage: https://genome.ucsc.edu/ mappings: biocontext: UCSC uniprot: UCSC wikidata: P2576 name: UCSC Genome Browser preferred_prefix: ucsc uri_format: ftp://hgdownload.cse.ucsc.edu/goldenPath/$1 umbbd.compound: description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information. example: c0001 homepage: http://umbbd.ethz.ch/ mappings: biocontext: UMBBD.COMPOUND miriam: umbbd.compound n2t: umbbd.compound wikidata: P8121 name: UM-BBD Compound part_of: umbbd pattern: ^c\d+$ preferred_prefix: umbbd.compound synonyms: - UM-BBD_compID uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1 umbbd.enzyme: description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information. example: e0333 homepage: http://umbbd.ethz.ch/ mappings: biocontext: UMBBD.ENZYME go: UM-BBD_enzymeID miriam: umbbd.enzyme n2t: umbbd.enzyme name: EAWAG Biocatalysis/Biodegradation Database part_of: umbbd pattern: ^e\d+$ preferred_prefix: umbbd.enzyme synonyms: - UM-BBD_enzymeID uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1 umbbd.pathway: description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information. example: ala homepage: http://umbbd.ethz.ch/ mappings: biocontext: UMBBD.PATHWAY go: UM-BBD_pathwayID miriam: umbbd.pathway n2t: umbbd.pathway name: EAWAG Biocatalysis/Biodegradation Database part_of: umbbd pattern: ^\w+$ preferred_prefix: umbbd.pathway synonyms: - UM-BBD_pathwayID uri_format: http://eawag-bbd.ethz.ch/$1/$1_map.html umbbd.reaction: description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information. example: r0001 homepage: http://umbbd.ethz.ch/ mappings: biocontext: UMBBD.REACTION go: UM-BBD_reactionID miriam: umbbd.reaction n2t: umbbd.reaction name: EAWAG Biocatalysis/Biodegradation Database part_of: umbbd pattern: ^r\d+$ preferred_prefix: umbbd.reaction synonyms: - UM-BBD_reactionID uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1 umbbd.rule: description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules. example: bt0001 homepage: http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules mappings: biocontext: UMBBD.RULE go: UM-BBD_ruleID miriam: umbbd.rule n2t: umbbd.rule name: EAWAG Biocatalysis/Biodegradation Database part_of: umbbd pattern: ^bt\d+$ preferred_prefix: umbbd.rule synonyms: - UM-BBD_ruleID uri_format: http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1 umls: description: The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank. example: C2584994 homepage: https://www.nlm.nih.gov/research/umls mappings: biocontext: UMLS miriam: umls n2t: umls wikidata: P2892 name: Unified Medical Language System Concept Unique Identifier pattern: ^C\d+$ preferred_prefix: umls synonyms: - UMLS - UMLS CUI - UMLS_CUI - umls.cui uri_format: http://linkedlifedata.com/resource/umls/id/$1 umls.aui: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An identifier for an atom; the smallest unit of naming in a source, viz, a specific string with specific code values and identifiers from a specific source. As such, they can be thought of as representing a single meaning with a source Atoms are the units of terminology that come from sources and form the building blocks of the concepts in the Metathesaurus. example: A0118748 homepage: https://www.nlm.nih.gov/research/umls name: Unified Medical Language System Atomic Unique Identifier pattern: ^A\d+$ preferred_prefix: umls.aui synonyms: - UMLS_ICD9CM_2005_AUI unigene: description: A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. example: '4900' homepage: http://www.ncbi.nlm.nih.gov/unigene mappings: biocontext: UNIGENE fairsharing: FAIRsharing.ge1c3p miriam: unigene n2t: unigene prefixcommons: unigene name: UniGene pattern: ^\d+$ preferred_prefix: unigene uri_format: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1 unii: description: The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information. example: 3G6A5W338E homepage: http://fdasis.nlm.nih.gov/srs/ mappings: biocontext: UNII cheminf: '000563' miriam: unii n2t: unii wikidata: P652 name: Unique Ingredient Identifier pattern: ^[A-Z0-9]+$ preferred_prefix: unii uri_format: http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=$1 unimod: description: Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide). download_owl: http://www.unimod.org/obo/unimod.obo example: '1200' homepage: http://www.unimod.org/ mappings: biocontext: UNIMOD fairsharing: FAIRsharing.zZHCUQ miriam: unimod n2t: unimod ols: unimod name: Unimod protein modification database for mass spectrometry pattern: ^\d+$ preferred_prefix: unimod uri_format: http://www.unimod.org/modifications_view.php?editid1=$1 uniparc: description: The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases. example: UPI000000000A homepage: https://www.ebi.ac.uk/uniparc/ mappings: biocontext: UNIPARC go: UniParc miriam: uniparc n2t: uniparc prefixcommons: uniparc name: UniProt Archive pattern: ^UPI[A-F0-9]{10}$ preferred_prefix: uniparc providers: - code: CURATOR_REVIEW description: UniParc through UniProt homepage: http://www.uniprot.org/uniparc/ name: UniParc through UniProt uri_format: https://www.uniprot.org/uniparc/$1 uri_format: https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$1 unipathway.compound: description: UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds. example: UPC04349 homepage: http://www.grenoble.prabi.fr/obiwarehouse/unipathway mappings: biocontext: UNIPATHWAY.COMPOUND miriam: unipathway.compound n2t: unipathway.compound name: UniPathway Compound pattern: ^UPC\d{5}$ preferred_prefix: unipathway.compound uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1 unipathway.reaction: description: UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions. example: UCR00226 homepage: http://www.grenoble.prabi.fr/obiwarehouse/unipathway mappings: biocontext: UNIPATHWAY.REACTION miriam: unipathway.reaction n2t: unipathway.reaction name: UniPathway Reaction pattern: ^UCR\d{5}$ preferred_prefix: unipathway.reaction uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1 uniprot: description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information. example: P0DP23 homepage: http://www.uniprot.org mappings: biocontext: UniProtKB cellosaurus: UniProtKB fairsharing: FAIRsharing.s1ne3g go: UniProtKB miriam: uniprot n2t: uniprot ncbi: UniProt prefixcommons: uniprot scholia: uniprot wikidata: P352 name: UniProt Protein pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ preferred_prefix: uniprot providers: - code: omnipath description: Molecular interations endpoint from OmniPathDB homepage: https://omnipathdb.org/ name: OmniPathDB uri_format: https://omnipathdb.org/interactions/?fields=sources,references&partners=$1 - code: iptmnet description: Protein post translational modification information homepage: https://research.bioinformatics.udel.edu/iptmnet name: iPTMnet uri_format: https://research.bioinformatics.udel.edu/iptmnet/entry/$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@UP - code: ncbi description: UniProt through NCBI homepage: https://www.ncbi.nlm.nih.gov/protein/ name: UniProt through NCBI uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 synonyms: - SwissProt - UP - UniProt - UniProtKB - Uniprot ID - uniprot/swiss-prot uri_format: http://purl.uniprot.org/uniprot/$1 uniprot.chain: description: This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein. example: PRO_0000016681 homepage: https://www.uniprot.org mappings: miriam: uniprot.chain name: UniProt Chain part_of: uniprot pattern: ^PRO_[0-9]{10}$ preferred_prefix: uniprot.chain synonyms: - UPPRO uri_format: http://purl.uniprot.org/annotation/$1 uniprot.disease: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary. download_obo: https://www.uniprot.org/diseases/?query=*&format=obo example: '04240' homepage: https://www.uniprot.org/diseases/ name: UniProt Diseases part_of: uniprot pattern: ^\d{5}$ preferred_prefix: uniprot.disease synonyms: - DI - SP_DI uri_format: https://www.uniprot.org/diseases/DI-$1 uniprot.isoform: description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information. example: Q5BJF6-3 homepage: http://www.uniprot.org/ mappings: biocontext: UNIPROT.ISOFORM miriam: uniprot.isoform n2t: uniprot.isoform name: UniProt Isoform part_of: uniprot pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\-\d+)$ preferred_prefix: uniprot.isoform providers: - code: CURATOR_REVIEW description: UniProt Isoform through Universal Protein Resource using Persistent URL system homepage: http://purl.uniprot.org/ name: UniProt Isoform through Universal Protein Resource using Persistent URL system uri_format: http://purl.uniprot.org/uniprot/$1 - code: CURATOR_REVIEW description: UniProt Isoform through UniParc homepage: http://www.uniprot.org/uniparc/ name: UniProt Isoform through UniParc uri_format: http://www.uniprot.org/uniparc/?query=$1 synonyms: - UPISO uri_format: http://www.uniprot.org/uniprot/$1 uniprot.keyword: description: UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries. download_obo: https://www.uniprot.org/keywords/?format=obo example: '1273' homepage: http://www.uniprot.org/keywords/ mappings: go: UniProtKB-KW name: UniProt Keywords part_of: uniprot pattern: ^\d{4}$ preferred_prefix: uniprot.keyword synonyms: - SP_KW - UniProtKB-KW - uniprot.keyword uri_format: https://www.uniprot.org/keywords/KW-$1 uniprot.location: description: The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms. download_obo: https://www.uniprot.org/locations/?query=*&format=obo example: '0002' homepage: https://www.uniprot.org/locations/ mappings: go: UniProtKB-SubCell name: UniProt Subcellular Locations part_of: uniprot pattern: ^\d+$ preferred_prefix: uniprot.location synonyms: - SP_SL - UPLOC - UniProtKB-SubCell uri_format: https://www.uniprot.org/locations/SL-$1 uniprot.ptm: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The post-translational modifications used in the UniProt knowledgebase (Swiss-Prot and TrEMBL). The definition of the post-translational modifications usage as well as other information is provided in the following format example: '0450' homepage: https://www.uniprot.org/docs/ptmlist name: UniProt Post-Translational Modification part_of: uniprot pattern: ^\d{4}$ preferred_prefix: uniprot.ptm references: - https://twitter.com/cthoyt/status/1510570256619778053 - https://www.uniprot.org/docs/ptmlist.txt synonyms: - PTM uniprot.resource: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources. example: '0174' homepage: https://www.uniprot.org/database/ name: UniProt Resource part_of: uniprot pattern: ^\d{4}$ preferred_prefix: uniprot.resource uri_format: https://www.uniprot.org/database/DB-$1 uniprot.tissue: description: The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified. example: 0285 homepage: https://www.uniprot.org/docs/tisslist.txt mappings: biocontext: TISSUELIST miriam: tissuelist n2t: tissuelist name: Tissue List part_of: uniprot pattern: ^\d{4}$ preferred_prefix: uniprot.tissue uri_format: https://www.uniprot.org/tissues/TS-$1 uniprot.var: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species.' example: 068078 homepage: https://web.expasy.org/variant_pages name: UniProt Variants part_of: uniprot pattern: ^\d+$ preferred_prefix: uniprot.var synonyms: - SP_VAR - UPVAR - UniProtKB_VAR uri_format: https://web.expasy.org/variant_pages/VAR_$1.html uniref: description: The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view. example: UniRef90_P00750 homepage: https://www.uniprot.org/ mappings: miriam: uniref name: UniRef pattern: ^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$ preferred_prefix: uniref uri_format: https://www.uniprot.org/uniref/$1 unirule: description: Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates. UniRule rules can annotate protein properties such as the protein name, function, catalytic activity, pathway membership, and subcellular location, along with sequence specific information, such as the positions of post-translational modifications and active sites. example: UR000124451 homepage: https://www.uniprot.org/unirule/ mappings: go: UniRule name: UniRule preferred_prefix: unirule uri_format: https://www.uniprot.org/unirule/$1 unists: description: UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences. example: '456789' homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists mappings: biocontext: UNISTS miriam: unists n2t: unists ncbi: UniSTS prefixcommons: unists name: Database of Sequence Tagged Sites pattern: ^\d+$ preferred_prefix: unists uri_format: https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1 unite: description: UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa. example: UDB000691 homepage: http://unite.ut.ee/ mappings: biocontext: UNITE fairsharing: FAIRsharing.cnwx8c miriam: unite n2t: unite ncbi: UNITE prefixcommons: unite name: Molecular database for the identification of fungi pattern: ^UDB\d{6}$ preferred_prefix: unite uri_format: http://unite.ut.ee/bl_forw.php?nimi=$1 unpd: comment: The website is dead, there are no places to get the source information except inside https://oolonek.github.io/ISDB/. contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true homepage: http://pkuxxj.pku.edu.cn/UNPD/ name: Universal Natural Products Database preferred_prefix: unpd references: - http://bioinf-applied.charite.de/supernatural_new/index.php?site=vendor_info&id=Universal%20Natural%20Products%20Database - https://pharmacognosy.in/the-universal-natural-products-database-unpd/ - https://pubs.acs.org/doi/abs/10.1021/acs.jnatprod.6b01093 - https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062839 - https://oolonek.github.io/ISDB/ uo: appears_in: - agro - ms - rbo - scdo banana: UO contact: email: g.gkoutos@gmail.com github: gkoutos name: George Gkoutos orcid: 0000-0002-2061-091X description: Ontology of standardized units download_obo: http://purl.obolibrary.org/obo/uo.obo download_owl: http://purl.obolibrary.org/obo/uo.owl example: 0000080 homepage: https://github.com/bio-ontology-research-group/unit-ontology license: CC BY 3.0 mappings: biocontext: UO bioportal: UO fairsharing: FAIRsharing.mjnypw miriam: uo n2t: uo obofoundry: UO ols: uo ontobee: UO prefixcommons: uo name: Units of measurement ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: UO repository: https://github.com/bio-ontology-research-group/unit-ontology uri_format: https://www.ebi.ac.uk/ols/ontologies/uo/terms?obo_id=UO:$1 version: '2020-03-10' upa: banana: UPA contact: email: Anne.Morgat@sib.swiss github: amorgat name: Anne Morgat orcid: 0000-0002-1216-2969 depends_on: - ro deprecated: true description: A manually curated resource for the representation and annotation of metabolic pathways download_obo: https://raw.githubusercontent.com/geneontology/unipathway/master/upa.obo download_owl: http://purl.obolibrary.org/obo/upa.owl example: UCR00513 homepage: https://github.com/geneontology/unipathway license: CC BY 3.0 mappings: biocontext: UNIPATHWAY bioportal: UPA go: UniPathway obofoundry: UPA ols: upa ontobee: UPA prefixcommons: unipathway uniprot: UniPathway name: Unipathway pattern: ^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$ preferred_prefix: UPA repository: https://github.com/geneontology/unipathway synonyms: - UPa - unipathway - unipathway.pathway uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1 version: '2018-12-12' upheno: banana: UPHENO contact: email: vasilevs@ohsu.edu github: nicolevasilevsky name: Nicole Vasilevsky orcid: 0000-0001-5208-3432 description: The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology. download_owl: https://github.com/obophenotype/upheno/blob/master/upheno.owl homepage: https://github.com/obophenotype/upheno license: CC0 1.0 mappings: biocontext: UPHENO bioportal: UPHENO fairsharing: FAIRsharing.r41qhx obofoundry: UPHENO ols: upheno ontobee: UPHENO name: Unified Phenotype Ontology no_own_terms: true preferred_prefix: UPHENO repository: https://github.com/obophenotype/upheno uri_format: http://purl.obolibrary.org/obo/UPHENO_$1 version: '2017-10-31' uspto: description: The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement. example: '4145692' homepage: http://patft.uspto.gov/netahtml/PTO/index.html mappings: biocontext: USPTO miriam: uspto n2t: uspto name: United States Patent and Trademark Office pattern: ^(D|PP|R|T|H|X|AI)?\d+$ preferred_prefix: uspto uri_format: http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1 validatordb: description: Database of validation results for ligands and non-standard residues in the Protein Data Bank. example: 2h6o homepage: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ mappings: biocontext: VALIDATORDB fairsharing: FAIRsharing.c9psgb miriam: validatordb n2t: validatordb name: ValidatorDB pattern: ^[A-Za-z0-9\/]+$ preferred_prefix: validatordb provides: pdb uri_format: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1 vandf: description: 'The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes. ' example: '4019477' homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF mappings: biolink: VANDF bioportal: VANDF fairsharing: FAIRsharing.xn3pb3 name: Veterans Administration National Drug File pattern: ^\d+$ preferred_prefix: vandf references: - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2244318/ vario: banana: VariO contact: email: mauno.vihinen@med.lu.se github: null name: Mauno Vihinen orcid: null description: The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level. download_obo: http://purl.obolibrary.org/obo/vario.obo download_owl: http://purl.obolibrary.org/obo/vario.owl example: '0376' homepage: http://variationontology.org mappings: biocontext: VARIO bioportal: VARIO fairsharing: FAIRsharing.65xkbs miriam: vario n2t: vario obofoundry: VariO ols: vario ontobee: VariO name: Variation Ontology namespace_in_lui: true pattern: ^\d+$ preferred_prefix: VariO providers: - code: CURATOR_REVIEW description: VariO at Lund University homepage: http://www.variationontology.org/ name: VariO at Lund University uri_format: http://www.ontobee.org/search?ontology=VariO&keywords=VariO_$1&submit=Search+terms uri_format: http://purl.obolibrary.org/obo/VARIO_$1 version: '2018-11-09' vbase2: description: The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes. example: humIGHV025 homepage: http://www.vbase2.org/vbase2.php mappings: biocontext: VBASE2 fairsharing: FAIRsharing.qvxhb1 miriam: vbase2 n2t: vbase2 ncbi: VBASE2 prefixcommons: vbase2 name: Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse pattern: ^\w+$ preferred_prefix: vbase2 uri_format: http://www.vbase2.org/vgene.php?id=$1 vbrc: description: The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis. example: '35742' homepage: http://vbrc.org/ mappings: biocontext: VBRC miriam: vbrc n2t: vbrc prefixcommons: vbrc name: Viral Bioinformatics Resource Center pattern: ^\d+$ preferred_prefix: vbrc uri_format: http://vbrc.org/gene_detail.asp?gene_id=$1 vcell: description: Models developed with the Virtual Cell (VCell) software prorgam. example: '201022999' homepage: https://health.uconn.edu/ mappings: miriam: vcell name: VCell Published Models pattern: ^\d{5,}$ preferred_prefix: vcell uri_format: https://vcell.org/biomodel-$1 vectorbase: description: 'VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis.' example: ISCW007415 homepage: https://www.vectorbase.org/ mappings: biocontext: VECTORBASE fairsharing: FAIRsharing.3etvdn miriam: vectorbase n2t: vectorbase ncbi: VectorBase prefixcommons: vectorbase name: Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens pattern: ^\D{4}\d{6}(\-\D{2})?$ preferred_prefix: vectorbase uri_format: https://vectorbase.org/vectorbase/app/record/gene/$1 vega: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A repository for high-quality gene models produced by the manual annotation of vertebrate genomes. example: OTTHUMG00000169812 homepage: https://vega.archive.ensembl.org/index.html mappings: fairsharing: FAIRsharing.mr293q prefixcommons: vega name: Vertebrate Genome Annotation Database preferred_prefix: vega synonyms: - VEGA uri_format: http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1 vegbank: description: 'VegBank is the vegetation plot database of the Ecological Society of America''s Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. ' example: VB.Ob.3736.GRSM125 homepage: http://vegbank.org/ mappings: miriam: vegbank name: VegBank pattern: ^VB\.[A-Za-z][A-Za-z]\..*$ preferred_prefix: vegbank uri_format: http://vegbank.org/cite/$1 vfb: description: An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster. example: '00000001' homepage: https://VirtualFlyBrain.org mappings: fairsharing: FAIRsharing.nzaz6z miriam: vfb n2t: vfb name: Virtual Fly Brain pattern: ^[0-9a-zA-Z]{8}$ preferred_prefix: vfb uri_format: http://virtualflybrain.org/reports/$1 vfdb.gene: description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes. example: VFG2154 homepage: http://www.mgc.ac.cn/VFs/ mappings: biocontext: VFDB.GENE miriam: vfdb.gene n2t: vfdb.gene name: VFDB Gene pattern: ^\w+$ preferred_prefix: vfdb.gene uri_format: http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1 vfdb.genus: description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus. example: Chlamydia homepage: http://www.mgc.ac.cn/VFs/ mappings: biocontext: VFDB.GENUS miriam: vfdb.genus n2t: vfdb.genus name: VFDB Genus pattern: ^\w+$ preferred_prefix: vfdb.genus uri_format: http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1 vgnc: description: The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee. example: VGNC:3792 homepage: https://vertebrate.genenames.org mappings: cellosaurus: VGNC fairsharing: FAIRsharing.5NhJFK miriam: vgnc ncbi: VGNC uniprot: VGNC name: Vertebrate Gene Nomenclature Committee pattern: ^((VGNC|vgnc):)?\d{1,9}$ preferred_prefix: vgnc uri_format: https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1 vhog: banana: VHOG deprecated: true download_obo: ftp://ftp.bgee.org/general/ontologies/vHOG.obo download_owl: http://purl.obolibrary.org/obo/vhog.owl example: '0000411' mappings: biocontext: VHOG bioportal: VHOG obofoundry: VHOG prefixcommons: vhog name: Vertebrate Homologous Organ Group Ontology pattern: ^\d{7}$ preferred_prefix: VHOG synonyms: - VHOG_RETIRED uri_format: http://purl.obolibrary.org/obo/VHOG_$1 viaf: description: The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web. example: '75121530' homepage: http://viaf.org mappings: miriam: viaf n2t: viaf scholia: viaf name: Virtual International Authority File pattern: ^\d+$ preferred_prefix: viaf uri_format: http://viaf.org/viaf/$1 vido: contact: email: johnbeverley2021@u.northwestern.edu github: johnbeve name: John Beverly orcid: 0000-0002-1118-1738 description: The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc. download_owl: http://purl.obolibrary.org/obo/2020-25-08/vido.owl example: '0001114' homepage: https://github.com/infectious-disease-ontology-extensions/ido-virus mappings: bioportal: VIDO ols: vido ontobee: VIDO name: The Virus Infectious Disease Ontology pattern: ^\d{7}$ preferred_prefix: vido repository: https://github.com/infectious-disease-ontology-extensions/ido-virus version: '2020-08-25' vipr: description: The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information. example: BeAn 70563 homepage: http://www.viprbrc.org/brc/home.do?decorator=vipr mappings: biocontext: VIPR fairsharing: FAIRsharing.2qx8n8 miriam: vipr n2t: vipr ncbi: ViPR name: Virus Pathogen Resource pattern: ^[A-Za-z 0-9]+$ preferred_prefix: vipr uri_format: http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena viralzone: description: ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures. example: '992' homepage: http://www.expasy.org/viralzone/ mappings: biocontext: VIRALZONE fairsharing: FAIRsharing.tppk10 miriam: viralzone n2t: viralzone name: ViralZone pattern: ^\d+$ preferred_prefix: viralzone uri_format: http://viralzone.expasy.org/all_by_protein/$1.html virsirna: description: The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region. example: virsi1909 homepage: http://crdd.osdd.net/servers/virsirnadb mappings: biocontext: VIRSIRNA miriam: virsirna n2t: virsirna name: VIRsiRNA pattern: ^virsi\d+$ preferred_prefix: virsirna uri_format: http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1 vmc: deprecated: true mappings: biolink: VMC name: Variation Modelling Collaboration preferred_prefix: vmc references: - https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.67hbe76b6a4z - https://github.com/ga4gh/vr-spec vmhgene: description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. example: '8639.1' homepage: https://www.vmh.life/ mappings: miriam: vmhgene name: VMH Gene pattern: ^[0-9]+\.[0-9]+$ preferred_prefix: vmhgene uri_format: https://www.vmh.life/#gene/$1 vmhmetabolite: description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. example: h2o homepage: https://www.vmh.life/ mappings: biocontext: VMHMETABOLITE miriam: vmhmetabolite n2t: vmhmetabolite name: VMH metabolite pattern: ^[a-zA-Z0-9_\(\_\)\[\]]+$ preferred_prefix: vmhmetabolite uri_format: https://www.vmh.life/#metabolite/$1 vmhreaction: description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. example: HEX1 homepage: https://www.vmh.life/ mappings: biocontext: VMHREACTION miriam: vmhreaction n2t: vmhreaction name: VMH reaction pattern: ^[a-zA-Z0-9_\(\_\)\[\]]+$ preferred_prefix: vmhreaction uri_format: https://www.vmh.life/#reaction/$1 vo: appears_in: - scdo banana: VO contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqunh He orcid: 0000-0001-9189-9661 description: The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine annotation, integrate various vaccine data, and support computer-assisted reasoning. VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities. download_owl: http://purl.obolibrary.org/obo/vo.owl example: 0000093 homepage: http://www.violinet.org/vaccineontology license: CC BY 3.0 mappings: biocontext: VO bioportal: VO fairsharing: FAIRsharing.zwtww5 obofoundry: VO ols: vo ontobee: VO prefixcommons: vo name: Vaccine Ontology pattern: ^\d{7}$ preferred_prefix: VO repository: https://github.com/vaccineontology/VO uri_format: http://purl.obolibrary.org/obo/VO_$1 version: 1.1.193 void: description: The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary. example: feature homepage: http://vocab.deri.ie/void mappings: biocontext: void name: Vocabulary of Interlinked Datasets preferred_prefix: void uri_format: http://rdfs.org/ns/void#$1 vsao: banana: VSAO contact: email: wasila.dahdul@usd.edu github: null name: Wasila Dahdul orcid: 0000-0003-3162-7490 deprecated: true description: Vertebrate skeletal anatomy ontology. download_owl: http://purl.obolibrary.org/obo/vsao.owl homepage: https://www.nescent.org/phenoscape/Main_Page mappings: biocontext: VSAO bioportal: VSAO obofoundry: VSAO name: Vertebrate Skeletal Anatomy Ontology preferred_prefix: VSAO synonyms: - VSAO_RETIRED uri_format: http://purl.obolibrary.org/obo/VSAO_$1 vsdb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source. example: '1868' homepage: https://sitem.herts.ac.uk/aeru/vsdb name: Veterinary Substances DataBase pattern: ^\d+$ preferred_prefix: vsdb uri_format: https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm vso: description: 'The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. ' example: '0000041' homepage: https://bioportal.bioontology.org/ontologies/VSO mappings: bioportal: VSO fairsharing: FAIRsharing.jjb2p2 prefixcommons: vso name: Vital Sign Ontology pattern: ^\d{7}$ preferred_prefix: vso uri_format: https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1 vt: appears_in: - scdo banana: VT contact: email: caripark@iastate.edu github: caripark name: Carissa Park orcid: 0000-0002-2346-5201 description: An ontology of traits covering vertebrates download_obo: https://github.com/AnimalGenome/vertebrate-trait-ontology/raw/master/current_release/vt.obo download_owl: http://purl.obolibrary.org/obo/vt.owl example: 0000685 homepage: https://github.com/AnimalGenome/vertebrate-trait-ontology license: CC BY 4.0 mappings: biocontext: VT bioportal: VT fairsharing: FAIRsharing.10gr18 obofoundry: VT ols: vt ontobee: VT prefixcommons: vt name: Vertebrate trait ontology pattern: ^\d{7}$ preferred_prefix: VT repository: https://github.com/AnimalGenome/vertebrate-trait-ontology uri_format: http://purl.obolibrary.org/obo/VT_$1 vto: banana: VTO contact: email: balhoff@renci.org github: balhoff name: Jim Balhoff orcid: 0000-0002-8688-6599 description: Comprehensive hierarchy of extinct and extant vertebrate taxa. download_obo: http://purl.obolibrary.org/obo/vto.obo download_owl: http://purl.obolibrary.org/obo/vto.owl example: '9008500' homepage: https://github.com/phenoscape/vertebrate-taxonomy-ontology license: CC0 1.0 mappings: biocontext: VTO bioportal: VTO fairsharing: FAIRsharing.akmeb9 obofoundry: VTO ols: vto ontobee: VTO name: Vertebrate Taxonomy Ontology pattern: ^\d{7}$ preferred_prefix: VTO repository: https://github.com/phenoscape/vertebrate-taxonomy-ontology uri_format: http://purl.obolibrary.org/obo/VTO_$1 version: '2020-11-13' vuid: comment: The example corresponds to acetaminophen contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Veterans Health Administration is America’s largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year. example: '4007166' homepage: https://www.va.gov/health name: Veterans Health Administration (VHA) unique identifier pattern: ^\d+$ preferred_prefix: vuid references: - https://academic.oup.com/jamia/article/17/4/432/866953 vz: description: ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries. example: '886' homepage: http://viralzone.expasy.org/ mappings: go: VZ prefixcommons: vz name: ViralZone pattern: ^\d+$ preferred_prefix: vz uri_format: https://viralzone.expasy.org/$1 wb.rnai: description: WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes. example: WBRNAi00086878 homepage: https://www.wormbase.org/ mappings: biocontext: WB.RNAI miriam: wb.rnai n2t: wb.rnai name: WormBase RNAi pattern: ^WBRNAi\d{8}$ preferred_prefix: wb.rnai uri_format: https://www.wormbase.org/species/c_elegans/rnai/$1 wbbt: banana: WBbt contact: email: raymond@caltech.edu github: raymond91125 name: Raymond Lee orcid: 0000-0002-8151-7479 description: Ontology about the gross anatomy of the C. elegans download_obo: http://purl.obolibrary.org/obo/wbbt.obo download_owl: http://purl.obolibrary.org/obo/wbbt.owl example: 0001290 homepage: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology license: CC BY 4.0 mappings: biocontext: WBBT biolink: WBbt bioportal: WB-BT fairsharing: FAIRsharing.phk7dd go: WBbt obofoundry: WBbt ols: wbbt ontobee: WBbt prefixcommons: wbbt name: C. elegans Gross Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: WBbt repository: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology synonyms: - WBbt uri_format: http://purl.obolibrary.org/obo/WBBT_$1 version: '2022-03-22' wbls: banana: WBls contact: email: cgrove@caltech.edu github: chris-grove name: Chris Grove orcid: 0000-0001-9076-6015 description: Ontology about the development and life stages of the C. elegans download_obo: http://purl.obolibrary.org/obo/wbls.obo download_owl: http://purl.obolibrary.org/obo/wbls.owl example: 0000690 homepage: https://github.com/obophenotype/c-elegans-development-ontology license: CC BY 4.0 mappings: biocontext: WBLS biolink: WBls bioportal: WB-LS fairsharing: FAIRsharing.sm90nh go: WBls obofoundry: WBls ols: wbls ontobee: WBLS prefixcommons: wbls name: C. elegans development ontology part_of: wormbase pattern: ^\d{7}$ preferred_prefix: WBls repository: https://github.com/obophenotype/c-elegans-development-ontology synonyms: - WBls uri_format: http://www.wormbase.org/get?name=$1 version: '2022-03-22' wbphenotype: banana: WBPhenotype contact: email: cgrove@caltech.edu github: chris-grove name: Chris Grove orcid: 0000-0001-9076-6015 description: Ontology about C. elegans and other nematode phenotypes download_obo: http://purl.obolibrary.org/obo/wbphenotype.obo download_owl: http://purl.obolibrary.org/obo/wbphenotype.owl example: 0000983 homepage: https://github.com/obophenotype/c-elegans-phenotype-ontology license: CC BY 4.0 mappings: biocontext: WBPhenotype bioportal: WB-PHENOTYPE fairsharing: FAIRsharing.agvc7y go: WBPhenotype obofoundry: WBPhenotype ols: wbphenotype ontobee: WBPhenotype prefixcommons: wbphenotype name: C. elegans phenotype part_of: wormbase pattern: ^\d{7}$ preferred_prefix: WBPhenotype repository: https://github.com/obophenotype/c-elegans-phenotype-ontology synonyms: - WBPhenotype uri_format: http://www.wormbase.org/get?name=$1 version: '2022-03-22' webelements: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Browser for the periodic table of the elements example: chromium homepage: https://www.webelements.com/ name: Web Elements pattern: ^\w+$ preferred_prefix: webelements uri_format: https://www.webelements.com/$1 wgs84: description: A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum example: latitude homepage: https://www.w3.org/2003/01/geo/wgs84_pos mappings: biolink: wgs name: WGS84 Geo Positioning preferred_prefix: wgs84 uri_format: http://www.w3.org/2003/01/geo/wgs84_pos#$1 wicell: description: Cell line collections example: ai10e-kctd13b homepage: https://www.wicell.org mappings: cellosaurus: WiCell name: WiCell Research Institute Cell Collection preferred_prefix: wicell uri_format: https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true wikidata: description: Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic. example: Q2207226 homepage: https://www.wikidata.org/ mappings: biocontext: WD_Entity biolink: WIKIDATA cellosaurus: Wikidata cheminf: '000567' fairsharing: FAIRsharing.6s749p miriam: wikidata n2t: wikidata name: Wikidata pattern: ^(Q|P)\d+$ preferred_prefix: wikidata providers: - code: scholia description: Scholia can generally resolve many Wikidata entries in the biomedical and bibliometric domains homepage: https://scholia.toolforge.org name: Scholia uri_format: https://scholia.toolforge.org/$1 synonyms: - WD_Entity - wd uri_format: http://www.wikidata.org/entity/$1 wikidata.property: description: 'Wikidata is a free and open knowledge base that can be read and edited by both humans and machines. Wikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. ' example: P4355 homepage: https://www.wikidata.org mappings: biocontext: WD_Prop biolink: WIKIDATA_PROPERTY name: Wikidata Property pattern: ^P\d+$ preferred_prefix: wikidata.property providers: - code: scholia description: Scholia can generally resolve many Wikidata entries in the biomedical and bibliometric domains homepage: https://scholia.toolforge.org name: Scholia uri_format: https://scholia.toolforge.org/$1 uri_format: https://www.wikidata.org/wiki/Property:$1 wikigenes: description: WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process. example: '3771877' homepage: http://www.wikigenes.org/ mappings: biocontext: WIKIGENES miriam: wikigenes n2t: wikigenes name: WikiGenes pattern: ^\d+$ preferred_prefix: wikigenes provides: ncbigene uri_format: http://www.wikigenes.org/e/gene/e/$1.html wikipathways: description: "WikiPathways is a resource providing an open and public collection\ \ of pathway maps created and curated by the community in a Wiki like style.\r\ \nAll content is under the Creative Commons Attribution 3.0 Unported license." example: WP732 homepage: http://www.wikipathways.org/ mappings: biocontext: WIKIPATHWAYS bioportal: WIKIPATHWAYS fairsharing: FAIRsharing.g7b4rj miriam: wikipathways n2t: wikipathways prefixcommons: wikipathways scholia: wikipathways wikidata: P2410 name: WikiPathways pattern: ^WP\d{1,5}(\_r\d+)?$ preferred_prefix: wikipathways 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/wikipathways/$1 uri_format: http://www.wikipathways.org/instance/$1 wikipedia.en: description: Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay. example: SM_UB-81 homepage: http://en.wikipedia.org/wiki/Main_Page mappings: biocontext: WIKIPEDIA.EN go: Wikipedia miriam: wikipedia.en n2t: wikipedia.en prefixcommons: wikipedia name: Wikipedia pattern: ^[A-Za-z-0-9_]+$ preferred_prefix: wikipedia.en providers: - code: CURATOR_REVIEW description: Wikipedia structured content through DBpedia homepage: http://wiki.dbpedia.org/ name: Wikipedia structured content through DBpedia uri_format: http://dbpedia.org/page/$1 synonyms: - wikipedia uri_format: http://en.wikipedia.org/wiki/$1 worfdb: description: WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends). example: T01B6.1 homepage: http://worfdb.dfci.harvard.edu/ mappings: biocontext: WORFDB miriam: worfdb n2t: worfdb ncbi: WorfDB prefixcommons: worfdb name: C. elegans ORFeome cloning project pattern: ^\w+(\.\d+)$ preferred_prefix: worfdb uri_format: http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1 wormbase: description: WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities. example: WBGene00000001 homepage: https://www.wormbase.org/ mappings: biocontext: WormBase biolink: WBVocab fairsharing: FAIRsharing.zx1td8 go: WB_REF miriam: wb n2t: wb ncbi: WormBase prefixcommons: wormbase uniprot: WormBase wikidata: P3860 name: WormBase database of nematode biology pattern: ^WB[A-Z][a-z]+\d+$ preferred_prefix: WormBase providers: - code: bioentitylink description: WormBase through BioEntity Link homepage: https://bioentity.link/ name: WormBase through BioEntity Link uri_format: https://bioentity.link/#/lexicon/public/$1 - code: agr description: WormBase through the Alliance of Genome Resources homepage: https://www.alliancegenome.org name: WormBase through the Alliance of Genome Resources uri_format: https://www.alliancegenome.org/gene/WB:$1 synonyms: - WB_REF - wb - wormbase uri_format: https://www.wormbase.org/get?name=$1 wormpep: description: Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project. example: CE28239 homepage: https://www.wormbase.org/db/seq/protein mappings: biocontext: WORMPEP miriam: wormpep n2t: wormpep prefixcommons: wormpep name: Wormpep pattern: ^CE\d{5}$ preferred_prefix: wormpep uri_format: https://www.wormbase.org/db/seq/protein?name=$1 worms: description: The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts. example: '146421' homepage: http://www.marinespecies.org/ mappings: biocontext: WORMS fairsharing: FAIRsharing.7g1bzj miriam: worms n2t: worms name: World Register of Marine Species pattern: ^\d+$ preferred_prefix: worms uri_format: http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1 wwf.ecoregion: comment: ENVO includes xrefs to this resource. See EnvironmentOntology/envo#658 contributor: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions. example: AT1402 homepage: https://www.worldwildlife.org/biomes mappings: wikidata: P1294 name: World Wildlife Fund Ecoregion pattern: ^AT\d+$ preferred_prefix: wwf.ecoregion reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - WWF uri_format: https://www.worldwildlife.org/ecoregions/$1 xao: appears_in: - xpo banana: XAO contact: email: Erik.Segerdell@cchmc.org github: seger name: Erik Segerdell orcid: 0000-0002-9611-1279 description: XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis. download_obo: http://purl.obolibrary.org/obo/xao.obo download_owl: http://purl.obolibrary.org/obo/xao.owl example: 0004486 homepage: http://www.xenbase.org/anatomy/xao.do?method=display license: CC BY 3.0 mappings: biocontext: XAO bioportal: XAO fairsharing: FAIRsharing.17zapb obofoundry: XAO ols: xao ontobee: XAO wikidata: P4495 name: Xenopus Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: XAO repository: https://github.com/xenopus-anatomy/xao uri_format: http://purl.obolibrary.org/obo/XAO_$1 version: '2021-03-04' xco: appears_in: - agro - ecto banana: XCO contact: email: jrsmith@mcw.edu github: jrsjrs name: Jennifer Smith orcid: 0000-0002-6443-9376 description: Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. download_obo: http://purl.obolibrary.org/obo/xco.obo download_owl: http://purl.obolibrary.org/obo/xco.owl example: 0000780 homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000 license: CC0 1.0 mappings: biocontext: XCO bioportal: XCO fairsharing: FAIRsharing.x39h5y obofoundry: XCO ols: xco ontobee: XCO prefixcommons: xco name: Experimental condition ontology pattern: ^\d{7}$ preferred_prefix: XCO repository: https://github.com/rat-genome-database/XCO-experimental-condition-ontology uri_format: http://purl.obolibrary.org/obo/XCO_$1 version: '2019-12-18' xenbase: description: Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions. example: XB-GENE-922462 homepage: https://www.xenbase.org/ mappings: biocontext: Xenbase biolink: Xenbase fairsharing: FAIRsharing.jrv6wj go: Xenbase miriam: xenbase n2t: xenbase ncbi: Xenbase prefixcommons: xenbase uniprot: Xenbase name: Xenbase pattern: ^XB\-\w+\-\d+$ preferred_prefix: xenbase uri_format: https://www.xenbase.org/common/xsearch.do?exactSearch=true&searchIn=7&searchValue=$1 ximbio: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Cell line collections example: '151022' homepage: https://ximbio.com mappings: cellosaurus: Ximbio name: Ximbio pattern: ^\d+$ preferred_prefix: ximbio uri_format: https://ximbio.com/reagent/$1 xl: deprecated: true description: A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry. download_owl: http://purl.obolibrary.org/obo/xl.owl homepage: http://www.psidev.info/groups/controlled-vocabularies mappings: biocontext: XL ols: xl ontobee: XL name: Cross-linker reagents ontology preferred_prefix: xl uri_format: http://purl.obolibrary.org/obo/XL_$1 xlmod: banana: XLMOD contact: email: lutz.fischer@tu-berlin.de github: lutzfischer name: Lutz Fischer orcid: 0000-0003-4978-0864 description: A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry. download_obo: https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo download_owl: http://purl.obolibrary.org/obo/xlmod.owl example: '00050' homepage: http://www.psidev.info/groups/controlled-vocabularies license: CC BY 3.0 mappings: bioportal: XLMOD obofoundry: XLMOD ols: xlmod ontobee: XLMOD name: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary pattern: ^\d{5}$ preferred_prefix: XLMOD repository: https://github.com/HUPO-PSI/xlmod-CV uri_format: http://purl.obolibrary.org/obo/XLMOD_$1 version: '2019-10-28' xmetdb: banana: XMETDB contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: Metabolites in the Xenobiotics Metabolism Database. example: '171' homepage: https://xmetdb.org name: Xenobiotics Metabolism Database pattern: ^\d+$ preferred_prefix: xmetdb uri_format: http://www.xmetdb.org/xmetdb/protocol/$1 xml: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Extensible Markup Language (XML) is a subset of SGML that is completely described in this document. Its goal is to enable generic SGML to be served, received, and processed on the Web in the way that is now possible with HTML. XML has been designed for ease of implementation and for interoperability with both SGML and HTML. example: lang homepage: https://www.w3.org/TR/xml/ mappings: biocontext: xml name: Extensible Markup Language preferred_prefix: xml uri_format: http://www.w3.org/XML/1998/namespace$1 xpo: banana: XPO contact: email: Erik.Segerdell@cchmc.org github: seger name: Erik Segerdell orcid: 0000-0002-9611-1279 depends_on: - bfo - chebi - cl - go - iao - pato - ro - xao description: XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis. download_obo: http://purl.obolibrary.org/obo/xpo.obo download_owl: http://purl.obolibrary.org/obo/xpo.owl example: '0100002' homepage: https://github.com/obophenotype/xenopus-phenotype-ontology license: CC BY 3.0 mappings: biolink: XPO bioportal: XPO obofoundry: XPO ols: xpo ontobee: XPO name: Xenopus Phenotype Ontology pattern: ^\d+$ preferred_prefix: XPO repository: https://github.com/obophenotype/xenopus-phenotype-ontology uri_format: http://purl.obolibrary.org/obo/XPO_$1 version: '2021-03-05' xsd: description: This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language. example: decimal homepage: http://www.w3.org/2001/XMLSchema mappings: biocontext: xsd name: XML Schema Definition preferred_prefix: xsd uri_format: http://www.w3.org/2001/XMLSchema#$1 xuo: appears_in: - hsapdv contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: XUO preferred_prefix: xuo ydpm: description: The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition. example: YAL001C homepage: http://www-deletion.stanford.edu/YDPM/ mappings: biocontext: YDPM miriam: ydpm n2t: ydpm prefixcommons: ydpm name: Yeast Deletion and the Mitochondrial Proteomics Project pattern: ^Y[A-Z]{2}\d+[CW]$ preferred_prefix: ydpm uri_format: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1 yeastintron: description: The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460]. example: SNR17A homepage: http://intron.ucsc.edu/yeast4.3/ mappings: biocontext: YEASTINTRON miriam: yeastintron n2t: yeastintron name: Yeast Intron Database v4.3 pattern: ^[A-Z0-9]+$ preferred_prefix: yeastintron uri_format: http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1 yetfasco: description: The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. example: YOR172W_571.0 homepage: http://yetfasco.ccbr.utoronto.ca/ mappings: biocontext: YETFASCO miriam: yetfasco n2t: yetfasco name: YeTFasCo pattern: ^\w+\_\d+(\.\d+)?$ preferred_prefix: yetfasco uri_format: http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1 yid: description: The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521]. example: SNR17A homepage: http://compbio.soe.ucsc.edu/yeast_introns.html mappings: biocontext: YID miriam: yid n2t: yid name: Yeast Intron Database v3 pattern: ^[A-Z0-9]+$ preferred_prefix: yid uri_format: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1 ymdb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast). example: YMDB00001 homepage: http://www.ymdb.ca mappings: fairsharing: FAIRsharing.tawpg2 name: Yeast Metabolome Database pattern: ^YMDB\d+$ preferred_prefix: ymdb uri_format: http://www.ymdb.ca/compounds/$1 ypo: banana: YPO contact: email: cherry@genome.stanford.edu github: null name: Mike Cherry orcid: 0000-0001-9163-5180 deprecated: true homepage: http://www.yeastgenome.org/ mappings: obofoundry: YPO ols: ypo name: Yeast phenotypes preferred_prefix: YPO uri_format: http://purl.obolibrary.org/obo/YPO_$1 yrcpdr: description: The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions. example: '2673500' homepage: http://www.yeastrc.org/pdr/ mappings: biocontext: YRCPDR fairsharing: FAIRsharing.karvzj miriam: yrcpdr n2t: yrcpdr name: YRC PDR pattern: ^\d+$ preferred_prefix: yrcpdr uri_format: http://yeastrc.org/pdr/viewProtein.do?id=$1 zea: banana: ZEA contact: email: Leszek@missouri.edu github: null name: Leszek Vincent orcid: 0000-0002-9316-2919 deprecated: true homepage: http://www.maizemap.org/ mappings: biocontext: ZEA bioportal: ZEA obofoundry: ZEA prefixcommons: zea name: Maize gross anatomy preferred_prefix: ZEA uri_format: http://purl.obolibrary.org/obo/ZEA_$1 zeco: appears_in: - mco banana: ZECO contact: email: ybradford@zfin.org github: ybradford name: Yvonne Bradford orcid: 0000-0002-9900-7880 description: Ontology of Zebrafish Experimental Conditions download_json: http://purl.obolibrary.org/obo/zeco.json download_obo: http://purl.obolibrary.org/obo/zeco.obo download_owl: http://purl.obolibrary.org/obo/zeco.owl example: '0000171' homepage: https://github.com/ybradford/zebrafish-experimental-conditions-ontology license: CC BY 3.0 mappings: biocontext: ZECO bioportal: ZECO fairsharing: FAIRsharing.np2wfz obofoundry: ZECO ols: zeco ontobee: ZECO name: Zebrafish Experimental Conditions Ontology pattern: ^\d{7}$ preferred_prefix: ZECO repository: https://github.com/ybradford/zebrafish-experimental-conditions-ontology uri_format: http://purl.obolibrary.org/obo/ZECO_$1 version: '2022-02-14' zfa: appears_in: - zp banana: ZFA contact: email: van_slyke@zfin.org github: cerivs name: Ceri Van Slyke orcid: 0000-0002-2244-7917 description: ZFA description. download_obo: http://purl.obolibrary.org/obo/zfa.obo download_owl: http://purl.obolibrary.org/obo/zfa.owl example: 0005926 homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources license: CC BY 3.0 mappings: biocontext: ZFA bioportal: ZFA fairsharing: FAIRsharing.s3r6sk obofoundry: ZFA ols: zfa ontobee: ZFA prefixcommons: zfa name: Zebrafish anatomy and development ontology pattern: ^\d{7}$ preferred_prefix: ZFA repository: https://github.com/cerivs/zebrafish-anatomical-ontology synonyms: - ZFA_RETIRED uri_format: http://purl.obolibrary.org/obo/ZFA_$1 version: '2022-03-15' zfin: description: ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN. example: ZDB-GENE-041118-11 homepage: http://zfin.org mappings: biocontext: ZFIN fairsharing: FAIRsharing.ybxnhg go: ZFIN miriam: zfin n2t: zfin ncbi: ZFIN prefixcommons: zfin uniprot: ZFIN wikidata: P3870 name: Zebrafish Information Network Gene pattern: ^ZDB\-\w+\-\d+\-\d+$ preferred_prefix: zfin providers: - code: bioentitylink description: ZFIN through BioEntity Link homepage: https://bioentity.link/ name: ZFIN through BioEntity Link uri_format: https://bioentity.link/#/lexicon/public/$1 - code: agr description: ZFIN through the Alliance of Genome Resources homepage: https://www.alliancegenome.org name: ZFIN through the Alliance of Genome Resources uri_format: https://test.alliancegenome.org/gene/ZFIN:$1 synonyms: - ZFIN uri_format: http://zfin.org/$1 zfs: banana: ZFS contact: email: van_slyke@zfin.org github: cerivs name: Ceri Van Slyke orcid: 0000-0002-2244-7917 description: Developmental stages of the Zebrafish download_obo: http://purl.obolibrary.org/obo/zfs.obo download_owl: http://purl.obolibrary.org/obo/zfs.owl example: '0000050' homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources license: CC BY 3.0 mappings: biocontext: ZFS bioportal: ZFS fairsharing: FAIRsharing.bc8ayj obofoundry: ZFS ols: zfs ontobee: ZFS name: Zebrafish developmental stages ontology pattern: ^\d{7}$ preferred_prefix: ZFS repository: https://github.com/cerivs/zebrafish-anatomical-ontology uri_format: http://purl.obolibrary.org/obo/ZFS_$1 version: '2020-03-10' zinc: description: ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. example: ZINC1084 homepage: http://zinc15.docking.org/ mappings: biocontext: ZINC miriam: zinc n2t: zinc wikidata: P2084 name: ZINC is not Commercial pattern: ^(ZINC)?\d+$ preferred_prefix: zinc uri_format: http://zinc15.docking.org/substances/$1 zp: banana: ZP contact: email: ybradford@zfin.org github: ybradford name: Yvonne Bradford orcid: 0000-0002-9900-7880 depends_on: - bfo - bspo - go - pato - ro - uberon - zfa description: The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism. download_obo: http://purl.obolibrary.org/obo/zp.obo download_owl: http://purl.obolibrary.org/obo/zp.owl example: 0019030 homepage: https://github.com/obophenotype/zebrafish-phenotype-ontology license: CC BY 3.0 mappings: biocontext: ZP bioportal: ZP obofoundry: ZP ols: zp ontobee: ZP name: Zebrafish Phenotype Ontology pattern: ^\d+$ preferred_prefix: ZP repository: https://github.com/obophenotype/zebrafish-phenotype-ontology uri_format: http://purl.obolibrary.org/obo/ZP_$1 version: '2021-12-12'