_3dmet: comment: Website has been down since 2023/2024 deprecated: true description: 3DMET is a database collecting three-dimensional structures of natural metabolites. example: B00162 homepage: http://www.3dmet.dna.affrc.go.jp/ keywords: - chemical - life science - metabolite - metabolomics - structure mappings: biocontext: 3DMET edam: '2635' fairsharing: FAIRsharing.5ab0n7 integbio: nbdc00351 miriam: 3dmet n2t: 3dmet prefixcommons: 3dmet wikidata: P2796 name: 3D Metabolites pattern: ^B\d{5}$ preferred_prefix: _3dmet providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/3dmet:$1 publications: - doi: 10.2142/biophysico.15.0_87 pmc: PMC5992871 pubmed: '29892514' title: 'Chemical curation to improve data accuracy: recent development of the 3DMET database' year: 2018 - doi: 10.1021/ci300309k pubmed: '23293959' title: 'Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures' year: 2013 synonyms: - 3dmet uri_format: http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1 _4dn.biosource: contact: email: Job.Dekker@umassmed.edu name: Job Dekker orcid: 0000-0001-5631-0698 description: The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases. example: 4DNSR73BT2A2 homepage: https://data.4dnucleome.org/biosources keywords: - dna - life science - protein mappings: cellosaurus: 4DN fairsharing: FAIRsharing.CugtbQ miriam: 4dn prefixcommons: 4dn name: 4D Nucleome Data Portal Biosource pattern: ^4DN[A-Z]{2}[A-Z0-9]{7}$ preferred_prefix: _4dn.biosource providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/4dn:$1 publications: - doi: 10.1038/nature23884 pmc: PMC5617335 pubmed: '28905911' title: The 4D nucleome project year: 2017 synonyms: - 4DN - 4dn.biosource twitter: 4dn_dcic uri_format: https://data.4dnucleome.org/biosources/$1 _4dn.replicate: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - email: laylamichan@ciencias.unam.mx github: lmichan name: Layla Michán Aguirre orcid: 0000-0002-5798-662X - email: mineromero2901@ciencias.unam.mx github: MinRo60 name: Minerva María Romero Pérez orcid: 0000-0002-6240-9325 - email: victorinolavida@ciencias.unam.mx github: Victorinolavida name: José Victorino Ruiz Lavida orcid: 0000-0001-5130-7705 description: Database portal containing replicate experiments of different assays and samples example: 4DNESWX1J3QU homepage: https://data.4dnucleome.org/experiment-set-replicates/ name: 4D Nucleome Data Portal Experiment Replicate preferred_prefix: _4dn.replicate synonyms: - 4dn.replicate uri_format: https://data.4dnucleome.org/experiment-set-replicates/$1 aaindex: contact: email: shuichi@hgc.jp github: skwsm name: Shuichi Kawashima orcid: 0000-0001-7883-3756 contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: Identifier of an entry from the AAindex database. example: BUNA790102 homepage: http://www.genome.ad.jp/aaindex/ keywords: - protein mappings: edam: '1128' integbio: nbdc00004 prefixcommons: aaindex name: AAindex preferred_prefix: aaindex providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/aaindex:$1 publications: - doi: 10.1093/nar/gkm998 pmc: PMC2238890 pubmed: '17998252' title: 'AAindex: amino acid index database, progress report 2008' year: 2007 references: - https://github.com/biopragmatics/bioregistry/pull/1098 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.genome.jp/dbget-bin/www_bget?aaindex:$1 aao: contact: email: david.c.blackburn@gmail.com name: David Blackburn orcid: 0000-0002-1810-9886 deprecated: true description: A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon. example: 0000138 homepage: http://github.com/seger/aao keywords: - anatomy - obo - ontology mappings: agroportal: AAO biocontext: AAO fairsharing: FAIRsharing.mxx5rp obofoundry: aao prefixcommons: aao name: Amphibian gross anatomy pattern: ^\d{7}$ preferred_prefix: AAO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/aao:$1 publications: - doi: 10.1186/2041-1480-5-21 pmc: PMC4089931 pubmed: '25009735' title: Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon year: 2014 - doi: 10.1142/9789812772435_0035 pubmed: '17992749' title: An anatomical ontology for amphibians year: 2007 rdf_uri_format: http://purl.obolibrary.org/obo/AAO_$1 uri_format: http://purl.obolibrary.org/obo/AAO_$1 abcam: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: Vendor for assays, cells, and antibodies example: ab275461 homepage: https://www.abcam.com mappings: cellosaurus: Abcam name: Abcam preferred_prefix: abcam references: - https://github.com/biopragmatics/bioregistry/pull/1098 uri_format: https://www.abcam.com/$1.html abcd: contact: email: Pierre.Cosson@unige.ch name: Pierre Cosson orcid: 0000-0002-4881-0358 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies example: AD834 homepage: https://web.expasy.org/abcd/ keywords: - immunology - molecular biology mappings: cellosaurus: ABCD fairsharing: FAIRsharing.Z8OKi5 uniprot: DB-0236 name: AntiBodies Chemically Defined database preferred_prefix: abcd publications: - doi: 10.1093/nar/gkz714 pmc: PMC6943046 pubmed: '31410491' title: 'The ABCD database: a repository for chemically defined antibodies' year: 2020 references: - https://github.com/biopragmatics/bioregistry/pull/1098 uri_format: https://web.expasy.org/abcd/ABCD_$1 abm: contributor_extras: - email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: Cell line collections (Providers) 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/search?query=$1 abs: contact: email: enrique.blanco@crg.eu name: Enrique Blanco orcid: 0000-0001-6261-7370 description: The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. example: A0014 homepage: http://genome.crg.es/datasets/abs2005/ keywords: - biology - gene - interaction - regulation mappings: biocontext: ABS edam: '2741' fairsharing: FAIRsharing.7mnebr miriam: abs n2t: abs pathguide: '217' prefixcommons: abs name: Annotated Regulatory Binding Sites pattern: ^A\d+$ preferred_prefix: abs providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/abs:$1 publications: - doi: 10.1093/nar/gkj116 pmc: PMC1347478 pubmed: '16381947' title: 'ABS: a database of Annotated regulatory Binding Sites from orthologous promoters' year: 2006 uri_format: http://genome.crg.es/datasets/abs2005/entries/$1.html absd: contact: email: nicolas.maillet@pasteur.fr name: Nicolas Maillet orcid: 0000-0003-1611-5243 contributor: email: palayoor.n@northeastern.edu github: nalikapalayoor name: Nalika Palayoor orcid: 0009-0008-8406-631X description: The AntiBody Sequence Database is a public dataset for antibody sequence data. It provides unique identifiers for antibody sequences, including both immunoglobulin and single-chain variable fragment sequences. These are are critical for immunological studies, and allows users to search and retrieve antibody sequences based on sequence similarity and specificity, and other biological properties. example: 81d0ea69a9ab134f6ba68314e982171a367d3ab739c85c5ba49701dd02170ed3 github_request_issue: 1362 homepage: https://absd.pasteur.cloud name: AntiBody Sequence Database pattern: ^[a-f0-9]{64}$ preferred_prefix: absd publications: - doi: 10.1093/nargab/lqae171 pmc: PMC11655285 pubmed: '39703430' title: AntiBody Sequence Database year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://absd.pasteur.cloud/antibody/$1 ac: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: Activity Streams is an open format specification for activity stream protocols, which are used to syndicate activities taken in social web applications and services, similar to those in Facebook's, Instagram's, and Twitter's. The standard provides a general way to represent activities. example: Add homepage: http://www.w3.org/ns/activitystreams keywords: - semantic web - social media name: Activity Streams preferred_prefix: ac references: - https://github.com/biopragmatics/bioregistry/pull/1098 uri_format: http://www.w3.org/ns/activitystreams#$1 aceview.worm: contact: email: mieg@ncbi.nlm.nih.gov name: Danielle Thierry-Mieg orcid: 0000-0001-9568-4211 description: AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression. example: aap-1 homepage: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm keywords: - dna - gene - rna mappings: biocontext: ACEVIEW.WORM miriam: aceview.worm n2t: aceview.worm prefixcommons: aceview.worm name: Aceview Worm pattern: ^[a-z0-9-]+$ preferred_prefix: aceview.worm providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/aceview.worm:$1 publications: - doi: 10.1186/gb-2006-7-s1-s12 pmc: PMC1810549 pubmed: '16925834' title: 'AceView: a comprehensive cDNA-supported gene and transcripts annotation' year: 2006 uri_format: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1 adcad: contact: email: brycemecum@gmail.com github: amoeba name: Bryce Mecum orcid: 0000-0002-0381-3766 contributor: email: j.harry.caufield@gmail.com github: caufieldjh name: Harry Caufield orcid: 0000-0001-5705-7831 description: An ontology to support disciplinary annotation of Arctic Data Center datasets. download_owl: http://aber-owl.net/media/ontologies/ADCAD/1/adcad.owl download_rdf: https://github.com/NCEAS/adc-disciplines/raw/main/ADCAD.ttl example: '00000' github_request_issue: 827 homepage: https://arcticdata.io/ keywords: - ontology license: CC-BY-4.0 mappings: aberowl: ADCAD bioportal: ADCAD name: Arctic Data Center Academic Disciplines Ontology pattern: ^\d{5}$ preferred_prefix: adcad repository: https://github.com/NCEAS/adc-disciplines reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://purl.dataone.org/odo/ADCAD_$1 addexbio: description: Cell line collections (Providers) 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=$1 addgene: contact: email: joanne.kamens@addgene.org name: Joanne Kamens orcid: 0000-0002-7000-1477 description: Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world. example: '50943' homepage: http://addgene.org/ keywords: - bio.tools - faseb list - life science - molecular biology - plasmid - repository - sequence alignment mappings: fairsharing: FAIRsharing.8hcczk integbio: nbdc00356 miriam: addgene n2t: addgene prefixcommons: addgene re3data: r3d100010741 rrid: Addgene name: Addgene Plasmid Repository pattern: ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$ preferred_prefix: addgene providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/addgene:$1 publications: - doi: 10.1093/nar/gku893 pmc: PMC4384007 pubmed: '25392412' title: 'The Addgene repository: an international nonprofit plasmid and data resource' year: 2014 - doi: 10.1038/505272a pubmed: '24429608' title: Repositories share key research tools year: 2014 - doi: 10.1038/nbt.2177 pubmed: '22491276' title: Addgene provides an open forum for plasmid sharing year: 2012 twitter: Addgene uri_format: http://addgene.org/$1 adms: contact: email: bert.van.nuffelen@tenforce.com github: bertvannuffelen name: Bert Van Nuffelen contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A vocabulary for describing semantic assets, defined as highly reusable metadata (e.g. XML1 schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies). example: Asset homepage: http://www.w3.org/ns/adms keywords: - metadata license: CC-BY-4.0 mappings: lov: adms name: Asset Description Metadata Schema Vocabulary preferred_prefix: adms repository: https://github.com/SEMICeu/ADMS/ uri_format: http://www.w3.org/ns/adms#$1 ado: contact: email: alpha.tom.kodamullil@scai.fraunhofer.de github: akodamullil name: Alpha Tom Kodamullil orcid: 0000-0001-9896-3531 contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 depends_on: - bfo description: Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining. download_owl: http://purl.obolibrary.org/obo/ado.owl example: '0000001' homepage: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO keywords: - alzheimer's disease - health science - obo - ontology license: CC-BY-4.0 mappings: aberowl: ADO bioportal: ADO fairsharing: FAIRsharing.ckd4rf obofoundry: ado ols: ado ontobee: ADO name: Alzheimer's Disease Ontology pattern: ^\d{7}$ preferred_prefix: ADO publications: - doi: 10.1016/j.jalz.2013.02.009 pubmed: '23830913' title: 'ADO: a disease ontology representing the domain knowledge specific to Alzheimer''s disease' year: 2013 rdf_uri_format: http://purl.obolibrary.org/obo/ADO_$1 references: - https://github.com/biopragmatics/bioregistry/pull/1098 repository: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO uri_format: http://purl.obolibrary.org/obo/ADO_$1 version: '2023-09-20' adw: contact: email: adw_geeks@umich.edu name: Animal Diversity Web technical staff contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 deprecated: true description: Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology. download_owl: http://aber-owl.net/media/ontologies/ADW/2/adw.owl example: Lycalopex_vetulus homepage: http://www.animaldiversity.org keywords: - anatomy - life science - obo - ontology - taxonomic classification mappings: aberowl: ADW agroportal: ADW biocontext: ADW bioportal: ADW fairsharing: FAIRsharing.t9fvdn miriam: adw n2t: adw obofoundry: adw name: Animal natural history and life history pattern: ^[A-Z_a-z]+$ preferred_prefix: ADW rdf_uri_format: http://purl.obolibrary.org/obo/ADW_$1 references: - https://github.com/biopragmatics/bioregistry/pull/1098 uri_format: https://animaldiversity.org/accounts/$1 aeo: appears_in: - ehdaa2 contact: email: J.Bard@ed.ac.uk name: Jonathan Bard contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 deprecated: true description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology download_obo: http://purl.obolibrary.org/obo/aeo.obo download_owl: http://purl.obolibrary.org/obo/aeo.owl example: '0001017' homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/ keywords: - anatomy - obo - ontology license: CC-BY-4.0 mappings: aberowl: AEO bartoc: '181' biocontext: AEO bioportal: AEO fairsharing: FAIRsharing.93ee19 obofoundry: aeo ols: aeo ontobee: AEO name: Anatomical Entity Ontology pattern: ^\d{7}$ preferred_prefix: AEO publications: - doi: 10.3389/fgene.2012.00018 pmc: PMC3278863 pubmed: '22347883' title: The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs year: 2012 rdf_uri_format: http://purl.obolibrary.org/obo/AEO_$1 references: - https://github.com/biopragmatics/bioregistry/pull/1098 repository: https://github.com/obophenotype/human-developmental-anatomy-ontology synonyms: - AEO_RETIRED uri_format: http://purl.obolibrary.org/obo/AEO_$1 version: '2014-12-05' aeon: contact: email: Philip.Stroemert@tib.eu github: StroemPhi name: Philip Strömert orcid: 0000-0002-1595-3213 contributor: email: Philip.Stroemert@tib.eu github: StroemPhi name: Philip Strömert orcid: 0000-0002-1595-3213 description: The academic event ontology, currently still in development and thus unstable, is an OBO compliant reference ontology for describing academic events such as conferences, workshops or seminars and their series. It is being developed as part of the [ConfIDent project](https://projects.tib.eu/confident/) to allow RDF representations of the academic events and series stored and curated in the [ConfIDent platform](https://www.confident-conference.org/index.php/main_page). download_owl: https://raw.githubusercontent.com/tibonto/aeon/main/aeon.owl example: '0000001' github_request_issue: 617 homepage: https://tibonto.github.io/aeon/ keywords: - ontology license: CC-BY-4.0 name: Academic Event Ontology pattern: ^\d{7}$ preferred_prefix: aeon repository: https://github.com/tibonto/aeon reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://purl.obolibrary.org/obo/AEON_$1 aero: contact: email: mcourtot@gmail.com name: Melanie Courtot orcid: 0000-0002-9551-6370 contributor_extras: - github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 deprecated: true description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events download_owl: http://purl.obolibrary.org/obo/aero.owl example: '0000125' homepage: http://purl.obolibrary.org/obo/aero keywords: - adverse reaction - biomedical science - electronic health record - health science - medicine - obo - ontology - preclinical studies license: CC-BY-3.0 mappings: aberowl: AERO biocontext: AERO bioportal: AERO fairsharing: FAIRsharing.rycy2x obofoundry: aero ols: aero name: Adverse Event Reporting Ontology pattern: ^\d{7}$ preferred_prefix: AERO rdf_uri_format: http://purl.obolibrary.org/obo/AERO_$1 references: - https://github.com/biopragmatics/bioregistry/pull/1098 uri_format: http://purl.obolibrary.org/obo/AERO_$1 affy.probeset: description: An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration. example: 243002_at homepage: http://www.affymetrix.com/ mappings: biocontext: AFFY.PROBESET miriam: affy.probeset n2t: affy.probeset togoid: AffyProbeset name: Affymetrix Probeset pattern: ^\d{4,}((_[asx])?_at)$ preferred_prefix: affy.probeset providers: - code: CURATOR_REVIEW description: Bio2RDF homepage: http://cu.affymetrix.bio2rdf.org/fct/ name: Bio2RDF uri_format: http://cu.affymetrix.bio2rdf.org/describe/?url=http://bio2rdf.org/affymetrix:$1 uri_format: https://www.affymetrix.com/LinkServlet?probeset=$1 afo: contact: email: more.info@allotrope.org name: Allotrope Foundation description: Allotrope Merged Ontology Suite download_owl: http://purl.allotrope.org/voc/afo/merged/REC/2024/12/merged-without-qudt-and-inferred homepage: https://www.allotrope.org/ keywords: - agricultural engineering - agriculture - biology - environmental science - food - food chemistry - forest management - ontology - veterinary medicine mappings: aberowl: AFO bioportal: AFO fairsharing: FAIRsharing.595710 ols: afo ontobee: AFO name: Allotrope Merged Ontology Suite no_own_terms: true preferred_prefix: afo version: 2024/12 afpo: contact: email: mcmelek@msn.com github: Melek-C name: Melek Chaouch orcid: 0000-0001-5868-4204 description: AfPO is an ontology that can be used in the study of diverse populations across Africa. It brings together publicly available demographic, anthropological and genetic data relating to African people in a standardised and structured format. The AfPO can be employed to classify African study participants comprehensively in prospective research studies. It can also be used to classify past study participants by mapping them using a language or ethnicity identifier or synonyms. download_json: http://purl.obolibrary.org/obo/afpo.json download_obo: http://purl.obolibrary.org/obo/afpo.obo download_owl: http://purl.obolibrary.org/obo/afpo.owl example: '0000440' homepage: https://github.com/h3abionet/afpo keywords: - obo - ontology license: CC-BY-4.0 mappings: aberowl: AFPO bioportal: AFPO obofoundry: afpo ontobee: AfPO name: African Population Ontology preferred_prefix: AfPO rdf_uri_format: http://purl.obolibrary.org/obo/AfPO_$1 repository: https://github.com/h3abionet/afpo uri_format: http://purl.obolibrary.org/obo/AfPO_$1 aftol.category: contact: email: davem@umn.edu name: David J. McLaughlin contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Categories in the AFTOL database example: '229' homepage: https://aftol.umn.edu name: Assembling the Fungal Tree of Life - Category preferred_prefix: aftol.category uri_format: https://aftol.umn.edu/glossary?category=$1 aftol.taxonomy: contact: email: davem@umn.edu name: David J. McLaughlin contributor_extras: - email: laylamichan@ciencias.unam.mx github: lmichan name: Layla Michán Aguirre orcid: 0000-0002-5798-662X description: The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species. example: '959' homepage: https://aftol.umn.edu mappings: biocontext: AFTOL.TAXONOMY miriam: aftol.taxonomy n2t: aftol.taxonomy name: Assembling the Fungal Tree of Life - Taxonomy pattern: ^\d+$ preferred_prefix: aftol.taxonomy uri_format: http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1 agilent.probe: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699.' example: A_24_P98555 homepage: https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt keywords: - transcriptomics name: Agilent Probe pattern: ^A_\d+_.+$ preferred_prefix: agilent.probe references: - http://www.cs.tau.ac.il/cgi-bin/cgiwrap/click/get.cgi/conversionFiles/conversion_human_14850_agilent2entrez.txt agricola: contact: email: judith.blake@jax.org github: judyblake name: Judith A Blake orcid: 0000-0001-8522-334X contributor_extras: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 - email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century. example: '50018' homepage: http://agricola.nal.usda.gov/ mappings: biocontext: AGRICOLA go: AGRICOLA_ID miriam: agricola n2t: agricola uniprot: DB-0266 name: Agricultural Online Access pattern: ^\d+$ preferred_prefix: agricola publications: - doi: 10.1093/nar/gkz813 pmc: PMC6943066 pubmed: '31552413' title: 'Alliance of Genome Resources Portal: unified model organism research platform' year: 2020 references: - https://github.com/biopragmatics/bioregistry/pull/1098 synonyms: - AGR - AGRICOLA_ID uri_format: https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1 agrkb: contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 contributor: github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 description: 'The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations. The Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location: - [ZFIN](https://zfin.org) - Zebrafish Information Network - [WormBase](https://wormbase.org) - [MGI](https://www.mgi.org) - Mouse Genome Informatics - [RGD](https://rgd.mcw.edu) - Rat Genome Database - [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database - [FlyBase](https://flybase.org) - [Xenbase](https://www.xenbase.org)' example: '100000000000001' github_request_issue: 359 homepage: https://www.alliancegenome.org keywords: - model organism database mappings: biolink: AGRKB name: Alliance of Genome Resources Knowledge Base pattern: ^[1-9][0-9]{14}$ preferred_prefix: agrkb reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.alliancegenome.org/accession/$1 agro: contact: email: m.a.laporte@cgiar.org github: marieALaporte name: Marie-Angélique Laporte orcid: 0000-0002-8461-9745 contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 depends_on: - bfo - envo - foodon - go - iao - ncbitaxon - obi - pato - peco - po - ro - to - uo - xco description: AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities download_obo: https://raw.githubusercontent.com/KrishnaTO/agro/master/agro.obo download_owl: http://purl.obolibrary.org/obo/agro.owl example: '00020007' homepage: https://github.com/AgriculturalSemantics/agro keywords: - agriculture - agronomy - cropping systems - farming systems research - obo - ontology - plant breeding license: CC-BY-4.0 mappings: aberowl: AGRO agroportal: AGRO biocontext: AGRO bioportal: AGRO fairsharing: FAIRsharing.m40bhw obofoundry: agro ols: agro ontobee: AGRO name: Agronomy Ontology pattern: ^\d{8}$ preferred_prefix: AGRO rdf_uri_format: http://purl.obolibrary.org/obo/AGRO_$1 references: - https://github.com/biopragmatics/bioregistry/pull/1098 repository: https://github.com/AgriculturalSemantics/agro uri_format: http://purl.obolibrary.org/obo/AGRO_$1 version: '2022-11-02' agrovoc: banana: c_ contact: email: agrovoc@fao.org name: AGROVOC Team contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages. example: '2842' homepage: https://data.apps.fao.org/catalog/organization/agrovoc keywords: - agriculture - botany - data management - environmental science - fisheries science - food - forest management - nutritional science - thesaurus mappings: agroportal: AGROVOC bartoc: '305' ecoportal: AGROVOC fairsharing: FAIRsharing.anpj91 wikidata: P8061 name: Agronomy Vocabulary pattern: ^[a-z0-9]+$ preferred_prefix: agrovoc publications: - doi: 10.4060/cb2838en title: AGROVOC year: 2021 - doi: 10.3390/engproc2021009017 title: 'How Agricultural Digital Innovation Can Benefit from Semantics: The Case of the AGROVOC Multilingual Thesaurus' year: 2021 - doi: 10.1016/j.compag.2020.105965 title: 'AGROVOC: The linked data concept hub for food and agriculture' year: 2022 rdf_uri_format: http://aims.fao.org/aos/agrovoc/$1 references: - http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_core.nt.zip - http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_lod.nt.zip - https://en.wikipedia.org/wiki/AGROVOC twitter: FAOAIMS uri_format: http://aims.fao.org/aos/agrovoc/c_$1 agsc: contact: email: srvoss@uky.edu name: Stephen Randal Voss orcid: 0000-0002-8332-3176 description: The Ambystoma Genetic Stock Center (AGSC) maintains a breeding colony of Mexican axolotls (Ambystoma mexicanum) and distributes axolotl embryos, larvae, and adults to laboratories and classrooms throughout the United States and abroad. [from homepage] example: 100E homepage: https://ambystoma.uky.edu/genetic-stock-center/ keywords: - adult - ambystoma - embryo - k-12 teacher - larvae - salamander mappings: rrid: AGSC name: Ambystoma Genetic Stock Center preferred_prefix: agsc publications: - pubmed: '16359543' uri_format: https://scicrunch.org/resolver/RRID:AGSC_$1 agsd: contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: A comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources. example: '4779' homepage: http://www.genomesize.com keywords: - dna - genome - life science mappings: fairsharing: FAIRsharing.efp5v2 prefixcommons: agsd re3data: r3d100012517 name: Animal Genome Size Database preferred_prefix: agsd providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/agsd:$1 references: - https://github.com/biopragmatics/bioregistry/pull/1098 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.genomesize.com/result_species.php?id=$1 aio: contact: email: MJoachimiak@lbl.gov github: realmarcin name: Marcin Pawel Joachimiak orcid: 0000-0001-8175-045X contributor: email: lindsey.anderson@pnnl.gov github: lnanderson name: Lindsey N. Anderson orcid: 0000-0002-8741-7823 description: This ontology models classes and relationships describing deep learning networks, their component layers and activation functions, as well as potential biases. download_json: https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.json download_obo: https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.obo download_owl: https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.owl example: Causal_Graphical_Model github_request_issue: 884 homepage: https://github.com/berkeleybop/artificial-intelligence-ontology keywords: - artificial intelligence - computational biology - hidden markov model - knowledge representation - machine learning - natural language processing - network model - ontology mappings: aberowl: AIO bioportal: AIO fairsharing: FAIRsharing.8d6247 name: The Artificial Intelligence Ontology preferred_prefix: aio publications: - doi: 10.48550/arxiv.2404.03044 title: 'The Artificial Intelligence Ontology: LLM-assisted construction of AI concept hierarchies' year: 2024 repository: https://github.com/berkeleybop reviewer: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://w3id.org/aio/$1 aism: appears_in: - colao - lepao contact: email: entiminae@gmail.com github: JCGiron name: Jennifer C. Girón orcid: 0000-0002-0851-6883 contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 depends_on: - bfo - bspo - caro - pato - ro - uberon description: The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research. download_json: http://purl.obolibrary.org/obo/aism.json download_obo: http://purl.obolibrary.org/obo/aism.obo download_owl: http://purl.obolibrary.org/obo/aism.owl example: '0000027' homepage: https://github.com/insect-morphology/aism keywords: - obo - ontology license: CC-BY-4.0 mappings: aberowl: AISM bioportal: AISM obofoundry: aism ols: aism ontobee: AISM name: Ontology for the Anatomy of the Insect SkeletoMuscular system pattern: ^\d{7}$ preferred_prefix: AISM rdf_uri_format: http://purl.obolibrary.org/obo/AISM_$1 references: - https://github.com/biopragmatics/bioregistry/pull/1098 repository: https://github.com/insect-morphology/aism uri_format: http://purl.obolibrary.org/obo/AISM_$1 version: '2024-06-20' alfred: comment: This resource doesn't exist on the web anymore contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 deprecated: true description: ALFRED has been designed to make allele frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases. example: LO362836C homepage: http://alfred.med.yale.edu keywords: - classification - genome mappings: prefixcommons: alfred name: The ALlele FREquency Database preferred_prefix: alfred providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/alfred:$1 publications: - doi: 10.1093/nar/gkg043 pmc: PMC165490 pubmed: '12519999' title: 'ALFRED: the ALelle FREquency Database. Update' year: 2003 references: - https://github.com/biopragmatics/bioregistry/pull/1098 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID=$1 allergome: contact: email: adriano.mari@allergome.org name: Adriano Mari orcid: 0000-0002-9137-1442 contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources. example: '1948' homepage: http://www.allergome.org/ keywords: - allergen - biomedical science - health science - life science - medicine mappings: biocontext: ALLERGOME fairsharing: FAIRsharing.w6cxgb integbio: nbdc01708 miriam: allergome n2t: allergome prefixcommons: allergome uniprot: DB-0160 name: Allergome pattern: ^\d+$ preferred_prefix: allergome providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/allergome:$1 publications: - doi: 10.1007/s11882-009-0055-9 pubmed: '19671381' title: 'Allergen databases: current status and perspectives' year: 2009 - doi: 10.1016/j.cellimm.2007.02.012 pubmed: '17434469' title: 'Bioinformatics applied to allergy: allergen databases, from collecting sequence information to data integration. The Allergome platform as a model' year: 2007 - pubmed: '17393720' title: 'Allergome: a unifying platform' year: 2006 references: - https://github.com/biopragmatics/bioregistry/pull/1098 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 contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease. example: app-d678n-tottori homepage: https://www.alzforum.org/mutations keywords: - alzheimer's disease - genes - variants name: Alzforum Mutations preferred_prefix: alzforum.mutation references: - https://github.com/biopragmatics/bioregistry/pull/1098 synonyms: - Alzforum_mut uri_format: https://www.alzforum.org/mutations/$1 alzgene: contact: email: bertram@helix.mgh.harvard.edu name: Lars Bertram orcid: 0000-0002-0108-124X description: The AlzGene database provides a comprehensive, unbiased and regularly updated field synopsis of genetic association studies performed in Alzheimer’s disease. In addition, hundreds of up-to-date meta-analyses are available for all eligible polymorphisms with sufficient data. example: '88' homepage: http://www.alzgene.org keywords: - gene mappings: prefixcommons: alzgene name: Alzheimer Gene Database preferred_prefix: alzgene providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/alzgene:$1 publications: - doi: 10.1038/ng1934 pubmed: '17192785' title: 'Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database' year: 2007 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.alzgene.org/geneoverview.asp?geneid=$1 amoebadb: contact: email: oharb@upenn.edu github: ramobrah name: Omar S. Harb orcid: 0000-0003-4446-6200 contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: EDI_244000 homepage: http://amoebadb.org/amoeba/ keywords: - functional genomics - genomics - model organism mappings: biocontext: AMOEBADB fairsharing: FAIRsharing.swbypy integbio: nbdc01207 miriam: amoebadb n2t: amoebadb prefixcommons: amoebadb re3data: r3d100012457 name: AmoebaDB pattern: ^EDI_\d+$ preferred_prefix: amoebadb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/amoebadb:$1 publications: - doi: 10.1093/nar/gkp941 pmc: PMC2808945 pubmed: '19914931' title: 'EuPathDB: a portal to eukaryotic pathogen databases' year: 2009 references: - https://github.com/biopragmatics/bioregistry/pull/1098 twitter: eupathdb uri_format: https://amoebadb.org/amoeba/app/record/gene/$1 amphx: contact: email: hescriva@obs-banyuls.fr github: hescriva name: Hector Escriva orcid: 0000-0001-7577-5028 contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 depends_on: - uberon description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). download_obo: http://purl.obolibrary.org/obo/amphx.obo download_owl: http://purl.obolibrary.org/obo/amphx.owl example: '1000160' homepage: https://github.com/EBISPOT/amphx_ontology keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: AMPHX bioportal: AMPHX obofoundry: amphx ols: amphx ontobee: AMPHX name: The Amphioxus Development and Anatomy Ontology pattern: ^\d+$ preferred_prefix: AMPHX rdf_uri_format: http://purl.obolibrary.org/obo/AMPHX_$1 references: - https://github.com/biopragmatics/bioregistry/pull/1098 repository: https://github.com/EBISPOT/amphx_ontology uri_format: http://purl.obolibrary.org/obo/AMPHX_$1 version: '2020-12-18' antibodyregistry: contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information. example: '493771' homepage: http://antibodyregistry.org/ keywords: - antibody - reagent - unique identifiers mappings: biocontext: ANTIBODYREGISTRY integbio: nbdc01696 miriam: antibodyregistry n2t: antibodyregistry rrid: AB name: Antibody Registry pattern: ^\d{6}$ preferred_prefix: antibodyregistry references: - https://github.com/biopragmatics/bioregistry/pull/1098 uri_format: http://antibodyregistry.org/AB_$1 antweb: description: AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures. example: casent0106247 homepage: http://www.antweb.org/ keywords: - anatomy - classification - life science mappings: biocontext: ANTWEB fairsharing: FAIRsharing.yk38tw integbio: nbdc01710 miriam: antweb n2t: antweb ncbi: AntWeb prefixcommons: antweb wikidata: P5299 name: AntWeb pattern: ^casent\d+(\-D\d+)?$ preferred_prefix: antweb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/antweb:$1 publications: - doi: 10.1038/424242b pubmed: '12867945' title: Ants join online colony to boost conservation efforts year: 2003 uri_format: http://www.antweb.org/specimen.do?name=$1 anzctr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: ' The Australian New Zealand Clinical Trials Registry (ANZCTR) is an online register of clinical trials being undertaken in Australia, New Zealand and elsewhere. The ANZCTR includes trials from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. In 2007 the ANZCTR was one of the first three trial registries to be recognised by the World Health Organization International Clinical Trials Registry Platform (WHO ICTRP) as a Primary Registry. WHO recognises registries as Primary Registries if they fulfil certain criteria with respect to data content, quality and validity, accessibility, unique identification, technical capacity and administration. The ANZCTR contributes data to the WHO ICTRP, which was developed in 2007. Trials from all ICTRP Primary Registries can be searched at: www.who.int/trialsearch. (from website)' example: ACTRN12623000498695 homepage: https://anzctr.org.au name: Australian New Zealand Clinical Trials Registry pattern: ^ACTRN\d+$ preferred_prefix: anzctr providers: - code: '' description: '' homepage: '' name: '' uri_format: https://anzctr.org.au/ACTRN$1.aspx references: - https://github.com/biopragmatics/bioregistry/pull/1098 synonyms: - ACTRN uri_format: https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=$1 aop: contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: International repository of Adverse Outcome Pathways. example: '98' homepage: https://aopwiki.org/ mappings: biocontext: AOP miriam: aop n2t: aop name: AOPWiki pattern: ^\d+$ preferred_prefix: aop references: - https://github.com/biopragmatics/bioregistry/pull/1098 uri_format: https://aopwiki.org/aops/$1 aop.events: description: International repository of Adverse Outcome Pathways. example: '3' homepage: https://aopwiki.org/ mappings: biocontext: AOP.EVENTS miriam: aop.events n2t: aop.events name: AOPWiki (Key Event) pattern: ^\d+$ preferred_prefix: aop.events uri_format: https://aopwiki.org/events/$1 aop.relationships: description: International repository of Adverse Outcome Pathways. example: '5' homepage: https://aopwiki.org/ mappings: biocontext: AOP.RELATIONSHIPS miriam: aop.relationships n2t: aop.relationships name: AOPWiki (Key Event Relationship) pattern: ^\d+$ preferred_prefix: aop.relationships uri_format: https://aopwiki.org/relationships/$1 aop.stressor: description: International repository of Adverse Outcome Pathways. example: '9' homepage: https://aopwiki.org/ mappings: biocontext: AOP.STRESSOR miriam: aop.stressor n2t: aop.stressor name: AOPWiki (Stressor) pattern: ^\d+$ preferred_prefix: aop.stressor uri_format: https://aopwiki.org/stressors/$1 apaonto: contact: email: awalker@apa.org name: Alvin Walker orcid: 0000-0003-1082-8760 contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: An ontology developed by the American Psychological Association (APA). Note that URIs in this ontology appear to have been generated with erroneous settings in Protege. download_owl: http://aber-owl.net/media/ontologies/APAONTO/4/apaonto.owl example: Abdomen homepage: https://bioportal.bioontology.org/ontologies/APAONTO keywords: - behavior - ontology - psychology mappings: aberowl: APAONTO bioportal: APAONTO fairsharing: FAIRsharing.gkw1w8 name: Psychology Ontology preferred_prefix: apaonto references: - https://github.com/biopragmatics/bioregistry/issues/528 - https://github.com/biopragmatics/bioregistry/pull/1098 uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1 apd: contact: email: gwang@unmc.edu name: Guangshun Wang orcid: 0000-0002-4841-7927 description: The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides. example: '01001' homepage: http://aps.unmc.edu/AP/ keywords: - biology - protein mappings: biocontext: APD fairsharing: FAIRsharing.ctwd7b miriam: apd n2t: apd prefixcommons: apd re3data: r3d100012901 name: Antimicrobial Peptide Database pattern: ^\d{5}$ preferred_prefix: apd providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/apd:$1 publications: - doi: 10.1093/nar/gkv1278 pmc: PMC4702905 pubmed: '26602694' title: 'APD3: the antimicrobial peptide database as a tool for research and education' year: 2015 - doi: 10.1093/nar/gkn823 pmc: PMC2686604 pubmed: '18957441' title: 'APD2: the updated antimicrobial peptide database and its application in peptide design' year: 2008 - doi: 10.1093/nar/gkh025 pmc: PMC308759 pubmed: '14681488' title: 'APD: the Antimicrobial Peptide Database' year: 2004 uri_format: http://aps.unmc.edu/AP/database/query_output.php?ID=$1 aphidbase.transcript: contact: email: fabrice.legeai@rennes.inra.fr name: Fabrice Legeai orcid: 0000-0002-6472-4839 description: AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information. example: ACYPI000159 homepage: http://www.aphidbase.com/aphidbase keywords: - genome mappings: biocontext: APHIDBASE.TRANSCRIPT miriam: aphidbase.transcript n2t: aphidbase.transcript prefixcommons: aphidbase name: AphidBase Transcript pattern: ^ACYPI\d{6}(-RA)?$ preferred_prefix: aphidbase.transcript providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/aphidbase:$1 publications: - doi: 10.1111/j.1365-2583.2009.00930.x pmc: PMC4372297 pubmed: '20482635' title: 'AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome' year: 2010 uri_format: http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1 apid.interactions: contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier. example: P01116 homepage: http://cicblade.dep.usal.es:8080/APID/ mappings: biocontext: APID.INTERACTIONS miriam: apid.interactions n2t: apid.interactions name: APID Interactomes pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ preferred_prefix: apid.interactions provides: uniprot references: - https://github.com/biopragmatics/bioregistry/pull/1098 uri_format: http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1 apo: contact: email: stacia@stanford.edu github: srengel name: Stacia R Engel orcid: 0000-0001-5472-917X contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi. download_obo: http://purl.obolibrary.org/obo/apo.obo download_owl: http://purl.obolibrary.org/obo/apo.owl example: 0000184 homepage: http://www.yeastgenome.org/ keywords: - cell biology - life cycle stage - life science - morphology - mutation - obo - ontology - phenotype - study design license: CC-BY-4.0 mappings: aberowl: APO biocontext: APO bioportal: APO fairsharing: FAIRsharing.dyqz3y obofoundry: apo ols: apo ontobee: APO name: Ascomycete phenotype ontology pattern: ^\d{7}$ preferred_prefix: APO publications: - doi: 10.1093/database/bap001 pmc: PMC2790299 pubmed: '20157474' title: New mutant phenotype data curation system in the Saccharomyces Genome Database year: 2009 rdf_uri_format: http://purl.obolibrary.org/obo/APO_$1 references: - https://github.com/biopragmatics/bioregistry/pull/1098 repository: https://github.com/obophenotype/ascomycete-phenotype-ontology twitter: yeastgenome uri_format: http://purl.obolibrary.org/obo/APO_$1 version: '2025-02-01' apollosv: appears_in: - scdo contact: email: hoganwr@gmail.com github: hoganwr name: William Hogan orcid: 0000-0002-9881-1017 description: An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. download_owl: http://purl.obolibrary.org/obo/apollo_sv.owl example: '00000443' homepage: https://github.com/ApolloDev/apollo-sv keywords: - biomedical science - ecology - epidemiology - infection - obo - ontology - pathogen - population genetics license: CC-BY-4.0 mappings: aberowl: APOLLO_SV bioportal: APOLLO-SV fairsharing: FAIRsharing.ngv2xx obofoundry: apollo_sv ols: apollo_sv ontobee: APOLLO_SV name: Apollo Structured Vocabulary pattern: ^\d{8}$ preferred_prefix: APOLLO_SV providers: - code: conflated description: This might be resulting from properties in Apollo SV actually trying to use appropriate identifiers homepage: http://purl.obolibrary.org name: OBO PURL in Parts uri_format: http://purl.obolibrary.org/obo/apollo_sv/dev/apollo_sv.owl#APOLLO_SV_$1 publications: - doi: 10.1186/s13326-016-0092-y pmc: PMC4989460 pubmed: '27538448' title: 'The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation' year: 2016 - pmc: PMC3900155 pubmed: '24551417' title: 'Apollo: giving application developers a single point of access to public health models using structured vocabularies and Web services' year: 2013 rdf_uri_format: http://purl.obolibrary.org/obo/APOLLO_SV_$1 repository: https://github.com/ApolloDev/apollo-sv uri_format: http://purl.obolibrary.org/obo/APOLLO_SV_$1 version: '2024-12-24' arachnoserver: contact: email: glenn.king@imb.uq.edu.au name: Glenn King orcid: 0000-0002-2308-2200 contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information. example: AS000060 homepage: http://www.arachnoserver.org/ keywords: - drug - life science - protein mappings: biocontext: ARACHNOSERVER edam: '2578' fairsharing: FAIRsharing.c54ywe integbio: nbdc01221 miriam: arachnoserver n2t: arachnoserver prefixcommons: arachnoserver re3data: r3d100012902 uniprot: DB-0145 name: ArachnoServer pattern: ^AS\d{6}$ preferred_prefix: arachnoserver providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/arachnoserver:$1 publications: - doi: 10.1093/bioinformatics/btx661 pubmed: '29069336' title: 'ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins' year: 2018 - doi: 10.1093/nar/gkq1058 pmc: PMC3013666 pubmed: '21036864' title: ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures year: 2010 references: - https://github.com/biopragmatics/bioregistry/pull/1141 uri_format: http://www.arachnoserver.org/toxincard.html?id=$1 araport: contact: email: hello@vivekkrish.com github: vivekkrish name: Vivek Krishnakuma orcid: 0000-0002-5227-0200 description: Website with general information about Arabidopsis and functionalities such as a genomic viewer example: AT5G05330 homepage: https://www.araport.org/ mappings: integbio: nbdc02433 miriam: tair.name ncbi: Araport pathguide: '768' uniprot: DB-0221 name: Arabidopsis Information Portal pattern: ^AT.G[0-9]{5}$ preferred_prefix: araport publications: - doi: 10.1093/nar/gku1200 pmc: PMC4383980 pubmed: '25414324' title: 'Araport: the Arabidopsis information portal' year: 2014 uri_format: https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1 archdb: contact: email: narcis.fernandez@gmail.com name: Narcis Fernandez-Fuentes orcid: 0000-0002-6421-1080 description: ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al. example: '39421' homepage: http://sbi.imim.es/archdb keywords: - classification - life science - protein mappings: fairsharing: FAIRsharing.tp9z4q integbio: nbdc01795 prefixcommons: archdb name: ArchDB preferred_prefix: archdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/archdb:$1 publications: - doi: 10.1093/nar/gkt1189 pmc: PMC3964960 pubmed: '24265221' title: 'ArchDB 2014: structural classification of loops in proteins' year: 2013 - doi: 10.1093/nar/gkh002 pmc: PMC308737 pubmed: '14681390' title: 'ArchDB: automated protein loop classification as a tool for structural genomics' year: 2004 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop=$1 ardb: description: The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes. example: CAE46076 homepage: http://ardb.cbcb.umd.edu/ mappings: biocontext: ARDB miriam: ardb n2t: ardb name: Antibiotic Resistance Genes Database pattern: ^[A-Z_]{3}[0-9]{4,}$ preferred_prefix: ardb references: - https://github.com/biopragmatics/bioregistry/pull/1141 uri_format: http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1 ark: banana: ark contact: email: jakkbl@gmail.com github: jkunze name: John Kunze orcid: 0000-0001-7604-8041 contributor_extras: - email: jakkbl@gmail.com github: jkunze name: John Kunze orcid: 0000-0001-7604-8041 - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: Archival Resource Keys (ARKs) serve as persistent identifiers, or stable, trusted references for information objects. Among other things, they aim to be web addresses (URLs) that don’t return 404 Page Not Found errors. The ARK Alliance is an open global community supporting the ARK infrastructure on behalf of research and scholarship. End users, especially researchers, rely on ARKs for long term access to the global scientific and cultural record. Since 2001 some 8.2 billion ARKs have been created by over 1000 organizations — libraries, data centers, archives, museums, publishers, government agencies, and vendors. They identify anything digital, physical, or abstract. ARKs are open, mainstream, non-paywalled, decentralized persistent identifiers that can be created by an organization as soon as it is registered with a NAAN (Name Assigning Authority Number). Once registered, an ARK organization can create unlimited numbers of ARKs and publicize them via the n2t.net global resolver or via their own local resolver. example: /53355/cl010066723 homepage: https://arks.org keywords: - centrally registered identifier - data management - data retrieval - subject agnostic logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaThDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--c69281eac0647c6b7a664f0932bee0d5fd27781d/gold_boat_arka.png?disposition=inline mappings: biocontext: ARK fairsharing: FAIRsharing.f928f1 miriam: ark n2t: ark mastodon: arks_org@fosstodon.org name: Archival Resource Key namespace_in_lui: true pattern: ^/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$ preferred_prefix: ark references: - https://n2t.net/e/about.html - https://github.com/biopragmatics/bioregistry/pull/1141 twitter: ARKsInTheOpen uri_format: http://n2t.net/ark:$1 aro: appears_in: - scdo contact: email: mcarthua@mcmaster.ca github: agmcarthur name: Andrew G. McArthur orcid: 0000-0002-1142-3063 contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: Antibiotic resistance genes and mutations download_obo: http://purl.obolibrary.org/obo/aro.obo download_owl: http://purl.obolibrary.org/obo/aro.owl example: '1000001' homepage: https://github.com/arpcard/aro keywords: - antibiotic resistance - antimicrobial - gene - genetics - mutation - obo - ontology license: CC-BY-4.0 mappings: aberowl: ARO biocontext: ARO bioportal: ARO fairsharing: FAIRsharing.d8fa2d obofoundry: aro ols: aro ontobee: ARO name: Antibiotic Resistance Ontology pattern: ^\d{7}$ preferred_prefix: ARO publications: - doi: 10.1093/nar/gkz935 pmc: PMC7145624 pubmed: '31665441' title: 'CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database' year: 2020 rdf_uri_format: http://purl.obolibrary.org/obo/ARO_$1 references: - https://github.com/biopragmatics/bioregistry/pull/1141 repository: https://github.com/arpcard/aro uri_format: http://purl.obolibrary.org/obo/ARO_$1 arrayexpress: contact: email: brazma@ebi.ac.uk name: Alvis Brazma orcid: 0000-0001-5988-7409 contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations. example: E-MEXP-1712 homepage: https://www.ebi.ac.uk/arrayexpress/ keywords: - expression - functional genomics - microarray - nucleotide mappings: biocontext: ARRAYEXPRESS cellosaurus: ArrayExpress fairsharing: FAIRsharing.6k0kwd integbio: nbdc00009 miriam: arrayexpress n2t: arrayexpress prefixcommons: arrayexpress re3data: r3d100010222 name: ArrayExpress pattern: ^[AEP]-\w{4}-\d+$ preferred_prefix: arrayexpress providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/arrayexpress:$1 - code: omicsdi description: ArrayExpress through OmicsDI homepage: https://www.omicsdi.org/ name: ArrayExpress through OmicsDI uri_format: https://www.omicsdi.org/dataset/arrayexpress-repository/$1 publications: - doi: 10.1093/nar/gky964 pmc: PMC6323929 pubmed: '30357387' title: ArrayExpress update - from bulk to single-cell expression data year: 2019 - doi: 10.1093/nar/gku1057 pmc: PMC4383899 pubmed: '25361974' title: ArrayExpress update--simplifying data submissions year: 2014 - doi: 10.1093/nar/gkg091 pmc: PMC165538 pubmed: '12519949' title: ArrayExpress--a public repository for microarray gene expression data at the EBI year: 2003 references: - https://github.com/biopragmatics/bioregistry/pull/1141 twitter: ArrayExpressEBI 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/$1 arraymap: contact: email: mbaudis@me.com github: mbaudis name: Michael Baudis orcid: 0000-0002-9903-4248 description: arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome. example: icdom:8500_3 homepage: https://www.arraymap.org keywords: - bioinformatics - biomedical science - genomics - life science mappings: biocontext: ARRAYMAP fairsharing: FAIRsharing.1fbc5y miriam: arraymap n2t: arraymap re3data: r3d100012630 name: ArrayMap pattern: ^[\w\-:,]{3,64}$ preferred_prefix: arraymap publications: - doi: 10.1093/nar/gkv1310 pmc: PMC4702916 pubmed: '26615188' title: 'The SIB Swiss Institute of Bioinformatics'' resources: focus on curated databases' year: 2015 - doi: 10.1093/nar/gku1123 pmc: PMC4383937 pubmed: '25428357' title: 'arrayMap 2014: an updated cancer genome resource' year: 2014 - doi: 10.1186/1471-2164-15-82 pmc: PMC3909908 pubmed: '24476156' title: Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens year: 2014 - doi: 10.1371/journal.pone.0036944 pmc: PMC3356349 pubmed: '22629346' title: 'arrayMap: a reference resource for genomic copy number imbalances in human malignancies' year: 2012 twitter: progenetix uri_format: https://www.arraymap.org/pgx:$1 arxiv: contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology. example: 0807.4956v1 homepage: https://arxiv.org/ keywords: - bibliography - preprints - publishing mappings: bartoc: '20434' biocontext: ARXIV miriam: arxiv n2t: arxiv prefixcommons: arxiv wikidata: P818 name: arXiv pattern: ^(\w+(\-\w+)?(\.\w+)?)?\d{4,7}(\.\d+(v\d+)?)?$ preferred_prefix: arxiv providers: - code: ar5iv description: Articles from arXiv.org as responsive HTML5 web pages. homepage: https://ar5iv.labs.arxiv.org/ name: ar5iv uri_format: https://ar5iv.org/abs/$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/arxiv:$1 - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/arxiv/$1 references: - https://github.com/biopragmatics/bioregistry/pull/1141 uri_format: https://arxiv.org/abs/$1 asap: contact: email: glasner@svm.vetmed.wisc.edu name: Jeremy D. Glasner orcid: 0000-0003-1848-4464 description: ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. example: ABE-0009634 homepage: http://asap.ahabs.wisc.edu/asap/home.php keywords: - comparative genomics - developmental biology - gene expression - genome - life science mappings: biocontext: ASAP fairsharing: FAIRsharing.anpa6 go: ASAP miriam: asap n2t: asap ncbi: ASAP prefixcommons: asap re3data: r3d100010666 name: A Systematic Annotation Package for Community Analysis of Genomes pattern: ^[A-Za-z0-9-]+$ preferred_prefix: asap providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/asap:$1 publications: - doi: 10.1093/nar/gkj164 pmc: PMC1347526 pubmed: '16381899' title: 'ASAP: a resource for annotating, curating, comparing, and disseminating genomic data' year: 2006 - doi: 10.1093/nar/gkg125 pmc: PMC165572 pubmed: '12519969' title: ASAP, a systematic annotation package for community analysis of genomes year: 2003 uri_format: http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1 ascl: contact: email: aallen@ascl.net name: Alice Allen orcid: 0000-0003-3477-2845 contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001). example: '1801.012' homepage: http://ascl.net/ keywords: - astrophysics and astronomy mappings: biocontext: ASCL fairsharing: FAIRsharing.wb0txg miriam: ascl n2t: ascl re3data: r3d100011865 name: Astrophysics Source Code Library pattern: ^[0-9\.]+$ preferred_prefix: ascl publications: - doi: 10.5334/jors.bv title: 'Looking before Leaping: Creating a Software Registry' year: 2015 twitter: asclnet uri_format: http://ascl.net/$1 asin: contributor_extras: - email: sumirp77@gmail.com github: sumirp name: Sumir H Pandit orcid: 0000-0002-1216-4761 description: Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue. example: 0471491039 homepage: https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182 mappings: biocontext: ASIN miriam: asin n2t: asin name: Amazon Standard Identification Number pattern: ^[0-9]{10}$ preferred_prefix: asin references: - https://github.com/biopragmatics/bioregistry/pull/1141 uri_format: https://amzn.com/$1 aspgd.locus: description: The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information. example: ASPL0000349247 homepage: http://www.aspgd.org/ mappings: biocontext: ASPGD.LOCUS biolink: AspGD go: AspGD_LOCUS miriam: aspgd.locus n2t: aspgd.locus name: Aspergillus Genome Database pattern: ^[A-Za-z_0-9]+$ 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: contact: email: kasschau@cgrb.oregonstate.edu name: Kristin D. Kasschau 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/ keywords: - genome - regulation - rna mappings: prefixcommons: asrp name: Arabidopsis Small RNA Project preferred_prefix: asrp providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/asrp:$1 publications: - doi: 10.1093/nar/gkm997 pmc: PMC2238918 pubmed: '17999994' title: 'Update of ASRP: the Arabidopsis Small RNA Project database' year: 2007 - doi: 10.1093/nar/gki127 pmc: PMC540081 pubmed: '15608278' title: 'ASRP: the Arabidopsis Small RNA Project Database' year: 2005 uri_format: http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1 astd: comment: This resource doesn't exist on the web anymore deprecated: true description: Identifier of an object from the ASTD database. example: ENSG00000136147 homepage: http://www.ebi.ac.uk/astd/ keywords: - alternative splicing - gene - transcript mappings: edam: '2367' prefixcommons: astd name: ASTD preferred_prefix: astd providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/astd:$1 provides: ensembl publications: - doi: 10.1016/j.ygeno.2008.11.003 pubmed: '19059335' title: 'ASTD: The Alternative Splicing and Transcript Diversity database' year: 2008 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.ebi.ac.uk/astd/geneview.html?acc=$1 asteraceaegd.genome: contact: email: greatchen@cdutcm.edu.cn name: Wei Chen orcid: 0000-0002-6857-7696 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: The AGD is an integrated database resource dedicated to collecting the genomic-related data of the Asteraceae family. This collection refers to the genomic data of Asteraceae species. example: '0002' github_request_issue: 1214 homepage: https://cbcb.cdutcm.edu.cn/AGD/ name: Asteraceae Genome Database pattern: ^\d{4}$ preferred_prefix: asteraceaegd.genome publications: - doi: 10.3389/fpls.2024.1445365 pmc: PMC11366637 pubmed: '39224843' title: 'Asteraceae genome database: a comprehensive platform for Asteraceae genomics' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://cbcb.cdutcm.edu.cn/AGD/genome/details/?id=$1 asteraceaegd.plant: contact: email: greatchen@cdutcm.edu.cn name: Wei Chen orcid: 0000-0002-6857-7696 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: The AGD is an integrated database resource dedicated to collecting the genomic-related data of the Asteraceae family. This collections refers to the broader phenotypic and genetic resources of Asteraceae plants. example: '0016' github_request_issue: 1214 homepage: https://cbcb.cdutcm.edu.cn/AGD/ name: Asteraceae Genome Database pattern: ^\d{4}$ preferred_prefix: asteraceaegd.plant publications: - doi: 10.3389/fpls.2024.1445365 pmc: PMC11366637 pubmed: '39224843' title: 'Asteraceae genome database: a comprehensive platform for Asteraceae genomics' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://cbcb.cdutcm.edu.cn/AGD/plant/details/?id=$1 atc: contact: email: whocc@fhi.no name: WHO Collaborating Centre for Drug Statistics Methodology description: The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels. example: A10BA02 homepage: http://www.whocc.no/atc_ddd_index/ keywords: - anatomical therapeutic chemical code - approved drug - biomedical science - chemical - chemical biology - drug - ontology - pharmacological family classification - pharmacology mappings: aberowl: ATC bartoc: '449' biocontext: ATC bioportal: ATC edam: '3103' fairsharing: FAIRsharing.1a27h8 hl7: 2.16.840.1.113883.6.73 miriam: atc n2t: atc prefixcommons: atc togoid: Atc wikidata: P267 name: Anatomical Therapeutic Chemical Classification System pattern: ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$ preferred_prefix: atc providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/atc:$1 publications: - pubmed: '7368387' title: '[New classification of drugs. The Medical list and the Drug catalogue are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code) in 1981]' year: 1980 - doi: 10.1007/s002280000200 pubmed: '11214783' title: Different versions of the anatomical therapeutic chemical classification system and the defined daily dose--are drug utilisation data comparable? year: 2000 synonyms: - ATC_code - ATTC uri_format: http://www.whocc.no/atc_ddd_index/?code=$1 atcc: description: The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences. example: '11303' example_extras: - ccl-1 - ccl-1.4 homepage: https://www.lgcstandards-atcc.org keywords: - epidemiology - life science - virology mappings: biocontext: ATCC cellosaurus: ATCC fairsharing: FAIRsharing.j0ezpm hl7: 2.16.840.1.113883.6.77 miriam: atcc n2t: atcc ncbi: ATCC name: American Type Culture Collection pattern: ^([a-zA-Z]+-)?\d+(\.\d)?$ preferred_prefix: atcc synonyms: - ATCC - ATCC number - ATCC(dna) - ATCC(in host) uri_format: https://www.atcc.org/products/$1 atcvet: description: The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use. example: QJ51RV02 homepage: http://www.whocc.no/atcvet/atcvet_index/ mappings: biocontext: ATCVET miriam: atcvet n2t: atcvet name: Anatomical Therapeutic Chemical Vetinary pattern: ^Q[A-Z0-9]+$ preferred_prefix: atcvet uri_format: http://www.whocc.no/atcvet/atcvet_index/?code=$1 atfdb.family: description: The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found. example: CUT homepage: http://www.bioguo.org/AnimalTFDB/family_index.php mappings: biocontext: ATFDB.FAMILY miriam: atfdb.family n2t: atfdb.family name: Animal TFDB Family pattern: ^\w+$ preferred_prefix: atfdb.family uri_format: http://www.bioguo.org/AnimalTFDB/family.php?fam=$1 ato: contact: email: david.c.blackburn@gmail.com name: David Blackburn orcid: 0000-0002-1810-9886 deprecated: true description: Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource download_obo: http://aber-owl.net/media/ontologies/ATO/2/ato.obo example: '0000000' homepage: http://www.amphibanat.org keywords: - obo - ontology - taxonomic classification - taxonomy mappings: aberowl: ATO biocontext: ATO bioportal: ATO fairsharing: FAIRsharing.ayjdsm obofoundry: ato name: Amphibian taxonomy pattern: ^\d{7}$ preferred_prefix: ATO rdf_uri_format: http://purl.obolibrary.org/obo/ATO_$1 uri_format: http://purl.obolibrary.org/obo/ATO_$1 atol: contact: email: pylebail@rennes.inra.fr name: Pierre-Yves LeBail orcid: 0000-0002-8310-5195 description: 'ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production.' download_owl: http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=atol.owl example: '0002233' homepage: http://www.atol-ontology.com keywords: - agriculture - animal husbandry - life science - livestock - ontology - phenotype mappings: aberowl: ATOL agroportal: ATOL bioportal: ATOL fairsharing: FAIRsharing.wsfk5z ols: atol name: Animal Trait Ontology for Livestock pattern: ^\d{7}$ preferred_prefix: atol uri_format: http://opendata.inra.fr/ATOL/ATOL_$1 version: '2018-09-13' autdb: description: AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder. example: ADA homepage: http://autism.mindspec.org/autdb/ mappings: biocontext: AUTDB miriam: autdb n2t: autdb name: AutDB pattern: ^[A-Z]+[A-Z-0-9]{2,}$ preferred_prefix: autdb uri_format: http://autism.mindspec.org/GeneDetail/$1 authenticus: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: ID of a researcher in Authenticus website example: P-008-GD6 homepage: https://www.authenticus.pt keywords: - person - researcher mappings: wikidata: P7834 name: Authenticus ID pattern: ^[A-Z]-[0-9A-Z]{3}-[0-9A-Z]{3}$ preferred_prefix: authenticus references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://www.authenticus.pt/$1 authorea.author: description: identifier for an author on the Authorea writing service example: '229233' homepage: https://www.authorea.com mappings: wikidata: P5039 name: Authorea author ID pattern: ^[1-9]\d*$ preferred_prefix: authorea.author uri_format: https://www.authorea.com/users/$1 babelon: contact: email: nicolas.matentzoglu@gmail.com github: matentzn name: Nicolas Matentzoglu orcid: 0000-0002-7356-1779 contributor: email: nicolas.matentzoglu@gmail.com github: matentzn name: Nicolas Matentzoglu orcid: 0000-0002-7356-1779 description: Babelon is a simple standard for managing ontology translations and language profiles. Profiles are managed as TSV files, see for example https://github.com/obophenotype/hpo-translations/tree/main/babelon. The goal of Babelon as a data model and vocabulary is to capture the minimum data required to capture important metadata such as confidence and precision of translation. example: translation_language github_request_issue: 903 homepage: https://monarch-initiative.github.io/babelon/ license: MIT name: Babelon pattern: ^[a-z][a-z0-9_]+[a-z0-9]$ preferred_prefix: babelon repository: https://github.com/monarch-initiative/babelon reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://w3id.org/babelon/$1 bacdive: contact: email: lorenz.reimer@dsmz.de name: Lorenz Reimer orcid: 0000-0002-7805-0660 description: BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. example: '131392' homepage: https://bacdive.dsmz.de/ keywords: - biodiversity - life science - microbiology mappings: fairsharing: FAIRsharing.aSszvY miriam: bacdive n2t: bacdive re3data: r3d100013060 wikidata: P2946 name: BacDive pattern: ^[0-9]+$ preferred_prefix: bacdive publications: - doi: 10.1093/nar/gky879 pmc: PMC6323973 pubmed: '30256983' title: 'BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis' year: 2019 - doi: 10.1016/j.jbiotec.2017.05.004 pubmed: '28487186' title: Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase year: 2017 - doi: 10.1093/nar/gkv983 pmc: PMC4702946 pubmed: '26424852' title: BacDive--The Bacterial Diversity Metadatabase in 2016 year: 2015 - doi: 10.1093/nar/gkt1058 pmc: PMC3965005 pubmed: '24214959' title: BacDive--the Bacterial Diversity Metadatabase year: 2013 uri_format: https://bacdive.dsmz.de/strain/$1 bacmap.biog: description: BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information. example: '1050' homepage: http://bacmap.wishartlab.com/ mappings: biocontext: BACMAP.BIOG miriam: bacmap.biog n2t: bacmap.biog name: BacMap Biography pattern: ^\d+$ preferred_prefix: bacmap.biog uri_format: http://bacmap.wishartlab.com/organisms/$1 bacmap.map: description: BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information. example: AP011135 homepage: http://bacmap.wishartlab.com/ mappings: biocontext: BACMAP.MAP miriam: bacmap.map n2t: bacmap.map name: BacMap Map pattern: ^\w+(\_)?\d+(\.\d+)?$ preferred_prefix: bacmap.map uri_format: http://bacmap.wishartlab.com/maps/$1/index.html bactibase: contact: email: ismail.fliss@fsaa.ulaval.ca name: Ismail Fliss orcid: 0000-0002-8467-9414 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria. example: BAC045 homepage: http://bactibase.hammamilab.org keywords: - life science - protein mappings: fairsharing: FAIRsharing.5f5mfm prefixcommons: bactibase re3data: r3d100012755 name: Bactibase preferred_prefix: bactibase providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/bactibase:$1 publications: - doi: 10.1186/1471-2180-10-22 pmc: PMC2824694 pubmed: '20105292' title: 'BACTIBASE second release: a database and tool platform for bacteriocin characterization' year: 2010 - doi: 10.1186/1471-2180-7-89 pmc: PMC2211298 pubmed: '17941971' title: 'BACTIBASE: a new web-accessible database for bacteriocin characterization' year: 2007 uri_format: http://bactibase.hammamilab.org/$1 bams: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: 'BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions.' homepage: https://bams1.org name: Brain Architecture Knowledge Management System Neuroanatomical Ontology preferred_prefix: bams references: - https://www.frontiersin.org/articles/10.3389/neuro.11.002.2008/full bao: contact: email: sschurer@med.miami.edu name: Stephan Schurer description: The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. download_owl: http://www.bioassayontology.org/bao/bao_complete.owl example: 0002989 homepage: http://bioassayontology.org keywords: - assay - biochemistry - biological process - biomedical science - cell - chemical entity - life science - molecular entity - ontology - protein - reagent - target mappings: aberowl: BAO biocontext: BAO bioportal: BAO fairsharing: FAIRsharing.mye76w miriam: bao n2t: bao ols: bao ontobee: BAO name: BioAssay Ontology pattern: ^\d{7}$ preferred_prefix: bao publications: - doi: 10.1186/2041-1480-5-s1-s5 pmc: PMC4108877 pubmed: '25093074' title: 'Evolving BioAssay Ontology (BAO): modularization, integration and applications' year: 2014 - doi: 10.1371/journal.pone.0049198 pmc: PMC3498356 pubmed: '23155465' title: Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO) year: 2012 - doi: 10.1186/1471-2105-12-257 pmc: PMC3149580 pubmed: '21702939' title: 'BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results' year: 2011 - doi: 10:1371/journal.pone.0049198 pubmed: '10' title: Digitoxin metabolism by rat liver microsomes year: 1975 repository: https://github.com/BioAssayOntology/BAO synonyms: - BAO uri_format: http://www.bioassayontology.org/bao#BAO_$1 version: 2.8.12 bartoc: contact: email: voss@gbv.de github: nichtich name: Jakob Voß orcid: 0000-0002-7613-4123 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - email: voss@gbv.de github: nichtich name: Jakob Voß orcid: 0000-0002-7613-4123 description: 'The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries. The main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO).' example: '241' homepage: https://bartoc.org keywords: - knowledge and information systems - ontology and terminology license: PDDL 1.0 mappings: bartoc: '2054' fairsharing: FAIRsharing.f1777e wikidata: P2689 name: Basic Register of Thesauri, Ontologies & Classifications owners: - name: Verbundzentrale des GBV partnered: false ror: 048vdhs48 pattern: ^[1-9][0-9]*$ preferred_prefix: bartoc rdf_uri_format: http://bartoc.org/en/node/$1 references: - https://github.com/biopragmatics/bioregistry/issues/783 repository: https://github.com/gbv/bartoc.org uri_format: https://bartoc.org/en/node/$1 bbkg: description: Blue Brain Project's published data as knowledge graphs and Web Studios. example: topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a homepage: https://portal.bluebrain.epfl.ch mappings: miriam: bbkg name: Blue Brain Project Knowledge Graph pattern: ^[-\w]+(?:\/[-\w]+)(?:\/\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b)$ 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:$1 bcbc: description: One of the many goals of the BCBC was to develop and maintain databases of useful research resources. A total of 813 different scientific resources were generated and submitted by BCBC investigators over the 14 years it existed. Information pertaining to 495 selected resources, judged to be the most scientifically-useful, has been converted into a static catalog, as shown below. In addition, the metadata for these 495 resources have been transferred to dkNET in the form of RDF descriptors, and all genomics data have been deposited to either ArrayExpress or GEO. [from homepage] example: '4623' homepage: http://www.betacell.org/ keywords: - adenovirus - antibody - basic research - basic science - beta cell - cell line - cell regeneration - cell replacement - cell reprogramming - data set - data sharing - embryonic stem cell - embryonic stem cell line - functional genomics - gene - gene expression - genomics - mouse - mouse embryonic stem cell line - mouse strain - pancreas - pancreatic development - pancreatic islet - pancreatic islet development - pancreatic islet function - protocol mappings: integbio: nbdc00375 rrid: BCBC name: Beta Cell Biology Consortium pattern: ^\d+$ preferred_prefix: bcbc uri_format: https://scicrunch.org/resolver/RRID:BCBC_$1 bcgo: contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 deprecated: true description: An application ontology built for beta cell genomics studies. download_owl: https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl example: '0000015' homepage: https://github.com/obi-bcgo/bcgo keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: BCGO biocontext: BCGO bioportal: BCGO cellosaurus: BCGO obofoundry: bcgo ols: bcgo ontobee: BCGO name: Beta Cell Genomics Ontology pattern: ^\d{7}$ preferred_prefix: BCGO rdf_uri_format: http://purl.obolibrary.org/obo/BCGO_$1 repository: https://github.com/obi-bcgo/bcgo uri_format: https://www.ebi.ac.uk/ols4/ontologies/bcgo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F$1 version: '2015-07-08' bcio: contact: email: srodriguez142857@gmail.com name: Sergio José Rodríguez Méndez orcid: 0000-0001-7203-8399 description: The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation. download_owl: http://humanbehaviourchange.org/ontology/bcio.owl example: '040000' homepage: https://www.humanbehaviourchange.org/ keywords: - ontology mappings: aberowl: BCI-O bioportal: BCI-O ols: bcio name: The Behaviour Change Intervention Ontology pattern: ^\d{6}$ preferred_prefix: bcio uri_format: https://w3id.org/BCI-ontology#$1 version: '2024-09-17' bco: appears_in: - fovt contact: email: rlwalls2008@gmail.com github: ramonawalls name: Ramona Walls orcid: 0000-0001-8815-0078 description: An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. download_owl: http://purl.obolibrary.org/obo/bco.owl example: 0000081 homepage: https://github.com/BiodiversityOntologies/bco keywords: - biodiversity - biological sample - biological sample annotation - ecology - environmental material - metagenomics - obo - ontology - taxonomic classification - taxonomy license: CC0-1.0 mappings: aberowl: BCO agroportal: BCO biocontext: BCO bioportal: BCO ecoportal: BCO fairsharing: FAIRsharing.8ktkqy obofoundry: bco ols: bco ontobee: BCO name: Biological Collections Ontology pattern: ^\d{7}$ preferred_prefix: BCO publications: - doi: 10.1371/journal.pone.0089606 pmc: PMC3940615 pubmed: '24595056' title: 'Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies' year: 2014 rdf_uri_format: http://purl.obolibrary.org/obo/BCO_$1 repository: https://github.com/BiodiversityOntologies/bco uri_format: http://purl.obolibrary.org/obo/BCO_$1 version: '2021-11-14' bcrc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Cell line collections (Providers) example: '60316' homepage: https://catalog.bcrc.firdi.org.tw keywords: - cell lines mappings: cellosaurus: BCRC name: BCRC Strain Collection Catalog pattern: ^\d+$ preferred_prefix: bcrc uri_format: https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1 bcrj: description: Cell line collections (Providers) example: 0278 homepage: https://bcrj.org.br/pesquisa/ mappings: cellosaurus: BCRJ name: Banco de Celulas do Rio de Janeiro pattern: ^\d{4}$ preferred_prefix: bcrj uri_format: https://bcrj.org.br/pesquisa/?search=$1 bdgp.est: description: The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI). example: EY223054.1 has_canonical: dbest homepage: https://www.ncbi.nlm.nih.gov/dbEST/index.html keywords: - genome mappings: biocontext: BDGP.EST miriam: bdgp.est n2t: bdgp.est ncbi: BDGP_EST prefixcommons: flybase.est name: Berkeley Drosophila Genome Project EST database pattern: ^\w+(\.)?(\d+)?$ preferred_prefix: bdgp.est providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/flybase.est:$1 uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1 bdgp.insertion: contact: email: spradling@ciwemb.edu name: Allan Spradling orcid: 0000-0002-5251-1801 description: BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element. example: KG09531 homepage: http://flypush.imgen.bcm.tmc.edu/pscreen/ keywords: - gene - sequence mappings: biocontext: BDGP.INSERTION miriam: bdgp.insertion n2t: bdgp.insertion prefixcommons: bdgp name: BDGP insertion DB pattern: ^\w+$ preferred_prefix: bdgp.insertion providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/bdgp:$1 publications: - doi: 10.1534/genetics.104.026427 pmc: PMC1470905 pubmed: '15238527' title: 'The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes' year: 2004 uri_format: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1 bdsc: description: The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research. example: '33607' homepage: https://bdsc.indiana.edu/about/mission.html keywords: - database - deficiency - deletion - disease model - duplication - faseb list - fly - gene - genetic - genetic analysis - genetic construct - germline - human disease model - insertion - invertebrate - mutation - protein trap - scientist - sequenced strain - somatic - stock - transposon - transposon insertion mappings: miriam: bdsc n2t: bdsc rrid: BDSC name: Bloomington Drosophila Stock Center pattern: ^\d+$ preferred_prefix: bdsc uri_format: https://bdsc.indiana.edu/stocks/$1 beetlebase: contact: email: sjbrown@ksu.edu name: Susan J. Brown orcid: 0000-0002-7984-0445 description: BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications. example: TC010103 homepage: http://beetlebase.org/ keywords: - computational biology - genome - life science mappings: biocontext: BEETLEBASE fairsharing: FAIRsharing.h5f091 integbio: nbdc01820 miriam: beetlebase n2t: beetlebase ncbi: BEETLEBASE prefixcommons: beetlebase re3data: r3d100010921 name: Tribolium Genome Database -- Insertion pattern: ^TC\d+$ preferred_prefix: beetlebase providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/beetlebase:$1 publications: - doi: 10.1093/nar/gkp807 pmc: PMC2808946 pubmed: '19820115' title: 'BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum' year: 2009 uri_format: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1 begdb: contact: email: pavel.hobza@uochb.cas.cz name: Pavel Hobza orcid: 0000-0001-5292-6719 description: The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods. example: '4214' homepage: http://www.begdb.com keywords: - life science mappings: biocontext: BEGDB fairsharing: FAIRsharing.nbe4fq miriam: begdb n2t: begdb re3data: r3d100011166 name: Benchmark Energy & Geometry Database pattern: ^[0-9]+$ preferred_prefix: begdb publications: - doi: 10.1135/cccc20081261 title: 'Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples' year: 2008 uri_format: http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1 beiresources: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Cell line collections (Providers) example: MRA-253 homepage: https://www.beiresources.org keywords: - cell lines mappings: cellosaurus: BEI_Resources name: BEI Resources preferred_prefix: beiresources synonyms: - BEI_Resources uri_format: https://www.beiresources.org/Catalog/cellBanks/$1.aspx bel: comment: INDRA uses bel as a catch-all for scomp/sfam contact: email: support@bel.bio name: William Hayes orcid: 0000-0003-0728-781X contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents. example: 9-1-1 Complex homepage: https://biological-expression-language.github.io/ keywords: - biology mappings: fairsharing: FAIRsharing.dp0jvd name: Biological Expression Language preferred_prefix: bel bfo: appears_in: - ado - agro - aism - cdno - colao - duo - ecocore - epio - foodon - fovt - hso - lepao - mco - ons - pcl - pco - psdo - rbo - uberon - xpo - zp contact: email: phismith@buffalo.edu github: phismith name: Barry Smith orcid: 0000-0003-1384-116X description: The upper level ontology upon which OBO Foundry ontologies are built. download_obo: http://purl.obolibrary.org/obo/bfo.obo download_owl: http://purl.obolibrary.org/obo/bfo.owl example: '0000001' homepage: http://ifomis.org/bfo/ keywords: - data retrieval - obo - ontology - subject agnostic license: CC-BY-4.0 logo: https://avatars2.githubusercontent.com/u/12972134?v=3&s=200 mappings: aberowl: BFO agroportal: BFO biocontext: BFO bioportal: BFO fairsharing: FAIRsharing.wcpd6f go: BFO obofoundry: bfo ols: bfo ontobee: BFO name: Basic Formal Ontology pattern: ^\d{7}$ preferred_prefix: BFO rdf_uri_format: http://purl.obolibrary.org/obo/BFO_$1 repository: https://github.com/BFO-ontology/BFO uri_format: http://purl.obolibrary.org/obo/BFO_$1 version: '2019-08-26' bgee.family: contributor_extras: - github: smoretti name: Sébastien Moretti orcid: 0000-0003-3947-488X deprecated: true description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species. example: ENSFM00500000270089 homepage: http://bgee.unil.ch/bgee/bgee mappings: biocontext: BGEE.FAMILY miriam: bgee.family n2t: bgee.family name: Bgee family pattern: ^(ENSFM|ENSGTV:)\d+$ preferred_prefix: bgee.family references: - https://github.com/biopragmatics/bioregistry/issues/889 uri_format: http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1 bgee.gene: contact: email: sebastien.moretti@sib.swiss github: smoretti name: Sebastien Moretti orcid: 0000-0003-3947-488X contributor_extras: - email: sebastien.moretti@sib.swiss github: smoretti name: Sebastien Moretti orcid: 0000-0003-3947-488X description: Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee. example: FBgn0000015 homepage: https://www.bgee.org keywords: - gene expression mappings: biocontext: BGEE.GENE miriam: bgee.gene n2t: bgee.gene prefixcommons: bgee name: Bgee gene pattern: ^[A-Za-z0-9]+$ preferred_prefix: bgee.gene providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/bgee:$1 references: - https://github.com/biopragmatics/bioregistry/issues/890 uri_format: https://www.bgee.org/gene/$1 bgee.organ: contributor_extras: - github: smoretti name: Sébastien Moretti orcid: 0000-0003-3947-488X deprecated: true description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures. example: EHDAA:2185 homepage: http://bgee.unil.ch/bgee/bgee mappings: biocontext: BGEE.ORGAN miriam: bgee.organ n2t: bgee.organ name: Bgee organ pattern: ^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\:\d+$ preferred_prefix: bgee.organ references: - https://github.com/biopragmatics/bioregistry/issues/889 uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1 bgee.stage: contributor_extras: - github: smoretti name: Sébastien Moretti orcid: 0000-0003-3947-488X deprecated: true description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages. example: HsapDO:0000004 homepage: http://bgee.unil.ch/bgee/bgee mappings: biocontext: BGEE.STAGE miriam: bgee.stage n2t: bgee.stage name: Bgee stage pattern: ^(FBvd|XtroDO|HsapDO|MmusDO)\:\d+$ preferred_prefix: bgee.stage references: - https://github.com/biopragmatics/bioregistry/issues/889 uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1 bibo: contact: email: fred@fgiasson.com github: fgiasson name: Frédérick Giasson contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Bibliographic Ontology Specification provides main concepts and properties for describing citations and bibliographic references (i.e. quotes, books, articles, etc) on the Semantic Web. example: authorList homepage: https://bibliontology.com/ keywords: - bibliometrics - catalogs mappings: lov: bibo zazuko: bibo name: The Bibliographic Ontology preferred_prefix: bibo uri_format: http://purl.org/ontology/bibo/$1 bido: contact: email: silvio.peroni@unibo.it github: essepuntato name: Silvio Peroni orcid: 0000-0003-0530-4305 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF. example: CategorialBibliometricData homepage: http://www.sparontologies.net/ontologies/bido keywords: - bibliography - citation - data model - report - subject agnostic mappings: fairsharing: FAIRsharing.d7f0a9 name: Bibliometric Data Ontology preferred_prefix: BiDO repository: https://github.com/sparontologies/bido twitter: sparontologies uri_format: http://purl.org/spar/bido/$1 bigg.compartment: description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments. example: c homepage: http://bigg.ucsd.edu/compartments/ license: http://bigg.ucsd.edu/license#license mappings: biocontext: BIGG.COMPARTMENT miriam: bigg.compartment n2t: bigg.compartment name: BiGG Compartment part_of: bigg pattern: ^c|cm|cx|e|f|g|h|i|im|l|m|mm|n|p|r|s|u|um|v|w|x|y$ 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 published genome-scale metabolic networks into a single database with a set of standardized 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 metabolites. example: 12dgr161 example_extras: - 12dgr161[c] homepage: http://bigg.ucsd.edu/universal/metabolites license: http://bigg.ucsd.edu/license#license mappings: biocontext: BIGG.METABOLITE miriam: bigg.metabolite n2t: bigg.metabolite name: BiGG Metabolite pattern: ^[a-z_A-Z0-9]+(\[[c|cm|cx|e|f|g|h|i|im|l|m|mm|n|p|r|s|u|um|v|w|x|y]\])?$ preferred_prefix: bigg.metabolite uri_format: http://bigg.ucsd.edu/models/universal/metabolites/$1 bigg.model: description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models. example: iECABU_c1320 homepage: http://bigg.ucsd.edu/models license: http://bigg.ucsd.edu/license#license mappings: biocontext: BIGG.MODEL miriam: bigg.model n2t: bigg.model name: BiGG Model pattern: ^[a-z_A-Z0-9]+$ preferred_prefix: bigg.model uri_format: http://bigg.ucsd.edu/models/$1 bigg.reaction: description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions. example: 13GS homepage: http://bigg.ucsd.edu/universal/reactions license: http://bigg.ucsd.edu/license#license mappings: biocontext: BIGG.REACTION miriam: bigg.reaction n2t: bigg.reaction name: BiGG Reaction pattern: ^[a-z_A-Z0-9]+$ preferred_prefix: bigg.reaction uri_format: http://bigg.ucsd.edu/models/universal/reactions/$1 bila: contact: email: henrich@embl.de github: ThorstenHen name: Thorsten Henrich orcid: 0000-0002-1548-3290 deprecated: true description: This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource. download_owl: http://purl.obolibrary.org/obo/bila.owl example: '0000000' homepage: http://4dx.embl.de/4DXpress keywords: - anatomy - gene expression - obo - ontology mappings: biocontext: BILA fairsharing: FAIRsharing.eqgjeq obofoundry: bila ols: bila prefixcommons: 4dxpress name: Bilateria anatomy pattern: ^\d{7}$ preferred_prefix: BILA providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/4dxpress:$1 publications: - doi: 10.1093/nar/gkm797 pmc: PMC2238840 pubmed: '17916571' title: '4DXpress: a database for cross-species expression pattern comparisons' year: 2007 rdf_uri_format: http://purl.obolibrary.org/obo/BILA_$1 uri_format: http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID=$1 version: '2019-06-12' bind: deprecated: true description: Accession number of an entry from the BIND database. example: '98346' homepage: http://bind.ca keywords: - interaction - pathway - small molecule mappings: biocontext: BIND edam: '1129' pathguide: '1' prefixcommons: bind name: BIND accession number preferred_prefix: bind providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/bind:$1 publications: - doi: 10.1093/nar/gkg056 pmc: PMC165503 pubmed: '12519993' title: 'BIND: the Biomolecular Interaction Network Database' year: 2003 - doi: 10.1093/bioinformatics/16.5.465 pubmed: '10871269' title: BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways year: 2000 uri_format: http://www.bind.ca/Action?identifier=bindid&idsearch=$1 bindingdb: contact: email: mgilson@health.ucsd.edu name: Michael K. Gilson orcid: 0000-0002-3375-1738 description: BindingDB is the first public database of protein-small molecule affinity data. example: e999 homepage: https://www.bindingdb.org keywords: - chemistry - computational chemistry - drug discovery - interaction - life science - medicinal chemistry - protein mappings: biocontext: BINDINGDB fairsharing: FAIRsharing.3b36hk miriam: bindingdb n2t: bindingdb pathguide: '50' prefixcommons: bindingdb re3data: r3d100012074 uniprot: DB-0127 name: BindingDB pattern: ^\w\d+$ preferred_prefix: bindingdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/bindingdb:$1 publications: - doi: 10.1093/nar/gkae1075 pubmed: '39574417' title: 'BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data' year: 2024 - doi: 10.1093/nar/gkv1072 pmc: PMC4702793 pubmed: '26481362' title: 'BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology' year: 2015 - doi: 10.1093/nar/gkl999 pmc: PMC1751547 pubmed: '17145705' title: 'BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities' year: 2006 uri_format: http://www.bindingdb.org/compact/$1 biocarta.pathway: description: BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps. example: h_aktPathway homepage: https://www.biocarta.com/ mappings: biocontext: BIOCARTA.PATHWAY miriam: biocarta.pathway n2t: biocarta.pathway name: BioCarta Pathway pattern: ^([hm]\_)?\w+Pathway$ preferred_prefix: biocarta.pathway uri_format: https://cgap.nci.nih.gov/Pathways/BioCarta/$1 biocatalogue.service: contact: email: carole.goble@manchester.ac.uk github: CaroleGoble name: Carole Goble orcid: 0000-0003-1219-2137 description: The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all. example: '614' homepage: https://www.biocatalogue.org/ keywords: - registry mappings: biocontext: BIOCATALOGUE.SERVICE miriam: biocatalogue.service n2t: biocatalogue.service prefixcommons: biocatalogue name: BioCatalogue Service pattern: ^\d+$ preferred_prefix: biocatalogue.service providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/biocatalogue:$1 publications: - doi: 10.1093/nar/gkq394 pmc: PMC2896129 pubmed: '20484378' title: 'BioCatalogue: a universal catalogue of web services for the life sciences' year: 2010 uri_format: https://www.biocatalogue.org/services/$1 biocompute: contact: email: mazumder@gwu.edu name: Raja Mazumder orcid: 0000-0001-8823-9945 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: BioCompute is shorthand for the IEEE 2791-2020 standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to facilitate communication. This pipeline documentation approach has been adopted by a few FDA centers. The goal is to ease the communication burdens between research centers, organizations, and industries. This web portal allows users to build a BioCompute Objects through the interface in a human and machine readable format. example: '000001' homepage: https://biocomputeobject.org name: Biocompute Object pattern: ^\d+$ preferred_prefix: biocompute publications: - pubmed: '27974626' title: BioCompute objects - a step towards evaluation and validation of bio-medical scientific computations year: 2017 repository: https://github.com/biocompute-objects/BCO_Specification uri_format: https://biocomputeobject.org/BCO_$1 biocyc: contact: email: pkarp@ai.sri.com github: pkarp111 name: Peter D. Karp orcid: 0000-0002-5876-6418 description: BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. example: ECOLI:CYT-D-UBIOX-CPLX homepage: http://biocyc.org keywords: - genome - pathway - sequence mappings: biocontext: BIOCYC edam: '2104' go: BioCyc integbio: nbdc00252 miriam: biocyc n2t: biocyc pathguide: '8' prefixcommons: biocyc uniprot: DB-0005 name: BioCyc collection of metabolic pathway databases pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$ preferred_prefix: biocyc providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/biocyc:$1 publications: - doi: 10.1093/bib/bbx085 pubmed: '29447345' - doi: 10.1093/nar/gkv1164 pmc: PMC4702838 pubmed: '26527732' title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases year: 2015 - doi: 10.1093/nar/gki892 pmc: PMC1266070 pubmed: '16246909' title: Expansion of the BioCyc collection of pathway/genome databases to 160 genomes year: 2005 uri_format: http://biocyc.org/getid?id=$1 biodeep: banana: BioDeep banana_peel: _ description: 'The BioDeep database is a comprehensive database of metabolite information in living organisms: by aggregating metabolite information from multiple public databases and large-scale natural language text mining work, we have built a large scale knowledge network for biological knowledge interpretation. By using the BioDeep database, it is possible to query such large scale metabolic knowledge network.' example: '00000000001' homepage: https://en.panomix.com/ mappings: miriam: biodeep name: BioDeep Database pattern: ^\d{11}$ preferred_prefix: biodeep uri_format: https://query.biodeep.cn/metabolite/$1 biodolphin: contact: email: andrew.mcshan@chemistry.gatech.edu name: Andrew C. McShan orcid: 0000-0002-3212-9867 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for lipid-protein interactions, including details about protein functions, protein families, lipid classifications, lipid-protein binding affinities, membrane association type, and atomic structures. example: BD1a05-A-A-IPM1 github_request_issue: 1327 homepage: https://biodolphin.chemistry.gatech.edu name: BioDolphin pattern: ^BD\d[a-zA-Z0-9]+-[A-Za-z]-[A-Za-z]-[A-Za-z0-9]+$ preferred_prefix: biodolphin publications: - doi: 10.1038/s42004-024-01384-z pmc: PMC11618342 pubmed: '39633021' title: BioDolphin as a comprehensive database of lipid-protein binding interactions year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://biodolphin.chemistry.gatech.edu/detail/$1 biofactoid: contact: email: jeffvin.wong@utoronto.ca github: jvwong name: Jeffrey Wong orcid: 0000-0002-8912-5699 contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: Biofactoid is a web-based system that empowers authors to capture and share machine-readable summaries of molecular-level interactions described in their publications. example: fdb8a927-45c3-48b7-9743-cbb5e16837fa github_request_issue: 700 homepage: https://biofactoid.org/ keywords: - biocuration - database - relationships license: CC0-1.0 mappings: miriam: biofactoid name: Biofactoid pattern: ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$ preferred_prefix: biofactoid publications: - doi: 10.7554/elife.68292 pmc: PMC8683078 pubmed: '34860157' title: Author-sourced capture of pathway knowledge in computable form using Biofactoid year: 2021 repository: https://github.com/PathwayCommons/factoid reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://biofactoid.org/document/$1 biogrid: contact: email: md.tyers@umontreal.ca name: Mike Tyers orcid: 0000-0002-9713-9994 description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. example: '31623' homepage: http://thebiogrid.org/ keywords: - biochemistry - bioinformatics - chemical biology - cheminformatics - gene - interaction - life science - protein - proteomics - systems biology mappings: biocontext: BIOGRID fairsharing: FAIRsharing.9d5f5r miriam: biogrid n2t: biogrid pathguide: '7' prefixcommons: biogrid re3data: r3d100010350 uniprot: DB-0184 name: BioGRID pattern: ^\d+$ preferred_prefix: biogrid providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/biogrid:$1 publications: - doi: 10.1002/pro.3978 pmc: PMC7737760 pubmed: '33070389' title: 'The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions' year: 2020 - doi: 10.1093/nar/gky1079 pmc: PMC6324058 pubmed: '30476227' title: 'The BioGRID interaction database: 2019 update' year: 2019 - doi: 10.1093/nar/gkq1116 pmc: PMC3013707 pubmed: '21071413' title: 'The BioGRID Interaction Database: 2011 update' year: 2010 - doi: 10.1093/nar/gkj109 pmc: PMC1347471 pubmed: '16381927' title: 'BioGRID: a general repository for interaction datasets' year: 2006 - doi: 10.1186/gb-2003-4-3-r23 pmc: PMC153463 pubmed: '12620108' title: 'The GRID: the General Repository for Interaction Datasets' year: 2003 repository: https://github.com/BioGRID twitter: biogrid uri_format: http://thebiogrid.org/$1 biogrid.interaction: contact: email: md.tyers@umontreal.ca name: Mike Tyers orcid: 0000-0002-9713-9994 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. example: '2649230' homepage: https://thebiogrid.org/ mappings: edam: '2628' name: BioGRID Interactions part_of: biogrid pattern: ^\d+$ preferred_prefix: biogrid.interaction twitter: biogrid uri_format: https://thebiogrid.org/interaction/$1 biokc: description: BioKC (Biological Knowledge Curation), is a web-based collaborative platform for the curation and annotation of biomedical knowledge following the standard data model from Systems Biology Markup Language (SBML). example: bkc640 homepage: https://wwwen.uni.lu/lcsb mappings: miriam: biokc name: BioKC pattern: ^bkc[0-9]*$ preferred_prefix: biokc uri_format: https://biokb.lcsb.uni.lu/fact/$1 biolegend: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: BioLegend is a life sciences supply vendor. example: '3403' homepage: https://www.biolegend.com keywords: - antibodies - assays - life sciences - reagents - vendor name: BioLegend pattern: ^\d+$ preferred_prefix: biolegend uri_format: https://www.biolegend.com/Default.aspx?ID=6664&productid=$1 biolink: contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations. download_owl: http://aber-owl.net/media/ontologies/BIOLINK/69/biolink.owl example: Gene homepage: https://biolink.github.io/biolink-model/ keywords: - biomedical science - functional genomics - medical biotechnology - medical informatics - ontology - translational medicine mappings: aberowl: BIOLINK biolink: biolink bioportal: BIOLINK fairsharing: FAIRsharing.ad9d85 miriam: biolink name: Biolink Model pattern: ^\S+$ preferred_prefix: biolink repository: https://github.com/biolink/biolink-model uri_format: https://w3id.org/biolink/vocab/$1 biomagresbank: description: A repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids. example: '10046' homepage: http://www.bmrb.wisc.edu/ keywords: - protein mappings: prefixcommons: biomagresbank name: BioMagResBank preferred_prefix: biomagresbank providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/biomagresbank:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId=$1 biominder: description: Database of the dielectric properties of biological tissues. example: aef4c195-9cf9-46db-a12a-7cfd1ff3eec3 homepage: https://datalab.rwth-aachen.de/MINDER mappings: biocontext: BIOMINDER miriam: biominder n2t: biominder name: Bio-MINDER Tissue Database pattern: ^[a-z0-9\-]+$ preferred_prefix: biominder uri_format: https://datalab.rwth-aachen.de/MINDER/resource/$1 biomodels.db: contact: email: mhucka@caltech.edu github: mhucka name: Michael Hucka orcid: 0000-0001-9105-5960 description: BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. example: BIOMD0000000048 homepage: https://www.ebi.ac.uk/biomodels/ keywords: - model mappings: biocontext: BIOMODELS.DB go: BIOMD miriam: biomodels.db n2t: biomodels.db prefixcommons: biomodels name: BioModels Database pattern: ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ preferred_prefix: biomodels.db providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/biomodels:$1 - code: omicsdi description: BioModels through OmicsDI homepage: https://www.omicsdi.org/ name: BioModels through OmicsDI uri_format: https://www.omicsdi.org/dataset/biomodels/$1 publications: - doi: 10.1093/nar/gkj092 pmc: PMC1347454 pubmed: '16381960' title: 'BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems' year: 2006 synonyms: - BIOMD uri_format: https://www.ebi.ac.uk/biomodels/$1 biomodels.kisao: banana: KISAO banana_peel: _ contact: email: jonrkarr@gmail.com github: jonrkarr name: Jonathan Karr orcid: 0000-0002-2605-5080 description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment. download_owl: http://purl.obolibrary.org/obo/kisao.owl example: '0000057' homepage: https://github.com/SED-ML/KiSAO keywords: - algorithm - bioinformatics - computer science - kinetic model - modeling and simulation - obo - ontology license: Artistic License 2.0 mappings: aberowl: KISAO biocontext: KISAO bioportal: KISAO fairsharing: FAIRsharing.jcg19w miriam: biomodels.kisao n2t: biomodels.kisao obofoundry: kisao ols: kisao ontobee: KISAO prefixcommons: kisao name: Kinetic Simulation Algorithm Ontology namespace_in_lui: true pattern: ^\d+$ preferred_prefix: biomodels.kisao providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/kisao:$1 - code: legacy description: This is the URI scheme used in the ontology but it does not resolve. homepage: https://www.biomodels.net name: Legacy Biomodels URL uri_format: https://www.biomodels.net/kisao/KISAO#KISAO_$1 publications: - doi: 10.1038/msb.2011.77 pmc: PMC3261705 pubmed: '22027554' title: Controlled vocabularies and semantics in systems biology year: 2011 rdf_uri_format: http://purl.obolibrary.org/obo/KISAO_$1 repository: https://github.com/SED-ML/KiSAO synonyms: - biomodels.kisao - kisao uri_format: http://purl.obolibrary.org/obo/KISAO_$1 version: '2.34' biomodels.teddy: banana: TEDDY banana_peel: _ contact: email: biomodels-net-support@lists.sf.net name: BioModels.net team description: The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. download_owl: http://svn.code.sf.net/p/teddyontology/code/teddy/tags/current/teddy-inferred.owl example: '0000066' homepage: http://teddyontology.sourceforge.net/ keywords: - modeling and simulation - neurophysiology - ontology - synthetic biology - systems biology mappings: aberowl: TEDDY biocontext: BIOMODELS.TEDDY bioportal: TEDDY fairsharing: FAIRsharing.w9jvbt miriam: biomodels.teddy n2t: biomodels.teddy ols: teddy prefixcommons: teddy name: Terminology for Description of Dynamics pattern: ^\d+$ preferred_prefix: biomodels.teddy providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/teddy:$1 publications: - doi: 10.1038/msb.2011.77 pmc: PMC3261705 pubmed: '22027554' title: Controlled vocabularies and semantics in systems biology year: 2011 repository: https://github.com/combine-org/combine-specifications/blob/main/specifications/teddy.md synonyms: - teddy uri_format: https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1 version: '2014-04-24' biomodels.vocabulary: description: Vocabulary used in the RDF representation of SBML models. example: rateRule homepage: http://biomodels.net/rdf/vocabulary.rdf mappings: biocontext: BIOMODELS.VOCABULARY miriam: biomodels.vocabulary n2t: biomodels.vocabulary name: SBML RDF Vocabulary pattern: ^[A-Za-z]+$ preferred_prefix: biomodels.vocabulary uri_format: http://biomodels.net/rdf/vocabulary.rdf#$1 bionumbers: description: BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data. example: '104674' homepage: https://bionumbers.hms.harvard.edu mappings: biocontext: BIONUMBERS edam: '2660' miriam: bionumbers n2t: bionumbers prefixcommons: bionumbers name: BioNumbers pattern: ^\d+$ preferred_prefix: bionumbers providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/bionumbers:$1 uri_format: https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1 biopixie: comment: This resource doesn't exist on the web anymore deprecated: true description: bioPIXIE is a novel system for biological data integration and visualization. It allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate. example: '12' homepage: http://pixie.princeton.edu/pixie/ keywords: - gene - interaction mappings: prefixcommons: biopixie name: biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology preferred_prefix: biopixie providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/biopixie:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://avis.princeton.edu/pixie/viewgraph.php?graphID=$1 bioportal: contact: email: jgraybeal@stanford.edu name: John Graybeal orcid: 0000-0001-6875-5360 description: BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. example: '1046' example_extras: - FBBi - SEPIO - pseudo homepage: http://bioportal.bioontology.org/ keywords: - life science - ontology - ontology and terminology mappings: biocontext: BIOPORTAL fairsharing: FAIRsharing.4m97ah integbio: nbdc02144 miriam: bioportal n2t: bioportal prefixcommons: bioportal re3data: r3d100012344 name: BioPortal pattern: ^(\d+)|(\w+)$ preferred_prefix: bioportal providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/bioportal:$1 publications: - doi: 10.1093/nar/gkr469 pmc: PMC3125807 pubmed: '21672956' title: 'BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications' year: 2011 - doi: 10.1093/nar/gkp440 pmc: PMC2703982 pubmed: '19483092' title: 'BioPortal: ontologies and integrated data resources at the click of a mouse' year: 2009 repository: http://github.com/ncbo twitter: bioontology uri_format: http://bioportal.bioontology.org/ontologies/$1 bioproject: contact: email: mizrachi@ncbi.nlm.nih.gov name: Ilene Karsch-Mizrachi orcid: 0000-0002-0289-7101 description: BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories. example: PRJDB3 homepage: https://www.ncbi.nlm.nih.gov/bioproject keywords: - life science mappings: biocontext: BIOPROJECT fairsharing: FAIRsharing.aqhv1y miriam: bioproject n2t: bioproject re3data: r3d100013330 togoid: Bioproject name: BioProject pattern: ^PRJ[DEN][A-Z]\d+$ preferred_prefix: bioproject publications: - doi: 10.1093/nar/gkr1163 pmc: PMC3245069 pubmed: '22139929' title: 'BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata' year: 2011 uri_format: https://www.ncbi.nlm.nih.gov/bioproject/?term=$1 bioregistry: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database. example: bioregistry homepage: https://bioregistry.io keywords: - bioinformatics - cheminformatics - computational biology - computational chemistry - life science - ontology and terminology mappings: bartoc: '18951' fairsharing: FAIRsharing.250a8c mastodon: bioregistry@fosstodon.org name: Bioregistry pattern: ^[A-Za-z_][A-Za-z0-9\.\-_]*$ preferred_prefix: bioregistry publications: - doi: 10.1101/2022.07.08.499378 title: Unifying the Identification of Biomedical Entities with the Bioregistry year: 2022 repository: https://github.com/biopragmatics/bioregistry twitter: bioregistry uri_format: https://bioregistry.io/registry/$1 bioregistry.collection: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Manually curated collections of resources stored in the bioregistry example: '0000001' homepage: https://bioregistry.io/collection keywords: - registry name: Bioregistry Collections pattern: ^\d{7}$ preferred_prefix: bioregistry.collection uri_format: https://bioregistry.io/collection/$1 bioregistry.registry: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Bioregistry's meta-registry example: miriam homepage: https://bioregistry.io/metaregistry/ keywords: - data integration - data science - metaregistry - registry name: Bioregistry Metaregistry preferred_prefix: bioregistry.registry uri_format: https://bioregistry.io/metaregistry/$1 bioregistry.schema: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Schema for the export of the Bioregistry as RDF example: '0000001' homepage: https://bioregistry.io/schema keywords: - registry name: Bioregistry Schema pattern: ^\d{7}$ preferred_prefix: bioregistry.schema uri_format: https://bioregistry.io/schema/#$1 biorxiv: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The bioRxiv is a preprint server for biology example: 2022.07.08.499378 example_extras: - 000091 - 000091v1 - 2022.07.08.499378v2 homepage: https://biorxiv.org keywords: - preprints - publishing mappings: go: bioRxiv wikidata: P3951 name: bioRxiv pattern: ^(\d{4}\.\d{2}\.\d{2}\.)?\d{6,8}(v\d{1,3})?$ preferred_prefix: biorxiv providers: - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/biorxiv/$1 rdf_uri_format: http://dx.doi.org/10.1101/$1 uri_format: https://www.biorxiv.org/content/10.1101/$1 biosample: contact: email: mizrachi@ncbi.nlm.nih.gov name: Ilene Karsch-Mizrachi orcid: 0000-0002-0289-7101 description: The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation. example: SAMEA2397676 homepage: https://www.ebi.ac.uk/biosamples/ keywords: - biology - biomaterial - cell - cell line - dna - gold standard - rna - stem cell mappings: biocontext: BIOSAMPLE cellosaurus: BioSamples fairsharing: FAIRsharing.qr6pqk miriam: biosample n2t: biosample re3data: r3d100012828 rrid: SAMN togoid: Biosample name: BioSample pattern: ^SAM[NED](\w)?\d+$ preferred_prefix: biosample providers: - code: ddbj description: BioSample at DNA Data Bank of Japan homepage: http://trace.ddbj.nig.ac.jp/biosample/ name: BioSample at DNA Data Bank of Japan uri_format: http://trace.ddbj.nig.ac.jp/BSSearch/biosample?acc=$1 - code: ncbi description: BioSample at NCBI homepage: http://www.ncbi.nlm.nih.gov/biosample name: BioSample at NCBI uri_format: http://www.ncbi.nlm.nih.gov/biosample?term=$1 publications: - doi: 10.1093/nar/gkr1163 pmc: PMC3245069 pubmed: '22139929' title: 'BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata' year: 2011 synonyms: - biosamples uri_format: https://www.ebi.ac.uk/biosamples/sample/$1 bioschemas: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. It does this by encouraging people in the life sciences to use Schema.org markup in their websites so that they are indexable by search engines and other services. Bioschemas encourages the consistent use of markup to ease the consumption of the contained markup across many sites. This structured information then makes it easier to discover, collate, and analyse distributed resources. [from BioSchemas.org] example: Dataset homepage: https://bioschemas.org mappings: biolink: bioschemas name: BioSchemas preferred_prefix: bioschemas repository: https://github.com/BioSchemas/specifications synonyms: - bioschema twitter: bioschemas uri_format: https://bioschemas.org/profiles/$1 biosimulations: description: BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools. example: Yeast-cell-cycle-Irons-J-Theor-Biol-2009 homepage: https://icahn.mssm.edu/ mappings: miriam: biosimulations re3data: r3d100013361 name: biosimulations pattern: ^[a-zA-Z0-9_-]{3,}$ preferred_prefix: biosimulations uri_format: https://biosimulations.org/projects/$1 biosimulators: contact: email: karr@mssm.edu name: Jonathan Karr orcid: 0000-0002-2605-5080 description: BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML). example: vcell homepage: https://biosimulators.org/ keywords: - computational biology - systems biology mappings: fairsharing: FAIRsharing.pwEima miriam: biosimulators re3data: r3d100013432 name: BioSimulators pattern: ^[a-zA-Z0-9-_]+$ preferred_prefix: biosimulators repository: https://github.com/biosimulators/Biosimulators/issues/new/choose uri_format: https://biosimulators.org/simulators/$1 biostudies: contact: email: ugis@ebi.ac.uk name: Ugis Sarkans orcid: 0000-0001-9227-8488 description: The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication. example: S-EPMC6266652 homepage: https://www.ebi.ac.uk/biostudies/ keywords: - biomedical science - life science mappings: fairsharing: FAIRsharing.mtjvme integbio: nbdc02279 miriam: biostudies n2t: biostudies re3data: r3d100012627 name: BioStudies database pattern: ^S-[A-Z]{4}[\-\_A-Z\d]+$ preferred_prefix: biostudies publications: - doi: 10.1093/nar/gkx965 pmc: PMC5753238 pubmed: '29069414' title: The BioStudies database-one stop shop for all data supporting a life sciences study year: 2018 - doi: 10.15252/msb.20156658 pmc: PMC4704487 pubmed: '26700850' title: The BioStudies database year: 2015 uri_format: https://www.ebi.ac.uk/biostudies/studies/$1 biosystems: contact: email: lewis.geer@nih.gov name: Aron Marchler-Bauer orcid: 0000-0003-1516-0712 contributor_extras: - email: egon.willighagen@gmail.com github: egonw name: Egon Willighagen orcid: 0000-0001-7542-0286 description: The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. example: '001' homepage: https://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html keywords: - biology - molecules - pathways - systems biology mappings: biocontext: BIOSYSTEMS fairsharing: FAIRsharing.w2eeqr integbio: nbdc00379 miriam: biosystems n2t: biosystems prefixcommons: biosystems re3data: r3d100011033 name: BioSystems pattern: ^\d+$ preferred_prefix: biosystems providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/biosystems:$1 publications: - doi: 10.1093/nar/gkp858 pmc: PMC2808896 pubmed: '19854944' title: The NCBI BioSystems database year: 2009 uri_format: https://www.ncbi.nlm.nih.gov/biosystems/$1 biotools: contact: email: haiiu@dtu.dk github: hansioan name: Hans Ienasescu orcid: 0000-0001-9727-2544 description: BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research. example: bioregistry homepage: https://bio.tools/ keywords: - bioinformatics - biology - biomedical science mappings: biocontext: BIOTOOLS fairsharing: FAIRsharing.63520c miriam: biotools n2t: biotools re3data: r3d100013668 name: BioTools pattern: ^[-A-Za-z0-9\_]*$ preferred_prefix: biotools publications: - doi: 10.1093/nar/gkv1116 pmc: PMC4702812 pubmed: '26538599' title: 'Tools and data services registry: a community effort to document bioinformatics resources' year: 2015 repository: http://github.com/bio-tools/biotoolsregistry/ uri_format: https://bio.tools/$1 biotop: contact: email: stefan.schulz@medunigraz.at github: steschu63 name: Stefan Schulz orcid: 0000-0001-7222-3287 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network download_owl: https://raw.githubusercontent.com/BioTopOntology/biotop/master/biotop.owl example: attachedTo github_request_issue: 1312 homepage: http://purl.org/biotop keywords: - biology - ontology license: CC-BY-3.0 mappings: lov: biotop name: BioTop preferred_prefix: biotop publications: - doi: 10.1093/bioinformatics/btp194 pmc: PMC2687948 pubmed: '19478019' title: 'Alignment of the UMLS semantic network with BioTop: methodology and assessment' year: 2009 - doi: 10.1093/bioinformatics/btn158 pmc: PMC2718636 pubmed: '18586729' title: The ontology of biological taxa year: 2008 repository: https://github.com/BioTopOntology/biotop/ uri_format: http://purl.org/biotop/biotop.owl#$1 biozil: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Redistributor of bilogics and biomedical supplies example: ls-c35719-120 homepage: https://www.biozol.de/en keywords: - biologics - life sciences - vendor name: BIOZIL preferred_prefix: biozil uri_format: https://www.biozol.de/en/product/$1 birnlex: comment: Part of the NeuroLex namespace now contact: email: wbug@ncmir.ucsd.edu name: William Bug contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. download_owl: http://aber-owl.net/media/ontologies/BIRNLEX/1/birnlex.owl example: '2023' homepage: https://bioportal.bioontology.org/ontologies/BIRNLEX keywords: - anatomy - biomedical science - disease - ontology - study design mappings: aberowl: BIRNLEX bioportal: BIRNLEX fairsharing: FAIRsharing.jedbbt name: Biomedical Informatics Research Network Lexicon pattern: ^\d+$ preferred_prefix: birnlex uri_format: http://uri.neuinfo.org/nif/nifstd/birnlex_$1 biro: contact: email: silvio.peroni@unibo.it github: essepuntato name: Silvio Peroni orcid: 0000-0003-0530-4305 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively. example: BibliographicRecord homepage: http://www.sparontologies.net/ontologies/biro keywords: - bibliography - citation - data model - report - spar - subject agnostic mappings: fairsharing: FAIRsharing.99da5f lov: biro name: Bibliographic Reference Ontology preferred_prefix: BiRO repository: https://github.com/sparontologies/biro twitter: sparontologies uri_format: http://purl.org/spar/biro/$1 bitbucket: description: Bitbucket is a Git-based source code repository hosting service owned by Atlassian. example: andreadega/systems-biology-compiler homepage: https://www.atlassian.com/ keywords: - knowledge and information systems - software engineering - subject agnostic mappings: fairsharing: FAIRsharing.fc3431 miriam: bitbucket re3data: r3d100013478 name: Bitbucket pattern: ^[0-9A-Za-z-_\.]+/[0-9A-Za-z-_\.]+$ preferred_prefix: bitbucket uri_format: https://bitbucket.org/$1 bitterdb.cpd: description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds. example: '46' homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php mappings: biocontext: BITTERDB.CPD miriam: bitterdb.cpd n2t: bitterdb.cpd name: BitterDB Compound pattern: ^\d+$ preferred_prefix: bitterdb.cpd uri_format: http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1 bitterdb.rec: description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors. example: '1' homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php mappings: biocontext: BITTERDB.REC miriam: bitterdb.rec n2t: bitterdb.rec name: BitterDB Receptor pattern: ^\d+$ preferred_prefix: bitterdb.rec uri_format: http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1 bko: comment: This resource also uses SBO terms and resolves them, e.g., http://www.sbgnbricks.org/BKO/full/entry/all/SBO:0000177/. contact: email: adrienrougny@gmail.com github: adrienrougny name: Adrien Rougny orcid: 0000-0002-2118-035X contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way. download_owl: http://aber-owl.net/media/ontologies/BKO/1/bko.owl example: '0000204' github_request_issue: 283 homepage: http://www.sbgnbricks.org/ keywords: - ontology mappings: aberowl: BKO bioportal: BKO name: SBGN Bricks data and ontology pattern: ^\d+$ preferred_prefix: bko reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1 bmrb: contact: email: markley@nmrfam.wisc.edu name: John L. Markley orcid: 0000-0003-1799-6134 description: BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy. example: '15000' homepage: http://www.bmrb.wisc.edu/ keywords: - structural biology mappings: fairsharing: FAIRsharing.p06nme integbio: nbdc00380 miriam: bmrb re3data: r3d100010191 uniprot: DB-0256 name: Biological Magnetic Resonance Data Bank pattern: ^(bmr|bmse|bmst)?[0-9]{1,6}$ preferred_prefix: bmrb publications: - doi: 10.1007/s10858-008-9221-y pmc: PMC2268728 pubmed: '18288446' title: 'BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions' year: 2008 - doi: 10.1093/nar/gkm957 pmc: PMC2238925 pubmed: '17984079' title: BioMagResBank year: 2007 uri_format: http://rest.bmrb.wisc.edu/bmrb/$1/html bmrb.restraint: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively. example: '28789' homepage: https://restraintsgrid.bmrb.io/NRG/MRGridServlet keywords: - chemistry - nmr - spectrometry name: NMR Restraints Grid pattern: ^\d+$ preferred_prefix: bmrb.restraint uri_format: https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1 bold.taxonomy: contact: email: phebert@uoguelph.ca name: Paul David Neil Hebert orcid: 0000-0002-3081-6700 description: The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information. example: '27267' homepage: http://www.boldsystems.org/ keywords: - dna mappings: biocontext: BOLD.TAXONOMY miriam: bold.taxonomy n2t: bold.taxonomy ncbi: BOLD prefixcommons: bold wikidata: P3606 name: BOLD Systems taxon pattern: ^\d+$ preferred_prefix: bold.taxonomy providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/bold:$1 publications: - doi: 10.1111/j.1471-8286.2007.01678.x pmc: PMC1890991 pubmed: '18784790' title: 'bold: The Barcode of Life Data System (http://www.barcodinglife.org)' year: 2007 uri_format: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1 bootstrep: contact: email: vlee@ebi.ac.uk name: Vivian Lee deprecated: true homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html keywords: - obo - ontology mappings: biocontext: BOOTSTREP obofoundry: bootstrep name: Gene Regulation Ontology preferred_prefix: BOOTSTREP rdf_uri_format: http://purl.obolibrary.org/obo/BOOTSTREP_$1 uri_format: http://purl.obolibrary.org/obo/BOOTSTREP_$1 bpdb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Database of biopesticides maintained by the University of Hertfordshire ' example: '2404' homepage: https://sitem.herts.ac.uk/aeru/bpdb/index.htm keywords: - biology - biopesticides - pesticides name: Bio-Pesticides DataBase pattern: ^\d+$ preferred_prefix: bpdb uri_format: https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm brenda: contact: email: D.Schomburg@tu-braunschweig.de name: Dietmar Schomburg orcid: 0000-0002-3354-822X description: BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. example: 1.1.1.1 homepage: https://www.brenda-enzymes.org/ keywords: - enzyme - life science mappings: biocontext: BRENDA fairsharing: FAIRsharing.etp533 go: BRENDA miriam: brenda n2t: brenda pathguide: '51' prefixcommons: brenda re3data: r3d100010616 name: BRENDA Enzyme pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ preferred_prefix: brenda providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/brenda:$1 provides: ec publications: - doi: 10.1016/j.jbiotec.2017.04.020 pubmed: '28438579' title: The BRENDA enzyme information system-From a database to an expert system year: 2017 - doi: 10.1093/nar/gku1068 pmc: PMC4383907 pubmed: '25378310' title: 'BRENDA in 2015: exciting developments in its 25th year of existence' year: 2014 - doi: 10.1093/nar/gks1049 pmc: PMC3531171 pubmed: '23203881' title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA' year: 2012 - doi: 10.1093/nar/gkq1089 pmc: PMC3013686 pubmed: '21062828' title: BRENDA, the enzyme information system in 2011 year: 2010 - doi: 10.1093/nar/gkn820 pmc: PMC2686525 pubmed: '18984617' title: 'BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009' year: 2008 - doi: 10.1093/nar/gkl972 pmc: PMC1899097 pubmed: '17202167' title: 'BRENDA, AMENDA and FRENDA: the enzyme information system in 2007' year: 2007 - doi: 10.1093/nar/gkh081 pmc: PMC308815 pubmed: '14681450' title: 'BRENDA, the enzyme database: updates and major new developments' year: 2004 - doi: 10.1016/s1096-7176(03)00008-9 pubmed: '12850129' title: Review of the BRENDA Database year: 2003 - doi: 10.1016/s0968-0004(01)02027-8 pubmed: '11796225' title: 'BRENDA: a resource for enzyme data and metabolic information' year: 2002 - doi: 10.1093/nar/30.1.47 pmc: PMC99121 pubmed: '11752250' title: BRENDA, enzyme data and metabolic information year: 2002 - doi: S0168-1656(17)30183-9 title: The BRENDA enzyme information system-From a database to an expert system. - doi: 10.1016/S1096-7176(03)00008-9 title: Review of the BRENDA Database. - doi: 10.1016/S0968-0004(01)02027-8 title: 'BRENDA: a resource for enzyme data and metabolic information.' uri_format: https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1 brenda.ligand: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Information for ligands in the BRENDA database. example: '278' homepage: https://www.brenda-enzymes.de/ligand.php keywords: - chemistry - structrual bioinformatics name: BRENDA Ligand pattern: ^\d+$ preferred_prefix: brenda.ligand uri_format: https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1 brenda.ligandgroup: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Information for ligand groups (chemical classes). example: '18030' homepage: https://www.brenda-enzymes.de/ligand.php keywords: - chemistry - grouping - structrual bioinformatics name: BRENDA Ligand Group pattern: ^\d+$ preferred_prefix: brenda.ligandgroup uri_format: https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1 bridgedb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A vocabulary about resources, similar to bioregistry.schema, venn, idot, etc. example: hasPrimaryUriPattern homepage: https://bridgedb.org name: BridgeDb Vocabulary preferred_prefix: bridgedb references: - https://github.com/bridgedb/BridgeDb/blob/master/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl uri_format: http://vocabularies.bridgedb.org/ops#$1 broad: description: Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae. example: S7000002168151102 homepage: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/ mappings: biocontext: BROAD miriam: broad n2t: broad name: Broad Fungal Genome Initiative pattern: ^S\d+$ preferred_prefix: broad uri_format: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1 bs: comment: An alernative vocabulary that has been aligned and integrated in Sequence Ontology (SO). contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library. download_obo: https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/subsets/biosapiens.obo example: '00042' homepage: https://github.com/The-Sequence-Ontology/SO-Ontologies keywords: - ontology name: Biosapiens Protein Feature Ontology pattern: ^\d+$ preferred_prefix: bs repository: https://github.com/The-Sequence-Ontology/SO-Ontologies uri_format: https://biopragmatics.github.io/providers/bs/$1 bspo: appears_in: - aism - colao - fovt - lepao - uberon - zp contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. download_json: http://purl.obolibrary.org/obo/bspo.json download_obo: https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo download_owl: http://purl.obolibrary.org/obo/bspo.owl example: 0000029 homepage: https://github.com/obophenotype/biological-spatial-ontology keywords: - anatomy - life science - obo - ontology license: CC-BY-3.0 mappings: aberowl: BSPO biocontext: BSPO bioportal: BSPO fairsharing: FAIRsharing.newa3z obofoundry: bspo ols: bspo ontobee: BSPO name: Biological Spatial Ontology pattern: ^\d{7}$ preferred_prefix: BSPO publications: - doi: 10.1186/2041-1480-5-34 pmc: PMC4137724 pubmed: '25140222' title: 'Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology' year: 2014 rdf_uri_format: http://purl.obolibrary.org/obo/BSPO_$1 repository: https://github.com/obophenotype/biological-spatial-ontology uri_format: http://purl.obolibrary.org/obo/BSPO_$1 version: '2023-05-27' bto: banana: BTO contact: email: c.dudek@tu-braunschweig.de github: chdudek name: Christian-Alexander Dudek orcid: 0000-0001-9117-7909 description: The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. download_json: http://purl.obolibrary.org/obo/bto.json download_obo: http://purl.obolibrary.org/obo/bto.obo download_owl: http://purl.obolibrary.org/obo/bto.owl example: 0000590 homepage: http://www.brenda-enzymes.org keywords: - cell - enzyme - enzymology - life science - obo - ontology - organ - reaction data - tissue license: CC-BY-4.0 mappings: aberowl: BTO biocontext: BTO bioportal: BTO cellosaurus: BTO fairsharing: FAIRsharing.1414v8 go: BTO miriam: bto n2t: bto obofoundry: bto ols: bto ontobee: BTO prefixcommons: bto wikidata: P5501 name: BRENDA Tissue Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: BTO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/bto:$1 - code: miriam_obo_legacy description: An old URI style for MIRIAM homepage: https://identifiers.org/ name: MIRIAM OBO Legacy uri_format: http://identifiers.org/obo.bto/BTO:$1 publications: - doi: 10.1093/nar/gky1048 pmc: PMC6323942 pubmed: '30395242' title: 'BRENDA in 2019: a European ELIXIR core data resource' year: 2019 - doi: 10.1093/nar/gku1068 pmc: PMC4383907 pubmed: '25378310' title: 'BRENDA in 2015: exciting developments in its 25th year of existence' year: 2014 - doi: 10.1093/nar/gks1049 pmc: PMC3531171 pubmed: '23203881' title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA' year: 2012 - doi: 10.1093/nar/gkq968 pmc: PMC3013802 pubmed: '21030441' title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources' year: 2010 - doi: 10.1093/nar/gkh081 pmc: PMC308815 pubmed: '14681450' title: 'BRENDA, the enzyme database: updates and major new developments' year: 2004 rdf_uri_format: http://purl.obolibrary.org/obo/BTO_$1 repository: https://github.com/BRENDA-Enzymes/BTO synonyms: - BTO uri_format: http://purl.obolibrary.org/obo/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?action=view&expt_id=$1 bugbase.protocol: description: BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols. example: '67' homepage: http://bugs.sgul.ac.uk/E-BUGS mappings: biocontext: BUGBASE.PROTOCOL miriam: bugbase.protocol n2t: bugbase.protocol name: BugBase Protocol pattern: ^\d+$ preferred_prefix: bugbase.protocol uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?action=view&protocol_id=$1 bykdb: contact: email: cozzone@ibcp.fr name: Alain J. Cozzone description: The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information. example: A0A009E7X8 homepage: https://bykdb.ibcp.fr/BYKdb/ keywords: - domain - life science - microbial - sequence mappings: biocontext: BYKDB fairsharing: FAIRsharing.jr30xc miriam: bykdb n2t: bykdb prefixcommons: bykdb name: Bacterial Tyrosine Kinase Database pattern: ^[A-Z0-9]+$ preferred_prefix: bykdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/bykdb:$1 provides: uniprot publications: - doi: 10.1016/s0378-1119(97)00554-4 pubmed: '9434192' title: Characterization of a bacterial gene encoding an autophosphorylating protein tyrosine kinase year: 1997 - doi: 10.1093/nar/gkr915 pmc: PMC3245071 pubmed: '22080550' title: 'BYKdb: the Bacterial protein tYrosine Kinase database' year: 2011 - doi: 10.1007/s00726-009-0237-8 pubmed: '19189200' title: 'Tyrosine-kinases in bacteria: from a matter of controversy to the status of key regulatory enzymes' year: 2009 - doi: 10.1093/bioinformatics/btn462 pubmed: '18772155' title: Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature year: 2008 uri_format: https://bykdb.ibcp.fr/data/html/annotated/$1.html c4o: contact: email: silvio.peroni@unibo.it github: essepuntato name: Silvio Peroni orcid: 0000-0003-0530-4305 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date. example: InTextReferencePointer homepage: http://www.sparontologies.net/ontologies/c4o keywords: - bibliography - citation - data model - report - spar - subject agnostic mappings: fairsharing: FAIRsharing.beb855 lov: c4o name: Citation Counting and Context Characterisation Ontology preferred_prefix: C4O repository: https://github.com/sparontologies/c4o twitter: sparontologies uri_format: http://purl.org/spar/c4o/$1 cabi: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Research and learning in agriculture, the environment and the applied life sciences example: '20000614040' github_request_issue: 1313 homepage: https://www.cabidigitallibrary.org name: CABI Digital Library pattern: ^\d+$ preferred_prefix: cabi uri_format: https://www.cabi.org/cabebooks/ebook/$1 cabri: contact: email: paolo.romano@hsanmartino.it name: Paolo Romano orcid: 0000-0003-4694-3883 description: CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it. example: dsmz_mutz-id:ACC 291 homepage: http://www.cabri.org/ keywords: - applied microbiology - medical microbiology - microbiology - molecular biology - molecular microbiology - virology mappings: biocontext: CABRI edam: '2380' fairsharing: FAIRsharing.qx2rvz miriam: cabri n2t: cabri ncbi: CABRI name: Common Access to Biological Resources and Information Project pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$ preferred_prefix: cabri providers: - code: 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] publications: - doi: 10.1002/cfg.376 pmc: PMC2447341 pubmed: '18629057' title: Interoperability of CABRI Services and Biochemical Pathways Databases year: 2004 - doi: 10.2165/00822942-200594030-00002 pubmed: '16231959' title: The role of informatics in the coordinated management of biological resources collections year: 2005 uri_format: http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1] cadsr: description: The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR. example: '3771992' homepage: https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki mappings: miriam: cadsr n2t: cadsr name: Cancer Data Standards Registry and Repository pattern: ^[0-9]*$ preferred_prefix: cadsr uri_format: https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1] caloha: contact: email: Paula.Duek@sib.swiss github: paulacalipho name: Paula Duek Roggli orcid: 0000-0002-0819-0473 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins. download_obo: https://raw.githubusercontent.com/calipho-sib/controlled-vocabulary/master/caloha.obo example: TS-0001 homepage: https://github.com/calipho-sib/controlled-vocabulary keywords: - anatomy - human - ontology - physiology license: CC-BY-4.0 name: CALIPHO Group Ontology of Human Anatomy pattern: ^TS-\d+$ preferred_prefix: caloha providers: - code: biopragmatics description: A static site generated from the CALOHA OBO flat file homepage: https://biopragmatics.github.io/providers name: Biopragmatics Browser uri_format: https://biopragmatics.github.io/providers/caloha/$1 references: - https://twitter.com/neXtProt_news/status/1350105997633867781 - https://github.com/biopragmatics/bioregistry/issues/721 repository: https://github.com/calipho-sib/controlled-vocabulary twitter: neXtProt_news uri_format: https://www.nextprot.org/term/$1 cameo: contact: email: torsten.schwede@unibas.ch name: Torsten Schwede orcid: 0000-0003-2715-335X description: The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB. example: 2019-08-03_00000089_1 homepage: https://cameo3d.org keywords: - life science mappings: biocontext: CAMEO fairsharing: FAIRsharing.dq34p2 miriam: cameo n2t: cameo name: Continuous Automated Model Evaluation pattern: ^[0-9\-_]+$ preferred_prefix: cameo publications: - doi: 10.1093/database/bat031 pmc: PMC3889916 pubmed: '23624946' title: The Protein Model Portal--a comprehensive resource for protein structure and model information year: 2013 uri_format: https://www.cameo3d.org/sp/targets/target/$1 cao: contact: email: williams.antony@epa.gov name: Antony Williams orcid: 0000-0002-2668-4821 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'An ontology developed as part of the Chemical Analysis Metadata Project (ChAMP) as a resource to semantically annotate standards developed using the ChAMP platform. (source: CAO ontology)' download_owl: https://champ.stuchalk.domains.unf.edu/images/ontology/cao.owl example: '000064' homepage: https://champ.stuchalk.domains.unf.edu keywords: - amino acid sequence - annotation - characterisation data heat - gene - genetics - life science - ontology - orthologous - phylogenetics - protein - transcript - transport and kinetic data license: CC-BY-3.0 mappings: aberowl: CAO bioportal: CAO fairsharing: FAIRsharing.wp0134 ols: cao name: Chemical Analysis Ontology pattern: ^\d+$ preferred_prefix: cao publications: - doi: 10.1126/science.278.5338.631 pubmed: '9381173' title: A genomic perspective on protein families year: 1997 uri_format: http://champ-project.org/images/ontology/cao.owl#CAO_$1 version: '0.2' caps: description: CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. example: '434' homepage: http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home mappings: biocontext: CAPS miriam: caps n2t: caps name: CAPS-DB pattern: ^\d+$ preferred_prefix: caps uri_format: http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1 carnegie.stage: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: One of the 23 stages of embryo development example: '20' github_request_issue: 1325 homepage: https://embryology.med.unsw.edu.au/embryology/index.php/Carnegie_Stages name: Carnegie Stage pattern: ^\d+$ preferred_prefix: carnegie.stage uri_format: https://embryology.med.unsw.edu.au/embryology/index.php/Carnegie_Stages#Stage_$1 caro: appears_in: - aism - colao - ehdaa2 - gallont - lepao - pco contact: email: haendel@ohsu.edu github: mellybelly name: Melissa Haendel orcid: 0000-0001-9114-8737 description: The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. download_json: http://purl.obolibrary.org/obo/caro.json download_obo: http://purl.obolibrary.org/obo/caro.obo download_owl: http://purl.obolibrary.org/obo/caro.owl example: '0000000' homepage: https://github.com/obophenotype/caro/ keywords: - anatomy - annotation - interoperability - life science - obo - ontology license: CC-BY-4.0 mappings: aberowl: CARO biocontext: CARO bioportal: CARO fairsharing: FAIRsharing.3kcgmr go: CARO obofoundry: caro ols: caro ontobee: CARO name: Common Anatomy Reference Ontology pattern: ^\d{7}$ preferred_prefix: CARO providers: - code: obo.1 description: This incorrect encoding was found inside IDO-COVID-19 homepage: http://purl.obolibrary.org name: Nonstandard OBO PURL uri_format: http://purl.obolibrary.org/obo/ido.owl/CARO_$1 publications: - doi: 10.1007/978-1-84628-885-2_16 title: CARO – The Common Anatomy Reference Ontology year: 2008 rdf_uri_format: http://purl.obolibrary.org/obo/CARO_$1 repository: https://github.com/obophenotype/caro uri_format: http://purl.obolibrary.org/obo/CARO_$1 version: '2023-03-15' cas: contact: email: ajacobs@cas.org name: Andrea Jacobs orcid: 0000-0001-9316-9400 description: CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information. example: 50-00-0 homepage: https://commonchemistry.cas.org/ keywords: - chemical - chemical entity - cheminformatics - structure mappings: biocontext: CAS cheminf: '000446' edam: '1002' fairsharing: FAIRsharing.r7Kwy7 go: CAS hl7: 2.16.840.1.113883.6.61 miriam: cas n2t: cas prefixcommons: cas wikidata: P231 name: CAS Registry Number pattern: ^\d{1,7}\-\d{2}\-\d$ preferred_prefix: cas providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/cas:$1 - code: hoelzel description: Vendor page homepage: https://www.hoelzel-biotech.com name: Hölzel Diagnostika uri_format: https://www.hoelzel-biotech.com/de/casinfo/cas/index/number/$1 - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/cas/$1 publications: - doi: 10.1021/acs.jcim.2c00268 pmc: PMC9199008 pubmed: '35559614' title: 'CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community' year: 2022 synonyms: - CASID - CAS_RN - SECONDARY_CAS_RN - cas_id uri_format: https://commonchemistry.cas.org/detail?cas_rn=$1 casspc: comment: Jim Balhoff said that Catalog of Fishes does not publish their data in a machine readable format, but a long time ago they sent a CSV dump to help in the development of TTO and VTO. These ontologies are effectively retired and CASSPC terms are only also used in Phenoscape. Note that the github request issue is not correct, since this was made on a commit (but, fishbase is related). contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 contributor_extras: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true example: '5359' github_request_issue: 149 homepage: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp mappings: go: CASSPC name: Eschmeyer's Catalog of Fishes pattern: ^\d+$ preferred_prefix: casspc reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1 cath: contact: email: c.orengo@ucl.ac.uk name: Christine Orengo orcid: 0000-0002-7141-8936 description: CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence. example: 1.10.8.10 homepage: http://www.cathdb.info keywords: - biology - classification - evolutionary biology - protein - structure mappings: biocontext: CATH edam: '2700' fairsharing: FAIRsharing.xgcyyn integbio: nbdc01888 miriam: cath n2t: cath prefixcommons: cath re3data: r3d100012629 name: CATH Protein Structural Domain Superfamily pattern: ^[1-6]\.[0-9]+\.[0-9]+\.[0-9]+$ preferred_prefix: cath providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/cath:$1 publications: - doi: 10.1016/s0969-2126(97)00260-8 pubmed: '9309224' title: CATH--a hierarchic classification of protein domain structures year: 1997 - doi: 10.1093/nar/gkae1087 pubmed: '39565206' title: 'CATH v4.4: major expansion of CATH by experimental and predicted structural data' year: 2024 - doi: 10.1093/nar/gkaa1079 pmc: PMC7778904 pubmed: '33237325' title: 'CATH: increased structural coverage of functional space' year: 2021 - doi: 10.1093/nar/gky1097 pmc: PMC6323983 pubmed: '30398663' title: 'CATH: expanding the horizons of structure-based functional annotations for genome sequences' year: 2019 - doi: 10.1093/nar/gkx1069 pmc: PMC5753370 pubmed: '29112716' title: 'Gene3D: Extensive prediction of globular domains in proteins' year: 2018 - doi: 10.1093/nar/gkw1098 pmc: PMC5210570 pubmed: '27899584' title: 'CATH: an expanded resource to predict protein function through structure and sequence' year: 2016 - doi: 10.1093/bioinformatics/btw473 pmc: PMC5018379 pubmed: '27477482' title: 'Functional classification of CATH superfamilies: a domain-based approach for protein function annotation' year: 2016 - doi: 10.1016/j.biochi.2015.08.004 pmc: PMC4678953 pubmed: '26253692' title: The history of the CATH structural classification of protein domains year: 2015 - doi: 10.1093/nar/gku947 pmc: PMC4384018 pubmed: '25348408' title: 'CATH: comprehensive structural and functional annotations for genome sequences' year: 2014 - pubmed: '11788987' title: 'The CATH protein family database: a resource for structural and functional annotation of genomes' year: 2002 twitter: CATHDatabase uri_format: http://www.cathdb.info/cathnode/$1 cath.domain: description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains. example: 1cukA01 homepage: http://www.cathdb.info/ mappings: biocontext: CATH.DOMAIN edam: '1040' miriam: cath.domain n2t: cath.domain name: CATH domain pattern: ^\w+$ preferred_prefix: cath.domain uri_format: http://www.cathdb.info/domain/$1 cath.superfamily: description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification. example: 1.10.10.200 homepage: http://www.cathdb.info/ mappings: biocontext: CATH.SUPERFAMILY miriam: cath.superfamily n2t: cath.superfamily name: CATH superfamily part_of: cath pattern: ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$ preferred_prefix: cath.superfamily uri_format: http://www.cathdb.info/cathnode/$1 cattleqtldb: description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs. example: '4685' homepage: https://www.animalgenome.org/QTLdb keywords: - dna - genome mappings: biocontext: CATTLEQTLDB miriam: cattleqtldb n2t: cattleqtldb prefixcommons: cattleqtldb name: Animal Genome Cattle QTL part_of: qtldb pattern: ^\d+$ preferred_prefix: cattleqtldb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/cattleqtldb:$1 uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 cazy: contact: email: nicolas.terrapon@univ-amu.fr github: gandarath name: Nicolas Terrapon orcid: 0000-0002-3693-6017 description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features. example: GT10 homepage: http://www.cazy.org/ keywords: - classification - glycomics - life science - polysaccharide mappings: biocontext: CAZY fairsharing: FAIRsharing.ntyq70 go: CAZY miriam: cazy n2t: cazy prefixcommons: cazy re3data: r3d100012321 uniprot: DB-0136 name: Carbohydrate Active EnZYmes pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$ preferred_prefix: cazy providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/cazy:$1 publications: - doi: 10.1093/nar/gkab1045 pubmed: '34850161' - doi: 10.1093/nar/gkt1178 pmc: PMC3965031 pubmed: '24270786' title: The carbohydrate-active enzymes database (CAZy) in 2013 year: 2013 - doi: 10.1093/nar/gkn663 pmc: PMC2686590 pubmed: '18838391' title: 'The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics' year: 2008 uri_format: http://www.cazy.org/$1.html cba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE.' example: '375364' homepage: http://www.cba.ac.cn keywords: - bibliography name: Chinese Biological Abstracts pattern: ^\d+$ preferred_prefix: cba uri_format: https://europepmc.org/article/CBA/$1 cbioportal: contact: email: gaoj@mskcc.org github: jjgao name: Jianjiong Gao orcid: 0000-0002-5739-1781 description: The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. example: laml_tcga_pub homepage: http://www.cbioportal.org keywords: - biomedical science - genomics - preclinical studies - proteomics mappings: fairsharing: FAIRsharing.6L6MjA miriam: cbioportal n2t: cbioportal name: The cBioPortal for Cancer Genomics pattern: ^[a-z0-9\_]+$ preferred_prefix: cbioportal publications: - doi: 10.1126/scisignal.2004088 pmc: PMC4160307 pubmed: '23550210' title: Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal year: 2013 - doi: 10.1158/2159-8290.cd-12-0095 pmc: PMC3956037 pubmed: '22588877' title: 'The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data' year: 2012 - doi: 10.1158/2159-8290.CD-12-0095 title: 'The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.' repository: https://github.com/cBioPortal/cbioportal twitter: cbioportal uri_format: https://www.cbioportal.org/study/summary?id=$1 cc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: ' The Creative Commons Rights Expression Language (ccREL) lets you describe copyright licenses in RDF. For more information on describing licenses in RDF and attaching those descriptions to digital works, see [ccREL](https://wiki.creativecommons.org/CC_REL) in the [Creative Commons wiki](https://wiki.creativecommons.org/).' download_rdf: https://creativecommons.org/schema.rdf example: Work homepage: https://creativecommons.org/ns keywords: - metadata license: CC0-1.0 mappings: aberowl: CC lov: cc zazuko: cc name: Creative Commons Rights Expression Language pattern: ^\w+$ preferred_prefix: cc twitter: cc_opensource uri_format: https://creativecommons.org/ns#$1 ccdc: description: The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC. example: '1829126' homepage: https://www.ccdc.cam.ac.uk/ mappings: miriam: ccdc name: CCDC Number pattern: ^\d{6,7}$ preferred_prefix: ccdc uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG ccds: contact: email: murphyte@ncbi.nlm.nih.gov name: Terence D. Murphy orcid: 0000-0001-9311-9745 description: The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations. example: CCDS12976 example_extras: - CCDS12976.1 homepage: http://www.ncbi.nlm.nih.gov/CCDS/ keywords: - gene - life science - protein mappings: biocontext: CCDS fairsharing: FAIRsharing.46s4nt integbio: nbdc00023 miriam: ccds n2t: ccds prefixcommons: ccds togoid: Ccds uniprot: DB-0187 name: Consensus CDS pattern: ^CCDS\d+(\.\d+)?$ preferred_prefix: ccds providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ccds:$1 publications: - doi: 10.1093/nar/gkx1031 pubmed: '29126148' - doi: 10.1101/gr.080531.108 pmc: PMC2704439 pubmed: '19498102' title: 'The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes' year: 2009 uri_format: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1 ccf: contact: email: katy@indiana.edu github: katyb name: Katy Börner orcid: 0000-0002-3321-6137 contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The Common Coordinate Framework (CCF) Ontology is an application ontology built to support the development of the Human Reference Atlas (HRA). It unifies vocabulary for HRA construction and usage—making it possible to ingest external data sources; supporting uniform tissue sample registration that includes the spatial positioning and semantic annotations within 3D reference organs; and supporting user-formulated cross-domain queries over tissue donor properties, anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology consists of three major ontologies. The Biological Structure Ontology records anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships between them. The ASCT+B tables are authored by human experts using templated Google Sheets. The biomarkers, cell types, and anatomical structures are mapped to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible. All relationships between anatomical structures and from cell types to anatomical structures are valid Uberon and CL relationships. The Spatial Ontology defines the shape, size, location, and rotation of experimental tissue and data major anatomical structures in the 3D Reference Object Library. The Specimen Ontology captures the sex, age, and other information on donors that provided tissue data used in the construction of the HRA. download_owl: http://aber-owl.net/media/ontologies/CCF/16/ccf.owl example: extraction_set github_request_issue: 879 homepage: https://bioportal.bioontology.org/ontologies/CCF keywords: - ontology license: CC-BY-4.0 mappings: aberowl: CCF bioportal: CCF ols: ccf re3data: r3d100012657 name: Human Reference Atlas Common Coordinate Framework Ontology pattern: ^\S+$ preferred_prefix: ccf rdf_uri_format: http://purl.org/ccf/$1 repository: https://github.com/hubmapconsortium/ccf-ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://bioportal.bioontology.org/ontologies/CCF/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fccf%2F$1 ccle: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Datasets around different cancer cell lines generated by the Broad Institute and Novartis example: BT20_BREAST homepage: https://www.cbioportal.org/study/summary?id=ccle_broad_2019 license: ODbL-1.0 mappings: cellosaurus: CCLE name: Cancer Cell Line Encyclopedia Cells preferred_prefix: ccle synonyms: - ccle.cell uri_format: https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1 cco: banana: CCO contact: email: kuiper@bio.ntnu.no github: makuintnu name: Martin Kuiper orcid: 0000-0002-1171-9876 description: The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process. download_obo: https://www.bio.ntnu.no/ontology/CCO/cco.obo download_owl: https://www.bio.ntnu.no/ontology/CCO/cco.owl example: '0000003' homepage: http://www.semantic-systems-biology.org/apo keywords: - cell - cell cycle - functional genomics - genomics - life science - molecular function - obo - ontology - proteomics mappings: aberowl: CCO bartoc: '20461' biocontext: CCO bioportal: CCO fairsharing: FAIRsharing.xhwrnr miriam: cco n2t: cco ols: cco prefixcommons: cco name: Cell Cycle Ontology namespace_in_lui: true pattern: ^\w+$ preferred_prefix: cco providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/cco:$1 publications: - doi: 10.1186/gb-2009-10-5-r58 pmc: PMC2718524 pubmed: '19480664' title: 'The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process' year: 2009 uri_format: https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:$1 ccrid: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Cell line databases/resources example: 4201PAT-CCTCC00348 homepage: http://www.cellresource.cn mappings: cellosaurus: CCRID name: National Experimental Cell Resource Sharing Platform preferred_prefix: ccrid uri_format: http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1 cdao: contact: email: balhoff@renci.org github: balhoff name: Jim Balhoff orcid: 0000-0002-8688-6599 description: a formalization of concepts and relations relevant to evolutionary comparative analysis download_owl: http://purl.obolibrary.org/obo/cdao.owl example: '0000072' homepage: https://github.com/evoinfo/cdao keywords: - bioinformatics - biomedical science - evolution - evolutionary biology - life science - molecular biology - obo - ontology - phylogenetics - taxonomy license: CC0-1.0 mappings: aberowl: CDAO agroportal: CDAO biocontext: CDAO bioportal: CDAO fairsharing: FAIRsharing.kay31r obofoundry: cdao ols: cdao ontobee: CDAO name: Comparative Data Analysis Ontology pattern: ^\d{7}$ preferred_prefix: CDAO publications: - doi: 10.4137/ebo.s2320 pmc: PMC2747124 pubmed: '19812726' title: Initial implementation of a comparative data analysis ontology year: 2009 rdf_uri_format: http://purl.obolibrary.org/obo/CDAO_$1 repository: https://github.com/evoinfo/cdao uri_format: http://purl.obolibrary.org/obo/CDAO_$1 version: '2024-01-25' cdd: description: The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. example: cd00400 homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd keywords: - earth science - geology - protein - structure mappings: biocontext: CDD edam: '2666' fairsharing: FAIRsharing.ea287c go: CDD integbio: nbdc00401 miriam: cdd n2t: cdd ncbi: CDD prefixcommons: cdd re3data: r3d100012041 uniprot: DB-0214 name: Conserved Domain Database at NCBI pattern: ^(cd)?\d{5}$ preferred_prefix: cdd providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/cdd:$1 publications: - doi: 10.1093/nar/gkac1096 pubmed: '36477806' - doi: 10.1093/nar/gku1221 pmc: PMC4383992 pubmed: '25414356' title: 'CDD: NCBI''s conserved domain database' year: 2014 - doi: 10.1093/nar/gkn845 pmc: PMC2686570 pubmed: '18984618' title: 'CDD: specific functional annotation with the Conserved Domain Database' year: 2008 uri_format: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 cdno: contact: email: landreshdz@gmail.com github: LilyAndres name: Liliana Andres Hernandez orcid: 0000-0002-7696-731X depends_on: - bfo - chebi - envo - pato - ro description: The CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. These terms are intended primarily to be associated with datasets that quantify concentration of chemical nutritional components derived from samples taken from any stage in the production of food raw materials (including from crops, livestock, fisheries) and through processing and supply chains. Additional knowledge associated with these dietary sources may be represented by terms that describe functional, physical and other attributes. Whilst recognising that dietary nutrients within food substrates may be present as complex and dynamic physical and chemical structures or mixtures, CDNO focuses on components typically quantified in an analytical chemistry laboratory. The primary CDNO class ‘dietary nutritional component’ contains hierarchical sets of terms organised to reflect commonly used classifications of chemical food composition. This class does not represent an exhaustive classification of chemical components, but focuses on structuring terms according to widely accepted categories. This class is independent of, but may be used in conjunction with, classes that describe ‘analytical methods’ for quantification, ‘physical properties’ or ‘dietary function’. Quantification data may be used and reported in research literature, to inform food composition tables and labelling, or for supply chain quality assurance and control. More specifically, terms within the ‘nutritional component concentration’ class may be used to represent quantification of components described in the ‘dietary nutritional component’ class. Concentration data are intended to be described in conjunction with post-composed metadata concepts, such as represented by the Food Ontology (FoodOn) ‘Food product by organism’, which derives from some food or anatomical entity and a NCBI organismal classification ontology (NCBITaxon) entity. The common vocabulary and relationships defined within CDNO should facilitate description, communication and exchange of material entity-derived nutritional composition datasets typically generated by analytical laboratories. The organisation of the vocabulary is structured to reflect common categories variously used by those involved in crop, livestock or other organismal production, associated R&D and breeding, as well as the food processing and supply sector, and nutritionists, inlcuding compilers and users of food composition databases. The CDNO therefore supports characterisation of genetic diversity and management of biodiversity collections, as well as sharing of knowledge relating to dietary composition between a wider set of researchers, breeders, farmers, processors and other stakeholders. Further development of the functional class should also assist in understanding how interactions between organismal genetic and environmental variation contribute to human diet and health in the farm to fork continuum. download_obo: http://purl.obolibrary.org/obo/cdno.obo download_owl: http://purl.obolibrary.org/obo/cdno.owl example: '0000013' homepage: https://cdno.info/ keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: CDNO agroportal: CDNO bioportal: CDNO obofoundry: cdno ols: cdno ontobee: CDNO name: Compositional Dietary Nutrition Ontology pattern: ^\d{7}$ preferred_prefix: CDNO publications: - doi: 10.3389/fnut.2022.928837 title: Establishing a Common Nutritional Vocabulary - From Food Production to Diet - doi: 10.1002/csc2.20092 title: Knowledge representation and data sharing to unlock crop variation for nutritional food security year: 2020 rdf_uri_format: http://purl.obolibrary.org/obo/CDNO_$1 repository: https://github.com/CompositionalDietaryNutritionOntology/cdno uri_format: http://purl.obolibrary.org/obo/CDNO_$1 version: '2024-11-12' cdpd: description: The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN). example: '63250' homepage: http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp mappings: biocontext: CDPD miriam: cdpd n2t: cdpd name: Canadian Drug Product Database pattern: ^\d+$ preferred_prefix: cdpd uri_format: http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1 cdt: appears_in: - ohd contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment. Note that CDT codes should look like D2150 but for some reason the ontology conversion that is reused across OBO rewrites them as CPT_000 + the four numbers without the leading D.' download_owl: https://raw.githubusercontent.com/oral-health-and-disease-ontologies/ohd-ontology/f19378ff192b6f9ea16133e85671e8359fc371cd/src/ontology/archive/CDTCodes%20as%20Classes_pruned.owl example: '1000001' homepage: https://www.ada.org/publications/CDT keywords: - ontology mappings: bartoc: '20299' hl7: 2.16.840.1.113883.6.116 name: Current Dental Terminology pattern: ^\d{7}$ preferred_prefix: cdt cell_biolabs: description: Cell line collections (Providers) example: AKR-270 homepage: https://www.cellbiolabs.com mappings: cellosaurus: Cell_Biolabs name: Cell Biolabs cell line products preferred_prefix: cell_biolabs uri_format: https://www.cellbiolabs.com/search?keywords=$1 cell_model_passport: description: Cell line databases/resources example: SIDM01262 homepage: https://cellmodelpassports.sanger.ac.uk/ mappings: cellosaurus: Cell_Model_Passport name: Sanger Cell Model Passports preferred_prefix: cell_model_passport uri_format: https://cellmodelpassports.sanger.ac.uk/passports/$1 cellbank.australia: description: CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world. example: ab-1-ha homepage: https://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/ mappings: cellosaurus: CBA name: CellBank Australia preferred_prefix: cellbank.australia uri_format: https://www.cellbankaustralia.com/$1.html cellimage: contact: email: dorloff@ncmir.ucsd.edu name: David N. Orloff orcid: 0000-0001-7594-0820 description: 'The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.' example: '24801' homepage: http://cellimagelibrary.org/ keywords: - cell biology - image - life science mappings: biocontext: CELLIMAGE fairsharing: FAIRsharing.8t18te miriam: cellimage n2t: cellimage prefixcommons: cellimage re3data: r3d100000023 name: Cell Image Library pattern: ^\d+$ preferred_prefix: cellimage providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/cellimage:$1 publications: - doi: 10.1093/nar/gks1257 pmc: PMC3531121 pubmed: '23203874' title: 'The cell: an image library-CCDB: a curated repository of microscopy data' year: 2012 twitter: CellImageLibrar uri_format: http://cellimagelibrary.org/images/$1 cellopub: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Cellosaurus identifeirs for publications, like Pubmed example: CLPUB00496 homepage: https://web.expasy.org/cellosaurus/ mappings: cellosaurus: CelloPub name: Cellosaurus Publication pattern: ^CLPUB\d+$ preferred_prefix: cellopub uri_format: https://web.expasy.org/cellosaurus/cellopub/$1 cellosaurus: banana: CVCL banana_peel: _ contact: email: Amos.Bairoch@sib.swiss github: AmosBairoch name: Amos Bairoch orcid: 0000-0003-2826-6444 description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.' download_obo: https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo example: '0440' homepage: https://cellosaurus.org keywords: - cell lines - controlled vocabularies - life science - ontologies - ontology - thesaurus license: CC-BY-4.0 mappings: biocontext: CELLOSAURUS cellosaurus: Cellosaurus fairsharing: FAIRsharing.hkk309 integbio: nbdc02180 miriam: cellosaurus n2t: cellosaurus re3data: r3d100013293 rrid: CVCL togoid: Cellosaurus wikidata: P3289 mastodon: cellosaurus@fediscience.org name: Cellosaurus pattern: ^[A-Z0-9]{4}$ preferred_prefix: cellosaurus providers: - code: legacy description: The legacy URI for the Cellosaurus website, updated on August 30, 2022 [ref](https://twitter.com/Cellosaurus/status/1564658792691810305). homepage: https://web.expasy.org/cellosaurus name: Legacy Endpoint uri_format: https://web.expasy.org/cellosaurus/CVCL_$1 - code: nextprot description: The neXtProt endpoint for exploring Cellosaurus homepage: https://www.nextprot.org/ name: neXtProt Cellosaurus Browser uri_format: https://www.nextprot.org/term/CVCL_$1 publications: - doi: 10.1002/ijc.32639 pubmed: '31444973' title: 'CLASTR: The Cellosaurus STR similarity search tool - A precious help for cell line authentication' year: 2019 - doi: 10.7171/jbt.18-2902-002 pmc: PMC5945021 pubmed: '29805321' title: The Cellosaurus, a Cell-Line Knowledge Resource year: 2018 repository: https://github.com/calipho-sib/cellosaurus synonyms: - CVCL twitter: cellosaurus uri_format: https://www.cellosaurus.org/CVCL_$1 cellosaurus.resource: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The set of prefixes used in the Cellosaurus resource example: 4DN homepage: https://web.expasy.org/cellosaurus/ keywords: - cell lines - cells - registry name: Cellosaurus Registry preferred_prefix: cellosaurus.resource uri_format: https://bioregistry.io/metaregistry/cellosaurus/$1 cellrepo: description: The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines example: '82' homepage: https://www.cellrepo.com/ mappings: miriam: cellrepo name: Cell Version Control Repository pattern: ^[0-9]+$ preferred_prefix: cellrepo uri_format: https://www.cellrepo.com/repositories/$1 cemo: contact: email: n.queralt_rosinach@lumc.nl github: NuriaQueralt name: Núria Queralt Rosinach orcid: 0000-0003-0169-8159 contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The covid-19 epidemiology and monitoring ontology (cemo) provides a common ontological model to make epidemiological quantitative data for monitoring the covid-19 outbreak machine-readable and interoperable to facilitate its exchange, integration and analysis, to eventually support evidence-based rapid response. download_json: https://raw.githubusercontent.com/cthoyt/covid19-epidemiology-ontology/add-artifacts/owl/cemo.json download_owl: https://raw.githubusercontent.com/NuriaQueralt/covid19-epidemiology-ontology/main/owl/cemo.owl example: secondary_attack_rate github_request_issue: 593 homepage: https://github.com/NuriaQueralt/covid19-epidemiology-ontology keywords: - ontology license: CC0-1.0 name: The COVID-19 epidemiology and monitoring ontology pattern: ^[0-9a-z_-]+$ preferred_prefix: cemo providers: - code: obo description: This represents misconfigured base IRIs, even though this ontology isn't an OBO Foundry ontology homepage: http://purl.obolibrary.org/obo/ name: Legacy OBO PURL uri_format: http://purl.obolibrary.org/obo/cemo.owl#$1 repository: https://github.com/NuriaQueralt/covid19-epidemiology-ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://biopragmatics.github.io/providers/cemo/$1 ceph: contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 deprecated: true description: An anatomical and developmental ontology for cephalopods download_obo: https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo download_owl: http://purl.obolibrary.org/obo/ceph.owl example: 0000109 homepage: https://github.com/obophenotype/cephalopod-ontology keywords: - anatomy - fisheries science - life cycle - obo - ontology - zoology license: CC-BY-3.0 mappings: aberowl: CEPH biocontext: CEPH bioportal: CEPH fairsharing: FAIRsharing.p58bm4 obofoundry: ceph ols: ceph ontobee: CEPH name: Cephalopod Ontology pattern: ^\d{7}$ preferred_prefix: CEPH rdf_uri_format: http://purl.obolibrary.org/obo/CEPH_$1 repository: https://github.com/obophenotype/cephalopod-ontology uri_format: http://purl.obolibrary.org/obo/CEPH_$1 version: '2016-01-12' cgd: contact: email: gsherloc@stanford.edu name: Gavin Sherlock orcid: 0000-0002-1692-4983 description: The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products. example: CAL0003079 homepage: http://www.candidagenome.org/ keywords: - eukaryotic - genome - life science - nucleotide mappings: biocontext: CGD fairsharing: FAIRsharing.j7j53 go: CGD integbio: nbdc00391 miriam: cgd n2t: cgd ncbi: CGD prefixcommons: cgd re3data: r3d100010617 uniprot: DB-0126 name: Candida Genome Database pattern: ^CAL\d{7}$ preferred_prefix: cgd providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/cgd:$1 publications: - doi: 10.1093/nar/gkw924 pmc: PMC5210628 pubmed: '27738138' title: 'The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data' year: 2016 - doi: 10.1093/nar/gkr945 pmc: PMC3245171 pubmed: '22064862' title: 'The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata' year: 2011 - doi: 10.1093/nar/gki003 pmc: PMC539957 pubmed: '15608216' title: The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information year: 2005 uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 cghdb: description: Cell line databases/resources example: 300165/p13898_2106T homepage: https://web.archive.org/web/20190222051223/http://www.cghtmd.jp/CGHDatabase/index_e.jsp mappings: cellosaurus: CGH-DB name: CGH Data Base preferred_prefix: cghdb cgnc: contact: email: fionamcc@arizona.edu name: Fiona M McCarthy orcid: 0000-0003-2175-5464 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans) example: '10087' homepage: http://birdgenenames.org/cgnc/ keywords: - gene license: CC-BY-4.0 mappings: cellosaurus: CGNC prefixcommons: cgnc re3data: r3d100012429 name: Chicken Gene Nomenclature Consortium pattern: ^\d+$ preferred_prefix: cgnc providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/cgnc:$1 publications: - doi: 10.1186/1471-2164-10-s2-s5 pmc: PMC2966335 pubmed: '19607656' title: The Chicken Gene Nomenclature Committee report year: 2009 synonyms: - BirdBase - CGNC uri_format: http://birdgenenames.org/cgnc/GeneReport?id=$1 cgsc: contact: email: kelly.hughes@utah.edu name: Kelly T. Hughes orcid: 0000-0003-1546-6746 description: The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. example: '74' homepage: http://cgsc.biology.yale.edu/index.php keywords: - gene - life science mappings: biocontext: CGSC fairsharing: FAIRsharing.1tbrdz go: CGSC miriam: cgsc n2t: cgsc prefixcommons: cgsc re3data: r3d100010585 name: Coli Genetic Stock Center pattern: ^\d+$ preferred_prefix: cgsc providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/cgsc:$1 publications: - doi: 10.1016/s0076-6879(06)21001-2 pubmed: '17352909' title: Strain collections and genetic nomenclature year: 2007 - doi: 10.1016/S0076-6879(06)21001-2 title: Strain collections and genetic nomenclature. 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/$1 chebi: appears_in: - cdno - chiro - ecocore - ecto - envo - fobi - foodon - genepio - maxo - mco - ons - pcl - proco - scdo - uberon - xpo banana: CHEBI contact: email: amalik@ebi.ac.uk github: amalik01 name: Adnan Malik orcid: 0000-0001-8123-5351 description: Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. download_obo: http://purl.obolibrary.org/obo/chebi.obo download_owl: http://purl.obolibrary.org/obo/chebi.owl example: '138488' homepage: http://www.ebi.ac.uk/chebi keywords: - biochemistry - chemical - chemistry - molecular entity - molecular structure - natural product - obo - ontology - small molecule - taxonomic classification license: CC-BY-4.0 logo: https://www.ebi.ac.uk/chebi/images/ChEBI_logo.png mappings: aberowl: CHEBI bartoc: '558' biocontext: CHEBI bioportal: CHEBI cellosaurus: ChEBI cheminf: '000407' edam: '1174' fairsharing: FAIRsharing.62qk8w go: CHEBI integbio: nbdc00027 miriam: chebi n2t: chebi obofoundry: chebi ols: chebi ontobee: CHEBI prefixcommons: chebi re3data: r3d100012626 togoid: Chebi wikidata: P683 name: Chemical Entities of Biological Interest namespace_in_lui: true pattern: ^\d+$ preferred_prefix: CHEBI providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/chebi:$1 - code: chebi-img description: Image server from chebi first_party: true 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 - code: iedb.antigen description: A comprehensive collection of data on immune epitopes, covering experimental data and resources, including antigens homepage: https://www.iedb.org/ name: Immune Epitope Database uri_format: https://www.iedb.org/antigen/ChEBI:$1 publications: - doi: 10.1093/nar/gkv1031 pmc: PMC4702775 pubmed: '26467479' title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites' year: 2015 - doi: 10.1093/nar/gks1146 pmc: PMC3531142 pubmed: '23180789' title: 'The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013' year: 2012 - doi: 10.1093/nar/gkp886 pmc: PMC2808869 pubmed: '19854951' title: 'Chemical Entities of Biological Interest: an update' year: 2009 - doi: 10.1002/0471250953.bi1409s26 pubmed: '19496059' title: 'ChEBI: an open bioinformatics and cheminformatics resource' year: 2009 - doi: 10.1093/nar/gkm791 pmc: PMC2238832 pubmed: '17932057' title: 'ChEBI: a database and ontology for chemical entities of biological interest' year: 2007 rdf_uri_format: http://purl.obolibrary.org/obo/CHEBI_$1 repository: https://github.com/ebi-chebi/ChEBI synonyms: - CHEBI - CHEBIID - ChEBI twitter: chebit uri_format: http://purl.obolibrary.org/obo/CHEBI_$1 version: '239' chembank: comment: This resource doesn't exist on the web anymore deprecated: true description: ChemBank is a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG). example: '1000000' homepage: http://chembank.broad.harvard.edu keywords: - chemical - metabolite mappings: biocontext: CHEMBANK biolink: ChemBank prefixcommons: chembank name: ChemBank preferred_prefix: chembank providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/chembank:$1 publications: - doi: 10.1093/nar/gkm843 pmc: PMC2238881 pubmed: '17947324' title: 'ChemBank: a small-molecule screening and cheminformatics resource database' year: 2007 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$1 chembl: contact: email: dmendez@ebi.ac.uk github: nclopezo name: David Mendez Lopez orcid: 0000-0002-0294-5484 description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. example: CHEMBL4303805 homepage: https://www.ebi.ac.uk/chembl keywords: - biochemistry - drug discovery - genomics - medicinal chemistry - molecules license: CC-BY-SA-3.0 mappings: cheminf: '000412' fairsharing: FAIRsharing.m3jtpg integbio: nbdc02555 miriam: chembl prefixcommons: chembl re3data: r3d100010539 uniprot: DB-0174 name: ChEMBL pattern: ^CHEMBL\d+$ preferred_prefix: chembl providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/chembl:$1 publications: - doi: 10.1093/nar/gky1075 pmc: PMC6323927 pubmed: '30398643' title: 'ChEMBL: towards direct deposition of bioassay data' year: 2019 - doi: 10.1093/nar/gkw1074 pmc: PMC5210557 pubmed: '27899562' title: The ChEMBL database in 2017 year: 2016 - doi: 10.1093/nar/gkt1031 pmc: PMC3965067 pubmed: '24214965' title: 'The ChEMBL bioactivity database: an update' year: 2013 - doi: 10.1093/nar/gkr777 pmc: PMC3245175 pubmed: '21948594' title: 'ChEMBL: a large-scale bioactivity database for drug discovery' year: 2011 repository: https://github.com/chembl/GLaDOS synonyms: - ChEMBL - ChEMBL_ID - chembl twitter: chembl uri_format: https://www.ebi.ac.uk/chembl/entity/$1 chembl.cell: contact: email: dmendez@ebi.ac.uk github: nclopezo name: David Mendez Lopez orcid: 0000-0002-0294-5484 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Chemistry resources example: CHEMBL3307800 homepage: https://www.ebi.ac.uk/chembldb keywords: - bioactivities - cell lines license: CC-BY-SA-3.0 mappings: cellosaurus: ChEMBL-Cells name: ChEMBL database of bioactive drug-like small molecules - Cell lines section part_of: chembl pattern: ^CHEMBL\d+$ preferred_prefix: chembl.cell synonyms: - ChEMBL-Cells uri_format: https://www.ebi.ac.uk/chembl/cell_line_report_card/$1 chembl.compound: contact: email: dmendez@ebi.ac.uk github: nclopezo name: David Mendez Lopez orcid: 0000-0002-0294-5484 description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. example: CHEMBL465070 homepage: https://www.ebi.ac.uk/chembldb/ license: CC-BY-SA-3.0 mappings: biocontext: CHEMBL.COMPOUND edam: '2646' miriam: chembl.compound n2t: chembl.compound togoid: ChemblCompound wikidata: P592 name: ChEMBL part_of: chembl pattern: ^CHEMBL\d+$ preferred_prefix: chembl.compound providers: - 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 rdf_uri_format: http://rdf.ebi.ac.uk/resource/chembl/molecule/$1 uri_format: https://www.ebi.ac.uk/chembl/compound/inspect/$1 chembl.target: contact: email: dmendez@ebi.ac.uk github: nclopezo name: David Mendez Lopez orcid: 0000-0002-0294-5484 description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. example: CHEMBL3467 homepage: https://www.ebi.ac.uk/chembldb/ license: CC-BY-SA-3.0 mappings: biocontext: CHEMBL.TARGET cellosaurus: ChEMBL-Targets miriam: chembl.target n2t: chembl.target togoid: ChemblTarget name: ChEMBL target part_of: chembl pattern: ^CHEMBL\d+$ preferred_prefix: chembl.target synonyms: - ChEMBL-Targets uri_format: https://www.ebi.ac.uk/chembl/target/inspect/$1 chemdb: contact: email: pfbaldi@uci.edu name: Pierre Baldi orcid: 0000-0001-8752-4664 description: ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. example: '3966782' homepage: http://cdb.ics.uci.edu/ keywords: - biochemistry - biomedical science - life science - preclinical studies - small molecule - systems biology mappings: biocontext: CHEMDB fairsharing: FAIRsharing.dstf7h miriam: chemdb n2t: chemdb prefixcommons: chemdb name: ChemDB pattern: ^\d+$ preferred_prefix: chemdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/chemdb:$1 publications: - doi: 10.1093/bioinformatics/btm341 pubmed: '17599932' title: ChemDB update--full-text search and virtual chemical space year: 2007 - doi: 10.1093/bioinformatics/bti683 pubmed: '16174682' title: 'ChemDB: a public database of small molecules and related chemoinformatics resources' year: 2005 uri_format: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1 chemicalbook: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A hybrid chemical enyclopedia and supplier advertizing system for chemicals. example: CB82546919 github_request_issue: 1311 homepage: https://www.chemicalbook.com name: Chemical Book preferred_prefix: chemicalbook synonyms: - ChemicalBookNo uri_format: https://www.chemicalbook.com/ChemicalProductProperty_IN_$1.htm chemidplus: description: ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. example: 57-27-2 homepage: https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp keywords: - biomedical science - chemistry - molecules - structure mappings: biocontext: CHEMIDPLUS edam: '2658' fairsharing: FAIRsharing.5949vn integbio: nbdc01837 miriam: chemidplus n2t: chemidplus prefixcommons: chemidplus name: ChemIDplus pattern: ^\d+\-\d+\-\d+$ preferred_prefix: chemidplus providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/chemidplus:$1 publications: - doi: 10.1300/j115v21n01_04 pubmed: '11989279' title: ChemIDplus-super source for chemical and drug information year: 2002 - doi: 10.1300/J115v21n01_04 title: ChemIDplus-super source for chemical and drug information. synonyms: - ChemIDplus uri_format: https://chem.nlm.nih.gov/chemidplus/rn/$1 cheminf: appears_in: - proco banana: CHEMINF contact: email: egon.willighagen@gmail.com github: egonw name: Egon Willighagen orcid: 0000-0001-7542-0286 description: The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals. download_owl: https://github.com/semanticchemistry/semanticchemistry/raw/master/ontology/cheminf.owl example: '000410' homepage: https://github.com/semanticchemistry/semanticchemistry keywords: - biochemistry - chemistry - life science - molecular entity - molecular structure - obo - ontology license: CC0-1.0 mappings: aberowl: CHEMINF biocontext: CHEMINF bioportal: CHEMINF fairsharing: FAIRsharing.sjhvyy miriam: cheminf obofoundry: cheminf ols: cheminf ontobee: CHEMINF name: Chemical Information Ontology namespace_in_lui: true pattern: ^\d{6}$ preferred_prefix: CHEMINF providers: - code: semanticscience description: Legacy URLs before conversion of CHEMINF to OBO PURLs homepage: http://semanticscience.org name: Semantic Science uri_format: http://semanticscience.org/resource/CHEMINF_$1 publications: - doi: 10.1371/journal.pone.0025513 pmc: PMC3184996 pubmed: '21991315' title: 'The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web' year: 2011 rdf_uri_format: http://purl.obolibrary.org/obo/CHEMINF_$1 repository: https://github.com/semanticchemistry/semanticchemistry uri_format: http://purl.obolibrary.org/obo/CHEMINF_$1 version: 2.1.0 chempro.competitor: contact: email: zhufeng@zju.edu.cn name: Feng Zhu orcid: 0000-0001-8069-0053 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for compounds that compete with probes for binding to target proteins. example: LDCM0160 github_request_issue: 1424 homepage: https://chemprosquare.idrblab.net name: ChemPro Competitor pattern: ^LDCM\d+$ preferred_prefix: chempro.competitor publications: - doi: 10.1093/nar/gkae943 pmc: PMC11701659 pubmed: '39436046' title: 'Chem(Pro)2: the atlas of chemoproteomic probes labelling human proteins' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://chemprosquare.idrblab.net/data/competitor/details/$1 chempro.probe: contact: email: zhufeng@zju.edu.cn name: Feng Zhu orcid: 0000-0001-8069-0053 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for chemoproteomic probes used to label human proteins in living cells. example: LDPC0032 github_request_issue: 1424 homepage: https://chemprosquare.idrblab.net name: ChemPro Probe pattern: ^LDPC\d+$ preferred_prefix: chempro.probe publications: - doi: 10.1093/nar/gkae943 pmc: PMC11701659 pubmed: '39436046' title: 'Chem(Pro)2: the atlas of chemoproteomic probes labelling human proteins' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://chemprosquare.idrblab.net/data/probe/details/$1 chempro.target: contact: email: zhufeng@zju.edu.cn name: Feng Zhu orcid: 0000-0001-8069-0053 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for human proteins that interact with chemoproteomic probes. example: LDTP03903 github_request_issue: 1424 homepage: https://chemprosquare.idrblab.net name: ChemPro Target pattern: ^LDTP\d+$ preferred_prefix: chempro.target publications: - doi: 10.1093/nar/gkae943 pmc: PMC11701659 pubmed: '39436046' title: 'Chem(Pro)2: the atlas of chemoproteomic probes labelling human proteins' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://chemprosquare.idrblab.net/data/target/details/$1 chemrof: contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: CHEMROF is an ontological framework for Chemical Entities Mixtures Reactions Ontological Framework. This OWL ontology is an automated Translation of the source LinkML schema, https://w3id.org/chemrof download_owl: http://aber-owl.net/media/ontologies/CHEMROF/4/chemrof.owl example: FullySpecifiedAtom homepage: https://chemkg.github.io/chemrof/ keywords: - ontology mappings: aberowl: CHEMROF bioportal: CHEMROF name: Chemical Entity Materials and Reactions Ontological Framework preferred_prefix: ChEMROF uri_format: https://chemkg.github.io/chemrof/$1 chemspider: contact: email: pencehe@oneonta.edu name: Harry E. Pence orcid: 0000-0002-0412-9018 description: ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources. example: '56586' homepage: http://www.chemspider.com/ keywords: - chemistry - life science - molecules - structure mappings: biocontext: CHEMSPIDER cheminf: '000405' edam: '1173' fairsharing: FAIRsharing.96f3gm integbio: nbdc01863 miriam: chemspider n2t: chemspider prefixcommons: chemspider re3data: r3d100010205 wikidata: P661 name: ChemSpider pattern: ^\d+$ preferred_prefix: chemspider providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/chemspider:$1 publications: - doi: 10.1021/ed100697w title: 'ChemSpider: An Online Chemical Information Resource' year: 2010 rdf_uri_format: http://rdf.chemspider.com/$1 synonyms: - ChemSpiderID - Chemspider twitter: ChemSpider uri_format: http://www.chemspider.com/Chemical-Structure.$1.html chickenqtldb: description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs. example: '14362' homepage: https://www.animalgenome.org/QTLdb keywords: - dna - genome mappings: biocontext: CHICKENQTLDB miriam: chickenqtldb n2t: chickenqtldb prefixcommons: chickenqtldb name: Animal Genome Chicken QTL part_of: qtldb pattern: ^\d+$ preferred_prefix: chickenqtldb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/chickenqtldb:$1 uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 chictr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Established in 2005 by professor Wu Taixiang and Li Youping team, West China Hospital, Sichuan University, and the Ministry of Health of China assigned it to be the representative of China to join WHO ICTRP in 2007. The Chinese Clinical Trial Registry provides the services include register for trials, consultation for trial design, central randomization for an allocation sequence, peer review for draft articles and training for peer reviewers. (from website) example: ChiCTR2300070727 homepage: https://www.chictr.org.cn logo: https://www.chictr.org.cn/images/top.jpg name: Chinese Clinical Trial Registry pattern: ^ChiCTR(-[A-Z]+-)?\d+$ preferred_prefix: chictr references: - https://www.chictr.org.cn/showproj.html?proj=187605 chiro: contact: email: vasilevs@ohsu.edu github: nicolevasilevsky name: Nicole Vasilevsky orcid: 0000-0001-5208-3432 depends_on: - chebi - go - hp - mp - ncbitaxon - pr - uberon description: CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes. download_obo: http://purl.obolibrary.org/obo/chiro.obo download_owl: http://purl.obolibrary.org/obo/chiro.owl homepage: https://github.com/obophenotype/chiro keywords: - obo - ontology license: CC0-1.0 mappings: aberowl: CHIRO bioportal: CHIRO obofoundry: chiro ols: chiro ontobee: CHIRO name: ChEBI Integrated Role Ontology no_own_terms: true preferred_prefix: CHIRO publications: - doi: 10.26434/chemrxiv.12591221 title: Extension of Roles in the ChEBI Ontology year: 2020 rdf_uri_format: http://purl.obolibrary.org/obo/CHIRO_$1 repository: https://github.com/obophenotype/chiro uri_format: http://purl.obolibrary.org/obo/CHIRO_$1 version: '2015-11-23' chmo: appears_in: - rbo - scdo contact: email: batchelorc@rsc.org github: batchelorc name: Colin Batchelor orcid: 0000-0001-5985-7429 description: CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI). download_obo: http://purl.obolibrary.org/obo/chmo.obo download_owl: http://purl.obolibrary.org/obo/chmo.owl example: 0002902 homepage: https://github.com/rsc-ontologies/rsc-cmo keywords: - assay - chemistry - chromatography - electron microscopy - mass spectrometry assay - obo - ontology license: CC-BY-4.0 mappings: aberowl: CHMO bartoc: '20509' biocontext: CHMO bioportal: CHMO fairsharing: FAIRsharing.9j4wh2 obofoundry: chmo ols: chmo ontobee: CHMO name: Chemical Methods Ontology pattern: ^\d{7}$ preferred_prefix: CHMO rdf_uri_format: http://purl.obolibrary.org/obo/CHMO_$1 repository: https://github.com/rsc-ontologies/rsc-cmo uri_format: http://purl.obolibrary.org/obo/CHMO_$1 version: '2022-04-19' chr: contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 contributor: email: jhc@lbl.gov github: caufieldjh name: Harry Caufield orcid: 0000-0001-5705-7831 description: The Chromosome Ontology is an automatically derived ontology of chromosomes and chromosome parts. download_json: https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.json download_obo: https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.obo download_owl: https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.owl example: 10090-chr10qC github_request_issue: 1265 homepage: https://github.com/monarch-initiative/monochrom keywords: - ontology license: BSD-3 mappings: aberowl: CHR biocontext: CHR bioportal: CHR name: Chromosome Ontology preferred_prefix: chr repository: https://github.com/monarch-initiative/monochrom reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 cido: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment. download_owl: https://github.com/CIDO-ontology/cido/raw/master/cido.owl example: '0000005' homepage: https://github.com/cido-ontology/cido keywords: - bioinformatics - covid-19 - disease - drug - drug discovery - drug interaction - drug repositioning - epidemiology - infection - obo - ontology - virology license: CC-BY-4.0 mappings: aberowl: CIDO bioportal: CIDO fairsharing: FAIRsharing.aVmpKl obofoundry: cido ols: cido ontobee: CIDO name: Coronavirus Infectious Disease Ontology pattern: ^\d{7}$ preferred_prefix: CIDO publications: - doi: 10.1186/s13326-022-00279-z pmc: PMC9585694 pubmed: '36271389' title: 'A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology' year: 2022 - doi: 10.1038/s41597-020-0523-6 pmc: PMC7293349 pubmed: '32533075' title: CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis year: 2020 rdf_uri_format: http://purl.obolibrary.org/obo/CIDO_$1 repository: https://github.com/cido-ontology/cido uri_format: http://purl.obolibrary.org/obo/CIDO_$1 version: '2024-02-16' cienciavitae: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier of scientific author in www.cienciavitae.pt example: 0C1F-DA6C-4B02 homepage: https://www.ciencia-id.pt keywords: - person - researcher mappings: wikidata: P7893 name: CIÊNCIAVITAE ID pattern: ^([0-9A-F]{4}-){2}[0-9A-F]{4}$ preferred_prefix: cienciavitae references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://www.cienciavitae.pt/$1 cio: contact: email: frederic.bastian@unil.ch github: fbastian name: Frédéric Bastian orcid: 0000-0002-9415-5104 description: An ontology to capture confidence information about annotations. download_obo: http://purl.obolibrary.org/obo/cio.obo download_owl: http://purl.obolibrary.org/obo/cio.owl example: '0000040' homepage: https://github.com/BgeeDB/confidence-information-ontology keywords: - annotation - biology - obo - ontology license: CC0-1.0 mappings: aberowl: CIO biocontext: CIO bioportal: CIO fairsharing: FAIRsharing.e3t0yw obofoundry: cio ols: cio ontobee: CIO name: Confidence Information Ontology pattern: ^\d{7}$ preferred_prefix: CIO publications: - doi: 10.1093/database/bav043 pmc: PMC4425939 pubmed: '25957950' title: 'The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations' year: 2015 rdf_uri_format: http://purl.obolibrary.org/obo/CIO_$1 repository: https://github.com/BgeeDB/confidence-information-ontology uri_format: http://purl.obolibrary.org/obo/CIO_$1 version: '2015-03-10' citexplore: contact: email: maria.taboada@usc.es name: Maria Taboada orcid: 0000-0002-2353-596X contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes. example: C6155 homepage: https://www.ebi.ac.uk/citexplore/ keywords: - biomedical science - brain - disease - genetics - lipid - phenotype - preclinical studies mappings: fairsharing: FAIRsharing.619eqr prefixcommons: citexplore name: CiteXplore preferred_prefix: citexplore providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/citexplore:$1 publications: - doi: 10.1097/mol.0b013e328362df13 pubmed: '23759795' title: Cerebrotendinous xanthomatosis year: 2013 references: - https://www.embl.de/aboutus/communication_outreach/media_relations/2006/061127_hinxton/ synonyms: - CTX uri_format: https://europepmc.org/article/CTX/$1 cito: contact: email: silvio.peroni@unibo.it github: essepuntato name: Silvio Peroni orcid: 0000-0003-0530-4305 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology that enables characterization of the nature or type of citations, both factually and rhetorically. example: sharesAuthorInstitutionWith homepage: http://www.sparontologies.net/ontologies/cito keywords: - citation - data model - knowledge and information systems - spar mappings: fairsharing: FAIRsharing.b220d4 lov: cito name: Citation Typing Ontology preferred_prefix: CiTO publications: - doi: 10.1016/j.websem.2012.08.001 title: 'FaBiO and CiTO: Ontologies for describing bibliographic resources and citations' year: 2012 repository: https://github.com/sparontologies/cito twitter: sparontologies uri_format: http://purl.org/spar/cito/$1 civic.aid: contact: email: mgriffit@wustl.edu github: malachig name: Malachi Griffith orcid: 0000-0002-6388-446X description: 'A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC.' example: '3' homepage: https://civicdb.org/ license: CC0-1.0 mappings: miriam: civic.aid name: CIViC Assertion part_of: civic pattern: ^[0-9]+$ preferred_prefix: civic.aid synonyms: - civic.assertion uri_format: https://civicdb.org/links/assertions/$1 civic.did: contact: email: mgriffit@wustl.edu github: malachig name: Malachi Griffith orcid: 0000-0002-6388-446X description: Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement. example: '46' homepage: https://civicdb.org/ license: CC0-1.0 mappings: miriam: civic.did name: CIViC Disease part_of: civic pattern: ^[0-9]+$ preferred_prefix: civic.did synonyms: - civic.disease uri_format: https://civicdb.org/links/diseases/$1 civic.eid: contact: email: mgriffit@wustl.edu github: malachig name: Malachi Griffith orcid: 0000-0002-6388-446X description: Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract). example: '1199' homepage: https://civicdb.org/ license: CC0-1.0 mappings: miriam: civic.eid name: CIViC Evidence part_of: civic pattern: ^[0-9]+$ preferred_prefix: civic.eid synonyms: - civic.evidence uri_format: https://civicdb.org/links/evidence/$1 civic.gid: contact: email: mgriffit@wustl.edu github: malachig name: Malachi Griffith orcid: 0000-0002-6388-446X description: A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus on emphasizing the clinical relevance from a molecular perspective rather than describing the biological function of the gene unless necessary to contextualize its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes, specific treatments for the gene’s associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis example: '272' homepage: https://civicdb.org/ license: CC0-1.0 mappings: miriam: civic.gid wikidata: P11277 name: CIViC gene part_of: civic pattern: ^[0-9]+$ preferred_prefix: civic.gid synonyms: - civic.gene uri_format: https://civicdb.org/links/gene/$1 civic.mpid: contact: email: mgriffit@wustl.edu github: malachig name: Malachi Griffith orcid: 0000-0002-6388-446X description: CIViC Molecular Profiles are combinations of one or more CIViC variants. Most Molecular Profiles are “Simple” Molecular Profiles comprised of a single variant. In most cases, these can be considered equivalent to the CIViC concept of a Variant. However, increasingly clinical significance must be considered in the context of multiple variants simultaneously. Complex Molecular Profiles in CIViC allow for curation of such variant combinations. Regardless of the nature of the Molecular Profile (Simple or Complex), it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional clinical relevance to be entered in CIViC. example: '559' homepage: https://civicdb.org/ license: CC0-1.0 mappings: miriam: civic.mpid name: CIViC Molecular Profile pattern: ^[0-9]+$ preferred_prefix: civic.mpid synonyms: - civic.molecularprofile uri_format: https://civicdb.org/links/molecular_profile/$1 civic.sid: contact: email: mgriffit@wustl.edu github: malachig name: Malachi Griffith orcid: 0000-0002-6388-446X description: In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source. example: '62' homepage: https://civicdb.org/ license: CC0-1.0 mappings: miriam: civic.sid name: CIViC Source part_of: civic pattern: ^[0-9]+$ preferred_prefix: civic.sid synonyms: - civic.source uri_format: https://civicdb.org/links/sources/$1 civic.tid: contact: email: mgriffit@wustl.edu github: malachig name: Malachi Griffith orcid: 0000-0002-6388-446X description: Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant. example: '14' homepage: https://civicdb.org/ license: CC0-1.0 mappings: miriam: civic.tid name: CIViC Therapy part_of: civic pattern: ^[0-9]+$ preferred_prefix: civic.tid synonyms: - civic.therapy uri_format: https://civicdb.org/links/drugs/$1 civic.vgid: contact: email: mgriffit@wustl.edu github: malachig name: Malachi Griffith orcid: 0000-0002-6388-446X description: Variant Groups in CIViC provide user-defined grouping of Variants within and between genes based on unifying characteristics. CIViC curators are required to define a cohesive rationale for grouping these variants together, summarize their relevance to cancer diagnosis, prognosis or treatment and highlight any treatments or cancers of particular relevance example: '16' homepage: https://civicdb.org/ license: CC0-1.0 mappings: miriam: civic.vgid name: CIViC Variant Group pattern: ^[0-9]+$ preferred_prefix: civic.vgid synonyms: - civic.variantgroup uri_format: https://civicdb.org/links/variant_group/$1 civic.vid: contact: email: mgriffit@wustl.edu github: malachig name: Malachi Griffith orcid: 0000-0002-6388-446X description: CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making. example: '12' homepage: https://civicdb.org/ license: CC0-1.0 mappings: miriam: civic.vid wikidata: P3329 name: CIViC variant part_of: civic pattern: ^[0-9]+$ preferred_prefix: civic.vid synonyms: - civic.variant uri_format: https://civicdb.org/links/variant/$1 cl: appears_in: - clo - ecao - ehdaa2 - go - mco - pcl - uberon - xpo banana: CL contact: email: addiehl@buffalo.edu github: addiehl name: Alexander Diehl orcid: 0000-0001-9990-8331 contributor_extras: - github: anitacaron name: Anita Caron orcid: 0000-0002-6523-4866 depends_on: - go - ncbitaxon - omo - pato - pr - ro - uberon description: The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi. download_json: http://purl.obolibrary.org/obo/cl.json download_obo: https://github.com/obophenotype/cell-ontology/raw/master/cl.obo download_owl: http://purl.obolibrary.org/obo/cl.owl example: '0000062' homepage: https://obophenotype.github.io/cell-ontology/ keywords: - anatomy - annotation - cell - cell biology - life science - morphology - obo - ontology license: CC-BY-4.0 logo: https://obofoundry.org/images/CL-logo.jpg mappings: aberowl: CL agroportal: CL biocontext: CL bioportal: CL cellosaurus: CL fairsharing: FAIRsharing.j9y503 go: CL miriam: cl n2t: cl obofoundry: cl ols: cl ontobee: CL prefixcommons: cl wikidata: P7963 name: Cell Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: CL providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/cl:$1 - code: cellguide description: CellGuide is a comprehensive resource for knowledge about cell types. homepage: https://cellxgene.cziscience.com/cellguide name: Cell Guide uri_format: https://cellxgene.cziscience.com/cellguide/CL_$1 - code: cellxgene description: Explore single cell data through the CZ CELLxGENE portal homepage: https://onto.cellxgene-labs.prod.si.czi.technology name: CELLxGENE uri_format: https://onto.cellxgene-labs.prod.si.czi.technology/a/ontology/CL/CL:$1 publications: - doi: 10.1186/s13326-016-0088-7 pmc: PMC4932724 pubmed: '27377652' title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability' year: 2016 - doi: 10.1186/1471-2105-12-6 pmc: PMC3024222 pubmed: '21208450' title: Logical development of the cell ontology year: 2011 rdf_uri_format: http://purl.obolibrary.org/obo/CL_$1 repository: https://github.com/obophenotype/cell-ontology twitter: CellOntology uri_format: http://purl.obolibrary.org/obo/CL_$1 version: '2025-02-13' clao: contact: email: lagonzalezmo@unal.edu.co github: luis-gonzalez-m name: Luis González-Montaña orcid: 0000-0002-9136-9932 depends_on: - ro description: 'CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).' download_obo: http://purl.obolibrary.org/obo/clao.obo download_owl: http://purl.obolibrary.org/obo/clao.owl example: 0000088 homepage: https://github.com/luis-gonzalez-m/Collembola keywords: - obo - ontology license: CC0-1.0 mappings: aberowl: CLAO bioportal: CLAO obofoundry: clao ols: clao ontobee: CLAO name: Collembola Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: CLAO rdf_uri_format: http://purl.obolibrary.org/obo/CLAO_$1 repository: https://github.com/luis-gonzalez-m/Collembola uri_format: http://purl.obolibrary.org/obo/CLAO_$1 version: '2021-09-27' classyfire: banana: C comment: There's a mismatch between the MIRIAM URI format string, which has a C prefix in front of class identifiers and the ontology which does not use them. description: ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API. download_obo: http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip example: 0004828 homepage: http://classyfire.wishartlab.com/ keywords: - ontology mappings: miriam: classyfire name: ClassyFire pattern: ^\d{7}$ preferred_prefix: classyfire synonyms: - CHEMONTID - chemont uri_format: http://classyfire.wishartlab.com/tax_nodes/C$1 clb: description: ChecklistBank is an index and repository for taxonomic and nomenclatural datasets example: '1010' homepage: https://www.checklistbank.org mappings: miriam: clb name: ChecklistBank pattern: ^[0-9]+(LR)?$ preferred_prefix: clb uri_format: https://www.checklistbank.org/dataset/$1 cldb: description: The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories. example: cl3603 homepage: http://bioinformatics.hsanmartino.it/hypercldb/indexes.html mappings: biocontext: CLDB cellosaurus: CLDB miriam: cldb n2t: cldb name: Cell Line Database pattern: ^(cl|tum)\d+$ preferred_prefix: cldb synonyms: - hypercldb uri_format: http://bioinformatics.hsanmartino.it/hypercldb/$1.html clingen.affiliation: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: ClinGen is a National Institutes of Health (NIH)-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This prefix provides identifiers for a panel of experts performing variant pathogenecity evaluation. example: '40135' github_request_issue: 1314 homepage: https://clinicalgenome.org/affiliation name: ClinGen Clinical Genome Expert Panel preferred_prefix: clingen.affiliation uri_format: https://clinicalgenome.org/affiliation/$1/ clingen.allele: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 description: ClinGen is a National Institutes of Health (NIH)-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This prefix provides and maintains identifiers for alleles. example: CA981206459 homepage: https://reg.clinicalgenome.org keywords: - alleles - genetics - mutations mappings: biolink: CAID name: ClinGen Allele Registry pattern: ^CA\d+$ preferred_prefix: clingen.allele references: - https://github.com/biopragmatics/bioregistry/issues/647 synonyms: - CAID - clingene uri_format: https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1 clingen.curation: banana: CCID banana_peel: ':' contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: ClinGen is a National Institutes of Health (NIH)-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This prefix provides identifiers for curations representing evidence aggregation and expert panel assertions based on standardized evaluation procedures example: '004126' github_request_issue: 1414 homepage: https://search.clinicalgenome.org/kb/gene-validity name: ClinGen Curation pattern: ^\d{6}$ preferred_prefix: clingen.curation reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://search.clinicalgenome.org/CCID:$1 clinicaltrials: description: ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries example: NCT00222573 homepage: https://clinicaltrials.gov/ keywords: - disease - drug - human license: https://clinicaltrials.gov/about-site/terms-conditions#availability mappings: biocontext: CLINICALTRIALS miriam: clinicaltrials n2t: clinicaltrials prefixcommons: clinicaltrials wikidata: P3098 name: ClinicalTrials.gov pattern: ^NCT\d{8}$ preferred_prefix: clinicaltrials providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/clinicaltrials:$1 - code: smartpatients description: Smart Patients is an online community for patients and their families. Join us to talk with other patients about the latest research for your condition. homepage: https://www.smartpatients.com name: Smart Patients uri_format: https://www.smartpatients.com/trials/$1 synonyms: - NCT - clinicaltrial - ctgov uri_format: https://www.clinicaltrials.gov/study/$1 clinvar: contact: email: maglott@ncbi.nlm.nih.gov name: Donna R. Maglott orcid: 0000-0001-7451-4467 description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier. example: '12345' homepage: http://www.ncbi.nlm.nih.gov/clinvar/ keywords: - biomedical science - clinical studies - genomics - preclinical studies mappings: biocontext: ClinVarVariant biolink: CLINVAR cellosaurus: ClinVar fairsharing: FAIRsharing.wx5r6f hl7: 2.16.840.1.113883.6.319 integbio: nbdc01514 miriam: clinvar n2t: clinvar re3data: r3d100013331 togoid: Clinvar wikidata: P1929 name: ClinVar Variation pattern: ^\d+$ preferred_prefix: clinvar publications: - doi: 10.1093/nar/gkt1113 pmc: PMC3965032 pubmed: '24234437' title: 'ClinVar: public archive of relationships among sequence variation and human phenotype' year: 2013 synonyms: - clinvar.variant - clinvar.variation uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1 clinvar.record: description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession. example: RCV000033555.3 homepage: http://www.ncbi.nlm.nih.gov/clinvar/ mappings: biocontext: CLINVAR.RECORD miriam: clinvar.record n2t: clinvar.record name: ClinVar Record part_of: clinvar pattern: ^RCV\d+(\.\d+)?$ preferred_prefix: clinvar.record uri_format: http://www.ncbi.nlm.nih.gov/clinvar/$1 clinvar.submission: description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession. example: SCV000151292 homepage: http://www.ncbi.nlm.nih.gov/clinvar/ mappings: biocontext: CLINVAR.SUBMISSION miriam: clinvar.submission n2t: clinvar.submission name: ClinVar Submission pattern: ^SCV\d+(\.\d+)?$ preferred_prefix: clinvar.submission uri_format: http://www.ncbi.nlm.nih.gov/clinvar?term=$1 clinvar.submitter: description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs). example: '26957' homepage: https://www.ncbi.nlm.nih.gov/clinvar/ mappings: miriam: clinvar.submitter name: ClinVar Submitter pattern: ^\d+$ preferred_prefix: clinvar.submitter uri_format: https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1 clo: appears_in: - mco contact: email: zhengj2007@gmail.com github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 depends_on: - cl - doid - ncbitaxon - uberon description: The Cell Line Ontology is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns. download_owl: http://purl.obolibrary.org/obo/clo.owl example: 0000091 homepage: https://github.com/CLO-Ontology/CLO keywords: - cell - cell biology - cell line - life science - morphology - obo - ontology license: CC-BY-3.0 mappings: aberowl: CLO biocontext: CLO bioportal: CLO cellosaurus: CLO fairsharing: FAIRsharing.4dvtcz miriam: clo obofoundry: clo ols: clo ontobee: CLO prefixcommons: clo wikidata: P2158 name: Cell Line Ontology pattern: ^\d{7}$ preferred_prefix: CLO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/clo:$1 - code: bioportal description: Our vision is that all biomedical knowledge and data are disseminated on the Internet using principled ontologies in such a way that the knowledge and data are semantically interoperable and useful for furthering biomedical science and clinical care. Our mission is to create software and support services for the application of principled ontologies in biomedical science and clinical care, ranging from tools for application developers to software for end-users. homepage: https://bioportal.bioontology.org name: Center for Biomedical Informatics Research, Stanford uri_format: https://bioportal.bioontology.org/ontologies/CLO/?p=classes&conceptid=http://purl.obolibrary.org/obo/CLO_$1 publications: - doi: 10.1186/2041-1480-5-37 pmc: PMC4387853 pubmed: '25852852' title: 'CLO: The cell line ontology' year: 2014 - doi: 10.1186/gb-2005-6-2-r21 pmc: PMC551541 pubmed: '15693950' title: An ontology for cell types year: 2005 rdf_uri_format: http://purl.obolibrary.org/obo/CLO_$1 repository: https://github.com/CLO-Ontology/CLO synonyms: - CLO uri_format: http://purl.obolibrary.org/obo/CLO_$1 version: 2.1.188 cls: description: Cell line collections (Providers) example: 300108/p3934_A-172 homepage: https://www.cytion.com/ mappings: cellosaurus: CLS name: Cell Lines Service preferred_prefix: cls uri_format: https://www.cytion.com/$1 clyh: contact: email: lucas.leclere@obs-vlfr.fr github: L-Leclere name: Lucas Leclere orcid: 0000-0002-7440-0467 depends_on: - iao - ro - uberon description: Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica. download_obo: http://purl.obolibrary.org/obo/clyh.obo download_owl: http://purl.obolibrary.org/obo/clyh.owl example: '1000100' homepage: https://github.com/EBISPOT/clyh_ontology keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: CLYH bioportal: CLYH obofoundry: clyh ols: clyh ontobee: CLYH name: Clytia hemisphaerica Development and Anatomy Ontology pattern: ^\d+$ preferred_prefix: CLYH rdf_uri_format: http://purl.obolibrary.org/obo/CLYH_$1 repository: https://github.com/EBISPOT/clyh_ontology uri_format: http://purl.obolibrary.org/obo/CLYH_$1 version: '2020-05-29' cmecs: contact: email: kate.rose@noaa.gov name: Kate Rose contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard. download_owl: http://aber-owl.net/media/ontologies/CMECS/2/cmecs.owl example: '595' homepage: https://cmecscatalog.org/cmecs keywords: - ecology - marine ecology - ontology mappings: aberowl: CMECS bioportal: CMECS ecoportal: CMECS name: Costal and Marine Ecological Classification Standard pattern: ^\d+$ preferred_prefix: cmecs references: - http://www.natureserve.org/sites/default/files/publications/files/cmecs_version_06-2012_final.pdf uri_format: https://cmecscatalog.org/cmecs/classification/unit/$1.html cmf: contact: email: engelsta@ohsu.edu name: Mark Engelstad orcid: 0000-0001-5889-4463 deprecated: true description: This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain homepage: https://code.google.com/p/craniomaxillofacial-ontology/ keywords: - obo - ontology mappings: aberowl: CMF biocontext: CMF obofoundry: cmf ontobee: CMF name: CranioMaxilloFacial ontology preferred_prefix: CMF rdf_uri_format: http://purl.obolibrary.org/obo/CMF_$1 uri_format: http://purl.obolibrary.org/obo/CMF_$1 cmo: appears_in: - scdo contact: email: jrsmith@mcw.edu github: jrsjrs name: Jennifer Smith orcid: 0000-0002-6443-9376 description: Morphological and physiological measurement records generated from clinical and model organism research and health programs. download_obo: http://purl.obolibrary.org/obo/cmo.obo download_owl: http://purl.obolibrary.org/obo/cmo.owl example: '0001350' homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html keywords: - biomedical science - disease - electronic health record - life science - model organism - obo - ontology - phenotype - preclinical studies license: CC0-1.0 logo: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif mappings: aberowl: CMO biocontext: CMO bioportal: CMO fairsharing: FAIRsharing.dq78pn obofoundry: cmo ols: cmo ontobee: CMO name: Clinical measurement ontology pattern: ^\d{7}$ preferred_prefix: CMO publications: - doi: 10.1186/2041-1480-4-26 pmc: PMC3882879 pubmed: '24103152' title: 'The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications' year: 2013 - doi: 10.3389/fgene.2012.00087 pmc: PMC3361058 pubmed: '22654893' title: Three ontologies to define phenotype measurement data year: 2012 rdf_uri_format: http://purl.obolibrary.org/obo/CMO_$1 repository: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology twitter: ratgenome uri_format: http://purl.obolibrary.org/obo/CMO_$1 version: '2.238' cmpo: contact: email: jupp@ebi.ac.uk name: Simon Jupp orcid: 0000-0002-0643-3144 description: CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. download_owl: http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl example: '0000435' homepage: http://www.ebi.ac.uk/cmpo keywords: - cell - cell biology - cellular component - microscopy - ontology - phenotype mappings: aberowl: CMPO bioportal: CMPO fairsharing: FAIRsharing.knp11s ols: cmpo name: Cellular Microscopy Phenotype Ontology pattern: ^\d{7}$ preferred_prefix: cmpo publications: - doi: 10.1186/s13326-016-0074-0 pmc: PMC4870745 pubmed: '27195102' title: The cellular microscopy phenotype ontology year: 2016 repository: https://github.com/EBISPOT/CMPO twitter: EBIOLS uri_format: http://www.ebi.ac.uk/cmpo/CMPO_$1 version: '2017-12-19' cnrs: comment: Motivated to add because of appearance in ROR contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier for an academic research group issued by the CNRS example: UMR7315 homepage: https://annuaire.cnrs.fr mappings: wikidata: P4550 name: French National Center for Scientific Research - Research Group Identifier pattern: ^(UMR|UMS|UMI|UPR|URA|USR|GDR|EA|FR|SNC|ERL|FRC|FRE|IFR|MOY)\d+$ preferred_prefix: cnrs uri_format: https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin?&p_lab=$1&p_origine_appel=u co_320: contact: email: j.detras@cgiar.org name: Jeffrey A. Detras orcid: 0000-0002-6680-578X description: Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables example: 0000618 homepage: https://cropontology.org/ontology/CO_320/Rice keywords: - agriculture - botany - food - life science - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_320 cropoct: CO_320 fairsharing: FAIRsharing.2jkxp5 ols: co_320 name: Rice ontology pattern: ^\d{7}$ preferred_prefix: CO_320 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_320:$1 version: '2019-10-09' co_321: contact: email: helpdesk@cropontology-curationtool.org name: Rosemary Shrestha orcid: 0000-0002-9399-8003 description: July 2018 example: 0000449 homepage: https://cropontology.org/ontology/CO_321/Wheat keywords: - agriculture - food - life science - phenotype license: CC-BY-4.0 mappings: agroportal: CO_321 cropoct: CO_321 fairsharing: FAIRsharing.czzmpg ols: co_321 name: Wheat ontology pattern: ^\d{7}$ preferred_prefix: CO_321 publications: - doi: 10.1093/aobpla/plq008 pmc: PMC3000699 pubmed: '22476066' title: 'Multifunctional crop trait ontology for breeders'' data: field book, annotation, data discovery and semantic enrichment of the literature' year: 2010 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_321:$1 version: '2019-10-09' co_322: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Maize Trait Dictionary in template 5 - CIMMYT- September 2016 example: '0000773' homepage: https://cropontology.org/ontology/CO_322/Maize keywords: - agriculture - botany - food - life science - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_322 cropoct: CO_322 fairsharing: FAIRsharing.eeyne8 ols: co_322 name: Maize ontology pattern: ^\d{7}$ preferred_prefix: CO_322 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_322:$1 version: '2019-10-09' co_323: contact: email: helpdesk@cropontology-curationtool.org name: Fawzy Nawar description: ICARDA - TDv5 - Sept 2018 example: '0000252' homepage: https://cropontology.org/ontology/CO_323/Barley keywords: - agriculture - botany - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_323 cropoct: CO_323 fairsharing: FAIRsharing.f69084 ols: co_323 name: Barley ontology pattern: ^\d{7}$ preferred_prefix: CO_323 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_323:$1 version: '2019-11-20' co_324: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Sorghum TDv5 - Oct 2019 example: '0000111' homepage: https://cropontology.org/ontology/CO_324/Sorghum keywords: - agriculture - botany - food - phenotype license: CC-BY-4.0 mappings: agroportal: CO_324 cropoct: CO_324 fairsharing: FAIRsharing.dxx0c ols: co_324 name: Sorghum ontology pattern: ^\d{7}$ preferred_prefix: CO_324 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_324:$1 version: '2019-10-09' co_325: contact: email: e.arnaud@cgiar.org name: Elizabeth Arnaud orcid: 0000-0002-6020-5919 description: Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019 example: 0000519 homepage: https://cropontology.org/ontology/CO_325/Banana keywords: - agriculture - food - life science - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_325 cropoct: CO_325 fairsharing: FAIRsharing.gdszhh ols: co_325 name: Banana ontology pattern: ^\d{7}$ preferred_prefix: CO_325 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_325:$1 version: '2019-10-09' co_326: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Draft version example: '0000254' homepage: https://cropontology.org/ontology/CO_326/Coconut license: CC-BY-4.0 mappings: agroportal: CO_326 cropoct: CO_326 ols: co_326 name: Coconut ontology pattern: ^\d{7}$ preferred_prefix: CO_326 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_326:$1 co_327: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016 example: 0000095 homepage: http://www.cropontology.org/ontology/CO_327/Pearl%20millet keywords: - agriculture - botany - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_327 cropoct: CO_327 fairsharing: FAIRsharing.4e3qh9 ols: co_327 name: Pearl millet ontology pattern: ^\d{7}$ preferred_prefix: CO_327 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_327:$1 co_330: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: CIP - potato ontology - december 2018 example: '0000106' homepage: https://cropontology.org/ontology/CO_330/Potato keywords: - agriculture - botany - life science - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_330 cropoct: CO_330 fairsharing: FAIRsharing.4fa657 ols: co_330 name: Potato ontology pattern: ^\d{7}$ preferred_prefix: CO_330 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_330:$1 version: '2019-10-09' co_331: contact: email: helpdesk@cropontology-curationtool.org name: Vilma Hualla Mamani orcid: 0000-0003-0595-5271 description: Sweet Potato Trait Dictionary in template v5 - CIP - November 2019 example: 0000088 homepage: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato keywords: - agriculture - botany - food - life science license: CC-BY-4.0 mappings: agroportal: CO_331 cropoct: CO_331 fairsharing: FAIRsharing.4g5qcw ols: co_331 name: Sweet Potato ontology pattern: ^\d{7}$ preferred_prefix: CO_331 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_331:$1 co_333: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: 'This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017.' example: '3000045' homepage: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology keywords: - agriculture - botany - food - life science - phenotype - plant breeding - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_333 cropoct: CO_333 fairsharing: FAIRsharing.af5655 ols: co_333 name: Beet Ontology ontology pattern: ^\d+$ preferred_prefix: CO_333 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_333:$1 co_334: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016 example: '0000070' homepage: https://cropontology.org/ontology/CO_334/Cassava keywords: - agriculture - botany - food - nutritional science - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_334 cropoct: CO_334 fairsharing: FAIRsharing.v06c4q ols: co_334 name: Cassava ontology pattern: ^\d{7}$ preferred_prefix: CO_334 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_334:$1 version: '2019-10-09' co_335: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: CIAT Common bean trait dictionary - version August 2014 example: 0000189 homepage: http://www.cropontology.org/ontology/CO_335/Common%20Bean keywords: - agriculture - botany - food license: CC-BY-4.0 mappings: agroportal: CO_335 cropoct: CO_335 fairsharing: FAIRsharing.a14123 ols: co_335 name: Common Bean ontology pattern: ^\d{7}$ preferred_prefix: CO_335 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_335:$1 co_336: contact: email: helpdesk@cropontology-curationtool.org name: Elizabeth Arnaud orcid: 0000-0002-6020-5919 description: Soybean Trait Dictionary in template v5 - IITA - July 2015 example: 0000339 homepage: https://cropontology.org/ontology/CO_336/Soybean keywords: - agriculture - food - life science - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_336 cropoct: CO_336 fairsharing: FAIRsharing.j75srj ols: co_336 name: Soybean ontology pattern: ^\d{7}$ preferred_prefix: CO_336 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_336:$1 co_337: contact: email: tm.shah@cgiar.org name: Trushar Shah orcid: 0000-0002-0091-7981 description: Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015 example: '0000054' homepage: https://cropontology.org/ontology/CO_337/Groundnut keywords: - agriculture - botany - food - life science - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_337 cropoct: CO_337 fairsharing: FAIRsharing.ge8y23 ols: co_337 name: Groundnut ontology pattern: ^\d{7}$ preferred_prefix: CO_337 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_337:$1 version: '2019-10-09' co_338: contact: email: tm.shah@cgiar.org name: Trushar Shah orcid: 0000-0002-0091-7981 description: Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015 example: 0000138 homepage: https://cropontology.org/ontology/CO_338/Chickpea keywords: - agriculture - botany - food - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_338 cropoct: CO_338 fairsharing: FAIRsharing.js20q3 ols: co_338 name: Chickpea ontology pattern: ^\d{7}$ preferred_prefix: CO_338 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_338:$1 version: '2019-10-09' co_339: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Lentil Trait Dictionary in template v5 - ICARDA - July 2015 example: '0000032' homepage: https://cropontology.org/ontology/CO_339/Lentil keywords: - agriculture - botany - food - life science - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_339 cropoct: CO_339 fairsharing: FAIRsharing.ry1ezg ols: co_339 name: Lentil ontology pattern: ^\d{7}$ preferred_prefix: CO_339 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_339:$1 version: '2019-10-09' co_340: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Cowpea Trait Dictionary in template v5 - IITA - August 2015 example: 0000639 homepage: https://cropontology.org/ontology/CO_340/Cowpea keywords: - agriculture - botany - food - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_340 cropoct: CO_340 fairsharing: FAIRsharing.31apg2 ols: co_340 name: Cowpea ontology pattern: ^\d{7}$ preferred_prefix: CO_340 publications: - doi: 10.3389/fphys.2012.00326 pmc: PMC3429094 pubmed: '22934074' title: Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice year: 2012 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_340:$1 version: '2019-10-09' co_341: contact: email: helpdesk@cropontology-curationtool.org name: Elizabeth Arnaud orcid: 0000-0002-6020-5919 description: Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015 example: '0000140' homepage: https://cropontology.org/ontology/CO_341/Pigeonpea keywords: - agriculture - botany - food - life science - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_341 cropoct: CO_341 fairsharing: FAIRsharing.ehe3yp ols: co_341 name: Pigeonpea ontology pattern: ^\d{7}$ preferred_prefix: CO_341 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_341:$1 version: '2019-11-18' co_343: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: version 2019 - pvs example: '0100010' homepage: https://cropontology.org/ontology/CO_343/Yam keywords: - agriculture - botany - food - life science - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_343 cropoct: CO_343 fairsharing: FAIRsharing.7e9cff ols: co_343 name: Yam ontology pattern: ^\d{7}$ preferred_prefix: CO_343 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_343:$1 version: '2019-10-09' co_345: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Brachiaria (forages) ontology TD v5 - Version Oct 2016 example: '0000127' homepage: https://cropontology.org/ontology/CO_345/Brachiaria keywords: - agriculture - botany - life science - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_345 cropoct: CO_345 fairsharing: FAIRsharing.9e9683 ols: co_345 name: Brachiaria ontology pattern: ^\d{7}$ preferred_prefix: CO_345 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_345:$1 version: '2019-10-09' co_346: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: oct 2016 example: 0000199 homepage: https://cropontology.org/ontology/CO_346/Mungbean keywords: - agriculture - food - life science - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_346 cropoct: CO_346 fairsharing: FAIRsharing.fgd5gq ols: co_346 name: Mungbean ontology pattern: ^\d{7}$ preferred_prefix: CO_346 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_346:$1 version: '2019-10-09' co_347: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: 'March 2017 version ' example: 0000108 homepage: http://www.cropontology.org/ontology/CO_347/Castor%20bean keywords: - agriculture - botany - food - life science - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_347 cropoct: CO_347 fairsharing: FAIRsharing.qrrvyk ols: co_347 name: Castor bean ontology pattern: ^\d{7}$ preferred_prefix: CO_347 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_347:$1 co_348: contact: email: helpdesk@cropontology-curationtool.org name: helpdesk cropontology description: Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France). example: '1100107' homepage: https://cropontology.org/ontology/CO_348/Brassica keywords: - agriculture - botany - life science - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_348 cropoct: CO_348 fairsharing: FAIRsharing.af7a2d ols: co_348 name: Brassica ontology pattern: ^\d+$ preferred_prefix: CO_348 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_348:$1 version: '2019-11-29' co_350: contact: email: helpdesk@cropontology-curationtool.org name: Jean-Luc Jannink orcid: 0000-0003-4849-628X description: Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo example: '0000215' homepage: https://cropontology.org/ontology/CO_350/Oat keywords: - agriculture - botany - life science - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_350 cropoct: CO_350 fairsharing: FAIRsharing.35e1c3 ols: co_350 name: Oat ontology pattern: ^\d{7}$ preferred_prefix: CO_350 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_350:$1 version: '2019-10-09' co_356: contact: email: helpdesk@cropontology-curationtool.org name: Eric Duchêne description: Grape Ontology including OIV and bioversity descriptors. INRA July 2017 example: '4000027' homepage: https://cropontology.org/ontology/CO_356/Vitis keywords: - agriculture - botany - life science - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_356 cropoct: CO_356 fairsharing: FAIRsharing.c7f4d7 ols: co_356 name: Vitis ontology pattern: ^\d+$ preferred_prefix: CO_356 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_356:$1 version: '2019-11-29' co_357: contact: email: celia.michotey@inrae.fr name: Célia Michotey orcid: 0000-0003-1877-1703 description: 'This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE.' example: '1000290' homepage: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology keywords: - botany - life science - phenotype license: CC-BY-4.0 mappings: agroportal: CO_357 cropoct: CO_357 fairsharing: FAIRsharing.2b04ae ols: co_357 name: Woody Plant Ontology ontology pattern: ^\d+$ preferred_prefix: CO_357 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_357:$1 co_358: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Cotton ontology from CottonGen database - June 2019 example: 0000139 homepage: https://cropontology.org/ontology/CO_358/Cotton license: CC-BY-4.0 mappings: agroportal: CO_358 cropoct: CO_358 ols: co_358 name: Cotton ontology pattern: ^\d{7}$ preferred_prefix: CO_358 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_358:$1 version: '2020-01-03' co_359: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: December 2019 example: 0000947 homepage: https://cropontology.org/ontology/CO_359/Sunflower license: CC-BY-4.0 mappings: agroportal: CO_359 cropoct: CO_359 ols: co_359 name: Sunflower ontology pattern: ^\d{7}$ preferred_prefix: CO_359 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_359:$1 co_360: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Sugar Kelp trait ontology example: '0000071' homepage: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait keywords: - botany - life science - marine environment - phenotype - plant phenotypes and traits license: CC-BY-4.0 mappings: agroportal: CO_360 cropoct: CO_360 fairsharing: FAIRsharing.1c1738 ols: co_360 name: Sugar Kelp trait ontology pattern: ^\d{7}$ preferred_prefix: CO_360 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_360:$1 co_365: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: developed by ICARDA - Dec 2018 example: '0000205' homepage: https://cropontology.org/ontology/CO_365/Fababean license: CC-BY-4.0 mappings: agroportal: CO_365 cropoct: CO_365 ols: co_365 name: Fababean ontology pattern: ^\d{7}$ preferred_prefix: CO_365 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_365:$1 version: '2019-10-15' co_366: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: version Dec 2019 example: '0000072' homepage: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut license: CC-BY-4.0 mappings: agroportal: CO_366 cropoct: CO_366 ols: co_366 name: Bambara groundnut ontology pattern: ^\d{7}$ preferred_prefix: CO_366 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_366:$1 co_367: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Quinoa Ontology database of the Crop Ontology (CO_367) of the Generation Challenge Program (GCP) describe traits variables of Quinoa Germinate Database http://germinate.quinoadb.org. Quinoa Phenotyping Consortium Creation Date 23.05.2021 example: '0000004' homepage: http://cropontology.org/term/CO_367:ROOT license: CC-BY-4.0 mappings: agroportal: CO_367 cropoct: CO_367 name: Quinoa Ontology pattern: ^\d{7}$ preferred_prefix: CO_367 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_367:$1 co_370: contact: email: ekaterina.chuprikova@eurac.edu name: Ekaterina Chuprikova orcid: 0000-0002-8981-0442 description: Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales. example: 0000890 homepage: http://cropontology.org/term/CO_370:ROOT license: CC-BY-4.0 mappings: agroportal: CO_370 cropoct: CO_370 name: Apple Ontology pattern: ^\d{7}$ preferred_prefix: CO_370 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_370:$1 cob: contact: email: bpeters@lji.org github: bpeters42 name: Bjoern Peters orcid: 0000-0002-8457-6693 description: COB brings together key terms from a wide range of OBO projects to improve interoperability. download_owl: http://purl.obolibrary.org/obo/cob.owl example: 0000080 homepage: https://obofoundry.org/COB/ keywords: - obo - ontology license: CC0-1.0 mappings: aberowl: COB bioportal: COB obofoundry: cob ols: cob ontobee: COB name: Core Ontology for Biology and Biomedicine pattern: ^\d{7}$ preferred_prefix: COB rdf_uri_format: http://purl.obolibrary.org/obo/COB_$1 repository: https://github.com/OBOFoundry/COB uri_format: http://purl.obolibrary.org/obo/COB_$1 version: '2025-02-20' coconut: comment: '@mSorok is the dev of the resource, hope I got it right!' contributor: email: adriano.rutz@ik.me github: adafede name: Adriano Rutz orcid: 0000-0003-0443-9902 description: COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a "flat" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties. example: CNP0171505 example_extras: - CNP0018459.2 github_request_issue: 221 homepage: https://coconut.naturalproducts.net keywords: - chemistry - natural producs - organic chemistry mappings: re3data: r3d100014517 name: COlleCtion of Open Natural ProdUcTs pattern: ^CNP\d{7}(\.\d+)?$ preferred_prefix: coconut publications: - doi: 10.1093/nar/gkae1063 pubmed: '39588778' title: 'COCONUT 2.0: a comprehensive overhaul and curation of the collection of open natural products database' year: 2024 - doi: 10.1186/s13321-020-00478-9 pmc: PMC7798278 pubmed: '33423696' title: 'COCONUT online: Collection of Open Natural Products database' year: 2021 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://coconut.naturalproducts.net/compound/coconut_id/$1 codelink: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release).' example: GE86325 homepage: https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt keywords: - microarray - transcriptomics name: GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray pattern: ^GE\d+$ preferred_prefix: codelink references: - https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-8060/A-GEOD-8060.adf.txt - https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt coexistence: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'COEXISTENCE - Thesaurus of intersectionality and decolonial issues: black studies, gender, sexuality and feminist studies' example: '163' github_request_issue: 1310 homepage: https://mamoura.eci.ufmg.br name: COEXISTENCE pattern: ^\d+$ preferred_prefix: coexistence uri_format: https://mamoura.eci.ufmg.br/tematres/vocab/index.php?tema=$1 cog: contact: email: cogs@ncbi.nlm.nih.gov name: Michael Y Galperin orcid: 0000-0002-2265-5572 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems.' example: COG0001 homepage: https://www.ncbi.nlm.nih.gov/research/cog/ keywords: - genome - life science - protein mappings: biolink: COG fairsharing: FAIRsharing.djsbw2 go: COG_Cluster miriam: cog prefixcommons: cog togoid: Cog name: Cluster of orthologous genes pattern: ^COG\d+$ preferred_prefix: cog providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/cog:$1 publications: - doi: 10.1126/science.278.5338.631 pubmed: '9381173' title: A genomic perspective on protein families year: 1997 - doi: 10.1093/nar/gku1223 pmc: PMC4383993 pubmed: '25428365' title: Expanded microbial genome coverage and improved protein family annotation in the COG database year: 2014 synonyms: - COG_Cluster uri_format: https://www.ncbi.nlm.nih.gov/research/cog/cog/$1 cog.category: contact: email: cogs@ncbi.nlm.nih.gov name: Michael Y Galperin orcid: 0000-0002-2265-5572 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Higher-level classifications of COG Pathways example: K homepage: https://www.ncbi.nlm.nih.gov/research/cog/ keywords: - pathways name: COG Categories 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 name: Michael Y Galperin orcid: 0000-0002-2265-5572 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. example: NAD%20biosynthesis homepage: https://www.ncbi.nlm.nih.gov/research/cog/pathways mappings: go: COG_Pathway name: COG Pathways part_of: cog preferred_prefix: cog.pathway uri_format: https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1 cohd: comment: not really sure where the source is. this also links to a system called athena. I was not able to figure out what COHD stands for. contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012 homepage: https://github.com/MIT-LCP/mimic-omop keywords: - clinical data - clinical trials - health - health sciences name: MIMIC III Database no_own_terms: true preferred_prefix: cohd repository: https://github.com/MIT-LCP/mimic-omop coi: contact: email: coi@bot.uc.pt name: COI Catalogue contributor: email: shah.tanay2@northeastern.edu github: tanayshah2 name: Tanay Shah orcid: 0009-0001-1912-5132 description: COI Catalogue is a herbarium with c. 800.000 specimens, organised in separate collections due to the research priorities over the years. example: '63812' github_request_issue: 1145 homepage: https://coicatalogue.uc.pt/index.php name: COI Catalogue preferred_prefix: coi publications: - doi: 10.1038/s41597-024-03520-9 pmc: PMC11193818 pubmed: '38909064' title: 'O armário: Fruiting phenology data for 4,462 plant taxa in Portugal (1926-2013)' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://coicatalogue.uc.pt/index.php?t=specimen&COINumber=$1 col: description: Identifier of a taxon or synonym in the Catalogue of Life example: 4QHKG homepage: https://www.checklistbank.org mappings: bartoc: '1915' miriam: col name: Catalogue of Life pattern: ^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$ preferred_prefix: col providers: - code: col description: The Catalogue of Life website providing a view onto the latest release of the COL Checklist. homepage: https://www.catalogueoflife.org name: Catalogue of Life (COL) uri_format: https://www.catalogueoflife.org/data/taxon/$1 uri_format: https://www.checklistbank.org/dataset/3LR/taxon/$1 col.taiwan: contributor: email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 description: Identifier (name code) for a taxon in the catalogue of life in taiwan example: '431472' github_request_issue: 466 homepage: http://taibnet.sinica.edu.tw/home.php mappings: wikidata: P3088 name: Catalogue of Life in Taiwan pattern: ^[1-9]\d{5}$ preferred_prefix: col.taiwan reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1 colao: contact: email: entiminae@gmail.com github: JCGiron name: Jennifer C. Giron orcid: 0000-0002-0851-6883 depends_on: - aism - bfo - bspo - caro - pato - ro - uberon description: The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. download_obo: http://purl.obolibrary.org/obo/colao.obo download_owl: http://purl.obolibrary.org/obo/colao.owl example: '0000000' homepage: https://github.com/insect-morphology/colao keywords: - obo - ontology license: CC-BY-4.0 mappings: aberowl: COLAO bioportal: COLAO obofoundry: colao ols: colao ontobee: COLAO name: Coleoptera Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: COLAO rdf_uri_format: http://purl.obolibrary.org/obo/COLAO_$1 repository: https://github.com/insect-morphology/colao uri_format: http://purl.obolibrary.org/obo/COLAO_$1 version: '2024-06-21' collagenmutdb: description: This database aims to record all published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP, FKBP10, LEPRE1 and PPIB genes. example: COL3A1 homepage: http://www.le.ac.uk/genetics/collagen/ keywords: - gene mappings: prefixcommons: cmd name: Collagen Mutation Database preferred_prefix: collagenmutdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/cmd:$1 provides: hgnc.symbol reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://eds.gene.le.ac.uk/home.php?select_db=$1 colonatlas: description: Cell line databases/resources example: ALA homepage: http://www.coloncanceratlas.org mappings: cellosaurus: ColonAtlas name: Colorectal Cancer Atlas preferred_prefix: colonatlas uri_format: http://www.coloncanceratlas.org/search_cell_line?cell_line=$1 combine.specifications: description: The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network. example: sed-ml.level-1.version-1 homepage: https://co.mbine.org/standards/ mappings: biocontext: COMBINE.SPECIFICATIONS miriam: combine.specifications n2t: combine.specifications name: COMBINE specifications pattern: ^\w+(\-|\.|\w)*$ preferred_prefix: combine.specifications uri_format: https://github.com/combine-org/combine-specifications/blob/main/specifications/$1.md come: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif. example: MOL000160 homepage: https://www.flymine.org/come keywords: - protein mappings: prefixcommons: come name: The Bioinorganic Motif Database preferred_prefix: come providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/come:$1 uri_format: https://www.flymine.org/come/entry?gn=$1 commoncoreontology: contact: email: mpjensen@buffalo.edu github: mark-jensen name: Mark Jensen orcid: 0000-0001-9228-8838 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The Common Core Ontologies (CCO) comprise twelve ontologies that are designed to represent and integrate taxonomies of generic classes and relations across all domains of interest. CCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained by the BFO framework, from which it inherits much of its basic semantic relationships.' example: DirectiveInformationContentEntity homepage: http://www.ontologyrepository.com keywords: - ontology - upper-level ontology license: CC-BY-4.0 name: Common Core Ontologies preferred_prefix: commoncoreontology repository: https://github.com/CommonCoreOntology/CommonCoreOntologies uri_format: http://www.ontologyrepository.com/CommonCoreOntologies/$1 complexportal: contact: email: bmeldal@ebi.ac.uk github: bmeldal-eg name: Birgit Meldal orcid: 0000-0003-4062-6158 description: A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases. example: CPX-263 homepage: https://www.ebi.ac.uk/complexportal license: CC0-1.0 mappings: biocontext: COMPLEXPORTAL biolink: ComplexPortal go: ComplexPortal miriam: complexportal n2t: complexportal re3data: r3d100013295 uniprot: DB-0228 wikidata: P7718 name: Complex Portal pattern: ^CPX-[0-9]+$ preferred_prefix: complexportal publications: - doi: 10.1093/nar/gky1001 pubmed: '30357405' - doi: 10.1093/nar/gku975 pmc: PMC4384031 pubmed: '25313161' title: The complex portal--an encyclopaedia of macromolecular complexes year: 2014 synonyms: - ComplexPortal uri_format: https://www.ebi.ac.uk/complexportal/complex/$1 comptox: description: The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks. example: DTXSID2021028 homepage: https://comptox.epa.gov/dashboard mappings: biocontext: COMPTOX miriam: comptox n2t: comptox wikidata: P3117 name: DSSTox substance pattern: ^DTXSID\d+$ preferred_prefix: comptox uri_format: https://comptox.epa.gov/dashboard/$1 compulyeast: description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record. example: O08709 homepage: http://compluyeast2dpage.dacya.ucm.es/ keywords: - protein mappings: biocontext: COMPULYEAST fairsharing: FAIRsharing.rbjs3e miriam: compulyeast n2t: compulyeast prefixcommons: compluyeast2dpage name: Compluyeast-2D-DB pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ preferred_prefix: compulyeast providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/compluyeast2dpage:$1 provides: uniprot uri_format: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1 conference: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The conference-ontology is a new self-contained ontology for modelleing knowledge about conferences. The conference-ontology adopts best ontology design practices (e.g., Ontology Design Patterns, ontology reuse and interlinking) and guarantees interoperability with SWC ontology and all other pertinent vocabularies. (from homepage) download_owl: https://w3id.org/scholarlydata/ontology/conference-ontology.owl example: isDocumentRelatedTo homepage: http://www.scholarlydata.org/ontology/doc/ keywords: - ontology license: CC-BY-3.0 name: Conference Ontology preferred_prefix: conference uri_format: https://w3id.org/scholarlydata/ontology/conference-ontology.owl#$1 confident.event: contact: email: Philip.Stroemert@tib.eu github: StroemPhi name: Philip Strömert orcid: 0000-0002-1595-3213 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating. example: 37af84f2-bfd7-4653-b608-eaff44febba6 github_request_issue: 519 homepage: https://www.confident-conference.org/index.php/Category:Event keywords: - conferences - meetings - metascience name: ConfIDent Event pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$ preferred_prefix: confident.event uri_format: https://www.confident-conference.org/index.php/Event:$1 confident.series: contact: email: Philip.Stroemert@tib.eu github: StroemPhi name: Philip Strömert orcid: 0000-0002-1595-3213 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating. example: AAC github_request_issue: 519 homepage: https://www.confident-conference.org/index.php/Category:Event_Series keywords: - conferences - grouping - meetings - metascience name: ConfIDent Event Series preferred_prefix: confident.series uri_format: https://www.confident-conference.org/index.php/Event_Series:$1 conoserver: contact: email: d.craik@imb.uq.edu.au name: David Craik orcid: 0000-0003-0007-6796 description: ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails. example: '2639' homepage: http://www.conoserver.org/ keywords: - life science - neurophysiology - statistics - synthetic biology mappings: biocontext: CONOSERVER fairsharing: FAIRsharing.y00hz4 miriam: conoserver n2t: conoserver uniprot: DB-0156 name: ConoServer pattern: ^\d+$ preferred_prefix: conoserver publications: - doi: 10.1093/nar/gkr886 pmc: PMC3245185 pubmed: '22058133' title: 'ConoServer: updated content, knowledge, and discovery tools in the conopeptide database' year: 2011 - doi: 10.1016/j.toxicon.2010.03.002 pubmed: '20211197' title: 'Conopeptide characterization and classifications: an analysis using ConoServer' year: 2010 - doi: 10.1093/bioinformatics/btm596 pubmed: '18065428' title: ConoServer, a database for conopeptide sequences and structures year: 2007 - doi: 10.1021/cb700091j pubmed: '17649970' title: Chemical modification of conotoxins to improve stability and activity year: 2007 - doi: 10.1152/physrev.00020.2003 pubmed: '14715910' title: 'Conus venoms: a rich source of novel ion channel-targeted peptides' year: 2004 uri_format: http://www.conoserver.org/?page=card&table=protein&id=$1 conso: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases. example: CONSO00010 homepage: https://pharmacome.github.io/conso/ keywords: - biology - life science - neurodegeneration - neuroscience - ontology name: Curation of Neurodegeneration Supporting Ontology pattern: ^CONSO\d{5}$ preferred_prefix: conso uri_format: https://pharmacome.github.io/conso/$1 cordis.article: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020). example: '436605' homepage: https://cordis.europa.eu/ name: CORDIS Article pattern: ^\d+$ preferred_prefix: cordis.article uri_format: https://cordis.europa.eu/article/id/$1 cordis.project: contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020). example: '817732' github_request_issue: 450 homepage: https://cordis.europa.eu/ name: CORDIS Project pattern: ^\d+$ preferred_prefix: cordis.project reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://cordis.europa.eu/project/id/$1 coriell: description: The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world. example: GM17027 homepage: http://ccr.coriell.org/ mappings: biocontext: Coriell cellosaurus: Coriell go: CORIELL miriam: coriell n2t: coriell name: Coriell Institute for Medical Research pattern: ^[A-Z]{2}\d+$ preferred_prefix: coriell uri_format: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1 corrdb: contact: email: zhu@iastate.edu name: Zhiliang Hu orcid: 0000-0002-6704-7538 description: A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies. example: '37232' homepage: https://www.animalgenome.org keywords: - animal genetics - genetics - life science - systems biology mappings: fairsharing: FAIRsharing.IziuCK miriam: corrdb re3data: r3d100011496 name: CorrDB pattern: ^[0-9]+$ preferred_prefix: corrdb uri_format: https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1 corum: contact: email: andreas.ruepp@helmholtz-muenchen.de name: Andreas Ruepp orcid: 0000-0003-1705-3515 description: The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded. example: '100' homepage: https://mips.helmholtz-muenchen.de/corum keywords: - bioinformatics - biology - protein mappings: biocontext: CORUM fairsharing: FAIRsharing.ohbpNw go: CORUM miriam: corum n2t: corum pathguide: '322' prefixcommons: corum uniprot: DB-0224 name: Comprehensive Resource of Mammalian protein complexes pattern: ^\d+$ preferred_prefix: corum providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/corum:$1 publications: - doi: 10.1093/nar/gkae1033 pubmed: '39526397' title: 'CORUM in 2024: protein complexes as drug targets' year: 2024 - doi: 10.1093/nar/gkac1015 pubmed: '36382402' - doi: 10.1093/nar/gky973 pmc: PMC6323970 pubmed: '30357367' title: 'CORUM: the comprehensive resource of mammalian protein complexes-2019' year: 2019 uri_format: https://mips.helmholtz-muenchen.de/corum/?complex_id=$1 cosmic: comment: Is this just HGNC Gene symbols? contact: email: jt6@sanger.ac.uk github: jgtate name: John G Tate orcid: 0000-0002-8315-6574 description: COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes. example: BRAF homepage: http://cancer.sanger.ac.uk/cosmic/ keywords: - biomedical science - genetics mappings: biocontext: COSMIC cellosaurus: Cosmic edam: '3264' fairsharing: FAIRsharing.s5zmbp miriam: cosmic n2t: cosmic name: COSMIC Gene pattern: ^[A-Z0-9][A-Z0-9-]*$ preferred_prefix: cosmic publications: - doi: 10.1093/nar/gky1015 pmc: PMC6323903 pubmed: '30371878' title: 'COSMIC: the Catalogue Of Somatic Mutations In Cancer' year: 2019 - doi: 10.1093/nar/gku1075 pmc: PMC4383913 pubmed: '25355519' title: 'COSMIC: exploring the world''s knowledge of somatic mutations in human cancer' year: 2014 - doi: 10.1093/nar/gkq929 pmc: PMC3013785 pubmed: '20952405' title: 'COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer' year: 2010 - doi: 10.1038/sj.bjc.6601894 pmc: PMC2409828 pubmed: '15188009' title: The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website year: 2004 uri_format: http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1 cosmic.cell: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer example: '906801' homepage: https://cancer.sanger.ac.uk/cell_lines/ mappings: cellosaurus: Cosmic-CLP name: COSMIC Cell Lines pattern: ^\d+$ preferred_prefix: cosmic.cell uri_format: https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1 covid19: contact: email: dylan.mcgagh@magd.ox.ac.uk name: Dylan McGagh orcid: 0000-0002-6772-2775 description: Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease. download_owl: http://aber-owl.net/media/ontologies/COVID19/3/covid19.owl example: SFB_COVID19_MW286762 homepage: https://covid19.sfb.uit.no keywords: - ontology mappings: aberowl: COVID19 bioportal: COVID19 miriam: covid19 name: COVID-19 Surveillance Ontology pattern: ^\w+_COVID19_[-\w]+$ preferred_prefix: covid19 uri_format: https://covid19.sfb.uit.no/api/records/$1 covoc: contact: email: zmp@ebi.ac.uk github: zoependlington name: Zoë May Pendlington orcid: 0000-0002-4071-8397 description: The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more. download_json: https://github.com/EBISPOT/covoc/releases/download/current/covoc.json download_obo: https://github.com/EBISPOT/covoc/releases/download/current/covoc.obo download_owl: https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl example: '0010034' homepage: https://github.com/EBISPOT/covoc keywords: - ontology mappings: ols: covoc name: CoVoc Coronavirus Vocabulary pattern: ^\d{7}$ preferred_prefix: covoc repository: https://github.com/EBISPOT/covoc uri_format: http://purl.obolibrary.org/obo/COVOC_$1 version: '2022-10-26' cp: appears_in: - cl comment: Part of cell ontology but deprecated, see https://github.com/obophenotype/cell-ontology/issues/572 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: Cellular Phenotypes preferred_prefix: cp cpc: description: The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013. example: A01M1/026 homepage: https://worldwide.espacenet.com/classification keywords: - atmospheric science - earth science - geodesy - geography - hydrogeology - meteorology mappings: biocontext: CPC fairsharing: FAIRsharing.e08886 miriam: cpc n2t: cpc name: Cooperative Patent Classification pattern: ^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H, Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$ preferred_prefix: cpc uri_format: https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1 cpt: contact: email: Intellectual.PropertyServices@ama-assn.org name: American Medical Association contributor: github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 contributor_extras: - github: colleenXu name: Colleen Xu orcid: 0000-0003-2975-882X description: Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)] example: '00103' github_request_issue: 357 homepage: https://www.aapc.com keywords: - biomedical science - health science - medicine - ontology mappings: aberowl: CPT biolink: CPT bioportal: CPT fairsharing: FAIRsharing.wpxab1 name: Current Procedural Terminology pattern: ^\d+$ preferred_prefix: cpt publications: - doi: 10.1136/neurintsurg-2014-011156 pubmed: '24589819' title: Current procedural terminology; a primer year: 2014 - doi: 10.1016/j.jacr.2007.10.004 pubmed: '18359442' title: 'CPT: an open system that describes all that you do' year: 2008 references: - https://github.com/biopragmatics/bioregistry/pull/358 - https://github.com/biolink/biolink-model/pull/993 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - ama-cpt uri_format: https://www.aapc.com/codes/cpt-codes/$1 cran: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Repository of packages for the R programming language example: ggplot2 homepage: https://cran.r-project.org/ mappings: wikidata: P5565 name: The Comprehensive R Archive Network preferred_prefix: cran uri_format: https://cran.r-project.org/web/packages/$1 crates: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A repository of software packages written in Rust. example: curies homepage: https://crates.io name: Crates.io preferred_prefix: crates uri_format: https://crates.io/crates/$1 creativebiolabs.antibody: contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Creative Biolabs Antigen provides identifiers for antibody-based entities such as recombinant, functional, engineered, and format-specific antibodies as well as antibody processing tools, which are essential for applications in diagnostics, therapeutics, and immunology. example: TAB-884 github_request_issue: 1257 homepage: https://www.creativebiolabs.net name: Creative Biolabs pattern: ^[a-zA-Z]+-[a-zA-Z0-9()]+(-[a-zA-Z0-9]*)?$ preferred_prefix: creativebiolabs.antibody reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 creativebiolabs.protein: contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Creative Biolabs Protein provides identifiers for protein-related entities, including therapeutic proteins, proteolytic enzymes, antibody-like scaffold proteins, soluble T cell receptors, and tetramers. example: VS-0724-CJ1 github_request_issue: 1257 homepage: https://www.creativebiolabs.net name: Creative Biolabs pattern: ^[a-zA-Z]+-[a-zA-Z0-9()]+(-[a-zA-Z0-9]*)?$ preferred_prefix: creativebiolabs.protein reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 credit: contact: email: liz.allen@f1000.com name: Liz Allen orcid: 0000-0002-9298-3168 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output. example: software homepage: https://credit.niso.org/ keywords: - citation - classification - data quality - publication - resource metadata - subject agnostic license: CC-BY-4.0 logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaUFCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--af4f02374db4f42007e6674ea2055ccaa36aa830/credit-icon-499x500-1.png?disposition=inline mappings: fairsharing: FAIRsharing.fe4816 name: CASRAI Contributor Roles Taxonomy pattern: ^(conceptualization|data-curation|formal-analysis|funding-acquisition|investigation|methodology|project-administration|resources|software|supervision|validation|visualization|writing-original-draft|writing-review-editing)$ preferred_prefix: credit publications: - doi: 10.1038/d41586-019-01715-4 pubmed: '31164773' title: Credit data generators for data reuse year: 2019 - doi: 10.1038/508312a pubmed: '24745070' title: 'Publishing: Credit where credit is due' year: 2014 - doi: 10.3789/ansi.niso.z39.104-2022 title: ANSI/NISO Z39.104-2022, CRediT, Contributor Roles Taxonomy year: 2022 - doi: 10.1087/20150211 title: 'Beyond authorship: attribution, contribution, collaboration, and credit' year: 2015 - doi: 10.1002/leap.1210 title: How can we ensure visibility and diversity in research contributions? How the Contributor Role Taxonomy (CRediT) is helping the shift from authorship to contributorship year: 2019 references: - https://casrai.org/credit/ twitter: contrib_roles uri_format: https://credit.niso.org/contributor-roles/$1 crisprdb: contact: email: Christine.Pourcel@u-psud.fr name: Christine Pourcel orcid: 0000-0002-8951-466X description: Repeated CRISPR ("clustered regularly interspaced short palindromic repeats") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data. example: '551115' homepage: http://crispr.i2bc.paris-saclay.fr/ keywords: - life science mappings: biocontext: CRISPRDB fairsharing: FAIRsharing.7sfedh integbio: nbdc02213 miriam: crisprdb n2t: crisprdb name: CRISPRdb pattern: ^[0-9]+$ preferred_prefix: crisprdb publications: - doi: 10.1093/nar/gkn228 pmc: PMC2447796 pubmed: '18442988' title: 'CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats' year: 2008 - doi: 10.1093/nar/gkm360 pmc: PMC1933234 pubmed: '17537822' title: 'CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats' year: 2007 - doi: 10.1186/1471-2105-8-172 pmc: PMC1892036 pubmed: '17521438' title: The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats year: 2007 uri_format: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1 cro: contact: email: whimar@ohsu.edu github: marijane name: Marijane White orcid: 0000-0001-5059-4132 description: A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. download_obo: https://raw.githubusercontent.com/data2health/contributor-role-ontology/master/cro.obo download_owl: http://purl.obolibrary.org/obo/cro.owl example: 0000038 homepage: https://github.com/data2health/contributor-role-ontology keywords: - obo - ontology license: CC BY 2.0 mappings: aberowl: CRO biocontext: CRO bioportal: CRO obofoundry: cro ols: cro ontobee: CRO name: Contributor Role Ontology pattern: ^\d{7}$ preferred_prefix: CRO rdf_uri_format: http://purl.obolibrary.org/obo/CRO_$1 repository: https://github.com/data2health/contributor-role-ontology uri_format: http://purl.obolibrary.org/obo/CRO_$1 version: '2019-12-11' crop2ml: description: CropMRespository is a database of soil and crop biophysical process models. example: '000000001' homepage: http://www.crop2ml.org mappings: miriam: crop2ml name: CropMRepository pattern: ^[0-9]{9}$ preferred_prefix: crop2ml uri_format: http://www.crop2ml.org/cropmdb/$1 cryoem: contact: email: isanchez@cnb.csic.es name: Carlos Oscar S. Sorzano orcid: 0000-0002-9473-283X description: Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles download_owl: http://scipion.i2pc.es/ontology/cryoem/releases/2021-03-09/cryoem.owl example: '0000052' homepage: http://scipion.i2pc.es/ontology/cryoem keywords: - electron microscopy - ontology - structural biology mappings: aberowl: CRYOEM bioportal: CRYOEM fairsharing: FAIRsharing.q47I0t ols: cryoem name: Cryo Electron Microscopy ontology pattern: ^\d{7}$ preferred_prefix: cryoem uri_format: http://scipion.i2pc.es/ontology/CRYOEM_$1 version: '2021-03-09' cryptodb: contact: email: jkissing@uga.edu name: Jessica Kissinger orcid: 0000-0003-4446-6200 description: CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: cgd7_230 homepage: https://cryptodb.org/cryptodb/ keywords: - functional genomics - genome - genomics - parasitology mappings: biocontext: CRYPTODB fairsharing: FAIRsharing.t3nprm integbio: nbdc01780 miriam: cryptodb n2t: cryptodb prefixcommons: cryptodb re3data: r3d100012265 name: CryptoDB pattern: ^\w+$ preferred_prefix: cryptodb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/cryptodb:$1 publications: - doi: 10.1007/978-1-4939-9748-0_10 pubmed: '31452162' title: Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org year: 2020 - doi: 10.1093/nar/gkj078 pmc: PMC1347441 pubmed: '16381902' title: 'CryptoDB: a Cryptosporidium bioinformatics resource update' year: 2006 twitter: VEuPathDB uri_format: https://cryptodb.org/cryptodb/app/record/gene/$1 csa: contact: email: nickf@ebi.ac.uk name: Nicholas Furnham orcid: 0000-0002-7532-1269 description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme. example: 1a05 homepage: https://www.ebi.ac.uk/thornton-srv/databases/CSA/ keywords: - enzyme - life science - structure mappings: biocontext: CSA fairsharing: FAIRsharing.2ajtcf miriam: csa n2t: csa prefixcommons: csa name: Catalytic Site Atlas pattern: ^[0-9][A-Za-z0-9]{3}$ preferred_prefix: csa providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/csa:$1 publications: - doi: 10.1093/nar/gkt1243 pmc: PMC3964973 pubmed: '24319146' title: 'The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes' year: 2013 - doi: 10.1093/nar/gkh028 pmc: PMC308762 pubmed: '14681376' title: 'The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data' year: 2004 uri_format: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1 csd: contact: email: support@ccdc.cam.ac.uk name: Support Email orcid: 0000-0002-6062-7492 description: The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode. example: PELNAW homepage: https://www.ccdc.cam.ac.uk/ keywords: - biochemistry - chemistry - organic chemistry - organic molecular chemistry mappings: fairsharing: FAIRsharing.vs7865 miriam: csd re3data: r3d100010197 name: Cambridge Structural Database pattern: ^[A-Z]{6}(\d{2})?$ preferred_prefix: csd publications: - doi: 10.1107/s2052520616003954 pmc: PMC4822653 pubmed: '27048719' title: The Cambridge Structural Database year: 2016 - doi: 10.1107/s0108768102003890 pubmed: '12037359' title: 'The Cambridge Structural Database: a quarter of a million crystal structures and rising' year: 2002 - doi: 10.1107/S2052520616003954 title: The Cambridge Structural Database. - doi: 10.1107/S0108768102003890 title: 'The Cambridge Structural Database: a quarter of a million crystal structures and rising' twitter: ccdc_cambridge uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG csp: contact: email: af8d@nih.gov name: Anita Ghebeles deprecated: true description: CRISP is a terminology used for indexing biomedical information. CRISP contains over 8,000 preferred terms that are grouped hierarchically into 11 domains. Note that while still available and included in Unified Medical Language System (UMLS), it has not been updated since 2006. example: 2004-2820 homepage: https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm keywords: - anatomy - biology - biomedical science - chemical biology - disease - food - medicine - ontology - social science mappings: aberowl: CRISP bioportal: CRISP fairsharing: FAIRsharing.1evfpc hl7: 2.16.840.1.113883.6.120 pathguide: '192' name: Computer Retrieval of Information on Science Projects Thesaurus preferred_prefix: csp publications: - pubmed: '8718842' title: Taking a bite out of CRISP. Strategies on using and conducting searches in the Computer Retrieval of Information on Scientific Projects database year: 1996 synonyms: - CRISP - CRISP Thesaurus - CRISP Thesaurus, 2006 - CSP2005 uri_format: http://purl.bioontology.org/ontology/CSP/$1 cst: description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways. example: Akt_PKB homepage: http://www.cellsignal.com/pathways/index.html keywords: - biomedical science - life science mappings: biocontext: CST fairsharing: FAIRsharing.n8pxvx hl7: 2.16.840.1.113883.6.62 miriam: cst n2t: cst pathguide: '193' name: Cell Signaling Technology Pathways pattern: ^[A-Za-z0-9_-]+$ preferred_prefix: cst uri_format: http://www.cellsignal.com/reference/pathway/$1.html cst.ab: description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products. example: '3305' homepage: http://www.cellsignal.com/catalog/index.html keywords: - pathway mappings: biocontext: CST.AB miriam: cst.ab n2t: cst.ab prefixcommons: cst name: Cell Signaling Technology Antibody pattern: ^\d+$ preferred_prefix: cst.ab providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/cst:$1 uri_format: http://www.cellsignal.com/products/$1.html cstr: description: 'CSTR is an identifier for Common Science and Technology Resources, to provide persistent identification services for the positioning, traceability, citation, statistics and evaluation of science and technology resources. ' example: 31253.11.sciencedb.j00001.00123 homepage: https://www.cstr.cn/en/ mappings: miriam: cstr name: Common Science and Technology Resources pattern: ^\w{5}\.\d{2}\..*$ preferred_prefix: cstr uri_format: https://cstr.cn/$1 ctcae: appears_in: - oae contact: email: ncictcaehelp@mail.nih.gov name: CTCAE Help contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: The Common Terminology Criteria for Adverse Events (CTCAE),[1] formerly called the Common Toxicity Criteria (CTC or NCI-CTC), are a set of criteria for the standardized classification of adverse effects of drugs used in cancer therapy. The CTCAE system is a product of the US National Cancer Institute (NCI). download_owl: http://aber-owl.net/media/ontologies/CTCAE/2/ctcae.owl example: E12768 homepage: https://evs.nci.nih.gov/ftp1/CTCAE/About.html keywords: - ontology mappings: aberowl: CTCAE bioportal: CTCAE name: Common Terminology Criteria for Adverse Events pattern: ^E\d+$ preferred_prefix: ctcae publications: - pmc: PMC5977606 pubmed: '29854250' title: 'Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs' year: 2018 references: - https://github.com/OAE-ontology/OAE/issues/8 - https://en.wikipedia.org/wiki/Common_Terminology_Criteria_for_Adverse_Events synonyms: - CTCAE ctd.chemical: description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. example: D001151 homepage: http://ctdbase.org/ mappings: biocontext: CTD.CHEMICAL biolink: CTD.CHEMICAL miriam: ctd.chemical n2t: ctd.chemical name: CTD Chemical part_of: ctd pattern: ^[CD]\d+$ preferred_prefix: ctd.chemical provides: mesh uri_format: http://ctdbase.org/detail.go?type=chem&acc=$1 ctd.disease: description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. example: D053716 homepage: http://ctdbase.org/ mappings: biocontext: CTD.DISEASE biolink: CTD.DISEASE miriam: ctd.disease n2t: ctd.disease name: CTD Disease part_of: ctd pattern: ^D\d+$ preferred_prefix: ctd.disease provides: mesh uri_format: http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1 ctd.gene: contact: email: apdavis3@ncsu.edu name: Allan Peter Davis orcid: 0000-0002-5741-7128 description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. example: '101' homepage: http://ctdbase.org/ mappings: biocontext: CTD.GENE biolink: CTD.GENE miriam: ctd.gene n2t: ctd.gene uniprot: DB-0140 name: CTD Gene part_of: ctd pattern: ^\d+$ preferred_prefix: ctd.gene provides: ncbigene publications: - doi: 10.1093/nar/gkaa891 pmc: PMC7779006 pubmed: '33068428' title: 'Comparative Toxicogenomics Database (CTD): update 2021' year: 2021 uri_format: http://ctdbase.org/detail.go?type=gene&acc=$1 cteno: contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 depends_on: - ro - uberon description: An anatomical and developmental ontology for ctenophores (Comb Jellies) download_obo: https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo download_owl: http://purl.obolibrary.org/obo/cteno.owl example: '0000047' homepage: https://github.com/obophenotype/ctenophore-ontology keywords: - anatomy - developmental biology - obo - ontology license: CC-BY-3.0 mappings: aberowl: CTENO biocontext: CTENO bioportal: CTENO fairsharing: FAIRsharing.mgxgza obofoundry: cteno ols: cteno ontobee: CTENO name: Ctenophore Ontology pattern: ^\d{7}$ preferred_prefix: CTENO rdf_uri_format: http://purl.obolibrary.org/obo/CTENO_$1 repository: https://github.com/obophenotype/ctenophore-ontology uri_format: http://purl.obolibrary.org/obo/CTENO_$1 version: '2016-10-19' ctis: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This website supports the undertaking and oversight of clinical trials in the European Union (EU) and European Economic Area (EEA). It is part of a broad initiative to transform the EU/EEA clinical trials environment in support of large clinical trials in multiple European countries, to the benefit of medical innovation and patients. (from homepage) example: 2023-503698-40-00 homepage: https://euclinicaltrials.eu/ name: Clinical Trials Information System pattern: ^\d{4}-\d+-\d+-\d+$ preferred_prefix: ctis uri_format: https://euclinicaltrials.eu/app/#/view/$1 cto: contact: email: alpha.tom.kodamullil@scai.fraunhofer.de github: akodamullil name: Dr. Alpha Tom Kodamullil orcid: 0000-0001-9896-3531 description: The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials. download_owl: http://purl.obolibrary.org/obo/cto.owl example: '0000022' homepage: https://github.com/ClinicalTrialOntology/CTO/ keywords: - biomedical science - disease - neurobiology - obo - ontology - preclinical studies license: CC-BY-4.0 mappings: aberowl: CTO bioportal: CTO fairsharing: FAIRsharing.qp211a obofoundry: cto ols: cto ontobee: CTO name: Clinical Trials Ontology pattern: ^\d{7}$ preferred_prefix: CTO publications: - pubmed: '35992013' title: 'CTO: a Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView' year: 2020 rdf_uri_format: http://purl.obolibrary.org/obo/CTO_$1 repository: https://github.com/ClinicalTrialOntology/CTO uri_format: http://purl.obolibrary.org/obo/CTO_$1 version: 1.0.0 ctri: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The mission of the Clinical Trials Registry-India (CTRI) is to ensure that all clinical trials conducted in India are prospectively registered, i.e. before the enrolment of the first participant. Additionally, post-marketing surveillance studies, BA/BE studies as well as clinical studies as part of PG thesis are also expected to be registered in the CTRI. (from homepage) Note that the identifier in this semantic space is not the one used in the webpages' example: CTRI/2023/04/052053 homepage: https://ctri.nic.in name: India Clinical Trials Registry pattern: ^CTRI/\d{4}/\d{2,3}/\d+$ preferred_prefix: ctri references: - https://www.ctri.nic.in/Clinicaltrials/pmaindet2.php?trialid=82487 uri_format: https://trialsearch.who.int/Trial2.aspx?TrialID=$1 cubedb: comment: website down as of 2021-10-04 deprecated: true description: Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available. example: AKR homepage: http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html mappings: biocontext: CUBEDB integbio: nbdc02094 miriam: cubedb n2t: cubedb name: Cube db pattern: ^[A-Za-z_0-9]+$ preferred_prefix: cubedb uri_format: http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/ cutg: description: Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank. example: '9606' homepage: http://www.kazusa.or.jp/codon/ keywords: - dna - gene mappings: prefixcommons: cutg name: Codon Usage Tabulated from GenBank preferred_prefix: cutg providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/cutg:$1 provides: ncbitaxon reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=$1 cvdo: contact: email: paul.fabry@usherbrooke.ca github: pfabry name: Paul Fabry orcid: 0000-0002-3336-2476 description: An ontology to describe entities related to cardiovascular diseases download_owl: http://purl.obolibrary.org/obo/cvdo.owl example: '0000546' homepage: https://github.com/OpenLHS/CVDO keywords: - cardiology - cardiovascular disease - obo - ontology license: CC-BY-4.0 mappings: aberowl: CVDO biocontext: CVDO bioportal: CVDO fairsharing: FAIRsharing.2basyz obofoundry: cvdo ols: cvdo ontobee: CVDO name: Cardiovascular Disease Ontology pattern: ^\d{7}$ preferred_prefix: CVDO rdf_uri_format: http://purl.obolibrary.org/obo/CVDO_$1 repository: https://github.com/OpenLHS/CVDO uri_format: http://purl.obolibrary.org/obo/CVDO_$1 version: '2024-05-17' cvx: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The CDC's National Center of Immunization and Respiratory Diseases (NCIRD) developed and maintains the CVX (vaccine administered) code set. The table below has the most up to date values. It includes both active and inactive vaccines available in the US. CVX codes for inactive vaccines allow transmission of historical immunization records. example: '54' homepage: https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx mappings: hl7: 2.16.840.1.113883.6.59 name: Vaccine administered code set pattern: ^\d+$ preferred_prefix: cvx uri_format: https://biopragmatics.github.io/providers/cvx/$1 d1id: description: DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences. example: 00030692-0FE1-4A1B-955E-A2E55D659267 homepage: https://www.dataone.org mappings: biocontext: D1ID miriam: d1id n2t: d1id name: DataONE pattern: ^\S+$ preferred_prefix: d1id uri_format: https://cn.dataone.org/cn/v2/resolve/{$1} dailymed: description: DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read. example: 973a9333-fec7-46dd-8eb5-25738f06ee54 homepage: https://dailymed.nlm.nih.gov/dailymed/ mappings: biocontext: DAILYMED miriam: dailymed n2t: dailymed prefixcommons: dailymed name: DailyMed pattern: ^[A-Za-z0-9-]+$ preferred_prefix: dailymed providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/dailymed:$1 uri_format: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1 daml.pt: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A representation of the periodic table of the elements in OWL, with both elements and a hierarchical classification. This is from the DARPA Agent Markup Language (DAML) project, which has been inactive since the mid 2000's. download_owl: https://www.daml.org/2003/01/periodictable/PeriodicTable.owl example: Be example_extras: - Metallic - Non-metallic github_request_issue: 1419 homepage: https://www.daml.org/2003/01/periodictable/ keywords: - ontology name: DAML Periodic Table of the Elements preferred_prefix: daml.pt uri_format: http://www.daml.org/2003/01/periodictable/PeriodicTable#$1 dandi: contact: email: yoh@dartmouth.edu name: Yaroslav Halchenko orcid: 0000-0003-3456-2493 description: 'DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable). DANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data. These data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.' example: '000017' homepage: https://dandiarchive.org/ keywords: - neurophysiology mappings: fairsharing: FAIRsharing.f2c119 miriam: dandi re3data: r3d100013638 name: Distributed Archives for Neurophysiology Data Integration pattern: ^\d{6}(\/\d+\.\d+\.\d+)?$ preferred_prefix: dandi repository: https://github.com/dandi/dandiarchive twitter: dandiarchive uri_format: https://dandiarchive.org/dandiset/$1 darc: contact: email: daniel.wilson@uni-hamburg.de name: Daniel N. Wilson orcid: 0000-0003-3816-3828 description: DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors. example: '1250' homepage: http://darcsite.genzentrum.lmu.de/darc/index.php keywords: - life science mappings: biocontext: DARC fairsharing: FAIRsharing.evfe2s miriam: darc n2t: darc name: Database of Aligned Ribosomal Complexes pattern: ^\d+$ preferred_prefix: darc publications: - doi: 10.1093/nar/gkr824 pmc: PMC3245104 pubmed: '22009674' title: 'The DARC site: a database of aligned ribosomal complexes' year: 2011 uri_format: http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1 dashr: contact: email: dashr@lisanwanglab.org name: Li-San Wang orcid: 0000-0002-3684-0031 description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records. example: hsa-mir-200a homepage: http://lisanwanglab.org/DASHR/ keywords: - life science mappings: biocontext: DASHR fairsharing: FAIRsharing.ztvs34 miriam: dashr n2t: dashr name: Database of small human noncoding RNAs pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ preferred_prefix: dashr publications: - doi: 10.1093/nar/gkv1188 pmc: PMC4702848 pubmed: '26553799' title: 'DASHR: database of small human noncoding RNAs' year: 2015 uri_format: http://lisanwanglab.org/DASHR/entry/$1 dashr.expression: description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression. example: hsa-mir-200a homepage: https://dashr1.lisanwanglab.org/show-expression-table.php?start=0 mappings: biocontext: DASHR.EXPRESSION miriam: dashr.expression n2t: dashr.expression name: DASHR expression pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ preferred_prefix: dashr.expression uri_format: https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable datacite: contact: email: silvio.peroni@unibo.it github: essepuntato name: Silvio Peroni orcid: 0000-0003-0530-4305 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF. download_owl: http://aber-owl.net/media/ontologies/DATACITE/2/datacite.owl example: AgentIdentifierScheme homepage: http://www.sparontologies.net/ontologies/datacite keywords: - bibliography - citation - data model - ontology - report - subject agnostic mappings: aberowl: DATACITE bioportal: DATACITE fairsharing: FAIRsharing.c06f1e name: DataCite Ontology preferred_prefix: DataCite repository: https://github.com/sparontologies/datacite twitter: datacite uri_format: http://purl.org/spar/datacite/$1 datacommons: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A large RDF store built from American governmental data. This semantic space has a mixture of direct terms and subspaces. example: Gene homepage: https://datacommons.org mappings: biolink: dcid name: Data Commons preferred_prefix: datacommons repository: https://github.com/datacommonsorg/website synonyms: - dcid uri_format: https://datacommons.org/browser/$1 datanator.gene: description: Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. example: K00973 homepage: https://datanator.info/ mappings: miriam: datanator.gene name: Datanator Gene part_of: datanator pattern: ^K[0-9]+$ preferred_prefix: datanator.gene uri_format: https://www.datanator.info/gene/$1 datanator.metabolite: description: Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. example: OUYCCCASQSFEME-MRVPVSSYSA-N homepage: https://datanator.info/ mappings: miriam: datanator.metabolite name: Datanator Metabolite part_of: datanator pattern: ^[A-Z\-]+$ preferred_prefix: datanator.metabolite uri_format: https://www.datanator.info/metabolite/$1 datanator.reaction: description: "\tDatanator is an integrated database of genomic and biochemical data\ \ designed to help investigators find data about specific molecules and reactions\ \ in specific organisms and specific environments for meta-analyses and mechanistic\ \ models. Datanator currently includes metabolite concentrations, RNA modifications\ \ and half-lives, protein abundances and modifications, and reaction kinetics\ \ integrated from several databases and numerous publications. The Datanator website\ \ and REST API provide tools for extracting clouds of data about specific molecules\ \ and reactions in specific organisms and specific environments, as well as data\ \ about similar molecules and reactions in taxonomically similar organisms." example: XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N homepage: https://icahn.mssm.edu/ mappings: miriam: datanator.reaction name: Datanator Reaction pattern: ^.*?--%3E.*?$ preferred_prefix: datanator.reaction uri_format: https://datanator.info/reaction/$1 datf: deprecated: true description: DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals. example: AT1G01030.1 homepage: http://datf.cbi.pku.edu.cn/ keywords: - regulation mappings: biocontext: DATF miriam: datf n2t: datf pathguide: '518' prefixcommons: datf name: Database of Arabidopsis Transcription Factors pattern: ^AT[1-5]G\d{5}(\.\d+)?$ preferred_prefix: datf providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/datf:$1 uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1 dbd: description: The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins. example: '0045310' homepage: http://www.transcriptionfactor.org/ keywords: - genome - regulation mappings: biocontext: DBD edam: '2716' miriam: dbd n2t: dbd pathguide: '496' prefixcommons: dbd name: Transcription Factor Database pattern: ^\d+$ preferred_prefix: dbd providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/dbd:$1 uri_format: http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD dbest: contact: email: tmjlowe@ucsc.edu name: Todd M Lowe orcid: 0000-0003-3253-6021 description: The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. example: BP100000 homepage: https://www.ncbi.nlm.nih.gov/nucest keywords: - bioinformatics - dna - life science mappings: biocontext: DBEST edam: '1105' fairsharing: FAIRsharing.v9fya8 integbio: nbdc00413 miriam: dbest n2t: dbest ncbi: dbEST prefixcommons: dbest re3data: r3d100010648 name: EST database maintained at the NCBI. pattern: ^([A-Z]+)?\d+(\.\d+)?$ preferred_prefix: dbest providers: - code: CURATOR_REVIEW description: dbEST through DNA Data Bank of Japan (DDBJ) homepage: http://www.ddbj.nig.ac.jp/ name: dbEST through DNA Data Bank of Japan (DDBJ) uri_format: http://getentry.ddbj.nig.ac.jp/getentry/na/$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/dbest:$1 - code: ebi description: dbEST through European Nucleotide Archive (ENA) homepage: https://www.ebi.ac.uk/ena name: dbEST through European Nucleotide Archive (ENA) uri_format: https://www.ebi.ac.uk/ena/data/view/$1 publications: - doi: 10.1038/ng0893-332 pubmed: '8401577' title: dbEST--database for "expressed sequence tags" year: 1993 uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1 dbg2introns: contact: email: zimmerly@ucalgary.ca name: Steven John Zimmerly description: The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. example: Cu.me.I1 homepage: http://webapps2.ucalgary.ca/~groupii/ keywords: - dna mappings: biocontext: DBG2INTRONS miriam: dbg2introns n2t: dbg2introns prefixcommons: mgiid name: DBG2 Introns pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$ preferred_prefix: dbg2introns providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mgiid:$1 publications: - doi: 10.1093/nar/gkr1043 pmc: PMC3245105 pubmed: '22080509' title: Database for bacterial group II introns year: 2011 uri_format: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1 dbgap: contact: email: feolo@ncbi.nlm.nih.gov github: mfeolo name: Michael Feolo orcid: 0000-0002-1650-5156 description: The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. example: phs000768.v2.p1 homepage: https://www.ncbi.nlm.nih.gov/gap/ keywords: - biomedical science - epigenetics - genetics mappings: biocontext: DBGAP cellosaurus: dbGAP fairsharing: FAIRsharing.88v2k0 integbio: nbdc00414 miriam: dbgap n2t: dbgap name: Database of Genotypes and Phenotypes pattern: ^phs[0-9]{6}(.v\d+.p\d+)?$ preferred_prefix: dbgap publications: - doi: 10.1093/nar/gkt1211 pmc: PMC3965052 pubmed: '24297256' title: 'NCBI''s Database of Genotypes and Phenotypes: dbGaP' year: 2013 - doi: 10.1038/ng1007-1181 pmc: PMC2031016 pubmed: '17898773' title: The NCBI dbGaP database of genotypes and phenotypes year: 2007 uri_format: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1 dblp.author: description: identifier for author entries in the DBLP computer science bibliography (use portion of DBLP person key after pid/) example: 199/2168 homepage: https://dblp.org/ mappings: wikidata: P2456 name: DBLP author ID preferred_prefix: dblp.author rdf_uri_format: https://dblp.org/pid/$1.rdf uri_format: https://dblp.org/pid/$1 dbmhc: appears_in: - cellosaurus deprecated: true description: Cell line databases/resources example: '48439' homepage: https://www.ncbi.nlm.nih.gov/gv/mhc/ mappings: cellosaurus: dbMHC integbio: nbdc01831 name: Database of human Major Histocompatibility Complex pattern: ^\d+$ preferred_prefix: dbmhc dbo: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki. example: careerPrizeMoney github_request_issue: 515 homepage: https://dbpedia.org/ontology keywords: - dbpedia - ontology mappings: zazuko: dbo name: DBPedia Ontology preferred_prefix: dbo uri_format: https://dbpedia.org/ontology/$1 dbpedia: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A semi-automatically generated knowledgebase example: Grenada github_request_issue: 1315 homepage: https://dbpedia.org mappings: re3data: r3d100011713 name: DBPedia preferred_prefix: dbpedia uri_format: http://dbpedia.org/resource/$1 dbpedia.property: appears_in: - fovt contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Properties in DBPedia. example: insertion github_request_issue: 1420 homepage: http://dbpedia.org/property name: DBPedia Property part_of: dbpedia preferred_prefix: dbpedia.property uri_format: http://dbpedia.org/property/$1 dbprobe: description: The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities. example: '1000000' homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe keywords: - nucleotide mappings: biocontext: DBPROBE edam: '2719' miriam: dbprobe n2t: dbprobe ncbi: dbProbe prefixcommons: dbprobe name: NCBI Probe database Public registry of nucleic acid reagents pattern: ^\d+$ preferred_prefix: dbprobe providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/dbprobe:$1 uri_format: https://www.ncbi.nlm.nih.gov/probe/?term=$1 dbsnp: contact: email: pruitt@ncbi.nlm.nih.gov name: Kim Dixon Pruitt orcid: 0000-0001-7950-1374 description: The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. example: rs121909098 homepage: https://www.ncbi.nlm.nih.gov/snp/ keywords: - genome - life science mappings: biocontext: dbSNP cellosaurus: dbSNP edam: '1106' fairsharing: FAIRsharing.edxb58 go: dbSNP hl7: 2.16.840.1.113883.6.284 integbio: nbdc00206 miriam: dbsnp n2t: dbsnp ncbi: dbSNP prefixcommons: dbsnp re3data: r3d100010652 togoid: Dbsnp uniprot: DB-0013 wikidata: P6861 name: dbSNP Reference SNP number pattern: ^rs\d+$ preferred_prefix: dbsnp providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/dbsnp:$1 - code: sib description: SNP2TFBS homepage: https://epd.expasy.org/ name: SNP2TFBS uri_format: https://epd.expasy.org/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1 publications: - doi: 10.1093/nar/gkaa892 pubmed: '33095870' - doi: 10.1093/nar/gkl1031 pmc: PMC1781113 pubmed: '17170002' title: Database resources of the National Center for Biotechnology Information year: 2006 - doi: 10.1093/nar/29.1.308 pmc: PMC29783 pubmed: '11125122' title: 'dbSNP: the NCBI database of genetic variation' year: 2001 repository: https://github.com/ncbi/dbsnp/tree/master/tutorials uri_format: https://www.ncbi.nlm.nih.gov/snp/$1 dbvar.study: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Studies in dbVar. example: nstd102 homepage: https://www.ncbi.nlm.nih.gov/dbvar name: Database of Genomic Structural Variation - Study preferred_prefix: dbvar.study synonyms: - dbvar.studies uri_format: https://www.ncbi.nlm.nih.gov/dbvar/studies/$1 dbvar.variant: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Variants in dbVar. example: nsv3875336 homepage: https://www.ncbi.nlm.nih.gov/dbvar name: Database of Genomic Structural Variation - Variant preferred_prefix: dbvar.variant synonyms: - dbvar.variants uri_format: https://www.ncbi.nlm.nih.gov/dbvar/variants/$1 dc: contact: email: kdurante@stanford.edu name: Kim Durante orcid: 0000-0001-9052-2854 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: 'Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. **Deprecation Notice**: While the `/elements/1.1/` namespace will be supported indefinitely, DCMI gently encourages use of the `/terms/` namespace (i.e., `dcterms`) ([source](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3)).' download_owl: http://aber-owl.net/media/ontologies/dcelements/1/dcelements.owl download_rdf: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_elements.rdf example: contributor homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ keywords: - annotation - biomedical science - life science - metadata - metadata standardization - ontology - resource metadata - subject agnostic mappings: aberowl: dcelements biocontext: dc bioportal: DC fairsharing: FAIRsharing.3nx7t lov: dce ols: dc zazuko: dc11 name: Dublin Core Elements (1.1) preferred_prefix: dc synonyms: - dc.elements - dc11 - dce - dcelem - elements uri_format: http://purl.org/dc/elements/1.1/$1 dc_cl: contact: email: Lindsay.Cowell@utsouthwestern.edu name: Lindsay Cowell orcid: 0000-0003-1617-8244 deprecated: true example: '0000003' homepage: http://www.dukeontologygroup.org/Projects.html keywords: - obo - ontology mappings: biocontext: DC_CL obofoundry: dc_cl name: Dendritic cell pattern: ^\d{7}$ preferred_prefix: DC_CL rdf_uri_format: http://purl.obolibrary.org/obo/DC_CL_$1 uri_format: http://purl.obolibrary.org/obo/DC_CL_$1 dcat: contact: email: kdurante@stanford.edu name: Kim Durante orcid: 0000-0001-9052-2854 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web download_owl: http://aber-owl.net/media/ontologies/DCAT/2/dcat.owl example: Dataset homepage: https://www.w3.org/ns/dcat keywords: - data management - ontology - subject agnostic - w3c rec mappings: aberowl: DCAT biocontext: dcat biolink: dcat bioportal: DCAT fairsharing: FAIRsharing.h4j3qm lov: dcat zazuko: dcat name: Data Catalog preferred_prefix: dcat repository: https://github.com/w3c/dxwg/ uri_format: http://www.w3.org/ns/dcat#$1 dcterms: contact: email: futo@stanford.edu name: Michelle Futornick contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. download_owl: http://aber-owl.net/media/ontologies/dcterms/1/dcterms.owl download_rdf: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_terms.rdf example: title homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ keywords: - metadata - metadata standardization - ontology - resource metadata - subject agnostic mappings: aberowl: dcterms biocontext: dcterms biolink: dct bioportal: DCTERMS fairsharing: FAIRsharing.9vtwjs lov: dcterms ols: dcterms zazuko: dcterms name: Dublin Core Metadata Initiative Terms preferred_prefix: dcterms synonyms: - dc.terms - dct - terms uri_format: http://purl.org/dc/terms/$1 dctypes: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. example: Collection homepage: https://dublincore.org/specifications/dublin-core/dcmi-terms/ mappings: biocontext: dctypes name: Dublin Core Types preferred_prefix: dctypes uri_format: http://purl.org/dc/dcmitype/$1 ddanat: contact: email: pfey@northwestern.edu github: pfey03 name: Petra Fey orcid: 0000-0002-4532-2703 description: A structured controlled vocabulary of anatomies of the slime-mold Dictyostelium discoideum. download_obo: http://purl.obolibrary.org/obo/ddanat.obo download_owl: http://purl.obolibrary.org/obo/ddanat.owl example: '0000006' homepage: http://dictybase.org/ keywords: - anatomy - cell - life science - obo - ontology - slime-mould license: CC0-1.0 mappings: aberowl: DDANAT biocontext: DDANAT bioportal: DDANAT fairsharing: FAIRsharing.z656ab go: DDANAT obofoundry: ddanat ols: ddanat ontobee: DDANAT prefixcommons: ddanat name: Dictyostelium discoideum anatomy pattern: ^\d{7}$ preferred_prefix: DDANAT providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ddanat:$1 publications: - doi: 10.1186/1471-2164-9-130 pmc: PMC2323390 pubmed: '18366659' title: An anatomy ontology to represent biological knowledge in Dictyostelium discoideum year: 2008 rdf_uri_format: http://purl.obolibrary.org/obo/DDANAT_$1 repository: https://github.com/dictyBase/migration-data twitter: dictybase uri_format: http://purl.obolibrary.org/obo/DDANAT_$1 ddc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Dewey Decimal Classification (DDC) system, devised by library pioneer Melvil Dewey in the 1870s and owned by OCLC since 1988, provides a dynamic structure for the organization of library collections. Now in its 23rd edition, and available in print and Web versions, the DDC is the world's most widely used library classification system. example: '325.4' example_extras: - '3' - '32' - '325' - 325.4-325.9 homepage: http://www.oclc.org/dewey/ mappings: bartoc: '241' name: Dewey Decimal Classification pattern: ^(([0-9][0-9]?|[0-9]{3}(-[0-9]{3})?|[0-9]{3}(-[0-9]{3}(:[0-9]+)?)?|[0-9]{3}\.[0-9]+(-[0-9]{3}\.[0-9]+(:[0-9]+)?)?|T[1-9][A-Z]?--[0-9]+(-T[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?|[1-9][A-Z]?--[0-9]+(-[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?)?)$ preferred_prefix: ddc ddinter.drug: contact: email: oriental-cds@163.com name: Dongsheng Cao orcid: 0000-0003-3604-3785 contributor: github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 description: Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety. example: DDInter20 github_request_issue: 492 homepage: http://ddinter.scbdd.com keywords: - chemistry - drugs - relationships license: CC-BY-NC-SA-4.0 name: Curated Drug-Drug Interactions Database - Drug pattern: ^DDInter\d+$ preferred_prefix: ddinter.drug reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://ddinter.scbdd.com/ddinter/drug-detail/$1 ddinter.interaction: contact: email: oriental-cds@163.com name: Dongsheng Cao orcid: 0000-0003-3604-3785 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety. example: '1122888' github_request_issue: 492 homepage: http://ddinter.scbdd.com keywords: - chemistry - drug-drug interactions - drugs - relationships license: CC-BY-NC-SA-4.0 name: Curated Drug-Drug Interactions Database - Interaction pattern: ^\d+$ preferred_prefix: ddinter.interaction uri_format: http://ddinter.scbdd.com/ddinter/interact/$1 ddpheno: contact: email: pfey@northwestern.edu github: pfey03 name: Petra Fey orcid: 0000-0002-4532-2703 description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. download_json: http://purl.obolibrary.org/obo/ddpheno.json download_obo: https://raw.githubusercontent.com/obophenotype/dicty-phenotype-ontology/master/ddpheno.obo download_owl: http://purl.obolibrary.org/obo/ddpheno.owl example: '0001417' homepage: http://dictybase.org/ keywords: - life science - obo - ontology - phenotype license: CC0-1.0 mappings: aberowl: DDPHENO biocontext: DDPHENO bioportal: DDPHENO fairsharing: FAIRsharing.9c1p18 obofoundry: ddpheno ols: ddpheno ontobee: DDPHENO name: Dictyostelium discoideum phenotype ontology pattern: ^\d{7}$ preferred_prefix: DDPHENO publications: - doi: 10.1387/ijdb.190226pf pmc: PMC7409682 pubmed: '31840793' title: dictyBase and the Dicty Stock Center (version 2.0) - a progress report year: 2019 - doi: 10.1007/978-1-62703-302-2_4 pmc: PMC3762881 pubmed: '23494302' title: 'One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012' year: 2013 rdf_uri_format: http://purl.obolibrary.org/obo/DDPHENO_$1 repository: https://github.com/obophenotype/dicty-phenotype-ontology twitter: dictybase uri_format: http://purl.obolibrary.org/obo/DDPHENO_$1 version: '2023-08-26' debio: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON. download_json: https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.json download_obo: https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.obo download_owl: https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.owl example: '0000001' homepage: https://biopragmatics.github.io/debio keywords: - ontology name: Decentralized Biomedical Ontology pattern: ^\d{7}$ preferred_prefix: debio providers: - code: obo2 description: Because it's not possible to configure the base URI with ROBOT/OWLAPI, this pops out homepage: http://purl.obolibrary.org name: Placeholder OBO PURL uri_format: http://purl.obolibrary.org/obo/debio_$1 synonyms: - DeBiO uri_format: https://biopragmatics.github.io/debio/$1 decipher: contact: email: ganesh.swaminathan@sanger.ac.uk name: Jawahar Swaminathan orcid: 0000-0002-0215-4084 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms example: '1' homepage: https://www.deciphergenomics.org/ keywords: - biomedical science - life science mappings: biocontext: DECIPHER fairsharing: FAIRsharing.l8Sf5x name: DECIPHER CNV Syndromes pattern: ^\d+$ preferred_prefix: decipher publications: - doi: 10.1093/nar/gkt937 pmc: PMC3965078 pubmed: '24150940' title: 'DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation' year: 2013 - doi: 10.1016/j.ajhg.2009.03.010 pmc: PMC2667985 pubmed: '19344873' title: 'DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources' year: 2009 uri_format: https://www.deciphergenomics.org/syndrome/$1 degradome: description: The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced. example: Ax1 homepage: http://degradome.uniovi.es/ mappings: biocontext: DEGRADOME miriam: degradome n2t: degradome name: Degradome Database pattern: ^[AMCST][0-9x][0-9]$ preferred_prefix: degradome uri_format: http://degradome.uniovi.es/cgi-bin/protease/$1 deims.activity: contact: email: christoph.wohner@umweltbundesamt.at github: stopopol name: Christoph Wohner orcid: 0000-0002-0655-3699 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Activities in DEIMS SDR example: 7dfd3f10-d410-45a4-983d-8fbd6dfbc374 github_request_issue: 1381 homepage: https://deims.org license: CC-BY-NC-4.0 name: Dynamic Ecological Information Management System - Site and Dataset Registry - Activity part_of: deims pattern: ^[0-9a-f\-]+$ preferred_prefix: deims.activity providers: - code: api description: A first-party API endpoint for an activity in DEIMS-SDR homepage: https://deims.org/api name: DEIMS-SDR API uri_format: https://deims.org/api/activities/$1 publications: - doi: 10.1016/j.ecoinf.2022.101708 pmc: PMC9461184 pubmed: '36105745' title: Designing and implementing a data model for describing environmental monitoring and research sites year: 2022 - doi: 10.1016/j.ecoinf.2020.101158 title: Towards interoperable research site documentation – Recommendations for information models and data provision year: 2020 - doi: 10.1016/j.ecoinf.2019.01.005 title: DEIMS-SDR – A web portal to document research sites and their associated data year: 2019 uri_format: https://deims.org/activity/$1 deims.dataset: contact: email: christoph.wohner@umweltbundesamt.at github: stopopol name: Christoph Wohner orcid: 0000-0002-0655-3699 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Datasets in DEIMS SDR example: bb0754dd-7e69-4b29-b348-3f8017f73d6b github_request_issue: 1381 homepage: https://deims.org license: CC-BY-NC-4.0 name: Dynamic Ecological Information Management System - Site and Dataset Registry - Dataset part_of: deims pattern: ^[0-9a-f\-]+$ preferred_prefix: deims.dataset providers: - code: api description: A first-party API endpoint for a dataset in DEIMS-SDR homepage: https://deims.org/api name: DEIMS-SDR API uri_format: https://deims.org/api/datasets/$1 publications: - doi: 10.1016/j.ecoinf.2022.101708 pmc: PMC9461184 pubmed: '36105745' title: Designing and implementing a data model for describing environmental monitoring and research sites year: 2022 - doi: 10.1016/j.ecoinf.2020.101158 title: Towards interoperable research site documentation – Recommendations for information models and data provision year: 2020 - doi: 10.1016/j.ecoinf.2019.01.005 title: DEIMS-SDR – A web portal to document research sites and their associated data year: 2019 uri_format: https://deims.org/dataset/$1 deims.location: contact: email: christoph.wohner@umweltbundesamt.at github: stopopol name: Christoph Wohner orcid: 0000-0002-0655-3699 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Locations in DEIMS SDR example: 85dc6019-9654-4ba0-8338-08c4ffe8fe47 github_request_issue: 1381 homepage: https://deims.org license: CC-BY-NC-4.0 name: Dynamic Ecological Information Management System - Site and Dataset Registry - Locations part_of: deims pattern: ^[0-9a-f\-]+$ preferred_prefix: deims.location providers: - code: api description: A first-party API endpoint for a location in DEIMS-SDR homepage: https://deims.org/api name: DEIMS-SDR API uri_format: https://deims.org/api/locations/$1 publications: - doi: 10.1016/j.ecoinf.2022.101708 pmc: PMC9461184 pubmed: '36105745' title: Designing and implementing a data model for describing environmental monitoring and research sites year: 2022 - doi: 10.1016/j.ecoinf.2020.101158 title: Towards interoperable research site documentation – Recommendations for information models and data provision year: 2020 - doi: 10.1016/j.ecoinf.2019.01.005 title: DEIMS-SDR – A web portal to document research sites and their associated data year: 2019 uri_format: https://deims.org/locations/$1 deims.network: contact: email: christoph.wohner@umweltbundesamt.at github: stopopol name: Christoph Wohner orcid: 0000-0002-0655-3699 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Networks in DEIMS SDR example: c3abdc60-49f1-49db-81fe-863b7dbb21d3 github_request_issue: 1381 homepage: https://deims.org license: CC-BY-NC-4.0 name: Dynamic Ecological Information Management System - Site and Dataset Registry - Network part_of: deims pattern: ^[0-9a-f\-]+$ preferred_prefix: deims.network publications: - doi: 10.1016/j.ecoinf.2022.101708 pmc: PMC9461184 pubmed: '36105745' title: Designing and implementing a data model for describing environmental monitoring and research sites year: 2022 - doi: 10.1016/j.ecoinf.2020.101158 title: Towards interoperable research site documentation – Recommendations for information models and data provision year: 2020 - doi: 10.1016/j.ecoinf.2019.01.005 title: DEIMS-SDR – A web portal to document research sites and their associated data year: 2019 uri_format: https://deims.org/networks/$1 deims.sensor: contact: email: christoph.wohner@umweltbundesamt.at github: stopopol name: Christoph Wohner orcid: 0000-0002-0655-3699 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Sensors in DEIMS SDR example: 2af339dd-a956-471f-9406-b0f74bacd579 github_request_issue: 1381 homepage: https://deims.org license: CC-BY-NC-4.0 name: Dynamic Ecological Information Management System - Site and Dataset Registry - Sensor part_of: deims pattern: ^[0-9a-f\-]+$ preferred_prefix: deims.sensor providers: - code: api description: A first-party API endpoint for a sensor in DEIMS-SDR homepage: https://deims.org/api name: DEIMS-SDR API uri_format: https://deims.org/api/sensors/$1 publications: - doi: 10.1016/j.ecoinf.2022.101708 pmc: PMC9461184 pubmed: '36105745' title: Designing and implementing a data model for describing environmental monitoring and research sites year: 2022 - doi: 10.1016/j.ecoinf.2020.101158 title: Towards interoperable research site documentation – Recommendations for information models and data provision year: 2020 - doi: 10.1016/j.ecoinf.2019.01.005 title: DEIMS-SDR – A web portal to document research sites and their associated data year: 2019 uri_format: https://deims.org/sensors/$1 deims.site: comment: This is an important resource for us in fields like environmental genomics. We frequently want to link metagenome samples to sites to make it easier to pull in environmental data to explore connections between environments, gene functions, community structure, etc. I will try and reach out to establish contacts with them contact: email: christoph.wohner@umweltbundesamt.at github: stopopol name: Christoph Wohner orcid: 0000-0002-0655-3699 contributor: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: DEIMS-SDR (Dynamic Ecological Information Management System - Site and dataset registry) is an information management system powered by eLTER. It allows you to discover long-term ecosystem research sites around the globe, along with the data gathered at those sites and the people and networks associated with them. DEIMS-SDR describes a wide range of sites, providing a wealth of information, including each site’s location, ecosystems, facilities, parameters measured and research themes. It is also possible to access a growing number of datasets and data products associated with the sites. example: 0e39569d-ff81-4b78-9c34-b07309504d80 github_request_issue: 1381 homepage: https://deims.org/ license: CC-BY-NC-4.0 name: Dynamic Ecological Information Management System - Site and dataset registry part_of: deims pattern: ^[0-9a-f\-]+$ preferred_prefix: deims.site providers: - code: api description: A first-party API endpoint for a site in DEIMS-SDR homepage: https://deims.org/api name: DEIMS-SDR API uri_format: https://deims.org/api/sites/$1 publications: - doi: 10.1016/j.ecoinf.2022.101708 pmc: PMC9461184 pubmed: '36105745' title: Designing and implementing a data model for describing environmental monitoring and research sites year: 2022 - doi: 10.1016/j.ecoinf.2020.101158 title: Towards interoperable research site documentation – Recommendations for information models and data provision year: 2020 - doi: 10.1016/j.ecoinf.2019.01.005 title: DEIMS-SDR – A web portal to document research sites and their associated data year: 2019 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - deims.id uri_format: https://deims.org/$1 deims.taxonomy: contact: email: christoph.wohner@umweltbundesamt.at github: stopopol name: Christoph Wohner orcid: 0000-0002-0655-3699 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Taxonomy in DEIMS SDR example: '21157' github_request_issue: 1381 homepage: https://deims.org license: CC-BY-NC-4.0 name: Dynamic Ecological Information Management System - Site and Dataset Registry - Taxonomy part_of: deims pattern: ^\d+$ preferred_prefix: deims.taxonomy publications: - doi: 10.1016/j.ecoinf.2022.101708 pmc: PMC9461184 pubmed: '36105745' title: Designing and implementing a data model for describing environmental monitoring and research sites year: 2022 - doi: 10.1016/j.ecoinf.2020.101158 title: Towards interoperable research site documentation – Recommendations for information models and data provision year: 2020 - doi: 10.1016/j.ecoinf.2019.01.005 title: DEIMS-SDR – A web portal to document research sites and their associated data year: 2019 uri_format: https://deims.org/taxonomy/term/$1 deo: contact: email: silvio.peroni@unibo.it github: essepuntato name: Silvio Peroni orcid: 0000-0003-0530-4305 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology that provides a structured vocabulary for rhetorical elements within documents (e.g., Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix). It is imported by DoCO. example: Reference homepage: http://www.sparontologies.net/ontologies/deo keywords: - bibliography - citation - data model - report - spar - subject agnostic mappings: fairsharing: FAIRsharing.39fd58 lov: deo name: Discourse Elements Ontology preferred_prefix: DEO publications: - doi: 10.3233/sw-150177 title: The Document Components Ontology (DoCO) year: 2016 repository: https://github.com/sparontologies/deo twitter: sparontologies uri_format: http://purl.org/spar/deo/$1 depmap: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells. example: ACH-000001 homepage: https://depmap.org/portal license: CC-BY-4.0 mappings: cellosaurus: DepMap name: DepMap Cell Lines pattern: ^ACH-\d+$ preferred_prefix: depmap uri_format: https://depmap.org/portal/cell_line/$1 depod: contact: email: depod@embl.de name: General Enquiries orcid: 0000-0003-3562-7869 description: The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources. example: PTPN1 homepage: http://www.depod.bioss.uni-freiburg.de keywords: - life science mappings: biocontext: DEPOD fairsharing: FAIRsharing.q9j2e3 miriam: depod n2t: depod pathguide: '584' re3data: r3d100011936 uniprot: DB-0190 name: Human Dephosphorylation Database pattern: ^[A-Z0-9]+$ preferred_prefix: depod provides: hgnc.symbol publications: - doi: 10.1093/database/baz133 pmc: PMC6911163 pubmed: '31836896' title: 'The human DEPhOsphorylation Database DEPOD: 2019 update' year: 2019 - doi: 10.1093/nar/gku1009 pmc: PMC4383878 pubmed: '25332398' title: 'The human DEPhOsphorylation database DEPOD: a 2015 update' year: 2014 - doi: 10.1126/scisignal.2003203 pubmed: '23674824' title: Elucidating human phosphatase-substrate networks year: 2013 uri_format: http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1 dermo: contact: email: pns12@hermes.cam.ac.uk github: PaulNSchofield name: Paul Schofield orcid: 0000-0002-5111-7263 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders download_obo: http://aber-owl.net/media/ontologies/DERMO/10/dermo.obo example: '0000000' homepage: https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x keywords: - dermatology - disease - ontology mappings: aberowl: DERMO bioportal: DERMO fairsharing: FAIRsharing.k008w7 name: Human Dermatological Disease Ontology pattern: ^\d{7}$ preferred_prefix: dermo publications: - doi: 10.1186/s13326-016-0085-x pmc: PMC4907256 pubmed: '27296450' title: DermO; an ontology for the description of dermatologic disease year: 2016 repository: https://github.com/dermatology-ontology/dermatology uri_format: http://purl.obolibrary.org/obo/DERMO_$1 dev.ga4ghdos: description: Assists in resolving data across cloud resources. example: 23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00 homepage: http://github.com/ga4gh/data-object-service-schemas mappings: biocontext: DEV.GA4GHDOS miriam: dev.ga4ghdos n2t: dev.ga4ghdos name: Development Data Object Service pattern: ^[a-zA-Z0-9\-:#\.]+$ preferred_prefix: dev.ga4ghdos uri_format: https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1 devtox: contact: email: rupert.kellner@item.fraunhofer.de name: Rupert Kellner orcid: 0000-0002-6807-8731 contributor: github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The DevTox Project harmonizes the nomenclature used to describe developmental anomalies in laboratory animals, assists in the visual recognition of developmental anomalies with the aid of photographs, and provides a historical control database of developmental effects in laboratory animals. example: '311935300' github_request_issue: 989 homepage: https://www.devtox.org/ name: DevTox pattern: ^\d+$ preferred_prefix: devtox publications: - doi: 10.1016/j.reprotox.2019.07.003 pmc: PMC8865445 pubmed: '31288076' title: 'Update of the DevTox data database for harmonized risk assessment and alternative methodologies in developmental toxicology: Report of the 9th Berlin Workshop on Developmental Toxicity' year: 2019 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.devtox.org/nomenclature/ml_manus.php?mno=$1 dg.4503: description: Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org example: 0000ffeb-36e0-4a29-b21d-84423bda979d homepage: https://gen3.biodatacatalyst.nhlbi.nih.gov mappings: miriam: dg.4503 name: BioData Catalyst pattern: ^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$ 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/$1 dggr: description: Organism supplier which collects Drosophila stocks from laboratories all over the world, maintains them, and provides them to researchers upon request. [from RRID] example: '918902' homepage: http://kyotofly.kit.jp/cgi-bin/stocks/data_search.cgi keywords: - drosophila - genetic resource - genomics - organism supplier mappings: rrid: DGGR name: Kyoto Stock Center pattern: ^\d+$ preferred_prefix: dggr uri_format: https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi?DB_NUM=1&DG_NUM=$1 dgrc: description: Cell line collections (Providers) example: '215' homepage: https://dgrc.bio.indiana.edu/cells/Catalog mappings: cellosaurus: DGRC integbio: nbdc00048 name: Drosophila Genomics Resource Center pattern: ^\d+$ preferred_prefix: dgrc uri_format: https://dgrc.bio.indiana.edu/product/View?product=$1 dhba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A controlled vocabulary to support the study of transcription in the developing human brain download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dhba.obo example: '10153' homepage: https://www.brainspan.org/ keywords: - ontology name: Developing Human Brain Atlas pattern: ^\d+$ preferred_prefix: DHBA providers: - code: biopragmatics description: A static site generated for the DHBA resource homepage: https://biopragmatics.github.io/providers name: Biopragmatics Browser uri_format: https://biopragmatics.github.io/providers/dhba/$1 uri_format: https://purl.brain-bican.org/ontology/dhbao/DHBA_$1 dialnet.article: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier of an article in Dialnet example: '262393' homepage: https://dialnet.unirioja.es mappings: wikidata: P1610 name: Dialnet article ID preferred_prefix: dialnet.article references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://dialnet.unirioja.es/servlet/articulo?codigo=$1 dialnet.author: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier of an author in Dialnet example: '241889' homepage: https://dialnet.unirioja.es keywords: - person - researcher mappings: wikidata: P1607 name: Dialnet author ID pattern: ^[1-9]\d*$ preferred_prefix: dialnet.author references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://dialnet.unirioja.es/servlet/autor?codigo=$1 dialnet.book: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier of a book in Dialnet example: '187021' homepage: https://dialnet.unirioja.es mappings: wikidata: P1608 name: Dialnet book ID preferred_prefix: dialnet.book references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://dialnet.unirioja.es/servlet/libro?codigo=$1 dialnet.journal: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier of a journal in Dialnet example: '1119' homepage: http://dialnet.unirioja.es mappings: wikidata: P1609 name: Dialnet journal ID pattern: ^[1-9]\d{0,6}$ preferred_prefix: dialnet.journal references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://dialnet.unirioja.es/servlet/revista?codigo=$1 dicom: contact: email: dclunie@dclunie.com name: David Clunie orcid: 0000-0002-2406-1145 description: DICOM Controlled Terminology download_owl: ftp://medical.nema.org/MEDICAL/Dicom/Resources/Ontology/DCM/dcm.owl example: '109082' homepage: http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html keywords: - anatomy - biomedical science - medicine - ontology mappings: bioportal: DCM fairsharing: FAIRsharing.b7z8by hl7: 1.2.840.10008.2.16.4 ols: dicom name: DICOM Controlled Terminology pattern: ^\d+$ preferred_prefix: dicom publications: - doi: 10.1007/s10278-013-9577-8 pmc: PMC3705029 pubmed: '23404629' title: 'Multi-series DICOM: an extension of DICOM that stores a whole study in a single object' year: 2013 - doi: 10.1016/j.crad.2005.07.003 pubmed: '16223609' title: 'DICOM demystified: a review of digital file formats and their use in radiological practice' year: 2005 uri_format: http://dicom.nema.org/resources/ontology/DCM/$1 version: 2025a_20250221 dictybase: contact: email: pfey@northwestern.edu github: pfey03 name: Petra Fey orcid: 0000-0002-4532-2703 description: A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics example: DDB0191090 homepage: http://dictybase.org keywords: - anatomy - comparative genomics - genome - life science license: CC-BY-SA-4.0 mappings: biocontext: dictyBase fairsharing: FAIRsharing.4shj9c go: dictyBase integbio: nbdc00420 ncbi: dictyBase prefixcommons: dictybase re3data: r3d100010586 uniprot: DB-0015 name: dictyBase preferred_prefix: dictybase providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/dictybase:$1 publications: - doi: 10.1007/978-1-62703-302-2_4 pmc: PMC3762881 pubmed: '23494302' title: 'One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012' year: 2013 - doi: 10.1093/nar/gks1064 pmc: PMC3531180 pubmed: '23172289' title: 'DictyBase 2013: integrating multiple Dictyostelid species' year: 2012 - doi: 10.1093/nar/gkh138 pmc: PMC308872 pubmed: '14681427' title: 'dictyBase: a new Dictyostelium discoideum genome database' year: 2004 synonyms: - dictyBase uri_format: http://dictybase.org/gene/$1 dictybase.est: description: The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information. example: DDB0016567 homepage: http://dictybase.org/ license: CC-BY-SA-4.0 mappings: biocontext: DICTYBASE.EST miriam: dictybase.est n2t: dictybase.est name: dictyBase Expressed Sequence Tag part_of: dictybase pattern: ^DDB\d+$ preferred_prefix: dictybase.est uri_format: http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1 dictybase.gene: description: The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information. example: DDB_G0267522 homepage: http://dictybase.org/ license: CC-BY-SA-4.0 mappings: biocontext: DICTYBASE.GENE miriam: dictybase.gene n2t: dictybase.gene name: Dictybase Gene part_of: dictybase pattern: ^DDB_G\d+$ preferred_prefix: dictybase.gene uri_format: http://dictybase.org/gene/$1 did: banana: did description: DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary. example: sov:WRfXPg8dantKVubE3HX8pw homepage: https://w3c-ccg.github.io/did-spec/ mappings: miriam: did n2t: did name: Decentralized Identifier namespace_in_lui: true pattern: ^[a-z0-9]+:[A-Za-z0-9.\-:]+$ preferred_prefix: did uri_format: https://uniresolver.io/#did:$1 dideo: contact: email: mbrochhausen@gmail.com github: mbrochhausen name: Mathias Brochhausen orcid: 0000-0003-1834-3856 description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology download_owl: http://purl.obolibrary.org/obo/dideo.owl example: 00000180 homepage: https://github.com/DIDEO/DIDEO keywords: - biochemistry - drug interaction - evidence - natural product - obo - ontology license: CC-BY-4.0 mappings: aberowl: DIDEO biocontext: DIDEO bioportal: DIDEO fairsharing: FAIRsharing.9y8f0n obofoundry: dideo ols: dideo ontobee: DIDEO name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology pattern: ^\d{8}$ preferred_prefix: DIDEO publications: - doi: 10.1186/s13326-018-0183-z pmc: PMC5944177 pubmed: '29743102' title: Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse year: 2018 - pmc: PMC5765984 pubmed: '29295242' title: Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies to Improve Evidence Base Curation year: 2017 - doi: 10.1016/j.knosys.2016.10.006 title: 'Conceptual models of drug-drug interactions: A summary of recent efforts' year: 2016 rdf_uri_format: http://purl.obolibrary.org/obo/DIDEO_$1 repository: https://github.com/DIDEO/DIDEO uri_format: http://purl.obolibrary.org/obo/DIDEO_$1 version: '2023-10-16' dinto: contact: email: maria.herrero@kcl.ac.uk name: Maria Herrero deprecated: true description: A formal represention for drug-drug interactions knowledge. download_owl: http://purl.obolibrary.org/obo/dinto.owl homepage: http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: DINTO biocontext: DINTO bioportal: DINTO obofoundry: dinto ontobee: DINTO name: The Drug-Drug Interactions Ontology preferred_prefix: DINTO publications: - doi: 10.1021/acs.jcim.5b00119 pubmed: '26147071' title: 'DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug-Drug Interactions and Their Mechanisms' year: 2015 rdf_uri_format: http://purl.obolibrary.org/obo/DINTO_$1 repository: https://github.com/labda/DINTO uri_format: http://purl.obolibrary.org/obo/DINTO_$1 dip: contact: email: david@mbi.ucla.edu name: David Eisenberg orcid: 0000-0003-2432-5419 description: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions example: DIP-743N homepage: https://dip.doe-mbi.ucla.edu/ keywords: - biology - interaction - protein mappings: biocontext: DIP edam: '2616' fairsharing: FAIRsharing.qje0v8 integbio: nbdc00049 miriam: dip n2t: dip pathguide: '3' prefixcommons: dip re3data: r3d100010670 uniprot: DB-0016 name: Database of Interacting Proteins pattern: ^DIP(\:)?\-\d{1,}[ENXS]$ preferred_prefix: dip providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/dip:$1 publications: - doi: 10.1093/nar/gkh086 pmc: PMC308820 pubmed: '14681454' title: 'The Database of Interacting Proteins: 2004 update' year: 2004 - doi: 10.1093/nar/30.1.303 pmc: PMC99070 pubmed: '11752321' title: 'DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions' year: 2002 - doi: 10.1093/nar/29.1.239 pmc: PMC29798 pubmed: '11125102' title: 'DIP: The Database of Interacting Proteins: 2001 update' year: 2001 - doi: 10.1093/nar/28.1.289 pmc: PMC102387 pubmed: '10592249' title: 'DIP: the database of interacting proteins' year: 2000 uri_format: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1 discoverx: description: Cell line collections (Providers) example: 95-0166C6 homepage: https://www.discoverx.com/product_types/cell-lines-primary-cells mappings: cellosaurus: DiscoverX name: DiscoverX cell line products preferred_prefix: discoverx uri_format: https://www.discoverx.com/catalogmanagement/catalog/?searchText=$1 disdriv: contact: email: lynn.schriml@gmail.com github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 description: Drivers of human diseases including environmental, maternal and social exposures. download_owl: http://purl.obolibrary.org/obo/disdriv.owl example: '0000000' homepage: http://www.disease-ontology.org keywords: - obo - ontology license: CC0-1.0 mappings: aberowl: DISDRIV bioportal: DISDRIV obofoundry: disdriv ols: disdriv ontobee: DISDRIV name: Disease Drivers Ontology pattern: ^\d+$ preferred_prefix: DISDRIV rdf_uri_format: http://purl.obolibrary.org/obo/DISDRIV_$1 repository: https://github.com/DiseaseOntology/DiseaseDriversOntology twitter: diseaseontology uri_format: http://purl.obolibrary.org/obo/DISDRIV_$1 version: '2023-12-15' diseaseclass: appears_in: - efo contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: Legacy disease classes that later became MONDO download_obo: https://github.com/obophenotype/human-disease-ontology/raw/master/src/experimental/missing-omc.obo example: 0000598 keywords: - ontology name: Disease Class pattern: ^\d{7}$ preferred_prefix: diseaseclass uri_format: https://biopragmatics.github.io/providers/diseaseclass/$1 diseasesdb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities.' example: '1784' homepage: http://www.diseasesdatabase.com/ mappings: wikidata: P557 name: Diseases Database pattern: ^\d+$ preferred_prefix: diseasesdb uri_format: https://www.diseasesdatabase.com/ddb$1.htm disprot: contact: email: silvio.tosatto@unipd.it name: Silvio C.E. Tosatto orcid: 0000-0003-4525-7793 description: DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature. example: DP00003 homepage: https://disprot.org/ keywords: - biology - biomedical science - protein - structural biology - structure mappings: biocontext: DISPROT edam: '2723' fairsharing: FAIRsharing.dt9z89 go: DisProt integbio: nbdc01798 miriam: disprot n2t: disprot prefixcommons: disprot re3data: r3d100010561 uniprot: DB-0017 name: DisProt pattern: ^DP\d{5}$ preferred_prefix: disprot providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/disprot:$1 publications: - doi: 10.1093/nar/gkab1082 pmc: PMC8728214 pubmed: '34850135' title: 'DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation' year: 2022 - doi: 10.1093/nar/gkz975 pmc: PMC7145575 pubmed: '31713636' title: 'DisProt: intrinsic protein disorder annotation in 2020' year: 2020 - doi: 10.1093/nar/gkw1056 pmc: PMC5210544 pubmed: '27899601' title: 'DisProt 7.0: a major update of the database of disordered proteins' year: 2016 - doi: 10.1093/nar/gkl893 pmc: PMC1751543 pubmed: '17145717' title: 'DisProt: the Database of Disordered Proteins' year: 2006 - doi: 10.1093/bioinformatics/bth476 pubmed: '15310560' title: 'DisProt: a database of protein disorder' year: 2004 repository: https://disprot.github.io/ twitter: disprot_db uri_format: https://disprot.org/$1 disprot.region: description: DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature. example: DP00086r013 homepage: https://www.disprot.org mappings: miriam: disprot.region name: DisProt region part_of: disprot pattern: ^DP\d{5}r\d{3}$ preferred_prefix: disprot.region uri_format: https://www.disprot.org/$1 dlxb: description: DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences. example: 6VDC956 homepage: https://doulix.com mappings: miriam: dlxb name: Linear double stranded DNA sequences part_of: dlx pattern: ^[A-Z0-9]{6,7}$ preferred_prefix: dlxb uri_format: https://doulix.com/biomodules/$1 dlxc: description: DOULIX lab-tested standard biological parts, in this case, full length constructs. example: M77F7JM homepage: https://doulix.com mappings: miriam: dlxc name: Circular double stranded DNA sequences composed part_of: dlx pattern: ^[A-Z0-9]{6,7}$ preferred_prefix: dlxc uri_format: https://doulix.com/constructs/$1 dmba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A controlled vocabulary to support the study of transcription in the developing mouse brain download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dmba.obo download_owl: https://purl.brain-bican.org/ontology/dmbao/releases/2025-02-10/dmbao.owl example: '15567' homepage: https://developingmouse.brain-map.org/ keywords: - ontology mappings: ols: dmba name: Developing Mouse Brain Atlas pattern: ^\d+$ preferred_prefix: DMBA providers: - code: biopragmatics description: Biopragmatics provider for DMBA homepage: https://biopragmatics.github.io/providers/dmba name: DMBA from Biopragmatics uri_format: https://biopragmatics.github.io/providers/dmba/$1 uri_format: https://purl.brain-bican.org/ontology/dmbao/DMBA_$1 version: '2025-02-10' doap: contact: email: edd@usefulinc.com github: ewilderj name: Edd Wilder-James contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: DOAP is a project to create an XML/RDF vocabulary to describe software projects, and in particular open source projects. download_rdf: http://usefulinc.com/ns/doap example: Project homepage: https://github.com/ewilderj/doap/wiki keywords: - metadata - rdf - semantic web - society mappings: lov: doap zazuko: doap name: Description of a Project preferred_prefix: doap references: - https://en.wikipedia.org/wiki/DOAP repository: https://github.com/ewilderj/doap uri_format: http://usefulinc.com/ns/doap#$1 dockerhub.repo: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Docker repository hosted on Docker Hub example: gitea/gitea homepage: https://hub.docker.com/ mappings: wikidata: P8778 name: Docker Hub repository preferred_prefix: dockerhub.repo references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://hub.docker.com/r/$1 dockerhub.user: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A user in DockerHub example: cthoyt homepage: https://hub.docker.com/ name: DockerHub User preferred_prefix: dockerhub.user uri_format: https://hub.docker.com/u/$1 doco: contact: email: silvio.peroni@unibo.it github: essepuntato name: Silvio Peroni orcid: 0000-0003-0530-4305 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology that provides a structured vocabulary written of document components, both structural (e.g., block, inline, paragraph, section, chapter) and rhetorical (e.g., introduction, discussion, acknowledgements, reference list, figure, appendix). example: Paragraph homepage: http://www.sparontologies.net/ontologies/doco keywords: - bibliography - citation - data model - report - spar - subject agnostic mappings: fairsharing: FAIRsharing.162003 lov: doco name: Document Components Ontology preferred_prefix: DoCO publications: - doi: 10.3233/sw-150177 title: The Document Components Ontology (DoCO) year: 2016 repository: https://github.com/sparontologies/doco twitter: sparontologies uri_format: http://purl.org/spar/doco/$1 doi: banana: doi comment: 'The [DOI resolution factsheet](https://www.doi.org/factsheets/DOIProxy.html) specifies that `https://doi.org/DOI` is the preferred format: > Users may resolve DOI names that are structured to use the DOI system Proxy Server (https://doi.org (preferred)). The resolution of the DOI name in this case depends on the use of URL syntax: the example DOI name doi:10.10.123/456 would be resolved from the address: "https://doi.org/10.123/456". Any standard browser encountering a DOI name in this form will be able to resolve it. The proxy service (both doi.org and the **earlier but no longer preferred** dx.doi.org) is accessible over IPv6, and supports DNSSEC. The proxy servers respond to HTTPS (**preferred**) as well as HTTP requests.' contributor_extras: - email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 - github: dhimmel name: Daniel Himmelstein orcid: 0000-0002-3012-7446 description: The Digital Object Identifier System is for identifying content objects in the digital environment. example: 10.1038/s41597-022-01807-3 example_extras: - 10.1016/j.foodchem.2008.11.065 - 10.1093/acprof:oso/9780195159561.001.1 - 10.1139/z02-135 - 10.1333/s00897980202a - 10.21/FQSQT4T3 homepage: https://www.doi.org/ keywords: - bibliography - centrally registered identifier - knowledge and information systems mappings: biocontext: DOI biolink: doi cellosaurus: DOI edam: '1188' fairsharing: FAIRsharing.hFLKCn go: DOI miriam: doi n2t: doi prefixcommons: doi wikidata: P356 name: Digital Object Identifier pattern: ^10.\d{2,9}/.*$ preferred_prefix: doi providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/doi:$1 - code: doi_http description: An alternate provider from the DOI website using HTTP homepage: https://www.doi.org name: Digital Object Identifier uri_format: http://doi.org/$1 - code: dx_doi_http description: An alternate provider from the DOI website using HTTP homepage: https://www.doi.org name: Digital Object Identifier uri_format: http://dx.doi.org/$1 - code: dx_doi_https description: An alternate provider from the DOI website using HTTPS homepage: https://www.doi.org name: Digital Object Identifier uri_format: https://dx.doi.org/$1 - code: miriam_legacy description: A legacy MIRIAM URI that does not follow the standard pattern homepage: https://identifiers.org name: Legacy MIRIAM URI uri_format: http://identifiers.org/DOI/$1 - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/doi/$1 rdf_uri_format: http://dx.doi.org/$1 references: - https://github.com/biopragmatics/bioregistry/issues/287 - https://github.com/biopragmatics/bioregistry/pull/316 uri_format: https://doi.org/$1 doid: appears_in: - clo - scdo banana: DOID contact: email: lynn.schriml@gmail.com github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. download_json: http://purl.obolibrary.org/obo/doid.json download_obo: https://github.com/DiseaseOntology/HumanDiseaseOntology/raw/main/src/ontology/doid.obo download_owl: http://purl.obolibrary.org/obo/doid.owl example: 0110974 homepage: http://www.disease-ontology.org keywords: - biomedical science - classification - disease - disease phenotype - disease process modeling - genetic disorder - human - infection - life science - mental health - obo - ontology license: CC0-1.0 logo: http://www.disease-ontology.org/media/images/DO_logo.jpg mappings: aberowl: DOID bartoc: '576' biocontext: DOID bioportal: DOID fairsharing: FAIRsharing.8b6wfq integbio: nbdc00261 miriam: doid n2t: doid obofoundry: doid ols: doid ontobee: DOID prefixcommons: do togoid: Doid wikidata: P699 name: Human Disease Ontology namespace_in_lui: true pattern: ^\d+$ preferred_prefix: DOID providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/do:$1 - code: hdo description: Human Disease Ontology at Northwestern University homepage: http://disease-ontology.org/ name: Human Disease Ontology at Northwestern University uri_format: http://disease-ontology.org/term/DOID:$1 - code: purl description: Legacy PURLs found in OAE homepage: http://purl.org/obo/owl/ name: Legacy PURL uri_format: http://purl.org/obo/owl/DOID#DOID_$1 publications: - doi: 10.1093/nar/gkad1051 pubmed: '37953304' title: 'The DO-KB Knowledgebase: a 20-year journey developing the disease open science ecosystem' year: 2023 - doi: 10.1093/nar/gkab1063 pmc: PMC8728220 pubmed: '34755882' title: The Human Disease Ontology 2022 update year: 2022 - doi: 10.1093/bib/bbab191 pmc: PMC8195003 pubmed: '34015823' title: COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model year: 2021 - doi: 10.7554/elife.52614 pmc: PMC7077981 pubmed: '32180547' title: Wikidata as a knowledge graph for the life sciences year: 2020 - doi: 10.1093/nar/gky1036 pmc: PMC6323956 pubmed: '30407590' title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence information' year: 2019 - doi: 10.1093/nar/gky1032 pmc: PMC6323977 pubmed: '30407550' title: 'Human Disease Ontology 2018 update: classification, content and workflow expansion' year: 2019 - doi: 10.1242/dmm.032839 pmc: PMC5897730 pubmed: '29590633' title: 'Disease Ontology: improving and unifying disease annotations across species' year: 2018 - doi: 10.1093/database/baw015 pmc: PMC4795929 pubmed: '26989148' title: Wikidata as a semantic framework for the Gene Wiki initiative year: 2016 - doi: 10.1016/j.ajhg.2015.05.020 pmc: PMC4572507 pubmed: '26119816' title: 'The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease' year: 2015 - doi: 10.1007/s00335-015-9576-9 pmc: PMC4602048 pubmed: '26093607' title: 'The Disease Ontology: fostering interoperability between biological and clinical human disease-related data' year: 2015 - doi: 10.1093/database/bav032 pmc: PMC4385274 pubmed: '25841438' title: Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis year: 2015 - doi: 10.1093/nar/gku1011 pmc: PMC4383880 pubmed: '25348409' title: 'Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data' year: 2014 - doi: 10.1093/nar/gkr972 pmc: PMC3245088 pubmed: '22080554' title: 'Disease Ontology: a backbone for disease semantic integration' year: 2011 - doi: 10.1186/1471-2164-10-s1-s6 pmc: PMC2709267 pubmed: '19594883' title: Annotating the human genome with Disease Ontology year: 2009 - doi: 10.1093/bioinformatics/btp193 pmc: PMC2687947 pubmed: '19478018' title: 'From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations' year: 2009 rdf_uri_format: http://purl.obolibrary.org/obo/DOID_$1 repository: https://github.com/DiseaseOntology/HumanDiseaseOntology synonyms: - do twitter: diseaseontology uri_format: http://purl.obolibrary.org/obo/DOID_$1 version: '2025-02-03' dolce: comment: This resource doesn't exist anymore contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering) is a foundational ontology developed as part of the WonderWeb Foundational Ontologies Library (WFOL). The development of this library has been guided by the need of a reliable set of foundational ontologies that can serve as 1) astarting point for building other ontologies, 2) a reference point for easy and rigorous comparisons among different ontological approaches, and 3) a rigorous basis for analyzing, harmonizing and integrating existing ontologies and metadata standards (by manually mapping them into some general module(s) in the library). DOLCE is the first module of WFOL and it is not a candidate for a universal standard ontology. Rather, it is intended as a starting point for comparing and elucidating the relationships with the other modules of the library, and also for clarifying the hidden assumptions underlying existing ontologies or linguistic resources such as WordNet. As reflected by its acronym, DOLCE has a clear cognitive bias, in the sense that it aims at capturing the ontological categories underlying natural language and human commonsense. DOLCE is an ontology that focuses on particulars in the sense that its domain of discourse is restricted to them. The project is complete, though the ontology remains available for use. homepage: http://www.loa.istc.cnr.it/dolce/overview.html keywords: - classification - computer science - knowledge and information systems - linguistics - subject agnostic mappings: fairsharing: FAIRsharing.ae8hpt name: Descriptive Ontology for Linguistic and Cognitive Engineering preferred_prefix: dolce dome: contact: email: silvio.tosatto@unipd.it github: silvio-tosatto name: Silvio Tosatto orcid: 0000-0003-4525-7793 contributor: email: palayoor.n@northeastern.edu github: nalikapalayoor name: Nalika Palayoor orcid: 0009-0008-8406-631X description: The DOME registry is a curated set of papers related to machine learning methods in biology, each with its own unique DOME identifier. example: dfyn1yvtz3 github_request_issue: 1374 homepage: https://registry.dome-ml.org mappings: miriam: dome name: DOME Registry pattern: ^[a-z0-9]{10}$ preferred_prefix: dome publications: - doi: 10.1093/gigascience/giae094 pmc: PMC11633452 pubmed: '39661723' title: 'DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://registry.dome-ml.org/review/$1 dommino: description: DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides. example: 2GC4 homepage: http://korkinlab.org/dommino mappings: biocontext: DOMMINO miriam: dommino n2t: dommino pathguide: '423' name: Database of Macromolecular Interactions pattern: ^[0-9][A-Za-z0-9]{3}$ preferred_prefix: dommino uri_format: http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1 door: description: DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes. example: '1398574' homepage: http://csbl.bmb.uga.edu/DOOR/operon.php keywords: - dna mappings: biocontext: DOOR miriam: door n2t: door prefixcommons: door re3data: r3d100014113 name: Database for Prokaryotic Operons pattern: ^\d+$ preferred_prefix: door providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/door:$1 uri_format: http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1 doqcs.model: contact: email: bhalla@ncbs.res.in github: upibhalla name: Upinder S. Bhalla orcid: 0000-0003-1722-5188 description: The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models. example: '57' homepage: http://doqcs.ncbs.res.in/ keywords: - model mappings: biocontext: DOQCS.MODEL miriam: doqcs.model n2t: doqcs.model prefixcommons: doqcs.model name: 'Database of Quantitative Cellular Signaling: Model' part_of: doqcs pattern: ^\d+$ preferred_prefix: doqcs.model providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/doqcs.model:$1 publications: - doi: 10.1093/bioinformatics/btf860 pubmed: '12584128' title: 'The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks' year: 2003 uri_format: http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1 doqcs.pathway: contact: email: bhalla@ncbs.res.in github: upibhalla name: Upinder S. Bhalla orcid: 0000-0003-1722-5188 description: The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways. example: '131' homepage: http://doqcs.ncbs.res.in/ keywords: - pathway mappings: biocontext: DOQCS.PATHWAY miriam: doqcs.pathway n2t: doqcs.pathway prefixcommons: doqcs.pathway name: 'Database of Quantitative Cellular Signaling: Pathway' part_of: doqcs pattern: ^\d+$ preferred_prefix: doqcs.pathway providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/doqcs.pathway:$1 publications: - doi: 10.1093/bioinformatics/btf860 pubmed: '12584128' title: 'The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks' year: 2003 uri_format: http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1 dpo: comment: DPO is a subset of terms from FBcv contact: email: cp390@cam.ac.uk github: Clare72 name: Clare Pilgrim orcid: 0000-0002-1373-1705 description: An ontology of commonly encountered and/or high level Drosophila phenotypes. download_json: http://purl.obolibrary.org/obo/dpo.json download_obo: http://purl.obolibrary.org/obo/dpo.obo download_owl: http://purl.obolibrary.org/obo/dpo.owl homepage: http://purl.obolibrary.org/obo/fbcv keywords: - obo - ontology license: CC-BY-4.0 mappings: aberowl: DPO bioportal: DPO obofoundry: dpo ols: dpo ontobee: DPO name: Drosophila Phenotype Ontology no_own_terms: true part_of: fbcv preferred_prefix: DPO publications: - doi: 10.1186/2041-1480-4-30 pmc: PMC3816596 pubmed: '24138933' title: The Drosophila phenotype ontology year: 2013 rdf_uri_format: http://purl.obolibrary.org/obo/FBcv_$1 repository: https://github.com/FlyBase/drosophila-phenotype-ontology uri_format: http://purl.obolibrary.org/obo/FBcv_$1 version: '2025-02-13' dpv: contact: email: mike.adams@bbsrc.ac.uk name: Michael J. Adams description: Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. example: '100' homepage: http://www.dpvweb.net/ keywords: - classification - gene - people - security mappings: biocontext: DPV integbio: nbdc02410 lov: dpv miriam: dpv n2t: dpv prefixcommons: dpvweb name: Description of Plant Viruses pattern: ^\d+$ preferred_prefix: dpv providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/dpvweb:$1 publications: - doi: 10.1093/nar/gkj023 pmc: PMC1347386 pubmed: '16381892' title: 'DPVweb: a comprehensive database of plant and fungal virus genes and genomes' year: 2006 uri_format: http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1 dpvocab: comment: The resource itself specifies a preferred prefix of `dpv` but this is already claimed in Bioregistry by the Description of Plant Viruses (https://bioregistry.io/registry/dpv). See also license discussion at https://github.com/w3c/dpv/issues/195. contact: email: me@harshp.com github: coolharsh55 name: Harshvardhan J. Pandit orcid: 0000-0002-5068-3714 contributor: email: jhc@lbl.gov github: caufieldjh name: Harry Caufield orcid: 0000-0001-5705-7831 contributor_extras: - email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 - email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 - email: arthit@gmail.com github: bact name: Arthit Suriyawongkul orcid: 0000-0002-9698-1899 description: The Data Privacy Vocabulary provides an ontology (classes and properties) and taxonomies of concepts to represent information regarding how personal data is processed in the form of an ontology or a knowledge graph. example: Duration github_request_issue: 1241 homepage: https://w3c.github.io/dpv/2.0/dpv license: W3C-20150513 name: Data Privacy Vocabulary preferred_prefix: dpvocab publications: - doi: 10.48550/arxiv.2404.13426 title: Data Privacy Vocabulary (DPV) -- Version 2 year: 2024 - doi: 10.1007/978-3-030-33246-4_44 title: Creating a Vocabulary for Data Privacy year: 2019 references: - https://github.com/biopragmatics/bioregistry/pull/1250 repository: https://github.com/w3c/dpv reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://w3id.org/dpv#$1 dragondb.allele: comment: Deprecated because the website is dead deprecated: true description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information. example: cho homepage: http://www.antirrhinum.net/ mappings: biocontext: DRAGONDB.ALLELE miriam: dragondb.allele n2t: dragondb.allele name: DragonDB Allele part_of: dragondb pattern: ^\w+$ preferred_prefix: dragondb.allele uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele dragondb.dna: comment: Deprecated because the website is dead deprecated: true description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information. example: 3hB06 homepage: http://www.antirrhinum.net/ mappings: biocontext: DRAGONDB.DNA miriam: dragondb.dna n2t: dragondb.dna name: DragonDB DNA part_of: dragondb pattern: ^\d\w+$ preferred_prefix: dragondb.dna uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA dragondb.locus: comment: Deprecated because the website is dead deprecated: true description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information. example: DEF homepage: http://www.antirrhinum.net/ mappings: biocontext: DRAGONDB.LOCUS miriam: dragondb.locus n2t: dragondb.locus name: DragonDB Locus part_of: dragondb pattern: ^\w+$ preferred_prefix: dragondb.locus uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus dragondb.protein: comment: Deprecated because the website is dead deprecated: true description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information. example: AMDEFA homepage: http://www.antirrhinum.net/ mappings: biocontext: DRAGONDB.PROTEIN miriam: dragondb.protein n2t: dragondb.protein name: DragonDB Protein part_of: dragondb pattern: ^\w+$ preferred_prefix: dragondb.protein uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide drduke: description: identifier for chemicals linked to information on occurrence in plants example: '19' homepage: https://phytochem.nal.usda.gov/phytochem/search/list mappings: wikidata: P10074 name: Dr. Duke's Phytochemical and Ethnobotanical Databases chemical preferred_prefix: drduke uri_format: https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1 drks: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The German Clinical Trials Register (DRKS) is the German WHO primary registry. It is competent for the registration of all patient-oriented clinical trials conducted in Germany. The DRKS now contains well over 14,000 studies. Currently, around 2,000 studies are added annually. (from website) example: DRKS00031815 homepage: http://drks.de name: German Clinical Trials Register pattern: ^DRKS\d+$ preferred_prefix: drks providers: - code: alt1 description: German Language Provider first_party: true homepage: http://drks.de name: German Language Provider uri_format: https://drks.de/search/de/trial/$1 - code: alt2 description: Legacy Provider first_party: true homepage: http://drks.de name: Legacy Provider uri_format: http://drks.de/en/trial/$1 uri_format: https://drks.de/search/en/trial/$1 dron: appears_in: - scdo contact: email: hoganwr@gmail.com github: hoganwr name: William Hogan orcid: 0000-0002-9881-1017 description: An ontology to support comparative effectiveness researchers studying claims data. download_json: http://purl.obolibrary.org/obo/dron.json download_obo: http://purl.obolibrary.org/obo/dron.obo download_owl: http://purl.obolibrary.org/obo/dron.owl example: '00023232' homepage: https://github.com/ufbmi/dron keywords: - approved drug - biomedical science - drug - obo - ontology - small molecule license: CC-BY-3.0 mappings: aberowl: DRON biocontext: DRON bioportal: DRON fairsharing: FAIRsharing.w5ntfd obofoundry: dron ols: dron ontobee: DRON name: The Drug Ontology pattern: ^\d{8}$ preferred_prefix: DRON publications: - doi: 10.1186/s13326-017-0121-5 pmc: PMC5335794 pubmed: '28253937' title: 'Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request' year: 2017 - doi: 10.1186/s13326-016-0048-2 pmc: PMC4836073 pubmed: '27096073' title: An accurate and precise representation of drug ingredients year: 2016 - doi: 10.1186/2041-1480-4-44 pmc: PMC3931349 pubmed: '24345026' title: Building a drug ontology based on RxNorm and other sources year: 2013 rdf_uri_format: http://purl.obolibrary.org/obo/DRON_$1 repository: https://github.com/ufbmi/dron uri_format: http://purl.obolibrary.org/obo/DRON_$1 version: '2024-12-20' drsanv0: description: 'This namespace is used for GA4GH Data Repository Service (DRS) access to the USA National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI), Genomic Analysis, Visualization and Informatics Lab-space (AnVIL) program data. AnVIL is a cloud-based genomic data sharing and analysis platform which facilitates integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by the National Institutes of Health (NIH) or by other agencies that support human genomics research. ' example: v2_1b0f158a-86e2-3887-b990-89e3cf2d9082 homepage: https://www.genome.gov/ mappings: miriam: drs.anv0 name: AnVIL DRS pattern: ^v2_[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$ preferred_prefix: drsanv0 uri_format: https://data.terra.bio/ga4gh/drs/v1/objects/$1 drsc: description: The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene. example: DRSC05221 homepage: http://flyrnai.org/ mappings: biocontext: DRSC miriam: drsc n2t: drsc name: Drosophila RNAi Screening Center pattern: ^DRSC\d+$ preferred_prefix: drsc uri_format: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1 drugbank: contact: email: david.wishart@ualberta.ca name: David Wishart orcid: 0000-0002-3207-2434 description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information. example: DB14938 homepage: http://www.drugbank.ca keywords: - biomedical science - drug - life science - protein mappings: bartoc: '18377' biocontext: DrugBank cellosaurus: DrugBank cheminf: '000406' edam: '2326' fairsharing: FAIRsharing.353yat integbio: nbdc01071 miriam: drugbank n2t: drugbank pathguide: '221' prefixcommons: drugbank re3data: r3d100010544 togoid: Drugbank uniprot: DB-0019 wikidata: P715 name: DrugBank pattern: ^DB\d{5}$ preferred_prefix: drugbank providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/drugbank:$1 publications: - doi: 10.1093/nar/gkad976 pubmed: '37953279' - doi: 10.1093/nar/gkt1068 pmc: PMC3965102 pubmed: '24203711' title: 'DrugBank 4.0: shedding new light on drug metabolism' year: 2013 - doi: 10.1093/nar/gkq1126 pmc: PMC3013709 pubmed: '21059682' title: 'DrugBank 3.0: a comprehensive resource for ''omics'' research on drugs' year: 2010 - doi: 10.1093/nar/gkm958 pmc: PMC2238889 pubmed: '18048412' title: 'DrugBank: a knowledgebase for drugs, drug actions and drug targets' year: 2007 - doi: 10.1093/nar/gkj067 pmc: PMC1347430 pubmed: '16381955' title: 'DrugBank: a comprehensive resource for in silico drug discovery and exploration' year: 2006 synonyms: - DRUGBANK_ID - DrugBank twitter: DrugBankDB uri_format: http://www.drugbank.ca/drugs/$1 drugbank.bioentity: description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database. example: BE0000048 homepage: http://www.drugbank.ca/targets mappings: biocontext: DRUGBANKV4.TARGET miriam: drugbankv4.target n2t: drugbankv4.target name: DrugBank Target v4 part_of: drugbank pattern: ^BE\d{7}$ preferred_prefix: drugbank.bioentity synonyms: - drugbank.target - drugbankv4.target uri_format: https://go.drugbank.com/bio_entities/$1 drugbank.category: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Close to 5K Categorizations for drugs, similar to ATCC. example: DBCAT000600 homepage: https://go.drugbank.com/categories keywords: - chemistry - drugs - metascience - topics name: DrugBank Drug Category part_of: drugbank pattern: ^DBCAT\d+$ preferred_prefix: drugbank.category uri_format: https://www.drugbank.ca/categories/$1 drugbank.condition: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Indications and other conditions in drugbank example: DBCOND0066902 homepage: https://go.drugbank.com name: DrugBank Condition pattern: ^DBCOND\d+$ preferred_prefix: drugbank.condition uri_format: https://go.drugbank.com/indications/$1 drugbank.metabolite: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Metabolites in drugbank example: DBMET02292 homepage: https://go.drugbank.com name: DrugBank Metabolite pattern: ^DBMET\d+$ preferred_prefix: drugbank.metabolite uri_format: https://go.drugbank.com/metabolites/$1 drugbank.reaction: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Reactions in drugbank example: '1537' homepage: https://go.drugbank.com name: DrugBank Reaction pattern: ^\d+$ preferred_prefix: drugbank.reaction uri_format: https://go.drugbank.com/reactions/$1 drugbank.salt: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets. example: DBSALT001211 homepage: http://www.drugbank.ca name: DrugBank Salts part_of: drugbank pattern: ^DBSALT\d{6}$ preferred_prefix: drugbank.salt uri_format: https://go.drugbank.com/salts/$1 drugcentral: contact: email: toprea@salud.unm.edu name: Tudor Oprea orcid: 0000-0002-6195-6976 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action. example: '307' homepage: http://drugcentral.org keywords: - biomedical science - drug development - drug discovery - drug repositioning - pharmacology - pharmacy license: CC-BY-SA-4.0 mappings: biolink: DrugCentral fairsharing: FAIRsharing.3me82d integbio: nbdc02192 miriam: drugcentral uniprot: DB-0239 wikidata: P11198 name: Drug Central pattern: ^\d+$ preferred_prefix: drugcentral publications: - doi: 10.1093/nar/gkac1085 pubmed: '36484092' - doi: 10.1093/nar/gky963 pmc: PMC6323925 pubmed: '30371892' title: 'DrugCentral 2018: an update' year: 2019 - doi: 10.1093/nar/gkw993 pmc: PMC5210665 pubmed: '27789690' title: 'DrugCentral: online drug compendium' year: 2016 synonyms: - Drug_Central uri_format: http://drugcentral.org/drugcard/$1 dsm4: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia] example: '315.1' example_extras: - '291.89' homepage: https://en.wikipedia.org/wiki/Diagnostic_and_Statistical_Manual_of_Mental_Disorders#DSM-IV-TR_(2000) mappings: hl7: 2.16.840.1.113883.6.126 wikidata: P663 name: Diagnostic and Statistical Manual of Mental Disorders (4th Edition) pattern: ^\d+\.\d+$ preferred_prefix: dsm4 synonyms: - dsm-iv dsm5: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia] example: '312.33' homepage: https://en.wikipedia.org/wiki/DSM-5 mappings: hl7: 2.16.840.1.113883.6.344 wikidata: P1930 name: Diagnostic and Statistical Manual of Mental Disorders (5th Edition) pattern: ^\d{3}\.\d{2}$ preferred_prefix: dsm5 references: - https://archive.org/details/diagnosticstatis0005unse synonyms: - dsm-v dsmz: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). The following designations are used as part of local unique identifiers: - `PC`: positive control - `NC`: negative control - `AS`: antiserum - `PV`: plant viruses - `RT`: recommended test - `ACC`: human or animal cell line - `DSM`: microorganism cell line' example: ACC-1 example_extras: - AS-0753 - DSM-2 - PC-0754 - PV-0998 - RT-0753 homepage: https://www.dsmz.de mappings: cellosaurus: DSMZCellDive re3data: r3d100010219 name: Deutsche Sammlung von Mikroorganismen und Zellkulturen pattern: ^(ACC|DSM|NC|PC|RT|AS|PV)-\d+$ preferred_prefix: dsmz synonyms: - DSMZCellDive uri_format: https://www.dsmz.de/collection/catalogue/details/culture/$1 dso: contact: email: evan@epatters.org github: epatters name: Evan Patterson orcid: 0000-0002-8600-949X contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Data Science Ontology is a research project of IBM Research AI and Stanford University Statistics. Its long-term objective is to improve the efficiency and transparency of collaborative, data-driven science. example: classification-model homepage: https://www.datascienceontology.org/ keywords: - data science - ontology name: Data Science Ontology preferred_prefix: dso repository: https://github.com/IBM/datascienceontology uri_format: https://www.datascienceontology.org/concept/$1 dto: appears_in: - pr contact: email: sschurer@med.miami.edu name: Stephan Schurer contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.' download_owl: http://aber-owl.net/media/ontologies/DTO/4/dto.owl example: '90000018' homepage: https://github.com/DrugTargetOntology/DTO keywords: - biomedical science - disease - drug discovery - drug target - ontology - protein mappings: aberowl: DTO bioportal: DTO fairsharing: FAIRsharing.tke3y2 name: Drug Target Ontology pattern: ^\d+$ preferred_prefix: dto publications: - doi: 10.1186/s13326-017-0161-x pmc: PMC5679337 pubmed: '29122012' title: Drug target ontology to classify and integrate drug discovery data year: 2017 repository: https://github.com/DrugTargetOntology/DTO uri_format: http://www.drugtargetontology.org/dto/DTO_$1 duo: appears_in: - scdo contact: email: mcourtot@gmail.com github: mcourtot name: Melanie Courtot orcid: 0000-0002-9551-6370 depends_on: - bfo - iao description: DUO is an ontology which represent data use conditions. download_owl: http://purl.obolibrary.org/obo/duo.owl example: '0000046' homepage: https://github.com/EBISPOT/DUO keywords: - biomedical science - metadata standardization - obo - ontology - subject agnostic license: CC-BY-4.0 logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdmdCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--9a42083efa91d79ee5c7ed8e7868db0f7faf0b76/DUO_logo_white_background.png?disposition=inline mappings: aberowl: DUO biocontext: DUO bioportal: DUO fairsharing: FAIRsharing.5dnjs2 obofoundry: duo ols: duo ontobee: DUO name: Data Use Ontology pattern: ^\d{7}$ preferred_prefix: DUO publications: - doi: 10.1016/j.xgen.2021.100028 pmc: PMC8591903 pubmed: '34820659' title: The Data Use Ontology to streamline responsible access to human biomedical datasets year: 2021 rdf_uri_format: http://purl.obolibrary.org/obo/DUO_$1 repository: https://github.com/EBISPOT/DUO uri_format: http://purl.obolibrary.org/obo/DUO_$1 version: '2021-02-23' dwc: contact: email: gtuco.btuco@gmail.com github: tucotuco name: John Wieczorek orcid: 0000-0003-1144-0290 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Darwin Core is a vocabulary standard for transmitting information about biodiversity. This document lists all terms in namespaces currently used in the vocabulary. example: Dataset github_request_issue: 1316 homepage: https://dwc.tdwg.org/list/ keywords: - biodiversity - biological sample annotation - geographical location - life science - taxonomic classification mappings: fairsharing: FAIRsharing.xvf5y3 name: Darwin Core Terms preferred_prefix: dwc publications: - doi: 10.1371/journal.pone.0102623 pubmed: '25099149' title: 'The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet' year: 2014 - doi: 10.3897/bdj.2.e1039 pubmed: '24723785' title: Linking multiple biodiversity informatics platforms with Darwin Core Archives year: 2014 - doi: 10.1371/journal.pone.0029715 pubmed: '22238640' title: 'Darwin Core: an evolving community-developed biodiversity data standard' year: 2012 repository: https://github.com/tdwg/dwc uri_format: http://rs.tdwg.org/dwc/terms/$1 eaglei: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Discovery tool for biomedical research resources available at institutions throughout the U.S. example: 0000012b-5661-2f63-2f73-b43980000000 homepage: https://hawaii.eagle-i.net mappings: cellosaurus: eagle-i re3data: r3d100011564 name: eagle-i preferred_prefix: eaglei uri_format: http://hawaii.eagle-i.net/i/$1 easychair.cfp: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Conferences in EasyChair example: SysBioCancer2022 homepage: https://easychair.org/cfp/ keywords: - conferences - metascience name: EasyChair Call for Paper preferred_prefix: easychair.cfp uri_format: https://easychair.org/cfp/$1 easychair.topic: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Call for paper topics in EasyChair example: '27106865' homepage: https://easychair.org/cfp/ keywords: - metascience - topics name: EasyChair Topic pattern: ^\d+$ preferred_prefix: easychair.topic uri_format: https://easychair.org/cfp/topic.cgi?tid=$1 ebisc: description: Cell line collections (Providers) example: ESi007-A example_extras: - EDi008-B homepage: https://www.ebisc.org mappings: cellosaurus: EBiSC name: European Bank for induced pluripotent Stem Cells pattern: ^E(S|D)i\d+-\w$ preferred_prefix: ebisc uri_format: https://cells.ebisc.org/$1 ec: comment: The Nomenclature Committee website does not yet contain an official policy regarding the use of dashes in the hierarchical categorization of enzymes, so the Bioregistry's regular expression is permissive and accepts both EC identifiers with dashes (e.g. 2.3.-.-) and without dashes (e.g., 2.3). This means you may have to do post-processing of EC identifiers in data integration scenarios. contact: email: kristian.axelsen@sib.swiss github: kaxelsen name: Kristian Axelsen orcid: 0000-0003-3889-2879 description: 'The Enzyme Nomenclature (also known as the Enzyme Commission Code) is a species-agnostic controlled vocabulary for specific enzymes and an associated hierarchical classification into 7 main categories. The Enzyme Nomenclature is maintained by the [Nomenclature Committee](https://iubmb.org/about/committees/nomenclature-committee/) of the International Union of Biochemistry and Molecular Biology (IUBMB). A detailed history of the nomenclature since the 1950s can be found [here](https://iubmb.qmul.ac.uk/enzyme/history.html). There are few notable resources providing access to the Enzyme Nomenclature:
WebsiteHomepageNotes
ExplorEnzhttps://www.enzyme-database.orgThis is the resources officially recommended by IUBMB
IUBMB (via by Queen Mary)https://iubmb.qmul.ac.uk/enzymeThis is a web-based version of the 1992 publication.
IntEnzhttps://www.ebi.ac.uk/intenz
ExPaSyhttps://enzyme.expasy.org
' example: 1.1.1.1 example_decoys: - '100' - '2.' - 2.n1 - 2.3. - 2.3.n1 - 2.3.1. - 2.3.1.n - 2.3.4.1. - 2.-.- - 2.- - 2.3.4.1.- example_extras: - '2' - 2.-.-.- - '2.3' - 2.3.-.- - 2.3.1 - 2.3.1.- - 2.3.1.n12 - 3.1.26.n2 - 3.4.24.B15 homepage: https://www.enzyme-database.org/ keywords: - biochemistry - centrally registered identifier - classification - enzyme - enzyme commission number - enzymology license: CC-BY-4.0 mappings: bartoc: '671' biocontext: EC-CODE edam: '1011' fairsharing: FAIRsharing.rfLD2u go: EC integbio: nbdc00508 miriam: ec-code n2t: ec-code pathguide: '106' prefixcommons: intenz re3data: r3d100010803 togoid: Ec uniprot: DB-0024 wikidata: P591 name: Enzyme Nomenclature owners: - name: International Union of Biochemistry and Molecular Biology partnered: false ror: 00910ay07 pattern: ^\d{1,2}(((\.\d{1,3}){1,3})|(\.\d+){2}\.[nB]\d{1,3}|\.-\.-\.-|\.\d{1,3}\.-\.-|\.\d{1,3}\.\d{1,3}\.-)?$ preferred_prefix: EC providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/intenz:$1 - code: expasy description: Enzyme nomenclature database, ExPASy (Expert Protein Analysis System) homepage: https://enzyme.expasy.org/ name: Enzyme nomenclature database, ExPASy (Expert Protein Analysis System) uri_format: https://enzyme.expasy.org/EC/$1 - code: expenz description: ExploreEnz at Trinity College homepage: http://www.enzyme-database.org/ name: ExploreEnz at Trinity College uri_format: http://www.enzyme-database.org/query.php?ec=$1 publications: - doi: 10.1093/nar/28.1.304 pmc: PMC102465 pubmed: '10592255' title: The ENZYME database in 2000 year: 2000 references: - https://github.com/biopragmatics/bioregistry/issues/681 synonyms: - EC - EC number - EC-CODE - ECCODE - EC_CODE - ec-code - eccode - intenz uri_format: https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1 ecacc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs). example: '90062901' homepage: https://www.phe-culturecollections.org.uk/collections/ecacc.aspx mappings: cellosaurus: ECACC name: European Collection of Authenticated Cell Culture pattern: ^\d+$ preferred_prefix: ecacc uri_format: https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1 ecao: contact: email: ettensohn@cmu.edu github: ettensohn name: Charles Ettensohn orcid: 0000-0002-3625-0955 depends_on: - cl - ro - uberon description: None download_obo: http://purl.obolibrary.org/obo/ecao.obo download_owl: http://purl.obolibrary.org/obo/ecao.owl example: 0107180 homepage: https://github.com/echinoderm-ontology/ecao_ontology keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: ECAO bioportal: ECAO obofoundry: ecao ols: ecao ontobee: ECAO name: The Echinoderm Anatomy and Development Ontology pattern: ^\d{7}$ preferred_prefix: ECAO rdf_uri_format: http://purl.obolibrary.org/obo/ECAO_$1 repository: https://github.com/echinoderm-ontology/ecao_ontology uri_format: http://purl.obolibrary.org/obo/ECAO_$1 version: '2024-08-22' ecg: contact: email: rwinslow@jhu.edu name: Raimond Winslow orcid: 0000-0003-1719-1651 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms. download_owl: http://aber-owl.net/media/ontologies/ECG/12/ecg.owl example: 000000159 homepage: https://bioportal.bioontology.org/ontologies/ECG keywords: - biomedical science - electrocardiography - heart - ontology mappings: aberowl: ECG bioportal: ECG fairsharing: FAIRsharing.azr389 name: Electrocardiogram Ontology pattern: ^\d+$ preferred_prefix: ecg publications: - doi: 10.1016/j.jbi.2010.08.007 pubmed: '20800107' title: Using an ECG reference ontology for semantic interoperability of ECG data year: 2010 synonyms: - ECGOntology uri_format: http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_$1 echinobase: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Echinobase supports the international research community by providing a centralized, integrated and easy to use web based resource to access the diverse and rich, functional genomics data of echinoderm species. example: '23159291' homepage: https://www.echinobase.org mappings: integbio: nbdc01512 name: Echinobase pattern: ^\d+$ preferred_prefix: echinobase uri_format: https://www.echinobase.org/entry/gene/showgene.do?method=display&geneId=$1 echobase: contact: email: gavin.thomas@york.ac.uk github: ghthomas name: Gavin H. Thomas orcid: 0000-0002-9763-1313 description: EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products. example: EB0170 homepage: http://www.york.ac.uk/ keywords: - gene - gene expression mappings: biocontext: ECHOBASE go: EchoBASE miriam: echobase n2t: echobase prefixcommons: echobase re3data: r3d100011646 uniprot: DB-0020 name: EchoBASE post-genomic database for Escherichia coli pattern: ^EB\d+$ preferred_prefix: echobase providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/echobase:$1 publications: - doi: 10.1093/nar/gki028 pmc: PMC539982 pubmed: '15608209' title: 'EchoBASE: an integrated post-genomic database for Escherichia coli' year: 2005 uri_format: http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1 ecmdb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes. example: ECMDB00005 homepage: https://ecmdb.ca mappings: pathguide: '386' name: E. coli Metabolite Database pattern: ^ECMDB\d+$ preferred_prefix: ecmdb synonyms: - ECMDB uri_format: http://ecmdb.ca/compounds/$1 ecn: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier for a chemical compound per EINECS or ELINCS example: 200-003-9 homepage: https://echa.europa.eu/information-on-chemicals mappings: cheminf: '000447' wikidata: P232 name: EC number pattern: ^\d{3}-\d{3}-\d$ preferred_prefix: ecn references: - https://github.com/biopragmatics/bioregistry/issues/257 - https://en.wikipedia.org/wiki/European_Community_number eco: banana: ECO contact: email: mgiglio@som.umaryland.edu github: mgiglio99 name: Michelle Giglio orcid: 0000-0001-7628-5565 description: Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity. download_obo: http://purl.obolibrary.org/obo/eco.obo download_owl: http://purl.obolibrary.org/obo/eco.owl example: 0007807 homepage: https://www.evidenceontology.org keywords: - assay - biocuration - biological sample annotation - computational biology - curated information - digital curation - evidence - life science - literature curation - obo - ontology - resource metadata - study design - text mining license: CC0-1.0 logo: https://avatars1.githubusercontent.com/u/12802432 mappings: aberowl: ECO bartoc: '1028' biocontext: ECO bioportal: ECO fairsharing: FAIRsharing.wvpgwn go: ECO miriam: eco n2t: eco obofoundry: eco ols: eco ontobee: ECO prefixcommons: eco wikidata: P3811 name: Evidence and Conclusion Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: ECO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/eco:$1 publications: - doi: 10.1093/nar/gkab1025 pmc: PMC8728134 pubmed: '34986598' title: 'ECO: the Evidence and Conclusion Ontology, an update for 2022' year: 2022 - doi: 10.1093/nar/gky1036 pmc: PMC6323956 pubmed: '30407590' title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence information' year: 2019 - doi: 10.1007/978-1-4939-3743-1_18 pmc: PMC6377151 pubmed: '27812948' title: 'The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations' year: 2017 - doi: 10.1093/database/bau075 pmc: PMC4105709 pubmed: '25052702' title: Standardized description of scientific evidence using the Evidence Ontology (ECO) year: 2014 - doi: 10.1142/9789812704856_0019 pubmed: '14992503' title: An evidence ontology for use in pathway/genome databases year: 2004 rdf_uri_format: http://purl.obolibrary.org/obo/ECO_$1 repository: https://github.com/evidenceontology/evidenceontology uri_format: http://purl.obolibrary.org/obo/ECO_$1 version: '2024-07-19' ecocore: contact: email: p.buttigieg@gmail.com github: pbuttigieg name: Pier Luigi Buttigieg orcid: 0000-0002-4366-3088 depends_on: - bfo - chebi - envo - go - iao - pato - pco - po - ro - uberon description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. download_obo: http://purl.obolibrary.org/obo/ecocore.obo download_owl: http://purl.obolibrary.org/obo/ecocore.owl example: '00000001' homepage: https://github.com/EcologicalSemantics/ecocore keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: ECOCORE biocontext: ECOCORE bioportal: ECOCORE obofoundry: ecocore ols: ecocore ontobee: ECOCORE name: An ontology of core ecological entities pattern: ^\d+$ preferred_prefix: ECOCORE rdf_uri_format: http://purl.obolibrary.org/obo/ECOCORE_$1 repository: https://github.com/EcologicalSemantics/ecocore uri_format: http://purl.obolibrary.org/obo/ECOCORE_$1 version: '2022-03-09' ecocyc: contact: email: pkarp@ai.sri.com github: pkarp111 name: Peter Karp orcid: 0000-0002-5876-6418 contributor_extras: - email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 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: https://ecocyc.org/ keywords: - biology mappings: fairsharing: FAIRsharing.65dmtr go: EcoCyc integbio: nbdc00262 ncbi: ECOCYC pathguide: '9' re3data: r3d100011277 name: EcoCyc preferred_prefix: ecocyc publications: - doi: 10.3389/fmicb.2021.711077 pmc: PMC8357350 pubmed: '34394059' title: The EcoCyc Database in 2021 year: 2021 - doi: 10.1093/nar/gkw1003 pmc: PMC5210515 pubmed: '27899573' title: 'The EcoCyc database: reflecting new knowledge about Escherichia coli K-12' year: 2016 - doi: 10.1128/ecosalplus.esp-0009-2013 pmc: PMC4243172 pubmed: '26442933' title: The EcoCyc Database year: 2014 - doi: 10.1093/nar/gks1027 pmc: PMC3531154 pubmed: '23143106' title: 'EcoCyc: fusing model organism databases with systems biology' year: 2012 - doi: 10.1128/ecosalplus.ESP-0009-2013 title: The EcoCyc Database. uri_format: https://ecocyc.org/gene?id=$1 ecogene: description: The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. example: EG10173 homepage: http://ecogene.org/ keywords: - genome - protein mappings: biocontext: EcoGene fairsharing: FAIRsharing.3q3kvn miriam: ecogene n2t: ecogene ncbi: EcoGene prefixcommons: ecogene re3data: r3d100010546 name: Database of Escherichia coli Sequence and Function pattern: ^EG\d+$ preferred_prefix: ecogene providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ecogene:$1 publications: - doi: 10.1093/nar/28.1.60 pmc: PMC102481 pubmed: '10592181' title: 'EcoGene: a genome sequence database for Escherichia coli K-12' year: 2000 uri_format: http://www.ecogene.org/gene/$1 ecolexicon: comment: No resolution - everything is in a single page app contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology. example: canal homepage: http://ecolexicon.ugr.es/en/index.htm keywords: - ecology - environmental science name: EcoLexicon preferred_prefix: ecolexicon ecoliwiki: contact: email: pkarp@ai.sri.com github: pkarp111 name: Peter D. Karp orcid: 0000-0002-5876-6418 description: EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes. example: aaeA homepage: http://ecoliwiki.net/colipedia/ keywords: - bioinformatics - genomics - life science - ontology and terminology mappings: biocontext: ECOLIWIKI fairsharing: FAIRsharing.tx95wa go: EcoliWiki integbio: nbdc02041 miriam: ecoliwiki n2t: ecoliwiki name: EcoliWiki from EcoliHub pattern: ^[A-Za-z0-9-]+$ preferred_prefix: ecoliwiki publications: - doi: 10.1016/j.tim.2009.04.004 pmc: PMC3575750 pubmed: '19576778' title: What we can learn about Escherichia coli through application of Gene Ontology year: 2009 uri_format: http://ecoliwiki.net/colipedia/index.php/$1:Gene ecso: contact: email: brycemecum@gmail.com github: amoeba name: Bryce Mecum orcid: 0000-0002-0381-3766 description: DataONE ontology of Carbon Flux measurements for MsTMIP and LTER Use Cases download_owl: https://raw.githubusercontent.com/DataONEorg/sem-prov-ontologies/run4/observation/d1-ECSO.owl example: '00000532' homepage: http://bioportal.bioontology.org/ontologies/ECSO keywords: - earth science - ecosystem - ecosystem science - ontology mappings: aberowl: ECSO bioportal: ECSO ecoportal: ECSO fairsharing: FAIRsharing.a4ww64 name: The Ecosystem Ontology pattern: ^\d+$ preferred_prefix: ecso repository: https://github.com/DataONEorg/sem-prov-ontologies uri_format: http://purl.dataone.org/odo/ECSO_$1 ecto: contact: email: annethessen@gmail.com github: diatomsRcool name: Anne Thessen orcid: 0000-0002-2908-3327 depends_on: - chebi - envo - exo - go - iao - maxo - nbo - ncbitaxon - ncit - pato - ro - uberon - xco description: ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology). download_json: http://purl.obolibrary.org/obo/ecto.json download_obo: http://purl.obolibrary.org/obo/ecto.obo download_owl: http://purl.obolibrary.org/obo/ecto.owl example: '0000001' homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology keywords: - diet - environmental science - exposure - obo - ontology license: CC0-1.0 logo: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/ecto-logos/ecto-logo_black-banner.png mappings: aberowl: ECTO agroportal: ECTO biolink: ECTO bioportal: ECTO fairsharing: FAIRsharing.6b77ac obofoundry: ecto ols: ecto ontobee: ECTO name: Environmental conditions, treatments and exposures ontology pattern: ^\d{7}$ preferred_prefix: ECTO publications: - doi: 10.1186/s13326-023-00283-x pubmed: '36823605' title: 'The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond' year: 2023 rdf_uri_format: http://purl.obolibrary.org/obo/ECTO_$1 repository: https://github.com/EnvironmentOntology/environmental-exposure-ontology uri_format: http://purl.obolibrary.org/obo/ECTO_$1 version: '2023-02-14' ecyano.entity: description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities. example: '23' homepage: http://www.e-cyanobacterium.org/bcs/entity/ mappings: biocontext: ECYANO.ENTITY miriam: ecyano.entity n2t: ecyano.entity name: E-cyanobacterium entity part_of: ecyano pattern: ^\d+$ preferred_prefix: ecyano.entity uri_format: https://www.e-cyanobacterium.org/bcs/entity/$1 ecyano.experiment: description: E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments. example: '18' homepage: https://www.e-cyanobacterium.org/experiments-repository/ mappings: miriam: ecyano.experiment name: E-cyanobacterium Experimental Data part_of: ecyano pattern: ^\d+$ preferred_prefix: ecyano.experiment uri_format: https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1 ecyano.model: description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models. example: '26' homepage: http://e-cyanobacterium.org/models/ mappings: biocontext: ECYANO.MODEL miriam: ecyano.model n2t: ecyano.model name: E-cyanobacterium model pattern: ^\d+$ preferred_prefix: ecyano.model uri_format: https://e-cyanobacterium.org/models/model/$1 ecyano.rule: description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules. example: '56' homepage: http://www.e-cyanobacterium.org/bcs/rule/ mappings: biocontext: ECYANO.RULE miriam: ecyano.rule n2t: ecyano.rule name: E-cyanobacterium rule part_of: ecyano pattern: ^\d+$ preferred_prefix: ecyano.rule uri_format: https://e-cyanobacterium.org/bcs/rule/$1 edam: contact: email: matus.kalas@uib.no github: matuskalas name: Matúš Kalaš orcid: 0000-0002-1509-4981 description: 'EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).' download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo download_owl: http://edamontology.org/1.25-20240924T0027Z-unstable(1.26) example: data_1664 homepage: http://edamontology.org keywords: - analysis - bioinformatics - data acquisition - data transformation - life science - obo - ontology - subject agnostic mappings: aberowl: EDAM agroportal: EDAM biocontext: EDAM bioportal: EDAM fairsharing: FAIRsharing.a6r7zs miriam: edam n2t: edam ols: edam ontobee: EDAM prefixcommons: edam name: EDAM Ontology pattern: ^(data|topic|operation|format)\_\d{4}$ preferred_prefix: edam providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/edam:$1 publications: - doi: 10.1093/bioinformatics/btt113 pmc: PMC3654706 pubmed: '23479348' title: 'EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats' year: 2013 - doi: 10.7490/f1000research.1118900.1 title: 'EDAM: the bioscientific data analysis ontology (update 2021)' year: 2021 - doi: 10.5281/zenodo.3899895 title: 'edamontology/edamontology: EDAM 1.25' year: 2020 rdf_uri_format: http://edamontology.org/$1 repository: https://github.com/edamontology/edamontology twitter: edamontology uri_format: https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1 version: 1.25-20240924T0027Z-unstable(1.26) edam.data: contact: email: matus.kalas@uib.no github: matuskalas name: Matúš Kalaš orcid: 0000-0002-1509-4981 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output. download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo example: '1664' homepage: http://edamontology.org keywords: - ontology mappings: biolink: EDAM-DATA name: EDAM Data part_of: edam pattern: ^\d+$ preferred_prefix: edam.data repository: https://github.com/edamontology/edamontology twitter: edamontology uri_format: http://edamontology.org/data_$1 edam.format: contact: email: matus.kalas@uib.no github: matuskalas name: Matúš Kalaš orcid: 0000-0002-1509-4981 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data. download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo example: '1915' homepage: http://edamontology.org keywords: - ontology mappings: biolink: EDAM-FORMAT name: EDAM Format part_of: edam pattern: ^\d+$ preferred_prefix: edam.format repository: https://github.com/edamontology/edamontology twitter: edamontology uri_format: http://edamontology.org/format_$1 edam.operation: contact: email: matus.kalas@uib.no github: matuskalas name: Matúš Kalaš orcid: 0000-0002-1509-4981 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.' download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo example: '0004' homepage: http://edamontology.org keywords: - ontology mappings: biolink: EDAM-OPERATION name: EDAM Operation part_of: edam pattern: ^\d+$ preferred_prefix: edam.operation repository: https://github.com/edamontology/edamontology twitter: edamontology uri_format: http://edamontology.org/operation_$1 edam.topic: contact: email: matus.kalas@uib.no github: matuskalas name: Matúš Kalaš orcid: 0000-0002-1509-4981 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other. download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo example: '0003' homepage: http://edamontology.org keywords: - ontology mappings: biolink: EDAM-TOPIC name: EDAM Topic part_of: edam pattern: ^\d+$ preferred_prefix: edam.topic repository: https://github.com/edamontology/edamontology twitter: edamontology uri_format: http://edamontology.org/topic_$1 edda: contact: email: tanja.bekhuis@tcbinfosci.com name: Tanja Bekhuis orcid: 0000-0002-8537-9077 description: Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries. download_owl: http://aber-owl.net/media/ontologies/EDDA/11/edda.owl example: health_care_quality_assessment homepage: https://bioportal.bioontology.org/ontologies/EDDA keywords: - medicine - ontology mappings: aberowl: EDDA bioportal: EDDA fairsharing: FAIRsharing.2ffmsb name: EDDA Study Designs Taxonomy preferred_prefix: edda uri_format: http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1 efo: contact: email: plwhetzel@gmail.com github: twhetzel name: Trish Whetzel orcid: 0000-0002-3458-4839 description: The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team. download_obo: http://www.ebi.ac.uk/efo/efo.obo download_owl: http://www.ebi.ac.uk/efo/efo.owl example: '0005147' homepage: http://www.ebi.ac.uk/efo keywords: - assay - experimental condition - experimental measurement - functional genomics - genome-wide association study - independent variable - ontology - study design license: Apache-2.0 mappings: aberowl: EFO agroportal: EFO biocontext: EFO biolink: EFO bioportal: EFO cellosaurus: EFO fairsharing: FAIRsharing.1gr4tz miriam: efo n2t: efo ols: efo ontobee: EFO wikidata: P11956 name: Experimental Factor Ontology owners: - name: European Bioinformatics Institute partnered: false ror: 02catss52 pattern: ^\d{7}$ preferred_prefix: EFO providers: - code: ebi description: EFO through Functional Genomics Group (EBI) homepage: https://www.ebi.ac.uk/efo/ name: EFO through Functional Genomics Group (EBI) uri_format: https://www.ebi.ac.uk/efo/EFO_$1 - code: ols.curie description: OLS via CURIE homepage: https://www.ebi.ac.uk/ols name: OLS uri_format: http://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_$1 publications: - doi: 10.1093/bioinformatics/btq099 pmc: PMC2853691 pubmed: '20200009' title: Modeling sample variables with an Experimental Factor Ontology year: 2010 repository: https://github.com/EBISPOT/efo/ uri_format: http://www.ebi.ac.uk/efo/EFO_$1 version: 3.75.0 ega.dataset: contact: email: tk2@ebi.ac.uk github: tk2 name: Thomas Keane orcid: 0000-0001-7532-6898 description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'. example: EGAD00000000001 homepage: https://ega-archive.org/ keywords: - biology - biomedical science - clinical studies - genomics - phenomics mappings: biocontext: EGA.DATASET fairsharing: FAIRsharing.mya1ff miriam: ega.dataset n2t: ega.dataset re3data: r3d100011242 name: European Genome-phenome Archive Dataset owners: - name: European Bioinformatics Institute partnered: false ror: 02catss52 pattern: ^EGAD\d{11}$ preferred_prefix: ega.dataset providers: - code: omicsdi description: EGA Dataset through OmicsDI homepage: https://www.omicsdi.org/ name: EGA Dataset through OmicsDI uri_format: https://www.omicsdi.org/dataset/ega/$1 publications: - doi: 10.1093/nar/gkab1059 pmc: PMC8728218 pubmed: '34791407' title: The European Genome-phenome Archive in 2021 year: 2022 - doi: 10.1038/ng.3312 pmc: PMC5426533 pubmed: '26111507' title: The European Genome-phenome Archive of human data consented for biomedical research year: 2015 twitter: EGAarchive uri_format: https://www.ebi.ac.uk/ega/datasets/$1 ega.study: description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets. example: EGAS00000000001 homepage: https://www.ebi.ac.uk/ega/studies mappings: biocontext: EGA.STUDY miriam: ega.study n2t: ega.study name: European Genome-phenome Archive Study pattern: ^EGAS\d{11}$ preferred_prefix: ega.study uri_format: https://www.ebi.ac.uk/ega/studies/$1 eggnog: contact: email: j.huerta@csic.es github: jhcepas name: Jaime Huerta-Cepas orcid: 0000-0003-4195-5025 description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).' example: veNOG12876 homepage: http://eggnog.embl.de/version_3.0/ keywords: - gene - life science mappings: biocontext: EGGNOG fairsharing: FAIRsharing.j1wj7d miriam: eggnog n2t: eggnog prefixcommons: eggnog uniprot: DB-0152 name: eggNOG pattern: ^\w+$ preferred_prefix: eggnog providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/eggnog:$1 publications: - doi: 10.1093/nar/gkac1022 pubmed: '36399505' - doi: 10.1093/nar/gkp951 pmc: PMC2808932 pubmed: '19900971' title: 'eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations' year: 2009 - doi: 10.1093/nar/gkm796 pmc: PMC2238944 pubmed: '17942413' title: 'eggNOG: automated construction and annotation of orthologous groups of genes' year: 2007 uri_format: http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1 ehda: contact: email: J.Bard@ed.ac.uk name: Jonathan Bard deprecated: true description: A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once. download_obo: http://aber-owl.net/media/ontologies/EHDA/6/ehda.obo example: '1' homepage: http://genex.hgu.mrc.ac.uk/ keywords: - anatomy - development - human - obo - ontology mappings: aberowl: EHDA biocontext: EHDA bioportal: EHDA obofoundry: ehda prefixcommons: ehda name: Human developmental anatomy, timed version pattern: ^\d+$ preferred_prefix: EHDA providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ehda:$1 rdf_uri_format: http://purl.obolibrary.org/obo/EHDA_$1 uri_format: http://purl.obolibrary.org/obo/EHDA_$1 ehdaa: contact: email: J.Bard@ed.ac.uk name: Jonathan Bard deprecated: true description: A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release. download_obo: http://aber-owl.net/media/ontologies/EHDAA/6/ehdaa.obo example: '1' homepage: http://genex.hgu.mrc.ac.uk/ keywords: - anatomy - development - human - obo - ontology mappings: aberowl: EHDAA biocontext: EHDAA bioportal: EHDAA obofoundry: ehdaa prefixcommons: ehdaa name: Human developmental anatomy, abstract version pattern: ^\d+$ preferred_prefix: EHDAA providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ehdaa:$1 rdf_uri_format: http://purl.obolibrary.org/obo/EHDAA_$1 uri_format: http://purl.obolibrary.org/obo/EHDAA_$1 ehdaa2: contact: email: J.Bard@ed.ac.uk name: Jonathan Bard depends_on: - aeo - caro - cl deprecated: true description: A structured controlled vocabulary of stage-specific anatomical structures of the developing human. download_obo: http://purl.obolibrary.org/obo/ehdaa2.obo download_owl: http://purl.obolibrary.org/obo/ehdaa2.owl example: '0000000' homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology keywords: - anatomy - animal organ development - biomedical science - life cycle stage - obo - ontology license: CC-BY-4.0 mappings: aberowl: EHDAA2 biocontext: EHDAA2 bioportal: EHDAA2 fairsharing: FAIRsharing.7zxrs6 obofoundry: ehdaa2 ols: ehdaa2 ontobee: EHDAA2 name: Human developmental anatomy, abstract pattern: ^\d{7}$ preferred_prefix: EHDAA2 publications: - doi: 10.1111/j.1469-7580.2012.01566.x pmc: PMC3482348 pubmed: '22973865' title: A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20) year: 2012 rdf_uri_format: http://purl.obolibrary.org/obo/EHDAA2_$1 repository: https://github.com/obophenotype/human-developmental-anatomy-ontology synonyms: - EHDAA2_RETIRED - HDAA2 - RETIRED_EHDAA2 uri_format: http://purl.obolibrary.org/obo/EHDAA2_$1 version: '2013-07-04' elm: contact: email: toby.gibson@embl.de name: Toby J Gibson orcid: 0000-0003-0657-5166 description: Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances. example: CLV_MEL_PAP_1 homepage: http://elm.eu.org/ keywords: - life science mappings: biocontext: ELM fairsharing: FAIRsharing.rj3kj5 miriam: elm n2t: elm uniprot: DB-0223 name: Eukaryotic Linear Motif Resource pattern: ^[A-Za-z_0-9]+$ preferred_prefix: elm publications: - doi: 10.1093/nar/gkab975 pubmed: '34718738' - doi: 10.1093/nar/gkz1030 pmc: PMC7145657 pubmed: '31680160' title: ELM-the eukaryotic linear motif resource in 2020 year: 2020 - doi: 10.1093/nar/gkv1291 pmc: PMC4702912 pubmed: '26615199' title: ELM 2016--data update and new functionality of the eukaryotic linear motif resource year: 2015 - doi: 10.1093/nar/gkr1064 pmc: PMC3245074 pubmed: '22110040' title: ELM--the database of eukaryotic linear motifs year: 2011 - doi: 10.1093/nar/gkg545 pmc: PMC168952 pubmed: '12824381' title: 'ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins' year: 2003 uri_format: http://elm.eu.org/elms/elmPages/$1.html emap: contact: email: Terry.Hayamizu@jax.org github: tfhayamizu name: Terry Hayamizu orcid: 0000-0002-0956-8634 deprecated: true description: A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). download_owl: http://purl.obolibrary.org/obo/emap.owl example: '1' homepage: http://emouseatlas.org keywords: - anatomy - development - mouse - obo - ontology mappings: biocontext: EMAP bioportal: EMAP obofoundry: emap ols: emap prefixcommons: emap.ontology name: Mouse gross anatomy and development, timed pattern: ^\d+$ preferred_prefix: EMAP providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/emap.ontology:$1 rdf_uri_format: http://purl.obolibrary.org/obo/EMAP_$1 uri_format: http://purl.obolibrary.org/obo/EMAP_$1 version: '2020-04-13' emapa: contact: email: Terry.Hayamizu@jax.org github: tfhayamizu name: Terry Hayamizu orcid: 0000-0002-0956-8634 description: An ontology for mouse anatomy covering embryonic development and postnatal stages. download_obo: http://purl.obolibrary.org/obo/emapa.obo download_owl: http://purl.obolibrary.org/obo/emapa.owl example: '26753' homepage: http://www.informatics.jax.org/expression.shtml keywords: - anatomy - developmental biology - obo - ontology license: CC-BY-4.0 mappings: aberowl: EMAPA bartoc: '549' biocontext: EMAPA bioportal: EMAPA fairsharing: FAIRsharing.j0fa1d go: EMAPA obofoundry: emapa ols: emapa ontobee: EMAPA name: Mouse Developmental Anatomy Ontology pattern: ^\d+$ preferred_prefix: EMAPA publications: - doi: 10.1016/s0925-4773(98)00069-0 pubmed: '9651497' title: An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature year: 1998 - doi: 10.1007/s00335-015-9584-9 pmc: PMC4602063 pubmed: '26208972' title: 'Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data' year: 2015 - doi: 10.1186/2041-1480-4-15 pmc: PMC3851555 pubmed: '23972281' title: 'EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update' year: 2013 - doi: 10.1016/b978-0-12-800043-4.00023-3 title: Textual Anatomics year: 2016 rdf_uri_format: http://purl.obolibrary.org/obo/EMAPA_$1 repository: https://github.com/obophenotype/mouse-anatomy-ontology synonyms: - EMAPA_RETIRED uri_format: http://purl.obolibrary.org/obo/EMAPA_$1 version: '2023-11-14' emaps: contact: email: Terry.Hayamizu@jax.org github: tfhayamizu name: Terry Hayamizu orcid: 0000-0002-0956-8634 contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 depends_on: - emapa description: EMAPA identifiers refer to developmental stage-independent mouse anatomical features, for instance, EMAPA:35178 resolves to the MGI's Mouse Developmental Anatomy Browser. EMAPS is an extension to EMAPA which introduces terms for different developmental stages of this generic EMAPA entry. EMAPS identifiers are constructed such that they are a concatenation of the EMAPA ID and a Theiler Stage (TS) number. For instance, EMAPA:35178 in TS 23 becomes EMAPS:3517823 example: '3517823' github_request_issue: 747 homepage: https://www.informatics.jax.org/vocab/gxd/anatomy/ name: Mouse Developmental Anatomy Ontology with Theiler Stage pattern: ^\d+$ preferred_prefix: EMAPS reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:$1 emdb: contact: email: help@emdatabank.org name: Ardan Patwardhan orcid: 0000-0001-7663-9028 description: The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community. example: EMD-1001 homepage: https://www.ebi.ac.uk/pdbe/emdb/ keywords: - epidemiology - structural biology - virology mappings: biocontext: EMDB edam: '1146' fairsharing: FAIRsharing.651n9j miriam: emdb n2t: emdb re3data: r3d100010562 uniprot: DB-0272 name: Electron Microscopy Data Bank owners: - name: European Bioinformatics Institute partnered: false ror: 02catss52 pattern: ^EMD-\d{4,5}$ preferred_prefix: emdb publications: - doi: 10.1093/nar/gkv1126 pmc: PMC4702818 pubmed: '26578576' title: EMDataBank unified data resource for 3DEM year: 2015 - doi: 10.1093/nar/gkq880 pmc: PMC3013769 pubmed: '20935055' title: 'EMDataBank.org: unified data resource for CryoEM' year: 2010 - doi: 10.1016/s0968-0004(02)02176-x pubmed: '12417136' title: New electron microscopy database and deposition system year: 2002 - doi: 10.1016/S0968-0004(02)02176-X title: New electron microscopy database and deposition system uri_format: https://www.ebi.ac.uk/pdbe/entry/emdb/$1 emea: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Product number for the European Medicines Agency example: EMEA/H/C/000181 homepage: https://www.ema.europa.eu/en/medicines name: European Medicines Evaluation Agency preferred_prefix: emea emmo: banana: EMMO banana_peel: _ contact: email: jesper.friis@sintef.no github: jesper-friis name: Jesper Friis orcid: 0000-0002-1560-809X contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) for applied sciences. It is based on physics, analytical philosophy and information and communication technologies. It has been instigated by materials science to provide a framework for knowledge capture that is consistent with scientific principles and methodologies. (from GitHub) download_rdf: https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl example: 03212fd7_abfd_4828_9c8e_62c293052d4b homepage: https://emmo-repo.github.io keywords: - communication science - industry - philosophy - physics license: CC-BY-4.0 logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdmtEIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--69489934048fba98feded162d24a8e3b36c9d370/EMMO.jpg?disposition=inline mappings: fairsharing: FAIRsharing.1bdf3c lov: emmo name: Elementary Multiperspective Material Ontology preferred_prefix: emmo repository: https://github.com/emmo-repo/EMMO uri_format: http://emmo.info/emmo#EMMO_$1 emmo.cif: contact: email: jesper.friis@sintef.no github: jesper-friis name: Jesper Friis orcid: 0000-0002-1560-809X contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A crystallography domain ontology based on EMMO and the CIF core dictionary. It is implemented as a formal language. (from https://nfdi4cat.org/services/ontologie-sammlung/) download_rdf: https://raw.githubusercontent.com/emmo-repo/CIF-ontology/main/ontology/cif-core.ttl example: _space_group_symop.operation_xyz example_extras: - o12 homepage: https://www.iucr.org/resources/cif name: Crystallographic Information Framework preferred_prefix: emmo.cif repository: https://github.com/emmo-repo/CIF-ontology uri_format: http://emmo.info/emmo/cif-core#$1 emolecules: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Catalog of purchasable reagents and building blocks example: '491187' homepage: https://reaxys.emolecules.com keywords: - chemistry - reagents - vendor name: Reaxys eMolecules pattern: ^\d+$ preferred_prefix: emolecules uri_format: https://reaxys.emolecules.com/cgi-bin/more?vid=$1 empiar: banana: EMPIAR banana_peel: '-' contact: email: ardan@ebi.ac.uk name: Ardan Patwardhan orcid: 0000-0001-7663-9028 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure example: '10595' homepage: https://www.ebi.ac.uk/pdbe/emdb keywords: - bioinformatics - biology mappings: fairsharing: FAIRsharing.dff3ef miriam: empiar name: Electron Microscopy Public Image Archive owners: - name: European Bioinformatics Institute partnered: false ror: 02catss52 pattern: ^\d+$ preferred_prefix: empiar publications: - doi: 10.1038/nmeth.3806 pubmed: '27067018' title: 'EMPIAR: a public archive for raw electron microscopy image data' year: 2016 uri_format: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1 emsl.project: contact: email: montana.smith@pnnl.gov github: mslarae13 name: Montana Smith orcid: 0000-0002-8683-0050 contributor: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: 'As a scientific user facility, the Environmental Molecular Sciences Laboratory (EMSL) provides expertise, instrumentation, and resources to 250 projects each year. Current and past projects supported through a variety of EMSL user proposal avenues are publicly searchable on the EMSL website. Project pages provide details including: - Research team and institution - The EMSL project DOI - Link to project data available in EMSLs Data Portal - Project type' example: '60141' github_request_issue: 835 homepage: https://www.emsl.pnnl.gov/projects name: Environmental Molecular Sciences Laboratory Project pattern: ^\d+$ preferred_prefix: emsl.project reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.emsl.pnnl.gov/project/$1 ena.embl: contact: email: datasubs@ebi.ac.uk name: Guy Cochrane orcid: 0000-0001-7954-7057 description: The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers. example: BN000065 has_canonical: insdc.run homepage: https://www.ebi.ac.uk/ena/ keywords: - biodiversity - bioinformatics - data management - dna - functional genomics - genomics - metagenomics - transcriptomics mappings: biocontext: ENA.EMBL fairsharing: FAIRsharing.dj8nt8 go: ENA integbio: nbdc00432 miriam: ena.embl n2t: ena.embl prefixcommons: ena re3data: r3d100010527 uniprot: DB-0022 name: European Nucleotide Archive owners: - name: European Bioinformatics Institute partnered: false ror: 02catss52 pattern: ^[A-Z]+[0-9]+(\.\d+)?$ 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 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ena:$1 publications: - doi: 10.1093/nar/gkaa1028 pmc: PMC7778925 pubmed: '33175160' title: The European Nucleotide Archive in 2020 year: 2021 - doi: 10.1093/nar/gkw1106 pmc: PMC5210577 pubmed: '27899630' title: European Nucleotide Archive in 2016 year: 2016 - doi: 10.1093/nar/gkv1323 pmc: PMC4702924 pubmed: '26657633' title: The International Nucleotide Sequence Database Collaboration year: 2015 - doi: 10.1093/nar/gkv1311 pmc: PMC4702917 pubmed: '26615190' title: Biocuration of functional annotation at the European nucleotide archive year: 2015 - doi: 10.1093/nar/gku1129 pmc: PMC4383942 pubmed: '25404130' title: Content discovery and retrieval services at the European Nucleotide Archive year: 2014 - doi: 10.1093/nar/gks1175 pmc: PMC3531187 pubmed: '23203883' title: Facing growth in the European Nucleotide Archive year: 2012 - doi: 10.1093/nar/gkh120 pmc: PMC308854 pubmed: '14681351' title: The EMBL Nucleotide Sequence Database year: 2004 synonyms: - ena twitter: enasequence uri_format: https://www.ebi.ac.uk/ena/browser/view/$1 encode: contact: email: gabdank@stanford.edu name: Idan Gabdank orcid: 0000-0001-5025-5886 description: The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. example: ENCSR163RYW homepage: https://www.encodeproject.org keywords: - epigenetics - functional genomics mappings: biocontext: ENCODE cellosaurus: ENCODE fairsharing: FAIRsharing.v0hbjs miriam: encode n2t: encode re3data: r3d100013051 name: Encyclopedia of DNA Elements pattern: ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$ preferred_prefix: encode publications: - doi: 10.1038/s41586-020-2493-4 pmc: PMC7410828 pubmed: '32728249' title: Expanded encyclopaedias of DNA elements in the human and mouse genomes year: 2020 - doi: 10.1038/s41586-020-2449-8 pmc: PMC7410827 pubmed: '32728248' title: Perspectives on ENCODE year: 2020 - doi: 10.1002/cpbi.89 pmc: PMC7307447 pubmed: '31751002' title: The ENCODE Portal as an Epigenomics Resource year: 2019 - doi: 10.1093/nar/gkz1062 pmc: PMC7061942 pubmed: '31713622' title: New developments on the Encyclopedia of DNA Elements (ENCODE) data portal year: 2020 - doi: 10.1093/nar/gkx1081 pmc: PMC5753278 pubmed: '29126249' title: 'The Encyclopedia of DNA elements (ENCODE): data portal update' year: 2018 - doi: 10.1371/journal.pone.0175310 pmc: PMC5389787 pubmed: '28403240' title: 'SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata' year: 2017 - doi: 10.1093/database/baw001 pmc: PMC4792520 pubmed: '26980513' title: Principles of metadata organization at the ENCODE data coordination center year: 2016 - doi: 10.1093/nar/gkv1160 pmc: PMC4702836 pubmed: '26527727' title: ENCODE data at the ENCODE portal year: 2015 - doi: 10.1093/database/bav010 pmc: PMC4360730 pubmed: '25776021' title: Ontology application and use at the ENCODE DCC year: 2015 - doi: 10.1093/nar/gks1172 pmc: PMC3531152 pubmed: '23193274' title: 'ENCODE data in the UCSC Genome Browser: year 5 update' year: 2012 - doi: 10.1093/nar/gkr1012 pmc: PMC3245183 pubmed: '22075998' title: 'ENCODE whole-genome data in the UCSC Genome Browser: update 2012' year: 2011 - doi: 10.1093/nar/gkq1017 pmc: PMC3013645 pubmed: '21037257' title: ENCODE whole-genome data in the UCSC genome browser (2011 update) year: 2010 - doi: 10.1093/nar/gkp961 pmc: PMC2808953 pubmed: '19920125' title: ENCODE whole-genome data in the UCSC Genome Browser year: 2009 - doi: 10.1093/nar/gkl1017 pmc: PMC1781110 pubmed: '17166863' title: The ENCODE Project at UC Santa Cruz year: 2006 - doi: 10.1126/science.1105136 pubmed: '15499007' title: The ENCODE (ENCyclopedia Of DNA Elements) Project year: 2004 uri_format: https://www.encodeproject.org/$1 enm: contact: email: egon.willighagen@maastrichtuniversity.nl name: Egon Willighagen orcid: 0000-0001-7542-0286 description: The eNanoMapper project (https://www.enanomapper.net/), NanoCommons project (https://www.nanocommons.eu/) and ACEnano project (http://acenano-project.eu/) are creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. download_owl: http://enanomapper.github.io/ontologies/releases/10.0/enanomapper.owl example: '8000221' homepage: http://www.enanomapper.net/ keywords: - chemical entity - health science - nanoparticle - nanosafety - ontology mappings: aberowl: ENM bioportal: ENM fairsharing: FAIRsharing.2gpf81 ols: enm name: eNanoMapper ontology pattern: ^\d+$ preferred_prefix: enm publications: - doi: 10.1186/s13326-015-0005-5 pmc: PMC4374589 pubmed: '25815161' title: 'eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment' year: 2015 uri_format: http://purl.enanomapper.org/onto/ENM_$1 version: '10.0' ensembl: contact: email: flicek@ebi.ac.uk name: Paul Flicek orcid: 0000-0002-3897-7955 description: Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms. example: ENSG00000139618 example_extras: - ENSG00000049246.14 - ENSG00000109819.9 - ENSG00000132326.12 - ENSG00000179094.16 - ENST00000264867.7 homepage: https://www.ensembl.org/ keywords: - biomedical science - comparative genomics - genome - genomics mappings: biocontext: ENSEMBL edam: '2610' fairsharing: FAIRsharing.fx0mw7 go: ENSEMBL integbio: nbdc00054 miriam: ensembl n2t: ensembl ncbi: ENSEMBL prefixcommons: ensembl re3data: r3d100010228 uniprot: DB-0023 wikidata: P594 mastodon: ensembl@genomic.social name: Ensembl Gene pattern: ^((ENS[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$ preferred_prefix: ensembl providers: - code: CURATOR_REVIEW description: Ensembl US East mirror homepage: http://useast.ensembl.org/ name: Ensembl US East mirror uri_format: http://useast.ensembl.org/id/$1 - code: CURATOR_REVIEW description: Ensembl Asia mirror homepage: http://asia.ensembl.org/ name: Ensembl Asia mirror uri_format: http://asia.ensembl.org/id/$1 - code: bgee description: Gene expression in various tissues homepage: https://bgee.org name: Bgee uri_format: https://bgee.org/?page=gene&gene_id=$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ensembl:$1 - code: ciliogenics description: CilioGenics is an integrated and open source, community friendly database for ciliary genes. homepage: https://ciliogenics.com name: CilioGenics uri_format: https://ciliogenics.com/?page=General%20info&query=$1 - code: gnomad description: The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community. homepage: https://gnomad.broadinstitute.org name: Genome Aggregation database uri_format: https://gnomad.broadinstitute.org/gene/$1 - code: opentargets.genetics description: Open Targets Genetics is a comprehensive tool highlighting variant-centric statistical evidence to allow both prioritisation of candidate causal variants at trait-associated loci and identification of potential drug targets. homepage: https://genetics.opentargets.org name: OpenTargets Genetics uri_format: https://genetics.opentargets.org/gene/$1 publications: - doi: 10.1093/nar/gkab1049 pmc: PMC8728283 pubmed: '34791404' title: Ensembl 2022 year: 2022 - doi: 10.1093/nar/gkz966 pmc: PMC7145704 pubmed: '31691826' title: Ensembl 2020 year: 2020 - doi: 10.1093/nar/gky1113 pmc: PMC6323964 pubmed: '30407521' title: Ensembl 2019 year: 2019 - doi: 10.1093/nar/gkw1104 pmc: PMC5210575 pubmed: '27899575' title: Ensembl 2017 year: 2016 - doi: 10.1093/database/baw093 pmc: PMC4919035 pubmed: '27337980' title: The Ensembl gene annotation system year: 2016 - doi: 10.1186/s13059-016-0974-4 pmc: PMC4893825 pubmed: '27268795' title: The Ensembl Variant Effect Predictor year: 2016 - doi: 10.1093/database/baw053 pmc: PMC4852398 pubmed: '27141089' title: Ensembl comparative genomics resources year: 2016 - doi: 10.1093/database/bav127 pmc: PMC4792531 pubmed: '26980512' title: ncRNA orthologies in the vertebrate lineage year: 2016 - doi: 10.1093/database/bav096 pmc: PMC4761110 pubmed: '26896847' title: Ensembl comparative genomics resources year: 2016 - doi: 10.1093/database/bav119 pmc: PMC4756621 pubmed: '26888907' title: Ensembl regulation resources year: 2016 - doi: 10.1093/nar/gkv1157 pmc: PMC4702834 pubmed: '26687719' title: Ensembl 2016 year: 2015 - doi: 10.1186/s13059-015-0621-5 pmc: PMC4407537 pubmed: '25887522' title: The ensembl regulatory build year: 2015 - doi: 10.1093/nar/gku1010 pmc: PMC4383879 pubmed: '25352552' title: Ensembl 2015 year: 2014 - doi: 10.1093/bioinformatics/btu613 pmc: PMC4271150 pubmed: '25236461' title: 'The Ensembl REST API: Ensembl Data for Any Language' year: 2014 - doi: 10.1093/bioinformatics/btt737 pmc: PMC3967112 pubmed: '24363377' title: 'WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis' year: 2013 - doi: 10.1093/nar/gkt1196 pmc: PMC3964975 pubmed: '24316576' title: Ensembl 2014 year: 2013 - doi: 10.1093/nar/gks1236 pmc: PMC3531136 pubmed: '23203987' title: Ensembl 2013 year: 2012 - doi: 10.1101/gr.135350.111 pmc: PMC3431492 pubmed: '22955987' title: 'GENCODE: the reference human genome annotation for The ENCODE Project' year: 2012 - doi: 10.1101/gr.137901.112 pmc: PMC3460200 pubmed: '22798491' title: Incorporating RNA-seq data into the zebrafish Ensembl genebuild year: 2012 - doi: 10.1093/nar/gkr991 pmc: PMC3245178 pubmed: '22086963' title: Ensembl 2012 year: 2011 - doi: 10.1093/database/bar030 pmc: PMC3170168 pubmed: '21785142' title: 'Ensembl BioMarts: a hub for data retrieval across taxonomic space' year: 2011 - doi: 10.1002/0471142905.hg0611s69 pmc: PMC3099348 pubmed: '21400687' title: Disease and phenotype data at Ensembl year: 2011 - doi: 10.1093/nar/gkq1064 pmc: PMC3013672 pubmed: '21045057' title: Ensembl 2011 year: 2010 - doi: 10.1093/bioinformatics/btq330 pmc: PMC2916720 pubmed: '20562413' title: Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor year: 2010 - doi: 10.1186/1471-2105-11-240 pmc: PMC2885371 pubmed: '20459813' title: 'eHive: an artificial intelligence workflow system for genomic analysis' year: 2010 - doi: 10.1186/1471-2105-11-238 pmc: PMC2882931 pubmed: '20459810' title: A database and API for variation, dense genotyping and resequencing data year: 2010 - doi: 10.1186/1471-2164-11-295 pmc: PMC2894802 pubmed: '20459808' title: 'Touring Ensembl: a practical guide to genome browsing' year: 2010 - doi: 10.1186/1471-2164-11-293 pmc: PMC2894800 pubmed: '20459805' title: Ensembl variation resources year: 2010 - doi: 10.1093/nar/gkp972 pmc: PMC2808936 pubmed: '19906699' title: Ensembl's 10th year year: 2009 - doi: 10.1093/nar/gkn828 pmc: PMC2686571 pubmed: '19033362' title: Ensembl 2009 year: 2008 - doi: 10.1101/gr.073585.107 pmc: PMC2652215 pubmed: '19029536' title: 'EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates' year: 2008 - doi: 10.1101/gr.076521.108 pmc: PMC2577868 pubmed: '18849525' title: Genome-wide nucleotide-level mammalian ancestor reconstruction year: 2008 - doi: 10.1093/nar/gkm988 pmc: PMC2238821 pubmed: '18000006' title: Ensembl 2008 year: 2007 - doi: 10.1093/bfgp/elm025 pubmed: '17967807' title: 'Genome browsing with Ensembl: a practical overview' year: 2007 - doi: 10.1093/nar/gkl996 pmc: PMC1761443 pubmed: '17148474' title: Ensembl 2007 year: 2006 - doi: 10.1038/ng0806-853a pmc: PMC2610433 pubmed: '16874317' title: 'TranscriptSNPView: a genome-wide catalog of mouse coding variation' year: 2006 - doi: 10.1093/nar/gkj133 pmc: PMC1347495 pubmed: '16381931' title: Ensembl 2006 year: 2006 - doi: 10.1093/nar/gki138 pmc: PMC540092 pubmed: '15608235' title: Ensembl 2005 year: 2005 - doi: 10.1016/j.tig.2004.04.002 pubmed: '15145580' title: Genome information resources - developments at Ensembl year: 2004 - doi: 10.1101/gr.1862204 pmc: PMC479129 pubmed: '15123595' title: 'ESTGenes: alternative splicing from ESTs in Ensembl' year: 2004 - doi: 10.1101/gr.1866304 pmc: PMC479128 pubmed: '15123594' title: The Ensembl computing architecture year: 2004 - doi: 10.1101/gr.1863004 pmc: PMC479125 pubmed: '15123591' title: 'The Ensembl Web site: mechanics of a genome browser' year: 2004 - doi: 10.1101/gr.1858004 pmc: PMC479124 pubmed: '15123590' title: The Ensembl automatic gene annotation system year: 2004 - doi: 10.1101/gr.1859804 pmc: PMC479123 pubmed: '15123589' title: The Ensembl analysis pipeline year: 2004 - doi: 10.1101/gr.1857204 pmc: PMC479122 pubmed: '15123588' title: The Ensembl core software libraries year: 2004 - doi: 10.1093/nar/gkg083 pmc: PMC165530 pubmed: '12519943' title: 'Ensembl 2002: accommodating comparative genomics' year: 2003 - doi: 10.1093/nar/30.1.38 pmc: PMC99161 pubmed: '11752248' title: The Ensembl genome database project year: 2002 - doi: doi:10.1093/nar/gku1010 title: Ensembl 2015 rdf_uri_format: http://rdf.ebi.ac.uk/resource/ensembl/$1 synonyms: - Ensembl twitter: ensembl uri_format: https://www.ensembl.org/id/$1 ensembl.bacteria: contact: email: flicek@ebi.ac.uk name: Paul Flicek orcid: 0000-0002-3897-7955 description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes. example: MU9_3181 homepage: https://bacteria.ensembl.org/ keywords: - comparative genomics - genome - genomics mappings: biocontext: ENSEMBL.BACTERIA fairsharing: FAIRsharing.zsgmvd integbio: nbdc00433 miriam: ensembl.bacteria n2t: ensembl.bacteria prefixcommons: ensembl.bacteria re3data: r3d100011195 uniprot: DB-0147 name: Ensembl Bacteria part_of: ensembl pattern: ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$ preferred_prefix: ensembl.bacteria providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ensembl.bacteria:$1 publications: - doi: 10.1093/nar/gkz890 pmc: PMC6943047 pubmed: '31598706' title: Ensembl Genomes 2020-enabling non-vertebrate genomic research year: 2020 - doi: 10.1093/nar/gkv1209 pmc: PMC4702859 pubmed: '26578574' title: 'Ensembl Genomes 2016: more genomes, more complexity' year: 2015 - doi: 10.1093/nar/gkp871 pmc: PMC2808935 pubmed: '19884133' title: 'Ensembl Genomes: extending Ensembl across the taxonomic space' year: 2009 twitter: ensemblgenomes uri_format: https://bacteria.ensembl.org/id/$1 ensembl.fungi: contact: email: flicek@ebi.ac.uk name: Paul Flicek orcid: 0000-0002-3897-7955 description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes. example: CADAFLAT00006211 homepage: https://fungi.ensembl.org/ keywords: - comparative genomics - genome - genomics mappings: biocontext: ENSEMBL.FUNGI fairsharing: FAIRsharing.bg5xqs go: EnsemblFungi integbio: nbdc00434 miriam: ensembl.fungi n2t: ensembl.fungi prefixcommons: ensembl.fungi re3data: r3d100011196 uniprot: DB-0148 name: Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi. part_of: ensembl pattern: ^[A-Z-a-z0-9]+$ preferred_prefix: ensembl.fungi providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ensembl.fungi:$1 publications: - doi: 10.1093/nar/gkz890 pmc: PMC6943047 pubmed: '31598706' title: Ensembl Genomes 2020-enabling non-vertebrate genomic research year: 2020 - doi: 10.1093/nar/gkv1209 pmc: PMC4702859 pubmed: '26578574' title: 'Ensembl Genomes 2016: more genomes, more complexity' year: 2015 twitter: ensemblgenomes uri_format: https://fungi.ensembl.org/id/$1 ensembl.metazoa: contact: email: flicek@ebi.ac.uk name: Paul Flicek orcid: 0000-0002-3897-7955 description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes. example: FBtr0084214 homepage: https://metazoa.ensembl.org/ keywords: - comparative genomics - genome - genomics mappings: biocontext: ENSEMBL.METAZOA fairsharing: FAIRsharing.c23cqq go: EnsemblMetazoa integbio: nbdc00435 miriam: ensembl.metazoa n2t: ensembl.metazoa prefixcommons: ensembl.metazoa re3data: r3d100011198 uniprot: DB-0149 name: Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa. pattern: ^\w+(\.)?\d+$ preferred_prefix: ensembl.metazoa providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ensembl.metazoa:$1 publications: - doi: 10.1093/nar/gkz890 pmc: PMC6943047 pubmed: '31598706' title: Ensembl Genomes 2020-enabling non-vertebrate genomic research year: 2020 - doi: 10.1093/nar/gkv1209 pmc: PMC4702859 pubmed: '26578574' title: 'Ensembl Genomes 2016: more genomes, more complexity' year: 2015 twitter: ensemblgenomes uri_format: https://metazoa.ensembl.org/id/$1 ensembl.plant: description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes. example: AT1G73965 homepage: https://plants.ensembl.org/ keywords: - genome mappings: biocontext: ENSEMBL.PLANT miriam: ensembl.plant n2t: ensembl.plant prefixcommons: ensembl.plant name: Ensembl Plants pattern: ^\w+(\.\d+)?(\.\d+)?$ preferred_prefix: ensembl.plant providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ensembl.plant:$1 uri_format: https://plants.ensembl.org/id/$1 ensembl.protist: description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes. example: PF3D7_1328700 homepage: https://protists.ensembl.org keywords: - genome mappings: biocontext: ENSEMBL.PROTIST miriam: ensembl.protist n2t: ensembl.protist prefixcommons: ensembl.protist name: Ensembl Protists pattern: ^\w+$ preferred_prefix: ensembl.protist providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ensembl.protist:$1 uri_format: https://protists.ensembl.org/id/$1 ensemblglossary: description: The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used. download_owl: http://ensembl.org/glossary/ensembl-glossary/releases/2023-01-04/ensembl-glossary.owl example: 0000198 homepage: http://ensembl.org/glossary keywords: - ontology mappings: ols: ensemblglossary name: Ensembl Glossary pattern: ^\d{7}$ preferred_prefix: ensemblglossary uri_format: http://ensembl.org/glossary/ENSGLOSSARY_$1 version: '2023-01-04' envipath: contact: email: admin@envipath.org name: Jörg Wicker orcid: 0000-0003-0533-3368 description: enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products. example: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea homepage: https://envipath.org/ keywords: - environmental science mappings: fairsharing: FAIRsharing.g0c5qn integbio: nbdc02011 miriam: envipath re3data: r3d100012715 name: enviPath pattern: ^[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}\/[\w-]+\/[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}$ preferred_prefix: envipath publications: - doi: 10.1186/s13321-021-00543-x pmc: PMC8414759 pubmed: '34479624' title: 'Holistic evaluation of biodegradation pathway prediction: assessing multi-step reactions and intermediate products' year: 2021 - doi: 10.1039/c6em00697c pubmed: '28229138' title: 'Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data' year: 2017 - doi: 10.1093/nar/gkv1229 pmc: PMC4702869 pubmed: '26582924' title: enviPath--The environmental contaminant biotransformation pathway resource year: 2015 - doi: 10.1039/C6EM00697C title: 'Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data' twitter: envipath uri_format: https://envipath.org/package/$1 envo: appears_in: - agro - cdno - ecocore - ecto - foodon - ons - pco - rbo - scdo - uberon banana: ENVO contact: email: pier.buttigieg@awi.de github: pbuttigieg name: Pier Luigi Buttigieg orcid: 0000-0002-4366-3088 depends_on: - chebi - foodon - go - ncbitaxon - pco - po - ro - uberon description: The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. download_json: http://purl.obolibrary.org/obo/envo.json download_obo: http://purl.obolibrary.org/obo/envo.obo download_owl: http://purl.obolibrary.org/obo/envo.owl example: 09200010 homepage: http://environmentontology.org/ keywords: - ecology - environmental material - environmental science - epidemiology - life science - marine metagenome - microbiome - nutritional science - obo - ontology license: CC0-1.0 logo: https://obofoundry.org/images/envo.png mappings: aberowl: ENVO agroportal: ENVO biocontext: ENVO bioportal: ENVO fairsharing: FAIRsharing.azqskx miriam: envo n2t: envo obofoundry: envo ols: envo ontobee: ENVO name: Environment Ontology namespace_in_lui: true pattern: ^\d{7,8}$ preferred_prefix: ENVO publications: - doi: 10.1186/s13326-016-0097-6 pmc: PMC5035502 pubmed: '27664130' title: 'The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation' year: 2016 - doi: 10.1093/database/baw005 pmc: PMC4761108 pubmed: '26896844' title: 'EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation' year: 2016 - doi: 10.7717/peerj.1470 pmc: PMC4690371 pubmed: '26713234' title: Emerging semantics to link phenotype and environment year: 2015 - doi: 10.1186/2041-1480-4-43 pmc: PMC3904460 pubmed: '24330602' title: 'The environment ontology: contextualising biological and biomedical entities' year: 2013 rdf_uri_format: http://purl.obolibrary.org/obo/ENVO_$1 repository: https://github.com/EnvironmentOntology/envo twitter: envoTweets uri_format: http://purl.obolibrary.org/obo/ENVO_$1 version: '2025-02-05' enzo: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Enzo Life Sciences is an antibody vendor. example: ALX-210-175 homepage: https://www.enzolifesciences.com keywords: - antibodies - life sciences - vendor name: Enzo Life Sciences preferred_prefix: enzo synonyms: - Enzo Life Sciences uri_format: https://www.enzolifesciences.com/$1 eo: appears_in: - foodon banana: EO contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp name: Pankaj Jaiswal orcid: 0000-0002-1005-8383 deprecated: true description: The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. download_obo: https://github.com/Planteome/plant-experimental-conditions-ontology/raw/refs/heads/master/peco.obo download_owl: https://github.com/Planteome/plant-experimental-conditions-ontology/raw/refs/heads/master/peco.owl example: '0007404' homepage: http://planteome.org/ keywords: - obo - ontology - plant license: CC-BY-4.0 logo: http://planteome.org/sites/default/files/garland_logo.PNG mappings: aberowl: EO agroportal: EO biocontext: EO miriam: eo n2t: eo obofoundry: eo prefixcommons: eo name: Plant Environment Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: EO providers: - code: CURATOR_REVIEW description: Plant Environment Ontology through Gramene homepage: http://archive.gramene.org/db/ontology/search_term?id=EO:0007359 name: Plant Environment Ontology through Gramene uri_format: http://archive.gramene.org/db/ontology/search?query=EO:$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/eo:$1 publications: - doi: 10.3732/ajb.1200222 pmc: PMC3492881 pubmed: '22847540' title: Ontologies as integrative tools for plant science year: 2012 rdf_uri_format: http://purl.obolibrary.org/obo/EO_$1 repository: https://github.com/Planteome/plant-environment-ontology uri_format: http://purl.obolibrary.org/obo/EO_$1 eol: contact: email: pylebail@rennes.inra.fr name: Pierre-Yves LeBail orcid: 0000-0002-8310-5195 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems. download_owl: http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=eol.owl example: 0001927 homepage: http://www.atol-ontology.com keywords: - agriculture - animal husbandry - environmental science - livestock - ontology - species-environment interaction mappings: aberowl: EOL agroportal: EOL bioportal: EOL fairsharing: FAIRsharing.w7bw2y ols: eol re3data: r3d100011663 name: Environment Ontology for Livestock pattern: ^\d{7}$ preferred_prefix: eol uri_format: http://purl.org/obo/owlEOL_$1 version: '2018-09-13' eol.schema: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Predicates in the Encyclopedia of Life data schema for describing animals, plants, and other organisms example: body_symmetry github_request_issue: 1421 homepage: https://eol.org/terms/glossary/ name: Encyclopedia of Life Schema preferred_prefix: eol.schema uri_format: http://eol.org/schema/terms/$1 eolife: contact: email: secretariat@eol.org name: EOL Secretariat orcid: 0000-0002-9943-2342 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A collaborative project intended to create an encyclopedia documenting all living species known to science example: '1044544' homepage: https://eol.org keywords: - biodiversity - biology - ecology - taxonomy mappings: fairsharing: FAIRsharing.3J6NYn re3data: r3d100010229 wikidata: P830 name: Encyclopedia of Life pattern: ^\d+$ preferred_prefix: eolife twitter: eol uri_format: https://eol.org/pages/$1 epawaste: contact: email: brennan.thomas@epa.gov name: Tom Brennan contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: This resource provides identifiers for listed hazardous wastes which are substances explicitly identified due to their potential harm to human health and the environment. These are categorized into four groups (F, K, P, and U) based on specific criteria, such as their source or inherent properties. example: F001 example_extras: - K001 - P001 - U001 github_request_issue: 1246 homepage: https://www.ecfr.gov/current/title-40/chapter-I/subchapter-I/part-261 name: EPA Hazardous Wastes pattern: ^[FKPU]\d{3}$ preferred_prefix: epawaste reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 epcc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Collection of European paediatric cardiac coding files homepage: https://www.aepc.org/european-paediatric-cardiac-coding name: European Paediatric Cardiac Codes preferred_prefix: epcc proprietary: true references: - https://www.cambridge.org/core/journals/cardiology-in-the-young/article/abs/european-paediatric-cardiac-codes-the-long-list-with-icd9-icd10-crossmapping-and-crossmap-to-epcc-short-list/FCA4DFCCB661298294A3D113FC79D5BE epd: contact: email: Philipp.Bucher@sib.swiss name: Philipp Bucher orcid: 0000-0002-0816-7775 contributor_extras: - email: sebastien.moretti@sib.swiss github: smoretti name: Sebastien Moretti orcid: 0000-0003-3947-488X description: The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. example: TA_H3 homepage: https://epd.expasy.org/epd/ keywords: - bioinformatics - biology mappings: biocontext: EPD edam: '2386' fairsharing: FAIRsharing.yk1krv integbio: nbdc00438 miriam: epd n2t: epd ncbi: EPD uniprot: DB-0205 name: Eukaryotic Promoter Database pattern: ^[A-Z-_0-9]+$ preferred_prefix: epd publications: - doi: 10.1093/nar/27.1.307 pmc: PMC148166 pubmed: '9847211' title: 'The Eukaryotic Promoter Database (EPD): recent developments' year: 1999 - doi: 10.1093/nar/26.1.353 pmc: PMC147208 pubmed: '9399872' title: The Eukaryotic Promoter Database EPD year: 1998 - doi: 10.1093/nar/14.24.10009 pmc: PMC341352 pubmed: '3808945' title: Compilation and analysis of eukaryotic POL II promoter sequences year: 1986 - doi: 10.1093/nar/gkx807 pmc: PMC5753345 pubmed: '28981707' title: 'The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics' year: 2018 - doi: 10.1093/nar/gkw1069 pmc: PMC5210552 pubmed: '27899657' title: 'The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms' year: 2016 - doi: 10.1093/nar/gku1111 pmc: PMC4383928 pubmed: '25378343' title: 'The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools' year: 2014 - doi: 10.1093/nar/gks1233 pmc: PMC3531148 pubmed: '23193273' title: EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era year: 2012 - doi: 10.1093/nar/gkj146 pmc: PMC1347508 pubmed: '16381980' title: 'EPD in its twentieth year: towards complete promoter coverage of selected model organisms' year: 2006 - doi: 10.1093/nar/gkh122 pmc: PMC308856 pubmed: '14681364' title: 'The Eukaryotic Promoter Database EPD: the impact of in silico primer extension' year: 2004 - doi: 10.1093/nar/30.1.322 pmc: PMC99099 pubmed: '11752326' title: 'The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data' year: 2002 - doi: 10.1093/nar/28.1.302 pmc: PMC102462 pubmed: '10592254' title: The eukaryotic promoter database (EPD) year: 2000 uri_format: https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0=$1 epio: contact: email: alpha.tom.kodamullil@scai.fraunhofer.de github: akodamullil name: Alpha Tom Kodamullil orcid: 0000-0001-9896-3531 depends_on: - bfo description: A application driven Epilepsy Ontology with official terms from the ILAE. download_owl: http://purl.obolibrary.org/obo/epio.owl example: '0000011' homepage: https://github.com/SCAI-BIO/EpilepsyOntology keywords: - obo - ontology license: CC-BY-4.0 mappings: aberowl: EPIO bioportal: EPIO obofoundry: epio ontobee: EPIO name: Epilepsy Ontology pattern: ^\d{7}$ preferred_prefix: EPIO rdf_uri_format: http://purl.obolibrary.org/obo/EPIO_$1 repository: https://github.com/SCAI-BIO/EpilepsyOntology uri_format: http://purl.obolibrary.org/obo/EPIO_$1 epo: contributor_extras: - github: djinnome name: Jeremy Zucker orcid: 0000-0002-7276-9009 deprecated: true description: An ontology designed to support the semantic annotation of epidemiology resources download_owl: https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/epidemiology-ontology/epo.owl homepage: https://code.google.com/p/epidemiology-ontology/ keywords: - obo - ontology mappings: biocontext: EPO obofoundry: epo ontobee: EPO name: Epidemiology Ontology preferred_prefix: EPO rdf_uri_format: http://purl.obolibrary.org/obo/EPO_$1 uri_format: http://purl.obolibrary.org/obo/EPO_$1 epso: contact: email: satyasahoo@ieee.org name: Satya S. Sahoo orcid: 0000-0001-9190-4256 description: 'The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. ' download_owl: http://aber-owl.net/media/ontologies/EPSO/3/epso.owl example: '0000400' homepage: http://prism.case.edu/prism/index.php/EpilepsyOntology keywords: - epilepsy - neurology - ontology - patient care mappings: aberowl: EPSO bioportal: EPSO fairsharing: FAIRsharing.ttprgy ontobee: EPSO name: Epilepsy and Seizure Ontology pattern: ^\d{7}$ preferred_prefix: epso publications: - doi: 10.1136/amiajnl-2013-001696 pmc: PMC3912711 pubmed: '23686934' title: 'Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care' year: 2013 uri_format: http://www.case.edu/EpilepsyOntology.owl#$1 erm: contact: email: egon.willighagen@gmail.com github: egonw name: Egon Willighagen orcid: 0000-0001-7542-0286 description: The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project. download_rdf: https://nanocommons.github.io/identifiers/registry example: ERM00000044 homepage: https://nanocommons.github.io/identifiers/ keywords: - chemical entity - materials informatics - nanotechnology mappings: cheminf: 000569 fairsharing: FAIRsharing.c26a4e miriam: erm n2t: erm name: European Registry of Materials pattern: ^ERM[0-9]{8}$ preferred_prefix: erm providers: - code: erm.database description: Database that provides links to onlnie information about materials with an European Registry of Materials (ERM) identifier homepage: https://nanocommons.github.io/erm-database/ name: ERM Identifier Database uri_format: https://nanocommons.github.io/erm-database/substance/erm/$1 publications: - doi: 10.1186/s13321-022-00614-7 pmc: PMC9400299 pubmed: '36002868' title: 'European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials' year: 2022 twitter: nanocommons uri_format: https://nanocommons.github.io/identifiers/registry#$1 ero: contact: email: Marc_Ciriello@hms.harvard.edu name: Marc Ciriello orcid: 0000-0002-3734-1859 deprecated: true description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. download_owl: http://purl.obolibrary.org/obo/ero.owl example: '0001655' homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology keywords: - biological sample - biomedical science - life science - obo - ontology - protocol - reagent - study design license: CC BY 2.0 mappings: aberowl: ERO biocontext: ERO bioportal: ERO fairsharing: FAIRsharing.nwgynk obofoundry: ero ols: ero ontobee: ERO name: eagle-i resource ontology pattern: ^\d{7}$ preferred_prefix: ERO publications: - doi: 10.1109/jcdl.2017.7991571 pmc: PMC5868434 pubmed: '29599662' title: 'Automating data citation: the eagle-i experience' year: 2017 - doi: 10.1093/database/bar067 pmc: PMC3308157 pubmed: '22434835' title: 'Research resources: curating the new eagle-i discovery system' year: 2012 rdf_uri_format: http://purl.obolibrary.org/obo/ERO_$1 uri_format: http://purl.obolibrary.org/obo/ERO_$1 version: '2016-07-27' eropmoscow: description: EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence database which strives to provide a high level of annotations (such as descriptions of the structure of an oligopeptide, its source and function, post-translational modifications, etc.). example: E00002 homepage: http://erop.inbi.ras.ru keywords: - protein mappings: integbio: nbdc00265 prefixcommons: eropmoscow name: Endogenous Regulatory OligoPeptide knowledgebase-Moscow preferred_prefix: eropmoscow providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/eropmoscow:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://erop.inbi.ras.ru/result2.php?PepName=$1 erv: description: Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features. example: THE1B homepage: https://herv.img.cas.cz/ mappings: biocontext: ERV miriam: erv n2t: erv name: Human Endogenous Retrovirus Database pattern: ^[A-Za-z0-9\-\_]+$ preferred_prefix: erv uri_format: https://herv.img.cas.cz/s/$1 esldb: description: eSLDB is a database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions. example: HS000015122 homepage: http://gpcr.biocomp.unibo.it/esldb keywords: - protein mappings: prefixcommons: esldb name: eukaryotic Subcellular Localization database preferred_prefix: esldb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/esldb:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice=$1 estdab: comment: Website is dead deprecated: true description: Cell line databases/resources example: '046' homepage: https://www.ebi.ac.uk/ipd/estdab/ mappings: cellosaurus: ESTDAB name: European Searchable Tumour Line Database owners: - name: European Bioinformatics Institute partnered: false ror: 02catss52 pattern: ^\d{3}$ preferred_prefix: estdab uri_format: https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1 eu89h: description: The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union. example: jrc-eurl-ecvam-chemagora homepage: http://data.jrc.ec.europa.eu/ mappings: biocontext: EU89H miriam: eu89h n2t: eu89h name: JRC Data Catalogue pattern: ^[a-z0-9\-_]+$ preferred_prefix: eu89h uri_format: http://data.europa.eu/89h/$1 eubopen: contact: email: tredup@pharmchem.uni-frankfurt.de name: Claudia Tredup orcid: 0000-0001-6518-3344 contributor: email: palayoor.n@northeastern.edu github: nalikapalayoor name: Nalika Palayoor orcid: 0009-0008-8406-631X description: EUbOPEN is a project focusing on organizing chemogenic library collections, advancing chemical probe discovery, profiling bioactive compounds, and making project data more accessible. example: EUB0000221 github_request_issue: 1378 homepage: https://gateway.eubopen.org name: Enabling and Unlocking Biology in the Open pattern: ^EUB\d{7}$ preferred_prefix: eubopen publications: - doi: 10.1039/d4md00735b pmc: PMC11605244 pubmed: '39618964' title: 'Toward target 2035: EUbOPEN - a public-private partnership to enable & unlock biology in the open' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://gateway.eubopen.org/compound/$1 euclinicaltrials: description: 'The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004. It also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.' example: 2008-005144-16 homepage: https://www.clinicaltrialsregister.eu/ mappings: biocontext: EUCLINICALTRIALS miriam: euclinicaltrials n2t: euclinicaltrials name: EU Clinical Trials pattern: ^\d{4}\-\d{6}\-\d{2}$ preferred_prefix: euclinicaltrials synonyms: - EUCTR uri_format: https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1 eugenes: contact: email: eugenes@iubio.bio.indiana.edu name: Don Gilbert orcid: 0000-0002-6646-7274 description: euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information. example: MGgn0008978 homepage: http://eugenes.org/ keywords: - genome - life science - ontology mappings: fairsharing: FAIRsharing.7fc5y6 prefixcommons: eugenes name: Eukaryotic Genes preferred_prefix: eugenes providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/eugenes:$1 publications: - doi: 10.1093/nar/30.1.145 pmc: PMC99146 pubmed: '11752277' title: 'euGenes: a eukaryote genome information system' year: 2002 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://eugenes.org:7072/.bin/fbidq.html?$1 eupath: appears_in: - scdo contact: email: jiezhen@med.umich.edu github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 deprecated: true description: The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available. download_owl: http://purl.obolibrary.org/obo/eupath.owl example: '0010316' homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology keywords: - biomedical science - epidemiology - functional genomics - microbiome - obo - ontology - population genetics license: CC-BY-4.0 logo: https://raw.githubusercontent.com/EuPathDB/communitysite/master/assets/images/VEuPathDB-logo-s.png mappings: aberowl: EUPATH biocontext: EUPATH bioportal: EUPATH fairsharing: FAIRsharing.9rhr9j obofoundry: eupath ols: eupath ontobee: EUPATH name: VEuPathDB ontology pattern: ^\d{7}$ preferred_prefix: EUPATH publications: - doi: 10.5281/zenodo.6685957 title: Malaria study data integration and information retrieval based on OBO Foundry ontologies year: 2016 rdf_uri_format: http://purl.obolibrary.org/obo/EUPATH_$1 repository: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology uri_format: http://purl.obolibrary.org/obo/EUPATH_$1 version: '2023-05-30' eurofir: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries. homepage: https://www.eurofir.org name: European Food Information Resource Network preferred_prefix: eurofir proprietary: true ev: appears_in: - cl contact: email: evoc@sanbi.ac.za name: eVOC mailing list deprecated: true description: Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment. example: '0100011' homepage: http://www.evocontology.org/ keywords: - anatomy - cell - development - experiment - obo - ontology mappings: biocontext: EV obofoundry: ev prefixcommons: evoc name: eVOC (Expressed Sequence Annotation for Humans) pattern: ^\d{7}$ preferred_prefix: EV providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/evoc:$1 rdf_uri_format: http://purl.obolibrary.org/obo/EV_$1 references: - https://twitter.com/Bgeedb/status/1350124337815281664 uri_format: http://www.evocontology.org/site/Main/BrowseEvoc?x_termid=$1 evm: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: eVOC mouse development stage preferred_prefix: evm references: - https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r229 evr: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'An open, community-driven registry of conference and event venues. EVR assigns persistent identifiers (PIDs) to make referencing venues FAIR. This is similar to how ORCID assigns PIDs to researchers and ROR assigns PIDs to research organizations. This benefits researchers assembling information about in-person conferences and events by enabling them to refer in an unambiguous way to the venue where it takes place. This repository follows the [Open Data, Open Code, Open Infrastructure (O3) principles](https://www.nature.com/articles/s41597-024-03406-w), meaning that the data and code are all in one repository that anyone can contribute to.' example: '0000001' github_request_issue: 1363 homepage: https://cthoyt.com/evr license: CC0-1.0 name: Event Venue Registry pattern: ^\d{7}$ preferred_prefix: evr repository: https://github.com/cthoyt/evr uri_format: https://cthoyt.com/evr/$1 exac.gene: description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information. example: ENSG00000169174 homepage: http://exac.broadinstitute.org/ mappings: biocontext: EXAC.GENE miriam: exac.gene n2t: exac.gene name: ExAC Gene pattern: ^ENSG\d{11}$ preferred_prefix: exac.gene uri_format: http://exac.broadinstitute.org/gene/$1 exac.transcript: description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information. example: ENST00000407236 homepage: http://exac.broadinstitute.org/ mappings: biocontext: EXAC.TRANSCRIPT miriam: exac.transcript n2t: exac.transcript name: ExAC Transcript pattern: ^ENST\d{11}$ preferred_prefix: exac.transcript uri_format: http://exac.broadinstitute.org/transcript/$1 exac.variant: description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information. example: 22-46615880-T-C homepage: http://exac.broadinstitute.org/ mappings: biocontext: EXAC.VARIANT miriam: exac.variant n2t: exac.variant name: ExAC Variant pattern: ^\d{1,2}\-\d+\-[GATC]\-[GATC]$ preferred_prefix: exac.variant uri_format: http://exac.broadinstitute.org/variant/$1 exo: appears_in: - ecto - scdo contact: email: annethessen@gmail.com github: diatomsRcool name: Anne Thessen orcid: 0000-0002-2908-3327 description: ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics. download_obo: http://purl.obolibrary.org/obo/exo.obo download_owl: http://purl.obolibrary.org/obo/exo.owl example: 0000078 homepage: https://github.com/CTDbase/exposure-ontology keywords: - disease - environmental science - epigenetics - exposure - obo - ontology - toxicology license: CC-BY-4.0 mappings: aberowl: EXO biocontext: EXO biolink: ExO bioportal: EXO fairsharing: FAIRsharing.6hna78 obofoundry: exo ols: exo ontobee: ExO name: Exposure ontology pattern: ^\d{7}$ preferred_prefix: ExO publications: - doi: 10.1021/es2033857 pmc: PMC3314380 pubmed: '22324457' title: 'Providing the missing link: the exposure science ontology ExO' year: 2012 rdf_uri_format: http://purl.obolibrary.org/obo/ExO_$1 repository: https://github.com/CTDbase/exposure-ontology synonyms: - ExO uri_format: http://purl.obolibrary.org/obo/ExO_$1 version: '2022-06-29' fabio: contact: email: silvio.peroni@unibo.it github: essepuntato name: Silvio Peroni orcid: 0000-0003-0530-4305 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references. download_owl: http://aber-owl.net/media/ontologies/FaBiO/1/fabio.owl example: d4e2515 homepage: https://github.com/sparontologies/fabio keywords: - bibliography - citation - data model - ontology - protocol - publication - report - spar - subject agnostic mappings: aberowl: FaBiO biolink: fabio ecoportal: FABIO fairsharing: FAIRsharing.2f3180 lov: fabio name: FaBiO, the FRBR-aligned Bibliographic Ontology preferred_prefix: fabio publications: - doi: 10.1016/j.websem.2012.08.001 title: 'FaBiO and CiTO: Ontologies for describing bibliographic resources and citations' year: 2012 rdf_uri_format: http://purl.org/spar/fabio/$1 repository: https://github.com/sparontologies/fabio twitter: sparontologies uri_format: https://sparontologies.github.io/fabio/current/fabio.html#$1 facebase: contact: email: ychai@usc.edu name: Yang Chai orcid: 0000-0003-2477-7247 description: FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects. example: FB00000917 homepage: https://www.facebase.org keywords: - anatomy - developmental biology - epigenetics - genetics - medicine mappings: biocontext: FACEBASE fairsharing: FAIRsharing.mqvqde integbio: nbdc02022 miriam: facebase n2t: facebase re3data: r3d100013263 name: FaceBase Data Repository pattern: ^FB\d{8}$ preferred_prefix: facebase publications: - doi: 10.1242/dev.191213 pmc: PMC7522026 pubmed: '32958507' title: 'FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research' year: 2020 uri_format: https://www.facebase.org/data/record/#1/isa:dataset/accession=$1 fairsharing: contact: email: allyson.lister@oerc.ox.ac.uk name: Allyson Lister orcid: 0000-0002-7702-4495 description: The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies. example: bsg-000052 example_extras: - FAIRsharing.CugtbQ homepage: https://fairsharing.org/ keywords: - agriculture - biomedical science - data governance - database management - earth science - environmental science - humanities - life science - natural science - ontology and terminology - policy mappings: biocontext: FAIRSHARING fairsharing: FAIRsharing.2abjs5 miriam: fairsharing n2t: fairsharing re3data: r3d100010142 mastodon: fairsharing@fediscience.org name: FAIRsharing pattern: ^(bsg-[dscp]?\d{6})|(FAIRsharing\.\w+)$ preferred_prefix: fairsharing publications: - doi: 10.1038/s41587-019-0080-8 pmc: PMC6785156 pubmed: '30940948' title: FAIRsharing as a community approach to standards, repositories and policies year: 2019 - doi: 10.1093/database/baw075 pmc: PMC4869797 pubmed: '27189610' title: 'BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences' year: 2016 - doi: 10.5281/zenodo.5106255 title: FAIRsharing, a FAIR-enabling service for repositories, standards and policies year: 2021 repository: https://github.com/FAIRsharing twitter: fairsharing_org uri_format: https://fairsharing.org/$1 fairsharing.organization: contact: email: allyson.lister@oerc.ox.ac.uk github: allysonlister name: Allyson Lister orcid: 0000-0002-7702-4495 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An organization in FAIRsharing, including universities, labs, etc. example: '3851' homepage: https://fairsharing.org name: FAIRsharing Organization part_of: fairsharing pattern: ^\d+$ preferred_prefix: fairsharing.organization uri_format: https://fairsharing.org/organisations/$1 fairsharing.user: contact: email: allyson.lister@oerc.ox.ac.uk github: allysonlister name: Allyson Lister orcid: 0000-0002-7702-4495 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A user of FAIRsharing example: '5112' homepage: https://fairsharing.org name: FAIRsharing User part_of: fairsharing pattern: ^\d+$ preferred_prefix: fairsharing.user uri_format: https://fairsharing.org/users/$1 faldo: contact: email: faldo@googlegroups.com name: FALDO group contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources download_owl: http://aber-owl.net/media/ontologies/FALDO/1/faldo.owl example: ForwardStrandPosition homepage: http://biohackathon.org/resource/faldo keywords: - binding site - gene feature - genetics - geography - nucleic acid sequence - ontology - sequence annotation - sequence feature mappings: aberowl: FALDO agroportal: FALDO biocontext: faldo bioportal: FALDO fairsharing: FAIRsharing.haxp7g lov: faldo name: 'Feature Annotation Location Description Ontology ' preferred_prefix: faldo publications: - doi: 10.1186/s13326-016-0067-z pmc: PMC4907002 pubmed: '27296299' title: 'FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation' year: 2016 repository: https://github.com/OBF/FALDO uri_format: http://biohackathon.org/resource/faldo#$1 fanta: contact: email: takeya.kasukawa@riken.jp name: Takeya Kasukawa contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Functional annotations of genomes for studying gene regulation, with a primary focus on cis-regulatory elements (CREs) such as promoters and enhancers. example: FCHS_301358 github_request_issue: 1328 homepage: https://fanta.bio name: Functional Genome Annotations with Transcriptional Activities pattern: ^FC(HS|MM)_\d+$ preferred_prefix: fanta publications: - doi: 10.1093/nar/gkae1047 pubmed: '39592010' title: 'Update of the FANTOM web resource: enhancement for studying noncoding genomes' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://fanta.bio/cre/$1 fao: contact: email: vw253@cam.ac.uk github: ValWood name: Val Wood orcid: 0000-0001-6330-7526 description: A structured controlled vocabulary for the anatomy of fungi. download_obo: http://purl.obolibrary.org/obo/fao.obo download_owl: http://purl.obolibrary.org/obo/fao.owl example: '0000001' homepage: https://github.com/obophenotype/fungal-anatomy-ontology/ keywords: - anatomy - fungi - life science - microbiology - obo - ontology license: CC0-1.0 mappings: aberowl: FAO biocontext: FAO bioportal: FAO fairsharing: FAIRsharing.xs6t67 obofoundry: fao ols: fao ontobee: FAO prefixcommons: fao name: Fungal gross anatomy pattern: ^\d{7}$ preferred_prefix: FAO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/fao:$1 rdf_uri_format: http://purl.obolibrary.org/obo/FAO_$1 repository: https://github.com/obophenotype/fungal-anatomy-ontology uri_format: http://purl.obolibrary.org/obo/FAO_$1 version: '2020-05-07' fao.asfis: comment: This resource is offered freely by FAO for download but no obvious licensing is indicated, and no caution about appropriate reuse. contributor: github: ddooley name: Damion Dooley orcid: 0000-0002-8844-9165 description: The FAO Statistics Team (NFISS) of Fisheries and Aquaculture Division collates world capture and aquaculture production statistics at either the species, genus, family, or higher taxonomic levels in 3,169 statistical categories (2022 data release) referred to as species items. ASFIS list of species includes 13,417 species items selected according to their interest or relation to fisheries and aquaculture. For each species item stored in a record, codes (ISSCAAP group, taxonomic and 3-alpha) and taxonomic information (scientific name, author(s), family, and higher taxonomic classification) are provided. An English name is available for most of the records, and about one third of them have also a French and Spanish name. Information is also provided about the availability of fishery production statistics on the species item in the FAO databases. (from homepage) example: '20560' github_request_issue: 872 homepage: https://www.fao.org/fishery/en/collection/asfis/en name: Aquatic Sciences and Fisheries Information System pattern: ^\d+$ preferred_prefix: fao.asfis reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - asfis uri_format: https://www.fao.org/fishery/en/species/$1 fbbi: contact: email: wawong@gmail.com github: wawong name: Willy Wong orcid: 0000-0002-8841-5870 deprecated: true description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. download_obo: http://aber-owl.net/media/ontologies/FBbi/14/fbbi.obo download_owl: http://purl.obolibrary.org/obo/fbbi.owl example: 00000268 homepage: http://cellimagelibrary.org/ keywords: - assay - biomedical science - experiment - image - imaging - life science - obo - ontology license: CC-BY-4.0 mappings: aberowl: FBbi biocontext: FBbi bioportal: FBbi fairsharing: FAIRsharing.ny3z9j obofoundry: fbbi ols: fbbi ontobee: FBbi prefixcommons: fbbi name: Biological Imaging Methods Ontology pattern: ^\d+$ preferred_prefix: FBbi providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/fbbi:$1 rdf_uri_format: http://purl.obolibrary.org/obo/FBbi_$1 repository: https://github.com/CRBS/Biological_Imaging_Methods_Ontology synonyms: - FBbi uri_format: http://purl.obolibrary.org/obo/FBbi_$1 version: '2020-11-06' fbbt: contact: email: cp390@cam.ac.uk github: Clare72 name: Clare Pilgrim orcid: 0000-0002-1373-1705 description: An ontology representing the gross anatomy of Drosophila melanogaster. download_json: http://purl.obolibrary.org/obo/fbbt.json download_obo: http://purl.obolibrary.org/obo/fbbt.obo download_owl: http://purl.obolibrary.org/obo/fbbt.owl example: 00007294 homepage: http://purl.obolibrary.org/obo/fbbt keywords: - anatomy - developmental biology - fly - gene expression - image - life cycle stage - life science - obo - ontology - phenotype license: CC-BY-4.0 mappings: aberowl: FBBT biocontext: FBbt bioportal: FB-BT fairsharing: FAIRsharing.y2qkst go: FBbt obofoundry: fbbt ols: fbbt ontobee: FBbt prefixcommons: fbbt name: Drosophila gross anatomy pattern: ^\d{8}$ preferred_prefix: FBbt providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/fbbt:$1 publications: - doi: 10.1186/2041-1480-4-32 pmc: PMC4015547 pubmed: '24139062' title: The Drosophila anatomy ontology year: 2013 - doi: 10.1093/bioinformatics/bts113 pubmed: '22402613' title: A strategy for building neuroanatomy ontologies year: 2012 - doi: 10.1093/bioinformatics/btr677 pubmed: '22180411' title: The Virtual Fly Brain browser and query interface year: 2011 - doi: 10.1093/nar/gkj068 pmc: PMC1347431 pubmed: '16381917' title: 'FlyBase: anatomical data, images and queries' year: 2006 rdf_uri_format: http://purl.obolibrary.org/obo/FBbt_$1 repository: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology synonyms: - FBbt - FBbt_root uri_format: http://purl.obolibrary.org/obo/FBbt_$1 version: '2025-02-13' fbcv: appears_in: - ontoavida contact: email: cp390@cam.ac.uk github: Clare72 name: Clare Pilgrim orcid: 0000-0002-1373-1705 description: A structured controlled vocabulary used for various aspects of annotation by FlyBase. download_json: http://purl.obolibrary.org/obo/fbcv.json download_obo: https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/fbcv.obo download_owl: http://purl.obolibrary.org/obo/fbcv.owl example: 0000586 homepage: http://purl.obolibrary.org/obo/fbcv keywords: - descriptor - expression data - fly - life science - obo - ontology - phenotype license: CC-BY-4.0 mappings: aberowl: FBCV biocontext: FBcv bioportal: FB-CV fairsharing: FAIRsharing.6tgyxf obofoundry: fbcv ols: fbcv ontobee: FBcv prefixcommons: fbcv name: FlyBase Controlled Vocabulary part_of: flybase pattern: ^\d{7}$ preferred_prefix: FBcv providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/fbcv:$1 publications: - doi: 10.1186/2041-1480-4-30 pmc: PMC3816596 pubmed: '24138933' title: The Drosophila phenotype ontology year: 2013 rdf_uri_format: http://purl.obolibrary.org/obo/FBcv_$1 repository: https://github.com/FlyBase/flybase-controlled-vocabulary synonyms: - FBcv uri_format: http://purl.obolibrary.org/obo/FBcv_$1 version: '2025-02-13' fbdv: contact: email: cp390@cam.ac.uk github: Clare72 name: Clare Pilgrim orcid: 0000-0002-1373-1705 description: A structured controlled vocabulary of the development of Drosophila melanogaster. download_json: http://purl.obolibrary.org/obo/fbdv.json download_obo: http://purl.obolibrary.org/obo/fbdv.obo download_owl: http://purl.obolibrary.org/obo/fbdv.owl example: '00000000' homepage: http://purl.obolibrary.org/obo/fbdv keywords: - development - developmental biology - fly - life cycle - life cycle stage - life science - obo - ontology license: CC-BY-4.0 mappings: aberowl: FBDV biocontext: FBdv bioportal: FB-DV fairsharing: FAIRsharing.p52pzj go: FBdv obofoundry: fbdv ols: fbdv ontobee: FBdv prefixcommons: fbdv name: Drosophila development pattern: ^\d{8}$ preferred_prefix: FBdv providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/fbdv:$1 rdf_uri_format: http://purl.obolibrary.org/obo/FBdv_$1 repository: https://github.com/FlyBase/drosophila-developmental-ontology synonyms: - FBdv uri_format: http://purl.obolibrary.org/obo/FBdv_$1 version: '2025-02-12' fbol: comment: Website down, checked on 2021-10-07 deprecated: true description: DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms. example: '2224' homepage: http://www.fungalbarcoding.org/ mappings: biocontext: FBOL miriam: fbol n2t: fbol ncbi: FBOL name: International Fungal Working Group Fungal Barcoding. pattern: ^\d+$ 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$1 fbsp: contact: email: cp390@cam.ac.uk github: Clare72 name: Clare Pilgrim orcid: 0000-0002-1373-1705 deprecated: true description: The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. download_obo: http://aber-owl.net/media/ontologies/FB-SP/7/fb-sp.obo download_owl: http://purl.obolibrary.org/obo/fbsp.owl example: '00000000' homepage: http://www.flybase.org/ keywords: - obo - ontology mappings: aberowl: FB-SP biocontext: FBSP bioportal: FB-SP obofoundry: fbsp ols: fbsp name: Fly taxonomy part_of: flybase pattern: ^\d{8}$ preferred_prefix: FBSP rdf_uri_format: http://purl.obolibrary.org/obo/FBSP_$1 uri_format: http://purl.obolibrary.org/obo/FBSP_$1 version: '2017-11-19' fbtc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The cell line vocabulary inside FlyBase example: 0000190 homepage: https://flybase.org mappings: cellosaurus: FlyBase_Cell_line name: Flybase Cell Line part_of: flybase pattern: ^\d{7}$ preferred_prefix: fbtc synonyms: - FlyBase_Cell_line uri_format: https://flybase.org/reports/FBtc$1 fcb: description: 'Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR). ' example: FCB005 homepage: https://w3id.org mappings: miriam: fcb name: the FAIR Cookbook pattern: ^FCB\d{3}$ 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?$1 fda.application: comment: The official FDA website doesn't appear to be able to resolve application IDs but these IDs do appear in some PDF documents, e.g., https://www.fda.gov/media/159183/download. contributor: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: This prefix is for FDA application identifiers. There are multiple types of FDA applications (https://www.fda.gov/drugs/how-drugs-are-developed-and-approved/types-applications), including New Drug Application (NDA). FDA.report provides access to all FDA databases, including applications, in a single portal, and can resolve FDA application identifiers. example: 070886 github_request_issue: 1146 homepage: https://fda.report/applications name: FDA Application pattern: ^\d{6}$ preferred_prefix: fda.application reviewer: email: tiago.lubiana.alves@usp.br github: lubianat name: Tiago Lubiana orcid: 0000-0003-2473-2313 uri_format: https://fda.report/applications/$1 fema: contact: email: staylor@vertosolutions.net name: Sean Taylor orcid: 0000-0002-7806-4173 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: FEMA provides identifiers for flavor ingredients deemed safe for food use. These entities include chemical compounds and natural substances used as flavoring agents, each reviewed by the FEMA Expert Panel for GRAS (Generally Recognized As Safe) status. The identifiers link to safety data and regulatory assessments, including evaluations by the U.S. FDA and, where applicable, the Joint FAO/WHO Expert Committee on Food Additives (JECFA). example: '4667' github_request_issue: 1247 homepage: https://www.femaflavor.org name: Flavor and Extract Manufacturers Association pattern: ^\d+$ preferred_prefix: fema reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 ferroliganddb: contact: email: guqiong@mail.sysu.edu.cn name: Qiong Gu contributor: email: shah.tanay2@northeastern.edu github: tanayshah2 name: Tanay Shah orcid: 0009-0001-1912-5132 description: FerroLigandDB is a meticulously curated, high-quality database of ferroptosis regulators, including inducers and inhibitors. example: '486' github_request_issue: 1145 homepage: https://ferr.gulab.org.cn/ name: FerroLigandDB preferred_prefix: ferroliganddb publications: - doi: 10.1021/acs.jcim.4c00525 pubmed: '38885636' title: 'FerroLigandDB: A Ferroptosis Ligand Database of Structure-Activity Relations' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://ferr.gulab.org.cn/browse/$1 fhir.implementation: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A set of guides on implementing various processes within hospitals or healthcare systems. example: immds homepage: https://hl7.org/fhir/us/ name: FHIR United States Implementation Guides preferred_prefix: fhir.implementation uri_format: https://hl7.org/fhir/us/$1 fideo: contact: email: georgeta.bordea@u-bordeaux.fr github: getbordea name: Georgeta Bordea orcid: 0000-0001-9921-8234 description: Food-Drug interactions automatically extracted from scientific literature download_owl: http://purl.obolibrary.org/obo/fideo.owl example: '00000021' homepage: https://gitub.u-bordeaux.fr/erias/fideo keywords: - obo - ontology license: CC0-1.0 mappings: aberowl: FIDEO bioportal: FIDEO obofoundry: fideo ols: fideo ontobee: FIDEO name: Food Interactions with Drugs Evidence Ontology pattern: ^\d{8}$ preferred_prefix: FIDEO rdf_uri_format: http://purl.obolibrary.org/obo/FIDEO_$1 repository: https://gitub.u-bordeaux.fr/erias/fideo uri_format: http://purl.obolibrary.org/obo/FIDEO_$1 version: '2023-12-18' fishbase.species: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years.' example: '6472' homepage: http://fishbase.org mappings: integbio: nbdc00270 re3data: r3d100010912 wikidata: P938 name: FishBase pattern: ^\d+$ preferred_prefix: fishbase.species synonyms: - fishbase uri_format: https://www.fishbase.ca/summary/$1 fivestars: contact: email: silvio.peroni@unibo.it github: essepuntato name: Silvio Peroni orcid: 0000-0003-0530-4305 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata. example: hasOpenAccessRating homepage: http://www.sparontologies.net/ontologies/fivestars keywords: - bibliography - citation - data model - report - subject agnostic mappings: fairsharing: FAIRsharing.6dfe9b name: Five Stars of Online Research Articles Ontology preferred_prefix: FiveStars publications: - doi: 10.1045/january2012-shotton title: The Five Stars of Online Journal Articles - a Framework for Article Evaluation year: 2012 repository: https://github.com/sparontologies/fivestars twitter: sparontologies fix: contact: email: amalik@ebi.ac.uk github: amalik01 name: Adnan Malik orcid: 0000-0001-8123-5351 deprecated: true description: An ontology of physico-chemical methods and properties. download_obo: http://purl.obolibrary.org/obo/fix.obo download_owl: http://purl.obolibrary.org/obo/fix.owl example: 0000390 homepage: https://www.ebi.ac.uk/chebi/ keywords: - chemistry - experiment - experimental measurement - obo - ontology - property - protocol mappings: aberowl: FIX biocontext: FIX bioportal: FIX fairsharing: FAIRsharing.wwy1ns obofoundry: fix ols: fix ontobee: FIX prefixcommons: fix name: Physico-chemical methods and properties owners: - name: European Bioinformatics Institute partnered: false ror: 02catss52 part_of: chebi pattern: ^\d{7}$ preferred_prefix: FIX providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/fix:$1 rdf_uri_format: http://purl.obolibrary.org/obo/FIX_$1 uri_format: http://purl.obolibrary.org/obo/FIX_$1 version: '2020-04-13' flopo: appears_in: - gallont contact: email: robert.hoehndorf@kaust.edu.sa github: leechuck name: Robert Hoehndorf orcid: 0000-0001-8149-5890 description: Traits and phenotypes of flowering plants occurring in digitized Floras download_owl: http://purl.obolibrary.org/obo/flopo.owl example: '0005250' homepage: https://github.com/flora-phenotype-ontology/flopoontology keywords: - biodiversity - botany - life cycle stage - obo - ontology - phenotype - plant anatomy license: CC0-1.0 mappings: aberowl: FLOPO agroportal: FLOPO biocontext: FLOPO bioportal: FLOPO fairsharing: FAIRsharing.ny9vnm obofoundry: flopo ols: flopo ontobee: FLOPO name: Flora Phenotype Ontology pattern: ^\d{7}$ preferred_prefix: FLOPO publications: - doi: 10.1186/s13326-016-0107-8 pmc: PMC5109718 pubmed: '27842607' title: 'The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants' year: 2016 - doi: 10.3897/bdj.2.e1125 pmc: PMC4092319 pubmed: '25057255' title: Enriched biodiversity data as a resource and service year: 2014 rdf_uri_format: http://purl.obolibrary.org/obo/FLOPO_$1 repository: https://github.com/flora-phenotype-ontology/flopoontology uri_format: http://purl.obolibrary.org/obo/FLOPO_$1 flowrepository: contact: email: rbrinkman@bccrc.ca name: Ryan Brinkman orcid: 0000-0002-9765-2990 description: FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field. example: FR-FCM-ZYGW homepage: https://flowrepository.org/ keywords: - biology - cell biology - life science mappings: fairsharing: FAIRsharing.veg2d6 integbio: nbdc01698 miriam: flowrepository n2t: flowrepository re3data: r3d100011280 name: FlowRepository pattern: ^FR\-FCM\-\w{4}$ preferred_prefix: flowrepository publications: - doi: 10.1002/cyto.a.22106 pubmed: '22887982' title: 'FlowRepository: a resource of annotated flow cytometry datasets associated with peer-reviewed publications' year: 2012 - doi: 10.1002/0471142956.cy1018s61 pubmed: '22752950' title: Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) compliant manuscript using the International Society for Advancement of Cytometry (ISAC) FCS file repository (FlowRepository.org) year: 2012 uri_format: https://flowrepository.org/id/$1 flu: contact: email: burkesquires@gmail.com name: R. Burke Squires orcid: 0000-0001-9666-6285 deprecated: true description: Starting in the fall of 2007, a collaborative group of influenza researchers have established an influenza ontology. The influenza ontology is an application ontology. Consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS) download_owl: http://purl.obolibrary.org/obo/flu.owl example: '0000404' homepage: http://purl.obolibrary.org/obo/flu/ keywords: - obo - ontology mappings: aberowl: FLU biocontext: FLU bioportal: FLU obofoundry: flu name: Influenza Ontology pattern: ^\d{7}$ preferred_prefix: FLU rdf_uri_format: http://purl.obolibrary.org/obo/FLU_$1 uri_format: http://purl.obolibrary.org/obo/FLU_$1 flybase: contact: email: vjenkins@morgan.harvard.edu name: Victoria K. Jenkins orcid: 0000-0002-1567-7626 description: FlyBase is the database of the Drosophila Genome Projects and of associated literature. example: FBgn0011293 homepage: http://flybase.org/ keywords: - allele - anatomy - bio.tools - bioinformatics - blast - comparative genomics - controlled term - dna - drosophilidae - expression - faseb list - functional genomics - gene - genetics - genome - genomics - genotype - image - image collection - interaction - life science - life-cycle - molecular biology - molecular genetics - movie - mutant - phenotype - rna-seq - sequence - stock - video resource license: CC-BY-4.0 mappings: biocontext: FlyBase cellosaurus: FlyBase edam: '1089' fairsharing: FAIRsharing.wrvze3 go: FB integbio: nbdc00064 miriam: fb n2t: fb ncbi: FLYBASE pathguide: '460' prefixcommons: flybase re3data: r3d100010591 rrid: FlyBase uniprot: DB-0026 wikidata: P3852 name: FlyBase Gene pattern: ^FB\w{2}\d{7}$ preferred_prefix: FlyBase providers: - code: agr description: FlyBase through the Alliance of Genome Resources homepage: https://www.alliancegenome.org name: FlyBase through the Alliance of Genome Resources uri_format: https://www.alliancegenome.org/gene/FB:$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/flybase:$1 publications: - doi: 10.1093/nar/27.1.85 pmc: PMC148103 pubmed: '9847148' title: The FlyBase database of the Drosophila Genome Projects and community literature year: 1999 - doi: 10.1093/nar/26.1.85 pmc: PMC147222 pubmed: '9399806' title: 'FlyBase: a Drosophila database' year: 1998 - doi: 10.1093/nar/25.1.63 pmc: PMC146418 pubmed: '9045212' title: 'FlyBase: a Drosophila database. The FlyBase consortium' year: 1997 - doi: 10.1093/nar/24.1.53 pmc: PMC145580 pubmed: '8594600' title: 'FlyBase: the Drosophila database' year: 1996 - pubmed: '8578603' - doi: 10.1093/nar/22.17.3456 pmc: PMC308301 pubmed: '7937045' title: FlyBase--the Drosophila database. The FlyBase Consortium year: 1994 - doi: 10.1242/dev.120.7.2077 pubmed: '7925011' title: FlyBase--the Drosophila genetic database year: 1994 - doi: 10.1093/nar/gkaa1026 pmc: PMC7779046 pubmed: '33219682' title: 'FlyBase: updates to the Drosophila melanogaster knowledge base' year: 2021 - doi: 10.1093/nar/gky1003 pmc: PMC6323960 pubmed: '30364959' title: 'FlyBase 2.0: the next generation' year: 2019 - doi: 10.1007/978-1-4939-7737-6_16 pmc: PMC5996772 pubmed: '29761468' title: Using FlyBase to Find Functionally Related Drosophila Genes year: 2018 - doi: 10.1002/cpbi.19 pmc: PMC5152691 pubmed: '27930807' title: Exploring FlyBase Data Using QuickSearch year: 2016 - doi: 10.1093/nar/gkw1016 pmc: PMC5210523 pubmed: '27799470' title: 'FlyBase at 25: looking to the future' year: 2016 - doi: 10.1242/dmm.023317 pmc: PMC4826978 pubmed: '26935103' title: FlyBase portals to human disease research using Drosophila models year: 2016 - doi: 10.1093/nar/gkv1046 pmc: PMC4702782 pubmed: '26467478' title: 'FlyBase: establishing a Gene Group resource for Drosophila melanogaster' year: 2015 - doi: 10.1534/g3.115.018929 pmc: PMC4528329 pubmed: '26109357' title: 'Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data' year: 2015 - doi: 10.1534/g3.115.018937 pmc: PMC4528330 pubmed: '26109356' title: 'Gene Model Annotations for Drosophila melanogaster: The Rule-Benders' year: 2015 - doi: 10.1093/nar/gku1099 pmc: PMC4383921 pubmed: '25398896' title: 'FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations' year: 2014 - doi: 10.1093/nar/gkt1092 pmc: PMC3964969 pubmed: '24234449' title: FlyBase 102--advanced approaches to interrogating FlyBase year: 2013 - doi: 10.1093/database/bas024 pmc: PMC3342516 pubmed: '22554788' title: Directly e-mailing authors of newly published papers encourages community curation year: 2012 - doi: 10.1093/nar/gkr1030 pmc: PMC3245098 pubmed: '22127867' title: FlyBase 101--the basics of navigating FlyBase year: 2011 - doi: 10.1093/nar/gkn788 pmc: PMC2686450 pubmed: '18948289' title: 'FlyBase: enhancing Drosophila Gene Ontology annotations' year: 2008 - doi: 10.1007/978-1-59745-583-1_3 pubmed: '18641940' title: 'FlyBase : a database for the Drosophila research community' year: 2008 - doi: 10.1093/nar/gkm930 pmc: PMC2238994 pubmed: '18160408' title: 'FlyBase: integration and improvements to query tools' year: 2007 - doi: 10.1093/nar/gkl827 pmc: PMC1669768 pubmed: '17099233' title: 'FlyBase: genomes by the dozen' year: 2006 - doi: 10.1093/nar/gkj068 pmc: PMC1347431 pubmed: '16381917' title: 'FlyBase: anatomical data, images and queries' year: 2006 - doi: 10.1093/nar/gki046 pmc: PMC540000 pubmed: '15608223' title: 'FlyBase: genes and gene models' year: 2005 - doi: 10.1093/nar/gkg094 pmc: PMC165541 pubmed: '12519974' title: The FlyBase database of the Drosophila genome projects and community literature year: 2003 - doi: 10.1093/nar/30.1.106 pmc: PMC99082 pubmed: '11752267' title: The FlyBase database of the Drosophila genome projects and community literature year: 2002 - pubmed: '11465064' - doi: 10.1093/nar/gkn788. title: 'FlyBase: enhancing Drosophila Gene Ontology annotations.' synonyms: - FB - FlyBase twitter: flybasedotorg uri_format: https://flybase.org/reports/$1 flybrain.ndb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A database of fly neurons and pathways with an associated 3D viewer. example: '10531' homepage: https://flybrain-ndb.virtualflybrain.org mappings: integbio: nbdc01446 name: FlyBrain Neuron Database pattern: ^\d+$ 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 flymine.chromosome: description: FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge. example: '1047874' homepage: http://www.flymine.org/ keywords: - gene expression - genome - protein mappings: prefixcommons: flymine name: FlyMine Chromosome Band preferred_prefix: flymine.chromosome providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/flymine:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.flymine.org/flymine/report/ChromosomeBand/$1 fma: banana: FMA contact: email: mejino@u.washington.edu name: Onard Mejino deprecated: true description: The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. download_owl: http://purl.obolibrary.org/obo/fma.owl example: '63189' homepage: http://si.washington.edu/projects/fma keywords: - anatomy - biomedical science - brain imaging - human - obo - ontology - owl - phenotype - radiology license: CC-BY-3.0 logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBYTg9IiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--16f323877b0cea5b9b3df9ea964ed441ad10cff1/fma.png?disposition=inline mappings: aberowl: FMA bartoc: '571' biocontext: FMA bioportal: FMA edam: '1182' fairsharing: FAIRsharing.x56jsy go: FMA hl7: 2.16.840.1.113883.6.119 integbio: nbdc00273 miriam: fma n2t: fma obofoundry: fma ols: fma ontobee: FMA prefixcommons: fma wikidata: P1402 name: Foundational Model of Anatomy namespace_in_lui: true pattern: ^\d+$ preferred_prefix: FMA providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/fma:$1 publications: - doi: 10.1016/j.artmed.2016.04.003 pmc: PMC4915823 pubmed: '27235801' title: 'From frames to OWL2: Converting the Foundational Model of Anatomy' year: 2016 - doi: 10.1016/j.websem.2007.12.001 pmc: PMC2500209 pubmed: '18688289' title: Translating the Foundational Model of Anatomy into OWL year: 2008 - doi: 10.1016/j.websem.2006.05.007 pmc: PMC2270940 pubmed: '18360535' title: 'The foundational model of anatomy in OWL: Experience and perspectives' year: 2006 - doi: 10.1109/iembs.2004.1404513 pubmed: '17271570' title: 'The foundational model of anatomy: a template for the symbolic representation of multi-scale physiological functions' year: 2004 - pmc: PMC1560487 pubmed: '16779026' title: 'Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study' year: 2005 - doi: 10.1016/j.jbi.2003.11.007 pubmed: '14759820' title: 'A reference ontology for biomedical informatics: the Foundational Model of Anatomy' year: 2003 rdf_uri_format: http://purl.obolibrary.org/obo/FMA_$1 repository: https://bitbucket.org/uwsig/fma synonyms: - FMAID - FMA_RETIRED uri_format: https://www.ebi.ac.uk/ols4/ontologies/fma/terms?obo_id=FMA:$1 version: '2020-04-13' foaf: contact: email: rafael.goncalves@stanford.edu name: Rafael Gonçalves contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people''s heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world.' download_owl: http://aber-owl.net/media/ontologies/foaf/1/foaf.owl example: familyName homepage: http://xmlns.com/foaf/spec/ keywords: - ontology - people mappings: aberowl: foaf biocontext: foaf biolink: foaf bioportal: FOAF lov: foaf zazuko: foaf name: Friend of a Friend preferred_prefix: foaf uri_format: http://xmlns.com/foaf/0.1/$1 fobi: contact: email: polcaes@gmail.com github: pcastellanoescuder name: Pol Castellano Escuder orcid: 0000-0001-6466-877X depends_on: - chebi - foodon description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data download_owl: http://purl.obolibrary.org/obo/fobi.owl example: 030719 example_extras: - '0142' - '07504' homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: FOBI agroportal: FOBI bioportal: FOBI obofoundry: fobi ols: fobi ontobee: FOBI name: Food-Biomarker Ontology pattern: ^\d{4,6}$ preferred_prefix: FOBI providers: - code: fobi.legacy description: An incorrect encoding of OBO purls homepage: http://purl.obolibrary.org/obo/fobi name: FOBI Hash uri_format: http://purl.obolibrary.org/obo/fobi.owl#FOBI:$1 publications: - doi: 10.1093/bioinformatics/btab626 pubmed: '34601570' title: 'The fobitools framework: the first steps towards food enrichment analysis' year: 2021 - doi: 10.1093/databa/baaa033 pmc: PMC7298227 pubmed: '32556148' title: 'FOBI: an ontology to represent food intake data and associate it with metabolomic data' year: 2020 rdf_uri_format: http://purl.obolibrary.org/obo/FOBI_$1 repository: https://github.com/pcastellanoescuder/FoodBiomarkerOntology uri_format: http://purl.obolibrary.org/obo/FOBI_$1 foodb.compound: description: FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds. example: FDB002100 homepage: https://foodb.ca/ mappings: biocontext: FOODB.COMPOUND biolink: foodb.compound miriam: foodb.compound n2t: foodb.compound re3data: r3d100012152 wikidata: P8117 name: FooDB compound pattern: ^FDB\d+$ preferred_prefix: foodb.compound synonyms: - foodb uri_format: http://foodb.ca/compounds/$1 foodb.food: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Foods in FooDB example: FOOD00020 homepage: https://foodb.ca/foods mappings: biolink: foodb.food name: FooDB Food pattern: ^FOOD\d+$ preferred_prefix: foodb.food uri_format: https://foodb.ca/foods/$1 foodex2: contact: email: data@food.gov.uk name: UK Food Standard Agency description: Food Type identifiers, supporting codes and vocabularies based on the EFSA FoodEx2 (https://www.efsa.europa.eu/en/data/data-standardisation) that are being tested in the development of the FSA's code and data standards repository. These codes may be used within FSA data. example: A0TMC homepage: https://data.food.gov.uk/codes/_foodtype mappings: agroportal: FOODEX2 name: Food Classification and Description System (from FSA Food Type identifiers) preferred_prefix: foodex2 uri_format: http://data.food.gov.uk/codes/foodtype/id/$1 foodon: appears_in: - agro - envo - fobi - maxo - one - ons banana: FOODON contact: email: damion_dooley@sfu.ca github: ddooley name: Damion Dooley orcid: 0000-0002-8844-9165 depends_on: - bfo - chebi - envo - eo - ncbitaxon - obi - ro - uberon description: FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies. download_obo: http://purl.obolibrary.org/obo/foodon.obo download_owl: http://purl.obolibrary.org/obo/foodon.owl example: 03307879 homepage: https://foodon.org/ keywords: - agriculture - botany - disease - environmental science - food - medicine - obo - ontology - sustainability license: CC-BY-4.0 mappings: aberowl: FOODON agroportal: FOODON biocontext: FOODON bioportal: FOODON fairsharing: FAIRsharing.dzxae miriam: foodon n2t: foodon obofoundry: foodon ols: foodon ontobee: FOODON name: The Food Ontology namespace_in_lui: true pattern: ^[0-9]{8}$ preferred_prefix: FOODON publications: - doi: 10.1038/s41538-018-0032-6 pmc: PMC6550238 pubmed: '31304272' title: 'FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration' year: 2018 - doi: 10.3389/fmicb.2017.01068 pmc: PMC5483436 pubmed: '28694792' title: 'Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance' year: 2017 rdf_uri_format: http://purl.obolibrary.org/obo/FOODON_$1 repository: https://github.com/FoodOntology/foodon uri_format: http://purl.obolibrary.org/obo/FOODON_$1 version: '2025-02-01' fossilworks.journal: contributor: email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 description: Identifier for a journal article in the fossilworks website example: '61467' github_request_issue: 468 homepage: http://fossilworks.org mappings: wikidata: P7720 name: Fossilworks Journal part_of: fossilworks pattern: ^\d+$ preferred_prefix: fossilworks.journal reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://fossilworks.org/?a=referenceInfo&reference_no=$1 fossilworks.taxon: contributor: email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 description: Identifier for an animal, plant, or microorganism from the fossilworks website example: '40565' github_request_issue: 469 homepage: http://www.fossilworks.org mappings: wikidata: P842 name: Fossilworks Taxon part_of: fossilworks pattern: ^[1-9]\d{0,5}$ preferred_prefix: fossilworks.taxon reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1 fovt: contact: email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 depends_on: - bco - bfo - bspo - iao - oba - pato - ro - uberon description: These are the terms that are improted for FOVT to describe vertebrate traits. download_obo: http://purl.obolibrary.org/obo/fovt.obo download_owl: http://purl.obolibrary.org/obo/fovt.owl example: 0000009 homepage: https://github.com/futres/fovt keywords: - obo - ontology license: CC0-1.0 mappings: aberowl: FOVT bioportal: FOVT ecoportal: FOVT obofoundry: fovt ols: fovt ontobee: FOVT name: FuTRES Ontology of Vertebrate Traits pattern: ^\d{7}$ preferred_prefix: FOVT rdf_uri_format: http://purl.obolibrary.org/obo/FOVT_$1 repository: https://github.com/futres/fovt uri_format: http://purl.obolibrary.org/obo/FOVT_$1 version: '2023-05-31' fplx: contact: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships. example: GPIb_IX_V homepage: https://sorgerlab.github.io/famplex/ keywords: - ontology license: CC0-1.0 mappings: aberowl: FPLX biocontext: FPLX bioportal: FPLX miriam: fplx n2t: fplx name: FamPlex pattern: ^[a-zA-Z0-9][A-Za-z0-9_]+$ preferred_prefix: fplx publications: - doi: 10.1186/s12859-018-2211-5 pmc: PMC6022344 pubmed: '29954318' title: 'FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining' year: 2018 synonyms: - famplex uri_format: https://sorgerlab.github.io/famplex/$1 fr: contact: email: silvio.peroni@unibo.it github: essepuntato name: Silvio Peroni orcid: 0000-0003-0530-4305 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology that enables the description of reviews of scientific articles and other scholarly resources. example: ReviewVersion homepage: http://www.sparontologies.net/ontologies/fr keywords: - bibliography - citation - data model - report - subject agnostic mappings: fairsharing: FAIRsharing.e7e609 name: FAIR* Reviews Ontology preferred_prefix: FR repository: https://github.com/sparontologies/fr twitter: sparontologies frapo: contact: email: silvio.peroni@unibo.it github: essepuntato name: Silvio Peroni orcid: 0000-0003-0530-4305 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc. example: Grant homepage: http://www.sparontologies.net/ontologies/frapo keywords: - academy - data model - funding bodies - grant application - report - research project - subject agnostic mappings: aberowl: FRAPO fairsharing: FAIRsharing.0a2576 lov: frapo name: Funding, Research Administration and Projects Ontology preferred_prefix: FRAPO repository: https://github.com/sparontologies/frapo twitter: sparontologies uri_format: http://purl.org/cerif/frapo/$1 frbr: contact: email: silvio.peroni@unibo.it github: essepuntato name: Silvio Peroni orcid: 0000-0003-0530-4305 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO. example: Expression homepage: http://www.sparontologies.net/ontologies/frbr keywords: - bibliography - citation - data model - frbr - report - subject agnostic mappings: fairsharing: FAIRsharing.b34b43 lov: frbr zazuko: frbr name: Functional Requirements for Bibliographic Records preferred_prefix: FRBR repository: https://github.com/sparontologies/frbr twitter: sparontologies uri_format: http://purl.org/vocab/frbr/core#$1 frbrer: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This is the element set of native RDF classes and properties described in the current text (Feb 2009) of the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model. (from https://www.iflastandards.info/fr/frbr/frbrer.html) download_rdf: http://iflastandards.info/ns/fr/frbr/frbrer.jsonld example: '1001' homepage: https://www.iflastandards.info/fr/frbr/frbrer keywords: - frbr mappings: lov: frbrer name: Functional Requirements for Bibliographic Records Entity-Relationship Model part_of: frbr preferred_prefix: frbrer uri_format: http://iflastandards.info/ns/fr/frbr/frbrer/$1 fsnp: description: The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification. example: rs17852708 homepage: http://compbio.cs.queensu.ca/F-SNP/ keywords: - dna - protein mappings: biocontext: FSNP miriam: fsnp n2t: fsnp prefixcommons: fsnp name: F-SNP pattern: ^rs\d+$ preferred_prefix: fsnp providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/fsnp:$1 uri_format: http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1 ftt: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific. example: '273' homepage: https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3 name: Feature Type Thesaurus pattern: ^\d+$ preferred_prefix: ftt references: - https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200 - https://github.com/EnvironmentOntology/envo/issues/1130 uri_format: https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1 funcbase.fly: description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data. example: '10194' homepage: http://func.mshri.on.ca/fly mappings: biocontext: FUNCBASE.FLY miriam: funcbase.fly n2t: funcbase.fly name: FuncBase Fly pattern: ^\d+$ preferred_prefix: funcbase.fly uri_format: http://func.mshri.on.ca/fly/genes/list_functional_scores/$1 funcbase.human: description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data. example: '119514' homepage: http://func.mshri.on.ca/human/ mappings: biocontext: FUNCBASE.HUMAN miriam: funcbase.human n2t: funcbase.human name: FuncBase Human pattern: ^\d+$ preferred_prefix: funcbase.human uri_format: http://func.mshri.on.ca/human/genes/list_functional_scores/$1 funcbase.mouse: description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse. example: '1351341' homepage: http://func.mshri.on.ca/mouse/ mappings: biocontext: FUNCBASE.MOUSE miriam: funcbase.mouse n2t: funcbase.mouse name: FuncBase Mouse pattern: ^\d+$ preferred_prefix: funcbase.mouse uri_format: http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1 funcbase.yeast: description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast. example: '2701' homepage: http://func.mshri.on.ca/yeast mappings: biocontext: FUNCBASE.YEAST miriam: funcbase.yeast n2t: funcbase.yeast name: FuncBase Yeast pattern: ^\d+$ preferred_prefix: funcbase.yeast uri_format: http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1 funderregistry: description: The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world. example: '100000001' homepage: https://www.crossref.org/ mappings: miriam: funderregistry name: FunderRegistry pattern: ^\d{9,9}$ preferred_prefix: funderregistry providers: - code: crossref.api description: Access funder data through the Crossref API homepage: https://api.crossref.org name: Crossref API uri_format: https://api.crossref.org/funders/$1 - code: doi description: Access funder data through a DOI for crossref funders. homepage: https://doi.org name: DOI uri_format: https://dx.doi.org/10.13039/501100000995 synonyms: - FundRef - crossref.funder uri_format: http://data.crossref.org/fundingdata/funder/10.13039/$1 fungidb: contact: email: jason.stajich@ucr.edu name: Jason E. Stajich orcid: 0000-0002-7591-0020 description: FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina. example: CNBG_0001 homepage: https://fungidb.org/fungidb keywords: - genomics mappings: biocontext: FUNGIDB fairsharing: FAIRsharing.xf30yc miriam: fungidb n2t: fungidb re3data: r3d100011906 name: FungiDB pattern: ^[A-Za-z_0-9]+$ preferred_prefix: fungidb publications: - doi: 10.1016/j.fgb.2016.04.002 pubmed: '27259951' title: Database whiplash, crowdsourcing, and FungiDB year: 2016 - doi: 10.1128/ec.00083-14 pmc: PMC4135733 pubmed: '24813190' title: Literature-based gene curation and proposed genetic nomenclature for cryptococcus year: 2014 - doi: 10.1093/nar/gkr918 pmc: PMC3245123 pubmed: '22064857' title: 'FungiDB: an integrated functional genomics database for fungi' year: 2011 - doi: 10.1128/EC.00083-14 title: Literature-based gene curation and proposed genetic nomenclature for cryptococcus. twitter: fungidb uri_format: https://fungidb.org/fungidb/app/record/gene/$1 fungorum: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier for a fungus taxon in Index Fungorum example: '154022' homepage: http://www.indexfungorum.org mappings: ncbi: Fungorum wikidata: P1391 name: Index Fungorum pattern: ^[1-9]\d{0,5}$ preferred_prefix: fungorum uri_format: http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1 fyeco: comment: Rather than admitting FYECO to the OBO foundry, we secure the prefix here at bioregistry. The FYECO namespace shows up in a lot of ingests (basically anywhere you ingest PomBase gene-phenotype data). Future work includes mapping FYECO to other OBO ontologies, but this is way ahead in the future. contact: email: vw253@cam.ac.uk github: ValWood name: Val Wood orcid: 0000-0001-6330-7526 contributor: email: vw253@cam.ac.uk github: ValWood name: Val Wood orcid: 0000-0001-6330-7526 description: PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase. example: '0000003' github_request_issue: 268 homepage: https://github.com/pombase/fypo mappings: biolink: FYECO name: Fission Yeast Experimental Conditions Ontology pattern: ^\d{7}$ preferred_prefix: FYECO repository: https://github.com/pombase/fypo reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 fyler: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'A hierarchical classification of congenital heart disease ' example: '4447' homepage: https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906 name: Fyler pattern: ^\d+$ preferred_prefix: fyler references: - https://github.com/obophenotype/human-phenotype-ontology/issues/2568 - https://github.com/obophenotype/human-phenotype-ontology/issues/2511 fypo: contact: email: vw253@cam.ac.uk github: ValWood name: Val Wood orcid: 0000-0001-6330-7526 description: A formal ontology of phenotypes observed in fission yeast. download_json: http://purl.obolibrary.org/obo/fypo.json download_obo: http://purl.obolibrary.org/obo/fypo.obo download_owl: http://purl.obolibrary.org/obo/fypo.owl example: '0001707' homepage: https://github.com/pombase/fypo keywords: - gene ontology enrichment - genetics - life science - obo - ontology - phenotype - phylogenetics license: CC-BY-4.0 logo: https://github.com/pombase/website/blob/master/src/assets/FYPO_logo_tiny.png mappings: aberowl: FYPO biocontext: FYPO biolink: FYPO bioportal: FYPO fairsharing: FAIRsharing.4vr0ys go: FYPO obofoundry: fypo ols: fypo ontobee: FYPO name: Fission Yeast Phenotype Ontology pattern: ^\d{7}$ preferred_prefix: FYPO publications: - doi: 10.1093/bioinformatics/btt266 pmc: PMC3694669 pubmed: '23658422' title: 'FYPO: the fission yeast phenotype ontology' year: 2013 rdf_uri_format: http://purl.obolibrary.org/obo/FYPO_$1 repository: https://github.com/pombase/fypo uri_format: http://purl.obolibrary.org/obo/FYPO_$1 version: '2025-01-14' ga4ghdos: description: Assists in resolving data across cloud resources. example: dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d homepage: http://github.com/ga4gh/data-object-service-schemas mappings: biocontext: GA4GHDOS miriam: ga4ghdos n2t: ga4ghdos name: Data Object Service pattern: ^[a-zA-Z0-9\-:#/\.]+$ preferred_prefix: ga4ghdos uri_format: https://dataguids.org/ga4gh/dos/v1/dataobjects/$1 gabi: contact: email: birgit.kersten@thuenen.de name: Birgit Kersten orcid: 0000-0001-9900-9133 description: GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'. example: '2679240' homepage: http://www.gabipd.org/ keywords: - gene - genome - plant mappings: biocontext: GABI miriam: gabi n2t: gabi ncbi: GABI prefixcommons: gabi name: Network of Different Plant Genomic Research Projects pattern: ^\w+$ preferred_prefix: gabi providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/gabi:$1 publications: - doi: 10.1093/nar/gkn611 pmc: PMC2686513 pubmed: '18812395' title: 'GabiPD: the GABI primary database--a plant integrative ''omics'' database' year: 2008 uri_format: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject gainesville.core: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Describes typical Computational Chemistry experiments, including Molecular Publications, Molecular Systems, Molecular Calculations download_owl: http://ontologies.makolab.com/gc06/gc.owl example: Aromatic homepage: http://ontologies.makolab.com/gc06/gc.html keywords: - ontology license: CC-BY-3.0 name: Gainesville Core Ontology preferred_prefix: gainesville.core references: - http://ontologies.makolab.com/gc/ uri_format: http://purl.org/gc/$1 galen: comment: I really tried, but could not figure out what GALEN stands for contact: email: j@deltaflow.com name: Julian Seidenberg deprecated: true description: A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic. download_owl: http://aber-owl.net/media/ontologies/GALEN/1/galen.owl example: MagnitudeValueType homepage: https://www.opengalen.org keywords: - ontology mappings: aberowl: GALEN bioportal: GALEN name: GALEN preferred_prefix: galen uri_format: http://www.co-ode.org/ontologies/galen#$1 gallont: contact: email: adeans@psu.edu github: adeans name: Andy Deans orcid: 0000-0002-2119-4663 depends_on: - caro - flopo - ncbitaxon - obi - pato - po - poro - ro description: Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls. download_json: http://purl.obolibrary.org/obo/gallont.json download_obo: http://purl.obolibrary.org/obo/gallont.obo download_owl: http://purl.obolibrary.org/obo/gallont.owl example: '0000001' homepage: https://adeans.github.io/gallont/ keywords: - obo - ontology license: CC0-1.0 mappings: aberowl: GALLONT agroportal: GALLONT bioportal: GALLONT obofoundry: gallont ontobee: GALLONT name: Plant Gall Ontology pattern: ^\d{7}$ preferred_prefix: GALLONT rdf_uri_format: http://purl.obolibrary.org/obo/GALLONT_$1 repository: https://github.com/adeans/gallont uri_format: http://purl.obolibrary.org/obo/GALLONT_$1 gard: contact: email: eric.sid@nih.gov github: ericsid name: Eric Sid orcid: 0000-0001-7697-3026 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease. example: '6038' homepage: https://rarediseases.info.nih.gov/diseases mappings: wikidata: P4317 name: Genetic and Rare Diseases Information Center pattern: ^\d+$ preferred_prefix: gard publications: - doi: 10.1080/02763869.2022.2131143 pubmed: '36394913' title: Genetic and Rare Diseases Information Center (GARD) year: 2022 - doi: 10.3233/trd-170011 pmc: PMC5685198 pubmed: '29152459' title: Marking 15 years of the Genetic and Rare Diseases Information Center year: 2017 synonyms: - GARD - Genetic and Rare Diseases Information Center uri_format: https://rarediseases.info.nih.gov/diseases/$1/index gateway: description: The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access. example: fd8d0743-344a-4758-bb97-f8ad84a37357 homepage: https://www.hdruk.ac.uk mappings: miriam: gateway name: Health Data Research Innovation Gateway pattern: ^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$ preferred_prefix: gateway uri_format: https://web.www.healthdatagateway.org/dataset/$1 gaz: appears_in: - scdo contact: email: lschriml@som.umaryland.edu github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 deprecated: true description: A gazetteer constructed on ontological principles. The countries are actively maintained. download_obo: http://purl.obolibrary.org/obo/gaz.obo download_owl: http://purl.obolibrary.org/obo/gaz.owl example: '00620027' homepage: http://environmentontology.github.io/gaz/ keywords: - environmental science - geographical location - obo - ontology license: CC0-1.0 mappings: aberowl: GAZ biocontext: GAZ bioportal: GAZ fairsharing: FAIRsharing.wkdjpb obofoundry: gaz ols: gaz ontobee: GAZ wikidata: P6778 name: Gazetteer pattern: ^\d{8}$ preferred_prefix: GAZ rdf_uri_format: http://purl.obolibrary.org/obo/GAZ_$1 repository: https://github.com/EnvironmentOntology/gaz uri_format: http://purl.obolibrary.org/obo/GAZ_$1 gbif: contact: email: timrobertson100@gmail.com github: timrobertson100 name: Tim Robertson orcid: 0000-0001-6215-3617 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity\ \ Information Facility—is international network and data infrastructure funded\ \ by the world's governments and aimed at providing anyone, anywhere, open access\ \ to data about all types of life on Earth." example: '4238' homepage: https://www.gbif.org/species keywords: - biodiversity - bioinformatics - marine biology - metagenomics - natural history - natural science - taxonomy mappings: fairsharing: FAIRsharing.zv11j3 integbio: nbdc00069 re3data: r3d100000039 wikidata: P846 name: Global Biodiversity Information Facility pattern: ^\d+$ preferred_prefix: gbif publications: - doi: 10.1371/journal.pone.0102623 pmc: PMC4123864 pubmed: '25099149' title: 'The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet' year: 2014 repository: https://github.com/gbif/ twitter: GBIF uri_format: https://www.gbif.org/species/$1 gcst: description: The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide. example: GCST000035 homepage: https://www.ebi.ac.uk mappings: miriam: gcst n2t: gcst name: GWAS Catalog owners: - name: European Bioinformatics Institute partnered: false ror: 02catss52 pattern: ^GCST\d{6}\d*$ preferred_prefix: gcst uri_format: https://www.ebi.ac.uk/gwas/studies/$1 gdc: description: The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis. example: ae8c77fe-e6c8-44d5-8265-4a38c637bbef homepage: https://gdc.cancer.gov mappings: biocontext: GDC miriam: gdc n2t: gdc name: Genomic Data Commons Data Portal pattern: ^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$ preferred_prefix: gdc uri_format: https://portal.gdc.cancer.gov/cases/$1 gdsc: description: The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies. example: '1242' homepage: https://www.cancerrxgene.org mappings: cellosaurus: GDSC miriam: gdsc n2t: gdsc name: Genomics of Drug Sensitivity in Cancer pattern: ^[0-9]+$ preferred_prefix: gdsc uri_format: https://www.cancerrxgene.org/translation/Drug/$1 gear: contact: email: jorvis@gmail.com github: jorvis name: Joshua Orvis orcid: 0000-0002-5705-5710 contributor: email: jorvis@gmail.com github: jorvis name: Joshua Orvis orcid: 0000-0002-5705-5710 description: The gEAR portal is a website for visualization and analysis of multi-omic data both in public and private domains. example: d.a59037e8 example_extras: - p.bfd178f5 github_request_issue: 728 homepage: https://umgear.org license: AGPL-3.0-only name: Gene Expression Analysis Resource pattern: ^[dp]\.[a-z0-9]{8}$ preferred_prefix: gear repository: https://github.com/IGS/gEAR reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://umgear.org/p?id=$1 gecko: contact: email: rbca.jackson@gmail.com github: beckyjackson name: Rebecca Jackson orcid: 0000-0003-4871-5569 description: An ontology to represent genomics cohort attributes. download_owl: http://purl.obolibrary.org/obo/gecko.owl example: '0000044' homepage: https://github.com/IHCC-cohorts/GECKO keywords: - biological sample - experimental measurement - genomics - life science - obo - ontology - statistics - survey license: CC-BY-4.0 mappings: aberowl: GECKO bioportal: GECKO fairsharing: FAIRsharing.3da56b obofoundry: gecko ols: gecko ontobee: GECKO name: Genomics Cohorts Knowledge Ontology pattern: ^\d{7}$ preferred_prefix: GECKO rdf_uri_format: http://purl.obolibrary.org/obo/GECKO_$1 repository: https://github.com/IHCC-cohorts/GECKO uri_format: http://purl.obolibrary.org/obo/GECKO_$1 version: '2021-01-18' gemet: contact: email: helpdesk@eionet.europa.eu name: Eionet Helpdesk contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts. example: '627' homepage: https://www.eionet.europa.eu/gemet/en/themes/ keywords: - biodiversity - ecology - environmental science mappings: agroportal: GEMET bartoc: '16' fairsharing: FAIRsharing.9091d9 name: General Multilingual Environmental Thesaurus pattern: ^\d+$ preferred_prefix: gemet providers: - code: gemet.multilingual description: An alternate URI that doesn't have the language encoded in it homepage: https://www.eionet.europa.eu/gemet name: GEMET Multilingual uri_format: http://www.eionet.europa.eu/gemet/concept/$1 uri_format: https://www.eionet.europa.eu/gemet/en/concept/$1 genatlas: description: GenAtlas is a database containing information on human genes, markers and phenotypes. example: HBB homepage: http://genatlas.medecine.univ-paris5.fr/ keywords: - disorder - gene - human - life science mappings: biocontext: GENATLAS fairsharing: FAIRsharing.pmg2vd integbio: nbdc00275 miriam: genatlas n2t: genatlas prefixcommons: genatlas uniprot: DB-0027 name: Genatlas pattern: ^\w+$ preferred_prefix: genatlas providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/genatlas:$1 publications: - doi: 10.1016/s0764-4469(99)80021-3 pubmed: '9835018' title: Genatlas database, genes and development defects year: 1998 - doi: 10.1006/mgme.1999.2867 pubmed: '10444337' title: 'Human genes involved in chromatin remodeling in transcription initiation, and associated diseases: An overview using the GENATLAS database' year: 1999 uri_format: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1 genbank: contact: email: nawrocke@ncbi.nlm.nih.gov github: nawrockie name: Eric P. Nawrocki orcid: 0000-0002-2497-3427 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). example: U49845 homepage: https://www.ncbi.nlm.nih.gov/genbank/ keywords: - bioinformatics - data management - dna - epidemiology - functional genomics - genomics - metagenomics - transcriptomics - virology mappings: biocontext: GenBank cheminf: '000304' edam: '2292' fairsharing: FAIRsharing.9kahy4 go: GenBank integbio: nbdc00276 prefixcommons: genbank re3data: r3d100010528 uniprot: DB-0028 name: GenBank preferred_prefix: genbank providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/genbank:$1 publications: - doi: 10.1093/nar/gkae1114 pubmed: '39558184' title: GenBank 2025 update year: 2024 - doi: 10.1186/s12859-020-3537-3 pmc: PMC7245624 pubmed: '32448124' title: 'VADR: validation and annotation of virus sequence submissions to GenBank' year: 2020 - doi: 10.1093/nar/gkz956 pmc: PMC7145611 pubmed: '31665464' title: GenBank year: 2020 - doi: 10.1093/nar/gky989 pmc: PMC6323954 pubmed: '30365038' title: GenBank year: 2019 - doi: 10.1093/nar/gkx1094 pmc: PMC5753231 pubmed: '29140468' title: GenBank year: 2018 - doi: 10.1093/nar/gkw1070 pmc: PMC5210553 pubmed: '27899564' title: GenBank year: 2016 - doi: 10.1093/nar/gkv1276 pmc: PMC4702903 pubmed: '26590407' title: GenBank year: 2015 - doi: 10.1093/nar/gku1216 pmc: PMC4383990 pubmed: '25414350' title: GenBank year: 2014 - doi: 10.1093/nar/gkt1030 pmc: PMC3965104 pubmed: '24217914' title: GenBank year: 2013 - doi: 10.1093/nar/gks1195 pmc: PMC3531190 pubmed: '23193287' title: GenBank year: 2012 - doi: 10.1093/nar/gkr1202 pmc: PMC3245039 pubmed: '22144687' title: GenBank year: 2011 - doi: 10.1093/nar/gkq1079 pmc: PMC3013681 pubmed: '21071399' title: GenBank year: 2010 - doi: 10.1093/nar/gkn723 pmc: PMC2686462 pubmed: '18940867' title: GenBank year: 2008 - doi: 10.1093/nar/gkm929 pmc: PMC2238942 pubmed: '18073190' title: GenBank year: 2007 - doi: 10.1093/nar/gkl1031 pmc: PMC1781113 pubmed: '17170002' title: Database resources of the National Center for Biotechnology Information year: 2006 uri_format: https://www.ncbi.nlm.nih.gov/nucleotide/$1 genbase: comment: 'CTH: this is a provider of the INSDC resources, not a new prefix.' contact: email: zhaoxuetong@big.ac.cn name: Xuetong Zhao orcid: 0000-0002-3019-8615 contributor: email: shah.tanay2@northeastern.edu github: tanayshah2 name: Tanay Shah orcid: 0009-0001-1912-5132 description: GenBase is a genetic sequence database that accepts user submissions (mRNA, genomic DNAs, ncRNA, or small genomes such as organelles, viruses, plasmids, phages from any organism) and integrates data from INSDC. example: C_AA001108.1 github_request_issue: 1140 homepage: https://ngdc.cncb.ac.cn/genbase/?lang=en mappings: re3data: r3d100014353 name: GenBase preferred_prefix: genbase reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://ngdc.cncb.ac.cn/genbase/search/gb/$1 gendis: comment: This resource doesn't exist on the web anymore deprecated: true description: Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases. example: '46946' homepage: http://caps.ncbs.res.in/gendis/home.html keywords: - classification - genome mappings: prefixcommons: gendis name: Genomic Distribution of structural Superfamilies preferred_prefix: gendis providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/gendis:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code=$1 genecards: contact: email: marilyn.safran@weizmann.ac.il name: Marilyn Safran orcid: 0000-0001-5424-1393 description: The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene. example: ABL1 homepage: http://www.genecards.org/ keywords: - genetics - genome - life science - transcriptomics mappings: biocontext: GENECARDS fairsharing: FAIRsharing.g7jbvn integbio: nbdc00242 miriam: genecards n2t: genecards prefixcommons: genecards re3data: r3d100012015 uniprot: DB-0030 name: GeneCards pattern: ^[A-Za-z-0-9_]+(\@)?$ preferred_prefix: genecards providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/genecards:$1 publications: - doi: 10.1016/s0168-9525(97)01103-7 pubmed: '9097728' title: 'GeneCards: integrating information about genes, proteins and diseases' year: 1997 - doi: 10.1186/s12864-016-2722-2 pmc: PMC4928145 pubmed: '27357693' title: 'VarElect: the phenotype-based variation prioritizer of the GeneCards Suite' year: 2016 - doi: 10.1002/cpbi.5 pubmed: '27322403' title: 'The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses' year: 2016 - doi: 10.1093/database/baw030 pmc: PMC4820835 pubmed: '27048349' title: Genic insights from integrated human proteomics in GeneCards year: 2016 - doi: 10.1089/omi.2015.0168 pmc: PMC4799705 pubmed: '26983021' title: 'GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data' year: 2016 - doi: 10.1093/database/bav006 pmc: PMC4343183 pubmed: '25725062' title: 'PathCards: multi-source consolidation of human biological pathways' year: 2015 - doi: 10.1093/database/baq020 pmc: PMC2938269 pubmed: '20689021' title: 'GeneCards Version 3: the human gene integrator' year: 2010 - doi: 10.1093/bioinformatics/18.11.1542 pubmed: '12424129' title: 'GeneCards 2002: towards a complete, object-oriented, human gene compendium' year: 2002 - doi: 10.1016/S0168-9525(97)01103-7 title: 'GeneCards: integrating information about genes, proteins and diseases.' uri_format: https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1 genecards.geneannot: description: GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Probe-sets are related to GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq and Ensembl mRNA sequences, while assigning sensitivity and specificity scores to each probe-set to gene match. example: GSTA1 homepage: http://genecards.weizmann.ac.il/geneannot/ keywords: - gene expression mappings: prefixcommons: geneannot name: 'GeneAnnot: Microarray Gene Annotation' preferred_prefix: genecards.geneannot providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/geneannot:$1 genecards.geneloc: description: GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources example: '17503' homepage: http://genecards.weizmann.ac.il/geneloc/ keywords: - genome mappings: prefixcommons: geneloc name: Gene Location preferred_prefix: genecards.geneloc providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/geneloc:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id=$1 genecards.genenote: description: GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E. example: GC06M052656 homepage: http://genecards.weizmann.ac.il/genenote/ keywords: - gene expression mappings: prefixcommons: genenote name: Gene Normal Tissue Expression preferred_prefix: genecards.genenote providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/genenote:$1 uri_format: http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl?keyword_type=2_gc_id&keyword=$1&data_type=norm2&results=yes genedb: deprecated: true description: GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed. example: LinJ.20.0070 homepage: https://www.genedb.org/ keywords: - genome - life science - sequence mappings: biocontext: GENEDB edam: '1035' fairsharing: FAIRsharing.j7esqq go: GeneDB integbio: nbdc00469 miriam: genedb n2t: genedb ncbi: GeneDB prefixcommons: genedb re3data: r3d100010626 wikidata: P3382 name: GeneDB pattern: ^[\w\d\.-]*$ preferred_prefix: genedb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/genedb:$1 publications: - doi: 10.1093/nar/gkh007 pmc: PMC308742 pubmed: '14681429' title: 'GeneDB: a resource for prokaryotic and eukaryotic organisms' year: 2004 uri_format: https://www.genedb.org/gene/$1 genefarm: contact: email: sebastien.aubourg@inrae.fr name: sébastien Aubourg orcid: 0000-0002-0695-4767 description: GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products. example: '4892' homepage: http://urgi.versailles.inra.fr/Genefarm/ keywords: - expression - genome - life science - nucleotide - sequence mappings: biocontext: GENEFARM fairsharing: FAIRsharing.2mayq0 miriam: genefarm n2t: genefarm prefixcommons: genefarm name: GeneFarm pattern: ^\d+$ preferred_prefix: genefarm providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/genefarm:$1 publications: - doi: 10.1093/nar/gki115 pmc: PMC540069 pubmed: '15608279' title: GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts year: 2005 uri_format: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1 genepio: contact: email: damion_dooley@sfu.ca github: ddooley name: Damion Dooley orcid: 0000-0002-8844-9165 depends_on: - chebi - ncbitaxon - po - ro - uberon description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. download_owl: http://purl.obolibrary.org/obo/genepio.owl example: 0001885 homepage: http://genepio.org/ keywords: - epidemiology - food - genome - genomics - obo - ontology - pathogen license: CC-BY-3.0 mappings: aberowl: GENEPIO biocontext: GENEPIO bioportal: GENEPIO fairsharing: FAIRsharing.y1mmbv obofoundry: genepio ols: genepio ontobee: GENEPIO name: Genomic Epidemiology Ontology pattern: ^\d{7}$ preferred_prefix: GENEPIO rdf_uri_format: http://purl.obolibrary.org/obo/GENEPIO_$1 repository: https://github.com/GenEpiO/genepio uri_format: http://purl.obolibrary.org/obo/GENEPIO_$1 version: '2024-12-18' genetree: contact: email: flicek@ebi.ac.uk name: Paul Flicek orcid: 0000-0002-3897-7955 description: Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl. example: ENSGT00550000074763 homepage: http://www.ensembl.org/ keywords: - classification - gene - protein mappings: biocontext: GENETREE miriam: genetree n2t: genetree prefixcommons: genetree uniprot: DB-0162 name: GeneTree pattern: ^ENSGT\d+$ preferred_prefix: genetree providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/genetree:$1 publications: - doi: 10.1093/database/bav096 pmc: PMC4761110 pubmed: '26896847' title: Ensembl comparative genomics resources year: 2016 - doi: 10.1093/nar/gkj133 pmc: PMC1347495 pubmed: '16381931' title: Ensembl 2006 year: 2006 uri_format: http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1 genewiki: contact: email: asu@scripps.edu github: andrewsu name: Andrew I Su orcid: 0000-0002-9859-4104 description: The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI. example: '1017' homepage: http://en.wikipedia.org/wiki/Gene_Wiki keywords: - genetics - life science mappings: biocontext: GENEWIKI fairsharing: FAIRsharing.t3snf integbio: nbdc00834 miriam: genewiki n2t: genewiki uniprot: DB-0180 name: Gene Wiki pattern: ^\d+$ preferred_prefix: genewiki provides: ncbigene publications: - doi: 10.1093/database/baw015 pmc: PMC4795929 pubmed: '26989148' title: Wikidata as a semantic framework for the Gene Wiki initiative year: 2016 - doi: 10.1093/nar/gkr925 pmc: PMC3245148 pubmed: '22075991' title: 'The Gene Wiki in 2011: community intelligence applied to human gene annotation' year: 2011 - doi: 10.1093/nar/gkp760 pmc: PMC2808918 pubmed: '19755503' title: 'The Gene Wiki: community intelligence applied to human gene annotation' year: 2009 - doi: 10.1371/journal.pbio.0060175 pmc: PMC2443188 pubmed: '18613750' title: A gene wiki for community annotation of gene function year: 2008 twitter: GeneWikiPulse uri_format: http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1 geno: contact: email: mhb120@gmail.com github: mbrush name: Matthew Brush orcid: 0000-0002-1048-5019 description: "GENO is an OWL model of genotypes, their more fundamental sequence\ \ components, and links to related biological and experimental entities. At present\ \ many parts of the model are exploratory and set to undergo refactoring. In\ \ addition, many classes and properties have GENO URIs but are place holders for\ \ classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI,\ \ etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype\ \ associations. This will support description of asserted and inferred relationships\ \ between a genotypes, phenotypes, and environments, and the evidence/provenance\ \ behind these associations. \n\nDocumentation is under development as well, and\ \ for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" download_json: http://purl.obolibrary.org/obo/geno.json download_obo: https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/develop/geno-full.obo download_owl: http://purl.obolibrary.org/obo/geno.owl example: '0000632' homepage: https://github.com/monarch-initiative/GENO-ontology/ keywords: - disease phenotype - genomics - genotype - obo - ontology license: CC-BY-4.0 mappings: aberowl: GENO biocontext: GENO bioportal: GENO fairsharing: FAIRsharing.kpbna7 obofoundry: geno ols: geno ontobee: GENO name: Genotype Ontology pattern: ^\d{7}$ preferred_prefix: GENO rdf_uri_format: http://purl.obolibrary.org/obo/GENO_$1 repository: https://github.com/monarch-initiative/GENO-ontology uri_format: http://purl.obolibrary.org/obo/GENO_$1 version: '2023-10-08' genpept: description: The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank. example: CAA71118.1 homepage: https://www.ncbi.nlm.nih.gov/protein mappings: biocontext: GENPEPT miriam: genpept n2t: genpept name: GenPept pattern: ^\w{3}\d{5}(\.\d+)?$ preferred_prefix: genpept uri_format: https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept genprop: description: Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome. example: GenProp0699 homepage: https://www.ebi.ac.uk/interpro/genomeproperties/ keywords: - classification - genome mappings: biocontext: GENPROP miriam: genprop n2t: genprop prefixcommons: jcvi.genprop name: Genome Properties owners: - name: European Bioinformatics Institute partnered: false ror: 02catss52 pattern: ^GenProp\d+$ preferred_prefix: genprop providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/jcvi.genprop:$1 uri_format: https://www.ebi.ac.uk/interpro/genomeproperties/#$1 geo: banana_peel: _ contact: email: barrett@ncbi.nlm.nih.gov name: Tanya Barrett orcid: 0000-0002-9448-8064 description: The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval. example: GDS1234 homepage: https://www.ncbi.nlm.nih.gov/geo/ keywords: - comparative genomics - epigenomics - gene expression - genome - genomics - life science - omics - phenomics - transcriptomics mappings: cellosaurus: GEO edam: '1147' fairsharing: FAIRsharing.5hc8vt go: GEO integbio: nbdc00080 miriam: geo n2t: geo prefixcommons: geo re3data: r3d100010283 name: NCBI Gene Expression Omnibus pattern: ^G(PL|SM|SE|DS)\d+$ preferred_prefix: geo providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/geo:$1 publications: - doi: 10.1093/nar/gks1193 pmc: PMC3531084 pubmed: '23193258' title: 'NCBI GEO: archive for functional genomics data sets--update' year: 2012 - doi: 10.1038/nbt1206-1471 pmc: PMC2270403 pubmed: '17160034' title: NCBI GEO standards and services for microarray data year: 2006 - doi: 10.1093/nar/30.1.207 pmc: PMC99122 pubmed: '11752295' title: 'Gene Expression Omnibus: NCBI gene expression and hybridization array data repository' year: 2002 - doi: 10.1038/35001676 pubmed: '10693778' title: One-stop shop for microarray data year: 2000 - doi: 10.5281/zenodo.5706412 title: 'MINSEQE: Minimum Information about a high-throughput Nucleotide SeQuencing Experiment - a proposal for standards in functional genomic data reporting' year: 2012 uri_format: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1 geogeo: banana: GEO banana_peel: _ contact: email: hoganwr@gmail.com github: hoganwr name: Bill Hogan orcid: 0000-0002-9881-1017 description: An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in "The US declared war on Germany" vs. the US in "The plane entered US airspace". download_owl: http://purl.obolibrary.org/obo/geo.owl example: '000000021' homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki keywords: - geographical location - human geography - obo - ontology - physical geography license: CC-BY-4.0 mappings: aberowl: GEO biocontext: GEO bioportal: GEO fairsharing: FAIRsharing.27rndz miriam: geogeo obofoundry: geo ols: geo ontobee: GEO name: Geographical Entity Ontology namespace_in_lui: true pattern: ^\d{9}$ preferred_prefix: GEOGEO rdf_uri_format: http://purl.obolibrary.org/obo/GEO_$1 repository: https://github.com/ufbmi/geographical-entity-ontology uri_format: http://purl.obolibrary.org/obo/GEO_$1 version: '2016-03-26' geonames: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge. example: '3532759' homepage: https://www.geonames.org keywords: - geographical location - geography - geoinformatics license: CC-BY-4.0 mappings: fairsharing: FAIRsharing.6dba71 re3data: r3d100010245 name: GeoNames pattern: ^\d+$ preferred_prefix: geonames synonyms: - Geomames - Geonamaes uri_format: https://www.geonames.org/$1 geonames.feature: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes. example: ADM1 homepage: https://www.geonames.org/export/codes.html license: CC-BY-4.0 name: GeoNames Feature Code preferred_prefix: geonames.feature uri_format: https://www.geonames.org/recent-changes/featurecode/$1/ gexo: contact: email: kuiper@bio.ntnu.no github: makuintnu name: Martin Kuiper orcid: 0000-0002-1171-9876 description: Gene Expression Ontology download_obo: https://www.bio.ntnu.no/ontology/GeXO/gexo.obo download_owl: https://www.bio.ntnu.no/ontology/GeXO/gexo.owl download_rdf: http://www.bio.ntnu.no/ontology/GeXO/gexo.rdf homepage: http://www.semantic-systems-biology.org/apo keywords: - expression data - gene expression - life science - ontology mappings: aberowl: GEXO bioportal: GEXO fairsharing: FAIRsharing.3e0sn4 ols: gexo name: Gene Expression Ontology no_own_terms: true preferred_prefix: gexo publications: - doi: 10.1186/s12859-014-0386-y pmc: PMC4279962 pubmed: '25490885' title: Finding gene regulatory network candidates using the gene expression knowledge base year: 2014 gfo: contact: email: heinrich.herre@imise.uni-leipzig.de name: Heinrich Herre contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The General Formal Ontology is a top-level ontology for conceptual modeling, which is being constantly further developed by Onto-Med. It includes elaborations of categories like objects, processes, time and space, properties, relations, roles, functions, facts, and situations. Moreover, we are working on an integration with the notion of levels of reality in order to more appropriately capture entities in the material, mental, and social areas. download_owl: http://www.onto-med.de/ontologies/gfo.owl example: projects_to homepage: https://www.onto-med.de/ontologies/gfo keywords: - biomedical science - life science - modeling and simulation - ontology mappings: aberowl: GFO bioportal: GFO fairsharing: FAIRsharing.175hsz name: General Formal Ontology preferred_prefix: gfo uri_format: http://www.onto-med.de/ontologies/gfo.owl#$1 ghr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA). example: saddan homepage: https://medlineplus.gov/genetics/condition name: Genetics Home Reference preferred_prefix: ghr uri_format: https://medlineplus.gov/genetics/condition/$1 giardiadb: contact: email: oharb@upenn.edu github: ramobrah name: Omar S. Harb orcid: 0000-0003-4446-6200 description: GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: GL50803_102438 homepage: https://giardiadb.org/giardiadb/ keywords: - eukaryotic - genome - genomics mappings: biocontext: GIARDIADB fairsharing: FAIRsharing.e7skwg integbio: nbdc01782 miriam: giardiadb n2t: giardiadb prefixcommons: giardiadb re3data: r3d100012458 name: GiardiaDB pattern: ^\w+$ preferred_prefix: giardiadb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/giardiadb:$1 publications: - doi: 10.1093/nar/gkn631 pmc: PMC2686445 pubmed: '18824479' title: 'GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis' year: 2008 twitter: EuPathDB uri_format: https://giardiadb.org/giardiadb/app/record/gene/$1 github: description: GitHub is an online host of Git source code repositories. example: biopragmatics/bioregistry example_extras: - biopragmatics - cthoyt homepage: https://github.com/ keywords: - knowledge and information systems - software engineering - subject agnostic mappings: fairsharing: FAIRsharing.c55d5e miriam: github re3data: r3d100010375 wikidata: P2037 name: GitHub username pattern: ^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$ preferred_prefix: github repository: https://services.github.com/ uri_format: https://github.com/$1 github.issue: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An issue in any public repository on GitHub. example: biopragmatics/bioregistry/424 homepage: https://github.com/ keywords: - knowledge and information systems - project management - software engineering - version control name: GitHub Issue preferred_prefix: github.issue uri_format: https://bioregistry.io/resolve/github/issue/$1 github.pull: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A pull request in any public repository on GitHub. example: biopragmatics/bioregistry/416 homepage: https://github.com/ keywords: - knowledge and information systems - project management - software engineering - version control name: GitHub Pull Request preferred_prefix: github.pull uri_format: https://bioregistry.io/resolve/github/pull/$1 gitlab: description: GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance. With GitLab, every team in your organization can collaboratively plan, build, secure, and deploy software to drive business outcomes faster with complete transparency, consistency and traceability. example: morpheus.lab/morpheus homepage: https://gitlab.com/ keywords: - knowledge and information systems - software engineering - subject agnostic mappings: fairsharing: FAIRsharing.530e61 miriam: gitlab name: GitLab pattern: ^.*/.*$ preferred_prefix: gitlab twitter: gitlab uri_format: https://gitlab.com/$1 glida.gpcr: description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors. example: ACM1_HUMAN homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ mappings: biocontext: GLIDA.GPCR miriam: glida.gpcr n2t: glida.gpcr name: GLIDA GPCR pattern: ^[A-Z-_0-9]+$ 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 glottolog: appears_in: - gsso contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: ' Comprehensive reference information for the world''s languages, especially the lesser known languages. [from homepage]' example: nort3314 github_request_issue: 1310 homepage: https://glottolog.org license: CC-BY-4.0 name: Glottolog preferred_prefix: glottolog uri_format: https://glottolog.org/resource/languoid/id/$1 glycoepitope: description: GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes. example: EP0311 homepage: https://www.glycoepitope.jp/epitopes/ mappings: biocontext: GLYCOEPITOPE integbio: nbdc00087 miriam: glycoepitope n2t: glycoepitope name: GlycoEpitope pattern: ^EP\d{4}$ preferred_prefix: glycoepitope uri_format: https://www.glycoepitope.jp/epitopes/$1 glycomapsdb: description: A database of GlycoMaps containing 2585 conformational maps. example: '6819' homepage: http://www.glycosciences.de/modeling/glycomapsdb/ keywords: - small molecule mappings: prefixcommons: glycomapsdb name: GlycoMapsDB preferred_prefix: glycomapsdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/glycomapsdb:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=$1 glycomedb: contact: email: rr@uga.edu github: ReneRanzinger name: René Ranzinger orcid: 0000-0003-3147-448X description: GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links. example: G77500AY has_canonical: glytoucan homepage: https://glytoucan.org/ keywords: - life science - molecules - small molecules - structure mappings: biocontext: GLYCOMEDB edam: '2664' fairsharing: FAIRsharing.k5k0yh integbio: nbdc00899 miriam: glycomedb n2t: glycomedb prefixcommons: glycomedb re3data: r3d100011527 name: GlycomeDB pattern: ^\w+$ preferred_prefix: glycomedb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/glycomedb:$1 publications: - doi: 10.1093/nar/gkq1014 pmc: PMC3013643 pubmed: '21045056' title: GlycomeDB--a unified database for carbohydrate structures year: 2010 - doi: 10.1093/glycob/cwp137 pubmed: '19759275' title: 'Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences' year: 2009 - doi: 10.1186/1471-2105-9-384 pmc: PMC2567997 pubmed: '18803830' title: GlycomeDB - integration of open-access carbohydrate structure databases year: 2008 uri_format: https://glytoucan.org/Structures/Glycans/$1 glyconavi: contact: email: issaku@noguchi.or.jp name: Issaku Yamada orcid: 0000-0001-9504-189X description: GlycoNAVI is a website for carbohydrate research. It consists of the "GlycoNAVI Database" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the "GlycoNAVI tools" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools. example: GN_G03681DA example_extras: - GN_GlyTouCan_G03681DA homepage: https://www.noguchi.or.jp/ keywords: - chemistry - glycomics - life science - organic chemistry mappings: fairsharing: FAIRsharing.wvp1t7 integbio: nbdc01174 miriam: glyconavi name: GlycoNAVI pattern: ^GN_[A-Za-z0-9_:]+$ preferred_prefix: glyconavi repository: https://glyconavi.github.io/doc/ uri_format: https://glyconavi.org/hub/?id=$1 glycopost: description: GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their "raw/processed" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines. example: GPST000024 homepage: https://glycopost.glycosmos.org keywords: - glycomics - life science mappings: fairsharing: FAIRsharing.2y1KMt miriam: glycopost name: GlycoPOST pattern: ^GPST[0-9]{6}$ preferred_prefix: glycopost uri_format: https://glycopost.glycosmos.org/entry/$1 glycosciencesdb: contact: email: thomas@luetteke-online.de github: glycosciences name: Thomas Lütteke orcid: 0000-0002-7140-9933 contributor: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: A database to support glycobiology and glycomics research. Its main focus is on 3D structures, including 3D structure models as well as references to PDB entries that feature carbohydrates. example: '1' github_request_issue: 537 homepage: http://www.glycosciences.de/database/ name: Glycosciences.DB pattern: ^\d+$ preferred_prefix: glycosciencesdb publications: - doi: 10.1093/nar/gky994 pmc: PMC6323918 pubmed: '30357361' title: 'Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update)' year: 2019 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - glycosciences.db uri_format: http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=$1 glytoucan: contact: email: rr@uga.edu github: ReneRanzinger name: René Ranzinger orcid: 0000-0003-3147-448X description: GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data. example: G00054MO homepage: https://glytoucan.org keywords: - glycomics - structural biology mappings: biocontext: GLYTOUCAN fairsharing: FAIRsharing.5Pze7l integbio: nbdc02434 miriam: glytoucan n2t: glytoucan re3data: r3d100012388 togoid: Glytoucan uniprot: DB-0254 name: GlyTouCan pattern: ^G[0-9]{5}[A-Z]{2}$ preferred_prefix: glytoucan providers: - code: glygen description: 'GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. ' homepage: https://www.glygen.org/ name: GlyGen uri_format: https://glygen.org/glycan/$1 publications: - doi: 10.1093/glycob/cwz080 pubmed: '31616925' - doi: 10.1093/glycob/cwx066 pmc: PMC5881658 pubmed: '28922742' title: 'GlyTouCan: an accessible glycan structure repository' year: 2017 - doi: 10.1093/nar/gkv1041 pmc: PMC4702779 pubmed: '26476458' title: GlyTouCan 1.0--The international glycan structure repository year: 2015 synonyms: - glygen twitter: glytoucan uri_format: https://glytoucan.org/Structures/Glycans/$1 gmd: contact: email: kopka@mpimp-golm.mpg.de name: Joachim Kopka orcid: 0000-0001-9675-4883 description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena. example: 68513255-fc44-4041-bc4b-4fd2fae7541d homepage: http://gmd.mpimp-golm.mpg.de/ keywords: - life science - metabolomics mappings: biocontext: GMD fairsharing: FAIRsharing.jykmkw miriam: gmd n2t: gmd re3data: r3d100011046 name: Golm Metabolome Database pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ preferred_prefix: gmd publications: - doi: 10.1007/s11306-010-0198-7 pmc: PMC2874469 pubmed: '20526350' title: Decision tree supported substructure prediction of metabolites from GC-MS profiles year: 2010 - doi: doi:10.1007/s11306-010-0198-7 title: Decision tree supported substructure prediction of metabolites from GC-MS profiles uri_format: http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx gmd.analyte: description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes. example: 4f0fa9b6-514f-4ff4-98cc-0009bc08eb80 homepage: http://gmd.mpimp-golm.mpg.de/ mappings: biocontext: GMD.ANALYTE miriam: gmd.analyte n2t: gmd.analyte name: Golm Metabolome Database Analyte pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ preferred_prefix: gmd.analyte uri_format: http://gmd.mpimp-golm.mpg.de/Analytes/$1 gmd.gcms: description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra. example: 53d583d8-40c6-40e1-9296-23f821cd77a5 homepage: http://gmd.mpimp-golm.mpg.de/ mappings: biocontext: GMD.GCMS miriam: gmd.gcms n2t: gmd.gcms name: Golm Metabolome Database GC-MS spectra pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ preferred_prefix: gmd.gcms uri_format: http://gmd.mpimp-golm.mpg.de/Spectrums/$1 gmd.profile: description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues. example: 10b38aaf-b977-4950-85b8-f4775f66658d homepage: http://gmd.mpimp-golm.mpg.de/ mappings: biocontext: GMD.PROFILE miriam: gmd.profile n2t: gmd.profile name: Golm Metabolome Database Profile pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ preferred_prefix: gmd.profile uri_format: http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1 gmd.ref: description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances. example: 8cf84adb-b4db-4807-ac98-0004247c35df homepage: http://gmd.mpimp-golm.mpg.de/ mappings: biocontext: GMD.REF miriam: gmd.ref n2t: gmd.ref name: Golm Metabolome Database Reference Substance pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ preferred_prefix: gmd.ref uri_format: http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1 gmelin: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s. example: '1466' homepage: https://link.springer.com/bookseries/562 mappings: edam: '1004' wikidata: P1578 name: Gmelins Handbuch der anorganischen Chemie pattern: ^[1-9][0-9]{3,6}$ preferred_prefix: gmelin proprietary: true references: - https://en.wikipedia.org/wiki/Gmelin_database gnd: description: The Gemeinsame Normdatei (Integrated Authority File) or GND is an international authority file for person names, subject headings and corporate bodies. It is used mainly for documentation in libraries and increasingly also by archives and museums. The GND is managed by the German National Library in cooperation with various regional library networks in German-speaking Europe and other partners. example: '117145750' homepage: https://lobid.org/ keywords: - culture - knowledge and information systems - publication - social science mappings: bartoc: '430' fairsharing: FAIRsharing.8337e2 miriam: gnd wikidata: P227 name: GND ID pattern: ^[0-9X\-]+$ preferred_prefix: gnd rdf_uri_format: https://d-nb.info/gnd/$1 twitter: gndnet uri_format: https://lobid.org/gnd/$1 gno: contact: email: nje5@georgetown.edu github: edwardsnj name: Nathan Edwards orcid: 0000-0001-5168-3196 description: An ontology for glycans based on GlyTouCan, but organized by subsumption. download_json: http://purl.obolibrary.org/obo/gno.json download_obo: http://purl.obolibrary.org/obo/gno.obo download_owl: http://purl.obolibrary.org/obo/gno.owl example: '10004892' example_extras: - G99373GG homepage: https://gnome.glyomics.org/ keywords: - obo - ontology license: CC-BY-4.0 mappings: aberowl: GNO bioportal: GNO obofoundry: gno ols: gno ontobee: GNO name: Glycan Naming and Subsumption Ontology pattern: ^(\d{8}|(\w+\d+\w+))$ preferred_prefix: GNO providers: - code: gno.composition description: GNOme composition browser homepage: https://gnome.glyomics.org/CompositionBrowser.html name: GNOme Composition Browser uri_format: https://gnome.glyomics.org/CompositionBrowser.html?focus=$1 - code: gno.structure description: GNOme structure browser homepage: https://gnome.glyomics.org/StructureBrowser.html name: GNOme Structure Viewer uri_format: https://gnome.glyomics.org/StructureBrowser.html?focus=$1 publications: - doi: 10.5281/zenodo.6678278 title: GNOme - Glycan Naming and Subsumption Ontology year: 2021 rdf_uri_format: http://purl.obolibrary.org/obo/GNO_$1 repository: https://github.com/glygen-glycan-data/GNOme synonyms: - gnome uri_format: http://purl.obolibrary.org/obo/GNO_$1 version: '2025-01-28' gnomad: contact: email: hrehm@mgh.harvard.edu github: heidirehm name: Heidi L. Rehm orcid: 0000-0002-6025-0015 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community (from https://gnomad.broadinstitute.org). example: 1-55516888-G-GA example_extras: - DUP_2_5708 - M-8602-T-C github_request_issue: 695 homepage: https://gnomad.broadinstitute.org license: CC0-1.0 mappings: integbio: nbdc02561 name: Genome Aggregation Database preferred_prefix: gnomad publications: - doi: 10.1038/s41586-020-2308-7 pmc: PMC7334197 pubmed: '32461654' title: The mutational constraint spectrum quantified from variation in 141,456 humans year: 2020 - doi: 10.1038/s41586-020-2287-8 pmc: PMC7334194 pubmed: '32461652' title: A structural variation reference for medical and population genetics year: 2020 uri_format: https://gnomad.broadinstitute.org/variant/$1 gnpis: contact: email: urgi-contact@versailles.inra.fr name: URGI Contact orcid: 0000-0003-3001-4908 description: GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. example: AY109603 homepage: https://urgi.versailles.inra.fr/gnpis/ keywords: - life science mappings: biocontext: GNPIS fairsharing: FAIRsharing.dw22y3 miriam: gnpis n2t: gnpis re3data: r3d100012647 name: GnpIS pattern: ^[A-Za-z0-9]+$ preferred_prefix: gnpis publications: - doi: 10.1093/database/bat058 pmc: PMC3746681 pubmed: '23959375' title: 'GnpIS: an information system to integrate genetic and genomic data from plants and fungi' year: 2013 uri_format: https://urgi.versailles.inra.fr/gnpis/#result/term=$1 gnps.task: contact: email: mingxun.wang@cs.ucr.edu github: mwang87 name: Mingxun Wang orcid: 0000-0001-7647-6097 contributor: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS) example: 4b848c342a4f4abc871bdf8a09a60807 github_request_issue: 833 homepage: https://gnps.ucsd.edu/ name: Global Natural Products Social Molecular Networking Task pattern: ^[a-f0-9]+$ preferred_prefix: gnps.task reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=$1 go: appears_in: - agro - chiro - cl - ecocore - ecto - envo - maxo - pcl - pco - planp - uberon - xpo - zp banana: GO contact: email: suzia@stanford.edu github: suzialeksander name: Suzi Aleksander orcid: 0000-0001-6787-2901 contributor_extras: - email: jmcl@ebi.ac.uk github: jamesamcl name: James Alastair McLaughlin orcid: 0000-0002-8361-2795 depends_on: - cl - ncbitaxon - ro - uberon description: The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. download_json: http://purl.obolibrary.org/obo/go.json download_obo: http://purl.obolibrary.org/obo/go.obo download_owl: http://purl.obolibrary.org/obo/go.owl example: '0032571' homepage: http://geneontology.org/ keywords: - annotation - biocuration - biological process - cellular component - data model - expression data - gene - gene functional annotation - gene ontology enrichment - knowledge representation - life science - molecular function - obo - ontology - protein - sequence annotation - transcript license: CC-BY-4.0 logo: https://obofoundry.org/images/go_logo.png mappings: aberowl: GO agroportal: GO bartoc: '572' biocontext: GO bioportal: GO edam: '1176' fairsharing: FAIRsharing.6xq0ee go: GO hl7: 2.16.840.1.113883.6.128 integbio: nbdc00074 miriam: go n2t: go ncbi: GO obofoundry: go ols: go ontobee: GO pathguide: '272' prefixcommons: go re3data: r3d100014165 togoid: Go uniprot: DB-0037 wikidata: P686 mastodon: go@genomic.social name: Gene Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: GO providers: - code: CURATOR_REVIEW description: GO Browser homepage: http://www.informatics.jax.org/searches/GO_form.shtml name: GO Browser uri_format: http://www.informatics.jax.org/searches/GO.cgi?id=GO:$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/go:$1 - code: go_site description: A non-PURL link through the GO site homepage: http://www.geneontology.org name: GO Site Link uri_format: http://www.geneontology.org/GO:$1 - code: jax description: The JAX endpoint for exploring GO homepage: http://www.informatics.jax.org name: Jackson Laboratories uri_format: http://www.informatics.jax.org/vocab/gene_ontology/GO:$1 - code: miriam_obo_legacy description: An old URI style for MIRIAM + GO homepage: https://identifiers.org/ name: MIRIAM OBO Legacy uri_format: http://identifiers.org/obo.go/GO:$1 - code: nextprot description: The neXtProt endpoint for exploring GO homepage: https://www.nextprot.org/ name: neXtProt GO Browser uri_format: https://www.nextprot.org/term/GO:$1 - code: pantherdb description: GO Browser in PantherDB homepage: http://www.pantherdb.org/panther name: PatherDB uri_format: http://www.pantherdb.org/panther/category.do?categoryAcc=GO:$1 - code: quickgo description: Gene Ontology browser from the EBI homepage: https://www.ebi.ac.uk/QuickGO/ name: QuickGO uri_format: https://www.ebi.ac.uk/QuickGO/term/GO:$1 - code: quickgo.legacy description: QuickGO (Gene Ontology browser) homepage: https://www.ebi.ac.uk/QuickGO/ name: QuickGO (Legacy URL) uri_format: https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:$1 publications: - doi: 10.1093/nar/gkaa1113 pmc: PMC7779012 pubmed: '33290552' title: 'The Gene Ontology resource: enriching a GOld mine' year: 2021 - doi: 10.1093/nar/gky1055 pmc: PMC6323945 pubmed: '30395331' title: 'The Gene Ontology Resource: 20 years and still GOing strong' year: 2019 - doi: 10.1093/nar/gku1179 pmc: PMC4383973 pubmed: '25428369' title: 'Gene Ontology Consortium: going forward' year: 2014 - doi: 10.1186/1471-2164-14-513 pmc: PMC3733925 pubmed: '23895341' title: 'Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology' year: 2013 - doi: 10.1093/nar/gks1050 pmc: PMC3531070 pubmed: '23161678' title: Gene Ontology annotations and resources year: 2012 - doi: 10.1093/nar/gkr1028 pmc: PMC3245151 pubmed: '22102568' title: 'The Gene Ontology: enhancements for 2011' year: 2011 - doi: 10.1093/nar/gkp1018 pmc: PMC2808930 pubmed: '19920128' title: 'The Gene Ontology in 2010: extensions and refinements' year: 2009 - doi: 10.1093/nar/gkh036 pmc: PMC308770 pubmed: '14681407' title: The Gene Ontology (GO) database and informatics resource year: 2004 - doi: 10.1038/75556 pmc: PMC3037419 pubmed: '10802651' title: 'Gene ontology: tool for the unification of biology. The Gene Ontology Consortium' year: 2000 rdf_uri_format: http://purl.obolibrary.org/obo/GO_$1 repository: https://github.com/geneontology/go-ontology synonyms: - gobp - gobpid - gocc - goccid - gomf - gomfid twitter: news4go uri_format: http://purl.obolibrary.org/obo/GO_$1 version: '2024-11-03' go.gpi: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 description: This describes the metadata schema for the Gene Product Information (GPI) files in the Gene Ontology, i.e., the local unique identifiers in this identifier space refer to the columns in GPI files. example: db-object-id homepage: http://geneontology.org/docs/gene-product-information-gpi-format/#db-object-id mappings: biolink: gpi name: Gene Product Information Schema part_of: go preferred_prefix: go.gpi uri_format: http://geneontology.org/docs/gene-product-information-gpi-format/#$1 go.model: description: GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform. example: 5fce9b7300001250 homepage: https://geneontology.org/go-cam mappings: go: gomodel name: Gene Ontology Causal Activity Model part_of: go preferred_prefix: go.model providers: - code: legacy description: This was the old URI for the GO CAM editor homepage: https://model.geneontology.org name: Legacy uri_format: http://noctua.geneontology.org/editor/graph/gomodel:$1 uri_format: https://model.geneontology.org/$1 go.ref: banana: GO_REF description: The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of "GO content" meetings at which substantial changes in the ontologies are discussed and made. example: '0000041' homepage: http://www.geneontology.org/cgi-bin/references.cgi mappings: biocontext: GO_REF go: GO_REF miriam: go_ref n2t: go.ref name: Gene Ontology Database references namespace_in_lui: true part_of: go pattern: ^\d{7}$ preferred_prefix: go.ref providers: - code: legacy description: The README file on GO's github repository has been replaced with a structured YAML file, so this URl is no longer available. homepage: https://github.com/geneontology/go-site/blob/master/metadata/gorefs.yaml name: Legacy uri_format: https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md#goref$1 uri_format: https://geneontology.org/GO_REF/$1 go.resource: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A database-specific registry supporting curation in the Gene Ontology example: CHEBI homepage: https://raw.githubusercontent.com/geneontology/go-site/master/metadata/db-xrefs.yaml name: Gene Ontology Registry part_of: go preferred_prefix: go.resource uri_format: https://bioregistry.io/metaregistry/go/$1 go.rule: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: GO Rules are a way of documenting the set of filters and reports that should apply to GAF annotation data. Some rules are expressed as SPARQL on a triplestore, some are code in the GAF parsing software, ontobio. example: '0000004' homepage: https://github.com/geneontology/go-site/tree/master/metadata/rules name: Gene Ontology Rules part_of: go pattern: ^\d{7}$ preferred_prefix: GORULE uri_format: https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-$1.md goa: contact: email: r.huntley@ucl.ac.uk github: rachhuntley name: Rachael P. Huntley orcid: 0000-0001-6718-3559 description: The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. example: P12345 homepage: https://www.ebi.ac.uk/GOA/ keywords: - biology - gene - life science - ontology - protein mappings: biocontext: GOA fairsharing: FAIRsharing.7zffgc integbio: nbdc00468 miriam: goa n2t: goa ncbi: GOA prefixcommons: goa name: Gene Ontology Annotation Database part_of: go pattern: ^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$ preferred_prefix: goa providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/goa:$1 provides: uniprot publications: - doi: 10.1093/nar/gku1113 pmc: PMC4383930 pubmed: '25378336' title: 'The GOA database: gene Ontology annotation updates for 2015' year: 2014 - doi: 10.1093/nar/gkn803 pmc: PMC2686469 pubmed: '18957448' title: The GOA database in 2009--an integrated Gene Ontology Annotation resource year: 2008 uri_format: https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1 goche: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Represent chemical entities having particular CHEBI roles download_owl: https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl example: '25512' homepage: https://github.com/geneontology/go-ontology keywords: - ontology name: GO Chemicals part_of: go pattern: ^\d+$ preferred_prefix: GOCHE rdf_uri_format: http://purl.obolibrary.org/obo/GOCHE_$1 references: - https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638472847049400 - https://github.com/geneontology/go-ontology/issues/19535 repository: https://github.com/geneontology/go-ontology synonyms: - go.chebi - go.chemical - go.chemicals uri_format: https://biopragmatics.github.io/providers/goche/$1 goeco: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported. example: IPI homepage: http://geneontology.org/docs/guide-go-evidence-codes/ name: GO Evidence Code part_of: go preferred_prefix: goeco gold: contact: email: tbreddy@lbl.gov github: TBKReddy name: TBK Reddy orcid: 0000-0002-0871-5567 description: 'The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.' example: Gs0000008 homepage: https://gold.jgi.doe.gov/ keywords: - genome - genomics - metabolomics - metagenomics - ontology and terminology - phylogenetics mappings: fairsharing: FAIRsharing.5q1p14 integbio: nbdc00483 miriam: gold prefixcommons: gold re3data: r3d100010808 name: Genomes Online Database pattern: ^[A-Z][a-z][0-9]+$ preferred_prefix: gold providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/gold:$1 publications: - doi: 10.1093/nar/gkae1000 pubmed: '39498478' title: 'Genomes OnLine Database (GOLD) v.10: new features and updates' year: 2024 - doi: 10.1093/nar/gkaa983 pmc: PMC7778979 pubmed: '33152092' title: 'Genomes OnLine Database (GOLD) v.8: overview and updates' year: 2021 - doi: 10.1093/nar/gky977 pmc: PMC6323969 pubmed: '30357420' title: 'Genomes OnLine database (GOLD) v.7: updates and new features' year: 2019 - doi: 10.1093/nar/gkp848 pmc: PMC2808860 pubmed: '19914934' title: 'The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata' year: 2009 - doi: 10.1093/nar/gkm884 pmc: PMC2238992 pubmed: '17981842' title: 'The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata' year: 2007 - doi: 10.1093/nar/29.1.126 pmc: PMC29859 pubmed: '11125068' title: 'Genomes OnLine Database (GOLD): a monitor of genome projects world-wide' year: 2001 - doi: 10.1093/bioinformatics/15.9.773 pubmed: '10498782' title: 'Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide' year: 1999 - doi: '11125068' title: 'Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.' uri_format: https://gold.jgi.doe.gov/resolver?id=$1 gold.genome: description: '- DEPRECATION NOTE - Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. The GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes.' example: Gi07796 homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi mappings: biocontext: GOLD.GENOME miriam: gold.genome n2t: gold.genome name: GOLD genome pattern: ^(Gi|Gc)\d+$ preferred_prefix: gold.genome uri_format: http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1 gold.meta: description: "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has\ \ been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold,\ \ and this namespace is kept here for support to already existing citations, new\ \ ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes OnLine\ \ Database)is a resource for centralized monitoring of genome and metagenome projects\ \ worldwide. It stores information on complete and ongoing projects, along with\ \ their associated metadata. This collection references metadata associated with\ \ samples." example: Gm00047 has_canonical: gold homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi mappings: biocontext: GOLD.META miriam: gold.meta n2t: gold.meta name: GOLD metadata pattern: ^Gm\d+$ preferred_prefix: gold.meta uri_format: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1 goldbook: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The Compendium is popularly referred to as the "Gold Book", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC "Colour Books" on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books. Terminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC''s Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry.' example: G02681 homepage: https://goldbook.iupac.org license: CC BY 4.0-NC-ND mappings: bartoc: '1884' wikidata: P4732 name: IUPAC Gold Book Compendium of Chemical Terminology pattern: ^[A-Z]{1,2}\d{5}$ preferred_prefix: goldbook providers: - code: goldbook.html description: This appears in REX homepage: http://goldbook.iupac.org name: GoldBook direct uri_format: http://goldbook.iupac.org/$1.html rdf_uri_format: http://dx.doi.org/10.1351/goldbook.$1 uri_format: https://goldbook.iupac.org/terms/view/$1 google.book: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Search the world's most comprehensive index of full-text books. example: qafeQTWIWmcC github_request_issue: 511 homepage: https://books.google.com mappings: wikidata: P675 name: Google Books preferred_prefix: google.book providers: - code: alt1 description: Alternate URL 1 homepage: https://books.google.com name: Alternate URL 1 uri_format: https://books.google.com/books/?id=$1 uri_format: https://books.google.com/books?id=$1 google.patent: contributor_extras: - email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date. example: US4145692 example_extras: - USRE38117E1 homepage: https://www.google.com/patents/ mappings: biocontext: GOOGLE.PATENT cellosaurus: Patent miriam: google.patent n2t: google.patent name: Google Patents pattern: ^[A-Z]{2,4}\d+([A-Z])?([0-9])?$ preferred_prefix: google.patent synonyms: - patent uri_format: https://www.google.com/patents/$1 google.scholar: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.' example: PjrpzUIAAAAJ homepage: https://scholar.google.com/ mappings: biolink: GSID wikidata: P1960 name: Google Scholar Researcher pattern: ^[-_0-9A-Za-z]{12}$ preferred_prefix: google.scholar uri_format: https://scholar.google.com/citations?user=$1 gorel: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO. download_owl: ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl example: '0002005' homepage: http://geneontology.org/docs/ontology-relations/ keywords: - ontology mappings: biolink: GOREL go: GOREL name: GO Relations pattern: ^\d{7}$ preferred_prefix: gorel providers: - code: obo.legacy description: Legacy OBO PURLs homepage: http://purl.obolibrary.org/obo/gorel.owl name: Legacy OBO uri_format: http://purl.obolibrary.org/obo/GOREL_$1 uri_format: http://purl.obolibrary.org/obo/GOREL_$1 gpcrdb: contact: email: david.gloriam@sund.ku.dk name: David Gloriam orcid: 0000-0002-4299-7561 description: The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models. example: RL3R1_HUMAN homepage: http://www.gpcrdb.org/ keywords: - life science - molecular biology - protein - small molecule mappings: biocontext: GPCRDB fairsharing: FAIRsharing.e4n3an integbio: nbdc00484 miriam: gpcrdb n2t: gpcrdb prefixcommons: gpcrdb uniprot: DB-0038 name: G protein-coupled receptor database pattern: ^\w+$ preferred_prefix: gpcrdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/gpcrdb:$1 publications: - doi: 10.1093/nar/26.1.275 pmc: PMC147194 pubmed: '9399852' title: 'GPCRDB: an information system for G protein-coupled receptors' year: 1998 - doi: 10.1093/nar/gkae1065 pubmed: '39558158' title: 'GPCRdb in 2025: adding odorant receptors, data mapper, structure similarity search and models of physiological ligand complexes' year: 2024 - doi: 10.1093/nar/gkaa1080 pmc: PMC7778909 pubmed: '33270898' title: 'GPCRdb in 2021: integrating GPCR sequence, structure and function' year: 2021 - doi: 10.1093/nar/gkx1109 pmc: PMC5753179 pubmed: '29155946' title: 'GPCRdb in 2018: adding GPCR structure models and ligands' year: 2018 - doi: 10.1111/bph.13509 pmc: PMC4919580 pubmed: '27155948' title: 'GPCRdb: the G protein-coupled receptor database - an introduction' year: 2016 - doi: 10.1093/nar/gkv1178 pmc: PMC4702843 pubmed: '26582914' title: 'GPCRdb: an information system for G protein-coupled receptors' year: 2015 - doi: 10.1093/nar/gkt1255 pmc: PMC3965068 pubmed: '24304901' title: 'GPCRDB: an information system for G protein-coupled receptors' year: 2013 - doi: 10.1093/nar/gkq1009 pmc: PMC3013641 pubmed: '21045054' title: 'GPCRDB: information system for G protein-coupled receptors' year: 2010 - doi: 10.1093/nar/gkg103 pmc: PMC165550 pubmed: '12520006' title: GPCRDB information system for G protein-coupled receptors year: 2003 - doi: 10.1093/nar/29.1.346 pmc: PMC29816 pubmed: '11125133' title: 'Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems' year: 2001 twitter: gpcrdb uri_format: https://gpcrdb.org/protein/$1 gpcrnava: description: The GPCR NaVa database describes sequence variants within the family of human G Protein-Coupled Receptors (GPCRs). GPCRs regulate many physiological functions and are the targets for most of today's medicines. The acronym NaVa stands for Natural Variant, which means any (non-artificial) variant that occurs in humans. example: '1150' homepage: http://nava.liacs.nl/ keywords: - pathway - protein mappings: prefixcommons: gnd name: GPCR Natural Variants database preferred_prefix: gpcrnava providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/gnd:$1 uri_format: http://nava.liacs.nl/cgi-bin/nava.py?id=$1 gpmdb: contact: email: rbeavis@thegpm.org github: RonBeavis name: Ronald C. Beavis (Ron Beavis) orcid: 0000-0001-5782-1000 description: The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. example: GPM32310002988 homepage: http://gpmdb.thegpm.org/ keywords: - bioinformatics - proteomics mappings: biocontext: GPMDB fairsharing: FAIRsharing.fhcmwq miriam: gpmdb n2t: gpmdb name: Global Proteome Machine Database pattern: ^GPM\d+$ preferred_prefix: gpmdb providers: - code: omicsdi description: GPMDB through OmicsDI homepage: https://www.omicsdi.org/ name: GPMDB through OmicsDI uri_format: https://www.omicsdi.org/dataset/gpmdb/$1 publications: - doi: 10.1021/pr049882h pubmed: '15595733' title: Open source system for analyzing, validating, and storing protein identification data year: 2004 twitter: GPMDB uri_format: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1 graingenes.reference: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A database for Triticeae and Avena references. example: WGS-95-1333 homepage: http://wheat.pw.usda.gov name: GrainGenes preferred_prefix: graingenes.reference uri_format: https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1 graingenes.symbol: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A database for Triticeae and Avena gene symbols. example: 1-FEH+w3 homepage: http://wheat.pw.usda.gov name: GrainGenes preferred_prefix: graingenes.symbol uri_format: http://wheat.pw.usda.gov/report?class=gene;name=$1 gramene.gene: description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene. example: GR:0080039 homepage: http://www.gramene.org/ mappings: biocontext: GRAMENE.GENE go: GR_GENE miriam: gramene.gene n2t: gramene.gene name: Gramene Gene pattern: ^GR\:\d+$ preferred_prefix: gramene.gene synonyms: - GR_GENE uri_format: http://www.gramene.org/db/genes/search_gene?acc=$1 gramene.growthstage: banana: GRO contact: email: po-discuss@plantontology.org name: Plant Ontology Administrators deprecated: true description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene. example: '0007133' homepage: http://www.gramene.org/plant_ontology/ keywords: - anatomy - obo - ontology mappings: biocontext: GRAMENE.GROWTHSTAGE bioportal: GRO-CPGA miriam: gro n2t: gramene.growthstage obofoundry: gro prefixcommons: gramene.po name: Gramene Growth Stage Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: GRO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/gramene.po:$1 rdf_uri_format: http://purl.obolibrary.org/obo/GRO_$1 synonyms: - cpga - gro-cpga uri_format: http://www.gramene.org/db/ontology/search?id=GRO:$1 gramene.protein: description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene. example: '78073' homepage: http://www.gramene.org/ mappings: biocontext: GRAMENE.PROTEIN go: GR_PROTEIN miriam: gramene.protein n2t: gramene.protein name: Gramene protein pattern: ^\d+$ preferred_prefix: gramene.protein synonyms: - GR_PROTEIN uri_format: http://www.gramene.org/db/protein/protein_search?protein_id=$1 gramene.qtl: description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene. example: CQG5 homepage: http://www.gramene.org/ mappings: biocontext: GRAMENE.QTL go: GR_QTL miriam: gramene.qtl n2t: gramene.qtl name: Gramene QTL pattern: ^\w+$ preferred_prefix: gramene.qtl synonyms: - GR_QTL uri_format: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1 gramene.reference: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Literature references in Gramene example: '6200' homepage: http://www.gramene.org name: Gramene Reference pattern: ^\d+$ preferred_prefix: gramene.reference synonyms: - gramene.ref uri_format: http://www.gramene.org/db/literature/pub_search?ref_id=$1 gramene.taxonomy: banana: GR_tax banana_peel: ':' description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene. example: 013681 homepage: http://www.gramene.org/ mappings: biocontext: GRAMENE.TAXONOMY miriam: gramene.taxonomy n2t: gramene.taxonomy name: Gramene Taxonomy pattern: ^\d+$ preferred_prefix: gramene.taxonomy uri_format: https://archive.gramene.org/db/ontology/search?id=GR_tax:$1 grassbase: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species. example: imp10873 github_request_issue: 218 homepage: https://www.kew.org/data/grasses-syn/index.htm mappings: wikidata: P1832 name: GrassBase pattern: ^(imp|gen)\d{5}$ preferred_prefix: grassbase uri_format: https://www.kew.org/data/grasses-db/www/$1 greengenes: contact: email: GLAndersen@lbl.gov name: Gary L Andersen orcid: 0000-0002-1618-9827 description: A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. example: '100000' homepage: http://greengenes.lbl.gov/ keywords: - genetics - life science - rna mappings: biocontext: GREENGENES fairsharing: FAIRsharing.bpxgb6 integbio: nbdc01824 miriam: greengenes n2t: greengenes ncbi: Greengenes prefixcommons: greengenes re3data: r3d100010549 name: 16S rRNA gene database pattern: ^\d+$ preferred_prefix: greengenes providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/greengenes:$1 publications: - doi: 10.1128/aem.03006-05 pmc: PMC1489311 pubmed: '16820507' title: Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB year: 2006 - doi: 10.1128/AEM.03006-05 title: Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. uri_format: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1 grid: description: International coverage of the world's leading research organisations, indexing 92% of funding allocated globally. example: grid.225360.0 homepage: https://www.grid.ac/ keywords: - data management mappings: biocontext: GRID fairsharing: FAIRsharing.0pUMYW miriam: grid n2t: grid name: Global Research Identifier Database pattern: ^grid\.[0-9]+\.[a-f0-9]{1,2}$ preferred_prefix: grid twitter: grid_ac uri_format: https://www.grid.ac/institutes/$1 grin: description: GRIN provides National Genetic Resources Program (NGRP) personnel and germplasm users continuous access to databases for the maintenance of passport, characterization, evaluation, inventory, and distribution data important for the effective management and utilization of national germplasm collections. example: '159787' homepage: http://www.ars-grin.gov/ keywords: - life science mappings: fairsharing: FAIRsharing.3axym7 prefixcommons: grin name: Germplasm Resources Information Network preferred_prefix: grin providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/grin:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=$1 grin.taxonomy: description: GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact. example: '19333' homepage: http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en mappings: biocontext: GRIN.TAXONOMY go: GRIN miriam: grin.taxonomy n2t: grin.taxonomy ncbi: GRIN wikidata: P1421 name: GRIN URL pattern: ^\d+$ preferred_prefix: grin.taxonomy uri_format: http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1 gro: contact: email: vlee@ebi.ac.uk name: Vivian Lee deprecated: true description: The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. download_owl: http://aber-owl.net/media/ontologies/GRO/5/gro.owl example: Lipid homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html keywords: - ontology mappings: aberowl: GRO bioportal: GRO name: Gene Regulation Ontology preferred_prefix: gro uri_format: http://www.bootstrep.eu/ontology/GRO#$1 grsdb: description: GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank. example: '10142' homepage: http://bioinformatics.ramapo.edu/GRSDB2/ keywords: - dna - rna mappings: biocontext: GRSDB miriam: grsdb n2t: grsdb prefixcommons: grsdb name: G-Rich Sequences Database pattern: ^\d+$ preferred_prefix: grsdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/grsdb:$1 uri_format: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1 gsfa: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The "Codex General Standard for Food Additives" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database. example: '174' homepage: http://www.fao.org/gsfaonline name: General Standard for Food Additives Online Database pattern: ^\d+$ preferred_prefix: gsfa synonyms: - FAO/WHO_standards uri_format: http://www.fao.org/gsfaonline/additives/details.html?id=$1 gsso: appears_in: - ontoavida - scdo banana: GSSO contact: email: kronkcj@mail.uc.edu github: Superraptor name: Clair Kronk orcid: 0000-0001-8397-8810 description: The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology. download_json: http://purl.obolibrary.org/obo/gsso.json download_obo: http://purl.obolibrary.org/obo/gsso.obo download_owl: http://purl.obolibrary.org/obo/gsso.owl example: 002368 homepage: https://gsso.research.cchmc.org/ keywords: - obo - ontology license: Apache 2.0 License mappings: aberowl: GSSO bioportal: GSSO miriam: gsso obofoundry: gsso ols: gsso ontobee: GSSO name: Gender, Sex, and Sexual Orientation Ontology namespace_in_lui: true pattern: ^\d{6}$ preferred_prefix: GSSO rdf_uri_format: http://purl.obolibrary.org/obo/GSSO_$1 repository: https://github.com/Superraptor/GSSO uri_format: http://purl.obolibrary.org/obo/GSSO_$1 version: 2.0.5 gtdb: contact: email: donovan.parks@gmail.com github: donovan-h-parks name: Donovan Parks orcid: 0000-0001-6662-9010 contributor: email: aireland@lbl.gov github: ialarmedalien name: AJ Ireland orcid: 0000-0003-1982-9065 description: The Genome Taxonomy Database (GTDB) is an initiative to establish a standardized microbial taxonomy based on genome phylogeny. example: g__Prochlorococcus_A github_request_issue: 1242 homepage: https://gtdb.ecogenomic.org license: CC-BY-SA-4.0 mappings: pathguide: '190' name: Genome Taxonomy Database pattern: ^[cdfgops]__\w+\S+$ preferred_prefix: gtdb publications: - doi: 10.1093/nar/gkab776 pmc: PMC8728215 pubmed: '34520557' title: 'GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy' year: 2021 - doi: 10.1038/s41564-021-00918-8 pubmed: '34155373' title: A standardized archaeal taxonomy for the Genome Taxonomy Database year: 2021 - doi: 10.1038/s41587-020-0501-8 pubmed: '32341564' title: A complete domain-to-species taxonomy for Bacteria and Archaea year: 2020 - doi: 10.1038/nbt.4229 pubmed: '30148503' title: A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life year: 2018 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://gtdb.ecogenomic.org/tree?r=$1 gtex: description: The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. example: BRIP1 homepage: https://www.gtexportal.org mappings: biocontext: GTEX biolink: GTEx miriam: gtex n2t: gtex name: Genotype-Tissue Expression pattern: ^\w.+$ preferred_prefix: gtex uri_format: https://www.gtexportal.org/home/gene/$1 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/$1 gudmap: contact: email: simon.harding@ed.ac.uk github: simondharding name: Simon Douglas Harding orcid: 0000-0002-9262-8318 description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract. example: Q-2958 homepage: http://www.gudmap.org/ keywords: - cell biology - developmental biology - genomics - molecular biology mappings: biocontext: GUDMAP fairsharing: FAIRsharing.910c39 miriam: gudmap n2t: gudmap re3data: r3d100012193 name: Genitourinary Development Molecular Anatomy Project pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$ preferred_prefix: gudmap publications: - doi: 10.1242/dev.063594 pmc: PMC3188593 pubmed: '21652655' title: The GUDMAP database--an online resource for genitourinary research year: 2011 - doi: 10.1681/asn.2007101078 pubmed: '18287559' title: 'GUDMAP: the genitourinary developmental molecular anatomy project' year: 2008 - doi: 10.1681/ASN.2007101078 title: 'GUDMAP: the genitourinary developmental molecular anatomy project.' twitter: GUDMAP uri_format: https://gudmap.org/id/$1 gwascentral.marker: description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker. example: HGVM15354 homepage: https://www.gwascentral.org/markers mappings: biocontext: GWASCENTRAL.MARKER miriam: gwascentral.marker n2t: gwascentral.marker name: GWAS Central Marker pattern: ^HGVM\d+$ preferred_prefix: gwascentral.marker uri_format: https://www.gwascentral.org/marker/$1 gwascentral.phenotype: description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype. example: HGVPM623 homepage: https://www.gwascentral.org/phenotypes mappings: biocontext: GWASCENTRAL.PHENOTYPE miriam: gwascentral.phenotype n2t: gwascentral.phenotype name: GWAS Central Phenotype pattern: ^HGVPM\d+$ preferred_prefix: gwascentral.phenotype uri_format: https://www.gwascentral.org/phenotype/$1 gwascentral.study: description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study. example: HGVST1828 homepage: https://www.gwascentral.org/studies keywords: - gene - genome mappings: biocontext: GWASCENTRAL.STUDY miriam: gwascentral.study n2t: gwascentral.study prefixcommons: hgvbase name: GWAS Central Study pattern: ^HGVST\d+$ preferred_prefix: gwascentral.study providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/hgvbase:$1 uri_format: https://www.gwascentral.org/study/$1 gxa.expt: description: The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments. example: E-MTAB-2037 homepage: https://www.ebi.ac.uk/gxa/ mappings: biocontext: GXA.EXPT miriam: gxa.expt n2t: gxa.expt name: GXA Expt owners: - name: European Bioinformatics Institute partnered: false ror: 02catss52 pattern: ^[AEP]-\w{4}-\d+$ preferred_prefix: gxa.expt providers: - code: omicsdi description: GXA Expt through OmicsDI homepage: https://www.omicsdi.org/ name: GXA Expt through OmicsDI uri_format: https://www.omicsdi.org/dataset/atlas-experiments/$1 uri_format: https://www.ebi.ac.uk/gxa/experiments/$1 gxa.gene: description: The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes. example: AT4G01080 homepage: https://www.ebi.ac.uk/gxa/ mappings: biocontext: GXA.GENE miriam: gxa.gene n2t: gxa.gene name: GXA Gene owners: - name: European Bioinformatics Institute partnered: false ror: 02catss52 pattern: ^\w+$ preferred_prefix: gxa.gene uri_format: https://www.ebi.ac.uk/gxa/genes/$1 habronattus: contact: email: peteremidford@yahoo.com name: Peter Midford orcid: 0000-0001-6512-3296 deprecated: true homepage: http://www.mesquiteproject.org/ontology/Habronattus/index.html keywords: - obo - ontology mappings: biocontext: HABRONATTUS obofoundry: habronattus name: Habronattus courtship preferred_prefix: HABRONATTUS rdf_uri_format: http://purl.obolibrary.org/obo/HABRONATTUS_$1 uri_format: http://purl.obolibrary.org/obo/HABRONATTUS_$1 hagr.genage: contact: email: jp@senescence.info name: Joao Pedro de Magalhaes orcid: 0000-0002-6363-2465 description: GenAge is a database of human and model organism genes related to longevity and aging, maintained by the Human Ageing Genomics Resources (HAGR) group. example: '0001' homepage: http://genomics.senescence.info/genes/ keywords: - aging - genes - longevity mappings: prefixcommons: genage name: The Ageing Gene Database preferred_prefix: hagr.genage providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/genage:$1 publications: - doi: 10.1093/nar/gks1155 pmc: PMC3531213 pubmed: '23193293' title: 'Human Ageing Genomic Resources: integrated databases and tools for the biology and genetics of ageing' year: 2012 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://genomics.senescence.info/genes/details.php?id=$1 hagr.gendr: contact: email: jp@senescence.info name: Joao Pedro de Magalhaes orcid: 0000-0002-6363-2465 description: 'GenDR is a database of genes associated with dietary restriction (DR). GenDR includes two datasets: 1) genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of DR; 2) genes robustly altered due to DR, derived from a meta-analysis of microarray DR studies in mammals' example: '2' homepage: http://genomics.senescence.info/diet/ keywords: - aging - dietary restriction - genes - longevity mappings: prefixcommons: gendr name: The Dietary Restriction Gene Database preferred_prefix: hagr.gendr providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/gendr:$1 publications: - doi: 10.1371/journal.pgen.1002834 pmc: PMC3415404 pubmed: '22912585' title: Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes year: 2012 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://genomics.senescence.info/diet/details.php?id=$1 hamap: contact: email: alan.bridge@isb-sib.ch name: Alan Bridge orcid: 0000-0003-2148-9135 description: HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries. example: MF_01400 homepage: https://hamap.expasy.org/ keywords: - life science - protein mappings: biocontext: HAMAP edam: '2766' fairsharing: FAIRsharing.63m4ss go: HAMAP miriam: hamap n2t: hamap prefixcommons: hamap uniprot: DB-0041 name: High-quality Automated and Manual Annotation of microbial Proteomes pattern: ^MF_\d+$ preferred_prefix: hamap providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/hamap:$1 publications: - doi: 10.1093/nar/gku1002 pmc: PMC4383873 pubmed: '25348399' title: 'HAMAP in 2015: updates to the protein family classification and annotation system' year: 2014 - doi: 10.1093/nar/gks1157 pmc: PMC3531088 pubmed: '23193261' title: HAMAP in 2013, new developments in the protein family classification and annotation system year: 2012 uri_format: https://hamap.expasy.org/unirule/$1 hancestro: contact: email: dwelter.ontologist@gmail.com github: daniwelter name: Danielle Welter orcid: 0000-0003-1058-2668 description: Human ancestry ontology for the NHGRI GWAS Catalog download_owl: http://purl.obolibrary.org/obo/hancestro.owl example: 0290 homepage: https://ebispot.github.io/hancestro/ keywords: - demographics - genome-wide association study - human genetics - obo - ontology - population genetics license: CC-BY-4.0 mappings: aberowl: HANCESTRO biolink: HANCESTRO bioportal: HANCESTRO fairsharing: FAIRsharing.rja8qp obofoundry: hancestro ols: hancestro ontobee: HANCESTRO name: Human Ancestry Ontology owners: - name: European Bioinformatics Institute partnered: false ror: 02catss52 pattern: ^\d{4}$ preferred_prefix: HANCESTRO providers: - code: legacy description: Legacy URI homepage: http://www.ebi.ac.uk/ancestro name: Legacy uri_format: http://www.ebi.ac.uk/ancestro/ancestro_$1 publications: - doi: 10.1186/s13059-018-1396-2 pmc: PMC5815218 pubmed: '29448949' title: A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog year: 2018 rdf_uri_format: http://purl.obolibrary.org/obo/HANCESTRO_$1 repository: https://github.com/EBISPOT/ancestro uri_format: http://purl.obolibrary.org/obo/HANCESTRO_$1 version: '2024-08-19' hao: contact: email: diapriid@gmail.com github: mjy name: Matt Yoder orcid: 0000-0002-5640-5491 description: A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) download_obo: http://purl.obolibrary.org/obo/hao.obo download_owl: http://purl.obolibrary.org/obo/hao.owl example: 0000187 homepage: http://hymao.org keywords: - anatomy - image - life science - obo - ontology license: CC0-1.0 mappings: aberowl: HAO biocontext: HAO bioportal: HAO fairsharing: FAIRsharing.kj3m5n obofoundry: hao ols: hao ontobee: HAO name: Hymenoptera Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: HAO publications: - doi: 10.1371/journal.pone.0015991 pmc: PMC3012123 pubmed: '21209921' title: A gross anatomy ontology for hymenoptera year: 2010 rdf_uri_format: http://purl.obolibrary.org/obo/HAO_$1 repository: https://github.com/hymao/hao uri_format: http://purl.obolibrary.org/obo/HAO_$1 version: '2023-06-01' hao.ref: contact: email: diapriid@gmail.com github: mjy name: Matt Yoder orcid: 0000-0002-5640-5491 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Literature references in the Hymenoptera Anatomy Ontology Portal example: '98127' github_request_issue: 1322 homepage: http://hymao.org name: Hymenoptera Anatomy Reference pattern: ^\d+$ preferred_prefix: hao.ref uri_format: http://api.hymao.org/api/ref/$1 hathitrust: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world. example: 008893080 github_request_issue: 510 homepage: https://www.hathitrust.org name: Hathi Trust Digital Library pattern: ^\d+$ preferred_prefix: hathitrust uri_format: https://catalog.hathitrust.org/Record/$1 hba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A controlled vocabulary to support the study of transcription in the human brain download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-hba.obo example: '4005' example_extras: - '265504410' homepage: https://human.brain-map.org keywords: - ontology name: Human Brain Atlas pattern: ^\d+$ preferred_prefix: HBA providers: - code: biopragmatics description: A static site generated for the HBA resource homepage: https://biopragmatics.github.io/providers name: Biopragmatics Browser uri_format: https://biopragmatics.github.io/providers/hba/$1 uri_format: https://purl.brain-bican.org/ontology/hbao/HBA_$1 hbvar: description: This is a relational database of information about hemoglobin variants and mutations that cause thalassemia. example: '2526' homepage: http://globin.cse.psu.edu/globin/hbvar keywords: - protein mappings: prefixcommons: hbvar name: A Database of Human Hemoglobin Variants and Thalassemias preferred_prefix: hbvar providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/hbvar:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=$1 hc.din: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A Drug Identification Number (DIN) is a computer-generated eight digit number assigned by Health Canada to a drug product prior to being marketed in Canada. It uniquely identifies all drug products sold in a dosage form in Canada and is located on the label of prescription and over-the-counter drug products that have been evaluated and authorized for sale in Canada. example: 02069237 homepage: https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/fact-sheets/drug-identification-number.html mappings: hl7: 2.16.840.1.113883.5.1105 name: Health Canada Drug Identification Number pattern: ^\d{8}$ preferred_prefix: hc.din references: - http://www.hc-sc.gc.ca/dhp-mps/prodpharma/databasdon/index-eng.php hc.npn: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Licensed Natural Health Products Database contains information about natural health products that have been issued a product licence by Health Canada. example: '18125' homepage: http://webprod.hc-sc.gc.ca/nhpid-bdipsn/search-rechercheReq.do?lang=eng mappings: hl7: 2.16.840.1.113883.5.1107 name: Health Canada Natural Product Number pattern: ^\d+$ preferred_prefix: hc.npn references: - https://www.canada.ca/en/health-canada/services/drugs-health-products/natural-non-prescription/applications-submissions/product-licensing/licensed-natural-health-products-database.html uri_format: http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id=$1 hc.trial: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Health Canada, through its Clinical Trials Database, is providing to the public a listing of specific information relating to phase I, II and III clinical trials in patients. The database is managed by Health Canada and provides a source of information about Canadian clinical trials involving human pharmaceutical and biological drugs. [from website] example: '239287' homepage: https://health-products.canada.ca/ctdb-bdec name: Health Canada Clinical Trials Database pattern: ^\d+$ preferred_prefix: hc.trial uri_format: https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo=$1 hcao: description: Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas. download_owl: http://ontology.data.humancellatlas.org/ontologies/hcao/releases/2023-05-16/hcao.owl homepage: https://www.humancellatlas.org keywords: - ontology mappings: ols: hcao name: Human Cell Atlas Ontology no_own_terms: true preferred_prefix: hcao hco: description: The Human Chromosome Ontology (HCO) provides simple and stable URIs for human reference genome versions to semantically identify human chromosomes. example: MT homepage: https://dbcls.rois.ac.jp/ mappings: miriam: hco name: Human Chromosome Ontology pattern: ^.+$ preferred_prefix: hco uri_format: http://biohackathon.org/resource/hco#$1 hcpcs: contact: email: Cynthia.Hake@cms.hhs.gov name: Cynthia Hake contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers. example: G8944 homepage: https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo keywords: - biomedical science - business administration - ontology mappings: aberowl: HCPCS biolink: HCPCS bioportal: HCPCS fairsharing: FAIRsharing.x81wz8 name: Healthcare Common Procedure Coding System preferred_prefix: hcpcs uri_format: http://purl.bioontology.org/ontology/HCPCS/$1 hcvdb: description: the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses. example: M58335 homepage: http://euhcvdb.ibcp.fr/euHCVdb/ keywords: - gene mappings: biocontext: HCVDB miriam: hcvdb n2t: hcvdb prefixcommons: hcv name: Hepatitis C Virus Database Project pattern: ^M\d{5}$ preferred_prefix: hcvdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/hcv:$1 uri_format: https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1 hdl: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Welcome to the web site of the Handle.Net Registry (HNR), run by Corporation for National Research Initiatives (CNRI). CNRI is a Multi-Primary Administrator (MPA) of the Global Handle Registry (GHR), authorized by the DONA Foundation to allot prefixes to users of the Handle System. The DONA Foundation is a non-profit organization based in Geneva that has taken over responsibility for the evolution of CNRI's Digital Object (DO) Architecture including outreach around the world. One of the Foundation's responsibilities is to administer and maintain the overall operation of the GHR, a task that was previously performed by CNRI. (from website) example: 2381/12775 example_extras: - 391/00-0000-0000-0009-3C7E-F homepage: https://www.handle.net/ keywords: - centrally registered identifier - subject agnostic mappings: fairsharing: FAIRsharing.0b7e54 name: Handle pattern: ^\d+/.+$ preferred_prefix: hdl synonyms: - handle uri_format: http://hdl.handle.net/$1 hdr: description: The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders. example: '63' homepage: http://research.nhgri.nih.gov/apps/homeodomain/web/ keywords: - genome mappings: biocontext: HDR miriam: hdr n2t: hdr pathguide: '307' prefixcommons: hdr name: Homeodomain Research pattern: ^\d+$ preferred_prefix: hdr providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/hdr:$1 uri_format: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1 hemonc: comment: It is unclear if identifiers can be resolved on the website but a spreadsheet of the terminology is available via the NCI at https://evs.nci.nih.gov/ftp1/HemOnc/HemOnc_Terminology.xls contributor: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: HemOnc.org is the largest freely available medical wiki of interventions, regimens, and general information relevant to the fields of hematology and oncology. example: '15543' github_request_issue: 1149 homepage: https://hemonc.org/ name: HemOnc Terminology pattern: ^\d+$ preferred_prefix: hemonc publications: - doi: 10.1016/j.jbi.2019.103239 pmc: PMC6697579 pubmed: '31238109' title: 'HemOnc: A new standard vocabulary for chemotherapy regimen representation in the OMOP common data model' year: 2019 reviewer: github: callahantiff name: Tiffany J. Callahan orcid: 0000-0002-8169-9049 hepro: contact: email: paul.fabry@usherbrooke.ca github: pfabry name: Paul Fabry orcid: 0000-0002-3336-2476 contributor: email: paul.fabry@usherbrooke.ca github: pfabry name: Paul Fabry orcid: 0000-0002-3336-2476 description: HEPRO is an ontology of informational entities and processes related to health procedures and health activities. download_json: https://github.com/OpenLHS/HEPRO/raw/main/HEPRO.json download_owl: https://github.com/OpenLHS/HEPRO/raw/main/HEPRO.owl example: '0000001' github_request_issue: 810 homepage: https://openlhs.github.io/HEPRO/ keywords: - ontology license: CC-BY-4.0 name: Health Procedure Ontology owners: - name: Université de Sherbrooke partnered: false ror: 00kybxq39 pattern: ^\d{7}$ preferred_prefix: HEPRO repository: https://github.com/OpenLHS/HEPRO reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://purl.obolibrary.org/obo/HEPRO_$1 hesa: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An identifier for institutions in the United Kingdom, used in GRID and ROR. example: '0154' homepage: https://www.hesa.ac.uk keywords: - bibliometrics - institution name: UK Higher Education Statistics Agency pattern: ^\d+$ preferred_prefix: hesa hgmd: description: The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases. example: CALM1 homepage: http://www.hgmd.cf.ac.uk/ac/index.php mappings: biocontext: HGMD edam: '3265' integbio: nbdc00097 miriam: hgmd n2t: hgmd name: Human Gene Mutation Database pattern: ^[A-Z_0-9]+$ preferred_prefix: hgmd uri_format: http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1 hgnc: contact: email: elspeth@genenames.org name: Elspeth Bruford orcid: 0000-0002-8380-5247 description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database. download_owl: http://aber-owl.net/media/ontologies/HGNC/1/hgnc.owl example: '16793' homepage: http://www.genenames.org keywords: - classification - gene - gene name - life science - non-coding rna - ontology - protein - pseudogene license: CC0-1.0 mappings: aberowl: HGNC biocontext: HGNC bioportal: HGNC cellosaurus: HGNC edam: '2298' fairsharing: FAIRsharing.amcv1e go: HGNC hl7: 2.16.840.1.113883.6.281 miriam: hgnc n2t: hgnc ncbi: HGNC prefixcommons: hgnc togoid: Hgnc uniprot: DB-0042 wikidata: P354 name: HUGO Gene Nomenclature Committee pattern: ^\d{1,5}$ preferred_prefix: hgnc providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/hgnc:$1 - code: gencc description: The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases. Curated gene-disease relationships are submitted by GenCC member organizations. The GenCC comprises organizations that currently provide online resources (e.g. ClinGen, DECIPHER, Genomics England PanelApp, OMIM, Orphanet, PanelApp Australia, TGMI’s G2P), as well as diagnostic laboratories that have committed to sharing their internal curated gene-level knowledge (e.g. Ambry, Illumina, Invitae, Myriad Women’s Health, Mass General Brigham Laboratory for Molecular Medicine). homepage: https://thegencc.org name: The Gene Curation Coalition uri_format: https://search.thegencc.org/genes/HGNC:$1 - code: indra description: A large scale database of biomedical statements. homepage: https://db.indra.bio name: INDRA Database publications: - doi: 10.15252/msb.202211325 pmc: PMC10167483 pubmed: '36938926' title: Automated assembly of molecular mechanisms at scale from text mining and curated databases year: 2023 - doi: 10.15252/msb.20177651 pmc: PMC5731347 pubmed: '29175850' title: From word models to executable models of signaling networks using automated assembly year: 2017 uri_format: https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@HGNC publications: - doi: 10.15252/msb.202211325 pmc: PMC10167483 pubmed: '36938926' title: Automated assembly of molecular mechanisms at scale from text mining and curated databases year: 2023 - doi: 10.1093/nar/gkaa980 pmc: PMC7779007 pubmed: '33152070' title: 'Genenames.org: the HGNC and VGNC resources in 2021' year: 2021 - doi: 10.1093/nar/gky930 pmc: PMC6324057 pubmed: '30304474' title: 'Genenames.org: the HGNC and VGNC resources in 2019' year: 2019 - doi: 10.1159/000131404 pubmed: '295268' title: International system for human gene nomenclature (1979) ISGN (1979) year: 1979 - doi: 10.15252/msb.20177651 pmc: PMC5731347 pubmed: '29175850' title: From word models to executable models of signaling networks using automated assembly year: 2017 uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1 hgnc.genefamily: description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families. example: '2029' has_canonical: hgnc.genegroup homepage: http://www.genenames.org license: CC0-1.0 mappings: biocontext: HGNC.GENEFAMILY miriam: hgnc.genefamily n2t: hgnc.genefamily name: HGNC gene family pattern: ^\d+$ preferred_prefix: hgnc.genefamily synonyms: - GFAM - HGNC_GROUP - hgnc.family uri_format: https://www.genenames.org/cgi-bin/genefamilies/set/$1 hgnc.genegroup: description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families. example: '141' homepage: https://www.genenames.org license: CC0-1.0 mappings: miriam: hgnc.genegroup name: HGNC Gene Group pattern: ^\d+$ preferred_prefix: hgnc.genegroup uri_format: https://www.genenames.org/data/genegroup/#!/group/$1 hgnc.symbol: description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol. example: DAPK1 homepage: https://www.genenames.org/ license: CC0-1.0 mappings: biocontext: HGNC.SYMBOL miriam: hgnc.symbol n2t: hgnc.symbol togoid: HgncSymbol wikidata: P353 name: HGNC gene symbol pattern: ^[A-Za-z-0-9_]+(\@)?$ preferred_prefix: hgnc.symbol providers: - code: cbgda description: A database of key host genes involved in the pathogenesis of different diseases identified through genome-wide CRISPR screens homepage: http://cbgda.zhounan.org/main name: CRISPR Based Gene-Disease Associations publications: - doi: 10.1093/database/baae077 pmc: PMC11363955 pubmed: '39213392' title: 'CBGDA: a manually curated resource for gene-disease associations based on genome-wide CRISPR' year: 2024 uri_format: http://cbgda.zhounan.org/geneinfo?gene=$1 - code: depmap description: DepMap summary of the given gene homepage: https://depmap.org name: DepMap Gene Summary uri_format: https://depmap.org/portal/gene/$1 - code: g2p description: A resource for linking genetic screening outputs to protein sequences and structures homepage: https://g2p.broadinstitute.org/ name: Genomics 2 Proteins Portal publications: - doi: 10.1038/s41592-024-02409-0 pmc: PMC11466821 pubmed: '39294369' title: 'Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures' year: 2024 uri_format: https://g2p.broadinstitute.org/gene/$1 - code: oncomx description: Mutation profiles for a gene homepage: https://oncomx.org name: OncoMX uri_format: https://oncomx.org/searchview/?gene=$1 - code: pathwaycommons description: Interactions between a given gene and other molecular entities homepage: https://www.pathwaycommons.org/ name: Pathway Commons Gene Interations uri_format: https://apps.pathwaycommons.org/interactions?source=$1 publications: - doi: 10.1038/s41592-024-02409-0 pmc: PMC11466821 pubmed: '39294369' title: 'Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures' year: 2024 - doi: 10.1093/database/baae077 pmc: PMC11363955 pubmed: '39213392' title: 'CBGDA: a manually curated resource for gene-disease associations based on genome-wide CRISPR' year: 2024 uri_format: https://www.genenames.org/data/gene-symbol-report/#!/symbol/$1 hgvs: contact: email: reecehart@gmail.com github: reece name: Reece Hart orcid: 0000-0003-3463-0775 contributor: email: miseming@sfu.ca github: miseminger name: Madeline Iseminger orcid: 0000-0002-0548-891X description: The HGVS Nomenclature is an internationally-recognized standard for the description of DNA, RNA and protein sequence variants. It is used to convey variants in clinical reports and to share variants in publications and databases. The HGVS Nomenclature is administered by the [HGVS Variant Nomenclature Committee (HVNC)](https://hgvs-nomenclature.org/stable/hvnc/) under the auspices of the [Human Genome Organization (HUGO)](https://hugo-int.org/). example: NP_003997.1:p.Trp24Cys example_extras: - GRCh38(chr11):g.112088970del - NC_000011.10(NM_001276503.2):c.169+998del - NC_000011.10:g.112088970del - NG_012337.3(NM_003002.4):c.274G>T - NG_012337.3(NM_003002.4):r.(274g>u) github_request_issue: 1032 homepage: https://hgvs-nomenclature.org/stable/background/simple/ mappings: hl7: 2.16.840.1.113883.6.282 wikidata: P3331 name: Human Genome Variation Society Nomenclature preferred_prefix: hgvs providers: - code: mutalyzer description: ' The Mutalyzer tool suite is designed to be of help when working with HGVS sequence variant nomenclature descriptions.' homepage: https://mutalyzer.nl name: LUMC Mutalyzer 3 uri_format: https://mutalyzer.nl/api/description_to_model/$1 publications: - doi: 10.1002/humu.22981 pubmed: '26931183' title: 'HGVS Recommendations for the Description of Sequence Variants: 2016 Update' year: 2016 - doi: 10.1093/bioinformatics/btu630 pmc: PMC4287946 pubmed: '25273102' title: A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature year: 2014 references: - https://github.com/biopragmatics/bioregistry/issues/460 repository: https://github.com/HGVSnomenclature/hgvs-nomenclature reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://reg.clinicalgenome.org/allele?hgvs=$1 hinv.locus: description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view. example: HIX0004394 homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp mappings: biocontext: HINV.LOCUS miriam: hinv.locus n2t: hinv.locus name: H-InvDb Locus pattern: ^HIX\d{7}(\.\d+)?$ 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: https://www.hipsci.org mappings: cellosaurus: HipSci name: Human Induced Pluripotent Stem Cells Initiative preferred_prefix: hipsci uri_format: https://www.hipsci.org/lines/#/lines/$1 hivreagentprogram: description: Cell line collections (Providers) example: ARP-1513 homepage: https://www.hivreagentprogram.org/ mappings: cellosaurus: HIVReagentProgram name: NIH HIV Reagent Program preferred_prefix: hivreagentprogram uri_format: https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx hl7.v2codesystem: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR. example: 0778 homepage: https://terminology.hl7.org/codesystems-v2.html name: HL7 V2 Code Systems pattern: ^\d+$ preferred_prefix: hl7.v2codesystem uri_format: http://terminology.hl7.org/CodeSystem/v2-$1 hl7.v3codesystem: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR. example: AcknowledgementCondition homepage: https://terminology.hl7.org/codesystems-v2.html name: HL7 V2 Code Systems pattern: ^\w+$ preferred_prefix: hl7.v3codesystem uri_format: https://terminology.hl7.org/CodeSystem-v3-$1 hmdb: contact: email: david.wishart@ualberta.ca github: DavidWishartLab name: David S. Wishart orcid: 0000-0002-3207-2434 description: The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data. example: HMDB00001 homepage: http://www.hmdb.ca/ keywords: - biochemistry - bioinformatics - chemical - human - life science - metabolite - metabolomics - molecular biology - omics - phenomics - proteomics mappings: biocontext: HMDB cheminf: 000408 edam: '2622' fairsharing: FAIRsharing.sye5js integbio: nbdc00909 miriam: hmdb n2t: hmdb pathguide: '244' prefixcommons: hmdb re3data: r3d100011285 togoid: Hmdb wikidata: P2057 name: Human Metabolome Database pattern: ^HMDB\d+$ preferred_prefix: hmdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/hmdb:$1 publications: - doi: 10.1093/nar/gkab1062 pmc: PMC8728138 pubmed: '34986597' title: 'HMDB 5.0: the Human Metabolome Database for 2022' year: 2022 - doi: 10.1093/nar/gkx1089 pmc: PMC5753273 pubmed: '29140435' title: 'HMDB 4.0: the human metabolome database for 2018' year: 2018 - doi: 10.1093/nar/gks1065 pmc: PMC3531200 pubmed: '23161693' title: HMDB 3.0--The Human Metabolome Database in 2013 year: 2012 - doi: 10.1093/nar/gkl923 pmc: PMC1899095 pubmed: '17202168' title: 'HMDB: the Human Metabolome Database' year: 2007 - doi: 10.1093/nar/gkn810 title: 'HMDB: a knowledgebase for the human metabolome' synonyms: - HMDB twitter: WishartLab uri_format: http://www.hmdb.ca/metabolites/$1 hms.lincs.antibody: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols. example: '80001' homepage: https://lincs.hms.harvard.edu/db/antibodies/ name: HMS Library of Integrated Network-based Cellular Signatures Antibodies pattern: ^8\d{4}$ preferred_prefix: hms.lincs.antibody uri_format: https://lincs.hms.harvard.edu/db/antibodies/$1 hms.lincs.cell: comment: this is NOT the same as lincs.cell. On https://lincs.hms.harvard.edu/db/cells/?search=MCF-10A&extra_form_shown=&dataset_types=, you can see there's a mapping to the other resource. contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols. example: '50583' homepage: https://lincs.hms.harvard.edu/db/cell/ name: HMS LINCS Cell pattern: ^5\d{4}$ preferred_prefix: hms.lincs.cell references: - https://github.com/identifiers-org/identifiers-org.github.io/issues/223 uri_format: https://lincs.hms.harvard.edu/db/cells/$1 hms.lincs.compound: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols. example: 10001-101 example_extras: - 11996-999 homepage: https://lincs.hms.harvard.edu/db/sm/ name: HMS LINCS Compound pattern: ^1\d{4}-\d{3}$ preferred_prefix: hms.lincs.compound synonyms: - HMS-LINCS - hmsl_id uri_format: https://lincs.hms.harvard.edu/db/sm/$1 hms.lincs.dataset: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 example: '20003' homepage: https://lincs.hms.harvard.edu/db/datasets/ name: HMS Library of Integrated Network-based Cellular Signatures Datasets pattern: ^2\d{4}$ preferred_prefix: hms.lincs.dataset uri_format: https://lincs.hms.harvard.edu/db/datasets/$1 hoelzel: contact: email: info@hoelzel.de name: Carsten Linder orcid: 0009-0009-3816-8777 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Hölzel is a life science reagent vendor based in Cologne, Germany. As a distributor, they offer products suitable for many kinds of research areas such as oncology, neuroscience, immunology, and more. Their portfolio consists of antibodies, recombinant proteins, inhibitors, ELISA-kits as well as other assays, arrays and kits. Their inhibitor portfolio can be easily accessed via the CAS-register catalog. example: 40592-R001-100 homepage: https://www.hoelzel-biotech.com keywords: - antibodies - assays - biologics - elisa-kits - inhibitors - life sciences - proteins - vendor logo: https://www.hoelzel-biotech.com/skin/frontend/ultimo/custom/images/logo.png name: Hölzel Diagnostika preferred_prefix: hoelzel synonyms: - hölzel uri_format: https://www.hoelzel-biotech.com/de/catalogsearch/result/?q=$1 hog: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc. download_obo: ftp://ftp.bgee.org/general/ontologies/HOG.obo example: '0000255' homepage: https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships keywords: - ontology name: Homologous Organ Groups pattern: ^\d{7}$ preferred_prefix: hog uri_format: https://biopragmatics.github.io/providers/hog/$1 hogenom: contact: email: perriere@biomserv.univ-lyon1.fr name: Guy Perrière orcid: 0000-0002-6850-6265 description: HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier. example: HBG284870 homepage: http://pbil.univ-lyon1.fr/databases/hogenom/ keywords: - classification - life science - phylogenetics - phylogeny - sequence mappings: biocontext: HOGENOM fairsharing: FAIRsharing.qe8tz8 integbio: nbdc01858 miriam: hogenom n2t: hogenom prefixcommons: hogenom uniprot: DB-0044 name: Database of Complete Genome Homologous Genes Families pattern: ^\w+$ preferred_prefix: hogenom providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/hogenom:$1 publications: - doi: 10.1186/1471-2105-10-s6-s3 pmc: PMC2697650 pubmed: '19534752' title: Databases of homologous gene families for comparative genomics year: 2009 - doi: 10.1101/gr.10.3.379 pmc: PMC311423 pubmed: '10720578' title: 'HOBACGEN: database system for comparative genomics in bacteria' year: 2000 - doi: 10.1186/1471-2105-10-S6-S3 title: Databases of homologous gene families for comparative genomics. uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1 hoip: comment: The ontology file was deleted in https://github.com/yuki-yamagata/hoip/commit/73fcfa114d71a76a984a9ce1166e50d7ebafe158, making it impossible to link to the ontology afterwards. contact: email: yuki.yamagata@riken.jp github: yuki-yamagata name: Yuki Yamagata orcid: 0000-0002-9673-1283 contributor: email: j.harry.caufield@gmail.com github: caufieldjh name: Harry Caufield orcid: 0000-0001-5705-7831 description: An ontology of processes triggered by homeostatic imbalance, with a focus on COVID-19 infectious processes. download_owl: https://github.com/yuki-yamagata/hoip/blob/c70ae6d4868ca951d075cec409e863fa4abe19b2/hoip_0308.owl example: 0040379 github_request_issue: 668 homepage: https://knowledge.brc.riken.jp/bioresource/ontology/HOIP keywords: - ontology license: CC-BY-4.0 mappings: aberowl: HOIP bioportal: HOIP name: Homeostasis imbalance process ontology pattern: ^\d{7}$ preferred_prefix: hoip repository: https://github.com/yuki-yamagata/hoip reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://purl.bioontology.org/ontology/HOIP/HOIP_$1 holofood.animal: contact: email: tgilbert@sund.ku.dk name: Tom Gilbert orcid: 0000-0002-5805-7195 contributor: email: palayoor.n@northeastern.edu github: nalikapalayoor name: Nalika Palayoor orcid: 0009-0008-8406-631X description: The HoloFood Data Portal centralizes access to datasets from the HoloFood project, which explores host microbiota interactions in salmon and chicken production. It links phenotypic data with microbiome samples and derived genomic resources and therefore simplifies data integration, supporting researchers in multiomics and microbiome studies. The identifiers in the animal semantic space correspond to animals that samples in the database are obtained from. example: SAMEA112904733 github_request_issue: 1400 homepage: https://www.holofooddata.org name: HoloFood animal pattern: ^SAMEA\d{9}$ preferred_prefix: holofood.animal publications: - doi: 10.1093/database/baae112 pmc: PMC11724189 pubmed: '39797569' title: 'HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production' year: 2025 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://www.holofooddata.org/animal/$1 holofood.sample: contact: email: tgilbert@sund.ku.dk name: Tom Gilbert orcid: 0000-0002-5805-7195 contributor: email: palayoor.n@northeastern.edu github: nalikapalayoor name: Nalika Palayoor orcid: 0009-0008-8406-631X description: The HoloFood Data Portal centralizes access to datasets from the HoloFood project, which explores host microbiota interactions in salmon and chicken production. It links phenotypic data with microbiome samples and derived genomic resources and therefore simplifies data integration, supporting researchers in multiomics and microbiome studies. The identifiers in the samples semantic space represent samples derived from animals in HoloFood trials. example: SAMEA10104908 github_request_issue: 1400 homepage: https://www.holofooddata.org name: HoloFood sample pattern: ^SAMEA\d{8}$ preferred_prefix: holofood.sample publications: - doi: 10.1093/database/baae112 pmc: PMC11724189 pubmed: '39797569' title: 'HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production' year: 2025 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://www.holofooddata.org/sample/$1 hom: contact: email: bgee@sib.swiss github: fbastian name: Frederic Bastian orcid: 0000-0002-9415-5104 description: This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. download_owl: http://purl.obolibrary.org/obo/hom.owl example: 0000049 homepage: https://github.com/BgeeDB/homology-ontology keywords: - anatomy - homologous - life cycle stage - life science - molecular entity - obo - ontology license: CC0-1.0 mappings: aberowl: HOM biocontext: HOM bioportal: HOM fairsharing: FAIRsharing.efv7gw obofoundry: hom ols: hom ontobee: HOM name: Homology Ontology pattern: ^\d{7}$ preferred_prefix: HOM publications: - doi: 10.1016/j.tig.2009.12.012 pubmed: '20116127' title: An ontology to clarify homology-related concepts year: 2010 rdf_uri_format: http://purl.obolibrary.org/obo/HOM_$1 repository: https://github.com/BgeeDB/homology-ontology uri_format: http://purl.obolibrary.org/obo/HOM_$1 version: '2015-01-07' homd.seq: contact: email: tchen@forsyth.org github: tsute name: Tsute Chen orcid: 0000-0001-6689-317X description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information. example: SEQF1003 homepage: http://www.homd.org/index.php keywords: - genome - microbial mappings: biocontext: HOMD.SEQ miriam: homd.seq n2t: homd.seq prefixcommons: homd.seq name: HOMD Sequence Metainformation pattern: ^SEQF\d+$ preferred_prefix: homd.seq providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/homd.seq:$1 publications: - doi: 10.1093/database/baq013 pmc: PMC2911848 pubmed: '20624719' title: 'The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information' year: 2010 uri_format: http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1 homd.taxon: contact: email: tchen@forsyth.org github: tsute name: Tsute Chen orcid: 0000-0001-6689-317X description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information. example: '811' homepage: http://www.homd.org/index.php keywords: - microbial - taxonomy mappings: biocontext: HOMD.TAXON miriam: homd.taxon n2t: homd.taxon ncbi: HOMD prefixcommons: homd.taxon name: Human Oral Microbiome Database pattern: ^\d+$ preferred_prefix: homd.taxon providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/homd.taxon:$1 publications: - doi: 10.1093/database/baq013 pmc: PMC2911848 pubmed: '20624719' title: 'The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information' year: 2010 uri_format: http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1 homologene: contact: email: sayers@ncbi.nlm.nih.gov name: Eric W. Sayers orcid: 0000-0001-8394-3802 description: HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. example: '1000' homepage: https://www.ncbi.nlm.nih.gov/homologene/ keywords: - gene - genome - life science mappings: biocontext: HOMOLOGENE fairsharing: FAIRsharing.mzc066 integbio: nbdc00101 miriam: homologene n2t: homologene prefixcommons: homologene togoid: Homologene wikidata: P593 name: HomoloGene pattern: ^\d+$ preferred_prefix: homologene providers: - code: 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 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/homologene:$1 publications: - doi: 10.1093/nar/gkq1172 pmc: PMC3013733 pubmed: '21097890' title: Database resources of the National Center for Biotechnology Information year: 2010 uri_format: https://www.ncbi.nlm.nih.gov/homologene/$1 homosaurus: appears_in: - gsso contact: email: adolphok@vcu.edu name: Keahi Kaʻiwalani Adolpho orcid: 0000-0003-1769-112X contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An international LGBTQ+ linked data vocabulary example: queerNewspapers github_request_issue: 1310 homepage: http://homosaurus.org license: CC BY NC-ND 4.0 name: Homosaurus preferred_prefix: homosaurus providers: - code: homosaurus.v2 description: Homosaurus API v2 homepage: https://homosaurus.org name: Homosaurus API v2 uri_format: http://homosaurus.org/v2/$1 - code: homosaurus.v3 description: Homosaurus API v3 homepage: https://homosaurus.org name: Homosaurus API v3 uri_format: http://homosaurus.org/v3/$1 repository: https://github.com/DigitalTransgenderArchive/homosaurus_site uri_format: http://homosaurus.org/terms/$1 horizon_discovery: description: Cell line collections (Providers) example: HD+118-001 homepage: https://horizondiscovery.com/ mappings: cellosaurus: Horizon_Discovery name: Horizon Discovery cell line collection preferred_prefix: horizon_discovery uri_format: https://horizondiscovery.com/en/search?searchterm=$1 hoso: contact: email: paul.fabry@usherbrooke.ca github: pfabry name: Paul Fabry orcid: 0000-0002-3336-2476 contributor: email: paul.fabry@usherbrooke.ca github: pfabry name: Paul Fabry orcid: 0000-0002-3336-2476 description: HOSO is an ontology of informational entities and processes related to healthcare organizations and services. example: '0000001' github_request_issue: 813 homepage: https://openlhs.github.io/HOSO/ license: CC-BY-4.0 name: Healthcare Organizations and Services Ontology pattern: ^\d{7}$ preferred_prefix: hoso repository: https://github.com/OpenLHS/HOSO reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 hovergen: contact: email: duret@biomserv.univ-lyon1.fr name: Laurent Duret orcid: 0000-0003-2836-3463 description: HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees. example: HBG004341 homepage: https://pbil.univ-lyon1.fr/databases/hovergen.php keywords: - dna - gene - life science - protein mappings: biocontext: HOVERGEN fairsharing: FAIRsharing.dg1f0e integbio: nbdc00284 miriam: hovergen n2t: hovergen prefixcommons: hovergen name: Homologous Vertebrate Genes Database pattern: ^HBG\d+$ preferred_prefix: hovergen providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/hovergen:$1 publications: - doi: 10.1093/bioinformatics/bti325 pubmed: '15713731' title: 'Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases' year: 2005 uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN hp: appears_in: - chiro - maxo - scdo banana: HP contact: email: dr.sebastian.koehler@gmail.com github: drseb name: Sebastian Koehler orcid: 0000-0002-5316-1399 description: The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. download_json: http://purl.obolibrary.org/obo/hp.json download_obo: http://purl.obolibrary.org/obo/hp.obo download_owl: http://purl.obolibrary.org/obo/hp.owl example: '0011140' homepage: http://www.human-phenotype-ontology.org/ keywords: - biomedical science - disease - genetics - obo - ontology - phenomics - phenotype - preclinical studies license: hpo logo: https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/logo/HPO-logo-black_small.png mappings: bartoc: '1937' biocontext: HPO fairsharing: FAIRsharing.kbtt7f hl7: 2.16.840.1.113883.6.339 integbio: nbdc02559 miriam: hp n2t: hp obofoundry: hp ols: hp ontobee: HP wikidata: P3841 mastodon: hpo@masto.ai name: Human Phenotype Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: HP publications: - doi: 10.1093/nar/gky1105 pmc: PMC6324074 pubmed: '30476213' title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources year: 2019 - doi: 10.1093/nar/gkw1039 pmc: PMC5210535 pubmed: '27899602' title: The Human Phenotype Ontology in 2017 year: 2016 - doi: 10.1016/j.ajhg.2015.05.020 pmc: PMC4572507 pubmed: '26119816' title: 'The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease' year: 2015 - doi: 10.1093/nar/gkt1026 pmc: PMC3965098 pubmed: '24217912' title: 'The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data' year: 2013 - doi: 10.1111/j.1399-0004.2010.01436.x pubmed: '20412080' title: The human phenotype ontology year: 2010 - doi: 10.1016/j.ajhg.2008.09.017 pmc: PMC2668030 pubmed: '18950739' title: 'The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease' year: 2008 rdf_uri_format: http://purl.obolibrary.org/obo/HP_$1 repository: https://github.com/obophenotype/human-phenotype-ontology synonyms: - hpo twitter: hp_ontology uri_format: http://purl.obolibrary.org/obo/HP_$1 version: '2025-01-16' hpa: contact: email: mathias.uhlen@scilifelab.se name: Mathias Uhlen orcid: 0000-0002-4858-8056 description: The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers. example: ENSG00000026508 homepage: http://www.proteinatlas.org/ keywords: - biomedical science - protein - proteomics - structure - systems biology - transcriptomics mappings: biocontext: HPA fairsharing: FAIRsharing.j0t0pe go: HPA miriam: hpa n2t: hpa prefixcommons: hpa re3data: r3d100010931 uniprot: DB-0046 name: Human Protein Atlas tissue profile information pattern: ^ENSG\d{11}$ preferred_prefix: hpa providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/hpa:$1 publications: - doi: 10.1126/science.aan2507 pubmed: '28818916' title: A pathology atlas of the human cancer transcriptome year: 2017 - doi: 10.1126/science.aal3321 pubmed: '28495876' title: A subcellular map of the human proteome year: 2017 - doi: 10.15252/msb.20155865 pmc: PMC4848759 pubmed: '27044256' title: Transcriptomics resources of human tissues and organs year: 2016 - doi: 10.1126/science.1260419 pubmed: '25613900' title: Proteomics. Tissue-based map of the human proteome year: 2015 - doi: 10.1038/nbt1210-1248 pubmed: '21139605' title: Towards a knowledge-based Human Protein Atlas year: 2010 - doi: 10.1002/path.2440 pubmed: '18853439' title: The Human Protein Atlas--a tool for pathology year: 2008 - doi: 10.1074/mcp.r800013-mcp200 pubmed: '18669619' title: A genecentric Human Protein Atlas for expression profiles based on antibodies year: 2008 - doi: 10.1074/mcp.m500279-mcp200 pubmed: '16127175' title: A human protein atlas for normal and cancer tissues based on antibody proteomics year: 2005 - doi: eaal3321 title: A subcellular map of the human proteome. - doi: 10.1074/mcp.R800013-MCP200 title: A genecentric Human Protein Atlas for expression profiles based on antibodies. - doi: 10.1074/mcp.M500279-MCP200 title: A human protein atlas for normal and cancer tissues based on antibody proteomics. twitter: ProteinAtlas uri_format: http://www.proteinatlas.org/$1 hpath: comment: 'This ontology used to be available in OLS3, but is no longer available in OLS4. The URI format string in this resource takes the form of an OBO PURL, but it is not itself registered with the OBO Foundry, and terms therefore redirect into http://ontologies.berkeleybop.org. This happens because the data is curated natively in the OBO Flat File Format from which CURIEs are automatically assumed to expand to OBO PURLs' contact: email: carlo.ravagli@novartis.com github: carloravagli name: Carlo Ravagli orcid: 0000-0001-8372-8387 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species. The original structure of the histopathology ontology was designed ab initio when the [INHAND](http://www.goreni.org/) manuscripts were not available. However, the ontology has been repetitively reviewed and updated to align with the subsequently published INHAND manuscripts. During this process cross references to INHAND lesion identifiers were added to the ontology. [from GitHub]' download_obo: https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo example: '2000191' homepage: https://github.com/Novartis/hpath keywords: - ontology name: Histopathology Ontology pattern: ^\d+$ preferred_prefix: hpath references: - https://github.com/biopragmatics/bioregistry/issues/927 repository: https://github.com/Novartis/hpath synonyms: - MC uri_format: http://purl.obolibrary.org/obo/MC_$1 hpm.peptide: description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra. example: '9606117' homepage: http://www.humanproteomemap.org/index.php mappings: biocontext: HPM.PEPTIDE miriam: hpm.peptide n2t: hpm.peptide name: Human Proteome Map Peptide pattern: ^\d+$ preferred_prefix: hpm.peptide uri_format: http://www.humanproteomemap.org/spectrum.php?pep_id=$1 hpm.protein: description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins. example: '1968' homepage: http://www.humanproteomemap.org/index.php mappings: biocontext: HPM.PROTEIN miriam: hpm.protein n2t: hpm.protein ncbi: HPM name: Human Proteome Map pattern: ^\d+$ preferred_prefix: hpm.protein uri_format: http://www.humanproteomemap.org/protein.php?hpm_id=$1 hprd: contact: email: pandey@jhmi.edu name: Akhilesh Pandey orcid: 0000-0001-9943-6127 description: The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. example: '00001' homepage: http://www.hprd.org/ keywords: - protein - structure mappings: biocontext: HPRD fairsharing: FAIRsharing.y2qws7 integbio: nbdc00103 miriam: hprd n2t: hprd pathguide: '14' prefixcommons: hprd re3data: r3d100010978 name: Human Protein Reference Database pattern: ^\d+$ preferred_prefix: hprd providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/hprd:$1 publications: - doi: 10.1093/nar/gkn892 pmc: PMC2686490 pubmed: '18988627' title: Human Protein Reference Database--2009 update year: 2008 uri_format: http://www.hprd.org/protein/$1 hpscreg: contact: email: stefanie.seltmann@ibmt.fraunhofer.de name: Stefanie Seltmann orcid: 0000-0002-8411-3226 description: hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines). example: BCRTi001-A homepage: https://hpscreg.eu/ keywords: - biomedical science - life science mappings: cellosaurus: hPSCreg fairsharing: FAIRsharing.7C0aVE miriam: hpscreg n2t: hpscreg re3data: r3d100012863 name: Human Pluripotent Stem Cell Registry pattern: ^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$ preferred_prefix: hpscreg publications: - doi: 10.1016/j.scr.2020.101887 pubmed: '32707486' title: 'Access to stem cell data and registration of pluripotent cell lines: The Human Pluripotent Stem Cell Registry (hPSCreg)' year: 2020 - doi: 10.1016/j.stemcr.2020.06.014 pmc: PMC7419703 pubmed: '32679065' title: A Manually Curated Database on Clinical Studies Involving Cell Products Derived from Human Pluripotent Stem Cells year: 2020 - doi: 10.1016/j.scr.2019.101539 pubmed: '31450190' title: 'A pathway for attesting ethical provenance of cell lines: Lessons from the European human pluripotent stem cell registry (hPSC' year: 2019 - doi: 10.1016/j.stemcr.2017.12.002 pmc: PMC5768986 pubmed: '29320760' title: A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells year: 2018 - doi: 10.1093/nar/gkv963 pmc: PMC4702942 pubmed: '26400179' title: hPSCreg--the human pluripotent stem cell registry year: 2015 - doi: S2213-6711(20)30235-6 title: A Manually Curated Database on Clinical Studies Involving Cell Products Derived from Human Pluripotent Stem Cells. - doi: S2213-6711(17)30531-3 title: A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells. - doi: S1873-5061(20)30188-4 title: 'Access to stem cell data and registration of pluripotent cell lines: The Human Pluripotent Stem Cell Registry (hPSCreg).' - doi: S1873-5061(19)30169-2 title: 'A pathway for attesting ethical provenance of cell lines: Lessons from the European human pluripotent stem cell registry (hPSC(reg)).' uri_format: https://hpscreg.eu/cell-line/$1 hsapdv: appears_in: - scdo contact: email: frederic.bastian@unil.ch github: fbastian name: Frédéric Bastian orcid: 0000-0002-9415-5104 description: Life cycle stages for Human download_obo: http://purl.obolibrary.org/obo/hsapdv.obo download_owl: http://purl.obolibrary.org/obo/hsapdv.owl example: 0000194 homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv keywords: - anatomy - developmental biology - life cycle stage - obo - ontology license: CC-BY-3.0 mappings: aberowl: HSAPDV biocontext: HSAPDV biolink: HsapDv bioportal: HSAPDV fairsharing: FAIRsharing.c6vhm3 obofoundry: hsapdv ols: hsapdv ontobee: HsapDv name: Human Developmental Stages pattern: ^\d{7}$ preferred_prefix: HsapDv rdf_uri_format: http://purl.obolibrary.org/obo/HsapDv_$1 repository: https://github.com/obophenotype/developmental-stage-ontologies synonyms: - HsapDv uri_format: http://purl.obolibrary.org/obo/HsapDv_$1 version: '2025-01-23' hsdb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. example: '5621' homepage: https://pubchem.ncbi.nlm.nih.gov/source/hsdb mappings: integbio: nbdc00930 wikidata: P2062 name: Hazardous Substances Data Bank pattern: ^\d+$ preferred_prefix: hsdb uri_format: https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1 hso: contact: email: fernanda.dorea@sva.se github: nandadorea name: Fernanda Dorea orcid: 0000-0001-8638-8525 depends_on: - bfo - ncbitaxon - obi - ro - uberon description: The health Surveillance Ontology (HSO) focuses on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance. download_owl: http://purl.obolibrary.org/obo/hso.owl example: '0000062' homepage: https://w3id.org/hso keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: HSO bioportal: HSO obofoundry: hso ols: hso ontobee: HSO name: Health Surveillance Ontology pattern: ^\d{7}$ preferred_prefix: HSO providers: - code: hso.legacy description: An incorrect encoding of OBO purls homepage: http://purl.obolibrary.org/obo/hso name: HSO Hash uri_format: http://purl.obolibrary.org/obo/hso.owl#HSO_$1 rdf_uri_format: http://purl.obolibrary.org/obo/HSO_$1 repository: https://github.com/SVA-SE/HSO uri_format: http://purl.obolibrary.org/obo/HSO_$1 version: '2021-12-13' hssp: contact: email: chris@sanderlab.org name: Chris Sander orcid: 0000-0001-6059-6270 description: HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein. example: 102l homepage: http://swift.cmbi.kun.nl/swift/hssp/ keywords: - clustering - protein - sequence mappings: biocontext: HSSP miriam: hssp n2t: hssp ncbi: HSSP prefixcommons: hssp name: Database of homology-derived secondary structure of proteins pattern: ^\w{4}$ preferred_prefix: hssp providers: - code: 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 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/hssp:$1 publications: - doi: 10.1093/nar/24.1.201 pmc: PMC145595 pubmed: '8594579' title: The HSSP database of protein structure-sequence alignments year: 1996 - pmc: PMC308328 pubmed: '7937066' title: The HSSP database of protein structure-sequence alignments year: 1994 uri_format: ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2 htn: contact: email: aellenhicks@gmail.com github: aellenhicks name: Amanda Hicks orcid: 0000-0002-1795-5570 description: An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines download_owl: http://purl.obolibrary.org/obo/htn.owl example: '00000014' homepage: https://github.com/aellenhicks/htn_owl keywords: - obo - ontology license: CC-BY-4.0 mappings: aberowl: HTN bioportal: HTN obofoundry: htn ols: htn ontobee: HTN name: Hypertension Ontology pattern: ^\d{8}$ preferred_prefix: HTN rdf_uri_format: http://purl.obolibrary.org/obo/HTN_$1 repository: https://github.com/aellenhicks/htn_owl uri_format: http://purl.obolibrary.org/obo/HTN_$1 huge: contact: email: ohara@kazusa.or.jp name: Osamu Ohara orcid: 0000-0002-3328-9571 description: The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. example: KIAA0001 homepage: http://www.kazusa.or.jp/huge/ keywords: - computational biology - dna - life science - protein - structure mappings: biocontext: HUGE fairsharing: FAIRsharing.zx2ztd integbio: nbdc00104 miriam: huge n2t: huge prefixcommons: huge uniprot: DB-0049 name: Human Unidentified Gene-Encoded pattern: ^KIAA\d{4}$ preferred_prefix: huge providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/huge:$1 publications: - doi: 10.1093/nar/gkh035 pmc: PMC308769 pubmed: '14681467' title: 'HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE' year: 2004 uri_format: https://www.kazusa.or.jp/huge/gfpage/$1 humap: contact: email: ksdrew@uic.edu github: ksdrew name: Kevin Drew orcid: 0000-0002-1260-4413 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The hu.MAP integrates several large scale protein interaction datasets to obtain a comprehensive view of protein complexes. example: huMAP3_04143.1 github_request_issue: 1249 homepage: https://humap3.proteincomplexes.org license: CC0-1.0 name: Human Protein Complex Map preferred_prefix: humap publications: - doi: 10.15252/msb.202010016 pmc: PMC8111494 pubmed: '33973408' title: 'hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies' year: 2021 - doi: 10.15252/msb.20167490 pmc: PMC5488662 pubmed: '28596423' title: Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes year: 2017 synonyms: - humap3 uri_format: https://humap3.proteincomplexes.org/displayComplexes?complex_key=$1 iao: appears_in: - agro - clyh - duo - ecocore - ecto - fovt - labo - maxo - mcro - pco - psdo - xpo contact: email: zhengj2007@gmail.com github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 description: An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch. download_obo: http://purl.obolibrary.org/obo/iao.obo download_owl: http://purl.obolibrary.org/obo/iao.owl example: '0000030' homepage: https://github.com/information-artifact-ontology/IAO/ keywords: - assay - biomedical science - data identity and mapping - data management - drug report - experimental measurement - knowledge and information systems - obo - ontology - protocol - reagent - study design - subject agnostic license: CC-BY-4.0 logo: https://avatars0.githubusercontent.com/u/13591168?v=3&s=200 mappings: aberowl: IAO biocontext: IAO bioportal: IAO fairsharing: FAIRsharing.gq1xtx go: IAO miriam: iao n2t: iao obofoundry: iao ols: iao ontobee: IAO name: Information Artifact Ontology pattern: ^\d{7}$ preferred_prefix: IAO providers: - code: legacy description: A URI from the semanticweb.og homepage: http://www.semanticweb.org name: Legacy URI uri_format: http://www.semanticweb.org/ontologies/2011/9/Ontology1317751904226.owl#IAO_$1 publications: - doi: 10.3233/978-1-61499-101-4-68 pubmed: '22874154' title: An information artifact ontology perspective on data collections and associated representational artifacts year: 2012 rdf_uri_format: http://purl.obolibrary.org/obo/IAO_$1 repository: https://github.com/information-artifact-ontology/IAO uri_format: http://purl.obolibrary.org/obo/IAO_$1 version: '2022-11-07' icd10: contact: email: info@who.int name: World Health Organization contributor_extras: - github: joeflack4 name: Joe Flack orcid: 0000-0002-2906-7319 - email: nicolas.matentzoglu@gmail.com github: matentzn name: Nicolas Matentzoglu orcid: 0000-0002-7356-1779 - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The 10th revision of the International Classification of Diseases (ICD) issued by the World Health Organization (WHO). ICD is formally named ''The International Statistical Classification of Diseases and Related Health Problems''. It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases. Note that the WHO version of ICD-10 is distinct from the ICD-10-CM (Clinical Modification) issued by the U.S. National Center for Health Statistics for use in the United States.' example: C34 example_decoys: - G00X - C34.90 - C4A.8 - C91.Z - C91.Z0 example_extras: - A01.1 - G00 - R25 - R25-R29 - R25.3 - V20 - XVIII homepage: https://icd.who.int/browse10 keywords: - biomedical science - classification - diagnosis - disease - epidemiology - global health - health science - ontology - taxonomy license: https://cdn.who.int/media/docs/default-source/publishing-policies/copyright/who-faq-licensing-icd-10.pdf mappings: aberowl: ICD10 bartoc: '447' biocontext: ICD biolink: ICD10 bioportal: ICD10 edam: '2611' fairsharing: FAIRsharing.nj16g hl7: 2.16.840.1.113883.6.3 miriam: icd n2t: icd prefixcommons: icd wikidata: P494 name: International Classification of Diseases, 10th Revision pattern: ^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\.[0-9]))?))$ preferred_prefix: icd10 providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/icd:$1 - code: icd10_2008 description: The 2008 revision of ICD-10 homepage: https://icd.who.int/browse10/2008/en# name: ICD-10 Version 2008 uri_format: https://icd.who.int/browse10/2008/en#/$1 - code: icd10_2010 description: The 2010 revision of ICD-10 homepage: https://icd.who.int/browse10/2010/en# name: ICD-10 Version 2010 uri_format: https://icd.who.int/browse10/2010/en#/$1 - code: icd10_2014 description: The 2014 revision of ICD-10 homepage: https://icd.who.int/browse10/2014/en# name: ICD-10 Version 2014 uri_format: https://icd.who.int/browse10/2014/en#/$1 - code: icd10_2015 description: The 2015 revision of ICD-10 homepage: https://icd.who.int/browse10/2015/en# name: ICD-10 Version 2015 uri_format: https://icd.who.int/browse10/2015/en#/$1 - code: icd10_2016 description: The 2016 revision of ICD-10 homepage: https://icd.who.int/browse10/2016/en# name: ICD-10 Version 2016 uri_format: https://icd.who.int/browse10/2016/en#/$1 - code: icdcodelookup description: This site is dedicated exclusively to helping you look up ICD-10 codes, quickly access the codes you use most, and become more comfortable with the new code set in general. homepage: https://icdcodelookup.com/icd-10/codes name: ICD Code Lookup uri_format: https://icdcodelookup.com/icd-10/codes/$1 synonyms: - ICD - ICD-10 - ICD10 - ICD10WHO uri_format: https://icd.who.int/browse10/2019/en#/$1 icd10cm: contact: email: pbrooks@hcfa.gov name: Patricia Brooks contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States issued by the National Center for Health Statistics (NCHS) and Centers for Medicare & Medicaid Services (CMS). example: F45.21 example_decoys: - C000 - c00 - C00-D499 - C00-99 - C34.90000 example_extras: - C00-D49 - C34 - C34.90 - C4A.8 - C91.Z - C91.Z0 - T37.0X1A - U49 homepage: https://www.icd10data.com/ICD10CM keywords: - biomedical science - diagnosis - disease - electronic health record - health science - medicine - morbidity - ontology mappings: aberowl: ICD10CM bioportal: ICD10CM fairsharing: FAIRsharing.hpvbxb hl7: 2.16.840.1.113883.6.90 wikidata: P4229 name: International Classification of Diseases, 10th Revision, Clinical Modification pattern: ^([A-Z][0-9][0-9AB]((-[A-Z][0-9][0-9AB])|(\.[0-9A-KXZ]([0-9A-EXYZ]([0-9A-HX][0-59A-HJKMNP-S]?)?)?)?))$ preferred_prefix: icd10cm providers: - code: bioportal.purl description: PURL from BioPortal homepage: http://purl.bioontology.org/ontology/ICD10CM name: BioPortal PURL uri_format: http://purl.bioontology.org/ontology/ICD10CM/$1 synonyms: - ICD10CM uri_format: https://icd.codes/icd10cm/$1 icd10pcs: contact: email: patricia.brooks2@cms.hhs.gov name: Pat Brooks contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis. 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 keywords: - biomedical science - classification - diagnosis - disease - electronic health record - epidemiology - health science - hospital - morbidity - ontology mappings: aberowl: ICD10PCS bioportal: ICD10PCS fairsharing: FAIRsharing.85k1jm hl7: 2.16.840.1.113883.6.4 wikidata: P1690 name: International Classification of Diseases, 10th Revision, Procedure Coding System preferred_prefix: icd10pcs uri_format: https://www.findacode.com/code.php?set=ICD10PCS&c=$1 icd11: comment: Clinical codes from an ICD-11 linearization (a structured subset of the ICD-11 Foundation tailored for specific use cases, such as morbidity or mortality coding), such as RA00.0, have their own namespace (icd11.code). contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - email: nicolas.matentzoglu@gmail.com github: matentzn name: Nicolas Matentzoglu orcid: 0000-0002-7356-1779 description: The ICD-11 Foundation is the comprehensive base layer of the International Classification of Diseases, encompassing all diagnostic concepts, definitions, and semantic relationships, designed for flexibility and adaptability across various use cases, including research, ontology development, and detailed health data analysis. example: '402558626' homepage: https://icd.who.int/ keywords: - biomedical science - diagnosis - disease - electronic health record - epidemiology - global health - health science - morbidity license: CC-BY-ND-3.0-IGO mappings: biolink: icd11.foundation fairsharing: FAIRsharing.97805c hl7: 2.16.840.1.113883.6.347 integbio: nbdc02556 wikidata: P7807 name: International Classification of Diseases, 11th Revision (Foundation Component) pattern: ^[1-9]\d*$ preferred_prefix: icd11 providers: - code: api description: This goes to an API endpoint. For more information, see https://icd.who.int/icdapi homepage: https://icd.who.int name: ICD 11 API Endpoint uri_format: http://id.who.int/icd/entity/$1 - code: foundation description: This goes to the Foundation interface to ICD11 homepage: https://icd.who.int/browse/2024-01/foundation name: ICD 11 Foundation uri_format: https://icd.who.int/browse/2024-01/foundation/en#$1 - code: mms description: This goes to the Mortality and Morbidity Statistics interface to ICD11 homepage: https://icd.who.int/browse/2024-01/mms name: ICD 11 Mortality and Morbidity Statistics uri_format: https://icd.who.int/browse/2024-01/mms/en#$1 rdf_uri_format: http://id.who.int/icd/entity/$1 references: - https://icd.who.int/docs/icd-api/license/ synonyms: - ICD-11 - ICD11 - icd11.foundation uri_format: https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1 icd11.code: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ICD-11 code is a standardized alphanumeric identifier used to classify and document diseases, conditions, and health-related issues for global healthcare and statistical purposes. example: NA06.8D example_extras: - CA71.2 - FB82.00 - XM34M9 github_request_issue: 1349 homepage: https://icd.who.int/en license: http://www.who.int/about/licensing/copyright_form/en name: ICD 11 Codes pattern: ^[0-9A-Z]+(\.[0-9A-Z]+)?$ preferred_prefix: icd11.code references: - https://github.com/biopragmatics/bioregistry/issues/1344 icd9: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics. example: '277.9' homepage: https://www.cdc.gov/nchs/icd/icd9.htm mappings: biolink: ICD9 hl7: 2.16.840.1.113883.6.42 wikidata: P493 name: International Classification of Diseases, 9th Revision pattern: ^(\d\d\d|V\d\d|E[8-9]\d\d)(\.\d{1,2})?$ preferred_prefix: icd9 synonyms: - ICD9 - ICD9_2005 - MTHICD9_2006 uri_format: http://www.icd9data.com/getICD9Code.ashx?icd9=$1 icd9cm: contact: email: pbrooks@hcfa.gov name: Patricia Brooks contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States. example: '784' homepage: https://www.cdc.gov/nchs/icd/icd9cm.htm keywords: - biomedical science - diagnosis - disease - epidemiology - health science - medicine - morbidity - ontology - preclinical studies mappings: aberowl: ICD9CM bioportal: ICD9CM fairsharing: FAIRsharing.10zsxb hl7: 2.16.840.1.113883.6.2 wikidata: P1692 name: International Classification of Diseases, 9th Revision, Clinical Modification pattern: ^([\dA-Z]\d{2}(\.\d{1,3}|))|(\d{2}(\.\d{1,2}|))$ preferred_prefix: icd9cm synonyms: - IC9CM - ICD9CM - ICD9CM_2005 - ICD9CM_2006 - ICDCM_2005 uri_format: http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1 icdc: contact: email: annika.jahnke-bornemann@uni-hamburg.de name: Annika Jahnke-Bornemann orcid: 0000-0001-7815-151X description: The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer. example: 000009 homepage: https://caninecommons.cancer.gov/#/ keywords: - atmospheric science - earth science - meteorology - oceanography - remote sensing - social science mappings: fairsharing: FAIRsharing.d95034 miriam: icdc re3data: r3d100010405 name: Integrated Canine Data Commons pattern: ^\d{6}$ preferred_prefix: icdc twitter: ICDC_Hamburg uri_format: https://caninecommons.cancer.gov/#/study/$1 icdo: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases example: 9861/3 homepage: https://www.who.int/classifications/icd/adaptations/oncology/en/ mappings: bartoc: '445' hl7: 2.16.840.1.113883.6.43 prefixcommons: icdo wikidata: P563 name: International Classification of Diseases for Oncology pattern: ^[8-9]\d{3}(/[0-3])?$ preferred_prefix: icdo providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/icdo:$1 synonyms: - ICD-O - ICDO uri_format: http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1 iceberg.cime: contact: email: hyou@sjtu.edu.cn name: Hong-Yu Ou orcid: 0000-0001-9439-1660 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements. example: '6' homepage: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_CIME.php?type=alpha&alpha=100 keywords: - biology - genomics name: ICEberg cis-integrative and mobilizable element part_of: iceberg pattern: ^\d+$ preferred_prefix: iceberg.cime publications: - doi: 10.1093/nar/gky1123 pmc: PMC6323972 pubmed: '30407568' title: 'ICEberg 2.0: an updated database of bacterial integrative and conjugative elements' year: 2019 - doi: 10.1093/nar/gkr846 pmc: PMC3244999 pubmed: '22009673' title: 'ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria' year: 2011 uri_format: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php?cime_id=$1_CIME iceberg.element: description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements. example: '100' homepage: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=alpha&alpha=100 mappings: biocontext: ICEBERG.ELEMENT miriam: iceberg.element n2t: iceberg.element name: ICEberg integrative and conjugative element part_of: iceberg pattern: ^\d+$ preferred_prefix: iceberg.element publications: - doi: 10.1093/nar/gky1123 pmc: PMC6323972 pubmed: '30407568' title: 'ICEberg 2.0: an updated database of bacterial integrative and conjugative elements' year: 2019 - doi: 10.1093/nar/gkr846 pmc: PMC3244999 pubmed: '22009673' title: 'ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria' year: 2011 synonyms: - iceberg.ice uri_format: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=$1 iceberg.family: contact: email: hyou@sjtu.edu.cn name: Hong-Yu Ou orcid: 0000-0001-9439-1660 description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families. example: '1' homepage: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_fam.php mappings: biocontext: ICEBERG.FAMILY miriam: iceberg.family n2t: iceberg.family name: ICEberg family part_of: iceberg pattern: ^\d+$ preferred_prefix: iceberg.family publications: - doi: 10.1093/nar/gky1123 pmc: PMC6323972 pubmed: '30407568' title: 'ICEberg 2.0: an updated database of bacterial integrative and conjugative elements' year: 2019 - doi: 10.1093/nar/gkr846 pmc: PMC3244999 pubmed: '22009673' title: 'ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria' year: 2011 uri_format: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id=$1 iceberg.ime: contact: email: hyou@sjtu.edu.cn name: Hong-Yu Ou orcid: 0000-0001-9439-1660 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements. example: '1' homepage: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_IME.php?type=alpha&alpha=100 keywords: - biology - genomics name: ICEberg integrative and mobilizable element part_of: iceberg pattern: ^\d+$ preferred_prefix: iceberg.ime publications: - doi: 10.1093/nar/gky1123 pmc: PMC6323972 pubmed: '30407568' title: 'ICEberg 2.0: an updated database of bacterial integrative and conjugative elements' year: 2019 - doi: 10.1093/nar/gkr846 pmc: PMC3244999 pubmed: '22009673' title: 'ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria' year: 2011 uri_format: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.php?ime_id=$1_IME icechem: description: 'The Integrated Chemical Environment (ICE) provides high-quality curated data and appropriate tools to support development and evaluation of new, revised, and alternative methods. ICE provides free online access to curated in vivo and in vitro test data, in silico toxicity predictions and chemical property data, reference chemical lists, and computational tools for chemical characterization and predicting toxicity. ICE supports the following: (i) Data integration: brings together available data, including data on formulations; (ii) Results exploration: enables dynamic, graphical exploration with publication-quality graphics; (iii) Data analysis: allows characterization of data using online workflows, and (iv) FAIR data access: data are findable, accessible, interoperable, and reusable.' example: DTXSID7032004 homepage: https://ice.ntp.niehs.nih.gov mappings: miriam: ice.chem name: Integrated Chemical Environment - Chemical data pattern: ^\d{2,7}-\d{2}-\d|DTXSID\d{7,9}|[A-Z]{14}-[A-Z]{8}[SN][A-Z]-[A-Z]$ preferred_prefix: icechem uri_format: https://ice.ntp.niehs.nih.gov/api/v1/search?chemid=$1 iceo: comment: ICEO is not consistent about its identfiers like ICEO:0000595:1 and ICEO:0000595_1 contact: email: liumeng94@sjtu.edu.cn github: Lemon-Liu name: Meng LIU orcid: 0000-0003-3781-6962 description: A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning. download_owl: http://purl.obolibrary.org/obo/iceo.owl example: '0000712_1' example_extras: - '0000712' homepage: https://github.com/ontoice/ICEO keywords: - obo - ontology license: CC-BY-4.0 mappings: aberowl: ICEO bioportal: ICEO obofoundry: iceo ols: iceo ontobee: ICEO name: Integrative and Conjugative Element Ontology pattern: ^\d{7}(_\d)?$ preferred_prefix: ICEO publications: - doi: 10.1038/s41597-021-01112-5 pmc: PMC8776819 pubmed: '35058462' title: ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements year: 2022 rdf_uri_format: http://purl.obolibrary.org/obo/ICEO_$1 repository: https://github.com/ontoice/ICEO uri_format: http://purl.obolibrary.org/obo/ICEO_$1 version: '2.1' icepo: contact: email: pascale.gaudet@isb-sib.ch github: pgaudet name: Pascale Gaudet orcid: 0000-0003-1813-6857 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. ' download_obo: https://download.nextprot.org/pub/current_release/controlled_vocabularies/icepo.obo example: '0000002' homepage: https://download.nextprot.org/pub/current_release/controlled_vocabularies/ keywords: - ontology name: Ion Channel Electrophysiology Ontology pattern: ^\d{7}$ preferred_prefix: icepo publications: - pmc: PMC4823818 title: 'ICEPO: the ion channel electrophysiology ontology' twitter: neXtProt_news uri_format: https://biopragmatics.github.io/providers/icepo/$1 icf: comment: This might be possible to roll directly into ICD11 contact: email: info@who.int name: The World Health Organization contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. As the functioning and disability of an individual occurs in a context, ICF also includes a list of environmental factors. ICF is the WHO framework for measuring health and disability at both individual and population levels. download_owl: http://aber-owl.net/media/ontologies/ICF/3/icf.owl example: '326705068' homepage: https://icd.who.int/dev11/l-icf/en keywords: - biomedical science - electronic health record - health science - medicine - ontology - primary health care mappings: aberowl: ICF bioportal: ICF fairsharing: FAIRsharing.7rngj0 hl7: 2.16.840.1.113883.6.254 name: International Classification of Functioning, Disability and Health pattern: ^\d+$ preferred_prefix: icf uri_format: https://icd.who.int/dev11/l-icf/en#/http://id.who.int/icd/entity/$1 iclc: description: Cell line collections (Providers) example: ATL98012 homepage: http://www.iclc.it mappings: cellosaurus: ICLC name: Interlab Cell Line Collection pattern: ^\w{3}\d+$ preferred_prefix: iclc uri_format: http://www.iclc.it/details/det_list.php?line_id=$1 icldb: contact: email: surjeet.arya@uky.edu name: Surjeet Kumar Arya orcid: 0000-0002-2212-4771 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: We have developed an online database describing the known cell lines from Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera that originated from crop pest insects. Cell line information has been primarily obtained from previous compilations of insect cell lines. (from homepage) example: 64ba homepage: https://entomology.ca.uky.edu/aginsectcellsdatabase mappings: cellosaurus: ICLDB name: Insect Cell Line Database preferred_prefix: icldb uri_format: https://entomology.ca.uky.edu/content/$1 ico: appears_in: - scdo contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field. download_owl: http://purl.obolibrary.org/obo/ico.owl example: '0000066' homepage: https://github.com/ICO-ontology/ICO keywords: - biomedical science - clinical studies - health science - medicine - obo - ontology license: CC-BY-3.0 mappings: aberowl: ICO biocontext: ICO bioportal: ICO fairsharing: FAIRsharing.b9znd5 obofoundry: ico ols: ico ontobee: ICO name: Informed Consent Ontology pattern: ^\d{7}$ preferred_prefix: ICO rdf_uri_format: http://purl.obolibrary.org/obo/ICO_$1 repository: https://github.com/ICO-ontology/ICO uri_format: http://purl.obolibrary.org/obo/ICO_$1 version: 1.0.187 ideal: contact: email: sfukuchi@maebashi-it.ac.jp github: sfukuchi name: Satoshi Fukuchi orcid: 0000-0002-5705-3061 description: IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. example: IID00001 homepage: https://www.ideal-db.org keywords: - biology mappings: biocontext: IDEAL fairsharing: FAIRsharing.h3y42f integbio: nbdc01456 miriam: ideal n2t: ideal pathguide: '701' uniprot: DB-0251 name: Intrinsically Disordered proteins with Extensive Annotations and Literature pattern: ^IID\d+$ preferred_prefix: ideal publications: - doi: 10.1093/nar/gkt1010 pmc: PMC3965115 pubmed: '24178034' title: IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners year: 2013 uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1 ido: appears_in: - scdo contact: email: Lindsay.Cowell@utsouthwestern.edu github: lgcowell name: Lindsay Cowell orcid: 0000-0003-1617-8244 contributor_extras: - email: github@yohannparis.com github: YohannParis name: Yohann Paris orcid: 0009-0006-6049-1392 description: Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases. download_owl: http://purl.obolibrary.org/obo/ido.owl example: '0000504' homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology keywords: - biomedical science - classification - disease - disease process modeling - molecular infection biology - obo - ontology - preclinical studies license: CC-BY-3.0 mappings: aberowl: IDO biocontext: IDO bioportal: IDO fairsharing: FAIRsharing.aae3v6 miriam: ido n2t: ido obofoundry: ido ols: ido ontobee: IDO name: Infectious Disease Ontology pattern: ^\d{7}$ preferred_prefix: IDO providers: - code: obo.1 description: This incorrect encoding was found inside IDO-COVID-19 homepage: http://purl.obolibrary.org name: Nonstandard OBO PURL uri_format: http://purl.obolibrary.org/obo/ido.owl/IDO_$1 publications: - doi: 10.1186/s13326-021-00245-1 pmc: PMC8286442 pubmed: '34275487' title: The Infectious Disease Ontology in the age of COVID-19 year: 2021 rdf_uri_format: http://purl.obolibrary.org/obo/IDO_$1 repository: https://github.com/infectious-disease-ontology/infectious-disease-ontology uri_format: http://purl.obolibrary.org/obo/IDO_$1 version: '2017-11-03' idocovid19: contact: email: johnbeverley2021@u.northwestern.edu github: johnbeve name: John Beverly orcid: 0000-0002-1118-1738 description: The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease. download_owl: https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19 example: 0001191 homepage: https://github.com/infectious-disease-ontology-extensions/ido-covid-19 keywords: - ontology mappings: aberowl: IDO-COVID-19 bioportal: IDO-COVID-19 ols: idocovid19 name: The COVID-19 Infectious Disease Ontology pattern: ^\d{7}$ preferred_prefix: idocovid19 providers: - code: obo1 description: This variation uses incorrect usage of dashes instead of underscores homepage: http://purl.obolibrary.org name: Incorrect OBO PURL variation 1 uri_format: http://purl.obolibrary.org/obo/IDO-COVID-19_$1 repository: https://github.com/infectious-disease-ontology-extensions/ido-covid-19 uri_format: http://purl.obolibrary.org/obo/COVIDO_$1 version: '2020-07-21' idoden: contact: email: elvira@imbb.forth.gr name: Elvira Mitraka orcid: 0000-0003-0719-3485 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology for dengue fever. download_owl: http://aber-owl.net/media/ontologies/IDODEN/6/idoden.owl example: '0003463' homepage: https://bioportal.bioontology.org/ontologies/IDODEN keywords: - medicine - ontology mappings: aberowl: IDODEN bioportal: IDODEN fairsharing: FAIRsharing.askzq4 name: Dengue Fever Ontology pattern: ^\d{7}$ preferred_prefix: idoden references: - https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003479 uri_format: http://purl.bioontology.org/ontology/IDODEN_$1 idog: contact: email: baoym@big.ac.cn name: Yiming Bao orcid: 0000-0002-9922-9723 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Provides the worldwide dog research community a variety of data services including access to genes, genomes, SNPs, breed/disease Traits, gene expression experiments, dog-guman homology, and literatur. In addition, iDog provides online tools for performing genomic data visualization and analyses. example: '4' homepage: https://ngdc.cncb.ac.cn/idog/ license: CC-BY-4.0 mappings: integbio: nbdc02480 re3data: r3d100012176 name: Integrated Resource for Domestic Dog pattern: ^\d+$ preferred_prefix: idog publications: - doi: 10.1093/nar/gky1041 pmc: PMC6323916 pubmed: '30371881' title: 'iDog: an integrated resource for domestic dogs and wild canids' year: 2019 references: - https://github.com/biopragmatics/bioregistry/pull/725 uri_format: https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=$1 idomal: appears_in: - scdo contact: email: topalis@imbb.forth.gr name: Pantelis Topalis orcid: 0000-0002-1635-4810 deprecated: true description: An application ontology to cover all aspects of malaria as well as the intervention attempts to control it. download_obo: http://purl.obolibrary.org/obo/idomal.obo download_owl: http://purl.obolibrary.org/obo/idomal.owl example: '0002350' example_extras: - '50000015' homepage: https://www.vectorbase.org/ontology-browser keywords: - biomedical science - disease - intervention design - life science - malaria - molecular infection biology - obo - ontology - pathogen license: CC0-1.0 mappings: aberowl: IDOMAL biocontext: IDOMAL bioportal: IDOMAL fairsharing: FAIRsharing.2q8c28 obofoundry: idomal ols: idomal ontobee: IDOMAL name: Malaria Ontology pattern: ^(5?)\d{7}$ preferred_prefix: IDOMAL publications: - doi: 10.1186/2041-1480-4-16 pmc: PMC3848731 pubmed: '24034841' title: 'IDOMAL: the malaria ontology revisited' year: 2013 - doi: 10.1186/1475-2875-9-230 pmc: PMC2925367 pubmed: '20698959' title: 'IDOMAL: an ontology for malaria' year: 2010 rdf_uri_format: http://purl.obolibrary.org/obo/IDOMAL_$1 repository: https://github.com/VEuPathDB-ontology/IDOMAL twitter: VectorBase uri_format: http://purl.obolibrary.org/obo/IDOMAL_$1 version: '2015-03-16' idoo: description: Identifiers.org Ontology example: DataCollection homepage: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology mappings: miriam: idoo n2t: idoo name: Identifiers.org Ontology pattern: ^[0-9a-zA-Z]+$ preferred_prefix: idoo uri_format: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1 idot: description: Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets. example: identifierPattern homepage: http://biomodels.net/vocab/idot.rdf mappings: biocontext: idot miriam: idot n2t: idot name: Identifiers.org Terms pattern: ^[A-Za-z]+$ preferred_prefix: idot uri_format: https://biomodels.net/vocab/idot.rdf#$1 idpo: contact: email: f.quaglia@ibiom.cnr.it github: federicaquaglia name: Federica Quaglia orcid: 0000-0002-0341-4888 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR. example: '00056' homepage: https://www.disprot.org/ontology keywords: - protein analysis - protein structure - proteins - proteomics - structural biochemistry - structural bioinformatics - structural biology mappings: fairsharing: FAIRsharing.bc973b name: Intrinsically Disordered Proteins Ontology pattern: ^\d{5}$ preferred_prefix: idpo publications: - doi: 10.1093/nar/gkad928 pubmed: '37904585' title: 'DisProt in 2024: improving function annotation of intrinsically disordered proteins' year: 2024 - doi: 10.1093/database/baae009 title: Best practices for the manual curation of intrinsically disordered proteins in DisProt year: 2024 uri_format: https://www.disprot.org/idpo/IDPO:$1 idr: contact: email: j.a.moore@dundee.ac.uk name: Josh Moore orcid: 0000-0003-4028-811X description: Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools. example: '0001' homepage: https://idr.openmicroscopy.org keywords: - biomedical science - botany - life science mappings: fairsharing: FAIRsharing.6wf1zw miriam: idr re3data: r3d100012435 name: Image Data Resource pattern: ^[0-9]{4}$ preferred_prefix: idr publications: - doi: 10.1038/nmeth.4326 pmc: PMC5536224 pubmed: '28775673' title: 'The Image Data Resource: A Bioimage Data Integration and Publication Platform' year: 2017 twitter: openmicroscopy uri_format: https://idr.openmicroscopy.org/search/?query=Name:idr$1 iedb.assay: contact: email: rvita@liai.org github: rvita name: Randi Vita orcid: 0000-0001-8957-7612 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for specific experimental assays that serve as evidence for immune-related studies. example: '1691753' github_request_issue: 1204 homepage: https://www.iedb.org/ keywords: - bioinformatics - immunology - life science mappings: fairsharing: FAIRsharing.c886cd integbio: nbdc00924 re3data: r3d100012702 name: Immune Epitope Database Assays part_of: iedb pattern: ^\d+$ preferred_prefix: iedb.assay publications: - doi: 10.1093/nar/gku938 pmc: PMC4384014 pubmed: '25300482' title: The immune epitope database (IEDB) 3.0 year: 2014 - doi: 10.1111/j.1365-2567.2012.03611.x pmc: PMC3461392 pubmed: '22681406' title: 'The immune epitope database: a historical retrospective of the first decade' year: 2012 - doi: 10.1093/nar/gkp1004 pmc: PMC2808938 pubmed: '19906713' title: The immune epitope database 2.0 year: 2009 - pubmed: '16312048' title: 'The immune epitope database and analysis resource: from vision to blueprint' year: 2004 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://www.iedb.org/assay/$1 iedb.epitope: contact: email: rvita@liai.org github: rvita name: Randi Vita orcid: 0000-0001-8957-7612 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for epitopes, which are the specific parts of antigens recognized by the immune system. example: '117395' github_request_issue: 1204 homepage: https://www.iedb.org/ keywords: - bioinformatics - immunology - life science - protein - small molecule mappings: fairsharing: FAIRsharing.c886cd integbio: nbdc00924 prefixcommons: tied re3data: r3d100012702 name: Immune Epitope Database Epitopes part_of: iedb pattern: ^\d+$ preferred_prefix: iedb.epitope providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/tied:$1 publications: - doi: 10.1093/nar/gku938 pmc: PMC4384014 pubmed: '25300482' title: The immune epitope database (IEDB) 3.0 year: 2014 - doi: 10.1111/j.1365-2567.2012.03611.x pmc: PMC3461392 pubmed: '22681406' title: 'The immune epitope database: a historical retrospective of the first decade' year: 2012 - doi: 10.1093/nar/gkp1004 pmc: PMC2808938 pubmed: '19906713' title: The immune epitope database 2.0 year: 2009 - pubmed: '16312048' title: 'The immune epitope database and analysis resource: from vision to blueprint' year: 2004 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://www.iedb.org/epitope/$1 iedb.mhc: contact: email: rvita@liai.org github: rvita name: Randi Vita orcid: 0000-0001-8957-7612 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for Major Histocompatibility Complex (MHC) restrictions of immune cells, detailing genetic factors that influence immune recognition. example: '86' github_request_issue: 1204 homepage: https://www.iedb.org/ keywords: - bioinformatics - immunology - life science mappings: fairsharing: FAIRsharing.c886cd integbio: nbdc00924 re3data: r3d100012702 name: Immune Epitope Database MHC Restrictions part_of: iedb pattern: ^\d+$ preferred_prefix: iedb.mhc publications: - doi: 10.1093/nar/gku938 pmc: PMC4384014 pubmed: '25300482' title: The immune epitope database (IEDB) 3.0 year: 2014 - doi: 10.1111/j.1365-2567.2012.03611.x pmc: PMC3461392 pubmed: '22681406' title: 'The immune epitope database: a historical retrospective of the first decade' year: 2012 - doi: 10.1093/nar/gkp1004 pmc: PMC2808938 pubmed: '19906713' title: The immune epitope database 2.0 year: 2009 - pubmed: '16312048' title: 'The immune epitope database and analysis resource: from vision to blueprint' year: 2004 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://www.iedb.org/mhc/$1 iedb.receptor: contact: email: rvita@liai.org github: rvita name: Randi Vita orcid: 0000-0001-8957-7612 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for immune receptors, representing receptor complexes or groups studied for their interactions with antigens or epitopes. example: '47' github_request_issue: 1204 homepage: https://www.iedb.org/ keywords: - bioinformatics - immunology - life science mappings: fairsharing: FAIRsharing.c886cd integbio: nbdc00924 re3data: r3d100012702 name: Immune Epitope Database Receptors part_of: iedb pattern: ^\d+$ preferred_prefix: iedb.receptor publications: - doi: 10.1093/nar/gku938 pmc: PMC4384014 pubmed: '25300482' title: The immune epitope database (IEDB) 3.0 year: 2014 - doi: 10.1111/j.1365-2567.2012.03611.x pmc: PMC3461392 pubmed: '22681406' title: 'The immune epitope database: a historical retrospective of the first decade' year: 2012 - doi: 10.1093/nar/gkp1004 pmc: PMC2808938 pubmed: '19906713' title: The immune epitope database 2.0 year: 2009 - pubmed: '16312048' title: 'The immune epitope database and analysis resource: from vision to blueprint' year: 2004 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://www.iedb.org/receptor/$1 iedb.reference: contact: email: rvita@liai.org github: rvita name: Randi Vita orcid: 0000-0001-8957-7612 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for references, typically linking to sources of evidence such as publications that support data within IEDB. example: '1038233' github_request_issue: 1204 homepage: https://www.iedb.org/ keywords: - bioinformatics - immunology - life science mappings: fairsharing: FAIRsharing.c886cd integbio: nbdc00924 miriam: iedb re3data: r3d100012702 name: Immune Epitope Database References part_of: iedb pattern: ^\d+$ preferred_prefix: iedb.reference publications: - doi: 10.1093/nar/gku938 pmc: PMC4384014 pubmed: '25300482' title: The immune epitope database (IEDB) 3.0 year: 2014 - doi: 10.1111/j.1365-2567.2012.03611.x pmc: PMC3461392 pubmed: '22681406' title: 'The immune epitope database: a historical retrospective of the first decade' year: 2012 - doi: 10.1093/nar/gkp1004 pmc: PMC2808938 pubmed: '19906713' title: The immune epitope database 2.0 year: 2009 - pubmed: '16312048' title: 'The immune epitope database and analysis resource: from vision to blueprint' year: 2004 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://www.iedb.org/reference/$1 ieee.author: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier for an author in IEEE Xplore example: '37271072100' homepage: https://ieeexplore.ieee.org keywords: - person - researcher mappings: wikidata: P6479 name: IEEE Xplore author ID pattern: ^[1-9]\d*$ preferred_prefix: ieee.author references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://ieeexplore.ieee.org/author/$1 ieee.document: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier for a document in IEEE Xplore example: '1580791' homepage: https://ieeexplore.ieee.org mappings: wikidata: P6480 name: IEEE Xplore document ID pattern: ^[1-9]\d*$ preferred_prefix: ieee.document references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://ieeexplore.ieee.org/document/$1 ietf.language: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Shorthand representations of languages and their subtypes example: en-GB example_extras: - aaf - ar-SA - en homepage: http://www.iana.org/assignments/language-subtag-registry/language-subtag-registry mappings: bartoc: '2022' wikidata: P305 name: Internet Engineering Task Force Language Tag pattern: ^\w{2,3}(-\w+)?$ preferred_prefix: ietf.language synonyms: - bcp47 iev: deprecated: true description: The Event Ontology is an ontology of pathways. It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure. example: '0000000' homepage: http://www.inoh.org keywords: - obo - ontology - pathway - structure mappings: biocontext: IEV obofoundry: iev prefixcommons: iev name: Event (INOH pathway ontology) pattern: ^\d{7}$ preferred_prefix: IEV providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/iev:$1 rdf_uri_format: http://purl.obolibrary.org/obo/IEV_$1 uri_format: http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IEV&id=$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=$1 igsn: contact: email: jens.klump@csiro.au github: jklump name: Jens Klump orcid: 0000-0001-5911-6022 description: IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents. example: AU124 homepage: https://ev.igsn.org/home keywords: - archaeology - citation - data management - earth science - environmental science - geochemistry - geology - hydrogeology - persistent identifier - physical samples - resource metadata logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaVVDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--4d19e53906f86cdaca6a9752fde1dd82276b7f22/igsn-original.jpg?disposition=inline mappings: fairsharing: FAIRsharing.c7f365 miriam: igsn n2t: igsn name: International Generic Sample Number pattern: ^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$ preferred_prefix: igsn publications: - doi: 10.5334/dsj-2023-005 title: 'Scaling Identifiers and their Metadata to Gigascale: An Architecture to Tackle the Challenges of Volume and Variety' year: 2023 - doi: 10.5334/dsj-2021-033 title: 'Towards Globally Unique Identification of Physical Samples: Governance and Technical Implementation of the IGSN Global Sample Number' year: 2021 - doi: 10.5334/dsj-2017-002 title: Utilizing the International Geo Sample Number Concept in Continental Scientific Drilling During ICDP Expedition COSC-1 year: 2017 - doi: 10.5281/zenodo.5118289 title: 'IGSN 2040 Summary Report: Defining the Future of the IGSN as a Global Persistent Identifier for Material Samples' year: 2021 - doi: 10.1007/978-3-030-85040-1_162 title: International Generic Sample Number year: 2023 repository: https://igsn.github.io/ uri_format: http://igsn.org/$1 igsr: contact: email: flicek@ebi.ac.uk name: Paul Flicek orcid: 0000-0002-3897-7955 description: 'The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project.' example: NA06985 homepage: https://www.internationalgenome.org/ keywords: - comparative genomics - genomics mappings: cellosaurus: IGSR fairsharing: FAIRsharing.4Vs9VM re3data: r3d100010180 name: International Genome Sample Resource preferred_prefix: igsr publications: - doi: 10.1093/nar/gkz836 pmc: PMC6943028 pubmed: '31584097' title: The International Genome Sample Resource (IGSR) collection of open human genomic variation resources year: 2020 - doi: 10.1038/nature15393 pmc: PMC4750478 pubmed: '26432245' title: A global reference for human genetic variation year: 2015 twitter: 1000genomes uri_format: https://www.internationalgenome.org/data-portal/sample/$1 ihw: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics. example: IHW09326 homepage: https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html mappings: cellosaurus: IHW name: International Histocompatibility Workshop cell lines pattern: ^IHW\d+$ preferred_prefix: ihw illumina.probe: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip. example: ILMN_129894 homepage: https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6790/A-GEOD-6790.adf.txt keywords: - transcriptomics name: Illumina Probe Identifier pattern: ^ILMN_\d+$ preferred_prefix: illumina.probe references: - https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-9184/A-GEOD-9184_comments.txt imanis: description: Cell line collections (Providers) example: CL070 homepage: https://www.imanislife.com/collections/cell-lines/ mappings: cellosaurus: Imanis name: Imanis Life Sciences cell line products preferred_prefix: imanis uri_format: https://www.imanislife.com/?s=$1 imdrf: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence. homepage: http://www.imdrf.org/ name: International Medical Device Regulators Forum no_own_terms: true preferred_prefix: imdrf references: - https://www.fda.gov/medical-devices/mandatory-reporting-requirements-manufacturers-importers-and-device-user-facilities/mdr-adverse-event-codes imex: banana: IM banana_peel: '-' contact: email: orchard@ebi.ac.uk github: sandraorchard name: Sandra Orchard orcid: 0000-0002-8878-3972 description: The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources. example: 19210-3 example_extras: - '19210' homepage: https://www.imexconsortium.org/ keywords: - interaction - molecule mappings: biocontext: IMEX miriam: imex n2t: imex pathguide: '422' prefixcommons: imex re3data: r3d100010669 name: International Molecular Exchange owners: - name: European Bioinformatics Institute partnered: false ror: 02catss52 pattern: ^\d+(-\d+)?$ preferred_prefix: imex providers: - code: CURATOR_REVIEW description: IMEx Consortium though Intact homepage: https://www.ebi.ac.uk/intact/ name: IMEx Consortium though Intact uri_format: https://imexcentral.org/icentral/imex/rec/$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/imex:$1 - code: intact.search description: Search page on IntAct homepage: https://www.ebi.ac.uk/intact name: IntAct Search uri_format: https://www.ebi.ac.uk/intact/search?query=IM-$1 publications: - doi: 10.1002/pmic.200700286 pubmed: '17893861' title: 'Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition' year: 2007 uri_format: https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-$1 img.gene: contact: email: nckyrpides@lbl.gov name: Nikos C. Kyrpides orcid: 0000-0002-6131-0462 description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information. example: '638309541' homepage: http://img.jgi.doe.gov/ keywords: - gene - genome mappings: biocontext: IMG.GENE miriam: img.gene n2t: img.gene prefixcommons: img.gene name: Integrated Microbial Genomes Gene pattern: ^\d+$ preferred_prefix: img.gene providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/img.gene:$1 publications: - doi: 10.1093/nar/gkm846 pmc: PMC2238897 pubmed: '17933782' title: 'The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions' year: 2007 uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1 img.taxon: contact: email: nckyrpides@lbl.gov name: Nikos C. Kyrpides orcid: 0000-0002-6131-0462 description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information. example: '648028003' homepage: http://img.jgi.doe.gov/ keywords: - genome - taxonomy mappings: biocontext: IMG.TAXON miriam: img.taxon n2t: img.taxon prefixcommons: img.taxon name: Integrated Microbial Genomes Taxon pattern: ^\d+$ preferred_prefix: img.taxon providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/img.taxon:$1 publications: - doi: 10.1093/nar/gkm846 pmc: PMC2238897 pubmed: '17933782' title: 'The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions' year: 2007 uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1 imgt.hla: contact: email: steven.marsh@ucl.ac.uk name: Steven G. E. Marsh orcid: 0000-0003-2855-4120 description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature. example: A*01:01:01:01 homepage: https://www.ebi.ac.uk/imgt/hla/allele.html keywords: - biomedical science - dna - immunogenetics - immunology - protein - rna mappings: biocontext: IMGT.HLA cellosaurus: IPD-IMGT/HLA edam: '2773' fairsharing: FAIRsharing.e28v7g go: IMGT_HLA integbio: nbdc00106 miriam: imgt.hla n2t: imgt.hla ncbi: IMGT/HLA prefixcommons: imgthla re3data: r3d100010804 name: IMGT/HLA human major histocompatibility complex sequence database owners: - name: European Bioinformatics Institute partnered: false ror: 02catss52 pattern: ^[A-Z0-9*:]+$ preferred_prefix: imgt.hla providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/imgthla:$1 publications: - doi: 10.1093/nar/gkz950 pmc: PMC7145640 pubmed: '31667505' title: IPD-IMGT/HLA Database year: 2020 - doi: 10.1093/nar/gku1161 pmc: PMC4383959 pubmed: '25414341' title: 'The IPD and IMGT/HLA database: allele variant databases' year: 2014 - doi: 10.1093/nar/gkn662 pmc: PMC2686596 pubmed: '18838392' title: The IMGT/HLA database year: 2008 - doi: 10.1007/978-1-60327-118-9_3 pubmed: '18449991' title: The IMGT/HLA database year: 2007 - doi: 10.1002/humu.20406 pubmed: '16944494' title: The IMGT/HLA and IPD databases year: 2006 - doi: 10.1093/nar/gkj088 pmc: PMC1347451 pubmed: '16381979' title: IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences year: 2006 - doi: 10.1093/nar/gkg070 pmc: PMC165517 pubmed: '12520010' title: 'IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex' year: 2003 - doi: 10.1093/nar/29.1.210 pmc: PMC29780 pubmed: '11125094' title: IMGT/HLA Database--a sequence database for the human major histocompatibility complex year: 2001 - doi: 10.1034/j.1399-0039.2000.550314.x pubmed: '10777106' title: IMGT/HLA database--a sequence database for the human major histocompatibility complex year: 2000 synonyms: - IPD-IMGT/HLA uri_format: https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1 imgt.ligm: contact: email: marie-paule.lefranc@umontpellier.fr name: Marie-Paule Lefranc orcid: 0000-0003-0116-9353 description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates. example: M94112 homepage: http://www.imgt.org/ keywords: - dna mappings: biocontext: IMGT.LIGM go: IMGT_LIGM miriam: imgt.ligm n2t: imgt.ligm ncbi: IMGT/LIGM prefixcommons: imgt.ligm name: ImMunoGeneTics database covering immunoglobulins and T-cell receptors pattern: ^M\d+$ preferred_prefix: imgt.ligm providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/imgt.ligm:$1 publications: - doi: 10.1093/nar/gkj088 pmc: PMC1347451 pubmed: '16381979' title: IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences year: 2006 uri_format: http://www.imgt.org/ligmdb/view?id=$1 imgt.primerdb: description: The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR). example: IPP900099 homepage: http://imgt.org/IMGTPrimerDB/ keywords: - dna mappings: prefixcommons: imgt.primerdb re3data: r3d100012535 name: IMGT/PRIMER-DB preferred_prefix: imgt.primerdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/imgt.primerdb:$1 uri_format: http://imgt.org/IMGTPrimerDB/Check_PrDB.pl?numacc0=$1&origin=view&source=PrList imotdb: comment: This resource doesn't exist on the web anymore deprecated: true description: The interacting motif database or iMOTdb , lists interacting motifs thatare identified for all structural entries in the PDB. The conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting the common motifs shared among all superfamily members. example: '53784' homepage: http://caps.ncbs.res.in/imotdb/ keywords: - interaction - protein mappings: pathguide: '207' prefixcommons: imotdb name: Database of Spatially Interacting Motifs in Proteins preferred_prefix: imotdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/imotdb:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode=$1 imr: contact: email: curator@inoh.org name: INOH curators deprecated: true description: MoleculeRole Ontology is an ontology for proteins/chemicals. It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data. example: '0000001' homepage: http://www.inoh.org keywords: - obo - ontology - protein - small molecule mappings: biocontext: IMR obofoundry: imr prefixcommons: imr name: Molecule role (INOH Protein name/family name ontology) pattern: ^\d{7}$ preferred_prefix: IMR providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/imr:$1 rdf_uri_format: http://purl.obolibrary.org/obo/IMR_$1 uri_format: http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id=$1 imsr.apb: description: 'The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. [from RRID]' example: '7345' homepage: https://pb.apf.edu.au/phenbank/homePage.html keywords: - allele - alteration - chromosome - database - embryo - gene - live mouse - murine - mutation - phenotype - sperm - strain - transgene - transgenic mappings: rrid: IMSR_APB name: NHMRC Australian PhenomeBank pattern: ^\d+$ preferred_prefix: imsr.apb uri_format: https://pb.apf.edu.au/phenbank/strain.html?id=$1 imsr_em: contact: email: d.smedley@qmul.ac.uk name: Damian Smedley orcid: 0000-0002-5836-9850 description: Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.With more than 8400 mutant mouse strains and asmall but increasing number of rat mutant strains available, EMMA is the primary mouse repository in Europe and the third largest non-profit repository worldwide. [from RRID] example: '11478' homepage: https://www.infrafrontier.eu/emma/ keywords: - mouse - mutant mouse repository - mutant mouse strain - mutant strain mappings: rrid: IMSR_EM name: European Mouse Mutant Archive pattern: ^\d+$ preferred_prefix: imsr_em publications: - pubmed: '19783817' - pubmed: '17709347' uri_format: https://www.infrafrontier.eu/emma/strain-search/straindetails/?q=$1 imsr_tac: description: Supplier of mice for research purposes. [from RRID] example: '1178' homepage: https://www.taconic.com/ keywords: - gene - genetic engineering - knockout - mice - model - mouse - repository - research - strain - subject - supply - transgenic mappings: rrid: IMSR_TAC name: Taconic Biosciences preferred_prefix: imsr_tac uri_format: https://scicrunch.org/resolver/RRID:IMSR_TAC_$1 inaturalist.observation: contributor: github: oolonek name: Pierre-Marie Allard orcid: 0000-0003-3389-2191 description: The identifier for an observation in iNaturalist example: '36010371' github_request_issue: 517 homepage: https://www.inaturalist.org/observations mappings: wikidata: P5683 name: iNaturalist Observation pattern: ^[1-9]\d*$ preferred_prefix: inaturalist.observation reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.inaturalist.org/observations/$1 inaturalist.place: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Identifier for a place in iNaturalist example: '7207' homepage: https://www.inaturalist.org/places mappings: wikidata: P7471 name: iNaturalist Place pattern: ^[1-9]\d*$ preferred_prefix: inaturalist.place uri_format: https://www.inaturalist.org/places/$1 inaturalist.taxon: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Identifier for a species in iNaturalist example: '21723' homepage: https://www.inaturalist.org/taxa mappings: wikidata: P3151 name: iNaturalist Taxonomy pattern: ^[1-9]\d{0,6}$ preferred_prefix: inaturalist.taxon uri_format: https://www.inaturalist.org/taxa/$1 inaturalist.user: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Identifier for a user in iNaturalist example: '1426686' homepage: https://www.inaturalist.org/users keywords: - person name: iNaturalist User pattern: ^[1-9]\d*$ preferred_prefix: inaturalist.user uri_format: https://www.inaturalist.org/users/$1 inchi: contact: email: jmg11@cam.ac.uk name: Stephen R. Heller orcid: 0000-0002-5538-8482 description: The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier. example: InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 homepage: http://www.chemspider.com/ keywords: - centrally registered identifier - chemical descriptor - chemical entity - chemical structure - cheminformatics - chemistry - knowledge and information systems - molecular entity - molecular structure logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBcUVFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--250afbf70b1e3f9c188231ff2fb50477040a71f5/inchi-wheel.png?disposition=inline mappings: biocontext: INCHI fairsharing: FAIRsharing.ddk9t9 miriam: inchi n2t: inchi wikidata: P234 name: InChI pattern: ^InChI\=1S?\/[A-Za-z0-9\.]+(\+[0-9]+)?(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,\/\?\;\.]+)*$ preferred_prefix: inchi providers: - code: CURATOR_REVIEW description: InChI through NIST homepage: http://webbook.nist.gov/chemistry name: InChI through NIST uri_format: http://webbook.nist.gov/cgi/cbook.cgi?$1 - code: ebi description: InChI through ChEBI homepage: https://www.ebi.ac.uk/chebi/ name: InChI through ChEBI uri_format: https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=$1 - code: um description: InChI through RDF Open Molecules homepage: http://rdf.openmolecules.net/ name: InChI through RDF Open Molecules uri_format: http://rdf.openmolecules.net/?$1 publications: - doi: 10.1186/s13321-021-00517-z pmc: PMC8147039 pubmed: '34030732' title: 'InChI version 1.06: now more than 99.99% reliable' year: 2021 - doi: 10.1186/s13321-015-0068-4 pmc: PMC4486400 pubmed: '26136848' title: InChI, the IUPAC International Chemical Identifier year: 2015 - doi: 10.1007/s10822-015-9854-3 pubmed: '26081259' title: Many InChIs and quite some feat year: 2015 - doi: 10.1186/s13321-024-00847-8 title: InChI isotopologue and isotopomer specifications year: 2024 repository: https://github.com/IUPAC-InChI/InChI twitter: inchi_trust uri_format: http://www.chemspider.com/$1 inchikey: description: The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI. example: RYYVLZVUVIJVGH-UHFFFAOYSA-N homepage: http://www.chemspider.com/ mappings: biocontext: INCHIKEY miriam: inchikey n2t: inchikey togoid: InchiKey wikidata: P235 name: InChIKey pattern: ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])?$ 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://legacy.chemspider.com/inchikey=$1 informall: appears_in: - doid contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The InformAll database was developed to provide a credible source of information on allergenic food materials of both plant and animal origin. example: '410' github_request_issue: 1311 homepage: http://research.bmh.manchester.ac.uk/informAll/ name: InformAll Allergenic Food Database pattern: ^\d+$ preferred_prefix: informall uri_format: http://research.bmh.manchester.ac.uk/informall/allergenic-food/?FoodId=$1 inhand: comment: This nomenclature is available via email. Truly a disgrace. contact: email: harkemaj@msu.edu name: Jack R Harkema orcid: 0000-0003-4682-0824 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The standard reference for nomenclature and diagnostic criteria in toxicologic pathology. homepage: https://www.goreni.org/gr3_nomenclature.php keywords: - biomedical science - disease - toxicity mappings: fairsharing: FAIRsharing.9gqfpm name: The International Harmonization of Nomenclature and Diagnostic criteria preferred_prefix: inhand proprietary: true publications: - doi: 10.1177/0192623309353423 pubmed: '20032296' title: Proliferative and nonproliferative lesions of the rat and mouse respiratory tract year: 2009 inn: comment: can not find a place to resolve to contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO. example: fluticasone homepage: https://www.who.int/teams/health-product-and-policy-standards/inn mappings: wikidata: P2275 name: International Nonproprietary Names preferred_prefix: inn synonyms: - INN_ID uri_format: https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1 innatedb: contact: email: david.lynn@flinders.edu.au name: David Lynn orcid: 0000-0003-4664-1404 description: InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactions and signaling responses involved in mammalian innate immunity. InnateDB incorporates information of the whole human, mouse and bovine interactomes by integrating interaction and pathway information from several of the major publicly available databases but aims to capture an improved coverage of the innate immunity interactome through manual curation. example: '20021' homepage: http://www.innatedb.ca/ keywords: - gene - immunology - interaction - life science - pathway - protein mappings: fairsharing: FAIRsharing.rb2drw integbio: nbdc01870 pathguide: '264' prefixcommons: innatedb re3data: r3d100010676 name: A Knowledge Resource for Innate Immunity Interactions and Pathways preferred_prefix: innatedb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/innatedb:$1 publications: - doi: 10.1093/nar/gks1147 pmc: PMC3531080 pubmed: '23180781' title: 'InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation' year: 2012 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 twitter: innatedb uri_format: http://www.innatedb.ca/getGeneCard.do?id=$1 ino: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles. download_owl: http://purl.obolibrary.org/obo/ino.owl example: '0000003' homepage: https://github.com/INO-ontology/ino keywords: - life science - molecular interaction - network model - obo - ontology license: CC-BY-3.0 mappings: aberowl: INO biolink: INO bioportal: INO fairsharing: FAIRsharing.mm72as obofoundry: ino ols: ino ontobee: INO name: Interaction Network Ontology pattern: ^\d{7}$ preferred_prefix: INO publications: - doi: 10.1186/s13040-016-0118-0 pmc: PMC5168857 pubmed: '28031747' title: The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature year: 2016 - doi: 10.1186/2041-1480-6-2 pmc: PMC4362819 pubmed: '25785184' title: Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions year: 2015 - doi: 10.1186/2041-1480-2-s2-s8 pmc: PMC3102897 pubmed: '21624163' title: Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology year: 2011 rdf_uri_format: http://purl.obolibrary.org/obo/INO_$1 repository: https://github.com/INO-ontology/ino uri_format: http://purl.obolibrary.org/obo/INO_$1 version: 1.1.13 insdc: description: The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. example: X58356 homepage: https://www.ncbi.nlm.nih.gov/Genbank/ keywords: - dna mappings: biocontext: INSDC integbio: nbdc02567 miriam: insdc n2t: insdc prefixcommons: insdc togoid: Insdc name: Nucleotide Sequence Database pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4,6}\d{8,10}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ preferred_prefix: insdc providers: - code: CURATOR_REVIEW description: INSDC through DDBJ homepage: http://www.ddbj.nig.ac.jp/ name: INSDC through DDBJ uri_format: https://getentry.ddbj.nig.ac.jp/getentry?database=ddbj&accession_number=$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/insdc:$1 - code: ebi description: INSDC through European Nucleotide Archive (ENA) homepage: https://www.ebi.ac.uk/ena/ name: INSDC through European Nucleotide Archive (ENA) uri_format: https://www.ebi.ac.uk/ena/data/view/$1 - code: ncbi description: INSDC through Nucleotide database at NCBI homepage: https://www.ncbi.nlm.nih.gov/nuccore/ name: INSDC through Nucleotide database at NCBI uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 publications: - doi: 10.1093/nar/gkae1058 pubmed: '39535044' title: 'The international nucleotide sequence database collaboration (INSDC): enhancing global participation' year: 2024 - doi: 10.1093/nar/18.6.1517 pmc: PMC330520 pubmed: '2326192' title: Recent changes in the GenBank On-line Service year: 1990 - doi: 10.1093/nar/gkl986 pmc: PMC1781245 pubmed: '17202161' title: GenBank year: 2007 - doi: 10.1093/nar/gkl913 pmc: PMC1897316 pubmed: '17148479' title: EMBL Nucleotide Sequence Database in 2006 year: 2006 - doi: 10.1126/science.298.5597.1333b pubmed: '12436968' title: Nucleotide sequence database policies year: 2002 uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 insdc.cds: description: The coding sequence or protein identifiers as maintained in INSDC. example: AAA35559 has_canonical: ncbiprotein homepage: http://getentry.ddbj.nig.ac.jp mappings: biocontext: INSDC.CDS miriam: insdc.cds n2t: insdc.cds name: INSDC CDS pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ preferred_prefix: insdc.cds providers: - code: CURATOR_REVIEW description: INSDC CDS through ENA homepage: https://www.ebi.ac.uk/ena name: INSDC CDS through ENA uri_format: https://www.ebi.ac.uk/ena/data/view/$1 - code: CURATOR_REVIEW description: INSDC CDS through NCBI homepage: https://www.ncbi.nlm.nih.gov/protein/ name: INSDC CDS through NCBI uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 uri_format: http://getentry.ddbj.nig.ac.jp/getentry/dad/$1 insdc.gca: description: The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage. example: GCA_000155495.1 has_canonical: ncbi.assembly homepage: https://www.ebi.ac.uk/ena/browse/genome-assembly-database mappings: biocontext: INSDC.GCA miriam: insdc.gca n2t: insdc.gca name: Genome assembly database - INSDC accessions pattern: ^GCA_[0-9]{9}(\.[0-9]+)?$ preferred_prefix: insdc.gca providers: - code: ncbi description: Genome assembly database NCBI homepage: https://www.ncbi.nlm.nih.gov/datasets/genome/ name: Genome assembly database NCBI uri_format: https://www.ncbi.nlm.nih.gov/datasets/genome/$1 uri_format: https://www.ebi.ac.uk/ena/data/view/$1 insdc.gcf: description: The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database RefSeq accessions does not extend to viroids and bacteriophage. example: GCF_000001405 has_canonical: ncbi.assembly homepage: https://www.ncbi.nlm.nih.gov/ mappings: miriam: refseq.gcf name: Genome assembly database - RefSeq accessions pattern: ^GCF_[0-9]{9}(\.[0-9]+)?$ preferred_prefix: insdc.gcf synonyms: - insdc.gcf uri_format: https://www.ncbi.nlm.nih.gov/datasets/genome/$1 insdc.run: comment: https://www.insdc.org/ is the authoritative source for INSDC. However, confusingly, they don't mention runs in this table. I think we should ask them to include. ENA is a partner and they have documentation [here](https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html). Runs | (E\|D\|S)RR[0-9]{6,} | ERR123456 -- | -- | -- contributor: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: An experimental run, served thrugh the ENA example: ERR436051 github_request_issue: 131 homepage: https://www.insdc.org/ name: International Nucleotide Sequence Database Collaboration (INSDC) Run pattern: ^(E|D|S)RR[0-9]{6,}$ preferred_prefix: insdc.run reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.ebi.ac.uk/ena/browser/view/$1 insdc.sra: contact: email: Hugh.Shanahan@rhul.ac.uk github: hughshanahan name: Hugh P Shanahan orcid: 0000-0003-1374-6015 description: 'The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.' example: SRX000007 homepage: https://www.ncbi.nlm.nih.gov/sra keywords: - biology - epidemiology - genomics - virology mappings: biocontext: INSDC.SRA fairsharing: FAIRsharing.g7t2hv miriam: insdc.sra n2t: insdc.sra re3data: r3d100010775 name: Sequence Read Archive pattern: ^[SED]R[APRSXZ]\d+$ preferred_prefix: insdc.sra providers: - code: ddbj description: DDBJ Sequence Read Archive (DRA) homepage: https://www.ddbj.nig.ac.jp/dra/index-e.html name: DDBJ Sequence Read Archive (DRA) uri_format: https://ddbj.nig.ac.jp/resource/sra-experiment/$1 - code: ebi description: European Nucleotide Archive (ENA) homepage: https://www.ebi.ac.uk/ena name: European Nucleotide Archive (ENA) uri_format: https://www.ebi.ac.uk/ena/data/view/$1 publications: - doi: 10.1186/s13742-015-0064-7 pmc: PMC4425880 pubmed: '25960871' title: Investigation into the annotation of protocol sequencing steps in the sequence read archive year: 2015 - doi: 10.1093/nar/gkr854 pmc: PMC3245110 pubmed: '22009675' title: 'The Sequence Read Archive: explosive growth of sequencing data' year: 2011 - doi: 10.1093/nar/gkm1000 pmc: PMC2238880 pubmed: '18045790' title: Database resources of the National Center for Biotechnology Information year: 2007 uri_format: https://www.ncbi.nlm.nih.gov/sra/$1 intact: contact: email: orchard@ebi.ac.uk name: Sandra Orchard orcid: 0000-0002-8878-3972 description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. example: EBI-2307691 homepage: https://www.ebi.ac.uk/intact/ keywords: - biology - interaction - protein license: CC-BY-4.0 mappings: biocontext: INTACT fairsharing: FAIRsharing.d05nwx go: IntAct integbio: nbdc00507 miriam: intact n2t: intact pathguide: '111' prefixcommons: intact re3data: r3d100010671 togoid: Intact uniprot: DB-0051 name: IntAct protein interaction database owners: - name: European Bioinformatics Institute partnered: false ror: 02catss52 pattern: ^EBI\-[0-9]+$ preferred_prefix: intact providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/intact:$1 publications: - doi: 10.1002/cpz1.70018 pubmed: '39401100' title: IntAct Database for Accessing IMEx's Contextual Metadata of Molecular Interactions year: 2024 - doi: 10.1093/nar/gkt1115 pmc: PMC3965093 pubmed: '24234451' title: The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases year: 2013 - doi: 10.1038/nmeth.1637 pmc: PMC3246345 pubmed: '21716279' title: 'PSICQUIC and PSISCORE: accessing and scoring molecular interactions' year: 2011 - doi: 10.1093/nar/gkp878 pmc: PMC2808934 pubmed: '19850723' title: The IntAct molecular interaction database in 2010 year: 2009 - doi: 10.1186/1741-7007-5-44 pmc: PMC2189715 pubmed: '17925023' title: Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions year: 2007 - doi: 10.1093/nar/gkh052 pmc: PMC308786 pubmed: '14681455' title: 'IntAct: an open source molecular interaction database' year: 2004 twitter: intact_project uri_format: https://www.ebi.ac.uk/intact/interaction/$1 intact.molecule: description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules. example: EBI-366083 homepage: https://www.ebi.ac.uk/intact/ mappings: biocontext: INTACT.MOLECULE miriam: intact.molecule n2t: intact.molecule name: IntAct Molecule pattern: ^EBI\-[0-9]+$ preferred_prefix: intact.molecule publications: - doi: 10.1002/cpz1.70018 pubmed: '39401100' title: IntAct Database for Accessing IMEx's Contextual Metadata of Molecular Interactions year: 2024 uri_format: https://www.ebi.ac.uk/intact/search?query=$1 integbio: contact: email: kwsm@dbcls.rois.ac.jp github: skwsm name: Shuichi Kawashima orcid: 0000-0001-7883-3756 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Integbio Database Catalog provides whereabouts information (URL), database description, biological species and other attributes (metadata) of Japanese and international life science databases to make it easier for users to find databases they need. This catalog has been developed as a part of the integration of life science databases promoted by four ministries in Japan: the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), The Ministry of Health, Labor, and Welfare (MHLW), the Ministry of Agriculture, Forestry, and Fisheries (MAFF), and the Ministry of Economy, Trade, and Industry of Japan (METI). (from https://integbio.jp/dbcatalog/en/about)' example: nbdc01071 homepage: https://integbio.jp/en/ license: CC0-1.0 logo: https://integbio.jp/templates/integbio/images/logo/logo.png name: Integbio pattern: ^nbdc\d+$ preferred_prefix: integbio uri_format: https://integbio.jp/dbcatalog/en/record/$1 interfil: description: The Intermediate Filament Database functions as a continuously updated review of the intermediate filament field and it is hoped that users will contribute to the development and expansion of the database on a regular basis. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants. example: NM_006262 homepage: http://www.interfil.org keywords: - genome mappings: prefixcommons: interfil name: Human Intermediate Filament Database preferred_prefix: interfil providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/interfil:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.interfil.org/details.php?id=$1 interlex: contact: email: mmartone@ucsd.edu github: memartone name: Maryann Elizabeth Martone orcid: 0000-0002-8406-3871 description: 'InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. ' example: 0101963 homepage: https://www.fdilab.org keywords: - anatomy - biomedical science - brain - imaging - neurobiology mappings: fairsharing: FAIRsharing.67sssf miriam: ilx wikidata: P696 name: InterLex pattern: ^[0-9]+$ preferred_prefix: interlex publications: - doi: 10.3389/fninf.2013.00018 pmc: PMC3757470 pubmed: '24009581' title: 'NeuroLex.org: an online framework for neuroscience knowledge' year: 2013 references: - https://github.com/AllenInstitute/nomenclature synonyms: - ILX uri_format: https://scicrunch.org/scicrunch/interlex/view/ilx_$1 interpro: contact: email: agb@ebi.ac.uk name: Alex Bateman orcid: 0000-0002-6982-4660 description: InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. example: IPR016380 homepage: http://www.ebi.ac.uk/interpro/index.html keywords: - bioinformatics - biology - domain - obo - ontology - protein license: CC0-1.0 mappings: biocontext: IPR biolink: interpro edam: '1133' fairsharing: FAIRsharing.pda11d go: InterPro integbio: nbdc00108 miriam: interpro n2t: interpro ncbi: InterPro obofoundry: ipr prefixcommons: interpro re3data: r3d100010798 togoid: Interpro uniprot: DB-0052 wikidata: P2926 name: InterPro pattern: ^IPR\d{6}$ 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 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/interpro:$1 publications: - doi: 10.1093/nar/gkae1082 pubmed: '39565202' title: 'InterPro: the protein sequence classification resource in 2025' year: 2024 - doi: 10.1093/nar/gkac993 pmc: PMC9825450 pubmed: '36350672' title: InterPro in 2022 year: 2023 - doi: 10.1093/nar/gkaa977 pmc: PMC7778928 pubmed: '33156333' title: 'The InterPro protein families and domains database: 20 years on' year: 2021 - doi: 10.1093/nar/gky1100 pmc: PMC6323941 pubmed: '30398656' title: 'InterPro in 2019: improving coverage, classification and access to protein sequence annotations' year: 2019 - doi: 10.1093/nar/gki106 pmc: PMC540060 pubmed: '15608177' title: InterPro, progress and status in 2005 year: 2005 rdf_uri_format: http://purl.obolibrary.org/obo/IPR_$1 repository: https://proteinswebteam.github.io/interpro-blog/ synonyms: - IP - IPR - InterPro twitter: InterProDB uri_format: https://www.ebi.ac.uk/interpro/entry/InterPro/$1 iobc: contact: email: kushida@biosciencedbc.jp github: kushidatatsuya name: Tatsuya Kushida orcid: 0000-0002-0784-4113 description: 'Interlinking Ontology for Biological Concepts (IOBC) contains approximately 80,000 biological concepts such as biological phenomena, diseases, molecular functions, gene products, chemicals, and medical cares, and approximately 20,000 related concepts such as earth science and environmental science. The concepts are structured by thirty-five relations such as has function, has role, has quality, and precedes. Each concept has both of English and Japanese labels. For further information including the developmental method, see papers in the PUBLICATIONS PAGE. The license for this ontology is specified in the Creative Commons Attribution-NonCommercial 4.0 International. If you use data from this ontology, please be sure attribute this ontology as follows: "Interlinking Ontology for Biological Concepts © National Bioscience Database Center licensed under CC Attribution-NonCommercial 4.0 International".' download_owl: http://aber-owl.net/media/ontologies/IOBC/25/iobc.owl example: '200906038218908385' example_extras: - AC21 - AC21_cat - OWLClass_00000000000000000321 homepage: https://github.com/kushidat/IOBC keywords: - ontology license: CC-BY-NC-4.0 mappings: aberowl: IOBC bioportal: IOBC name: Interlinking Ontology for Biological Concepts preferred_prefix: iobc publications: - doi: 10.1007/s00354-019-00074-y title: Interconnection of Biological Knowledge Using NikkajiRDF and Interlinking Ontology for Biological Concepts year: 2019 repository: https://github.com/kushidat/IOBC uri_format: http://purl.jp/bio/4/id/$1 ipi: deprecated: true description: IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI maintaisn a database of cross references between the primary data sources, it provides minimally redundant but complete sets of proteins for featured species, and it maintains stable and unique identifiers. example: IPI00000001 homepage: http://www.ebi.ac.uk/IPI keywords: - protein mappings: biocontext: IPI integbio: nbdc00911 prefixcommons: ipi name: International Protein Index preferred_prefix: ipi providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ipi:$1 publications: - doi: 10.1002/pmic.200300721 pubmed: '15221759' title: 'The International Protein Index: an integrated database for proteomics experiments' year: 2004 uri_format: http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$1&format=default irct: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Iranian Registry of Clinical Trials. This is a Primary Registry in the WHO Registry Network set up with the help from the Ministry of Health and Medical Education (MOHME) and hosted by Iran University of Medical Sciences (IUMS). (from homepage) Note that the website uses a different identifier then the one reported in this semantic space.' example: IRCT20080904001199N7 homepage: https://en.irct.ir/ name: Iranian Registry of Clinical Trials pattern: ^IRCT\d+N\d+$ preferred_prefix: irct references: - https://en.irct.ir/trial/65035 ird.segment: contact: email: richard.scheuermann@nih.gov github: scheuerm name: Richard H. Scheuermann orcid: 0000-0003-1355-892X description: Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s). example: CY077097 homepage: http://www.fludb.org/ keywords: - gene - protein mappings: biocontext: IRD.SEGMENT miriam: ird.segment n2t: ird.segment prefixcommons: ird.segment name: IRD Segment Sequence pattern: ^\w+(\_)?\d+(\.\d+)?$ preferred_prefix: ird.segment providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ird.segment:$1 publications: - doi: 10.1093/nar/gkm905 pmc: PMC2238987 pubmed: '17965094' title: 'BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence' year: 2007 uri_format: http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1 irefweb: contact: email: shoshana@sickkids.ca name: Shoshana J. Wodak orcid: 0000-0002-0701-6545 description: 'iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.' example: '617102' homepage: http://wodaklab.org/iRefWeb/ keywords: - interaction - life science - protein mappings: biocontext: IREFWEB fairsharing: FAIRsharing.t31wcb miriam: irefweb n2t: irefweb pathguide: '300' prefixcommons: irefweb re3data: r3d100012725 name: iRefWeb pattern: ^\d+$ preferred_prefix: irefweb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/irefweb:$1 publications: - doi: 10.1093/database/baq023 pmc: PMC2963317 pubmed: '20940177' title: 'iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence' year: 2010 twitter: wodaklab uri_format: http://wodaklab.org/iRefWeb/interaction/show/$1 iresite: contact: email: martin.pospisek@natur.cuni.cz name: Martin Pospíšek orcid: 0000-0002-9490-8911 description: The IRESite database presents information about experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract the eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure. example: '322' homepage: http://www.iresite.org keywords: - life science - regulation - rna mappings: fairsharing: FAIRsharing.kd39j4 integbio: nbdc01752 prefixcommons: iresite name: Database of experimentally verified IRES structures preferred_prefix: iresite providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/iresite:$1 publications: - doi: 10.1093/nar/gkp981 pmc: PMC2808886 pubmed: '19917642' title: IRESite--a tool for the examination of viral and cellular internal ribosome entry sites year: 2009 - doi: 10.1093/nar/gkj081 pmc: PMC1347444 pubmed: '16381829' title: 'IRESite: the database of experimentally verified IRES structures (www.iresite.org)' year: 2006 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.iresite.org/IRESite_web.php?page=view&entry_id=$1 iro: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true example: 0000008 name: Insect Resistance Ontology pattern: ^\d{7}$ preferred_prefix: iro uri_format: https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1 isbn: description: The International Standard Book Number (ISBN) is for identifying printed books. example: '9781584885658' homepage: http://isbndb.com/ keywords: - bibliography mappings: biocontext: ISBN-13 biolink: isbn edam: '2634' go: ISBN miriam: isbn n2t: isbn prefixcommons: isbn name: International Standard Book Number pattern: ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ preferred_prefix: isbn providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/isbn:$1 - code: google.isbn description: Google Books provider for ISBN numbers homepage: https://books.google.com name: Google Books uri_format: https://books.google.com/books?isbn=$1 - code: worldcat description: ISBN database at WorldCat homepage: http://www.worldcat.org/ name: ISBN database at WorldCat uri_format: http://www.worldcat.org/isbn/$1 synonyms: - ISBN-10 - ISBN-13 uri_format: http://isbndb.com/search-all.html?kw=$1 ised: description: ISED catalogues the influenza sequence and epitope information obtained in countries worldwide and currently hosts a total of 49368 influenza A and 4761 influenza B virus sequence data including pandemic A/H1N1 2009 virus sequences collected in 42 countries, and a total of 545 amantadine-resistant influenza virus sequences collected in Korea. example: AY209920 homepage: http://influenza.korea.ac.kr keywords: - protein mappings: prefixcommons: ised name: Influenza Sequence and Epitope Database preferred_prefix: ised providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ised:$1 isfinder: contact: email: patricia.siguier@univ-tlse3.fr name: Patricia Siguier orcid: 0000-0003-1620-6495 description: ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available. example: ISA1083-2 homepage: http://www-is.biotoul.fr/i keywords: - gene - life science - sequence mappings: biocontext: ISFINDER fairsharing: FAIRsharing.xhpc3h integbio: nbdc00510 miriam: isfinder n2t: isfinder ncbi: ISFinder prefixcommons: isfinder name: Insertion sequence elements database pattern: ^IS\w+(\-\d)?$ preferred_prefix: isfinder providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/isfinder:$1 publications: - doi: 10.1093/nar/gkj014 pmc: PMC1347377 pubmed: '16381877' title: 'ISfinder: the reference centre for bacterial insertion sequences' year: 2006 uri_format: https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1 isni: description: 'ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC. The mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described.' example: 000000012281955X homepage: http://www.isni.org mappings: bartoc: '20464' biolink: isni miriam: isni n2t: isni wikidata: P213 name: International Standard Name Identifier pattern: ^[0-9]{15}[0-9X]{1}$ preferred_prefix: isni providers: - code: isni.short description: Unqualified ISNI URI homepage: http://www.isni.org name: ISNI short uri_format: http://www.isni.org/$1 uri_format: http://www.isni.org/isni/$1 iso.3166: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An identifier for a country in numeric format per ISO 3166-1 example: '554' homepage: https://www.iso.org/iso-3166-country-codes.html mappings: wikidata: P299 name: ISO 3166-1 Country Code pattern: ^\d+$ preferred_prefix: iso.3166 uri_format: https://data.who.int/countries/$1 iso15926: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The primary purpose of ISO 15926 is to provide a foundation ontology to support the integration and sharing of data related to the lifecycle of a process plant in such a way that it is consistent, unambiguous, and minimizing the number of ways something could be expressed. Further purpose of ISO 15926-14 is to meet needs for OWL 2 ontologies that are based on ISO 15926-2, that enable efficient reasoning and that capture lifecycle information. A specific purpose is to demonstrate lifecycle modelling through a representation of the lifecycle model of ISO/IEC 81346-1. Another specific purpose is to exemplify how this standard can be used to develop industrial ontologies through various real-world use cases from industry. (from https://nfdi4cat.org/services/ontologie-sammlung/) download_rdf: https://github.com/uwasystemhealth/modular_ontologies/raw/master/LIS-14.ttl example: activityBoundOf homepage: https://15926.org/home/ name: ISO 15926-14 preferred_prefix: iso15926 uri_format: http://standards.iso.org/iso/15926/part14/$1 isrctn: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The ISRCTN registry is a primary clinical trial registry recognised by WHO and ICMJE that accepts all clinical research studies (whether proposed, ongoing or completed), providing content validation and curation and the unique identification number necessary for publication. All study records in the database are freely accessible and searchable. (from homepage) example: ISRCTN10175490 homepage: https://www.isrctn.com/ name: International Traditional Medicine Clinical Trial Registry pattern: ^ISRCTN\d+$ preferred_prefix: isrctn providers: - code: doi description: DOI resolution of ISRCTN homepage: https://doi.org/10.1186 name: DOI uri_format: https://doi.org/10.1186/$1 uri_format: https://www.isrctn.com/$1 issn: description: The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books. example: 0745-4570 homepage: https://portal.issn.org mappings: biocontext: ISSN biolink: issn go: ISSN miriam: issn n2t: issn name: International Standard Serial Number pattern: ^\d{4}-\d{3}[\dX]$ preferred_prefix: issn providers: - code: 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 istransbase: contact: email: oriental-cds@163.com name: Dongsheng Cao contributor: email: shah.tanay2@northeastern.edu github: tanayshah2 name: Tanay Shah orcid: 0009-0001-1912-5132 description: ISTransbase is a highly reliable and accessible database that focuses on inhibitors and substrates of drug transporters, offering a wealth of vital information encompassing experimental methods, transport parameters, and references. example: IST028 github_request_issue: 1145 homepage: https://istransbase.scbdd.com/ name: ISTransbase preferred_prefix: istransbase publications: - doi: 10.1093/database/baae053 pmc: PMC11214160 pubmed: '38943608' title: 'ISTransbase: an online database for inhibitor and substrate of drug transporters' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://istransbase.scbdd.com/database/trans/$1 itis: contact: email: itiswebmaster@itis.gov name: Gerald Guala orcid: 0000-0002-4972-3782 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world. example: '589462' homepage: https://www.itis.gov/ keywords: - biodiversity - life science - taxonomy license: CC0-1.0 mappings: bartoc: '17791' fairsharing: FAIRsharing.t19hpa integbio: nbdc00916 re3data: r3d100011213 wikidata: P815 name: Integrated Taxonomic Information System pattern: ^\d+$ preferred_prefix: itis uri_format: https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1 itmctr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The International Traditional Medicine Clinical Trial Registry (ITMCTR) is a non-profit online register of clinical trials being conducted in the field of traditional medicine. It isoperated by the China Academy of Chinese Medical Sciences and The China Center For Evidence Based Traditional Chinese Medicine. It is recognized as a Primary Registry of WHO, and contributes data to the WHO ICTRP. (from website) example: ITMCTR2023000002 homepage: http://itmctr.ccebtcm.org.cn logo: http://itmctr.ccebtcm.org.cn/Content/images/ny_logo.png name: International Traditional Medicine Clinical Trial Registry pattern: ^ITMCTR\d+$ preferred_prefix: itmctr ito: banana: ITO banana_peel: _ contact: email: matthias.samwald@meduniwien.ac.at name: Matthias Samwald orcid: 0000-0002-4855-2571 description: The Intelligence Task Ontology (ITO) provides a comprehensive map of machine intelligence tasks, as well as broader human intelligence or hybrid human/machine intelligence tasks. download_owl: http://aber-owl.net/media/ontologies/ITO/17/ito.owl example: '01625' homepage: https://openbiolink.github.io/ITOExplorer/ keywords: - artificial intelligence - machine learning - natural language processing - ontology mappings: aberowl: ITO bioportal: ITO fairsharing: FAIRsharing.89e853 miriam: ito name: Intelligence Task Ontology pattern: ^\d+$ preferred_prefix: ito publications: - doi: 10.1038/s41597-022-01435-x pmc: PMC9205953 pubmed: '35715466' title: A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks year: 2022 - doi: 10.5281/zenodo.5561989 title: Intelligence Task Ontology and Knowledge Graph (ITO) year: 2022 - doi: 10.48550/arxiv.2110.01434 title: A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks year: 2021 repository: https://github.com/OpenBioLink/ITO uri_format: https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:ITO_$1 iuphar.family: description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits. example: '78' homepage: http://www.guidetopharmacology.org/ keywords: - protein license: CC-BY-SA-4.0 mappings: biocontext: IUPHAR.FAMILY miriam: iuphar.family n2t: iuphar.family prefixcommons: iuphar.family name: IUPHAR family pattern: ^\d+$ preferred_prefix: iuphar.family providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/iuphar.family:$1 synonyms: - IUPHARfam uri_format: http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1 iuphar.ligand: description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands. example: '1755' homepage: http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all license: CC-BY-SA-4.0 mappings: biocontext: IUPHAR.LIGAND biolink: GTOPDB miriam: iuphar.ligand n2t: iuphar.ligand togoid: IupharLigand wikidata: P595 name: Guide to Pharmacology Ligand pattern: ^\d+$ preferred_prefix: iuphar.ligand synonyms: - IUPHAR_LIGAND - IUPHAR_LIGAND_ID uri_format: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1 iuphar.receptor: contact: email: simon.harding@igmm.ed.ac.uk github: simondharding name: Simon D Harding orcid: 0000-0002-9262-8318 description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits. example: '101' homepage: http://www.guidetopharmacology.org/targets.jsp license: CC-BY-SA-4.0 mappings: biocontext: IUPHAR.RECEPTOR go: IUPHAR_RECEPTOR miriam: iuphar.receptor n2t: iuphar.receptor uniprot: DB-0182 wikidata: P5458 name: Guide to Pharmacology Target pattern: ^\d+$ preferred_prefix: iuphar.receptor publications: - doi: 10.1093/nar/gkab1010 pmc: PMC8689838 pubmed: '34718737' title: 'The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials' year: 2022 - doi: 10.1111/j.1476-5381.2012.02141.x pmc: PMC3575771 pubmed: '23003568' title: GuideToPharmacology.org--an update year: 2012 synonyms: - IUPHAR_GPCR - IUPHARobj uri_format: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1 ivdb: description: IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively. example: E13035 homepage: http://influenza.psych.ac.cn/ keywords: - dna - gene - genome mappings: prefixcommons: ivdb name: Influenza Virus Database preferred_prefix: ivdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ivdb:$1 uri_format: http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id=$1 jax: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Information about the C57BL/6J. Includes genetic background and disease data. example: '004435' homepage: https://www.jax.org/strain keywords: - gene - genetic engineering - knockout - life science - mice - model - mouse - repository - research - strain - subject - supply mappings: biocontext: JAX fairsharing: FAIRsharing.5701h1 rrid: IMSR_JAX name: Jackson Laboratories Strain pattern: ^\d{6}$ 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 synonyms: - jaxMiceUID uri_format: http://jaxmice.jax.org/strain/$1.html jcggdb: description: JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc. example: JCGG-STR008690 homepage: http://jcggdb.jp/index_en.html mappings: biocontext: JCGGDB integbio: nbdc01164 miriam: jcggdb n2t: jcggdb name: Japan Consortium for Glycobiology and Glycotechnology Database pattern: ^JCGG-STR\d{6}$ preferred_prefix: jcggdb uri_format: http://jcggdb.jp/idb/jcggdb/$1 jcm: description: The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2. example: '17254' homepage: http://www.jcm.riken.go.jp/ keywords: - life science - microbial - taxonomy mappings: biocontext: JCM fairsharing: FAIRsharing.h2wrt2 miriam: jcm n2t: jcm ncbi: JCM prefixcommons: jcm name: Japan Collection of Microorganisms pattern: ^\d+$ preferred_prefix: jcm providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/jcm:$1 uri_format: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1 jcrb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Cell line collections (Providers) example: JCRB1355 homepage: https://cellbank.nibiohn.go.jp mappings: cellosaurus: JCRB name: JRBC Cell Bank pattern: ^JCRB\d+$ preferred_prefix: jcrb uri_format: https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1 jcsd: contributor_extras: - email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST). example: J55.713G homepage: http://jglobal.jst.go.jp/en/ keywords: - drug mappings: biocontext: JCSD miriam: jcsd n2t: jcsd prefixcommons: nikkaji name: Japan Chemical Substance Dictionary pattern: ^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$ preferred_prefix: jcsd providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/nikkaji:$1 - code: stirdf description: Appears in iobc homepage: http://stirdf.jst.go.jp name: Unknown uri_format: http://stirdf.jst.go.jp/cde/nikkaji/$1 synonyms: - Nikkaji number - nikkaji uri_format: http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1 jecfa: contact: email: kpetersen@who.int name: Kim Petersen contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: JECFA provides identifiers for flavors, food additives, contaminants, toxicants, and veterinary drugs. Each entry includes chemical details, acceptable or tolerable intake limits, and links to related reports and monographs. example: '2116' github_request_issue: 1247 homepage: https://apps.who.int/food-additives-contaminants-jecfa-database mappings: wikidata: P9557 name: Joint FAO/WHO Expert Committee on Food Additives pattern: ^\d+$ preferred_prefix: jecfa reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 jgi.proposal: contact: email: sewilson@lbl.gov name: Steven E. Wilson orcid: 0000-0002-8489-208X contributor: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 contributor_extras: - email: aclum@lbl.gov github: aclum name: Alicia Clum orcid: 0000-0002-5004-3362 description: Identifiers for proposals/projects at the Joint Genome Institute example: '502930' github_request_issue: 853 homepage: https://genome.jgi.doe.gov/portal/ name: Joint Genome Institute Proposals pattern: ^\d+$ preferred_prefix: jgi.proposal publications: - doi: 10.1128/msystems.00804-20 pmc: PMC8269246 pubmed: '34006627' title: DOE JGI Metagenome Workflow year: 2021 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue=$1 jrct: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This system submits an implementation plan to the Minister of Health, Labor and Welfare for clinical research conducted at medical institutions, etc. based on the provisions of the 'Clinical Research Act' and the 'Act on Ensuring Safety of Regenerative Medicine, etc.' It is a system for performing notification procedures such as In addition, based on the clinical research practice standards stipulated in the same law, we disclose information that the World Health Organization (WHO) requires to be disclosed, information that ensures the transparency of the research process, and information that contributes to the selection of participation in clinical research by the public. (translated from website) example: jRCTs041220087 homepage: https://jrct.niph.go.jp name: Japan Registry of Clinical Trials pattern: ^jRCT\w?\d+$ preferred_prefix: jrct providers: - code: '' description: '' homepage: '' name: '' uri_format: https://jrct.niph.go.jp/latest-detail/$1 uri_format: https://jrct.niph.go.jp/en-latest-detail/$1 jstor: description: JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration. example: '3075966' homepage: http://www.jstor.org/ mappings: biocontext: JSTOR go: JSTOR miriam: jstor n2t: jstor name: Digital archive of scholarly articles pattern: ^\d+$ preferred_prefix: jstor uri_format: http://www.jstor.org/stable/$1 jws: contact: email: brettolivier@gmail.com github: bgoli name: Brett G. Olivier orcid: 0000-0002-5293-5321 description: JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser. example: achcar11 homepage: http://jjj.biochem.sun.ac.za/models/ keywords: - model - pathway mappings: biocontext: JWS miriam: jws n2t: jws prefixcommons: jws name: JWS Online pattern: ^\w+$ preferred_prefix: jws providers: - code: CURATOR_REVIEW description: JWS Online Model Repository at Manchester homepage: http://jjj.mib.ac.uk/models 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/ - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/jws:$1 publications: - doi: 10.1093/bioinformatics/bth200 pubmed: '15072998' title: Web-based kinetic modelling using JWS Online year: 2004 uri_format: https://jjj.bio.vu.nl/models/$1 kaggle: description: Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions. example: nasa/kepler-exoplanet-search-results homepage: https://kaggle.com mappings: miriam: kaggle n2t: kaggle re3data: r3d100012705 name: Kaggle pattern: ^[0-9a-zA-Z\-]+\/[0-9a-zA-Z\-]+$ preferred_prefix: kaggle uri_format: https://www.kaggle.com/$1 kaken: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier for researchers in Japan used in goverment-based research funding (from 1980s) example: '00011461' homepage: https://nrid.nii.ac.jp/ja/search/?kw= keywords: - person - researcher mappings: wikidata: P9776 name: e-Rad researcher number pattern: ^\d{8}$ preferred_prefix: kaken references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://nrid.nii.ac.jp/ja/nrid/10000$1 kclb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Cell line collections (Providers) example: '10020.2' homepage: https://cellbank.snu.ac.kr/english mappings: cellosaurus: KCLB name: Korean Cell Line Bank preferred_prefix: kclb uri_format: https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1 kcris: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The Clinical Research Information Service (CRIS) is a non-profit online registration system for clinical trials (researches) to be conducted in Korea. It has been established at the Korea Disease Control and Prevention Agency (KDCA) with support from the Ministry of Health and Welfare (MOHW). It joined the WHO International Clinical Trials Registry Platform (ICTRP) as 11th member of Primary Registry. (from about page) Note that the web page that resolves this trial does not correspond to the semantic space' example: KCT0008394 homepage: https://cris.nih.go.kr name: Korean Clinical Research Information Service pattern: ^KCT\d+$ preferred_prefix: kcris references: - https://cris.nih.go.kr/cris/search/detailSearchEn.do?seq=23973 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 biolink: KEGG cheminf: 000409 go: KEGG integbio: nbdc00530 miriam: kegg n2t: kegg pathguide: '16' uniprot: DB-0053 name: Kyoto Encyclopedia of Genes and Genomes pattern: ^([CHDEGTMKR]\d+)|(\w+:[\w\d\.-]*)|([a-z]{3,5})|(\w{2,4}\d{5})$ preferred_prefix: kegg publications: - doi: 10.1093/nar/gkw1092 pmc: PMC5210567 pubmed: '27899662' title: 'KEGG: new perspectives on genomes, pathways, diseases and drugs' year: 2016 synonyms: - KEGG uri_format: http://www.kegg.jp/entry/$1 kegg.brite: description: KEGG BRITE is a collection of hierarchical classifications (see new hierarchies and last updates) representing our knowledge on various aspects of biological systems. In contrast to KEGG PATHWAY, which is limited to molecular interactions and reactions, KEGG BRITE incorporates many different types of relationships. example: ko00071 homepage: http://www.genome.jp/kegg/brite.html keywords: - classification - ontology - pathway mappings: biolink: KEGG.BRITE integbio: nbdc00115 prefixcommons: kegg.brite name: KEGG BRITE part_of: kegg preferred_prefix: kegg.brite providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/kegg.brite:$1 uri_format: http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br$1 kegg.compound: contact: email: kanehisa@kuicr.kyoto-u.ac.jp name: Minoru Kanehisa orcid: 0000-0001-6123-540X description: KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life. example: C12345 homepage: https://www.genome.jp/kegg/ligand.html keywords: - small molecule mappings: biocontext: KEGG.COMPOUND edam: '2605' integbio: nbdc00814 miriam: kegg.compound n2t: kegg.compound prefixcommons: kegg.compound wikidata: P665 name: KEGG Compound part_of: kegg pattern: ^C\d+$ preferred_prefix: kegg.compound providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/kegg.compound:$1 publications: - doi: 10.1002/0471250953.bi0112s38 pubmed: '22700311' title: Using the KEGG database resource year: 2012 synonyms: - KEGG COMPOUND - KEGG.COMPOUND uri_format: https://www.kegg.jp/entry/$1 kegg.dgroup: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: " KEGG DGROUP contains structurally and functionally related groups\ \ of D number entries in KEGG DRUG. There are five types of drug groups.\n\n \ \ Chemical - grouped as identical chemical structures with minor variations\ \ of salts, hydration states, etc.\n Structure - grouped as similar chemical\ \ structures having the same skeleton, etc.\n Target - grouped by drug targets\n\ \ Class - drug classes often representing similar mechanisms of action\n \ \ Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing\ \ enzymes and transporters\n\nChemical groups are often used for identifying essentially\ \ the same active ingredients of drugs in different countries." example: DG00301 homepage: http://www.genome.jp/kegg/reaction/ mappings: biolink: KEGG.DGROUP name: KEGG Drug Group part_of: kegg pattern: ^DG\d+$ preferred_prefix: kegg.dgroup references: - https://github.com/prefixcommons/prefixes/pull/4 synonyms: - KEGG_DGROUP - KEGG_DRUG_GROUP kegg.disease: description: The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system. example: H00076 homepage: http://www.genome.jp/kegg/disease/ keywords: - classification mappings: biocontext: KEGG.DISEASE integbio: nbdc00813 miriam: kegg.disease n2t: kegg.disease prefixcommons: kegg.disease name: KEGG Disease part_of: kegg pattern: ^H\d+$ preferred_prefix: kegg.disease providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/kegg.disease:$1 uri_format: http://www.kegg.jp/entry/$1 kegg.drug: contact: email: kanehisa@kuicr.kyoto-u.ac.jp name: Minoru Kanehisa orcid: 0000-0001-6123-540X description: KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules. example: D00123 homepage: https://www.genome.jp/kegg/drug/ keywords: - small molecule mappings: biocontext: KEGG.DRUG edam: '2609' integbio: nbdc00812 miriam: kegg.drug n2t: kegg.drug prefixcommons: kegg.drug wikidata: P665 name: KEGG Drug part_of: kegg pattern: ^D\d+$ preferred_prefix: kegg.drug providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/kegg.drug:$1 publications: - doi: 10.1093/nar/gkj102 pmc: PMC1347464 pubmed: '16381885' title: 'From genomics to chemical genomics: new developments in KEGG' year: 2006 synonyms: - KEGG DRUG - KEGG.DRUG uri_format: https://www.kegg.jp/entry/$1 kegg.environ: deprecated: true description: KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable. example: ev:E00032 homepage: http://www.genome.jp/kegg/drug/environ.html mappings: biocontext: KEGG.ENVIRON integbio: nbdc01059 miriam: kegg.environ n2t: kegg.environ name: KEGG Environ part_of: kegg pattern: ^(ev\:)?E\d+$ preferred_prefix: kegg.environ synonyms: - KEGG.EDRUG uri_format: http://www.kegg.jp/entry/$1 kegg.enzyme: description: KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links. homepage: http://www.genome.jp/dbget-bin/www_bfind?enzyme mappings: biolink: KEGG.ENZYME go: KEGG_ENZYME name: KEGG Enzyme part_of: kegg preferred_prefix: kegg.enzyme provides: ec uri_format: http://www.genome.jp/dbget-bin/www_bget?ec:$1 kegg.genes: contact: email: kanehisa@kuicr.kyoto-u.ac.jp name: Minoru Kanehisa orcid: 0000-0001-6123-540X description: KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources. example: bsu:BSU01340 homepage: http://www.genome.jp/kegg/genes.html keywords: - dna - gene - protein mappings: biocontext: KEGG.GENES biolink: KEGG.GENES miriam: kegg.genes n2t: kegg.genes prefixcommons: kegg.gene wikidata: P665 name: KEGG Genes part_of: kegg pattern: ^\w+:[\w\d\.-]*$ preferred_prefix: kegg.genes providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/kegg.gene:$1 publications: - doi: 10.1093/nar/gkj102 pmc: PMC1347464 pubmed: '16381885' title: 'From genomics to chemical genomics: new developments in KEGG' year: 2006 uri_format: http://www.kegg.jp/entry/$1 kegg.genome: contact: email: kanehisa@kuicr.kyoto-u.ac.jp name: Minoru Kanehisa orcid: 0000-0001-6123-540X description: KEGG Genome is a collection of organisms whose genomes have been completely sequenced. example: T06648 homepage: http://www.genome.jp/kegg/catalog/org_list.html license: https://www.kegg.jp/kegg/legal.html mappings: biocontext: KEGG.GENOME integbio: nbdc00816 miriam: kegg.genome n2t: kegg.genome prefixcommons: kegg.genome wikidata: P665 name: KEGG Genome part_of: kegg pattern: ^(T0\d+|\w{3,5})$ preferred_prefix: kegg.genome providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/kegg.genome:$1 publications: - doi: 10.1093/nar/gkr988 pmc: PMC3245020 pubmed: '22080510' title: KEGG for integration and interpretation of large-scale molecular data sets year: 2011 synonyms: - kegg_genome - kegg_genomes uri_format: http://www.kegg.jp/entry/$1 kegg.glycan: contact: email: kanehisa@kuicr.kyoto-u.ac.jp name: Minoru Kanehisa orcid: 0000-0001-6123-540X description: KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways. example: G00123 homepage: https://www.genome.jp/kegg/glycan/ keywords: - small molecule mappings: biocontext: KEGG.GLYCAN edam: '2613' integbio: nbdc00533 miriam: kegg.glycan n2t: kegg.glycan prefixcommons: kegg.glycan name: KEGG Glycan part_of: kegg pattern: ^G\d+$ preferred_prefix: kegg.glycan providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/kegg.glycan:$1 publications: - doi: 10.1093/glycob/cwj010 pubmed: '16014746' title: KEGG as a glycome informatics resource year: 2005 uri_format: https://www.kegg.jp/entry/$1 kegg.ligand: comment: This database has been discontinued by KEGG. It now lives inside the compound database deprecated: true homepage: http://www.genome.ad.jp/kegg/docs/upd_ligand.html mappings: go: KEGG_LIGAND name: KEGG LIGAND part_of: kegg preferred_prefix: kegg.ligand uri_format: http://www.genome.jp/dbget-bin/www_bget?cpd:$1 kegg.metagenome: contact: email: kanehisa@kuicr.kyoto-u.ac.jp name: Minoru Kanehisa orcid: 0000-0001-6123-540X description: The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species. example: T30002 homepage: http://www.genome.jp/kegg/catalog/org_list3.html keywords: - genome mappings: biocontext: KEGG.METAGENOME miriam: kegg.metagenome n2t: kegg.metagenome prefixcommons: kegg.metagenome name: KEGG Metagenome part_of: kegg pattern: ^T3\d+$ preferred_prefix: kegg.metagenome providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/kegg.metagenome:$1 publications: - doi: 10.1093/nar/gkr988 pmc: PMC3245020 pubmed: '22080510' title: KEGG for integration and interpretation of large-scale molecular data sets year: 2011 uri_format: http://www.kegg.jp/entry/$1 kegg.module: description: KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules. example: M00002 homepage: http://www.kegg.jp/kegg/module.html mappings: biocontext: KEGG.MODULE integbio: nbdc01428 miriam: kegg.module n2t: kegg.module name: KEGG Module part_of: kegg pattern: ^([a-z]{3,5}_)?M\d{5}$ preferred_prefix: kegg.module uri_format: http://www.kegg.jp/entry/$1 kegg.orthology: description: KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms. example: K00001 homepage: http://www.genome.jp/kegg/ko.html keywords: - classification - pathway mappings: biocontext: KEGG.ORTHOLOGY miriam: kegg.orthology n2t: kegg.orthology prefixcommons: kegg.orthology name: KEGG Orthology part_of: kegg pattern: ^K\d+$ preferred_prefix: kegg.orthology providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/kegg.orthology:$1 uri_format: http://www.kegg.jp/entry/$1 kegg.pathway: contact: email: kanehisa@kuicr.kyoto-u.ac.jp name: Minoru Kanehisa orcid: 0000-0001-6123-540X description: KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks. example: rsk00410 homepage: https://www.genome.jp/kegg/pathway.html keywords: - pathway mappings: biocontext: KEGG.PATHWAY biolink: KEGG.PATHWAY edam: '2343' go: KEGG_PATHWAY miriam: kegg.pathway n2t: kegg.pathway prefixcommons: kegg.pathway wikidata: P665 name: KEGG Pathways Database part_of: kegg pattern: ^\w{2,4}\d{5}$ preferred_prefix: kegg.pathway providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/kegg.pathway:$1 publications: - doi: 10.1002/0471250953.bi0112s38 pubmed: '22700311' title: Using the KEGG database resource year: 2012 synonyms: - KEGG-path - KEGG_PATHWAY uri_format: https://www.kegg.jp/entry/$1 kegg.rclass: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns. example: RC00001 homepage: http://www.genome.jp/kegg/reaction/ mappings: biolink: KEGG.RCLASS integbio: nbdc00860 name: KEGG Reaction Class part_of: kegg pattern: ^RC\d+$ preferred_prefix: kegg.rclass references: - https://github.com/prefixcommons/prefixes/pull/2 synonyms: - KEGG_RCLASS - KEGG_REACTION_CLASS kegg.reaction: contact: email: kanehisa@kuicr.kyoto-u.ac.jp name: Minoru Kanehisa orcid: 0000-0001-6123-540X description: KEGG reaction contains our knowledge on the universe of reactions that are relevant to life. example: R00100 homepage: https://www.genome.jp/kegg/reaction/ keywords: - enzyme - pathway mappings: biocontext: KEGG.REACTION edam: '2608' go: KEGG_REACTION integbio: nbdc00818 miriam: kegg.reaction n2t: kegg.reaction prefixcommons: kegg.reaction wikidata: P665 name: KEGG Reaction part_of: kegg pattern: ^R\d+$ preferred_prefix: kegg.reaction providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/kegg.reaction:$1 publications: - doi: 10.1002/0471250953.bi0112s38 pubmed: '22700311' title: Using the KEGG database resource year: 2012 rdf_uri_format: http://www.kegg.jp/entry/$1 synonyms: - KEGG_REACTION uri_format: https://www.kegg.jp/entry/$1 kerafast: description: Cell line collections (Providers) example: EJH014 homepage: https://www.kerafast.com/ mappings: cellosaurus: Kerafast name: Kerafast cell lines preferred_prefix: kerafast uri_format: https://www.kerafast.com/Search?SearchTerm="$1" kestrelo: contact: email: lindsey.anderson@pnnl.gov github: lnanderson name: Lindsey N. Anderson orcid: 0000-0002-8741-7823 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology for harmonizing and extending severeral existing resources in the vaccine and immunology domains example: '0000001' homepage: https://gitlab.pnnl.gov/kestrel/kestrel_ontology name: KESTREL Ontology pattern: ^\d{7}$ preferred_prefix: kestrelo uri_format: http://purl.obolibrary.org/obo/kestrelo_$1 knapsack: description: 'KNApSAcK provides information on metabolites and the taxonomic class with which they are associated.' example: C00000001 homepage: http://www.knapsackfamily.com/KNApSAcK/ mappings: biocontext: KNAPSACK integbio: nbdc00545 miriam: knapsack n2t: knapsack wikidata: P2064 name: KNApSAcK pattern: ^C\d{8}$ 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 (Providers) example: KC-0979 homepage: https://www.kyinno.com/ mappings: cellosaurus: KYinno name: KYinno cell lines preferred_prefix: kyinno uri_format: https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf labo: contact: email: paul.fabry@usherbrooke.ca github: pfabry name: Paul Fabry orcid: 0000-0002-3336-2476 depends_on: - iao - obi - ogms - omiabis - omrse - opmi description: LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents. download_owl: http://purl.obolibrary.org/obo/labo.owl example: '0000124' homepage: https://github.com/OpenLHS/LABO keywords: - obo - ontology license: CC-BY-4.0 mappings: aberowl: LABO bioportal: LABO obofoundry: labo ols: labo ontobee: LABO name: clinical LABoratory Ontology pattern: ^\d{7}$ preferred_prefix: LABO publications: - doi: 10.5281/zenodo.6522019 title: 'LABO: An ontology for laboratory test prescription and reporting' year: 2019 rdf_uri_format: http://purl.obolibrary.org/obo/LABO_$1 repository: https://github.com/OpenLHS/LABO uri_format: http://purl.obolibrary.org/obo/LABO_$1 version: '2021-06-08' langual: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Langual stands for "langua alimentaria" or "language of food". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970''s by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases' example: B2067 github_request_issue: 507 homepage: https://www.langual.org name: Langua aLimentaria Thesaurus pattern: ^B\d+$ preferred_prefix: langual uri_format: https://www.langual.org/langual_thesaurus.asp?termid=$1 lattes: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: number for the Lattes Platform entry on the person or group. Relationship between entry and subject must be supported by a source example: 0061106995455595 homepage: https://lattes.cnpq.br keywords: - person - researcher mappings: wikidata: P1007 name: Lattes Platform number pattern: ^\d{16}$ preferred_prefix: lattes references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://lattes.cnpq.br/$1 lbctr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Lebanese Clinical Trials Registry is an online register of clinical trials being undertaken in Lebanon. It includes trials that target humans from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. (from homepage) example: LBCTR2023015204 homepage: https://lbctr.moph.gov.lb/ name: Lebanon Clinical Trials Registry pattern: ^LBCTR\d+$ preferred_prefix: lbctr references: - https://lbctr.moph.gov.lb/Trials/Details/5204 lbo: contact: email: caripark@iastate.edu github: caripark name: Carissa Park orcid: 0000-0002-2346-5201 description: A vocabulary for cattle, chicken, horse, pig, and sheep breeds. download_obo: https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.obo download_owl: https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.owl example: 0000487 homepage: http://bioportal.bioontology.org/ontologies/LBO keywords: - animal breeding - animal husbandry - genetics - genomics - ontology mappings: aberowl: LBO agroportal: LBO bioportal: LBO fairsharing: FAIRsharing.309v57 ols: lbo name: Livestock Breed Ontology pattern: ^\d{7}$ preferred_prefix: lbo rdf_uri_format: http://purl.obolibrary.org/obo/LBO_$1 repository: https://github.com/AnimalGenome/livestock-breed-ontology uri_format: https://bioportal.bioontology.org/ontologies/LBO/?p=classes&conceptid=http://purl.obolibrary.org/obo/LBO_$1 lccn: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: LCCN Permalinks are persistent URLs for bibliographic records in the LC Catalog and authority records in LC Authorities. These links are constructed using the record's LCCN (or Library of Congress Control Number), an identifier assigned by the Library of Congress to bibliographic and authority records. LCCN Permalinks are also available for citation records in the Handbook for Latin American Studies (HLAS). [from homepage] example: '2011488555' github_request_issue: 1310 homepage: https://lccn.loc.gov name: Library of Congress Control Number pattern: ^\d+$ preferred_prefix: lccn uri_format: https://lccn.loc.gov/$1 lcsh: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Library of Congress Subject Headings (LCSH) has been actively maintained since 1898 to catalog materials held at the Library of Congress. (from homepage) example: nb2018006591 homepage: https://id.loc.gov/authorities keywords: - subject agnostic mappings: bartoc: '454' fairsharing: FAIRsharing.d31795 wikidata: P244 name: Library of Congress Subject Headings pattern: ^\w{1,2}\d{8,10}$ preferred_prefix: lcsh rdf_uri_format: http://id.loc.gov/authorities/names/$1 synonyms: - lcnaf - lcnafid uri_format: https://id.loc.gov/authorities/$1 leafsnap: description: identifier for a tree species of the United States and Canada on the Leafsnap electronic field guide example: Amelanchier laevis homepage: http://leafsnap.com/ mappings: wikidata: P10538 name: Leafsnap preferred_prefix: leafsnap uri_format: http://leafsnap.com/species/$1/ lei: description: Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland. example: HWUPKR0MPOU8FGXBT394 homepage: https://www.gleif.org/ mappings: miriam: lei n2t: lei name: Global LEI Index pattern: ^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$ preferred_prefix: lei uri_format: https://www.gleif.org/lei/$1 lepao: contact: email: lagonzalezmo@unal.edu.co github: luis-gonzalez-m name: Luis A. Gonzalez-Montana orcid: 0000-0002-9136-9932 depends_on: - aism - bfo - bspo - caro - pato - ro - uberon description: The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. download_obo: http://purl.obolibrary.org/obo/lepao.obo download_owl: http://purl.obolibrary.org/obo/lepao.owl example: '0000005' homepage: https://github.com/insect-morphology/lepao keywords: - obo - ontology license: CC-BY-4.0 mappings: aberowl: LEPAO bioportal: LEPAO obofoundry: lepao ols: lepao ontobee: LEPAO name: Lepidoptera Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: LEPAO rdf_uri_format: http://purl.obolibrary.org/obo/LEPAO_$1 repository: https://github.com/insect-morphology/lepao uri_format: http://purl.obolibrary.org/obo/LEPAO_$1 version: '2023-02-18' lgai.cede: description: LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR). example: LGCEDe-S-000002244 homepage: https://www.lgresearch.ai mappings: miriam: lgai.cede name: LG Chemical Entity Detection Dataset (LGCEDe) pattern: ^LGCEDe-S-\d{9}$ preferred_prefix: lgai.cede uri_format: https://s3.us-east-2.amazonaws.com/lg.cede/$1 lgic: comment: Website is gone deprecated: true description: The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available. example: 5HT3Arano homepage: https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php keywords: - gene - protein - sequence mappings: biocontext: LGIC miriam: lgic n2t: lgic prefixcommons: lgicdb name: Ligand-Gated Ion Channel database pattern: ^\w+$ preferred_prefix: lgic providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/lgicdb:$1 publications: - doi: 10.1093/nar/27.1.340 pmc: PMC148177 pubmed: '9847222' title: The Ligand Gated Ion Channel Database year: 1999 uri_format: https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php licebase: contact: email: Inge.Jonassen@uib.no name: Inge Jonassen orcid: 0000-0003-4110-0748 description: Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects. example: EMLSAT00000003403 homepage: https://licebase.org keywords: - life science mappings: biocontext: LICEBASE fairsharing: FAIRsharing.c7w81a integbio: nbdc02217 miriam: licebase n2t: licebase re3data: r3d100013547 name: LiceBase pattern: ^[A-Za-z0-9\-\/]+$ preferred_prefix: licebase uri_format: https://licebase.org/?q=$1 ligandbook: description: Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community. example: '785' homepage: https://ligandbook.org/ mappings: miriam: ligandbook n2t: ligandbook name: LigandBook pattern: ^[0-9]+$ preferred_prefix: ligandbook uri_format: https://ligandbook.org/package/$1 ligandbox: description: LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. example: D00001 homepage: http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en mappings: biocontext: LIGANDBOX integbio: nbdc00551 miriam: ligandbox n2t: ligandbox name: LigandBox pattern: ^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$ preferred_prefix: ligandbox uri_format: http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1 ligandexpo: contact: email: jwest@rcsb.rutgers.edu name: John Westbrook orcid: 0000-0002-6686-5475 description: Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. example: ABC homepage: http://ligand-depot.rutgers.edu/index.html keywords: - chemical - interaction - life science - nucleic acid - protein - structure mappings: biocontext: LIGANDEXPO fairsharing: FAIRsharing.2ma4gq integbio: nbdc01864 miriam: ligandexpo n2t: ligandexpo pathguide: '154' prefixcommons: ligandexpo name: Ligand Expo pattern: ^(\w){3}$ preferred_prefix: ligandexpo providers: - code: 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 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ligandexpo:$1 publications: - doi: 10.1093/bioinformatics/bth214 pubmed: '15059838' title: 'Ligand Depot: a data warehouse for ligands bound to macromolecules' year: 2004 uri_format: http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid ligea: comment: This might just be a provider for CCLE description: Polymorphism and mutation databases example: CCLE_867 homepage: http://hpc-bioinformatics.cineca.it/fusion/main mappings: cellosaurus: LiGeA name: Cancer cell LInes GEne fusions portAl preferred_prefix: ligea uri_format: http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1 limore: description: Cell line databases/resources example: Li7 homepage: https://www.picb.ac.cn/limore/home mappings: cellosaurus: LIMORE name: Liver Cancer Model Repository preferred_prefix: limore uri_format: https://www.picb.ac.cn/limore/cellLines/single?para=$1 lincs.cell: description: 'The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.' example: LCL-2085 homepage: http://lincsportal.ccs.miami.edu/cells/ mappings: biocontext: LINCS.CELL cellosaurus: LINCS_LDP miriam: lincs.cell n2t: lincs.cell name: LINCS Cell pattern: ^(LCL|LDC|ES|LSC|LPC)-\d+$ preferred_prefix: lincs.cell synonyms: - LINCS_LDP uri_format: http://lincsportal.ccs.miami.edu/cells/#/view/$1 lincs.data: description: The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level). example: LDS-1110 homepage: http://lincsportal.ccs.miami.edu/datasets/ mappings: biocontext: LINCS.DATA miriam: lincs.data n2t: lincs.data name: LINCS Data pattern: ^[EL]D[SG]-\d+$ preferred_prefix: lincs.data providers: - code: omicsdi description: Lincs through OmicsDI homepage: https://www.omicsdi.org/ name: Lincs through OmicsDI uri_format: https://www.omicsdi.org/dataset/lincs/$1 uri_format: http://lincsportal.ccs.miami.edu/datasets/#/view/$1 lincs.protein: description: The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins. example: '200282' homepage: http://lincs.hms.harvard.edu/db/proteins/ mappings: biocontext: LINCS.PROTEIN miriam: lincs.protein n2t: lincs.protein name: LINCS Protein pattern: ^\d+$ preferred_prefix: lincs.protein uri_format: https://lincs.hms.harvard.edu/db/proteins/$1 lincs.smallmolecule: description: The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC). example: LSM-6306 homepage: http://lincsportal.ccs.miami.edu/SmallMolecules/ mappings: biocontext: LINCS.SMALLMOLECULE miriam: lincs.smallmolecule n2t: lincs.smallmolecule name: LINCS Small Molecule pattern: ^LSM-\d+$ preferred_prefix: lincs.smallmolecule synonyms: - lincs uri_format: http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1 linguist: description: Registry of programming languages for the Linguist program for detecting and highlighting programming languages. example: Python homepage: https://github.com/github/linguist mappings: miriam: linguist name: Linguist pattern: ^[a-zA-Z0-9 +#'*]+$ preferred_prefix: linguist repository: https://github.com/github/linguist uri_format: https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1 linguist.gold: comment: This resource has been deprecated and was last released in 2010. The homepage links to a zip folder that includes an OWL artifact, but it doesn't follow any typical standards. The ontology browser is not perfect, it only works for classes. contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true example: Term github_request_issue: 1310 homepage: https://linguistlist.org/gold/ name: Genderal Ontology for Linguistic Description preferred_prefix: linguist.gold rdf_uri_format: http://purl.org/linguistics/gold/$1 uri_format: https://lambdamusic.github.io/ontospy-examples/gold-2010owl/class-gold$1.html linkedin: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier for a person, on the LinkedIn website example: deborahlehr homepage: https://www.linkedin.com keywords: - person - researcher mappings: wikidata: P6634 name: LinkedIn personal profile ID pattern: ^[\w0-9\-&_'’\.]+$ preferred_prefix: linkedin references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://www.linkedin.com/in/$1 linkml: comment: 'Closes #508' contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks. example: SchemaDefinition github_request_issue: 512 homepage: https://linkml.io/linkml-model/docs/SchemaDefinition/ keywords: - data integration - ontology and terminology mappings: biolink: linkml fairsharing: FAIRsharing.cb7086 name: LinkML preferred_prefix: linkml publications: - doi: 10.5281/zenodo.5598314 title: 'linkml/linkml-model: v1.5.2' year: 2023 repository: https://github.com/linkml/ twitter: linkml_data uri_format: https://w3id.org/linkml/$1 lipidbank: contact: email: e-yasugi@umin.ac.jp name: Etsuko Yasugi orcid: 0000-0003-1898-4426 description: LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. example: BBA0001 homepage: http://lipidbank.jp/index.html keywords: - life science - lipid - molecule - structure mappings: biocontext: LIPIDBANK edam: '2665' fairsharing: FAIRsharing.bdn9br integbio: nbdc00126 miriam: lipidbank n2t: lipidbank prefixcommons: lipidbank name: LipidBank pattern: ^\w+\d+$ preferred_prefix: lipidbank providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/lipidbank:$1 publications: - pubmed: '12058481' title: '[LIPIDBANK for Web, the newly developed lipid database]' year: 2002 uri_format: http://lipidbank.jp/cgi-bin/detail.cgi?id=$1 lipidmaps: contact: email: edennis@ucsd.edu name: 0000-0003-3738-3140 orcid: 0000-0003-3738-3140 description: The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy. example: LMPR0102010012 homepage: http://www.lipidmaps.org keywords: - biomedical science - endocrinology - life science - lipid - structure - systems biology - taxonomy mappings: biocontext: LIPIDMAPS cheminf: '000564' edam: '2625' fairsharing: FAIRsharing.cpneh8 miriam: lipidmaps n2t: lipidmaps pathguide: '503' prefixcommons: lipidmaps re3data: r3d100012315 togoid: Lipidmaps wikidata: P2063 name: LIPID MAPS pattern: ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$ preferred_prefix: lipidmaps providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/lipidmaps:$1 - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/lipidmaps/$1 publications: - doi: 10.1194/jlr.r800095-jlr200 pmc: PMC2674711 pubmed: '19098281' title: Update of the LIPID MAPS comprehensive classification system for lipids year: 2008 - doi: 10.1093/nar/gkm324 pmc: PMC1933166 pubmed: '17584797' title: LIPID MAPS online tools for lipid research year: 2007 - doi: 10.1093/nar/gkl838 pmc: PMC1669719 pubmed: '17098933' title: 'LMSD: LIPID MAPS structure database' year: 2006 - doi: 10.1194/jlr.e400004-jlr200 pubmed: '15722563' title: A comprehensive classification system for lipids year: 2005 - doi: 10.1194/jlr.R800095-JLR200 title: Update of the LIPID MAPS comprehensive classification system for lipids. synonyms: - LIPID MAPS - LIPID_MAPS_class - LIPID_MAPS_instance twitter: lipidmaps uri_format: http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1 lipro: contact: email: bakerc@unb.ca name: Christopher Baker orcid: 0000-0003-4004-6479 deprecated: true description: An ontology representation of the LIPIDMAPS nomenclature classification. download_owl: http://aber-owl.net/media/ontologies/LIPRO/4/lipro.owl keywords: - obo - ontology mappings: aberowl: LIPRO biocontext: LIPRO bioportal: LIPRO obofoundry: lipro name: Lipid Ontology preferred_prefix: LIPRO rdf_uri_format: http://purl.obolibrary.org/obo/LIPRO_$1 uri_format: http://purl.obolibrary.org/obo/LIPRO_$1 lncipedia: contact: email: pieter.mestdagh@ugent.be github: OncoRNALab name: Pieter Mestdagh orcid: 0000-0001-7821-9684 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A comprehensive compendium of human long non-coding RNAs example: SNHG3 homepage: https://lncipedia.org keywords: - life science mappings: fairsharing: FAIRsharing.84c1a7 name: LNCipedia preferred_prefix: lncipedia publications: - doi: 10.1093/nar/gkv295 pmc: PMC4417186 pubmed: '25829178' title: 'An update on LNCipedia: a database for annotated human lncRNA sequences' year: 2015 - doi: 10.1093/nar/gku1060 pmc: PMC4383901 pubmed: '25378313' title: 'An update on LNCipedia: a database for annotated human lncRNA sequences' year: 2014 - doi: 10.1093/nar/gks915 pmc: PMC3531107 pubmed: '23042674' title: 'LNCipedia: a database for annotated human lncRNA transcript sequences and structures' year: 2012 loggerhead: contact: email: peteremidford@yahoo.com name: Peter Midford orcid: 0000-0001-6512-3296 deprecated: true homepage: http://www.mesquiteproject.org/ontology/Loggerhead/index.html keywords: - obo - ontology mappings: biocontext: LOGGERHEAD obofoundry: loggerhead name: Loggerhead nesting preferred_prefix: LOGGERHEAD rdf_uri_format: http://purl.obolibrary.org/obo/LOGGERHEAD_$1 uri_format: http://purl.obolibrary.org/obo/LOGGERHEAD_$1 loinc: contact: email: loinc@regenstrief.org name: LOINC Support contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The international standard for identifying health measurements, observations, and documents. example: LL379-9 homepage: https://loinc.org/ keywords: - assay - biomedical science - diagnosis - genetic disorder - genetic polymorphism - life science - ontology - phenotype - preclinical studies license: https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf mappings: aberowl: LOINC bartoc: '1897' biolink: LOINC bioportal: LOINC fairsharing: FAIRsharing.2mk2zb hl7: 2.16.840.1.113883.6.1 wikidata: P4338 name: Logical Observation Identifiers Names and Codes pattern: ^(\d|\w)+-\d$ preferred_prefix: loinc publications: - doi: 10.1016/s1386-5056(98)00089-6 pubmed: '9749897' title: Combining laboratory data sets from multiple institutions using the logical observation identifier names and codes (LOINC) year: 1998 - doi: 10.1093/jamia/ocu012 pmc: PMC5566197 pubmed: '25656513' title: Supporting interoperability of genetic data with LOINC year: 2015 - doi: 10.1016/j.jbi.2012.01.005 pmc: PMC3376691 pubmed: '22285984' title: Enabling international adoption of LOINC through translation year: 2012 rdf_uri_format: http://loinc.org/rdf/$1 synonyms: - LNC twitter: LOINC uri_format: https://loinc.org/$1 lonza: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Contains information about cells and data sheets related to transfection. example: '968' homepage: https://knowledge.lonza.com mappings: cellosaurus: Lonza name: Lonza pattern: ^\d+$ preferred_prefix: lonza uri_format: https://knowledge.lonza.com/cell?id=$1 loop: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier for a person, in the Loop database of researcher impact example: '1859' homepage: https://loop.frontiersin.org/ keywords: - person - researcher mappings: wikidata: P2798 name: Loop ID pattern: ^[1-9]\d*$ preferred_prefix: loop references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://loop.frontiersin.org/people/$1/overview loqate: contact: email: maya.schuldiner@weizmann.ac.il github: Maya-Schuldiner-lab name: Maya Schuldiner orcid: 0000-0001-9947-115X description: The data presented here is a result of systematically tracking the localization and abundance of 5330 yeast proteins at single-cell resolution under three different stress conditions (DTT, H2O2 and nitrogen starvation) using the GFP-tagged yeast library example: '1001' homepage: http://www.weizmann.ac.il/molgen/loqate/ mappings: prefixcommons: loqate name: The localization and quantitation atlas of the yeast proteome preferred_prefix: loqate providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/loqate:$1 publications: - doi: 10.1093/nar/gkt933 pmc: PMC3965041 pubmed: '24150937' title: LoQAtE--Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast year: 2013 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.weizmann.ac.il/molgen/loqate/gene/view/$1 lotus: comment: IDs are actually leading to the structural part of LOTUS only, which might change in the future. Will adapt the regexp in case. contact: email: adriano.rutz@ik.me github: adafede name: Adriano Rutz orcid: 0000-0003-0443-9902 contributor: email: adriano.rutz@ik.me github: adafede name: Adriano Rutz orcid: 0000-0003-0443-9902 description: LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry. example: LTS0004651 github_request_issue: 222 homepage: https://lotus.naturalproducts.net keywords: - chemistry - drugs - metabolites logo: https://upload.wikimedia.org/wikipedia/commons/6/64/Lotus_initiative_logo.svg name: LOTUS Initiative for Open Natural Products Research pattern: ^LTS\d{7}$ preferred_prefix: lotus reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://lotus.naturalproducts.net/compound/lotus_id/$1 lpt: contact: email: caripark@iastate.edu github: caripark name: Carissa Park orcid: 0000-0002-2346-5201 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit. download_obo: https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.obo download_owl: https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.owl example: '0000156' homepage: https://github.com/AnimalGenome/livestock-product-trait-ontology keywords: - animal husbandry - ontology - phenotype mappings: aberowl: LPT agroportal: LPT biocontext: LPT bioportal: LPT fairsharing: FAIRsharing.g78mbm name: Livestock Product Trait Ontology pattern: ^\d+$ preferred_prefix: lpt repository: https://github.com/AnimalGenome/livestock-product-trait-ontology uri_format: http://purl.obolibrary.org/obo/LPT_$1 lrg: banana: LRG banana_peel: _ description: A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI. example: '1' homepage: http://www.lrg-sequence.org/ mappings: biocontext: LRG hl7: 2.16.840.1.113883.6.283 integbio: nbdc02566 miriam: lrg n2t: lrg togoid: Lrg name: Locus Reference Genomic pattern: ^\d+$ preferred_prefix: lrg providers: - code: 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 east) homepage: http://useast.ensembl.org/ name: Locus Reference Genomic through Ensembl mirror (US east) uri_format: http://useast.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1 uri_format: http://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml lspci: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions) example: '1' homepage: https://labsyspharm.github.io/lspci/ keywords: - chemistry - drugs - metabolites name: Laboratory of Systems Pharmacology Compound pattern: ^\d+$ preferred_prefix: lspci uri_format: https://labsyspharm.github.io/lspci/$1 lter: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Ecological terms example: '182' homepage: https://vocab.lternet.edu/vocab/vocab/index.php name: Long Term Ecological Research Controlled Vocabulary pattern: ^\d+$ preferred_prefix: lter uri_format: https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1 lw: description: The LifeWatch Metadata Catalogues plays a crucial role in managing metadata for digital objects, including Datasets, Services, Workflows and Virtual Research Environments. This catalogue serves as the central repository, ensuring that resources are accessible and reusable by stakeholders. example: 6e3b1371-59d7-481a-9db4-cd0d0de98436 homepage: https://metadatacatalogue.lifewatch.eu/ mappings: miriam: lw name: LifeWatch Metadata Catalogue pattern: ^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$ preferred_prefix: lw uri_format: https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/$1 m4i: contact: email: dorothea.iglezakis@ub.uni-stuttgart.de github: doigl name: Dorothea Iglezakis orcid: 0000-0002-8524-0569 contributor: email: giacomo.lanza@ptb.de github: Zack-83 name: Giacomo Lanza orcid: 0000-0002-2239-3955 description: The ontology Metadata4Ing is developed within the NFDI Consortium NFDI4Ing with the aim of providing a thorough framework for the semantic description of research data, with a particular focus on engineering sciences and neighbouring disciplines. This ontology allows a description of the whole data generation process (experiment, observation, simulation), embracing the object of investigation, all sample and data manipulation procedures, a summary of the data files and the information contained, and all personal and institutional roles. The subordinate classes and relations can be built according to the two principles of inheritance and modularity. "Inheritance" means that a subclass inherits all properties of its superordinate class, possibly adding some new ones. Modularity means that all expansions are independent of each other; this makes possible for instance to generate expanded ontologies for any possible combinations of method × object of research. download_owl: https://nfdi4ing.pages.rwth-aachen.de/metadata4ing/metadata4ing/ontology.xml download_rdf: https://nfdi4ing.pages.rwth-aachen.de/metadata4ing/metadata4ing/ontology.ttl example: Method github_request_issue: 970 homepage: https://w3id.org/nfdi4ing/metadata4ing/ keywords: - academy - engineering science - metadata - ontology license: CC-BY-4.0 mappings: bartoc: '20402' fairsharing: FAIRsharing.f8b3ec lov: m4i wikidata: Q111516803 zazuko: m4i mastodon: nfdi4ing@nfdi.social name: Metadata4Ing owners: - name: Nationale Forschungsdateninfrastruktur partnered: false ror: 05qj6w324 pattern: ^\w+$ preferred_prefix: m4i repository: https://git.rwth-aachen.de/nfdi4ing/metadata4ing/metadata4ing/ reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://w3id.org/nfdi4ing/metadata4ing#$1 ma: banana: MA contact: email: Terry.Hayamizu@jax.org github: tfhayamizu name: Terry Hayamizu orcid: 0000-0002-0956-8634 description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus) download_obo: http://purl.obolibrary.org/obo/ma.obo download_owl: http://purl.obolibrary.org/obo/ma.owl example: '0002502' homepage: https://github.com/obophenotype/mouse-anatomy-ontology keywords: - anatomy - mouse - obo - ontology - organ - tissue license: CC-BY-4.0 mappings: aberowl: MA biocontext: MA bioportal: MA fairsharing: FAIRsharing.pdwqcr go: MA miriam: ma n2t: ma obofoundry: ma ols: ma ontobee: MA prefixcommons: ma name: Mouse adult gross anatomy namespace_in_lui: true pattern: ^\d+$ preferred_prefix: MA providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ma:$1 publications: - doi: 10.1186/gb-2005-6-3-r29 pmc: PMC1088948 pubmed: '15774030' title: 'The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data' year: 2005 rdf_uri_format: http://purl.obolibrary.org/obo/MA_$1 repository: https://github.com/obophenotype/mouse-anatomy-ontology uri_format: http://purl.obolibrary.org/obo/MA_$1 version: '2017-02-07' macie: contact: email: gemma.l.holliday@gmail.com github: GLHolliday79 name: Gemma L. Holliday orcid: 0000-0002-6731-6398 description: MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved. example: M0001 homepage: https://www.ebi.ac.uk/thornton-srv/m-csa/about/ keywords: - enzyme - life science - pathway mappings: biocontext: MACIE edam: '2641' fairsharing: FAIRsharing.7xkx69 miriam: macie n2t: macie prefixcommons: macie name: Mechanism, Annotation and Classification in Enzymes pattern: ^M\d{4}$ preferred_prefix: macie providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/macie:$1 publications: - doi: 10.1093/nar/gkl774 pmc: PMC1634735 pubmed: '17082206' title: 'MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms' year: 2006 - doi: 10.1093/bioinformatics/bti693 pmc: PMC2748267 pubmed: '16188925' title: 'MACiE: a database of enzyme reaction mechanisms' year: 2005 uri_format: https://www.ebi.ac.uk/thornton-srv/m-csa/search/?s=$1 maggot: description: Sharing descriptive Metadata is the first essential step towards Open Scientific Data. With this in mind, Maggot was specifically designed to annotate datasets by creating a metadata file to attach to the storage space. Indeed, it allows users to easily add descriptive metadata to datasets produced within a collective of people (research unit, platform, multi-partner project, etc.). This approach fits perfectly into a data management plan as it addresses the issues of data organization and documentation, data storage and frictionless metadata sharing within this same collective and beyond. example: frim1 homepage: https://eng-bfp.bordeaux-aquitaine.hub.inrae.fr/resources/metabolome-platform mappings: miriam: maggot name: Maggot pattern: ^[A-Za-z0-9]+$ preferred_prefix: maggot uri_format: https://pmb-bordeaux.fr/maggot/metadata/$1 maizegdb.locus: contact: email: margaret.woodhouse@usda.gov github: margaretwoodhouse name: Margaret R. Woodhouse orcid: 0000-0003-2164-8300 description: MaizeGDB is the maize research community's central repository for genetics and genomics information. example: '25011' homepage: http://www.maizegdb.org/ keywords: - dna - genetics - genome - genomics - life science mappings: biocontext: MAIZEGDB.LOCUS fairsharing: FAIRsharing.aq280w go: MaizeGDB_Locus integbio: nbdc00129 miriam: maizegdb.locus n2t: maizegdb.locus ncbi: MaizeGDB prefixcommons: maizegdb re3data: r3d100010795 uniprot: DB-0058 name: MaizeGDB Locus pattern: ^\d+$ preferred_prefix: maizegdb.locus providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/maizegdb:$1 publications: - doi: 10.1186/s12870-021-03173-5 pubmed: '34416864' - doi: 10.3389/fpls.2019.01050 pmc: PMC6724615 pubmed: '31555312' title: 'MaizeDIG: Maize Database of Images and Genomes' year: 2019 - doi: 10.1093/nar/gky1046 pmc: PMC6323944 pubmed: '30407532' title: 'MaizeGDB 2018: the maize multi-genome genetics and genomics database' year: 2019 - doi: 10.1007/978-1-4939-3167-5_9 pubmed: '26519406' title: 'MaizeGDB: The Maize Genetics and Genomics Database' year: 2016 - doi: 10.1093/nar/gkv1007 pmc: PMC4702771 pubmed: '26432828' title: 'MaizeGDB update: new tools, data and interface for the maize model organism database' year: 2015 - doi: 10.1155/2008/496957 pmc: PMC2518694 pubmed: '18769488' title: 'MaizeGDB: The maize model organism database for basic, translational, and applied research' year: 2008 - doi: 10.1093/nar/gkl1048 pmc: PMC1899092 pubmed: '17202174' title: MaizeGDB's new data types, resources and activities year: 2007 synonyms: - MaizeGDB uri_format: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1 mamo: banana: MAMO banana_peel: _ contact: email: n.lenovere@gmail.com name: Nicolas Le Novere orcid: 0000-0002-6309-7327 deprecated: true description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. download_owl: http://purl.obolibrary.org/obo/mamo.owl download_rdf: https://raw.githubusercontent.com/EBISPOT/mamo/main/mamo.rdf example: '0000026' homepage: http://sourceforge.net/p/mamo-ontology/wiki/Home/ keywords: - computational biology - mathematics - modeling and simulation - obo - ontology - systems biology license: Artistic License 2.0 mappings: aberowl: MAMO biocontext: MAMO bioportal: MAMO fairsharing: FAIRsharing.kbz5jh miriam: mamo n2t: mamo obofoundry: mamo ols: mamo ontobee: MAMO name: Mathematical modeling ontology pattern: ^\d{7}$ preferred_prefix: MAMO rdf_uri_format: http://purl.obolibrary.org/obo/MAMO_$1 repository: http://sourceforge.net/p/mamo-ontology uri_format: http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1 version: '2023-02-03' mampol: description: The Mammalia Polymorphism Database is a secondary database designed to provide a collection of all the existing polymorphic sequences in the MammaliaOnline query interfaces facilitate data interrogation by different polymorphism parameter values and keyword queries (based on SQL searches). example: MAMpol005339 homepage: http://mampol.uab.es keywords: - dna mappings: prefixcommons: mampol name: Mammalia Polymorphism Database preferred_prefix: mampol providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mampol:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://mampol.uab.es/cgi-bin/MamPol_s2.pl?Accession=$1 mao: contact: email: julie@igbmc.u-strasbg.fr name: Julie Thompson deprecated: true description: An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment. example: '0000061' homepage: http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html keywords: - alignment - obo - ontology - sequence mappings: biocontext: MAO obofoundry: mao prefixcommons: mao name: Multiple alignment pattern: ^\d{7}$ preferred_prefix: MAO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mao:$1 rdf_uri_format: http://purl.obolibrary.org/obo/MAO_$1 uri_format: http://purl.obolibrary.org/obo/MAO_$1 markerdb: contact: email: dwishart@ualberta.ca github: DavidWishartLab name: David S. Wishart orcid: 0000-0002-3207-2434 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: MarkerDB is a freely available electronic database that attempts to consolidate information on all known clinical and pre-clinical biomarkers into a single resource. It provides identifiers for known clinical and pre-clinical biomarkers. Each entry provides detailed annotations, including biomarker descriptions, associated conditions, specificity, sensitivity, molecular structures, chromosomal locations, and clinical approval status. example: MDB00000001 github_request_issue: 1330 homepage: https://markerdb.ca name: MarkerDB pattern: ^MDB\d{8}$ preferred_prefix: markerdb publications: - doi: 10.1093/nar/gkae1056 pubmed: '39535054' title: 'MarkerDB 2.0: a comprehensive molecular biomarker database for 2025' year: 2024 - doi: 10.1093/nar/gkaa1067 pmc: PMC7778954 pubmed: '33245771' title: 'MarkerDB: an online database of molecular biomarkers' year: 2021 reviewer: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 massbank: contact: email: tobias.schulze@ufz.de github: tsufz name: Tobias Schulze orcid: 0000-0002-9744-8914 description: MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da). example: MSBNK-IPB_Halle-PB000166 homepage: http://www.massbank.jp keywords: - chemistry - life science - physics mappings: biocontext: MASSBANK fairsharing: FAIRsharing.dk451a integbio: nbdc00298 miriam: massbank n2t: massbank wikidata: P6689 name: MassBank pattern: ^MSBNK-[0-9a-zA-Z_]+-[A-Z0-9_]+$ preferred_prefix: massbank providers: - code: massbankeu description: MassBank in Europe homepage: https://massbank.eu/ name: MassBank in Europe uri_format: https://massbank.eu/MassBank/RecordDisplay?id=$1 publications: - doi: 10.1002/jms.1777 pubmed: '20623627' title: 'MassBank: a public repository for sharing mass spectral data for life sciences' year: 2010 repository: https://github.com/MassBank uri_format: https://massbank.jp/RecordDisplay?id=$1 massive: contact: email: miw023@ucsd.edu name: Mingxun Wang orcid: 0000-0001-7647-6097 description: MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. example: MSV000082131 homepage: https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp keywords: - functional genomics - metabolomics - metaproteomics - omics - phenomics - proteomics mappings: biocontext: MASSIVE fairsharing: FAIRsharing.LYsiMd miriam: massive n2t: massive uniprot: DB-0241 name: MassIVE pattern: ^MSV\d+$ preferred_prefix: massive providers: - code: omicsdi description: MassIVE through OmicsDI homepage: https://www.omicsdi.org/ name: MassIVE through OmicsDI uri_format: https://www.omicsdi.org/dataset/massive/$1 publications: - doi: 10.1038/s41592-020-0955-0 pmc: PMC7541731 pubmed: '32929271' title: 'MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets' year: 2020 - doi: 10.1093/nar/gkz984 pmc: PMC7145525 pubmed: '31686107' title: 'The ProteomeXchange consortium in 2020: enabling ''big data'' approaches in proteomics' year: 2020 - doi: 10.1016/j.cels.2018.08.004 pmc: PMC6279426 pubmed: '30172843' title: Assembling the Community-Scale Discoverable Human Proteome year: 2018 - doi: 10.1093/nar/gkw936 pmc: PMC5210636 pubmed: '27924013' title: 'The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition' year: 2016 - doi: 10.1038/nbt.3597 pmc: PMC5321674 pubmed: '27504778' title: Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking year: 2016 repository: https://ccms-ucsd.github.io/MassIVEDocumentation uri_format: https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1 mastodon: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: address on the Mastodon decentralized social network (the form is 'user@server.domain' without a leading '@') example: jz@mamot.fr homepage: https://mastodon.social mappings: wikidata: P4033 name: Mastodon pattern: ^[A-Za-z0-9_]+([A-Za-z0-9_\.]+[A-Za-z0-9_]+)?@[\d\w\.\-]+[0-9a-z]+$ preferred_prefix: mastodon uri_format: https://fedirect.toolforge.org/?id=$1 mat: contact: email: j.bard@ed.ac.uk name: Jonathan Bard deprecated: true description: Minimal set of terms for anatomy download_obo: http://aber-owl.net/media/ontologies/MAT/3/mat.obo example: '0000000' keywords: - obo - ontology mappings: aberowl: MAT biocontext: MAT bioportal: MAT obofoundry: mat name: Minimal Anatomical Terminology pattern: ^\d{7}$ preferred_prefix: MAT rdf_uri_format: http://purl.obolibrary.org/obo/MAT_$1 uri_format: http://purl.obolibrary.org/obo/MAT_$1 matrixdb: appears_in: - complexportal contact: email: sylvie.ricard-blum@univ-lyon1.fr github: ricardblum name: Sylvie Ricard-Blum orcid: 0000-0001-9263-1851 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides example: MULT_4_VAR1_bovine homepage: http://matrixdb.univ-lyon1.fr/ keywords: - biology - interaction - protein - small molecule mappings: fairsharing: FAIRsharing.91yrz6 integbio: nbdc01222 pathguide: '298' prefixcommons: matrixdb re3data: r3d100010672 name: MatrixDB preferred_prefix: matrixdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/matrixdb:$1 publications: - doi: 10.1093/nar/gky1035 pmc: PMC6324007 pubmed: '30371822' title: 'MatrixDB: integration of new data with a focus on glycosaminoglycan interactions' year: 2019 - doi: 10.1093/nar/gku1091 pmc: PMC4383919 pubmed: '25378329' title: 'MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities' year: 2014 - doi: 10.1093/nar/gkq830 pmc: PMC3013758 pubmed: '20852260' title: MatrixDB, the extracellular matrix interaction database year: 2010 - doi: 10.1093/bioinformatics/btp025 pmc: PMC2647840 pubmed: '19147664' title: MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions year: 2009 uri_format: http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1 matrixdb.association: description: MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations. example: P00747__P07355 homepage: https://matrixdb.univ-lyon1.fr/ mappings: biocontext: MATRIXDB.ASSOCIATION miriam: matrixdb.association n2t: matrixdb.association name: MatrixDB Association pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$ preferred_prefix: matrixdb.association uri_format: https://matrixdb.univ-lyon1.fr/association/$1 mavedb: comment: This is an interesting one as the full IDs as they appear on the page are of the form `urn:mavedb:00000011-a` suggesting this is the preferred URI expansion for identification purposes. However, mavedb hasn't been registered with IANA https://www.iana.org/assignments/urn-namespaces/urn-namespaces.xhtml contact: email: alan.rubin@wehi.edu.au github: afrubin name: Alan Rubin orcid: 0000-0003-1474-605X contributor: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: Some IDs may represent experiment sets, e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011 Others represent genomic regions (specifically deep mutational scans thereof) e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011-a example: 00000011-a example_extras: - '00000011' github_request_issue: 1045 homepage: https://www.mavedb.org name: Multiplexed Assays of Variant Effect Database pattern: ^\S+$ preferred_prefix: mavedb publications: - doi: 10.1186/s13059-025-03476-y pmc: PMC11753097 pubmed: '39838450' title: 'MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays' year: 2025 - doi: 10.1186/s13059-019-1845-6 pmc: PMC6827219 pubmed: '31679514' title: 'MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect' year: 2019 repository: https://github.com/VariantEffect/mavedb-api reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.mavedb.org/#/experiments/urn:mavedb:$1 maxo: appears_in: - ecto contact: email: Leigh.Carmody@jax.org github: LCCarmody name: Leigh Carmody orcid: 0000-0001-7941-2961 depends_on: - chebi - foodon - go - hp - iao - nbo - obi - ro - uberon description: An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations. download_json: http://purl.obolibrary.org/obo/maxo.json download_obo: http://purl.obolibrary.org/obo/maxo.obo download_owl: http://purl.obolibrary.org/obo/maxo.owl example: 0000008 homepage: https://github.com/monarch-initiative/MAxO keywords: - medicine - obo - ontology - rare disease license: CC-BY-4.0 logo: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/maxo-logos/maxo_logo_black-banner.png mappings: aberowl: MAXO biolink: MAXO bioportal: MAXO fairsharing: FAIRsharing.945c78 miriam: maxo obofoundry: maxo ols: maxo ontobee: MAXO name: Medical Action Ontology pattern: ^\d{7}$ preferred_prefix: MAXO publications: - doi: 10.1101/2023.07.13.23292612 pubmed: '37503136' title: 'The Medical Action Ontology: A Tool for Annotating and Analyzing Treatments and Clinical Management of Human Disease' year: 2023 rdf_uri_format: http://purl.obolibrary.org/obo/MAXO_$1 repository: https://github.com/monarch-initiative/MAxO twitter: MonarchInit uri_format: http://purl.obolibrary.org/obo/MAXO_$1 version: '2024-07-29' mba: contact: email: cellsemantics@gmail.com name: Allen Institute for Brain Science contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A controlled vocabulary to support the study of transcription in the mouse brain download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-mba.obo download_owl: https://purl.brain-bican.org/ontology/mbao/releases/2025-02-10/mbao.owl example: '688' homepage: https://mouse.brain-map.org keywords: - ontology mappings: bioportal: ABA-AMB ols: mba name: Mouse Brain Atlas pattern: ^\d+$ preferred_prefix: MBA providers: - code: biopragmatics description: Biopragmatics provider for MBA homepage: https://biopragmatics.github.io/providers/mba name: MBA from Biopragmatics uri_format: https://biopragmatics.github.io/providers/mba/$1 uri_format: https://purl.brain-bican.org/ontology/mbao/MBA_$1 version: '2025-02-10' mcc: contact: email: usha@molecularconnections.com name: Usha Mahadevan deprecated: true description: Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive of machine-interpretable definitions of basic concepts in the domain and relations among them. The need for ontologies that provide a systematic arrangement of available data and allow cross talk across various related domains is gaining momentum. In this backdrop, we have developed a comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format. example: ThoracicArtery homepage: http://www.molecularconnections.com keywords: - ontology mappings: bioportal: MCCL name: Cell Line Ontology [derivative] preferred_prefix: mcc uri_format: http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#$1 mco: contact: email: citlalli.mejiaalmonte@gmail.com github: citmejia name: Citlalli Mejía-Almonte orcid: 0000-0002-0142-5591 depends_on: - bfo - chebi - cl - clo - micro - ncbitaxon - ncit - obi - omit - omp - pato - peco - uberon - zeco description: Microbial Conditions Ontology is an ontology... download_obo: http://purl.obolibrary.org/obo/mco.obo download_owl: http://purl.obolibrary.org/obo/mco.owl example: 0000858 homepage: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: MCO bioportal: MCO obofoundry: mco ols: mco ontobee: MCO name: Microbial Conditions Ontology pattern: ^\d+$ preferred_prefix: MCO rdf_uri_format: http://purl.obolibrary.org/obo/MCO_$1 repository: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology uri_format: http://purl.obolibrary.org/obo/MCO_$1 version: '2019-05-15' mcro: banana: MCRO contact: email: muamith@utmb.edu github: ProfTuan name: Tuan Amith orcid: 0000-0003-4333-1857 depends_on: - iao - swo description: 'An ontology representing the model card structure, he aim of this work is to describe machine learning models to communicate information about specific details about the model (trade offs, intended users, licensing, etc.). ' download_owl: http://purl.obolibrary.org/obo/mcro.owl example: '0000001' homepage: https://github.com/UTHealth-Ontology/MCRO keywords: - obo - ontology license: CC-BY-4.0 mappings: aberowl: MCRO bioportal: MCRO miriam: mcro obofoundry: mcro ontobee: MCRO name: Model Card Report Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: MCRO publications: - doi: 10.1186/s12859-022-04797-6 title: Toward a standard formal semantic representation of the model card report rdf_uri_format: http://purl.obolibrary.org/obo/MCRO_$1 repository: https://github.com/UTHealth-Ontology/MCRO uri_format: https://www.ebi.ac.uk/ols4/ontologies/mcro/classes?obo_id=MCRO:$1 mdl: appears_in: - xlmod contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The MDL number contains a unique identification number for each reaction and variation. The format is RXXXnnnnnnnn. R indicates a reaction, XXX indicates which database contains the reaction record. The numeric portion, nnnnnnnn, is an 8-digit number. [wikipedia] example: MFCD00011659 github_request_issue: 1311 homepage: https://en.wikipedia.org/wiki/Chemical_file_format#MDL_number name: Molecular Design Limited Hash pattern: ^\w{4}\d{8}$ preferred_prefix: mdl references: - https://en.wikipedia.org/wiki/Chemical_file_format#MDL_number mdm: contact: email: bernd.mueller@zbmed.de name: Bernd Müller orcid: 0000-0003-3062-8192 description: The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems. download_owl: http://aber-owl.net/media/ontologies/MDM/4/mdm.owl example: '4776' homepage: https://medical-data-models.org/ keywords: - biomedical science - medicine - ontology - translational medicine mappings: aberowl: MDM biocontext: MDM bioportal: MDM fairsharing: FAIRsharing.wnk2eq miriam: mdm n2t: mdm re3data: r3d100013816 name: Medical Data Models pattern: ^\d+$ preferred_prefix: mdm publications: - doi: 10.1093/database/bav121 pmc: PMC4750548 pubmed: '26868052' title: 'Portal of medical data models: information infrastructure for medical research and healthcare' year: 2016 uri_format: https://medical-data-models.org/forms/$1 meddra: contact: email: mssohelp@meddra.org name: MedDRA MSSO description: The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT). example: '10015919' homepage: http://bioportal.bioontology.org/ontologies/MEDDRA keywords: - biomedical science - disease - medicine - ontology - preclinical studies mappings: aberowl: MEDDRA bartoc: '1237' biocontext: MEDDRA bioportal: MEDDRA fairsharing: FAIRsharing.ad3137 hl7: 2.16.840.1.113883.6.163 integbio: nbdc02564 miriam: meddra n2t: meddra togoid: Meddra wikidata: P3201 name: Medical Dictionary for Regulatory Activities Terminology pattern: ^\d+$ preferred_prefix: meddra publications: - doi: 10.1016/s1386-5056(00)00062-9 pubmed: '10961570' title: The use of a medical dictionary for regulatory activities terminology (MedDRA) in prescription-event monitoring in Japan (J-PEM) year: 2000 - doi: 10.2165/00002018-199920020-00002 pubmed: '10082069' title: The medical dictionary for regulatory activities (MedDRA) year: 1999 rdf_uri_format: http://purl.bioontology.org/ontology/MDRFRE/$1 synonyms: - MEDRA - MeDRA - MedDRA - Medical Dictionary for Regulatory Activities uri_format: http://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid=$1 medgen: description: MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder. example: '760050' homepage: https://www.ncbi.nlm.nih.gov/medgen/ mappings: biocontext: MedGen biolink: medgen integbio: nbdc02560 miriam: medgen n2t: medgen ncbi: MedGen togoid: Medgen name: Human Medical Genetics pattern: ^[CN]*\d{4,7}$ preferred_prefix: medgen uri_format: https://www.ncbi.nlm.nih.gov/medgen/$1 mediadive.ingredient: contact: email: joerg.overmann@dsmz.de name: Jörg Overmann orcid: 0000-0003-3909-7201 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about] example: '13' github_request_issue: 941 homepage: https://mediadive.dsmz.de/solutions license: CC-BY-4.0 name: MediaDive Ingredient pattern: ^\d+$ preferred_prefix: mediadive.ingredient uri_format: https://mediadive.dsmz.de/ingredients/$1 mediadive.medium: contact: email: joerg.overmann@dsmz.de name: Jörg Overmann orcid: 0000-0003-3909-7201 contributor: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about] example: '77' example_extras: - 54b github_request_issue: 941 homepage: https://mediadive.dsmz.de/media license: CC-BY-4.0 mappings: miriam: mediadive.medium name: MediaDive Medium pattern: ^\d+\w?$ preferred_prefix: mediadive.medium reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://mediadive.dsmz.de/medium/$1 mediadive.solution: contact: email: joerg.overmann@dsmz.de name: Jörg Overmann orcid: 0000-0003-3909-7201 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about] example: S6 github_request_issue: 941 homepage: https://mediadive.dsmz.de/solutions license: CC-BY-4.0 name: MediaDive Solution pattern: ^S\d+$ preferred_prefix: mediadive.solution uri_format: https://mediadive.dsmz.de/solutions/$1 medlineplus: contact: email: custserv@nlm.nih.gov name: NLM Customer Service description: MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language. example: 002804 homepage: http://www.nlm.nih.gov/medlineplus/ keywords: - biomedical science - disease - health science - medicine - ontology logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaEFGIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--611e307f6ed5ae6a6f06017953d913cdcacc490b/Screenshot%20from%202024-10-04%2017-49-50.png?disposition=inline mappings: aberowl: MEDLINEPLUS biocontext: MEDLINEPLUS bioportal: MEDLINEPLUS fairsharing: FAIRsharing.bf8dsb hl7: 2.16.840.1.113883.6.173 integbio: nbdc00836 miriam: medlineplus n2t: medlineplus name: MedlinePlus Health Topics pattern: ^\d+$ preferred_prefix: medlineplus providers: - code: medlineplus.fp description: First-party version of medline plus. homepage: https://medlineplus.gov name: MedLine Plus home page uri_format: https://medlineplus.gov/ency/article/$1.htm uri_format: http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm merops.clan: contact: email: ndr@ebi.ac.uk name: Neil D Rawlings orcid: 0000-0001-5557-7665 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. example: IA homepage: https://www.ebi.ac.uk/merops name: MEROPS Clan part_of: merops preferred_prefix: merops.clan publications: - doi: 10.1093/nar/gkx1134 pmc: PMC5753285 pubmed: '29145643' title: The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database year: 2018 references: - https://github.com/biopragmatics/bioregistry/issues/439 uri_format: https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=$1 merops.entry: contact: email: ndr@ebi.ac.uk name: Neil D Rawlings orcid: 0000-0001-5557-7665 description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors. example: I31.952 example_extras: - S01.001 - XM02.001 homepage: http://merops.sanger.ac.uk/index.htm keywords: - biomedical science - enzyme - life science - protein - structure mappings: biocontext: MEROPS.INHIBITOR edam: '2629' fairsharing: FAIRsharing.2s4n8r go: MEROPS miriam: merops.inhibitor n2t: merops.inhibitor prefixcommons: merops name: MEROPS Entry pattern: ^[SCTAGMNUIX]{1,2}\d{2}\.([AB]\d{2}|\d{3})$ preferred_prefix: merops.entry providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/merops:$1 publications: - doi: 10.1093/nar/27.1.325 pmc: PMC148173 pubmed: '9847218' title: 'MEROPS: the peptidase database' year: 1999 - doi: 10.1042/bj2900205 pmc: PMC1132403 pubmed: '8439290' title: Evolutionary families of peptidases year: 1993 - doi: 10.1093/nar/gkx1134 pmc: PMC5753285 pubmed: '29145643' title: The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database year: 2018 - doi: 10.1093/nar/gkv1118 pmc: PMC4702814 pubmed: '26527717' title: Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors year: 2015 - doi: 10.1016/j.biochi.2015.10.003 pmc: PMC4756867 pubmed: '26455268' title: Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation year: 2015 - doi: 10.1093/nar/gkr987 pmc: PMC3245014 pubmed: '22086950' title: 'MEROPS: the database of proteolytic enzymes, their substrates and inhibitors' year: 2011 - doi: 10.1093/nar/gkm954 pmc: PMC2238837 pubmed: '17991683' title: 'MEROPS: the peptidase database' year: 2007 references: - https://github.com/biopragmatics/bioregistry/issues/439 synonyms: - merops.inhibitor uri_format: https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1 merops.family: contact: email: ndr@ebi.ac.uk name: Neil D Rawlings orcid: 0000-0001-5557-7665 description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families. example: S1 homepage: http://merops.sanger.ac.uk/index.htm mappings: biocontext: MEROPS.FAMILY miriam: merops.family n2t: merops.family name: MEROPS Family part_of: merops pattern: ^[SCTAGMNU]\d+$ preferred_prefix: merops.family publications: - doi: 10.1093/nar/gkx1134 pmc: PMC5753285 pubmed: '29145643' title: The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database year: 2018 references: - https://github.com/biopragmatics/bioregistry/issues/439 uri_format: https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1 merriamwebster: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Online Dictionary example: buccal_gland github_request_issue: 1310 homepage: https://www.merriam-webster.com name: Merriam Webster Dictionary preferred_prefix: merriamwebster synonyms: - merriam_webster uri_format: https://www.merriam-webster.com/dictionary/$1 mesh: contact: email: custserv@nlm.nih.gov name: NLM Customer Service contributor_extras: - github: rombaum name: Roman Baum orcid: 0000-0001-5246-9351 description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc. example: C063233 example_extras: - D000001 homepage: http://id.nlm.nih.gov/mesh/ keywords: - bioinformatics - biomedical science - classification - data model - data retrieval - life science - literature curation - metascience - ontology - topics license: CC0-1.0 logo: https://meshb.nlm.nih.gov/public/img/meshLogo.jpg mappings: aberowl: MESH bartoc: '391' biocontext: MESH biolink: MESH bioportal: MESH cellosaurus: MeSH edam: '1177' fairsharing: FAIRsharing.qnkw45 go: MeSH hl7: 2.16.840.1.113883.6.177 integbio: nbdc00132 miriam: mesh n2t: mesh prefixcommons: mesh togoid: Mesh wikidata: P486 name: Medical Subject Headings pattern: ^(C|D|M)\d{6,9}$ preferred_prefix: mesh providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mesh:$1 - code: bioportal.purl description: The BioPortal version of MeSH. Should be re-coded to `bioportal`, see https://github.com/biopragmatics/bioregistry/pull/1066. homepage: https://bioportal.bioontology.org/ontologies/MESH name: BioPortal uri_format: http://purl.bioontology.org/ontology/MESH/$1 - code: mesh.2008 description: Appears in birnlex homepage: http://id.nlm.nih.gov/mesh/ name: Legacy 2008 MeSH URL uri_format: http://www.nlm.nih.gov/cgi/mesh/2008/MB_cgi?field=uid&term=$1 - code: mesh.json-ld description: The MeSH version in JSON-LD. first_party: true homepage: http://id.nlm.nih.gov/mesh/ name: Medical Subject Headings (JSON-LD) uri_format: https://id.nlm.nih.gov/mesh/$1.json-ld - code: mesh.n3 description: The MeSH version in N3. first_party: true homepage: http://id.nlm.nih.gov/mesh/ name: Medical Subject Headings (N3) uri_format: https://id.nlm.nih.gov/mesh/$1.n3 - code: mesh.ttl description: The MeSH version in TTL. first_party: true homepage: http://id.nlm.nih.gov/mesh/ name: Medical Subject Headings (TTL) uri_format: https://id.nlm.nih.gov/mesh/$1.ttl - code: ncbi description: MeSH via National Library of Medicine homepage: https://www.nlm.nih.gov/ name: MeSH via National Library of Medicine uri_format: https://www.ncbi.nlm.nih.gov/mesh/?term=$1 publications: - pmc: PMC197951 pubmed: '13982385' title: Medical subject headings year: 1963 rdf_uri_format: http://id.nlm.nih.gov/mesh/$1 synonyms: - MESH - MESHA - MESHC - MESHCS - MESHD - MESHPP - MESH_DESCRIPTOR_UI - MESH_SUPPLEMENTAL_RECORD_UI - MSH - MSH2010_2010_02_22 - meshUID uri_format: https://meshb.nlm.nih.gov/record/ui?ui=$1 mesh.2012: description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012. example: '17186' homepage: http://www.nlm.nih.gov/mesh/ mappings: biocontext: MESH.2012 miriam: mesh.2012 n2t: mesh.2012 name: MeSH 2012 pattern: ^[A-Za-z0-9]+$ preferred_prefix: mesh.2012 provides: mesh uri_format: http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded mesh.2013: description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013. example: '17165' homepage: http://www.nlm.nih.gov/mesh/ mappings: biocontext: MESH.2013 miriam: mesh.2013 n2t: mesh.2013 name: MeSH 2013 pattern: ^[A-Za-z0-9]+$ preferred_prefix: mesh.2013 provides: mesh uri_format: http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded mesh.vocab: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump example: term homepage: https://hhs.github.io/meshrdf/ name: Medical Subject Headings Vocabulary part_of: mesh preferred_prefix: mesh.vocab references: - https://id.nlm.nih.gov/mesh/query repository: https://github.com/HHS/meshrdf uri_format: http://id.nlm.nih.gov/mesh/vocab#$1 metabolights: description: MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies. example: MTBLS1 homepage: https://www.ebi.ac.uk/metabolights/ mappings: biocontext: METABOLIGHTS cellosaurus: MetaboLights integbio: nbdc02124 miriam: metabolights n2t: metabolights re3data: r3d100011556 wikidata: P3890 name: MetaboLights Compound pattern: ^MTBLS\d+$ 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/$1 metacyc.compound: contact: email: pkarp@ai.sri.com github: pkarp111 name: Peter Karp orcid: 0000-0002-5876-6418 description: MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. example: CPD-10330 homepage: https://metacyc.org keywords: - life science - metabolomics - systems biology mappings: biocontext: METACYC.COMPOUND biolink: MetaCyc fairsharing: FAIRsharing.yytevr go: MetaCyc integbio: nbdc00907 miriam: metacyc.compound n2t: metacyc.compound pathguide: '10' re3data: r3d100011294 name: Metabolic Encyclopedia of metabolic and other pathways pattern: ^[A-Za-z0-9+_.%-:]+$ preferred_prefix: metacyc.compound publications: - doi: 10.1093/nar/gkv1164 pmc: PMC4702838 pubmed: '26527732' title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases year: 2015 - doi: 10.1093/nar/gkt1103 pmc: PMC3964957 pubmed: '24225315' title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases year: 2013 - doi: 10.1093/nar/gkr1014 pmc: PMC3245006 pubmed: '22102576' title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases year: 2011 synonyms: - MetaCyc twitter: BioCyc uri_format: https://metacyc.org/compound?orgid=META&id=$1 metacyc.pathway: contact: email: pkarp@ai.sri.com github: pkarp111 name: Peter Karp orcid: 0000-0002-5876-6418 contributor: github: hrshdhgd name: Harshad Hegde orcid: 0000-0002-2411-565X description: 'MetaCyc is a database of non-redundant, experimentally elucidated metabolic pathways and enzymes. It also contains reactions, chemical compounds, and genes. It stores predominantly qualitative information rather than quantitative data, although it does contain some quantitative data such as enzyme kinetics data. MetaCyc is [curated](http://www.biocyc.org/glossary.shtml?sid=biocyc14-3908554027#Curation) from the scientific experimental literature according to an [extensive process](https://metacyc.org/MetaCycUserGuide.shtml#TAG:__tex2page_sec_4)]. The majority of pathways occurring in it are from microorganisms and plants. MetaCyc stores thousands of additional enzyme-catalyzed reactions that have not yet been assigned an EC number' example: 12DICHLORETHDEG-PWY github_request_issue: 1012 homepage: https://metacyc.org name: Metabolic Encyclopedia for Pathway/Genome Databases preferred_prefix: metacyc.pathway publications: - pubmed: '31586394' title: The MetaCyc database of metabolic pathways and enzymes - a 2019 update year: 2019 - pubmed: '23746312' title: The challenge of constructing, classifying, and representing metabolic pathways year: 2013 - pubmed: '21523460' title: A survey of metabolic databases emphasizing the MetaCyc family year: 2011 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://metacyc.org/META/NEW-IMAGE?object=$1 metacyc.reaction: contact: email: pkarp@ai.sri.com github: pkarp111 name: Peter Karp orcid: 0000-0002-5876-6418 description: MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. example: RXN-14904 homepage: https://metacyc.org mappings: biocontext: METACYC.REACTION biolink: metacyc.reaction miriam: metacyc.reaction n2t: metacyc.reaction name: MetaCyc Reaction pattern: ^[A-Za-z0-9+_.%-:]+$ preferred_prefix: metacyc.reaction uri_format: https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1 metanetx.chemical: description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components. example: MNXM1723 homepage: https://www.metanetx.org/ mappings: biocontext: METANETX.CHEMICAL miriam: metanetx.chemical n2t: metanetx.chemical name: MetaNetX chemical pattern: ^(MNXM\d+|BIOMASS|WATER)$ preferred_prefix: metanetx.chemical uri_format: https://www.metanetx.org/chem_info/$1 metanetx.compartment: description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments. example: MNXC15 homepage: https://www.metanetx.org/ mappings: biocontext: METANETX.COMPARTMENT miriam: metanetx.compartment n2t: metanetx.compartment name: MetaNetX compartment pattern: ^(MNX[CD]\d+|BOUNDARY|IN|OUT)$ preferred_prefix: metanetx.compartment uri_format: https://www.metanetx.org/comp_info/$1 metanetx.reaction: description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions. example: MNXR101574 homepage: https://www.metanetx.org/ mappings: biocontext: METANETX.REACTION biolink: METANETX.REACTION miriam: metanetx.reaction n2t: metanetx.reaction name: MetaNetX reaction pattern: ^(MNXR\d+|EMPTY)$ preferred_prefix: metanetx.reaction uri_format: https://www.metanetx.org/equa_info/$1 metatlas: contact: email: mihail.anton@chalmers.se github: mihai-sysbio name: Mihail Anton orcid: 0000-0002-7753-9042 contributor: email: mihail.anton@chalmers.se github: mihai-sysbio name: Mihail Anton orcid: 0000-0002-7753-9042 description: A resource for exploring metabolism, starting with a set of of community-curated genome-scale metabolic models of human and model organisms, enriched with pathway maps and other tools for easy browsing and analysis. example: MAM01234c example_decoys: - MAR11851c example_extras: - MAR11851 github_request_issue: 495 homepage: https://metabolicatlas.org keywords: - chemistry - metabolites - reactions mappings: miriam: metatlas name: Metabolic Atlas pattern: ^(MAM\d{5}\w)|(MAR\d{5})$ preferred_prefix: metatlas reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://metabolicatlas.org/identifier/MetabolicAtlas/$1 metatlas.metabolite: contact: email: mihail.anton@chalmers.se github: mihai-sysbio name: Mihail Anton orcid: 0000-0002-7753-9042 contributor: email: mihail.anton@chalmers.se github: mihai-sysbio name: Mihail Anton orcid: 0000-0002-7753-9042 description: A subspace of Metabolic Atlas for compartment-specific records for metabolites. example: MAM01234c github_request_issue: 495 homepage: https://metabolicatlas.org keywords: - chemistry - metabolites name: Metabolic Atlas Metabolite part_of: metatlas pattern: ^MAM\d{5}\w$ preferred_prefix: metatlas.metabolite reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://metabolicatlas.org/identifier/MetabolicAtlas/$1 metatlas.reaction: contact: email: mihail.anton@chalmers.se github: mihai-sysbio name: Mihail Anton orcid: 0000-0002-7753-9042 contributor: email: mihail.anton@chalmers.se github: mihai-sysbio name: Mihail Anton orcid: 0000-0002-7753-9042 description: A subspace of Metabolic Atlas for reactions. example: MAR11851 github_request_issue: 495 homepage: https://metabolicatlas.org keywords: - chemistry - reactions name: Metabolic Atlas Reaction part_of: metatlas pattern: ^MAR\d{5}$ preferred_prefix: metatlas.reaction reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://metabolicatlas.org/identifier/MetabolicAtlas/$1 metlin: description: The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry. example: '1455' homepage: http://masspec.scripps.edu/ mappings: biocontext: METLIN miriam: metlin n2t: metlin re3data: r3d100012311 name: Metabolite and Tandem Mass Spectrometry Database pattern: ^\d{4}$ preferred_prefix: metlin uri_format: http://metlin.scripps.edu/metabo_info.php?molid=$1 metnetdb: description: The MetNet database (MetNetDB) contains information on networks of metabolic and regulatory and interactions in Arabidopsis. Types of interactions in MetNetDB include transcription, translation, protein modification, assembly, allosteric regulation, translocation from one subcellular compartment to another. example: '377369' homepage: http://www.metnetdb.org/MetNet_db.htm keywords: - dna - interaction - pathway - protein - regulation - rna - small molecule mappings: pathguide: '234' prefixcommons: metnetdb name: Metabolic Network Exchange Database preferred_prefix: metnetdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/metnetdb:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://metnetonline.org/browse_pathway2.php?pthID=$1 mex: description: A public place to process, interpret and share GC/MS metabolomics datasets. example: '36' homepage: https://www.metabolome-express.org/ mappings: biocontext: MEX miriam: mex n2t: mex name: Metabolome Express pattern: ^\d+$ preferred_prefix: mex providers: - code: omicsdi description: Metabolome Express through OmicsDI homepage: https://www.omicsdi.org/ name: Metabolome Express through OmicsDI uri_format: https://www.omicsdi.org/dataset/metabolome_express/MEX$1 uri_format: https://www.metabolome-express.org/datasetview.php?datasetid=$1 mf: contact: email: janna.hastings@gmail.com github: jannahastings name: Janna Hastings orcid: 0000-0002-3469-4923 description: The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning. download_owl: http://purl.obolibrary.org/obo/mf.owl example: 0000091 homepage: https://github.com/jannahastings/mental-functioning-ontology keywords: - biomedical science - cognition - cognitive neuroscience - mental health - obo - ontology license: CC-BY-3.0 mappings: aberowl: MF biocontext: MF bioportal: MF fairsharing: FAIRsharing.4gm9gt obofoundry: mf ols: mf ontobee: MF name: Mental Functioning Ontology pattern: ^\d{7}$ preferred_prefix: MF rdf_uri_format: http://purl.obolibrary.org/obo/MF_$1 repository: https://github.com/jannahastings/mental-functioning-ontology uri_format: http://purl.obolibrary.org/obo/MF_$1 version: '2022-07-19' mfmo: contact: email: druzinsk@uic.edu github: RDruzinsky name: Robert Druzinsky orcid: 0000-0002-1572-1316 depends_on: - uberon deprecated: true description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors. download_owl: http://purl.obolibrary.org/obo/mfmo.owl example: 0000208 homepage: https://github.com/rdruzinsky/feedontology keywords: - anatomy - obo - ontology license: CC-BY-3.0 mappings: aberowl: MFMO biocontext: MFMO bioportal: MFMO fairsharing: FAIRsharing.669cnk obofoundry: mfmo ols: mfmo ontobee: MFMO name: Mammalian Feeding Muscle Ontology pattern: ^\d{7}$ preferred_prefix: MFMO providers: - code: conflated description: A conflated URL with parts. homepage: http://purl.obolibrary.org name: OBO PURL Parts uri_format: http://purl.obolibrary.org/obo/mfmo.owl#MFMO_$1 rdf_uri_format: http://purl.obolibrary.org/obo/MFMO_$1 repository: https://github.com/RDruzinsky/feedontology uri_format: http://purl.obolibrary.org/obo/MFMO_$1 version: '2013-11-16' mfo: contact: email: henrich@embl.de github: ThorstenHen name: Thorsten Henrich orcid: 0000-0002-1548-3290 deprecated: true description: A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes. download_obo: http://aber-owl.net/media/ontologies/MFO/14/mfo.obo download_owl: http://purl.obolibrary.org/obo/mfo.owl example: '0000001' homepage: http://ani.embl.de:8080/mepd/ keywords: - anatomy - development - fish - obo - ontology mappings: aberowl: MFO biocontext: MFO bioportal: MFO obofoundry: mfo prefixcommons: mfo name: Medaka fish anatomy and development pattern: ^\d{7}$ preferred_prefix: MFO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mfo:$1 rdf_uri_format: http://purl.obolibrary.org/obo/MFO_$1 uri_format: http://purl.obolibrary.org/obo/MFO_$1 mfoem: contact: email: janna.hastings@gmail.com github: jannahastings name: Janna Hastings orcid: 0000-0002-3469-4923 description: An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings. download_owl: http://purl.obolibrary.org/obo/mfoem.owl example: '000204' homepage: https://github.com/jannahastings/emotion-ontology keywords: - biomedical science - emotion - mental health - obo - ontology license: CC-BY-3.0 mappings: aberowl: MFOEM biocontext: MFOEM bioportal: MFOEM fairsharing: FAIRsharing.dx30m8 obofoundry: mfoem ols: mfoem ontobee: MFOEM name: Emotion Ontology pattern: ^\d{6}$ preferred_prefix: MFOEM publications: - doi: 10.1186/2041-1480-5-38 pmc: PMC4417517 pubmed: '25937879' title: Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference year: 2014 rdf_uri_format: http://purl.obolibrary.org/obo/MFOEM_$1 repository: https://github.com/jannahastings/emotion-ontology uri_format: http://purl.obolibrary.org/obo/MFOEM_$1 version: '2025-01-06' mfomd: contact: email: janna.hastings@gmail.com github: jannahastings name: Janna Hastings orcid: 0000-0002-3469-4923 description: The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF). download_owl: http://purl.obolibrary.org/obo/mfomd.owl example: '0000046' homepage: https://github.com/jannahastings/mental-functioning-ontology keywords: - disease - obo - ontology - psychiatry license: CC-BY-3.0 mappings: aberowl: MFOMD biocontext: MFOMD bioportal: MFOMD fairsharing: FAIRsharing.q053vb obofoundry: mfomd ols: mfomd ontobee: MFOMD name: Mental Disease Ontology pattern: ^\d{7}$ preferred_prefix: MFOMD rdf_uri_format: http://purl.obolibrary.org/obo/MFOMD_$1 repository: https://github.com/jannahastings/mental-functioning-ontology uri_format: http://purl.obolibrary.org/obo/MFOMD_$1 version: '2020-04-26' mge: banana: mge deprecated: true description: ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. example: '2' homepage: http://aclame.ulb.ac.be/ keywords: - gene - genome - life science mappings: biocontext: ACLAME edam: '2631' fairsharing: FAIRsharing.5tfcy8 integbio: nbdc00355 miriam: mge n2t: mge prefixcommons: aclame name: Aclame namespace_in_lui: true pattern: ^\d+$ preferred_prefix: mge providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/aclame:$1 publications: - doi: 10.1093/nar/gkp938 pmc: PMC2808911 pubmed: '19933762' title: 'ACLAME: a CLAssification of Mobile genetic Elements, update 2010' year: 2009 - doi: 10.1093/nar/gkh084 pmc: PMC308818 pubmed: '14681355' title: 'ACLAME: a CLAssification of Mobile genetic Elements' year: 2004 synonyms: - aclame uri_format: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1 mgi: banana: MGI contact: email: joel.richardson@jax.org github: JoelRichardson name: Joel Richardson orcid: 0000-0003-3342-5753 description: The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data. example: '6017782' homepage: http://www.informatics.jax.org/ keywords: - animal model - blast - data analysis service - expression - function - gene - gene expression - genetics - genome - genotype - gold standard - human disease - human health - image - life science - model - molecular neuroanatomy resource - ontology and terminology - orthology - pathology - pathway - phenotype - recombinase - sequence - single nucleotide polymorphism - strain - tumor license: CC-BY-4.0 mappings: biocontext: MGI cellosaurus: MGI edam: '3274' fairsharing: FAIRsharing.fcwyhz go: MGI integbio: nbdc00568 miriam: mgi n2t: mgi ncbi: MGI prefixcommons: mgi re3data: r3d100010266 rrid: MGI uniprot: DB-0060 wikidata: P671 name: Mouse Genome Informatics namespace_in_lui: true pattern: ^\d+$ preferred_prefix: MGI providers: - code: agr description: MGI through the Alliance of Genome Resources homepage: https://www.alliancegenome.org name: MGI through the Alliance of Genome Resources uri_format: https://www.alliancegenome.org/gene/MGI:$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mgi:$1 - code: mgi.marker description: MGI Marker homepage: http://www.informatics.jax.org/marker name: MGI Marker uri_format: http://www.informatics.jax.org/marker/MGI:$1 publications: - doi: 10.1126/science.8091224 pubmed: '8091224' title: A database for mouse development year: 1994 - doi: 10.1093/nar/gky1056 pmc: PMC6323923 pubmed: '30407599' title: Mouse Genome Database (MGD) 2019 year: 2019 - doi: 10.1093/nar/gky922 pmc: PMC6324054 pubmed: '30335138' title: 'The mouse Gene Expression Database (GXD): 2019 update' year: 2019 - doi: 10.1093/ilar/ilx013 pmc: PMC5886341 pubmed: '28838066' title: 'Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse' year: 2017 - doi: 10.1007/978-1-4939-6427-7_3 pubmed: '27933520' title: 'Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research' year: 2017 - doi: 10.1093/nar/gkw1040 pmc: PMC5210536 pubmed: '27899570' title: 'Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse' year: 2016 - doi: 10.1093/nar/gkt1225 pmc: PMC3964950 pubmed: '24285300' title: 'The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse' year: 2013 - doi: 10.1093/nar/gks1115 pmc: PMC3531104 pubmed: '23175610' title: 'The mouse genome database: genotypes, phenotypes, and models of human disease' year: 2012 - doi: 10.1093/nar/gkr974 pmc: PMC3245042 pubmed: '22075990' title: 'The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse' year: 2011 - pubmed: '19274630' - pubmed: '18428715' - doi: 10.1093/nar/gki113 pmc: PMC540067 pubmed: '15608240' title: 'The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology' year: 2005 synonyms: - MGD - MGI twitter: mgi_mouse uri_format: http://www.informatics.jax.org/accession/MGI:$1 mgnify.analysis: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Analyses of microbiome data within MGnify example: MGYA00002270 homepage: https://www.ebi.ac.uk/metagenomics/ name: MGnify Analysis pattern: ^MGYA\d+$ preferred_prefix: mgnify.analysis uri_format: https://www.ebi.ac.uk/metagenomics/analyses/$1 mgnify.proj: description: MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis. example: ERP004492 homepage: https://www.ebi.ac.uk/metagenomics mappings: miriam: mgnify.proj n2t: mgnify.proj name: MGnify Project pattern: ^[A-Z]+[0-9]+$ preferred_prefix: mgnify.proj uri_format: https://www.ebi.ac.uk/metagenomics/projects/$1 mgnify.samp: description: The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples. example: SRS086444 homepage: https://www.ebi.ac.uk/metagenomics mappings: miriam: mgnify.samp n2t: mgnify.samp name: MGnify Sample pattern: ^[A-Z]+[0-9]+$ preferred_prefix: mgnify.samp uri_format: https://www.ebi.ac.uk/metagenomics/samples/$1 mi: banana: MI contact: email: luana.licata@gmail.com github: luanalicata name: Luana Licata orcid: 0000-0001-5084-9000 description: The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative. download_obo: http://purl.obolibrary.org/obo/mi.obo download_owl: http://purl.obolibrary.org/obo/mi.owl example: 0058 homepage: https://github.com/HUPO-PSI/psi-mi-CV keywords: - interaction - life science - molecular interaction - molecule - obo - ontology - protein - protein interaction license: CC-BY-4.0 mappings: aberowl: MI biocontext: PSIMI biolink: MI bioportal: MI fairsharing: FAIRsharing.8qzmtr go: PSI-MI miriam: mi n2t: psimi obofoundry: mi ols: mi ontobee: MI prefixcommons: psi.mi name: Molecular Interactions Controlled Vocabulary namespace_in_lui: true pattern: ^\d{4}$ preferred_prefix: MI providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/psi.mi:$1 publications: - doi: 10.1038/nbt926 pubmed: '14755292' title: The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data year: 2004 rdf_uri_format: http://purl.obolibrary.org/obo/MI_$1 repository: https://github.com/HUPO-PSI/psi-mi-CV synonyms: - PSI-MI uri_format: http://purl.obolibrary.org/obo/MI_$1 miaa: comment: same as MAT contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: Minimal Information About Anatomy ontology preferred_prefix: miaa references: - https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/rols/inst/doc/rols.pdf miapa: contact: email: hilmar.lapp@duke.edu github: hlapp name: Hilmar Lapp orcid: 0000-0001-9107-0714 description: 'The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies. This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project''s main page at http://evoio.org/wiki/MIAPA.' download_owl: http://purl.obolibrary.org/obo/miapa.owl example: '0000010' homepage: http://www.evoio.org/wiki/MIAPA keywords: - life science - obo - ontology - phylogenetics - phylogeny license: CC0-1.0 mappings: aberowl: MIAPA biocontext: MIAPA bioportal: MIAPA fairsharing: FAIRsharing.ca48xs obofoundry: miapa ols: miapa ontobee: MIAPA name: Minimum Anformation About a Phylogenetic Analysis Ontology pattern: ^\d{7}$ preferred_prefix: MIAPA publications: - doi: 10.1089/omi.2006.10.231 pmc: PMC3167193 pubmed: '16901231' title: 'Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)' year: 2006 rdf_uri_format: http://purl.obolibrary.org/obo/MIAPA_$1 repository: https://github.com/evoinfo/miapa uri_format: http://purl.obolibrary.org/obo/MIAPA_$1 mibig: contact: email: kblin@biosustain.dtu.dk github: kblin name: Kai Blin orcid: 0000-0003-3764-6051 contributor: email: zdoucmm@gmail.com github: mmzdouc name: Mitja M. Zdouc orcid: 0000-0001-6534-6609 description: MIBiG (Minimum Information about a Biosynthetic Gene Cluster) is a data repository and associated data standard designed to describe biosynthetic gene clusters involved in the production of specialized metabolites. It also stores data on measured biological activities and links to other resources such as NCBI, NPAtlas, and ChEBI. MIBiG is used as a reference database, knowledgebase, and training dataset for machine learning. example: BGC0000001 github_request_issue: 1407 homepage: https://mibig.secondarymetabolites.org license: CC-BY-4.0 name: Minimum Information about a Biosynthetic Gene Cluster data repository pattern: ^BGC\d{7}$ preferred_prefix: mibig publications: - doi: 10.1093/nar/gkae1115 pmc: PMC11701617 pubmed: '39657789' title: 'MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration' year: 2024 repository: https://github.com/mibig-secmet/mibig-json reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://mibig.secondarymetabolites.org/go/$1 micro: appears_in: - mco contact: email: carrine.blank@umontana.edu github: carrineblank name: Carrine Blank orcid: 0000-0002-2100-6351 deprecated: true description: An ontology of prokaryotic phenotypic and metabolic characters download_owl: http://purl.obolibrary.org/obo/micro.owl example: 0002999 homepage: https://github.com/carrineblank/MicrO keywords: - assay - bioinformatics - cell culture - microbiology - obo - ontology - phenotype license: CC BY 2.0 mappings: aberowl: MICRO biocontext: MICRO fairsharing: FAIRsharing.brhpb0 obofoundry: micro ols: micro ontobee: MICRO name: Ontology of Prokaryotic Phenotypic and Metabolic Characters pattern: ^\d{7}$ preferred_prefix: MICRO publications: - doi: 10.1186/s13326-016-0060-6 pmc: PMC4830071 pubmed: '27076900' title: 'MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions' year: 2016 rdf_uri_format: http://purl.obolibrary.org/obo/MICRO_$1 repository: https://github.com/carrineblank/MicrO uri_format: http://purl.obolibrary.org/obo/MICRO_$1 version: 1.5.1 microscope: contact: email: cmedigue@genoscope.cns.fr name: MEDIGUE Claudine orcid: 0000-0002-3905-1054 description: MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. example: '5601141' homepage: http://www.genoscope.cns.fr/agc/microscope keywords: - comparative genomics - life science mappings: biocontext: MICROSCOPE fairsharing: FAIRsharing.3t5qc3 miriam: microscope n2t: microscope re3data: r3d100012928 name: MicroScope pattern: ^\d+$ preferred_prefix: microscope publications: - doi: 10.1093/nar/gks1194 pmc: PMC3531135 pubmed: '23193269' title: MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data year: 2012 uri_format: http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1 microsporidia: contact: email: oharb@upenn.edu github: ramobrah name: Omar Harb orcid: 0000-0003-4446-6200 description: MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: ECU03_0820i homepage: http://microsporidiadb.org/micro/ keywords: - eukaryotic - genome mappings: biocontext: MICROSPORIDIA miriam: microsporidia n2t: microsporidia prefixcommons: microsporidia name: MicrosporidiaDB pattern: ^\w+$ preferred_prefix: microsporidia providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/microsporidia:$1 publications: - doi: 10.1093/nar/gkp941 pmc: PMC2808945 pubmed: '19914931' title: 'EuPathDB: a portal to eukaryotic pathogen databases' year: 2009 uri_format: http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 millipore: description: Cell line collections (Providers) example: SCC111 homepage: https://www.merckmillipore.com/ mappings: cellosaurus: Millipore name: Merck Millipore (EMD Millipore) preferred_prefix: millipore uri_format: https://www.merckmillipore.com/catalogue/item/$1 mimodb: contact: email: hj@uestc.edu.cn name: Jian Huang orcid: 0000-0003-2314-7104 description: MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank. example: '1' homepage: http://immunet.cn/bdb/ keywords: - interaction - life science - protein mappings: biocontext: MIMODB fairsharing: FAIRsharing.bv0zjz miriam: mimodb n2t: mimodb prefixcommons: mimodb name: MimoDB pattern: ^\d+$ preferred_prefix: mimodb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mimodb:$1 publications: - doi: 10.1093/nar/gkv1100 pmc: PMC4702802 pubmed: '26503249' title: 'BDB: biopanning data bank' year: 2015 - doi: 10.1093/nar/gkr922 pmc: PMC3245166 pubmed: '22053087' title: 'MimoDB 2.0: a mimotope database and beyond' year: 2011 - doi: 10.3390/molecules15118279 pmc: PMC6259156 pubmed: '21079566' title: 'MimoDB: a new repository for mimotope data derived from phage display technology' year: 2010 uri_format: http://immunet.cn/bdb/index.php/mimoset/$1 minid: contact: email: foster@uchicago.edu name: Ian Foster orcid: 0000-0003-2129-5269 description: Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. example: b97957 homepage: https://fair-research.org keywords: - citation - data retrieval - publication - subject agnostic mappings: biocontext: MINID fairsharing: FAIRsharing.d099fb miriam: minid n2t: minid name: Minimal Viable Identifier pattern: ^[A-Za-z0-9]+$ preferred_prefix: minid publications: - doi: 10.1371/journal.pone.0213013 pubmed: '30973881' title: 'Reproducible big data science: A case study in continuous FAIRness' year: 2019 - doi: 10.1371/journal.pone.0294883 title: 'Correction: Reproducible big data science: A case study in continuous FAIRness' year: 2023 uri_format: https://hdl.handle.net/hdl:20.500.12582/$1 minid.test: description: 'Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. ' example: 3SBPLMKKVEVR homepage: https://fair-research.org mappings: miriam: minid.test name: MINID Test pattern: ^[A-Za-z0-9]+$ preferred_prefix: minid.test uri_format: https://hdl.handle.net/hdl:20.500.12633/$1 mint: banana: MINT banana_peel: '-' contact: email: luana.licata@gmail.com name: Luana Licata orcid: 0000-0001-5084-9000 description: The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals. example: '6978836' homepage: https://mint.bio.uniroma2.it keywords: - interaction - life science - protein - proteomics mappings: biocontext: MINT edam: '2615' fairsharing: FAIRsharing.2bdvmk miriam: mint n2t: mint pathguide: '17' prefixcommons: mint re3data: r3d100010414 uniprot: DB-0158 name: Molecular Interaction Database pattern: ^\d{1,7}$ preferred_prefix: mint providers: - code: CURATOR_REVIEW description: The Molecular INTeraction database (MINT) homepage: http://mint.bio.uniroma2.it/mint/ name: The Molecular INTeraction database (MINT) uri_format: https://mint.bio.uniroma2.it/index.php/results-interactions/?id=$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mint:$1 publications: - doi: 10.1093/nar/gkr930 pmc: PMC3244991 pubmed: '22096227' title: 'MINT, the molecular interaction database: 2012 update' year: 2011 - doi: 10.1093/nar/gkp983 pmc: PMC2808973 pubmed: '19897547' title: 'MINT, the molecular interaction database: 2009 update' year: 2009 - doi: 10.1093/nar/gkl950 pmc: PMC1751541 pubmed: '17135203' title: 'MINT: the Molecular INTeraction database' year: 2006 - doi: 10.1016/s0014-5793(01)03293-8 pubmed: '11911893' title: 'MINT: a Molecular INTeraction database' year: 2002 twitter: MINT_database uri_format: https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-$1 mipmod: contact: email: rsankar@iitk.ac.in name: Ramasubbu Sankararamakrishnan orcid: 0000-0002-8527-5614 description: MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures. example: HOSAPI0399 homepage: http://bioinfo.iitk.ac.in/MIPModDB keywords: - protein - structure mappings: biocontext: MIPMOD miriam: mipmod n2t: mipmod prefixcommons: mipmod name: MIPModDB pattern: ^\w+$ preferred_prefix: mipmod providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mipmod:$1 publications: - doi: 10.1093/nar/gkr914 pmc: PMC3245135 pubmed: '22080560' title: 'MIPModDB: a central resource for the superfamily of major intrinsic proteins' year: 2011 uri_format: http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1 mir: banana: MIR description: The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or "PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources. example: '00100037' homepage: https://registry.identifiers.org/registry mappings: biocontext: MIR miriam: mir n2t: mir name: Identifiers.org Registry namespace_in_lui: true pattern: ^\d{8}$ preferred_prefix: mir uri_format: https://registry.identifiers.org/registry?query=MIR:$1 mirbase: contact: email: sam.griffiths-jones@manchester.ac.uk github: samgriffithsjones name: Sam Griffiths-Jones orcid: 0000-0001-6043-807X description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). example: MI0026471 homepage: http://www.mirbase.org/ keywords: - biology - gene - rna license: public domain mappings: biocontext: MIRBASE biolink: mirbase edam: '2642' fairsharing: FAIRsharing.hmgte8 integbio: nbdc00136 miriam: mirbase n2t: mirbase ncbi: miRBase pathguide: '210' prefixcommons: mirbase re3data: r3d100010566 togoid: Mirbase wikidata: P2870 name: miRBase pre-miRNA pattern: ^MI\d{7}$ preferred_prefix: mirbase providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mirbase:$1 publications: - doi: 10.1093/nar/gky1141 pmc: PMC6323917 pubmed: '30423142' title: 'miRBase: from microRNA sequences to function' year: 2019 - doi: 10.1093/nar/gkt1181 pmc: PMC3965103 pubmed: '24275495' title: 'miRBase: annotating high confidence microRNAs using deep sequencing data' year: 2013 - doi: 10.1093/nar/gkq1027 pmc: PMC3013655 pubmed: '21037258' title: 'miRBase: integrating microRNA annotation and deep-sequencing data' year: 2010 - doi: 10.1093/nar/gkm952 pmc: PMC2238936 pubmed: '17991681' title: 'miRBase: tools for microRNA genomics' year: 2007 - doi: 10.1093/nar/gkj112 pmc: PMC1347474 pubmed: '16381832' title: 'miRBase: microRNA sequences, targets and gene nomenclature' year: 2006 - doi: 10.1093/nar/gkh023 pmc: PMC308757 pubmed: '14681370' title: The microRNA Registry year: 2004 uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1 mirbase.family: 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/ license: public domain name: miRBase Families preferred_prefix: mirbase.family synonyms: - MIRBASE_FAMILY uri_format: http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1 mirbase.mature: description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence. example: MIMAT0046872 homepage: http://www.mirbase.org/ keywords: - nucleotide - sequence license: public domain mappings: biocontext: MIRBASE.MATURE miriam: mirbase.mature n2t: mirbase.mature prefixcommons: mirbase.mature wikidata: P2871 name: miRBase mature miRNA pattern: ^MIMAT\d{7}$ preferred_prefix: mirbase.mature providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mirbase.mature:$1 synonyms: - MIRBASEM uri_format: http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1 mirex: contact: email: wmk@amu.edu.pl name: Wojciech M. Karlowski orcid: 0000-0002-8086-5404 description: mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages. example: 165a homepage: http://comgen.pl/mirex/?page=home keywords: - life science mappings: biocontext: MIREX fairsharing: FAIRsharing.q3b39v integbio: nbdc02064 miriam: mirex n2t: mirex name: mirEX pattern: ^\d+(\w+)?$ preferred_prefix: mirex publications: - doi: 10.1186/s12870-015-0533-2 pmc: PMC4490709 pubmed: '26141515' title: mirEX 2.0 - an integrated environment for expression profiling of plant microRNAs year: 2015 - doi: 10.1093/nar/gkr878 pmc: PMC3245179 pubmed: '22013167' title: 'mirEX: a platform for comparative exploration of plant pri-miRNA expression data' year: 2011 uri_format: http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes mirgenedb: contact: email: BastianFromm@gmail.com name: Bastian Fromm orcid: 0000-0003-0352-3037 contributor: email: palayoor.n@northeastern.edu github: nalikapalayoor name: Nalika Palayoor orcid: 0009-0008-8406-631X description: mircoRNA Gene Database is a collection of animal microRNA genes. This database allows researchers to analyze mircoRNA properties like secondary structure and features in a phylogenetic context. example: Hsa-Let-7-P2a3 github_request_issue: 1393 homepage: https://mirgenedb.org/ name: microRNA Gene Database pattern: ^[a-zA-Z0-9]+(-[a-zA-Z0-9]+)+$ preferred_prefix: mirgenedb publications: - doi: 10.1093/nar/gkae1094 pmc: PMC11701709 pubmed: '39673268' title: 'MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models' year: 2025 - doi: 10.1093/nar/gkab1101 pmc: PMC8728216 pubmed: '34850127' title: 'MirGeneDB 2.1: toward a complete sampling of all major animal phyla' year: 2022 - doi: 10.1093/nar/gkz885 pmc: PMC6943042 pubmed: '31598695' title: 'MirGeneDB 2.0: the metazoan microRNA complement' year: 2020 - doi: 10.1146/annurev-genet-120213-092023 pmc: PMC4743252 pubmed: '26473382' title: A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome year: 2015 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://mirgenedb.org/browse?qtype=mgid&org=ALL&query=$1 miriam: contact: email: n.lenovere@gmail.com name: Nicolas Le Novère orcid: 0000-0002-6309-7327 description: Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain. example: pubmed homepage: https://www.ebi.ac.uk keywords: - biochemistry - biomedical science - life science mappings: edam: '1162' fairsharing: FAIRsharing.ap169a miriam: identifiers.namespace name: Identifiers.org namespace pattern: ^[0-9a-z_:\.-]+$ preferred_prefix: miriam publications: - doi: 10.1093/nar/gkr1097 pmc: PMC3245029 pubmed: '22140103' title: 'Identifiers.org and MIRIAM Registry: community resources to provide persistent identification' year: 2011 - doi: 10.1186/1752-0509-1-58 pmc: PMC2259379 pubmed: '18078503' title: 'MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology' year: 2007 - doi: 10.1038/nbt1156 pubmed: '16333295' title: Minimum information requested in the annotation of biochemical models (MIRIAM) year: 2005 synonyms: - identifiers.namespace uri_format: https://registry.identifiers.org/registry/$1 miriam.collection: banana: MIR deprecated: true description: MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections. example: 00000008 homepage: https://www.ebi.ac.uk/miriam/ mappings: biocontext: MIRIAM.COLLECTION miriam: miriam.collection n2t: miriam.collection name: MIRIAM Registry collection part_of: miriam pattern: ^000\d{5}$ preferred_prefix: miriam.collection uri_format: https://www.ebi.ac.uk/miriam/main/$1 miriam.resource: banana: MIR deprecated: true description: MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases. example: '00100005' homepage: https://www.ebi.ac.uk/miriam/ keywords: - registry mappings: biocontext: MIRIAM.RESOURCE miriam: miriam.resource n2t: miriam.resource prefixcommons: miriam.resource name: MIRIAM Legacy Registry Identifier part_of: miriam pattern: ^001\d{5}$ preferred_prefix: miriam.resource providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/miriam.resource:$1 publications: - doi: 10.1186/1752-0509-1-58 pmc: PMC2259379 pubmed: '18078503' title: 'MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology' year: 2007 uri_format: https://resolver.api.identifiers.org/resolveMirId/$1 mirnao: contact: email: topalis@imbb.forth.gr name: Pantelis Topalis orcid: 0000-0002-1635-4810 deprecated: true description: An application ontology for use with miRNA databases. download_owl: http://aber-owl.net/media/ontologies/MIRNAO/11/mirnao.owl homepage: http://code.google.com/p/mirna-ontology/ keywords: - obo - ontology license: CC0-1.0 mappings: aberowl: MIRNAO biocontext: MIRNAO bioportal: MIRNAO obofoundry: mirnao ontobee: miRNAO name: microRNA Ontology preferred_prefix: MIRNAO rdf_uri_format: http://purl.obolibrary.org/obo/MIRNAO_$1 uri_format: http://purl.obolibrary.org/obo/MIRNAO_$1 mirnest: contact: email: miszcz@amu.edu.pl name: Michael Szcześniak orcid: 0000-0002-6050-9525 description: miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species. example: MNEST029358 homepage: http://rhesus.amu.edu.pl/mirnest/copy/ keywords: - expression - genomics - life science - prediction mappings: biocontext: MIRNEST fairsharing: FAIRsharing.5pfx4r integbio: nbdc01703 miriam: mirnest n2t: mirnest prefixcommons: mirnest name: miRNEST pattern: ^MNEST\d+$ preferred_prefix: mirnest providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mirnest:$1 publications: - doi: 10.1093/nar/gkt1156 pmc: PMC3965105 pubmed: '24243848' title: 'miRNEST 2.0: a database of plant and animal microRNAs' year: 2013 - doi: 10.1093/nar/gkr1159 pmc: PMC3245016 pubmed: '22135287' title: 'miRNEST database: an integrative approach in microRNA search and annotation' year: 2011 uri_format: http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1 miro: contact: email: louis@imbb.forth.gr name: Christos Louis orcid: 0000-0003-2497-2210 deprecated: true description: Application ontology for entities related to insecticide resistance in mosquitos download_obo: http://purl.obolibrary.org/obo/miro.obo download_owl: http://purl.obolibrary.org/obo/miro.owl example: '40000617' homepage: https://github.com/VEuPathDB-ontology/MIRO keywords: - insecticide resistance - life science - mutation - obo - ontology - phenotype mappings: aberowl: MIRO biocontext: MIRO bioportal: MIRO fairsharing: FAIRsharing.sjf113 obofoundry: miro ols: miro ontobee: MIRO name: Mosquito insecticide resistance pattern: ^\d{8}$ preferred_prefix: MIRO publications: - doi: 10.1371/journal.pntd.0000465 pmc: PMC2694272 pubmed: '19547750' title: 'MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide resistance in mosquito disease vectors' year: 2009 rdf_uri_format: http://purl.obolibrary.org/obo/MIRO_$1 repository: https://github.com/VEuPathDB-ontology/MIRO uri_format: http://purl.obolibrary.org/obo/MIRO_$1 version: '2014-05-14' mirtarbase: contact: email: ken.sd.hsu@gmail.com name: Sheng-Da Hsu orcid: 0000-0002-8214-1696 contributor_extras: - email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. example: MIRT000002 homepage: https://mirtarbase.cuhk.edu.cn/ keywords: - life science mappings: biocontext: MIRTARBASE fairsharing: FAIRsharing.f0bxfg integbio: nbdc01217 miriam: mirtarbase n2t: mirtarbase pathguide: '715' wikidata: P2646 name: mirTarBase pattern: ^MIRT\d{6}$ preferred_prefix: mirtarbase publications: - doi: 10.1093/nar/gkab1079 pmc: PMC8728135 pubmed: '34850920' title: 'miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions' year: 2022 - doi: 10.1093/nar/gkz896 pmc: PMC7145596 pubmed: '31647101' title: 'miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database' year: 2020 - doi: 10.1093/nar/gkx1067 pmc: PMC5753222 pubmed: '29126174' title: 'miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions' year: 2018 - doi: 10.1093/nar/gkv1258 pmc: PMC4702890 pubmed: '26590260' title: 'miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database' year: 2016 - doi: 10.1093/nar/gkt1266 pmc: PMC3965058 pubmed: '24304892' title: 'miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions' year: 2014 - doi: 10.1093/nar/gkq1107 pmc: PMC3013699 pubmed: '21071411' title: 'miRTarBase: a database curates experimentally validated microRNA-target interactions' year: 2010 references: - https://github.com/biopragmatics/bioregistry/pull/940 uri_format: https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid=$1 mirte: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs example: miR-1 homepage: http://www.russelllab.org/miRNAs/ name: miRNA Target Prediction at EMBL preferred_prefix: mirte mite: contact: email: zdoucmm@gmail.com github: mmzdouc name: Mitja M. Zdouc orcid: 0000-0001-6534-6609 contributor: email: zdoucmm@gmail.com github: mmzdouc name: Mitja M. Zdouc orcid: 0000-0001-6534-6609 description: MITE (Minimum Information about a Tailoring Enzyme) is a data repository and associated data standard designed to capture the reaction- and substrate-specificities of tailoring enzymes. Community-driven and fully expert-reviewed, it represents enzymatic reactions using reaction SMARTS and links to established resources such as UniProt, NCBI GenPept, Rhea, and MIBiG. MITE serves as a knowledgebase for enzyme and pathway annotation, in silico biosynthesis, and machine learning applications. example: MITE0000001 github_request_issue: 1405 homepage: https://mite.bioinformatics.nl license: CC0-1.0 name: Minimum Information about a Tailoring Enzyme data repository pattern: ^MITE\d{7}$ preferred_prefix: mite publications: - doi: 10.26434/chemrxiv-2024-78mtl title: The Minimum Information about a Tailoring Enzyme/Maturase data standard for capturing natural product biosynthesis year: 2024 repository: https://github.com/mite-standard/mite_data reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://mite.bioinformatics.nl/repository/$1 mixs: comment: 'Some things to be decided before granting - [ ] should the prefix be mixs, gsc.mixs, MIxS, MIXS, ...? - [ ] MIxS terms are most commonly identified by a short computable stable label, e.g ph_regm. The GSC CIG team are creating numeric identifiers, e.g. MIXS:0001056 - Should we support both schemes? - If we do, should these be different prefixes? I would strongly recommend this. E.g. mixs.term:ph_regm, mixs:0001056. We can then have different regex patterns for both Additional notes: - The http://gensc.org/ns/mixs/ will likely changes to a w3id.org URI that will also serve as a semweb identifier - It currently redirects to the tdwg wiki but this is I assume temporary' contact: email: rlwalls2008@gmail.com github: ramonawalls name: Ramona Walls orcid: 0000-0001-8815-0078 contributor: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 contributor_extras: - email: chris@gigasciencejournal.com github: only1chunts name: Chris Hunter orcid: 0000-0002-1335-0881 - email: lindsey.anderson@pnnl.gov github: lnanderson name: Lindsey N. Anderson orcid: 0000-0002-8741-7823 description: The GSC family of minimum information standards (checklists) – Minimum Information about any (x) Sequence (MIxS). MIxS identifiers are for terms describing an aspect of an environmental sample. download_owl: http://aber-owl.net/media/ontologies/MIXS/5/mixs.owl example: '0001056' github_request_issue: 151 homepage: https://www.gensc.org/pages/standards/all-terms.html keywords: - ontology mappings: aberowl: MIXS bioportal: MIXS fairsharing: FAIRsharing.9aa0zp name: Minimal Information about any Sequence pattern: ^\d{7}$ preferred_prefix: mixs providers: - code: github description: MIxS LinkML schema homepage: https://genomicsstandardsconsortium.github.io/mixs name: MIxS LinkML schema uri_format: https://genomicsstandardsconsortium.github.io/mixs/$1 publications: - doi: 10.1038/nbt.1823 pmc: PMC3367316 pubmed: '21552244' title: Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications year: 2011 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://w3id.org/mixs/$1 mlc: description: MLCommons Association artifacts, including benchmark results, datasets, and saved models. example: 0.7-123 homepage: https://mlcommons.org/en/ mappings: miriam: mlc name: MLCommons Association pattern: ^[0-9a-zA-Z\.\-\_]+$ preferred_prefix: mlc uri_format: https://www.mlcommons.org/mlc-id/$1 mmdb: contact: email: siqian.he@nih.gov name: Siqian He orcid: 0000-0002-1707-4167 description: The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites. example: '50885' homepage: http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure keywords: - dna - interaction - protein - small molecule - structure mappings: biocontext: MMDB edam: '2667' miriam: mmdb n2t: mmdb pathguide: '508' prefixcommons: mmdb name: Molecular Modeling Database pattern: ^\d{1,5}$ preferred_prefix: mmdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mmdb:$1 publications: - doi: 10.1093/nar/gkl952 pmc: PMC1751549 pubmed: '17135201' title: 'MMDB: annotating protein sequences with Entrez''s 3D-structure database' year: 2006 uri_format: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1 mmmp.biomaps: description: A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma. example: '37' homepage: http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp keywords: - interaction - molecule - pathway mappings: biocontext: MMMP:BIOMAPS biolink: mmmp.biomaps miriam: mmmp.biomaps n2t: biomaps prefixcommons: mmmp name: Melanoma Molecular Map Project Biomaps pattern: ^\d+$ preferred_prefix: mmmp.biomaps providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mmmp:$1 synonyms: - mmmp:biomaps uri_format: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1 mmo: contact: email: jrsmith@mcw.edu github: jrsjrs name: Jennifer Smith orcid: 0000-0002-6443-9376 description: A representation of the variety of methods used to make clinical and phenotype measurements. download_obo: http://purl.obolibrary.org/obo/mmo.obo download_owl: http://purl.obolibrary.org/obo/mmo.owl example: '0000574' homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 keywords: - biomedical science - life science - model organism - obo - ontology - phenotype - preclinical studies license: CC0-1.0 mappings: aberowl: MMO biocontext: MMO bioportal: MMO fairsharing: FAIRsharing.bgkyd7 obofoundry: mmo ols: mmo ontobee: MMO name: Measurement method ontology pattern: ^\d{7}$ preferred_prefix: MMO publications: - doi: 10.1186/2041-1480-4-26 pmc: PMC3882879 pubmed: '24103152' title: 'The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications' year: 2013 - doi: 10.3389/fgene.2012.00087 pmc: PMC3361058 pubmed: '22654893' title: Three ontologies to define phenotype measurement data year: 2012 rdf_uri_format: http://purl.obolibrary.org/obo/MMO_$1 repository: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology twitter: ratgenome uri_format: http://purl.obolibrary.org/obo/MMO_$1 version: '2.146' mmp.cat: description: MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples. example: MMP743597.11 homepage: https://mmp.sfb.uit.no/databases/marcat/ mappings: biocontext: MMP.CAT miriam: mmp.cat n2t: mmp.cat name: MarCat pattern: ^MMP\d+.\d+$ 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/$1 mmrrc: contact: email: f.grieder@nih.gov name: Franziska B. Grieder orcid: 0000-0002-3070-8224 description: The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections. example: '70' homepage: https://www.mmrrc.org keywords: - biology - cryopreserved - database - embryonic stem cell - embryonic stem cell line - faseb list - mouse strain - mutant - mutant mouse strain - stem cell - transgenic mappings: biocontext: MMRRC cellosaurus: MMRRC fairsharing: FAIRsharing.9dpd18 miriam: mmrrc n2t: mmrrc re3data: r3d100013715 rrid: MMRRC name: Mutant Mouse Resource and Research Centers pattern: ^\d+$ preferred_prefix: mmrrc publications: - pubmed: '12102564' title: 'Mutant Mouse Regional Resource Center Program: a resource for distribution of mouse models for biomedical research' year: 2002 twitter: mmrc uri_format: http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1 mmsinc: description: MMSsINC is a database of commercially-available compounds for virtual screening and chemoinformatic applications. MMsINC contains over 4 million non-redundant chemical compounds in 3D formats. example: MMs00000001 homepage: http://mms.dsfarm.unipd.it/MMsINC keywords: - small molecule - structure mappings: prefixcommons: mmsinc name: MMsINC preferred_prefix: mmsinc providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mmsinc:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php?mmscode=$1 mmsl: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included. example: '3355' homepage: https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html mappings: hl7: 2.16.840.1.113883.6.175 name: Multum MediSource Lexicon pattern: ^\d+$ preferred_prefix: mmsl synonyms: - MMSL_CODE mmusdv: contact: email: frederic.bastian@unil.ch github: fbastian name: Frédéric Bastian orcid: 0000-0002-9415-5104 description: Life cycle stages for Mus Musculus download_obo: http://purl.obolibrary.org/obo/mmusdv.obo download_owl: http://purl.obolibrary.org/obo/mmusdv.owl example: '0000066' homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv keywords: - anatomy - developmental biology - embryology - life cycle stage - obo - ontology license: CC-BY-3.0 mappings: aberowl: MMUSDV biocontext: MMUSDV biolink: MmusDv bioportal: MMUSDV fairsharing: FAIRsharing.zchb68 obofoundry: mmusdv ols: mmusdv ontobee: MmusDv name: Mouse Developmental Stages pattern: ^\d{7}$ preferred_prefix: MmusDv rdf_uri_format: http://purl.obolibrary.org/obo/MmusDv_$1 repository: https://github.com/obophenotype/developmental-stage-ontologies synonyms: - MmusDv uri_format: http://purl.obolibrary.org/obo/MmusDv_$1 version: '2025-01-23' mo: contact: email: stoeckrt@pcbi.upenn.edu name: Chris Stoeckert orcid: 0000-0002-5714-991X deprecated: true description: The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. download_owl: http://purl.obolibrary.org/obo/mo.owl example: ArrayGroup homepage: http://mged.sourceforge.net/ontologies/MGEDontology.php keywords: - obo - ontology mappings: aberowl: MO biocontext: MO bioportal: MO miriam: mo n2t: mo obofoundry: mo name: Microarray experimental conditions pattern: ^\w+$ preferred_prefix: MO rdf_uri_format: http://purl.obolibrary.org/obo/MO_$1 uri_format: https://mged.sourceforge.net/ontologies/MGEDontology.php#$1 mobidb: contact: email: silvio.tosatto@unipd.it name: Silvio C.E. Tosatto orcid: 0000-0003-4525-7793 description: MobiDB is a database of protein disorder and mobility annotations. example: P10636 homepage: https://mobidb.org keywords: - biology - biomedical science mappings: biocontext: MOBIDB fairsharing: FAIRsharing.jwra3e integbio: nbdc01956 miriam: mobidb n2t: mobidb pathguide: '623' uniprot: DB-0183 name: MobiDB pattern: ^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$ preferred_prefix: mobidb provides: uniprot publications: - doi: 10.1093/nar/gkae969 pubmed: '39470701' title: 'MOBIDB in 2025: integrating ensemble properties and function annotations for intrinsically disordered proteins' year: 2024 - doi: 10.1093/nar/gkac1065 pubmed: '36416266' - doi: 10.1093/nar/gkaa1058 pmc: PMC7779018 pubmed: '33237329' title: 'MobiDB: intrinsically disordered proteins in 2021' year: 2021 - doi: 10.1093/nar/gkx1071 pmc: PMC5753340 pubmed: '29136219' title: 'MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins' year: 2018 - doi: 10.1093/nar/gku982 pmc: PMC4384034 pubmed: '25361972' title: 'MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins' year: 2014 - doi: 10.1093/bioinformatics/bts327 pubmed: '22661649' title: 'MobiDB: a comprehensive database of intrinsic protein disorder annotations' year: 2012 uri_format: https://mobidb.org/$1 mod: banana: MOD contact: email: pierre-alain.binz@chuv.ch github: pabinz name: Pierre-Alain Binz orcid: 0000-0002-0045-7698 description: The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications. download_obo: http://purl.obolibrary.org/obo/mod.obo download_owl: http://purl.obolibrary.org/obo/mod.owl example: '01467' homepage: http://www.psidev.info/MOD keywords: - enzymatic reaction - life science - molecule - obo - ontology - protein - structure license: CC-BY-4.0 mappings: aberowl: PSIMOD biocontext: MOD bioportal: PSIMOD fairsharing: FAIRsharing.2m4ms9 go: PSI-MOD miriam: mod n2t: mod obofoundry: mod ols: mod ontobee: MOD prefixcommons: psi.mod name: Protein modification namespace_in_lui: true pattern: ^\d{5}$ preferred_prefix: MOD providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/psi.mod:$1 publications: - doi: 10.1038/nbt0808-864 pubmed: '18688235' title: The PSI-MOD community standard for representation of protein modification data year: 2008 rdf_uri_format: http://purl.obolibrary.org/obo/MOD_$1 repository: https://github.com/HUPO-PSI/psi-mod-CV synonyms: - PSI-MOD uri_format: http://purl.obolibrary.org/obo/MOD_$1 version: 1.031.6 modeldb: contact: email: perry.miller@yale.edu name: Perry Miller orcid: 0000-0002-5176-943X description: ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment. example: '45539' homepage: https://modeldb.science keywords: - computational biology - life science - neurobiology mappings: biocontext: MODELDB edam: '2669' fairsharing: FAIRsharing.5rb3fk integbio: nbdc02085 miriam: modeldb n2t: modeldb prefixcommons: modeldb re3data: r3d100011330 name: ModelDB pattern: ^\d+$ preferred_prefix: modeldb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/modeldb:$1 publications: - doi: 10.1136/jamia.1996.97084512 pmc: PMC116323 pubmed: '8930855' title: 'ModelDB: an environment for running and storing computational models and their results applied to neuroscience' year: 1996 - doi: 10.1007/s10827-016-0623-7 pmc: PMC5279891 pubmed: '27629590' title: 'Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience' year: 2016 - doi: 10.1023/b:jcns.0000023869.22017.2e pmc: PMC3732827 pubmed: '15218350' title: 'ModelDB: A Database to Support Computational Neuroscience' year: 2004 - doi: 10.1385/ni:1:1:135 pmc: PMC3728921 pubmed: '15055399' title: 'ModelDB: making models publicly accessible to support computational neuroscience' year: 2003 - doi: 10.1385/NI:1:1:135 title: 'ModelDB: making models publicly accessible to support computational neuroscience.' - doi: 10.1023/B:JCNS.0000023869.22017.2e title: 'ModelDB: A Database to Support Computational Neuroscience.' twitter: SenseLabProject uri_format: https://modeldb.science/$1 modeldb.concept: description: Concept used by ModelDB, an accessible location for storing and efficiently retrieving computational neuroscience models. example: '3639' homepage: https://www.yale.edu mappings: miriam: modeldb.concept name: ModelDB concept pattern: ^\d+$ preferred_prefix: modeldb.concept uri_format: https://senselab.med.yale.edu/ModelDB/ModelList?id=$1 moid: description: M3G stands for “Metadata Management and distribution system for Multiple GNSS Networks”. M3G allows to upload, validate, and distribute GNSS station metadata such as IGS-style site logs, information about local networks, DOIs, nominal data provision, data licenses attached to the daily RINEX data, etc... example: station.6051b2f8b9142a5b8c676342 homepage: https://www.astro.oma.be/en/ mappings: miriam: moid name: Metadata Management and distribution system for Multiple GNSS Networks pattern: ^[a-zA-Z0-9]+\.[a-f0-9]{24}$ preferred_prefix: moid uri_format: https://gnss-metadata.eu/MOID/$1 molbase: description: Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier. example: 128796-39-4 homepage: http://www.molbase.com/ mappings: biocontext: MOLBASE miriam: molbase n2t: molbase name: Molbase pattern: ^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$ preferred_prefix: molbase uri_format: http://www.molbase.com/en/index.php?app=search&search_keyword=$1 molbase.sheffield: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students. example: '1868' homepage: https://winter.group.shef.ac.uk/molbase/ name: MolBase pattern: ^\d+$ preferred_prefix: molbase.sheffield molbic.cellline: contact: email: zhufeng@zju.edu.cn name: Feng Zhu orcid: 0000-0001-8069-0053 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: MolBiC provides information about cell-based molecular bioactivities along with associated compounds, proteins and cell lines. This prefix maintains identifiers for cell lines used in assays measuring molecular bioactivity, linking them to associated compounds and proteins. example: CL000025 github_request_issue: 1418 homepage: https://molbic.idrblab.net name: MolBiC Cell Line pattern: ^CL\d+$ preferred_prefix: molbic.cellline publications: - doi: 10.1093/nar/gkae868 pubmed: '39373530' title: 'MolBiC: the cell-based landscape illustrating molecular bioactivities' year: 2025 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://molbic.idrblab.net/data/cellline/details/$1 molbic.compound: contact: email: zhufeng@zju.edu.cn name: Feng Zhu orcid: 0000-0001-8069-0053 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: MolBiC provides information about cell-based molecular bioactivities along with associated compounds, proteins and cell lines. This prefix maintains identifiers for chemical compounds with experimentally validated bioactivity in cellular contexts. example: CP0041613 github_request_issue: 1418 homepage: https://molbic.idrblab.net name: MolBiC Compound pattern: ^CP\d+$ preferred_prefix: molbic.compound publications: - doi: 10.1093/nar/gkae868 pmc: PMC11701603 pubmed: '39373530' title: 'MolBiC: the cell-based landscape illustrating molecular bioactivities' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://molbic.idrblab.net/data/compound/details/$1 molbic.protein: contact: email: zhufeng@zju.edu.cn name: Feng Zhu orcid: 0000-0001-8069-0053 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: MolBiC provides information about cell-based molecular bioactivities along with associated compounds, proteins and cell lines. This prefix maintains identifiers for proteins that serve as molecular targets in cell-based bioactivity measurements. example: PT00819 github_request_issue: 1418 homepage: https://molbic.idrblab.net name: MolBiC Protein pattern: ^PT\d+$ preferred_prefix: molbic.protein publications: - doi: 10.1093/nar/gkae868 pubmed: '39373530' title: 'MolBiC: the cell-based landscape illustrating molecular bioactivities' year: 2025 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://molbic.idrblab.net/data/protein/details/$1 molmedb: contact: email: karel.berka@upol.cz github: KarelBerka name: Karel Berka orcid: 0000-0001-9472-2589 contributor_extras: - email: dominik.martinat@gmail.com github: DominikMartinat name: Dominik Martinat orcid: 0000-0001-6611-7883 description: 'MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations. ' example: MM00040 homepage: http://www.upol.cz/en/ keywords: - biochemistry - cheminformatics - chemistry - computational chemistry - molecular biology - molecular chemistry - molecular dynamics - molecular physical chemistry mappings: fairsharing: FAIRsharing.CWzk3C miriam: molmedb name: MolMeDB pattern: ^[m,M]{2}[0-9]{5}[0-9]*$ preferred_prefix: molmedb repository: https://github.com/MolMeDB/MolMeDB uri_format: https://molmedb.upol.cz/mol/$1 molmovdb: description: The Molecular Movements Database lists motions in proteins and other macromolecules. It is arranged around a multi-level classification scheme and includes motions of loops, domains, and subunits. example: f665230-5267 homepage: http://bioinfo.mbb.yale.edu/MolMovDB/ keywords: - classification - protein - small molecule - structure mappings: integbio: nbdc00573 prefixcommons: molmovdb name: Database of Macromolecular Movements preferred_prefix: molmovdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/molmovdb:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.molmovdb.org/cgi-bin/morph.cgi?ID=$1 mondo: contact: email: nicole@tislab.org github: nicolevasilevsky name: Nicole Vasilevsky orcid: 0000-0001-5208-3432 description: The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. download_json: http://purl.obolibrary.org/obo/mondo.json download_obo: http://purl.obolibrary.org/obo/mondo.obo download_owl: http://purl.obolibrary.org/obo/mondo.owl example: '0000001' homepage: https://monarch-initiative.github.io/mondo keywords: - biocuration - infectious disease medicine - medicine - obo - ontology license: CC-BY-4.0 logo: https://raw.githubusercontent.com/monarch-initiative/mondo/master/docs/images/mondo_logo_black-stacked-small.png mappings: aberowl: MONDO biocontext: MONDO bioportal: MONDO fairsharing: FAIRsharing.b2979t integbio: nbdc02563 miriam: mondo obofoundry: mondo ols: mondo ontobee: MONDO togoid: Mondo wikidata: P5270 mastodon: monarch_initiative@genomic.social name: Mondo Disease Ontology pattern: ^\d{7}$ preferred_prefix: MONDO providers: - code: clinicalgenome description: Clinical genome condition homepage: https://search.clinicalgenome.org name: Clinical Genome uri_format: https://search.clinicalgenome.org/kb/conditions/MONDO:$1 publications: - doi: 10.1093/nar/gkw1128 pubmed: '27899636' title: 'The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species' year: 2016 - doi: 10.1101/2022.04.13.22273750 title: 'Mondo: Unifying diseases for the world, by the world' year: 2022 rdf_uri_format: http://purl.obolibrary.org/obo/MONDO_$1 repository: https://github.com/monarch-initiative/mondo twitter: MonarchInit uri_format: http://purl.obolibrary.org/obo/MONDO_$1 version: '2025-02-04' mop: contact: email: batchelorc@rsc.org github: batchelorc name: Colin Batchelor orcid: 0000-0001-5985-7429 description: MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation. download_obo: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.obo download_owl: http://purl.obolibrary.org/obo/mop.owl example: 0000079 homepage: https://github.com/rsc-ontologies/rxno keywords: - molecular chemistry - obo - ontology - reaction data license: CC-BY-4.0 mappings: aberowl: MOP bartoc: '20466' biocontext: MOP bioportal: MOP fairsharing: FAIRsharing.mct09a obofoundry: mop ols: mop ontobee: MOP name: Molecular Process Ontology pattern: ^\d{7}$ preferred_prefix: MOP rdf_uri_format: http://purl.obolibrary.org/obo/MOP_$1 repository: https://github.com/rsc-ontologies/rxno uri_format: http://purl.obolibrary.org/obo/MOP_$1 version: '2022-05-11' morpheus: description: 'The Morpheus model repository is an open-access data resource to store, search and retrieve unpublished and published computational models of spatio-temporal and multicellular biological systems, encoded in the MorpheusML language and readily executable with the Morpheus software. ' example: M0001 homepage: https://morpheus.gitlab.io/ mappings: miriam: morpheus name: Morpheus model repository pattern: ^M[0-9]{4,}$ preferred_prefix: morpheus uri_format: https://morpheus.gitlab.io/models/$1 mosaic: contact: email: brycemecum@gmail.com github: amoeba name: Bryce Mecum orcid: 0000-0002-0381-3766 contributor: email: j.harry.caufield@gmail.com github: caufieldjh name: Harry Caufield orcid: 0000-0001-5705-7831 description: An ontology used to describe data resources in the Arctic Data Center (https://arcticdata.io). download_owl: https://ontologies.dataone.org/MOSAiC.owl example: '00005643' github_request_issue: 636 homepage: https://ontologies.dataone.org/MOSAiC.html keywords: - ontology license: CC-BY-4.0 mappings: aberowl: MOSAIC bioportal: MOSAIC name: MOSAiC Ontology pattern: ^\d{8}$ preferred_prefix: mosaic repository: https://github.com/DataONEorg/sem-prov-ontologies reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://purl.dataone.org/odo/MOSAIC_$1 mp: appears_in: - chiro - scdo banana: MP contact: email: pheno@jax.org github: sbello name: Sue Bello orcid: 0000-0003-4606-0597 description: The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways. download_json: http://purl.obolibrary.org/obo/mp.json download_obo: http://purl.obolibrary.org/obo/mp.obo download_owl: http://purl.obolibrary.org/obo/mp.owl example: '0005452' homepage: https://www.informatics.jax.org/vocab/mp_ontology/ keywords: - behavior - developmental biology - life science - mammalian - obo - ontology - phenotype - physiology license: CC-BY-4.0 logo: https://raw.githubusercontent.com/mgijax/mammalian-phenotype-ontology/main/logo/2024_MP_logo_RGB_ICON_color.png mappings: aberowl: MP biocontext: MP bioportal: MP fairsharing: FAIRsharing.kg1x4z miriam: mp n2t: mp obofoundry: mp ols: mp ontobee: MP prefixcommons: mp togoid: Mp name: Mammalian Phenotype Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: MP providers: - code: CURATOR_REVIEW description: Mammalian Phenotype Ontology at The Jackson Lab homepage: http://www.informatics.jax.org/ name: Mammalian Phenotype Ontology at The Jackson Lab uri_format: http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mp:$1 - code: nextprot description: The neXtProt endpoint for exploring MP homepage: https://www.nextprot.org name: neXtProt MP Browser uri_format: https://www.nextprot.org/term/MP:$1 publications: - doi: 10.1186/s13326-015-0009-1 pmc: PMC4378007 pubmed: '25825651' title: Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens year: 2015 - doi: 10.1007/s00335-012-9421-3 pmc: PMC3463787 pubmed: '22961259' title: The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data year: 2012 - doi: 10.1002/wsbm.44 pmc: PMC2801442 pubmed: '20052305' title: 'The mammalian phenotype ontology: enabling robust annotation and comparative analysis' year: 2009 - doi: 10.1186/gb-2004-6-1-r7 pmc: PMC549068 pubmed: '15642099' title: The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information year: 2004 rdf_uri_format: http://purl.obolibrary.org/obo/MP_$1 repository: https://github.com/mgijax/mammalian-phenotype-ontology uri_format: http://purl.obolibrary.org/obo/MP_$1 version: '2025-01-30' mpath: contact: email: pns12@hermes.cam.ac.uk github: PaulNSchofield name: Paul Schofield orcid: 0000-0002-5111-7263 description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes download_obo: https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo download_owl: http://purl.obolibrary.org/obo/mpath.owl example: '728' homepage: http://www.pathbase.net keywords: - anatomy - biomedical science - disease - genetic strain - histology - mouse - mutation - obo - ontology - phenotype license: CC-BY-3.0 mappings: aberowl: MPATH biocontext: MPATH bioportal: MPATH fairsharing: FAIRsharing.3wbgm0 integbio: nbdc01568 obofoundry: mpath ols: mpath ontobee: MPATH prefixcommons: mpath name: Mouse pathology ontology pattern: ^\d+$ preferred_prefix: MPATH providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mpath:$1 publications: - doi: 10.1177/0300985810374845 pmc: PMC3038412 pubmed: '20587689' title: Pathbase and the MPATH ontology. Community resources for mouse histopathology year: 2010 rdf_uri_format: http://purl.obolibrary.org/obo/MPATH_$1 repository: https://github.com/PaulNSchofield/mpath synonyms: - MPATH uri_format: http://purl.obolibrary.org/obo/MPATH_$1 version: '2020-05-19' mpid: contact: email: jgoll@emmes.com name: Johannes B. Goll orcid: 0000-0002-9968-4080 description: The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts. example: '172' homepage: http://www.jcvi.org/mpidb/about.php keywords: - interaction - life science - protein - small molecule mappings: biocontext: MPID fairsharing: FAIRsharing.eyjkws miriam: mpid n2t: mpid pathguide: '559' prefixcommons: mpi name: Microbial Protein Interaction Database pattern: ^\d+$ preferred_prefix: mpid providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mpi:$1 - code: ebi description: Microbial Protein Interaction Database subset through IntAct homepage: https://www.ebi.ac.uk/intact/ name: Microbial Protein Interaction Database subset through IntAct uri_format: https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$1 publications: - doi: 10.1093/bioinformatics/btn285 pmc: PMC2638870 pubmed: '18556668' title: 'MPIDB: the microbial protein interaction database' year: 2008 synonyms: - mpidb uri_format: http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1 mpio: contact: email: mbrochhausen@uams.edu github: mbrochhausen name: Mathias Brochhausen orcid: 0000-0003-1834-3856 description: An ontology of minimum information regarding potential drug-drug interaction information. download_owl: http://purl.obolibrary.org/obo/mpio.owl example: '0000004' homepage: https://github.com/MPIO-Developers/MPIO keywords: - obo - ontology license: CC-BY-4.0 mappings: aberowl: MPIO biocontext: MPIO bioportal: MPIO obofoundry: mpio ols: mpio ontobee: MPIO name: Minimum PDDI Information Ontology pattern: ^\d{7}$ preferred_prefix: MPIO rdf_uri_format: http://purl.obolibrary.org/obo/MPIO_$1 repository: https://github.com/MPIO-Developers/MPIO uri_format: http://purl.obolibrary.org/obo/MPIO_$1 version: '2023-10-17' mro: contact: email: bpeters@lji.org github: bpeters42 name: Bjoern Peters orcid: 0000-0002-8457-6693 description: The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions. download_owl: http://purl.obolibrary.org/obo/mro.owl example: '0000634' homepage: https://github.com/IEDB/MRO keywords: - immune system - immunology - major histocompatibility complex - obo - ontology license: CC-BY-3.0 mappings: aberowl: MRO biocontext: MRO fairsharing: FAIRsharing.k893xa obofoundry: mro ols: mro ontobee: MRO name: MHC Restriction Ontology pattern: ^\d{7}$ preferred_prefix: MRO publications: - doi: 10.1186/s13326-016-0045-5 pmc: PMC4709943 pubmed: '26759709' title: An ontology for major histocompatibility restriction year: 2016 rdf_uri_format: http://purl.obolibrary.org/obo/MRO_$1 repository: https://github.com/IEDB/MRO uri_format: http://purl.obolibrary.org/obo/MRO_$1 version: '2025-02-13' ms: banana: MS contact: email: joshua.adam.klein@gmail.com github: mobiusklein name: Joshua Klein orcid: 0000-0003-1279-6838 depends_on: - pato - uo description: The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. download_obo: http://purl.obolibrary.org/obo/ms.obo download_owl: http://purl.obolibrary.org/obo/ms.owl example: '1000560' homepage: http://www.psidev.info/groups/controlled-vocabularies keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: MS biocontext: MS bioportal: MS miriam: ms n2t: ms obofoundry: ms ols: ms ontobee: MS name: Mass spectrometry ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: MS publications: - doi: 10.1093/database/bat009 pmc: PMC3594986 pubmed: '23482073' title: The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary year: 2013 rdf_uri_format: http://purl.obolibrary.org/obo/MS_$1 repository: https://github.com/HUPO-PSI/psi-ms-CV uri_format: http://purl.obolibrary.org/obo/MS_$1 version: 4.1.190 msigdb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can example: M1 homepage: https://www.gsea-msigdb.org license: CC-BY-4.0 mappings: biolink: MSigDB integbio: nbdc02550 name: Molecular Signatures Database pattern: ^M\d+$ preferred_prefix: msigdb providers: - code: biopragmatics description: An OBO to Website of MMSigDB homepage: https://biopragmatics.github.io/providers/msigdb/ name: MMSigDB from Biopragmatics uri_format: https://biopragmatics.github.io/providers/msigdb/$1 synonyms: - msig uri_format: https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/$1 msio: contact: email: philippe.rocca-serra@oerc.ox.ac.uk name: Philippe Rocca-Serra orcid: 0000-0001-9853-5668 description: an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies. download_owl: https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl example: '0000111' homepage: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO keywords: - annotation - experimental measurement - mass spectrum - metabolomics - nmr - nuclear magnetic resonance (nmr) spectroscopy - omics - omics data analysis - ontology mappings: fairsharing: FAIRsharing.4c7f91 ols: msio name: Metabolomics Standards Initiative Ontology pattern: ^\d{7}$ preferred_prefix: msio publications: - doi: 10.1007/s11306-007-0069-z title: 'Metabolomics standards initiative: ontology working group work in progress' year: 2007 repository: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO uri_format: http://purl.obolibrary.org/obo/MSIO_$1 version: 1.0.1 mtbd: description: The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, and information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors. example: '1374' homepage: http://tumor.informatics.jax.org keywords: - dna - gene expression mappings: prefixcommons: mtbd name: Mouse Tumor Biology Database preferred_prefix: mtbd providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mtbd:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key=$1 multicellds: contact: email: samuel.friedman@cammlab.org name: Samuel Friedman orcid: 0000-0001-8003-6860 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata. example: MCDS_S_0000000001 homepage: http://multicellds.org/MultiCellDB.php keywords: - life science mappings: fairsharing: FAIRsharing.pqzyd5 name: MultiCellDS preferred_prefix: multicellds uri_format: http://multicellds.org/MultiCellDB/$1 multicellds.cell_line: description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata. example: MCDS_L_0000000001 homepage: http://multicellds.org/MultiCellDB.php mappings: biocontext: MULTICELLDS.CELL_LINE miriam: multicellds.cell_line n2t: multicellds.cell_line name: MultiCellDS Digital Cell Line part_of: multicellds pattern: ^MCDS_L_[a-zA-Z0-9]{1,10}$ preferred_prefix: multicellds.cell_line uri_format: http://multicellds.org/MultiCellDB/$1 multicellds.collection: description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections). example: MCDS_C_0000000001 homepage: http://multicellds.org/MultiCellDB.php mappings: biocontext: MULTICELLDS.COLLECTION miriam: multicellds.collection n2t: multicellds.collection name: MultiCellDS collection part_of: multicellds pattern: ^MCDS_C_[a-zA-Z0-9]{1,10}$ preferred_prefix: multicellds.collection uri_format: http://multicellds.org/MultiCellDB/$1 multicellds.snapshot: description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data. example: MCDS_S_0000000001 homepage: http://multicellds.org/MultiCellDB.php mappings: biocontext: MULTICELLDS.SNAPSHOT miriam: multicellds.snapshot n2t: multicellds.snapshot name: MultiCellDS Digital snapshot part_of: multicellds pattern: ^MCDS_S_[a-zA-Z0-9]{1,10}$ preferred_prefix: multicellds.snapshot uri_format: http://multicellds.org/MultiCellDB/$1 mvx: contributor: email: lindsey.anderson@pnnl.gov github: lnanderson name: Lindsey Anderson orcid: 0000-0002-8741-7823 description: The CDC's National Center for Immunization and Respiratory Diseases ([NCIRD](https://www.cdc.gov/ncird/)) developed and maintains HL7 Table 0227, Manufacturers of Vaccines (MVX). It includes both active and inactive manufacturers of vaccines in the US. Inactive MVX codes allow transmission of historical immunization records. When [MVX code is paired with a CVX code](https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=tradename) (vaccine administered code), the specific trade named vaccine may be indicated. example: ASZ github_request_issue: 986 homepage: https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=mvx mappings: hl7: 2.16.840.1.113883.6.60 name: Manufacturers of Vaccines pattern: ^\w+$ preferred_prefix: mvx reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.12.227&code=$1 mw.project: description: Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC). example: PR000001 homepage: http://www.metabolomicsworkbench.org/ mappings: biocontext: MW.PROJECT miriam: mw.project n2t: mw.project name: Metabolomics Workbench Project pattern: ^PR[0-9]{6}$ preferred_prefix: mw.project uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1 mw.study: description: Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC). example: ST000900 homepage: http://www.metabolomicsworkbench.org/ mappings: biocontext: MW.STUDY miriam: mw.study n2t: mw.study name: Metabolomics Workbench Study pattern: ^ST[0-9]{6}$ preferred_prefix: mw.study providers: - code: omicsdi description: Metabolomics Workbench Study through OmicsDI homepage: https://www.omicsdi.org/ name: Metabolomics Workbench Study through OmicsDI uri_format: https://www.omicsdi.org/dataset/metabolomics_workbench/$1 uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1 myco.lepra: description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information. example: ML0224 homepage: http://mycobrowser.epfl.ch/leprosy.html keywords: - genome - sequence mappings: biocontext: MYCO.LEPRA miriam: myco.lepra n2t: myco.lepra prefixcommons: myco.lepra name: MycoBrowser leprae pattern: ^ML\w+$ preferred_prefix: myco.lepra providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/myco.lepra:$1 uri_format: http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1 myco.marinum: description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information. example: MMAR_2462 homepage: http://mycobrowser.epfl.ch/marinolist.html keywords: - genome - sequence mappings: biocontext: MYCO.MARINUM miriam: myco.marinum n2t: myco.marinum prefixcommons: myco.marinum name: MycoBrowser marinum pattern: ^MMAR\_\d+$ preferred_prefix: myco.marinum providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/myco.marinum:$1 uri_format: http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1 myco.smeg: description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information. example: MSMEG_3769 homepage: http://mycobrowser.epfl.ch/smegmalist.html keywords: - genome - sequence mappings: biocontext: MYCO.SMEG miriam: myco.smeg n2t: myco.smeg prefixcommons: myco.smeg name: MycoBrowser smegmatis pattern: ^MSMEG\w+$ preferred_prefix: myco.smeg providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/myco.smeg:$1 uri_format: http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1 myco.tuber: contact: email: stewart.cole@epfl.ch name: Stewart Thomas Cole orcid: 0000-0003-1400-5585 description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information. example: Rv1908c homepage: http://tuberculist.epfl.ch/ keywords: - dna - genome - protein mappings: biocontext: MYCO.TUBER miriam: myco.tuber n2t: myco.tuber ncbi: TubercuList prefixcommons: tuberculist uniprot: DB-0106 name: TubercuList knowledge base pattern: ^Rv\d{4}(A|B|c)?$ preferred_prefix: myco.tuber providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/tuberculist:$1 publications: - doi: 10.1016/j.tube.2010.09.006 pubmed: '20980200' title: 'The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes' year: 2010 synonyms: - TubercuList uri_format: http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1 mycobank: contact: email: vrobert@unistra.fr name: Vincent Robert orcid: 0000-0002-9370-4677 contributor_extras: - email: carlosm@ebi.ac.uk github: CarMoreno name: Carlos Moreno orcid: 0000-0003-0066-1717 description: MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations. example: '349124' homepage: http://www.mycobank.org/ keywords: - biology - classification - taxonomy mappings: biocontext: MYCOBANK fairsharing: FAIRsharing.v8se8r integbio: nbdc01815 miriam: mycobank n2t: mycobank ncbi: MycoBank prefixcommons: mycobank re3data: r3d100011222 name: Fungal Nomenclature and Species Bank pattern: ^\d+$ preferred_prefix: mycobank providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/mycobank:$1 publications: - doi: 10.5598/imafungus.2013.04.02.16 pmc: PMC3905949 pubmed: '24563843' title: MycoBank gearing up for new horizons year: 2013 uri_format: https://www.mycobank.org/page/Name%20details%20page/$1 mzspec: banana: mzspec contact: email: gerhard.mayer@rub.de github: germa name: Gerhard Mayer orcid: 0000-0002-1767-2343 contributor_extras: - email: lindsey.anderson@pnnl.gov github: lnanderson name: Lindsey N. Anderson orcid: 0000-0002-8741-7823 description: The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it. example: PXD002255:ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2 homepage: http://www.psidev.info/usi keywords: - data governance - data identity and mapping - data retrieval - lipidomics - mass spectrum - metabolomics - omics data analysis - proteomics mappings: biocontext: MZSPEC fairsharing: FAIRsharing.b549b8 miriam: mzspec n2t: mzspec name: Universal Spectrum Identifier namespace_in_lui: true pattern: ^.+$ preferred_prefix: mzspec providers: - code: 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 - code: ebi description: PRIDE is a database of PRoteomics IDEntifications. It contains protein and peptide identifications (including details of post-translational modifications) together with the mass spectrometric evidence supporting these identifications. PRIDE acts as a repository for mass spectrometry data, specifically the fragment ion spectra used to identify peptide sequences. homepage: https://www.ebi.ac.uk/pride name: PRIDE uri_format: https://www.ebi.ac.uk/pride/archive/usi?usi=mzspec:$1 publications: - doi: 10.1038/s41592-021-01184-6 pmc: PMC8405201 pubmed: '34183830' title: Universal Spectrum Identifier for mass spectra year: 2021 repository: https://github.com/HUPO-PSI/usi uri_format: http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1 n2t: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ARK resolver as well as resolver built with common prefixes as in Identifiers.org example: chebi homepage: https://n2t.net name: Name-to-Thing preferred_prefix: n2t uri_format: 'https://n2t.net/$1:' namerxn: contact: email: gregory.landrum@phys.chem.ethz.ch github: greglandrum name: Gregory Landrum orcid: 0000-0001-6279-4481 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO). example: 4.2.78 homepage: https://www.nextmovesoftware.com/namerxn.html keywords: - chemistry - reactions - text mining name: NameRXN preferred_prefix: namerxn proprietary: true publications: - doi: 10.1021/acs.jmedchem.6b00153 pubmed: '27028220' title: 'Big Data from Pharmaceutical Patents: A Computational Analysis of Medicinal Chemists'' Bread and Butter' year: 2016 - doi: 10.1038/s42256-020-00284-w title: Mapping the space of chemical reactions using attention-based neural networks year: 2021 references: - https://www.nextmovesoftware.com/products/HazELNutPoster.pdf - https://twitter.com/cthoyt/status/1443929184745758723 nando: banana: NANDO contact: email: takatter@dbcls.rois.ac.jp name: Terue Takatsuki description: Nanbyo Disease Ontology (NANDO) is the ontology creating a comprehensive hierarchical controlled vocabulary for intractable and rare disease (i.e., nanbyo) representation in Japan. download_owl: http://aber-owl.net/media/ontologies/NANDO/16/nando.owl example: '1200031' homepage: https://nanbyodata.jp/ keywords: - ontology mappings: aberowl: NANDO bioportal: NANDO miriam: nando togoid: Nando name: Nanbyo Disease Ontology namespace_in_lui: true pattern: ^\d+$ preferred_prefix: nando uri_format: https://nanbyodata.jp/disease/NANDO:$1 napdi: contact: email: rdb20@pitt.edu name: Richard Boyce orcid: 0000-0002-2993-2085 description: The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs). example: '28' homepage: https://repo.napdi.org/ keywords: - biomedical science - pharmacology mappings: biocontext: NAPDI fairsharing: FAIRsharing.y9x8wk miriam: napdi n2t: napdi name: Natural Product-Drug Interaction Research Data Repository pattern: ^[0-9]+$ preferred_prefix: napdi publications: - doi: 10.1186/s13326-018-0183-z pmc: PMC5944177 pubmed: '29743102' title: Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse year: 2018 uri_format: https://repo.napdi.org/study/$1 napp: contact: email: daniel.gautheret@u-psud.fr name: Daniel Gautheret orcid: 0000-0002-1508-8469 description: NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters. example: '351' homepage: http://napp.u-psud.fr/ keywords: - clustering - genomics - nucleotide mappings: biocontext: NAPP fairsharing: FAIRsharing.vr52p3 miriam: napp n2t: napp prefixcommons: napp name: Nucleic Acids Phylogenetic Profiling pattern: ^\d+$ preferred_prefix: napp providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/napp:$1 publications: - doi: 10.1093/nar/gkr807 pmc: PMC3245103 pubmed: '21984475' title: 'NAPP: the Nucleic Acid Phylogenetic Profile Database' year: 2011 - doi: 10.1101/gr.089714.108 pmc: PMC2694484 pubmed: '19237465' title: Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles year: 2009 uri_format: http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1 narcis: description: NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases. example: oai:cwi.nl:4725 homepage: http://www.narcis.nl keywords: - subject agnostic mappings: biocontext: NARCIS fairsharing: FAIRsharing.f63h4k integbio: nbdc01862 miriam: narcis n2t: narcis name: National Academic Research and Collaborations Information System pattern: ^oai\:cwi\.nl\:\d+$ preferred_prefix: narcis uri_format: http://www.narcis.nl/publication/RecordID/$1 nasaosdr.biospecimen: contact: email: sylvain.v.costes@nasa.gov name: Sylvain V Costes orcid: 0000-0002-8542-2389 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for biospecimens used in experiments that investigate biological and health responses of terrestrial life to spaceflight example: '7943' github_request_issue: 1298 homepage: https://www.nasa.gov/osdr name: NASA Open Science Data Repository Biospecimen pattern: ^\d+$ preferred_prefix: nasaosdr.biospecimen publications: - doi: 10.1093/nar/gkae1116 pubmed: '39558178' title: 'NASA open science data repository: open science for life in space' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://osdr.nasa.gov/bio/repo/data/biospecimens/$1 nasaosdr.experiment: contact: email: sylvain.v.costes@nasa.gov name: Sylvain V Costes orcid: 0000-0002-8542-2389 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for space-related data from experiments that investigate biological and health responses of terrestrial life to spaceflight example: OS-27 github_request_issue: 1298 homepage: https://www.nasa.gov/osdr name: NASA Open Science Data Repository Experiment pattern: ^OS-\d+$ preferred_prefix: nasaosdr.experiment publications: - doi: 10.1093/nar/gkae1116 pubmed: '39558178' title: 'NASA open science data repository: open science for life in space' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://osdr.nasa.gov/bio/repo/data/experiments/$1 nasaosdr.hardware: contact: email: sylvain.v.costes@nasa.gov name: Sylvain V Costes orcid: 0000-0002-8542-2389 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for hardware used in experiments that investigate biological and health responses of terrestrial life to spaceflight example: '2011' github_request_issue: 1298 homepage: https://www.nasa.gov/osdr name: NASA Open Science Data Repository Hardware pattern: ^\d+$ preferred_prefix: nasaosdr.hardware publications: - doi: 10.1093/nar/gkae1116 pubmed: '39558178' title: 'NASA open science data repository: open science for life in space' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://osdr.nasa.gov/bio/repo/data/hardware/$1 nasaosdr.mission: contact: email: sylvain.v.costes@nasa.gov name: Sylvain V Costes orcid: 0000-0002-8542-2389 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for missions associated with experiments that investigate biological and health responses of terrestrial life to spaceflight example: ARCBedrest example_extras: - Bion 11 - STS-46 github_request_issue: 1298 homepage: https://www.nasa.gov/osdr name: NASA Open Science Data Repository Mission pattern: ^.+$ preferred_prefix: nasaosdr.mission publications: - doi: 10.1093/nar/gkae1116 pubmed: '39558178' title: 'NASA open science data repository: open science for life in space' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://osdr.nasa.gov/bio/repo/data/missions/$1 nasaosdr.payload: contact: email: sylvain.v.costes@nasa.gov name: Sylvain V Costes orcid: 0000-0002-8542-2389 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for payloads associated with experiments that investigate biological and health responses of terrestrial life to spaceflight example: VEG-03D example_extras: - HyperG2-SIMBA2 - NanoRacks-UF-Squids-1 - PSE.02 github_request_issue: 1298 homepage: https://www.nasa.gov/osdr name: NASA Open Science Data Repository Payload pattern: ^.+$ preferred_prefix: nasaosdr.payload publications: - doi: 10.1093/nar/gkae1116 pubmed: '39558178' title: 'NASA open science data repository: open science for life in space' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://osdr.nasa.gov/bio/repo/data/payloads/$1 nasaosdr.study: comment: NASA OSDR is NASA's new integrated life sciences data archive which encompasses NASA GeneLAB (ngl), their old database for omics data. The studies from ngl are relabelled with new identifier formats, thus this is curated as a new prefix contact: email: sylvain.v.costes@nasa.gov name: Sylvain V Costes orcid: 0000-0002-8542-2389 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for space-related data from studies that investigate biological and health responses of terrestrial life to spaceflight example: OSD-678 github_request_issue: 1298 homepage: https://www.nasa.gov/osdr name: NASA Open Science Data Repository Study pattern: ^OSD-\d+$ preferred_prefix: nasaosdr.study publications: - doi: 10.1093/nar/gkae1116 pubmed: '39558178' title: 'NASA open science data repository: open science for life in space' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://osdr.nasa.gov/bio/repo/data/studies/$1 nasaosdr.subject: contact: email: sylvain.v.costes@nasa.gov name: Sylvain V Costes orcid: 0000-0002-8542-2389 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for subjects of experiments that investigate biological and health responses of terrestrial life to spaceflight example: '58' github_request_issue: 1298 homepage: https://www.nasa.gov/osdr name: NASA Open Science Data Repository Subject pattern: ^\d+$ preferred_prefix: nasaosdr.subject publications: - doi: 10.1093/nar/gkae1116 pubmed: '39558178' title: 'NASA open science data repository: open science for life in space' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://osdr.nasa.gov/bio/repo/data/subjects/$1 nasc: contact: email: sean@arabidopsis.org.uk name: Sean May orcid: 0000-0001-5282-3250 description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. example: N1899 homepage: http://arabidopsis.info/ keywords: - genome - life science mappings: biocontext: NASC fairsharing: FAIRsharing.2sqcxs miriam: nasc n2t: nasc prefixcommons: nasc re3data: r3d100010906 name: NASC code pattern: ^(\w+)?\d+$ preferred_prefix: nasc providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/nasc:$1 publications: - doi: 10.1093/nar/gkh133 pmc: PMC308867 pubmed: '14681484' title: 'NASCArrays: a repository for microarray data generated by NASC''s transcriptomics service' year: 2004 twitter: NascArabidopsis uri_format: http://arabidopsis.info/StockInfo?NASC_id=$1 nbn: description: The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier. example: urn:nbn:fi:tkk-004781 homepage: http://nbn-resolving.org/resolve_urn.htm mappings: biocontext: NBN miriam: nbn n2t: nbn name: National Bibliography Number pattern: ^(urn|URN):(nbn|NBN)(:[A-Za-z_0-9]+)*.+$ preferred_prefix: nbn uri_format: http://nbn-resolving.org/resolver?identifier=$1&verb=redirect nbo: appears_in: - ecto - maxo - pcl - scdo - uberon contact: email: g.gkoutos@bham.ac.uk github: gkoutos name: George Gkoutos orcid: 0000-0002-2061-091X description: An ontology of human and animal behaviours and behavioural phenotypes download_obo: https://github.com/obo-behavior/behavior-ontology/raw/master/nbo.obo download_owl: http://purl.obolibrary.org/obo/nbo.owl example: '0000564' homepage: https://github.com/obo-behavior/behavior-ontology/ keywords: - behavior - obo - ontology - phenotype - social and behavioural science - systemic neuroscience license: CC-BY-3.0 mappings: aberowl: NBO biocontext: NBO bioportal: NBO fairsharing: FAIRsharing.pktgc6 obofoundry: nbo ols: nbo ontobee: NBO name: Neuro Behavior Ontology pattern: ^\d{7}$ preferred_prefix: NBO publications: - doi: 10.1007/s00335-013-9481-z pubmed: '24177753' title: Analyzing gene expression data in mice with the Neuro Behavior Ontology year: 2013 - doi: 10.1016/b978-0-12-388408-4.00004-6 pubmed: '23195121' title: 'The neurobehavior ontology: an ontology for annotation and integration of behavior and behavioral phenotypes' year: 2012 rdf_uri_format: http://purl.obolibrary.org/obo/NBO_$1 repository: https://github.com/obo-behavior/behavior-ontology uri_format: http://purl.obolibrary.org/obo/NBO_$1 version: '2023-07-04' nbrc: description: NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information. example: '00001234' homepage: http://www.nbrc.nite.go.jp/e/index.html keywords: - microbial - microbiology - taxonomy mappings: biocontext: NBRC fairsharing: FAIRsharing.ftamrc miriam: nbrc n2t: nbrc ncbi: NBRC prefixcommons: nbrc name: NITE Biological Resource Center pattern: ^\d+$ preferred_prefix: nbrc providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/nbrc:$1 uri_format: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1 ncats.bioplanet: contact: email: ruili.huang@nih.gov name: Ruili Huang orcid: 0000-0001-8886-8311 contributor: github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 description: The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays. example: '3' github_request_issue: 445 homepage: https://tripod.nih.gov/bioplanet/ mappings: biolink: ncats.bioplanet name: National Center for Advancing Translation Sciences BioPlanet pattern: ^\d+$ preferred_prefix: ncats.bioplanet publications: - doi: 10.3389/fphar.2019.00445 pmc: PMC6524730 pubmed: '31133849' title: The NCATS BioPlanet - An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics year: 2019 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 twitter: ncats_nih_gov uri_format: https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1 ncats.drug: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 - github: vdancik name: Vlado Dancik orcid: 0000-0002-5970-6660 - github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 description: 'The National Center for Advancing Translational Sciences](http://www.ncats.nih.gov/) (NCATS) has developed Inxight Drugs as a comprehensive portal for drug development information. NCATS Inxight Drugs contains information on ingredients in medicinal products, including: - US Approved Drugs - Marketed Drugs - Investigational Drugs - Other Substances' example: '44259' example_extras: - 1IJV77EI07 homepage: https://drugs.ncats.io/ mappings: biolink: ncats.drug name: NCATS Drugs preferred_prefix: ncats.drug synonyms: - inxight - inxight-drugs uri_format: https://drugs.ncats.io/drug/$1 ncbi.assembly: description: A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. example: GCF_000005845.2 homepage: https://www.ncbi.nlm.nih.gov/ mappings: biocontext: NCBIAssembly miriam: assembly re3data: r3d100012688 name: Assembly pattern: ^[a-zA-Z0-9_\.]+$ preferred_prefix: ncbi.assembly uri_format: https://www.ncbi.nlm.nih.gov/datasets/genome/$1 ncbi.gc: comment: 'see comment here: https://github.com/obophenotype/ncbitaxon/issues/47' contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries. example: '11' homepage: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html license: public domain name: Genetic Code pattern: ^\d+$ preferred_prefix: ncbi.gc references: - https://github.com/obophenotype/ncbitaxon/issues/47 synonyms: - gc - gc_id uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1 ncbi.genome: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations. example: '51' homepage: https://www.ncbi.nlm.nih.gov/genome mappings: biocontext: NCBIGenome edam: '2787' re3data: r3d100010785 name: NCBI Genome pattern: ^\d+$ preferred_prefix: ncbi.genome uri_format: https://www.ncbi.nlm.nih.gov/genome/$1 ncbi.resource: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources example: ECOCYC homepage: https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/ name: NCBI Registry preferred_prefix: ncbi.resource uri_format: https://bioregistry.io/metaregistry/ncbi/$1 ncbibook: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. ' example: NBK331 homepage: https://www.ncbi.nlm.nih.gov/books name: NCBI Bookshelf pattern: ^NBK\d+$ preferred_prefix: ncbibook uri_format: https://www.ncbi.nlm.nih.gov/books/$1 ncbidrs: description: 'This is the namespace for the archive of sequence and other files provided by NCBI e.g. in SRA and dbGaP. These files are related to objects in the sequencing data model managed under the insdc.sra namespace. ' example: 72ff6ff882ec447f12df018e6183de59 homepage: https://www.ncbi.nlm.nih.gov/ mappings: miriam: ncbidrs name: NCBI Data Repository Service pattern: ^[0-9a-fA-F]{32}$ preferred_prefix: ncbidrs uri_format: https://locate.be-md.ncbi.nlm.nih.gov/ga4gh/drs/v1/objects/$1 ncbigene: contact: email: murphyte@ncbi.nlm.nih.gov name: Terence D. Murphy orcid: 0000-0001-9311-9745 contributor_extras: - email: rcameron@sfu.com github: cmrn-rhi name: Rhiannon Cameron orcid: 0000-0002-9578-0788 description: Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis. example: '100010' homepage: https://www.ncbi.nlm.nih.gov/gene keywords: - dna - gene - genetics - genome - genomics mappings: biocontext: NCBIGene biolink: NCBIGene edam: '1027' fairsharing: FAIRsharing.5h3maw go: NCBIGene hl7: 2.16.840.1.113883.6.340 integbio: nbdc00073 miriam: ncbigene n2t: ncbigene ncbi: GeneID prefixcommons: ncbigene re3data: r3d100010650 togoid: Ncbigene uniprot: DB-0118 wikidata: P351 name: NCBI Gene owners: - name: National Center for Biotechnology Information partnered: false ror: 02meqm098 pattern: ^\d+$ preferred_prefix: NCBIGene providers: - code: CURATOR_REVIEW description: Bio2RDF homepage: http://ncbigene.bio2rdf.org/fct name: Bio2RDF uri_format: http://ncbigene.bio2rdf.org/describe/?url=http://bio2rdf.org/ncbigene:$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ncbigene:$1 - code: marrvel description: Helps browse potential orthologs in model organisms for a given gene homepage: http://marrvel.org name: Model organism Aggregated Resources for Rare Variant ExpLoration uri_format: http://marrvel.org/model/gene/$1 - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/ncbi-gene/$1 publications: - doi: 10.1093/nar/gku1055 pubmed: '25355515' - doi: 10.1093/nar/gkq1237 pmc: PMC3013746 pubmed: '21115458' title: 'Entrez Gene: gene-centered information at NCBI' year: 2010 - doi: 10.1093/nar/gki031 pmc: PMC539985 pubmed: '15608257' title: 'Entrez Gene: gene-centered information at NCBI' year: 2005 rdf_uri_format: http://purl.uniprot.org/geneid/$1 references: - https://github.com/biopragmatics/bioregistry/issues/983 synonyms: - EGID - EntrezGene - GeneID - NCBIGene - NCBI_GeneID - entrez - entrez gene/locuslink - nihgeneid uri_format: https://www.ncbi.nlm.nih.gov/gene/$1 ncbigi: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A GI number (for GenInfo Identifier, sometimes written in lower case, _gi_) is a simple series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Version number of the sequence record. Each time a sequence record is changed, it is assigned a new GI number. example: '568815597' has_canonical: genbank homepage: https://www.ncbi.nlm.nih.gov/genbank/sequenceids/ mappings: biocontext: NCBIGI edam: '2314' go: NCBI_gi ncbi: GI name: GenInfo Identifier owners: - name: National Center for Biotechnology Information partnered: false ror: 02meqm098 pattern: ^\d+$ preferred_prefix: ncbigi references: - https://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html - https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/Format/exercises/qa_accession_vs_gi.html synonyms: - NCBI_gi - ncbi.gi uri_format: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$1 ncbiortholog: comment: We do not currently have the source code for our ortholog resource available publicly, although we are looking at how to split it off and make it available in the next year. We are now in the process of adding this tag to the INSDC list for use in annotations, so I'd like to mirror that tag in bioregistry. contact: email: murphyte@ncbi.nlm.nih.gov github: murphyte name: Terence Murphy orcid: 0000-0001-9311-9745 contributor: email: murphyte@ncbi.nlm.nih.gov github: murphyte name: Terence Murphy orcid: 0000-0001-9311-9745 description: Database of one-to-one ortholog information provided by the NCBI as a subset of their Gene resource. Used for users to access ortholog information for over 1000 species of vertebrates and arthropods. example: '2' github_request_issue: 1181 homepage: https://www.ncbi.nlm.nih.gov/gene/ license: US gov't public domain name: NCBI Orthologs pattern: ^\d+$ preferred_prefix: ncbiortholog reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://www.ncbi.nlm.nih.gov/gene/$1/ortholog ncbiprotein: description: The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. example: CAA71118.1 homepage: https://www.ncbi.nlm.nih.gov/protein keywords: - protein mappings: biocontext: NCBIProtein go: NCBI_NP integbio: nbdc00636 miriam: ncbiprotein n2t: ncbiprotein prefixcommons: ncbi.protein re3data: r3d100010776 name: NCBI Protein owners: - name: National Center for Biotechnology Information partnered: false ror: 02meqm098 pattern: ^\w+_?\d+(.\d+)?$ preferred_prefix: NCBIProtein providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ncbi.protein:$1 uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 ncbitaxon: appears_in: - agro - chiro - cl - clo - ecto - envo - foodon - gallont - genepio - go - hso - mco - ons - pcl - pco - uberon - vbo contact: email: schoch2@ncbi.nlm.nih.gov github: fbastian name: Conrad L Schoch orcid: 0000-0003-1839-5322 description: The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined. download_json: http://purl.obolibrary.org/obo/ncbitaxon.json download_obo: http://purl.obolibrary.org/obo/ncbitaxon.obo download_owl: http://purl.obolibrary.org/obo/ncbitaxon.owl example: '2170610' homepage: https://github.com/obophenotype/ncbitaxon keywords: - classification - dna - life science - obo - ontology - phylogenetics - protein - structure - taxonomic classification - taxonomy license: CC0-1.0 mappings: aberowl: NCBITAXON agroportal: NCBITAXON bartoc: '509' biocontext: TAXONOMY bioportal: NCBITAXON cellosaurus: NCBI_TaxID edam: '1179' fairsharing: FAIRsharing.fj07xj go: NCBITaxon hl7: 2.16.840.1.113883.6.205 miriam: taxonomy n2t: taxonomy ncbi: taxon obofoundry: ncbitaxon ols: ncbitaxon ontobee: NCBITaxon prefixcommons: taxonomy re3data: r3d100010415 togoid: Taxonomy wikidata: P685 name: NCBI Taxonomy owners: - name: National Center for Biotechnology Information partnered: false ror: 02meqm098 pattern: ^\d+$ preferred_prefix: NCBITaxon providers: - code: CURATOR_REVIEW description: Taxonomy through UniProt PURL homepage: https://www.uniprot.org/taxonomy/ name: Taxonomy through UniProt PURL uri_format: https://purl.uniprot.org/taxonomy/$1 - code: CURATOR_REVIEW description: Bio2RDF homepage: https://bio2rdf.org/ name: Bio2RDF uri_format: https://bio2rdf.org/taxonomy:$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/taxonomy:$1 - code: ebi description: European Nucleotide Archive (ENA) homepage: https://www.ebi.ac.uk/ena/ name: European Nucleotide Archive (ENA) uri_format: https://www.ebi.ac.uk/ena/data/view/Taxon:$1 - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/ncbi-taxon/$1 publications: - doi: 10.1093/database/baaa062 pmc: PMC7408187 pubmed: '32761142' title: 'NCBI Taxonomy: a comprehensive update on curation, resources and tools' year: 2020 - doi: 10.1093/nar/gkx1094 pmc: PMC5753231 pubmed: '29140468' title: GenBank year: 2018 - doi: 10.1093/nar/gkr1178 pmc: PMC3245000 pubmed: '22139910' title: The NCBI Taxonomy database year: 2011 rdf_uri_format: http://purl.obolibrary.org/obo/NCBITaxon_$1 repository: https://github.com/obophenotype/ncbitaxon synonyms: - NCBI Taxonomy - NCBITaxon - NCBITaxonomyID - NCBI_Taxon_ID - NCBI_taxid - TAX - TaxonomyID - ncbiTaxUID - taxid - taxon - taxonomy - uniprot.taxonomy uri_format: http://purl.obolibrary.org/obo/NCBITaxon_$1 version: '2024-11-25' nci.drug: description: identifier of an entry in the NCI Drug Dictionary example: beta-carotene homepage: https://www.cancer.gov/publications/dictionaries/cancer-drug mappings: wikidata: P11623 name: NCI Drug Dictionary ID preferred_prefix: nci.drug uri_format: https://www.cancer.gov/publications/dictionaries/cancer-drug/def/$1 ncim: description: NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical. example: C0026339 homepage: http://ncim.nci.nih.gov/ mappings: biocontext: NCIM miriam: ncim n2t: ncim name: NCI Metathesaurus owners: - name: National Cancer Institute partnered: false ror: 040gcmg81 pattern: ^C\d+$ preferred_prefix: ncim uri_format: http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1 ncit: appears_in: - ecto - mco - ontoavida - scdo contact: email: haendel@ohsu.edu github: mellybelly name: Melissa Haendel orcid: 0000-0001-9114-8737 description: NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code. download_obo: http://purl.obolibrary.org/obo/ncit.obo download_owl: http://purl.obolibrary.org/obo/ncit.owl example: C138986 homepage: https://github.com/NCI-Thesaurus/thesaurus-obo-edition keywords: - biomedical science - cancer - disease - obo - ontology - preclinical studies - thesaurus - translational medicine license: CC-BY-4.0 mappings: aberowl: NCIT biocontext: NCIT bioportal: NCIT cellosaurus: NCIt fairsharing: FAIRsharing.4cvwxa hl7: 2.16.840.1.113883.6.206 integbio: nbdc02651 miriam: ncit n2t: ncit obofoundry: ncit ols: ncit ontobee: NCIT prefixcommons: ncit wikidata: P1748 name: NCI Thesaurus owners: - name: National Cancer Institute partnered: false ror: 040gcmg81 pattern: ^C\d+$ preferred_prefix: NCIT providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ncit:$1 - code: evs description: Links to a no-longer existing OWL file homepage: https://ncit.nci.nih.gov/ncitbrowser/ name: Legacy NCBI OWL uri_format: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#$1 publications: - doi: 10.3233/ao-2008-0051 pmc: PMC2753293 pubmed: '19789731' title: 'Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages' year: 2008 - doi: 10.3233/978-1-60750-949-3-33 pubmed: '15360769' title: 'NCI Thesaurus: using science-based terminology to integrate cancer research results' year: 2004 rdf_uri_format: http://purl.obolibrary.org/obo/NCIT_$1 repository: https://github.com/NCI-Thesaurus/thesaurus-obo-edition synonyms: - NCI - NCI2004_11_17 - NCIT - NCIT_Thesaurus - NCIThesaurus - NCITm - NCITt - NCI_Thesaurus - NCIt - NCit - ncithesaurus uri_format: http://purl.obolibrary.org/obo/NCIT_$1 version: '2024-05-07' ncro: contact: email: huang@southalabama.edu github: Huang-OMIT name: Jingshan Huang orcid: 0000-0003-2408-2883 description: An ontology for non-coding RNA, both of biological origin, and engineered. download_obo: https://raw.githubusercontent.com/OmniSearch/ncro/master/src/ontology/ncro.obo download_owl: http://purl.obolibrary.org/obo/ncro.owl example: 0002927 homepage: http://omnisearch.soc.southalabama.edu/w/index.php/Ontology keywords: - genomics - non-coding rna - obo - ontology license: CC-BY-4.0 mappings: aberowl: NCRO biocontext: NCRO bioportal: NCRO fairsharing: FAIRsharing.vppyga obofoundry: ncro ols: ncro ontobee: NCRO name: Non-Coding RNA Ontology pattern: ^\d{7}$ preferred_prefix: NCRO publications: - doi: 10.1186/s13326-016-0066-0 pmc: PMC4857245 pubmed: '27152146' title: 'The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology' year: 2016 rdf_uri_format: http://purl.obolibrary.org/obo/NCRO_$1 repository: https://github.com/OmniSearch/ncro uri_format: http://purl.obolibrary.org/obo/NCRO_$1 ndc: description: The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily. example: 0002-1975-61 homepage: http://www.accessdata.fda.gov/scripts/cder/ndc/ mappings: biocontext: NDC hl7: 2.16.840.1.113883.6.69 miriam: ndc n2t: ndc wikidata: P3640 name: National Drug Code pattern: ^\d+\-\d+\-\d+$ preferred_prefix: ndc providers: - code: CURATOR_REVIEW description: Bio2RDF homepage: http://ndc.bio2rdf.org/fct name: Bio2RDF uri_format: http://ndc.bio2rdf.org/describe/?url=http://bio2rdf.org/ndc:$1 uri_format: http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1 nddf: contact: email: cs@firstdatabank.com name: First DataBank Customer Support contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: FDB MedKnowledge encompasses medications approved by the U.S. Food and Drug Administration, and information on commonly-used over-the-counter and alternative therapy agents such as herbals, nutraceuticals and dietary supplements. example: 002678 homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDDF keywords: - biomedical science - chemical entity - drug - medicinal chemistry - ontology license: https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf mappings: aberowl: NDDF biolink: NDDF bioportal: NDDF fairsharing: FAIRsharing.8qcbs0 hl7: 2.16.840.1.113883.6.208 name: National Drug Data File pattern: ^\d{6}$ preferred_prefix: nddf uri_format: http://purl.bioontology.org/ontology/NDDF/$1 ndex: contact: email: rpillich@ucsd.edu name: Rudolf T. Pillich orcid: 0000-0001-8682-0568 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 keywords: - epidemiology - life science - microbiology mappings: fairsharing: FAIRsharing.8nq9t6 re3data: r3d100012690 name: Network Data Exchange preferred_prefix: ndex publications: - doi: 10.1002/cpz1.258 pmc: PMC8544027 pubmed: '34570431' title: 'NDEx: Accessing Network Models and Streamlining Network Biology Workflows' year: 2021 - doi: 10.1158/0008-5472.can-17-0606 pmc: PMC5679399 pubmed: '29092941' title: 'NDEx 2.0: A Clearinghouse for Research on Cancer Pathways' year: 2017 - doi: 10.1007/978-1-4939-6783-4_13 pubmed: '28150243' title: 'NDEx: A Community Resource for Sharing and Publishing of Biological Networks' year: 2017 - doi: 10.1016/j.cels.2015.10.001 pmc: PMC4649937 pubmed: '26594663' title: NDEx, the Network Data Exchange year: 2015 - doi: 10.1158/0008-5472.CAN-17-0606 title: 'NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.' repository: https://github.com/ndexbio twitter: NDExProject uri_format: https://www.ndexbio.org/viewer/networks/$1 ndfrt: contact: email: michael.lincoln@va.gov name: Michael J. Lincoln MD contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction].' example: N0000001662 homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDFRT keywords: - biomedical science - chemical entity - drug name - health science - medicine - ontology - physiology mappings: aberowl: NDFRT bioportal: NDFRT fairsharing: FAIRsharing.901nkj hl7: 2.16.840.1.113883.6.209 ontobee: NDF-RT prefixcommons: ndfrt wikidata: P2115 name: National Drug File - Reference Terminology pattern: ^N[0-9]{10}$ preferred_prefix: ndfrt providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ndfrt:$1 publications: - pmc: PMC1480331 pubmed: '14728237' title: Adequacy of representation of the National Drug File Reference Terminology Physiologic Effects reference hierarchy for commonly prescribed medications year: 2003 rdf_uri_format: http://purl.bioontology.org/ontology/NDFRT/$1 synonyms: - NUI - ndf-rt uri_format: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NDFRT&code=$1 nembase: comment: This resource doesn't exist on the web anymore deprecated: true description: NEMBASE is a comprehensive Nematode Transcriptome Database. NEMBASE4 includes robust protein predictions (NemPep4), and protein families for 63 nematode species, over 600,000 ESTs and over 250,000 proteins. example: NBC00001 homepage: http://www.nematodes.org keywords: - dna - protein - rna mappings: prefixcommons: nembase name: Nematode & Neglected Genomics preferred_prefix: nembase providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/nembase:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.nematodes.org/nembase4/cluster.php?cluster=$1 nemo: description: This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects. example: smp-m3w9hbe homepage: https://www.nemoarchive.org mappings: miriam: nemo name: Neuroscience Multi-Omic BRAIN Initiative Data pattern: ^[a-z]{3}-[a-km-z0-9]{7}$ preferred_prefix: nemo uri_format: https://assets.nemoarchive.org/$1 nemo2: contact: email: gfrishkoff@gsu.edu name: Gwen Frishkoff orcid: 0000-0003-0612-0970 description: Neural ElectroMagnetic Ontology (NEMO) describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters). FAIRsharing curators have been unable to contact the project developers, and as such this record has been marked as Uncertain. Please contact us if you have any information on this resource. download_owl: http://aber-owl.net/media/ontologies/NEMO/24/nemo.owl example: 0000196 homepage: http://aimlab.cs.uoregon.edu/NEMO/web/index.html keywords: - brain - cognition - cognitive neuroscience - electroencephalography - imaging - interoperability - life science - neurobiology - neuron - ontology mappings: aberowl: NEMO bioportal: NEMO fairsharing: FAIRsharing.n66krd name: Neural ElectroMagnetic Ontology preferred_prefix: nemo2 publications: - doi: 10.4056/sigs.2025347 pmc: PMC3235514 pubmed: '22180824' title: 'Minimal Information for Neural Electromagnetic Ontologies (MINEMO): A standards-compliant method for analysis and integration of event-related potentials (ERP) data' year: 2011 - doi: 10.1038/npre.2009.3458.1 title: 'Development of Neural Electromagnetic Ontologies (NEMO): Ontology-based Tools for Representation and Integration of Event-related Brain Potentials' year: 2009 uri_format: http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_$1 neurolex: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex). example: '4' homepage: https://github.com/SciCrunch/NIF-Ontology keywords: - classification - neuroscience - ontology license: CC BY-4.0 mappings: biocontext: NEUROLEX miriam: neurolex n2t: neurolex prefixcommons: neurolex name: 'NIF Standard Ontology: Neurolex' part_of: nif pattern: ^\d+$ preferred_prefix: neurolex providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/neurolex:$1 publications: - doi: 10.1007/s12021-008-9032-z pmc: PMC2743139 pubmed: '18975148' title: 'The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience' year: 2008 repository: https://github.com/SciCrunch/NIF-Ontology synonyms: - NLX - nlx twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_$1 neuromorpho: contact: email: Ascoli@gmu.edu name: Giorgio Ascoli orcid: 0000-0002-0964-676X description: NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons. example: Rosa2 homepage: http://neuromorpho.org/index.jsp keywords: - anatomy - structure mappings: biocontext: NEUROMORPHO edam: '2657' miriam: neuromorpho n2t: neuromorpho prefixcommons: neuromorpho name: NeuroMorpho pattern: ^\w+$ preferred_prefix: neuromorpho providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/neuromorpho:$1 publications: - doi: 10.1038/nrn1885 pubmed: '16552417' title: 'Mobilizing the base of neuroscience data: the case of neuronal morphologies' year: 2006 uri_format: http://neuromorpho.org/neuron_info.jsp?neuron_name=$1 neuronames: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it. example: '268' homepage: http://braininfo.rprc.washington.edu/ mappings: wikidata: P4394 name: NeuroNames pattern: ^\d+$ preferred_prefix: neuronames providers: - code: neuronames.alt1 description: Alternate URI inside neuronames, appearning in birnlex homepage: http://braininfo.rprc.washington.edu name: Neuronames Alternate 1 uri_format: http://braininfo.rprc.washington.edu/Scripts/hiercentraldirectory.aspx?ID=$1 references: - https://en.wikipedia.org/wiki/NeuroNames synonyms: - neuroname uri_format: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1 neurondb: description: 'NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.' example: '265' homepage: http://senselab.med.yale.edu/NeuronDB/ keywords: - anatomy - cellular neuroscience - comparative neurobiology - computational neuroscience - molecular neuroscience - neurobiology - neurophysiology - structure mappings: biocontext: NEURONDB edam: '2656' fairsharing: FAIRsharing.45a10e miriam: neurondb n2t: neurondb prefixcommons: neurondb name: NeuronDB pattern: ^\d+$ preferred_prefix: neurondb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/neurondb:$1 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/$1 nextdb: description: NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones. example: 6b1 homepage: http://nematode.lab.nig.ac.jp/ keywords: - dna - gene expression - genome - life science mappings: biocontext: NEXTDB fairsharing: FAIRsharing.xz5m1a integbio: nbdc00594 miriam: nextdb n2t: nextdb ncbi: NextDB prefixcommons: nextdb name: Nematode Expression Pattern DataBase pattern: ^[A-Za-z0-9]+$ preferred_prefix: nextdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/nextdb:$1 uri_format: http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1 nextprot: contact: email: monique.zahn@sib.swiss name: Monique Zahn orcid: 0000-0001-7961-6091 description: neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases. example: NX_O00165 homepage: https://www.nextprot.org/ keywords: - life science - proteomics mappings: biocontext: NEXTPROT fairsharing: FAIRsharing.62evqh integbio: nbdc02107 miriam: nextprot n2t: nextprot uniprot: DB-0161 name: nextProt pattern: ^NX_\w+$ preferred_prefix: nextprot publications: - doi: 10.1093/nar/gkz995 pmc: PMC7145669 pubmed: '31724716' title: 'The neXtProt knowledgebase in 2020: data, tools and usability improvements' year: 2020 - doi: 10.1093/nar/gkw1062 pmc: PMC5210547 pubmed: '27899619' title: 'The neXtProt knowledgebase on human proteins: 2017 update' year: 2016 - doi: 10.1093/nar/gku1178 pmc: PMC4383972 pubmed: '25593349' title: 'The neXtProt knowledgebase on human proteins: current status' year: 2015 - doi: 10.1021/pr300830v pubmed: '23205526' title: 'neXtProt: organizing protein knowledge in the context of human proteome projects' year: 2012 - doi: 10.1093/nar/gkr1179 pmc: PMC3245017 pubmed: '22139911' title: 'neXtProt: a knowledge platform for human proteins' year: 2011 - doi: 10.1093/nar/gkw1062. title: 'The neXtProt knowledgebase on human proteins: 2017 update.' - doi: 10.1093/nar/gku1178. title: 'The neXtProt knowledgebase on human proteins: current status.' - doi: 10.1021/pr300830v. title: 'neXtProt: organizing protein knowledge in the context of human proteome projects.' synonyms: - NXP twitter: neXtProt_news uri_format: https://www.nextprot.org/db/entry/$1 nextprot.family: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: "NeXtProt is a comprehensive human-centric discovery platform, offering\ \ its users a seamless integration of and navigation through protein-related data.\ \ \n(Developed by the SIB Swiss Institute of Bioinformatics)" example: '01406' homepage: https://www.nextprot.org/ name: neXtProt family pattern: ^\d+$ preferred_prefix: nextprot.family synonyms: - NXPFA twitter: neXtProt_news uri_format: https://www.nextprot.org/term/FA-$1 nfdi.core: contact: email: joerg.waitelonis@fiz-karlsruhe.de github: joergwa name: Jörg Waitelonis orcid: 0000-0001-7192-7143 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A mid-level ontology for representing metadata related to NFDI resources, including individuals, organizations, projects, data portals, and more download_owl: https://github.com/ISE-FIZKarlsruhe/nfdicore/raw/refs/heads/main/nfdicore.owl download_rdf: https://github.com/ISE-FIZKarlsruhe/nfdicore/raw/refs/heads/main/nfdicore.ttl example: '0000106' github_request_issue: 1448 homepage: https://ise-fizkarlsruhe.github.io/nfdicore/ keywords: - ontology license: CC0-1.0 name: NFDI Core Ontology pattern: ^\d+$ preferred_prefix: nfdi.core repository: https://github.com/ISE-FIZKarlsruhe/nfdicore uri_format: https://nfdi.fiz-karlsruhe.de/ontology/NFDI_$1 nfdi4chem.ontocape: comment: This ontology ecosystem is near unusable contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: OntoCAPE is a large-scale ontology for the domain of Computer Aided Process Engineering (CAPE). Represented in a formal, machine-interpretable ontology language, OntoCAPE captures consensual knowledge of the process engineering domain in a generic way such that it can be reused and shared by groups of people and across software systems. On the basis of OntoCAPE, novel software support for various engineering activities can be developed; possible applications include the systematic management and retrieval of simulation models and design documents, electronic procurement of plant equipment, mathematical modeling, as well as the integration of design data from distributed sources. homepage: https://www.avt.rwth-aachen.de/cms/AVT/Forschung/Software/~ipts/OntoCape/ license: GPL-2.0 name: Ontology for computer aided process engineering preferred_prefix: nfdi4chem.ontocape nfdi4chem.osmo: comment: locked behind a private GitLab instance contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: OSMO is an ontologization and extension of MODA, a workflow metadata standard that constitutes a mandatory requirement within a number of European calls and projects in the context of materials modelling. OSMO was developed within the Horizon 2020 project VIMMP (Virtual Materials Marketplace) and is part of a larger effort in ontology engineering driven by the European Materials Modelling Council, with the European Materials and Modelling Ontology (EMMO) as its core. (from https://nfdi4cat.org/services/ontologie-sammlung/) homepage: https://zenodo.org/record/5237774#.YXq72hxCRGo name: Ontology for simulation, modelling, and optimization preferred_prefix: nfdi4chem.osmo ngbo: contact: email: dal.alghamdi92@gmail.com github: dalalghamdi name: Dalia Alghamdi orcid: 0000-0002-2801-0767 description: 'Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.' download_owl: http://purl.obolibrary.org/obo/ngbo.owl example: '6000122' homepage: https://github.com/Dalalghamdi/NGBO keywords: - obo - ontology license: CC-BY-4.0 mappings: aberowl: NGBO bioportal: NGBO obofoundry: ngbo ols: ngbo ontobee: NGBO name: Next Generation Biobanking Ontology pattern: ^\d{7}$ preferred_prefix: NGBO rdf_uri_format: http://purl.obolibrary.org/obo/NGBO_$1 repository: https://github.com/Dalalghamdi/NGBO uri_format: http://purl.obolibrary.org/obo/NGBO_$1 version: '2024-08-27' ngl: description: NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA. example: GLDS-141 homepage: https://genelab-data.ndc.nasa.gov/genelab/ mappings: biocontext: NGL miriam: ngl n2t: ngl name: NASA GeneLab pattern: ^GLDS-\d+$ preferred_prefix: ngl uri_format: https://genelab-data.ndc.nasa.gov/genelab/accession/$1 nhcdr: description: Cell line collections (Providers) example: ND50028 homepage: https://stemcells.nindsgenetics.org mappings: cellosaurus: NHCDR name: NINDS Human Cell and Data Repository preferred_prefix: nhcdr uri_format: https://stemcells.nindsgenetics.org?line=$1 niaest: contact: email: dawood@helix.nih.gov name: Dawood B. Dudekula orcid: 0000-0002-4054-1827 description: A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones. example: J0705A10 homepage: http://lgsun.grc.nia.nih.gov/cDNA/ keywords: - dna - life science mappings: biocontext: NIAEST fairsharing: FAIRsharing.xwqg9h miriam: niaest n2t: niaest ncbi: niaEST prefixcommons: niaest name: NIA Mouse cDNA Project pattern: ^\w\d{4}\w\d{2}(\-[35])?$ preferred_prefix: niaest providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/niaest:$1 publications: - doi: 10.1016/j.crvi.2003.09.008 pubmed: '14744099' title: The NIA cDNA project in mouse stem cells and early embryos year: 2003 uri_format: http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1 niaid.chemdb: description: ID in NIAID ChemDB example: 059486 homepage: http://chemdb.niaid.nih.gov mappings: wikidata: P2065 name: NIAID ChemDB ID preferred_prefix: niaid.chemdb uri_format: http://chemdb.niaid.nih.gov/CompoundDetails.aspx?AIDSNO=$1 nif.cell: contact: email: smtifahim@gmail.com name: Fahim Imam orcid: 0000-0003-4752-543X deprecated: true description: Neuronal cell types download_owl: http://aber-owl.net/media/ontologies/NIFCELL/15/nifcell.owl homepage: http://neuinfo.org/ keywords: - obo - ontology mappings: aberowl: NIFCELL biocontext: NIF_CELL bioportal: NIFCELL obofoundry: nif_cell name: NIF Cell part_of: nif preferred_prefix: NIF_CELL rdf_uri_format: http://purl.obolibrary.org/obo/NIF_CELL_$1 uri_format: http://purl.obolibrary.org/obo/NIF_CELL_$1 nif.dysfunction: contact: email: smtifahim@gmail.com name: Fahim Imam orcid: 0000-0003-4752-543X deprecated: true homepage: http://neuinfo.org/ keywords: - obo - ontology mappings: biocontext: NIF_DYSFUNCTION obofoundry: nif_dysfunction name: NIF Dysfunction part_of: nif preferred_prefix: NIF_DYSFUNCTION rdf_uri_format: http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1 uri_format: http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1 nif.ext: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: NIFEXT covers IRIs that were "external" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed. example: '7123' homepage: https://github.com/SciCrunch/NIF-Ontology license: CC BY-4.0 name: 'NIF Standard Ontology: External' part_of: nif pattern: ^\d+$ preferred_prefix: nif.ext repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NIFEXT twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nifext_$1 nif.grossanatomy: contact: email: smtifahim@gmail.com name: Fahim Imam orcid: 0000-0003-4752-543X deprecated: true homepage: http://neuinfo.org/ keywords: - obo - ontology mappings: biocontext: NIF_GROSSANATOMY obofoundry: nif_grossanatomy name: NIF Gross Anatomy part_of: nif preferred_prefix: NIF_GROSSANATOMY rdf_uri_format: http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1 uri_format: http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1 nif.std: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing. download_owl: http://aber-owl.net/media/ontologies/NIFSTD/23/nifstd.owl example: BAMSC981 homepage: https://github.com/SciCrunch/NIF-Ontology keywords: - neuroscience - ontology license: CC BY-4.0 mappings: aberowl: NIFSTD bioportal: NIFSTD fairsharing: FAIRsharing.vgw1m6 name: NIF Standard Ontology part_of: nif pattern: ^BAMSC\d+$ preferred_prefix: nif.std publications: - doi: 10.1007/s12021-008-9032-z pmc: PMC2743139 pubmed: '18975148' title: 'The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience' year: 2008 repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NIFSTD twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/$1 nihhesc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The NIH registration number should be used on all NIH competing applications and annual progress reports to identify the stem cell line proposed for use. Identify the specific line(s) from the Registry using the NIH Registration Number (e.g., 0001), in the specified location in the application (from homepage) example: NIHhESC-10-0083 homepage: https://grants.nih.gov/stem_cells/registry/current.htm mappings: cellosaurus: NIHhESC name: NIH Human Embryonic Stem Cell Registry preferred_prefix: nihhesc uri_format: https://grants.nih.gov/stem_cells/registry/current.htm?ID=$1 nihreporter.project: contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding. example: '10343835' github_request_issue: 400 homepage: https://reporter.nih.gov/ name: NIH RePORTER pattern: ^\d+$ preferred_prefix: nihreporter.project reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://reporter.nih.gov/project-details/$1 nist: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species. homepage: https://webbook.nist.gov/chemistry/ name: NIST Chemistry WebBook no_own_terms: true preferred_prefix: nist synonyms: - NIST - NIST Chemistry WebBook nist.codata: description: identifier for a physical constant example: c homepage: http://physics.nist.gov/cuu/Constants/index.html mappings: wikidata: P1645 name: NIST/CODATA ID preferred_prefix: nist.codata uri_format: http://physics.nist.gov/cgi-bin/cuu/Value?$1 nkos: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'NKOS is devoted to the discussion of the functional and data model for enabling knowledge organization systems/services (KOS), such as classification systems, thesauri, gazetteers, and ontologies, as networked interactive information services to support the description and retrieval of diverse information resources through the Internet. Knowledge Organization Systems/Services (KOS) model the underlying semantic structure of a domain. Embodied as Web-based services, they can facilitate resource discovery and retrieval. They act as semantic road maps and make possible a common orientation by indexers and future users (whether human or machine). -- Douglas Tudhope, Traugott Koch (2004).' download_rdf: https://nkos.dublincore.org/nkos.rdf example: alignedWith homepage: http://w3id.org/nkos name: Networked Knowledge Organization Systems/Services/Structures preferred_prefix: nkos uri_format: http://w3id.org/nkos/$1 nlfff: description: Nonlinear Force-Free Field Three-Dimensional Magnetic Fields Data of Solar Active Regions Database example: '345201101230312003' homepage: https://nlfff.dataset.deepsolar.space/en/ mappings: miriam: nlfff name: NLFFF Database pattern: ^[0-9]+$ preferred_prefix: nlfff uri_format: http://database.deepsolar.space:18080/dbs/nlfff/$1 nlm: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The NLM Catalog provides access to NLM bibliographic data for journals, books, audiovisuals, computer software, electronic resources and other materials. Links to the library's holdings in LocatorPlus, NLM's online public access catalog, are also provided. [from homepage] example: '101775319' homepage: https://www.ncbi.nlm.nih.gov/nlmcatalog license: public domain mappings: bartoc: '528' biolink: NLMID name: National Library of Medicine Catalog pattern: ^\d+$ preferred_prefix: nlm uri_format: https://www.ncbi.nlm.nih.gov/nlmcatalog/$1 nlm.publisher: appears_in: - nlm contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Publisher short codes appearin in the NLM Catalog. example: wiley github_request_issue: 1318 homepage: https://ftp.ncbi.nlm.nih.gov/pubmed/xmlprovidernames.txt license: public domain name: NLM Publisher Codes preferred_prefix: nlm.publisher nlx.anat: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: NLXANAT covers anatomy terms. Almost all terms are also in Uberon. example: 090201 homepage: https://scicrunch.org/scicrunch/interlex/dashboard keywords: - anatomy name: NeuroLex Anatomy part_of: nif pattern: ^\d+$ preferred_prefix: nlx.anat reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1 nlx.br: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999). example: '145' homepage: https://github.com/SciCrunch/NIF-Ontology keywords: - anatomy - brain regions - neuroscience license: CC BY-4.0 name: 'NIF Standard Ontology: Brain Regions' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.br repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXBR twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_br_$1 nlx.cell: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: NLXCELL conatins cell types with a focus on neuron types. example: 091005 homepage: https://github.com/SciCrunch/NIF-Ontology keywords: - cell lines - cell types - cells - neuroscience license: CC BY-4.0 name: 'NIF Standard Ontology: Cell Types' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.cell repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXCELL twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1 nlx.chem: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: NLXCHEM covers chemicals. Most classes are also in ChEBI. example: 090801 homepage: https://github.com/SciCrunch/NIF-Ontology keywords: - chemistry license: CC BY-4.0 name: 'NIF Standard Ontology: Chemical' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.chem repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXCHEM twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1 nlx.dys: appears_in: - mondo contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc. example: '20090602' homepage: https://scicrunch.org/scicrunch/interlex/dashboard keywords: - disease - disorders - phenotypes name: NeuroLex Dysfunction part_of: nif pattern: ^\d+$ preferred_prefix: nlx.dys reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1 nlx.func: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: NLXFUNC covers terms for cognitive function. example: '90801' homepage: https://github.com/SciCrunch/NIF-Ontology keywords: - neuroscience license: CC BY-4.0 name: 'NIF Standard Ontology: Cognitive Function' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.func repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXFUNC twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_func_$1 nlx.inv: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis. example: '90901' homepage: https://github.com/SciCrunch/NIF-Ontology keywords: - data analysis - funding agencies license: CC BY-4.0 name: 'NIF Standard Ontology: Investigations' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.inv repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXINV twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1 nlx.mol: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system. example: '90806' homepage: https://github.com/SciCrunch/NIF-Ontology keywords: - biology - chemistry - neuroscience - proteins license: CC BY-4.0 name: 'NIF Standard Ontology: Molecules' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.mol repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXMOL twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1 nlx.oen: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results). example: '0001000' homepage: https://github.com/SciCrunch/NIF-Ontology keywords: - neuroscience license: CC BY-4.0 name: 'NIF Standard Ontology: OEN Terms in Neurolex' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.oen repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXOEN twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/oen_$1 nlx.org: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: NLXORG covers organisms. example: 090701 homepage: https://github.com/SciCrunch/NIF-Ontology keywords: - taxonomy license: CC BY-4.0 name: 'NIF Standard Ontology: Organisms' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.org repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXORG twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1 nlx.qual: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO). example: '100810' homepage: https://github.com/SciCrunch/NIF-Ontology keywords: - dispositions - qualities license: CC BY-4.0 name: 'NIF Standard Ontology: Qualities' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.qual repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXQUAL twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1 nlx.res: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites example: 090924 homepage: https://github.com/SciCrunch/NIF-Ontology keywords: - software and information systems license: CC BY-4.0 name: 'NIF Standard Ontology: Digital Resources' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.res repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXRES twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_res_$1 nlx.sub: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO). example: 090803 homepage: https://github.com/SciCrunch/NIF-Ontology keywords: - cellular components license: CC BY-4.0 mappings: go: NIF_Subcellular name: 'NIF Standard Ontology: Subcellular Entities' part_of: nif pattern: ^\d+$ preferred_prefix: nlx.sub repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NLXSUB - nif_subcellular twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1 nmdc: contact: email: donny@polyneme.xyz github: dwinston name: Donny Winston orcid: 0000-0002-8424-0604 contributor: email: donny@polyneme.xyz github: dwinston name: Donny Winston orcid: 0000-0002-8424-0604 contributor_extras: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem. example: y3ax-8bq3-60 github_request_issue: 130 homepage: https://microbiomedata.org/ keywords: - microbiome mappings: miriam: nmdc name: National Microbiome Data Collaborative pattern: ^.{2,}$ preferred_prefix: nmdc providers: - code: web description: Direct link homepage: https://drs.microbiomedata.org name: NMDC Web Page uri_format: https://drs.microbiomedata.org/objects/$1 rdf_uri_format: https://w3id.org/nmdc/$1 references: - https://github.com/biopragmatics/bioregistry/pull/982 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://w3id.org/nmdc/$1 nmpdr: comment: This resource doesn't exist on the web anymore deprecated: true description: The NMPDR provided curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma. example: fig|306254.1.peg.183 homepage: http://www.nmpdr.org keywords: - genome mappings: ncbi: NMPDR prefixcommons: nmpdr name: National Microbial Pathogen Data Resource preferred_prefix: nmpdr providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/nmpdr:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature=$1 nmr: banana: NMR contact: email: schober@imbi.uni-freiburg.de github: DSchober name: Daniel Schober orcid: 0000-0001-8014-6648 deprecated: true description: nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi. download_owl: https://nmrml.org/cv/stable/nmrCV.owl example: '1000003' homepage: http://msi-ontology.sourceforge.net/ keywords: - nmr - obo - ontology - owl mappings: aberowl: NMR biocontext: NMR bioportal: NMR miriam: nmr n2t: nmr obofoundry: nmr ols: nmrcv prefixcommons: nmr name: NMR-instrument specific component of metabolomics investigations namespace_in_lui: true pattern: ^\d+$ preferred_prefix: NMR providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/nmr:$1 rdf_uri_format: http://purl.obolibrary.org/obo/NMR_$1 synonyms: - nmrcv uri_format: https://www.ebi.ac.uk/ols4/ontologies/nmrcv/terms?curie=NMR:$1 version: 1.1.0 nmrshiftdb2: contact: email: stefan.kuhn@dmu.ac.uk name: Stefan Kuhn orcid: 0000-0002-5990-4157 contributor_extras: - email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. example: '234' homepage: https://nmrshiftdb.nmr.uni-koeln.de keywords: - analytical chemistry mappings: fairsharing: FAIRsharing.nYaZ1N miriam: nmrshiftdb2 re3data: r3d100010316 wikidata: P9405 name: NMRShiftDB structure pattern: ^[0-9]+$ preferred_prefix: nmrshiftdb2 publications: - doi: 10.1002/mrc.4263 pubmed: '25998807' title: 'Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories' year: 2015 - doi: 10.1016/j.phytochem.2004.08.027 pubmed: '15464159' title: NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database year: 2004 - doi: 10.1021/ci0341363 pubmed: '14632418' title: NMRShiftDB-constructing a free chemical information system with open-source components year: 2003 synonyms: - NMRShiftDB uri_format: https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1 noaa: contributor: email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 description: Identifier for a species on the noaa fisheries website example: long-finned-pilot-whale github_request_issue: 456 homepage: https://www.fisheries.noaa.gov/species-directory mappings: wikidata: P6049 name: NOAA Fisheries Species Directory pattern: ^[a-z]+(\-[a-z]+)*$ preferred_prefix: noaa reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.fisheries.noaa.gov/species/$1 noaa.cameo: description: CAMEO Chemicals is a database of hazardous chemical datasheets that emergency responders and planners can use to get response recommendations and predict hazards—such as explosions or toxic fumes. example: '19757' homepage: https://cameochemicals.noaa.gov mappings: wikidata: P11931 name: CAMEO Chemicals ID pattern: ^\d*$ preferred_prefix: noaa.cameo uri_format: https://cameochemicals.noaa.gov/chemical/$1 nomen: contact: email: diapriid@gmail.com github: mjy name: Matt Yoder orcid: 0000-0002-5640-5491 description: NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature. download_owl: http://purl.obolibrary.org/obo/nomen.owl example: 0000295 homepage: https://github.com/SpeciesFileGroup/nomen keywords: - obo - ontology license: CC0-1.0 mappings: aberowl: NOMEN bioportal: NOMEN obofoundry: nomen ols: nomen ontobee: NOMEN name: A nomenclatural ontology for biological names pattern: ^\d{7}$ preferred_prefix: NOMEN rdf_uri_format: http://purl.obolibrary.org/obo/NOMEN_$1 repository: https://github.com/SpeciesFileGroup/nomen uri_format: http://purl.obolibrary.org/obo/NOMEN_$1 noncodev3: contact: email: biozy@ict.ac.cn name: Yi Zhao orcid: 0000-0001-6049-8347 description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4. example: '377550' homepage: http://www.noncode.org/ keywords: - expression - nucleotide mappings: biocontext: NONCODEV3 miriam: noncodev3 n2t: noncodev3 prefixcommons: noncode name: NONCODE v3 pattern: ^\d+$ preferred_prefix: noncodev3 providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/noncode:$1 publications: - doi: 10.1093/nar/gkr1175 pmc: PMC3245065 pubmed: '22135294' title: 'NONCODE v3.0: integrative annotation of long noncoding RNAs' year: 2011 uri_format: http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1 noncodev4.gene: description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions. example: NONHSAG00001 homepage: http://www.bioinfo.org/NONCODEv4/ mappings: biocontext: NONCODEV4.GENE miriam: noncodev4.gene n2t: noncodev4.gene name: NONCODE v4 Gene pattern: ^NONHSAG\d{5}$ 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=$1 nord: appears_in: - mondo contact: email: sean@skm.digital github: skm16 name: Sean Roberts contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A website containing information about rare diseases, powered by Wordpress. example: '1693' github_request_issue: 1375 homepage: https://rarediseases.org name: National Organization for Rare Disorders pattern: ^\d+$ preferred_prefix: nord references: - https://github.com/monarch-initiative/mondo/issues/8588 uri_format: https://rarediseases.org/?p=$1 norine: contact: email: maude.pupin@univ-lille.fr name: Maude Pupin orcid: 0000-0003-3197-0715 description: Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings. example: NOR00681 homepage: http://bioinfo.lifl.fr/norine/ keywords: - life science - protein mappings: biocontext: NORINE fairsharing: FAIRsharing.gf8yhy miriam: norine n2t: norine prefixcommons: norine name: Nonribosomal Peptides Database pattern: ^NOR\d+$ preferred_prefix: norine providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/norine:$1 publications: - doi: 10.1093/nar/gkz1000 pmc: PMC7145658 pubmed: '31691799' title: 'Norine: update of the nonribosomal peptide resource' year: 2020 - doi: 10.1093/nar/gkm792 pmc: PMC2238963 pubmed: '17913739' title: 'NORINE: a database of nonribosomal peptides' year: 2007 uri_format: 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/$1 npass: comment: This resource does not have an explicit license. The [lotus database](https://github.com/lotusnprod/lotus-processor/blob/main/docs/licenses/npass.md) inferred that the CC-BY-NC license from the paper might be good enough for applying to the data itself. contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data. ' example: NPC139585 homepage: http://bidd.group/NPASS/ license: CC-BY-NC name: Natural Product Activity and Species Source Database pattern: ^NPC\d+$ preferred_prefix: npass uri_format: https://bidd.group/NPASS/compound.php?compoundID=$1 npatlas: contact: email: rliningt@sfu.ca name: Roger Linington orcid: 0000-0003-1818-4971 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for microbially derived natural products that contains compound structures, producing organism taxonomy, biosynthetic and chemical properties. example: NPA000001 github_request_issue: 1295 homepage: https://www.npatlas.org name: The Natural Products Atlas pattern: ^NPA\d{6}$ preferred_prefix: npatlas publications: - doi: 10.1093/nar/gkae1093 pubmed: '39588755' title: 'The Natural Products Atlas 3.0: extending the database of microbially derived natural products' year: 2024 - doi: 10.1093/nar/gkab941 pmc: PMC8728154 pubmed: '34718710' title: 'The Natural Products Atlas 2.0: a database of microbially-derived natural products' year: 2021 - doi: 10.1021/acscentsci.9b00806 pmc: PMC6891855 pubmed: '31807684' title: 'The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery' year: 2019 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://www.npatlas.org/explore/compounds/$1 npm: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A repository of software packages written in Javascript, TypeScript, and related. example: '@biopragmatics/curies' example_extras: - ansi-pad homepage: https://www.npmjs.com name: Node Package Manager preferred_prefix: npm uri_format: https://www.npmjs.com/package/$1 npo: contact: email: nathan.baker@pnnl.gov github: sobolevnrm name: Nathan Baker orcid: 0000-0002-5892-6506 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy. download_owl: http://aber-owl.net/media/ontologies/NPO/31/npo.owl example: '1731' homepage: https://bioportal.bioontology.org/ontologies/NPO keywords: - life science - molecular entity - nanoparticle - ontology - structure mappings: aberowl: NPO bioportal: NPO fairsharing: FAIRsharing.vy0p71 name: NanoParticle Ontology pattern: ^\d+$ preferred_prefix: npo publications: - doi: 10.1016/j.jbi.2010.03.001 pmc: PMC3042056 pubmed: '20211274' title: NanoParticle Ontology for cancer nanotechnology research year: 2010 repository: https://github.com/sobolevnrm/npo uri_format: http://purl.bioontology.org/ontology/npo#NPO_$1 nrfc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The NRFC was established at ICAR-National Bureau of Fish Genetic Resources, Lucknow in the form of a research project entitled ‘Establishment of a National Repository at NBFGR, Lucknow for conservation and characterization of fish cell lines’ during 09 November, 2010 to 08 November, 2014 with the financial support from Department of Biotechnology, Govt. of India, New Delhi. NRFC aims to receive, authenticate, store and supply the fish cell lines to the researchers and academicians for Research & Development works and to serve as a National Referral Centre for fish cell lines in the country. NRFC also aims to provide need-based support for training and education to stakeholders. (from homepage) example: NRFC051 homepage: https://mail.nbfgr.res.in/nrfc/index.php mappings: cellosaurus: NRFC name: National Repository of Fish Cell Lines pattern: ^NRFC\d+$ preferred_prefix: nrfc nsc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Identifier used by the Cancer Chemotherapy National Service Center. example: '27223' homepage: https://wiki.nci.nih.gov/display/NCIDTPdata/Chemical+Data mappings: cheminf: '000565' name: USA National Service Center Number pattern: ^\d+$ preferred_prefix: nsc references: - https://pubchem.ncbi.nlm.nih.gov/source/DTP/NCI uri_format: https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist=$1 nsf.award: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Information about research projects that NSF has funded since 1989 can be found by searching the Award Abstracts database. The information includes abstracts that describe the research, and names of principal investigators and their institutions. The database includes both completed and in-process research. example: '1458400' homepage: https://www.nsf.gov/awards/about.jsp name: National Science Foundation Award pattern: ^\d+$ preferred_prefix: nsf.award uri_format: https://www.nsf.gov/awardsearch/showAward?AWD_ID=$1 nsrrc: description: Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research. [from RRID] example: '0005' homepage: http://www.nsrrc.missouri.edu/ keywords: - biomaterial manufacture - breeding - consulting - cryopreservation - fetal fibroblast - fetus - fibroblast - genetically modified pig - genetics - genome - genotyping - health monitoring - live animal - phenotyping - pig - reproduction - tissue mappings: rrid: NSRRC name: National Swine Resource and Research Center pattern: ^\d+$ preferred_prefix: nsrrc uri_format: https://nsrrc.missouri.edu/nsrrc$1info/ nucc.characteristic: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Provider Characteristics code set is for use with health care provider information for enrollment and credentialing transactions and their corresponding responses. It is intended to provide codified responses to questions presented to a health care provider applying to or registering with an entity and to report the outcome of such application or registration. It may also be used for responses to inquiries regarding provider participation or registration in a program or plan. example: 2A example_extras: - '10' - '11' homepage: https://nucc.org/index.php/code-sets-mainmenu-41/provider-characteristics-mainmenu-39 name: National Uniform Claim Committee Characteristic pattern: ^\d(\d|\w)$ preferred_prefix: nucc.characteristic nucc.taxonomy: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: "The Health Care Provider Taxonomy code set is an external, nonmedical\ \ data code set designed for use in an electronic environment, specifically within\ \ the ASC X12N Health Care transactions. This includes the transactions mandated\ \ under HIPAA.\n\nThe taxonomy code is a unique alphanumeric code, ten characters\ \ in length. The code set is structured into three distinct \"Levels\" including\ \ Provider Grouping, Classification, and Area of Specialization.\n\n - **Level\ \ I, Provider Grouping** A major grouping of service(s) or occupation(s) of health\ \ care providers. For example: Allopathic & Osteopathic Physicians, Dental Providers,\ \ Hospitals, etc.\n - **Level II, Classification** A more specific service or\ \ occupation related to the Provider Grouping. For example, the Classification\ \ for Allopathic & Osteopathic Physicians is based upon the General Specialty\ \ Certificates as issued by the appropriate national boards. The following boards\ \ will however, have their general certificates appear as Level III areas of specialization\ \ strictly due to display limitations of the code set for Boards that have multiple\ \ general certificates: Medical Genetics, Preventive Medicine, Psychiatry & Neurology,\ \ Radiology, Surgery, Otolaryngology, Pathology.\n - **Level III, Area of Specialization**\ \ A more specialized area of the Classification in which a provider chooses to\ \ practice or make services available. For example, the Area of Specialization\ \ for provider grouping Allopathic & Osteopathic Physicians is based upon the\ \ Subspecialty Certificates as issued by the appropriate national boards." example: 207LH0002X homepage: https://taxonomy.nucc.org name: National Uniform Claim Committee Taxonomy pattern: ^\d{3}\w(\w|\d_)\d{4}X$ preferred_prefix: nucc.taxonomy references: - https://www.nucc.org/images/stories/CSV/nucc_taxonomy_221.csv - https://www.nucc.org nucleardb: comment: Note that the typo from MIRIAM has spread to several other sources contact: email: vriend@cmbi.ru.nl name: Gert Vriend orcid: 0000-0002-1067-7053 description: NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs. example: prgr_human homepage: http://www.receptors.org/nucleardb/ keywords: - classification mappings: biocontext: NUCLEARBD integbio: nbdc00599 miriam: nuclearbd n2t: nuclearbd prefixcommons: nucleardb name: NucleaRDB pattern: ^\w+\_\w+$ preferred_prefix: nucleardb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/nucleardb:$1 publications: - doi: 10.1093/nar/gkr960 pmc: PMC3245090 pubmed: '22064856' title: 'NucleaRDB: information system for nuclear receptors' year: 2011 synonyms: - nuclearbd uri_format: http://www.receptors.org/nucleardb/proteins/$1 nucleotide: description: The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery. example: '880798137' has_canonical: insdc homepage: https://www.ncbi.nlm.nih.gov/ mappings: integbio: nbdc00600 miriam: nucleotide name: Nucleotide pattern: ^[a-zA-Z0-9_\.]+$ preferred_prefix: nucleotide uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 nxr: description: National stock center for X. laevis and X. tropicalis and training center for advanced technologies (e.g. husbandry, cell biology, imaging, genetics, transgenesis, genomics). [from RRID] example: '0024' homepage: http://www.mbl.edu/xenopus/ keywords: - laevis - tropicalis - xenopus mappings: rrid: NXR name: National Xenopus Resource pattern: ^\d+$ preferred_prefix: nxr uri_format: https://scicrunch.org/resolver/RRID:NXR_$1 nztcs: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - email: sumirp77@gmail.com github: SumirHPandit name: Sumir Pandit orcid: 0000-0002-1216-4761 description: identifier for species classified under the New Zealand Threat Classification System example: '11061' homepage: https://nztcs.org.nz/ keywords: - taxon - taxonomy license: CC-BY-4.0 mappings: wikidata: P9889 name: New Zealand Threat Classification System pattern: ^[1-9]\d{3,7}$ preferred_prefix: nztcs references: - https://github.com/biopragmatics/bioregistry/pull/1083 uri_format: https://nztcs.org.nz/nztcs-species/$1 oa: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture. download_owl: http://aber-owl.net/media/ontologies/OA/4/oa.owl example: sourceDateStart homepage: http://www.w3.org/ns/oa keywords: - ontology - quality mappings: aberowl: OA biocontext: oa bioportal: OA lov: oa zazuko: oa name: Web Annotation Ontology preferred_prefix: oa uri_format: http://www.w3.org/ns/oa#$1 oae: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqunh He orcid: 0000-0001-9189-9661 description: The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc. download_owl: http://purl.obolibrary.org/obo/oae.owl example: 0002959 homepage: https://github.com/OAE-ontology/OAE/ keywords: - adverse reaction - biomedical science - drug - obo - ontology - vaccine license: CC-BY-3.0 mappings: aberowl: OAE biocontext: OAE bioportal: OAE fairsharing: FAIRsharing.tw4q8x obofoundry: oae ols: oae ontobee: OAE name: Ontology of Adverse Events pattern: ^\d{7}$ preferred_prefix: OAE publications: - doi: 10.1186/2041-1480-5-29 pmc: PMC4120740 pubmed: '25093068' title: 'OAE: The Ontology of Adverse Events' year: 2014 rdf_uri_format: http://purl.obolibrary.org/obo/OAE_$1 repository: https://github.com/OAE-ontology/OAE uri_format: http://purl.obolibrary.org/obo/OAE_$1 version: 1.2.47 oarcs: contact: email: mjyoder@illinois.edu github: mjy name: Matt Yoder orcid: 0000-0002-5640-5491 description: OArCS is an ontology describing the Arthropod ciruclatory system. download_owl: http://purl.obolibrary.org/obo/oarcs.owl example: 0000029 homepage: https://github.com/aszool/oarcs keywords: - anatomy - angiology - obo - ontology license: CC-BY-3.0 mappings: aberowl: OARCS biocontext: OARCS bioportal: OARCS fairsharing: FAIRsharing.yqn857 obofoundry: oarcs ols: oarcs ontobee: OARCS name: Ontology of Arthropod Circulatory Systems pattern: ^\d{7}$ preferred_prefix: OARCS publications: - doi: 10.1093/sysbio/syw108 pubmed: '28123116' title: The First Organ-Based Ontology for Arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its Integration into a Novel Formalization Scheme for Morphological Descriptions year: 2017 rdf_uri_format: http://purl.obolibrary.org/obo/OARCS_$1 repository: https://github.com/aszool/oarcs uri_format: http://purl.obolibrary.org/obo/OARCS_$1 version: '2019-04-18' oba: appears_in: - fovt contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO. download_json: http://purl.obolibrary.org/obo/oba.json download_obo: http://purl.obolibrary.org/obo/oba.obo download_owl: http://purl.obolibrary.org/obo/oba.owl example: '0000001' example_extras: - VT0003769 homepage: https://github.com/obophenotype/bio-attribute-ontology keywords: - biology - obo - ontology license: CC0-1.0 mappings: aberowl: OBA agroportal: OBA biocontext: OBA bioportal: OBA fairsharing: FAIRsharing.mp0rwf obofoundry: oba ols: oba ontobee: OBA name: Ontology of Biological Attributes pattern: ^(VT)?\d{7}$ preferred_prefix: OBA publications: - doi: 10.1007/s00335-023-09992-1 pubmed: '37076585' title: The Ontology of Biological Attributes (OBA)-computational traits for the life sciences year: 2023 - doi: 10.1101/2023.01.26.525742 pmc: PMC9900877 pubmed: '36747660' title: The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences year: 2023 rdf_uri_format: http://purl.obolibrary.org/obo/OBA_$1 repository: https://github.com/obophenotype/bio-attribute-ontology uri_format: http://purl.obolibrary.org/obo/OBA_$1 version: '2025-01-14' oban: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: It is an ontology model used to describe associations between biomedical entities in triple format based on W3C specification. OBAN is a generic association representation model that loosely couples a subject and object (e.g. disease and its associated phenotypes supported by the source of evidence for that association) via a construction of class OBAN:association. [from GitHub] download_owl: https://raw.githubusercontent.com/EBISPOT/OBAN/master/ontology/oban_core.owl download_rdf: https://raw.githubusercontent.com/EBISPOT/OBAN/master/ontology/oban_core.ttl example: provenance homepage: https://github.com/EBISPOT/OBAN keywords: - ontology mappings: biocontext: OBAN biolink: OBAN name: Open Biomedical Annotations pattern: ^\w+$ preferred_prefix: oban repository: https://github.com/EBISPOT/OBAN uri_format: http://purl.org/oban/$1 obci: contact: email: dan5@georgetown.edu github: nataled name: Darren A. Natale orcid: 0000-0001-5809-9523 contributor: email: dan5@georgetown.edu github: nataled name: Darren A. Natale orcid: 0000-0001-5809-9523 description: The Ontology for Biomarkers of Clinical Interest (OBCI) formally defines biomarkers for diseases, phenotypes, and effects. download_owl: https://proteininformationresource.org/staff/nataled/OBCI/obci.owl example: '000000001' github_request_issue: 1174 homepage: https://github.com/clinical-biomarkers/OBCI keywords: - ontology name: Ontology for Biomarkers of Clinical Interest pattern: ^\d+$ preferred_prefix: obci reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: http://purl.obolibrary.org/obo/OBCI_$1 obcs: banana: OBCS contact: email: jiezhen@med.umich.edu github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 description: OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI) download_owl: http://purl.obolibrary.org/obo/obcs.owl example: '0000121' homepage: https://github.com/obcs/obcs keywords: - biology - biomedical science - medical informatics - medicine - obo - ontology - statistics - vaccine license: CC-BY-4.0 mappings: aberowl: OBCS biocontext: OBCS bioportal: OBCS fairsharing: FAIRsharing.5p12xh miriam: obcs obofoundry: obcs ols: obcs ontobee: OBCS name: Ontology of Biological and Clinical Statistics namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: OBCS publications: - doi: 10.1186/s13326-016-0100-2 pmc: PMC5024438 pubmed: '27627881' title: The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis year: 2016 rdf_uri_format: http://purl.obolibrary.org/obo/OBCS_$1 repository: https://github.com/obcs/obcs uri_format: http://purl.obolibrary.org/obo/OBCS_$1 version: '2023-12-08' obi: appears_in: - agro - foodon - gallont - hso - labo - maxo - mco - one - ons - proco - rbo - scdo banana: OBI banana_peel: ':' contact: email: bpeters@lji.org github: bpeters42 name: Bjoern Peters orcid: 0000-0002-8457-6693 description: The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO). download_obo: https://github.com/obi-ontology/obi/raw/master/views/obi.obo download_owl: http://purl.obolibrary.org/obo/obi.owl example: 0400109 homepage: http://obi-ontology.org keywords: - assay - biomedical science - data transformation - device - functional genomics - life science - obo - ontology - protocol - reagent - report - study design license: CC-BY-4.0 logo: https://svn.code.sf.net/p/obi/code/trunk/web/htdocs/images/obi-lotext.png mappings: aberowl: OBI biocontext: OBI bioportal: OBI fairsharing: FAIRsharing.284e1z go: OBI miriam: obi n2t: obi obofoundry: obi ols: obi ontobee: OBI prefixcommons: obi name: Ontology for Biomedical Investigations namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: OBI providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/obi:$1 publications: - doi: 10.1371/journal.pone.0154556 pmc: PMC4851331 pubmed: '27128319' title: The Ontology for Biomedical Investigations year: 2016 - doi: 10.1093/database/bau132 pmc: PMC4309925 pubmed: '25632945' title: 'Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach' year: 2015 - doi: 10.1186/2041-1480-4-s1-s6 pmc: PMC3633001 pubmed: '23734660' title: 'Query enhancement through the practical application of ontology: the IEDB and OBI' year: 2013 - doi: 10.4056/sigs.1994602 pmc: PMC3235517 pubmed: '22180825' title: Minimum Information about a Genotyping Experiment (MIGEN) year: 2011 - doi: 10.1186/2041-1480-1-s1-s7 pmc: PMC2903726 pubmed: '20626927' title: Modeling biomedical experimental processes with OBI year: 2010 rdf_uri_format: http://purl.obolibrary.org/obo/OBI_$1 repository: https://github.com/obi-ontology/obi uri_format: http://purl.obolibrary.org/obo/OBI_$1 version: '2025-01-09' obib: contact: email: jmwhorton@uams.edu github: jmwhorton name: Justin Whorton orcid: 0009-0003-4268-6207 description: The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology. download_owl: http://purl.obolibrary.org/obo/obib.owl example: 0000389 homepage: https://github.com/biobanking/biobanking keywords: - biobank - health science - obo - ontology license: CC-BY-4.0 mappings: aberowl: OBIB biocontext: OBIB bioportal: OBIB fairsharing: FAIRsharing.bxc508 obofoundry: obib ols: obib ontobee: OBIB name: Ontology for Biobanking pattern: ^\d{7}$ preferred_prefix: OBIB publications: - doi: 10.1186/s13326-016-0068-y pmc: PMC4855778 pubmed: '27148435' title: OBIB-a novel ontology for biobanking year: 2016 rdf_uri_format: http://purl.obolibrary.org/obo/OBIB_$1 repository: https://github.com/biobanking/biobanking uri_format: http://purl.obolibrary.org/obo/OBIB_$1 version: '2023-04-05' obo: contact: email: nicolas.matentzoglu@gmail.com github: matentzn name: Nicolas Matentzoglu orcid: 0000-0002-7356-1779 description: The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies. example: uberon example_extras: - go - uberon.owl homepage: http://www.obofoundry.org/ keywords: - biology - health - ontology and terminology mappings: biocontext: OBO fairsharing: FAIRsharing.847069 integbio: nbdc00305 lov: obo name: Open Biological and Biomedical Ontologies preferred_prefix: obo publications: - doi: 10.1038/nbt1346 pmc: PMC2814061 pubmed: '17989687' title: 'The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration' year: 2007 rdf_uri_format: http://purl.obolibrary.org/obo/$1 references: - https://github.com/biopragmatics/bioregistry/pull/913 - https://github.com/biopragmatics/bioregistry/issues/910 repository: https://github.com/OBOFoundry/OBOFoundry.github.io twitter: OBOFoundry uri_format: http://purl.obolibrary.org/obo/$1 oboe: contact: email: brycemecum@gmail.com github: amoeba name: Bryce Mecum orcid: 0000-0002-0381-3766 contributor: github: StroemPhi name: Philip Strömert orcid: 0000-0002-1595-3213 description: The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations. download_owl: https://raw.githubusercontent.com/NCEAS/oboe/refs/heads/master/oboe.owl example: Characteristic github_request_issue: 1276 homepage: https://github.com/NCEAS/oboe keywords: - biodiversity - ecology - environmental science - observations - ontology license: CC-BY-3.0 mappings: aberowl: OBOE agroportal: OBOE bioportal: OBOE ecoportal: OBOE fairsharing: FAIRsharing.5970hq name: The Extensible Observation Ontology preferred_prefix: oboe publications: - doi: 10.1016/j.ecoinf.2007.05.004 pmc: PMC8612252 pubmed: '34817235' title: An ontology for describing and synthesizing ecological observation data year: 2007 repository: https://github.com/NCEAS/oboe reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#$1 oboinowl: contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties download_obo: http://www.geneontology.org/formats/oboInOwl.obo download_owl: http://www.geneontology.org/formats/oboInOwl.owl example: hasDbXref example_extras: - hasBroadSynonym - hasExactSynonym - hasNarrowSynonym homepage: https://github.com/geneontology/go-ontology/tree/master/contrib keywords: - life science - ontology mappings: biocontext: oboInOwl biolink: oboformat fairsharing: FAIRsharing.aa0eat ols: oboinowl name: OBO in OWL pattern: ^\w+$ preferred_prefix: oboInOwl references: - https://github.com/biopragmatics/bioregistry/pull/973 - https://github.com/geneontology/go-site/issues/2157 repository: https://github.com/geneontology/go-ontology synonyms: - oboformat - oio uri_format: http://www.geneontology.org/formats/oboInOwl#$1 obv: description: The Austrian Library Network (OBV) is the largest network of scientific and administrative libraries in Austria with 70 participants, representing more than 90 individual institutions - including the Austrian National Library, university libraries, the colleges of education, individual ministries, numerous technical colleges and other important collections. example: AC00963334 homepage: https://www.obvsg.at/ mappings: bartoc: '20430' miriam: obv name: Austrian Library Network pattern: ^AC[0-9]{8}$ preferred_prefix: obv uri_format: https://permalink.obvsg.at/$1 occ: description: The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law. example: br/1 homepage: https://w3id.org/oc/corpus mappings: miriam: occ n2t: occ name: OpenCitations Corpus pattern: ^[a-z][a-z]/[0-9]+$ preferred_prefix: occ uri_format: https://w3id.org/oc/corpus/$1 occo: contact: email: zhengj2007@gmail.com github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 description: An ontology representing occupations. It is designed to facilitate harmonization of existing occupation standards, such as the US Bureau of Labor Statistics Standard Occupational Classification (US SOC), the International Standard Classification of Occupations (ISCO), the UK National Statistics Standard Occupational Classification (UK SOC), and the European Skills, Competences, Qualifications and Occupations (ESCO) of the European Union. download_owl: http://purl.obolibrary.org/obo/occo.owl example: '00000001' homepage: https://github.com/Occupation-Ontology/OccO keywords: - obo - ontology license: CC-BY-4.0 mappings: aberowl: OCCO bioportal: OCCO obofoundry: occo ontobee: OCCO name: Occupation Ontology pattern: ^\d+$ preferred_prefix: OCCO rdf_uri_format: http://purl.obolibrary.org/obo/OCCO_$1 repository: https://github.com/Occupation-Ontology/OccO uri_format: http://purl.obolibrary.org/obo/OCCO_$1 oci: description: 'Each OCI (Open Citation Identifier) has a simple structure: oci:-, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entity - see https://doi.org/10.6084/m9.figshare.7127816.v2 for additional information. In each OCI, the first is the identifier for the citing bibliographic resource, while the second is the identifier for the cited bibliographic resource.' example: 01027931310-01022252312 homepage: http://opencitations.net mappings: biocontext: OCI miriam: oci n2t: oci name: Open Citation Identifier pattern: ^0[1-9]+0[0-9]+-0[1-9]+0[0-9]+$ preferred_prefix: oci uri_format: https://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/$1/datapackage?links=1 odamexplorer: description: 'ODAM (Open Data for Access and Mining) is an Experimental data table management software (EDTMS) to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines. ODAM allows datasets to be explored and then extracted in whole or in part as needed. For more information/explanation, see ODAM User''s Guide : https://inrae.github.io/ODAM/' example: frim1 homepage: https://eng-bfp.bordeaux-aquitaine.hub.inrae.fr/ mappings: miriam: odam.explorer name: ODAM Data explorer pattern: ^[A-Za-z][A-Za-z0-9]+$ preferred_prefix: odamexplorer uri_format: https://pmb-bordeaux.fr/dataexplorer/?ds=$1 odc.sci: contact: email: jgrethe@ucsd.edu name: Jeffrey Grethe orcid: 0000-0001-5212-7052 description: The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data. example: '602' homepage: https://odc-sci.org keywords: - biomedical science - neurobiology - neurology - neuroscience mappings: fairsharing: FAIRsharing.M6Ruz3 miriam: odc.sci re3data: r3d100014071 name: Open Data Commons for Spinal Cord Injury pattern: ^[0-9]*$ preferred_prefix: odc.sci publications: - doi: 10.1089/neu.2019.6674 pmc: PMC7071068 pubmed: '31608767' title: 'FAIR SCI Ahead: The Evolution of the Open Data Commons for Pre-Clinical Spinal Cord Injury Research' year: 2019 - doi: 10.1016/j.expneurol.2017.05.012 pmc: PMC6448396 pubmed: '28576567' title: Developing a data sharing community for spinal cord injury research year: 2017 - doi: 10.1038/ncomms9581 pmc: PMC4634208 pubmed: '26466022' title: Topological data analysis for discovery in preclinical spinal cord injury and traumatic brain injury year: 2015 - doi: 10.1038/nn.3838 pmc: PMC4728080 pubmed: '25349910' title: 'Big data from small data: data-sharing in the ''long tail'' of neuroscience' year: 2014 - doi: 10.1089/neu.2014.3399 pmc: PMC4186058 pubmed: '25077610' title: Development of a database for translational spinal cord injury research year: 2014 - doi: 10.1371/journal.pone.0059712 pmc: PMC3609747 pubmed: '23544088' title: Derivation of multivariate syndromic outcome metrics for consistent testing across multiple models of cervical spinal cord injury in rats year: 2013 - doi: 10.1007/s12975-011-0121-1 pmc: PMC3236294 pubmed: '22207883' title: 'Syndromics: a bioinformatics approach for neurotrauma research' year: 2011 - doi: S0014-4886(17)30137-1 title: Developing a data sharing community for spinal cord injury research. uri_format: https://odc-sci.org/data/$1 odc.tbi: description: The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data. example: '408' homepage: https://odc-tbi.org mappings: miriam: odc.tbi name: Open Data Commons for Traumatic Brain Injury pattern: ^[0-9]*$ preferred_prefix: odc.tbi uri_format: https://odc-tbi.org/data/$1 odor: description: OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors example: '74' homepage: http://senselab.med.yale.edu/OdorDB mappings: biocontext: ODOR miriam: odor n2t: odor name: Odor Molecules DataBase pattern: ^\d+$ preferred_prefix: odor uri_format: http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5 odrl: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The ODRL Vocabulary and Expression defines a set of concepts and terms (the vocabulary) and encoding mechanism (the expression) for permissions and obligations statements describing digital content usage based on the ODRL Information Model. download_rdf: https://www.w3.org/ns/odrl/2/ODRL22.rdf example: assetConcepts homepage: http://www.w3.org/ns/odrl/2 keywords: - metadata mappings: lov: odrl name: Open Digital Rights Language Ontology preferred_prefix: odrl uri_format: http://www.w3.org/ns/odrl/2/$1 oecd.template: comment: The identifiers have two numbers separated by a dot. The first one corresponds to the template number which can be found on the homepage. The second number referes to the row within the corresponding spreadsheet. contributor: github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The Organisation for Economic Co-operation and Development (OECD) Harmonised Templates (OHTs) are standard data formats for reporting information used for the risk assessment of chemicals, mainly studies done on chemicals to determine their properties or effects on human health and the environment, but also for storing data on use and exposure. example: '74.186' github_request_issue: 997 homepage: https://www.oecd.org/ehs/templates/ name: OECD Harmonised Templates pattern: ^\d+\.\d+$ preferred_prefix: oecd.template references: - https://github.com/biopragmatics/bioregistry/issues/991 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 ogg: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. download_owl: http://purl.obolibrary.org/obo/ogg.owl example: '3000887619' homepage: https://bitbucket.org/hegroup/ogg keywords: - biology - gene - gene name - genome - life science - obo - ontology license: CC-BY-3.0 mappings: aberowl: OGG biocontext: OGG bioportal: OGG fairsharing: FAIRsharing.zmx7nn obofoundry: ogg ols: ogg ontobee: OGG name: The Ontology of Genes and Genomes pattern: ^\d+$ preferred_prefix: OGG rdf_uri_format: http://purl.obolibrary.org/obo/OGG_$1 repository: https://bitbucket.org/hegroup/ogg uri_format: http://purl.obolibrary.org/obo/OGG_$1 version: 1.0.59 ogi: contact: email: linikujp@gmail.com github: linikujp name: Asiyah Yu Lin orcid: 0000-0002-5379-5359 deprecated: true description: "OGI formalized the genomic element by defining an upper class 'genetic\ \ interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous\ \ physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.)\ \ between and including two points (Nucleic Acid Base Residue) on a chromosome\ \ or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated\ \ paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology”\ \ Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary\ \ Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\n\ Yu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI)\ \ to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding\ \ of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam,\ \ Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons\ \ (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology\ \ Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th-\ \ Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n" download_owl: http://purl.obolibrary.org/obo/ogi.owl example: 0000019 homepage: https://code.google.com/archive/p/ontology-for-genetic-interval/ keywords: - obo - ontology mappings: aberowl: OGI biocontext: OGI bioportal: OGI obofoundry: ogi ols: ogi ontobee: OGI name: Ontology for genetic interval pattern: ^\d{7}$ preferred_prefix: OGI rdf_uri_format: http://purl.obolibrary.org/obo/OGI_$1 synonyms: - OGI.owl uri_format: http://purl.obolibrary.org/obo/OGI_$1 version: '2.0' ogms: appears_in: - labo - scdo contact: email: baeverma@jcvi.org github: BAevermann name: Brian Aevermann orcid: 0000-0003-1346-1327 description: 'The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: ''disease'', ''disorder'', ''disease course'', ''diagnosis'', ''patient'', and ''healthcare provider''. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.' download_obo: http://purl.obolibrary.org/obo/ogms.obo download_owl: http://purl.obolibrary.org/obo/ogms.owl example: '0000031' homepage: https://github.com/OGMS/ogms keywords: - biomedical science - cancer - diagnosis - disease - disease phenotype - medicine - obo - ontology license: CC-BY-4.0 logo: https://avatars2.githubusercontent.com/u/12973154?s=200&v=4 mappings: aberowl: OGMS bartoc: '216' biocontext: OGMS bioportal: OGMS fairsharing: FAIRsharing.rvz0m9 obofoundry: ogms ols: ogms ontobee: OGMS name: Ontology for General Medical Science pattern: ^\d{7}$ preferred_prefix: OGMS publications: - pubmed: '25991121' title: Biomarkers in the ontology for general medical science year: 2015 - doi: 10.1186/2041-1480-4-42 pmc: PMC4028878 pubmed: '24314207' title: The neurological disease ontology year: 2013 - pmc: PMC3041577 pubmed: '21347182' title: Toward an ontological treatment of disease and diagnosis year: 2009 rdf_uri_format: http://purl.obolibrary.org/obo/OGMS_$1 repository: https://github.com/OGMS/ogms synonyms: - ogms/OMRE uri_format: http://purl.obolibrary.org/obo/OGMS_$1 version: '2021-08-19' ogsf: contact: email: linikujp@gmail.com github: linikujp name: Asiyah Yu Lin orcid: 0000-0002-5379-5359 deprecated: true description: An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process. download_owl: http://purl.obolibrary.org/obo/ogsf.owl example: '0000025' homepage: https://github.com/linikujp/OGSF keywords: - adverse reaction - biomedical science - disease - epidemiology - genetic disorder - genetics - obo - ontology license: CC-BY-3.0 mappings: aberowl: OGSF biocontext: OGSF bioportal: OGSF fairsharing: FAIRsharing.egv2cz obofoundry: ogsf ols: ogsf ontobee: OGSF name: Ontology of Genetic Susceptibility Factor pattern: ^\d{7}$ preferred_prefix: OGSF publications: - doi: 10.1186/2041-1480-5-19 pmc: PMC4068904 pubmed: '24963371' title: The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events year: 2014 - pubmed: '20847592' title: Ontology driven modeling for the knowledge of genetic susceptibility to disease year: 2009 rdf_uri_format: http://purl.obolibrary.org/obo/OGSF_$1 repository: https://github.com/linikujp/OGSF uri_format: http://purl.obolibrary.org/obo/OGSF_$1 version: '2.0' ohd: contact: email: wdduncan@gmail.com github: wdduncan name: Bill Duncan orcid: 0000-0001-9625-1899 description: The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies. download_owl: http://purl.obolibrary.org/obo/ohd.owl example: '0000006' homepage: https://purl.obolibrary.org/obo/ohd/home keywords: - dentistry - medicine - obo - ontology - oral surgery license: CC-BY-4.0 mappings: aberowl: OHD biocontext: OHD bioportal: OHD fairsharing: FAIRsharing.bg7bb6 obofoundry: ohd ols: ohd ontobee: OHD name: Oral Health and Disease Ontology pattern: ^\d{7}$ preferred_prefix: OHD publications: - doi: 10.1186/s13326-020-00222-0 pmc: PMC7439527 pubmed: '32819435' title: Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology year: 2020 rdf_uri_format: http://purl.obolibrary.org/obo/OHD_$1 repository: https://github.com/oral-health-and-disease-ontologies/ohd-ontology uri_format: http://purl.obolibrary.org/obo/OHD_$1 version: '2024-06-21' ohmi: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions. download_owl: http://purl.obolibrary.org/obo/ohmi.owl example: '0000460' homepage: https://github.com/ohmi-ontology/ohmi keywords: - host - life science - microbiome - obo - ontology license: CC-BY-4.0 mappings: aberowl: OHMI biocontext: OHMI bioportal: OHMI fairsharing: FAIRsharing.cz9cnp obofoundry: ohmi ols: ohmi ontobee: OHMI name: Ontology of Host-Microbiome Interactions pattern: ^\d{7}$ preferred_prefix: OHMI rdf_uri_format: http://purl.obolibrary.org/obo/OHMI_$1 repository: https://github.com/ohmi-ontology/ohmi uri_format: http://purl.obolibrary.org/obo/OHMI_$1 version: '2019-09-17' ohpi: contact: email: edong@umich.edu github: e4ong1031 name: Edison Ong orcid: 0000-0002-5159-414X description: OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration). download_owl: http://purl.obolibrary.org/obo/ohpi.owl example: '9001411' homepage: https://github.com/OHPI/ohpi keywords: - bioinformatics - biomedical science - host - infection - obo - ontology - pathogen license: CC-BY-4.0 mappings: aberowl: OHPI bioportal: OHPI fairsharing: FAIRsharing.vxpUJ6 obofoundry: ohpi ols: ohpi ontobee: OHPI name: Ontology of Host Pathogen Interactions pattern: ^\d+$ preferred_prefix: OHPI publications: - doi: 10.1093/nar/gky999 pmc: PMC6324020 pubmed: '30365026' title: 'Victors: a web-based knowledge base of virulence factors in human and animal pathogens' year: 2019 rdf_uri_format: http://purl.obolibrary.org/obo/OHPI_$1 repository: https://github.com/OHPI/ohpi uri_format: http://purl.obolibrary.org/obo/OHPI_$1 version: '2019-09-30' oid: contributor_extras: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes. example: 2.16.840 example_extras: - '2' - '2.16' - 2.16.840.1 - 2.16.840.1.113883 - 2.16.840.1.113883.6 - 2.16.840.1.113883.6.88 homepage: http://www.oid-info.com/introduction.htm mappings: miriam: oid n2t: oid name: ISO Object Identifier pattern: ^[\d.]+$ preferred_prefix: oid providers: - code: oid_www description: OID w/ WWW homepage: http://www.oid-info.com name: OID w/ WWW uri_format: http://www.oid-info.com/get/$1 - code: orange description: Mirror of OID site from Orange homepage: https://oid-rep.orange-labs.fr name: Mirror of OID site from Orange uri_format: https://oid-rep.orange-labs.fr/get/$1 references: - https://en.wikipedia.org/wiki/Object_identifier uri_format: http://oid-info.com/get/$1 olatdv: contact: email: frederic.bastian@unil.ch github: fbastian name: Frédéric Bastian orcid: 0000-0002-9415-5104 deprecated: true description: Life cycle stages for Medaka download_obo: http://purl.obolibrary.org/obo/olatdv.obo download_owl: http://purl.obolibrary.org/obo/olatdv.owl example: '0000210' homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv keywords: - aquaculture - developmental biology - life cycle stage - life science - obo - ontology license: CC-BY-3.0 mappings: aberowl: OLATDV biocontext: OLATDV bioportal: OLATDV fairsharing: FAIRsharing.c86z66 obofoundry: olatdv ols: olatdv ontobee: OlatDv name: Medaka Developmental Stages pattern: ^\d{7}$ preferred_prefix: OlatDv rdf_uri_format: http://purl.obolibrary.org/obo/OlatDv_$1 repository: https://github.com/obophenotype/developmental-stage-ontologies uri_format: http://purl.obolibrary.org/obo/OlatDv_$1 om: contact: email: hajo.rijgersberg@wur.nl name: Hajo Rijgersberg description: The Ontology of units of Measure (OM) 2.0 models concepts and relations important to scientific research. It has a strong focus on units, quantities, measures, and dimensions. download_owl: http://aber-owl.net/media/ontologies/OM/33/om.owl download_rdf: https://raw.githubusercontent.com/HajoRijgersberg/OM/master/om-2.0.rdf example: Dimension homepage: https://github.com/HajoRijgersberg/OM keywords: - ontology mappings: aberowl: OM agroportal: OM bioportal: OM ols: om ontobee: OM name: Ontology of units of Measure preferred_prefix: om repository: https://github.com/HajoRijgersberg/OM uri_format: http://www.ontology-of-units-of-measure.org/resource/om-2/$1 version: 2.0.58 oma.grp: description: OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs. example: LCSCCPN homepage: https://omabrowser.org/cgi-bin/gateway.pl mappings: biocontext: OMA.GRP miriam: oma.grp n2t: oma.grp name: OMA Group pattern: ^[A-Z]+$ preferred_prefix: oma.grp uri_format: https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1 oma.hog: banana: HOG description: 'Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. ' example: 0459895 homepage: https://omabrowser.org mappings: miriam: oma.hog name: OMA HOGs namespace_in_lui: true pattern: ^[0-9]{7}(\.[0-9a-z.]+)?(_[0-9]+)?$ preferred_prefix: oma.hog uri_format: https://omabrowser.org/oma/hog/HOG:$1 oma.protein: description: OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records. example: HUMAN16963 homepage: https://omabrowser.org/oma/home/ mappings: biocontext: OMA.PROTEIN miriam: oma.protein n2t: oma.protein togoid: OmaProtein name: OMA Protein pattern: ^[A-Z0-9]{5}\d+$ preferred_prefix: oma.protein uri_format: https://omabrowser.org/oma/vps/$1 omia: contact: email: imke.tammen@sydney.edu.au github: ImkeTammen name: Imke Tammen orcid: 0000-0002-5520-6597 contributor_extras: - email: imke.tammen@sydney.edu.au github: ImkeTammen name: Imke Tammen orcid: 0000-0002-5520-6597 description: Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources). The 'omia' prefix is used for phenes, either across species (omia:001000) or in a specific species (omia:001000-9615) example: '001000' example_extras: - 001000-9615 homepage: https://omia.org keywords: - classification - disorders - gene - model organism database - traits mappings: biocontext: OMIA integbio: nbdc00153 miriam: omia n2t: omia prefixcommons: omia name: Online Mendelian Inheritance in Animals pattern: ^\d{6}(-\d+)?$ preferred_prefix: omia providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/omia:$1 publications: - doi: 10.1007/s00335-024-10059-y pubmed: '39143381' title: 'Online Mendelian Inheritance in Animals (OMIA): a genetic resource for vertebrate animals' year: 2024 synonyms: - OMIA uri_format: https://omia.org/phene/omia:$1 omia.variant: contact: email: imke.tammen@sydney.edu.au github: ImkeTammen name: Imke Tammen orcid: 0000-0002-5520-6597 contributor_extras: - email: imke.tammen@sydney.edu.au github: ImkeTammen name: Imke Tammen orcid: 0000-0002-5520-6597 description: Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources). The 'omia.variant' prefix is used for genetic variants associated with phenes listed in OMIA example: '1710' example_extras: - '620' homepage: https://omia.org keywords: - disorders - model organism database - traits mappings: biocontext: OMIA integbio: nbdc00153 name: OMIA variants pattern: ^\d+$ preferred_prefix: omia.variant publications: - doi: 10.1007/s00335-024-10059-y pubmed: '39143381' title: 'Online Mendelian Inheritance in Animals (OMIA): a genetic resource for vertebrate animals' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://omia.org/variant/omia.variant:$1 omiabis: appears_in: - labo contact: email: mbrochhausen@gmail.com name: Mathias Brochhausen orcid: 0000-0003-1834-3856 deprecated: true description: An ontological version of MIABIS (Minimum Information About BIobank data Sharing) download_owl: http://purl.obolibrary.org/obo/omiabis.owl example: 0001079 homepage: https://github.com/OMIABIS/omiabis-dev keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: OMIABIS biocontext: OMIABIS bioportal: OMIABIS obofoundry: omiabis ols: omiabis ontobee: OMIABIS name: Ontologized MIABIS pattern: ^\d{7}$ preferred_prefix: OMIABIS rdf_uri_format: http://purl.obolibrary.org/obo/OMIABIS_$1 repository: https://github.com/OMIABIS/omiabis-dev uri_format: http://purl.obolibrary.org/obo/OMIABIS_$1 version: '2014-05-28' omid: description: Every entity in OpenCitations Meta (https://opencitations.net/meta) is assigned persistent internal identifier called OpenCitations Meta Identifier (OMID). The OMID has structure [[entity_type_abbreviation]]/[[supplier_prefix]][[sequential_number]]. For example, the first journal article ever processed has OMID br/0601 (the full URI is https://w3id.org/oc/meta/br/0601), where br is the abbreviation of bibliographic resource, and 060 corresponds to the supplier prefix, helpful in recognising at a glance the index it belongs to (i.e., OpenCitations Meta). Finally, 1 indicates that this is the index's first bibliographic resource ever minted. example: br/0601 homepage: http://opencitations.net/ mappings: miriam: omid name: OpenCitations Meta Identifier pattern: ^[a-z][a-z]/06[1-9]*0[1-9][0-9]*$ preferred_prefix: omid uri_format: https://w3id.org/oc/meta/$1 omim: contact: email: ahamosh@jhmi.edu github: ahamosh name: Ada Hamosh orcid: 0000-0002-1780-5230 description: Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. example: '603903' homepage: https://omim.org/ keywords: - biomedical science - disease - disease process modeling - gene - gene expression - genetic disorder - genotype - ontology - phenotype license: https://www.omim.org/help/agreement mappings: aberowl: OMIM biocontext: OMIM bioportal: OMIM edam: '1153' fairsharing: FAIRsharing.b084yh go: OMIM hl7: 2.16.840.1.113883.6.174 integbio: nbdc00154 miriam: mim n2t: mim ncbi: MIM prefixcommons: omim uniprot: DB-0062 wikidata: P492 name: Online Mendelian Inheritance in Man pattern: ^\d+$ 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 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/omim:$1 - code: legacy description: This is the actual endpoint for OMIM entries homepage: https://www.omim.org name: OMIM uri_format: https://www.omim.org/entry/$1 - code: miriam_legacy description: Legacy URLs for identifiers.org homepage: http://identifiers.org name: MIRIAM Legacy uri_format: http://identifiers.org/omim/$1 - code: ncbi.omim description: An NCBI endpoint for OMIM entries homepage: http://www.ncbi.nlm.nih.gov/omim name: NCBI uri_format: http://www.ncbi.nlm.nih.gov/omim/$1 - code: purl description: An extra purl that was registred, but probably won't be used. homepage: https://www.omim.org name: OMIM PURL (not in use) uri_format: https://purl.org/mim/MIM:$1 - code: purl2 description: An extra purl that was registred, but probably won't be used. homepage: https://www.omim.org name: OMIM PURL (not in use) uri_format: https://omim.org/OMIM:$1 publications: - doi: 10.1093/nar/gky1151 pubmed: '30445645' - doi: 10.1093/nar/gku1205 pmc: PMC4383985 pubmed: '25428349' title: 'OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders' year: 2014 - doi: 10.1093/nar/gki033 pmc: PMC539987 pubmed: '15608251' title: Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders year: 2005 references: - https://github.com/biopragmatics/bioregistry/issues/497 synonyms: - OMIM - mim uri_format: https://omim.org/MIM:$1 omim.ps: banana: PS contact: email: ahamosh@jhmi.edu github: ahamosh name: Ada Hamosh orcid: 0000-0002-1780-5230 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 description: A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome. example: '214100' homepage: https://www.omim.org/phenotypicSeriesTitles/all license: https://www.omim.org/help/agreement mappings: biolink: OMIM.PS name: OMIM Phenotypic Series part_of: omim pattern: ^\d+$ preferred_prefix: omim.ps providers: - code: legacy description: This is the actual endpoint for OMIM phenotypic series entries homepage: https://www.omim.org name: OMIM uri_format: https://omim.org/phenotypicSeries/PS$1 synonyms: - MIMPS - OMIMPS - PS - mim.ps uri_format: https://omim.org/MIM:PS$1 omit: appears_in: - mco contact: email: huang@southalabama.edu github: Huang-OMIT name: Jingshan Huang orcid: 0000-0003-2408-2883 description: The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). download_obo: https://raw.githubusercontent.com/OmniSearch/omit/master/src/ontology/omit.obo download_owl: http://purl.obolibrary.org/obo/omit.owl example: 0000069 homepage: http://omit.cis.usouthal.edu/ keywords: - annotation - biology - cell - computational biological predictions - gene - gene prediction - life science - micro rna - molecular entity - molecular interaction - obo - ontology - protein - regulation of gene expression license: CC-BY-3.0 mappings: aberowl: OMIT biocontext: OMIT bioportal: OMIT fairsharing: FAIRsharing.mf91p5 miriam: omit n2t: omit obofoundry: omit ols: omit ontobee: OMIT name: Ontology for MicroRNA Target pattern: ^\d{7}$ preferred_prefix: OMIT publications: - doi: 10.1186/s13326-016-0064-2 pmc: PMC4863347 pubmed: '27175225' title: 'OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data' year: 2016 - doi: 10.1371/journal.pone.0100855 pmc: PMC4099014 pubmed: '25025130' title: 'OMIT: dynamic, semi-automated ontology development for the microRNA domain' year: 2014 - doi: 10.1007/s11095-011-0573-8 pubmed: '21879385' title: 'OMIT: a domain-specific knowledge base for microRNA target prediction' year: 2011 rdf_uri_format: http://purl.obolibrary.org/obo/OMIT_$1 repository: https://github.com/OmniSearch/omit synonyms: - OMIT uri_format: http://purl.obolibrary.org/obo/OMIT_$1 version: dev omo: appears_in: - cl - pcl - uberon contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO). download_owl: http://purl.obolibrary.org/obo/omo.owl example: '0003003' homepage: https://github.com/information-artifact-ontology/ontology-metadata keywords: - obo - ontology license: CC0-1.0 mappings: aberowl: OMO bioportal: OMO obofoundry: omo ols: omo ontobee: OMO name: OBO Metadata Ontology pattern: ^\d{7}$ preferred_prefix: OMO rdf_uri_format: http://purl.obolibrary.org/obo/OMO_$1 repository: https://github.com/information-artifact-ontology/ontology-metadata uri_format: http://purl.obolibrary.org/obo/OMO_$1 version: '2024-11-13' omon: contributor: email: oga.t@northeastern.edu github: tomo-oga name: Tomohiro Oga orcid: 0009-0001-6787-3995 description: The new national clinical trials registry of the Netherlands example: '53367' github_request_issue: 1157 homepage: https://onderzoekmetmensen.nl/en logo: https://onderzoekmetmensen.nl/themes/custom/trialregister/logo.svg name: Overview of Medical Research in the Netherlands pattern: ^\d{5}$ preferred_prefix: omon reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://onderzoekmetmensen.nl/en/trial/$1 omop: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - email: nicolas.matentzoglu@gmail.com github: matentzn name: Nicolas Matentzoglu orcid: 0000-0002-7356-1779 description: The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format. example: '1' homepage: https://www.ohdsi.org/data-standardization/the-common-data-model/ name: Observational Medical Outcomes Partnership pattern: ^\d+$ preferred_prefix: omop providers: - code: ohdsi.api description: Programmatic access to OMOP terms homepage: http://api.ohdsi.org name: OHDSI API uri_format: http://api.ohdsi.org/WebAPI/vocabulary/concept/$1 - code: ohdsi.data description: ' https://faircookbook.elixir-europe.org/content/recipes/applied-examples/ehden-ohdsi.html suggests https://data.ohdsi.org/concept/ as another uri expansion but it does not resolve.' homepage: https://data.ohdsi.org/concept name: OHDSI Data Endpoint uri_format: https://data.ohdsi.org/concept/$1 references: - https://github.com/callahantiff/OMOP2OBO - https://github.com/biopragmatics/bioregistry/issues/599 - https://github.com/biopragmatics/bioregistry/pull/600 synonyms: - OMOP uri_format: https://athena.ohdsi.org/search-terms/terms/$1 omp: appears_in: - mco contact: email: jimhu@tamu.edu github: jimhu-tamu name: James C. Hu orcid: 0000-0001-9016-2684 description: An ontology of phenotypes covering microbes download_obo: http://purl.obolibrary.org/obo/omp.obo download_owl: http://purl.obolibrary.org/obo/omp.owl example: '0005067' homepage: http://microbialphenotypes.org keywords: - biology - data mining - microbiology - obo - ontology - phenotype license: CC-BY-3.0 mappings: aberowl: OMP biocontext: OMP bioportal: OMP fairsharing: FAIRsharing.cc3f2x obofoundry: omp ols: omp ontobee: OMP name: Ontology of Microbial Phenotypes pattern: ^\d{7}$ preferred_prefix: OMP publications: - doi: 10.1186/s12866-014-0294-3 pmc: PMC4287307 pubmed: '25433798' title: An ontology for microbial phenotypes year: 2014 rdf_uri_format: http://purl.obolibrary.org/obo/OMP_$1 repository: https://github.com/microbialphenotypes/OMP-ontology uri_format: http://purl.obolibrary.org/obo/OMP_$1 version: '2024-03-25' omrse: appears_in: - labo contact: email: hoganwr@gmail.com github: hoganwr name: Bill Hogan orcid: 0000-0002-9881-1017 description: The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations. download_json: http://purl.obolibrary.org/obo/omrse.json download_obo: https://github.com/ufbmi/OMRSE/raw/master/omrse-full.obo download_owl: http://purl.obolibrary.org/obo/omrse.owl example: '00000022' homepage: https://github.com/mcwdsi/OMRSE/wiki/OMRSE-Overview keywords: - biomedical science - demographics - health science - hospital - obo - ontology - patient care - social science license: CC-BY-4.0 mappings: aberowl: OMRSE biocontext: OMRSE bioportal: OMRSE fairsharing: FAIRsharing.z0p37e obofoundry: omrse ols: omrse ontobee: OMRSE name: Ontology for Modeling and Representation of Social Entities pattern: ^\d{8}$ preferred_prefix: OMRSE publications: - doi: 10.1186/s13326-016-0087-8 pmc: PMC4942889 pubmed: '27406187' title: 'The ontology of medically related social entities: recent developments' year: 2016 rdf_uri_format: http://purl.obolibrary.org/obo/OMRSE_$1 repository: https://github.com/mcwdsi/OMRSE uri_format: http://purl.obolibrary.org/obo/OMRSE_$1 version: '2024-11-25' omx.dataset: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: OncoMX is a knowledgebase for exploring cancer biomarkers in the context of related cancer and healthy data. This resource is for datasets within OncoMX. example: 000059 homepage: https://data.oncomx.org name: OncoMX Dataset pattern: ^\d+$ preferred_prefix: omx.dataset uri_format: https://data.oncomx.org/OMX_$1 oncotree: appears_in: - efo contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research. example: BLL homepage: http://oncotree.mskcc.org keywords: - cancer - clinical decision support systems - oncology name: OncoTree preferred_prefix: oncotree uri_format: http://oncotree.mskcc.org/api/tumorTypes/search/code/$1 one: contact: email: chenyangnutrition@gmail.com github: cyang0128 name: Chen Yang orcid: 0000-0001-9202-5309 depends_on: - foodon - obi - ons description: An ontology to standardize research output of nutritional epidemiologic studies. download_owl: http://purl.obolibrary.org/obo/one.owl example: '0001021' homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies keywords: - diet - epidemiology - metabolomics - nutritional science - obo - ontology license: CC-BY-4.0 mappings: aberowl: ONE bioportal: ONE fairsharing: FAIRsharing.USxx0K obofoundry: one ols: one ontobee: ONE name: Ontology for Nutritional Epidemiology pattern: ^\d{7}$ preferred_prefix: ONE publications: - doi: 10.3390/nu11061300 pmc: PMC6628051 pubmed: '31181762' title: 'An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content' year: 2019 rdf_uri_format: http://purl.obolibrary.org/obo/ONE_$1 repository: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies uri_format: http://purl.obolibrary.org/obo/ONE_$1 ons: appears_in: - one contact: email: francesco.vitali@ibba.cnr.it github: FrancescoVit name: Francesco Vitali orcid: 0000-0001-9125-4337 depends_on: - bfo - chebi - envo - foodon - ncbitaxon - obi - ro - uberon description: An ontology for description of concepts in the nutritional studies domain. download_owl: http://purl.obolibrary.org/obo/ons.owl example: '0000060' homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies keywords: - biomedical science - nutritional science - obo - ontology license: CC-BY-4.0 mappings: aberowl: ONS agroportal: ONS bioportal: ONS fairsharing: FAIRsharing.rfec93 obofoundry: ons ols: ons ontobee: ONS name: Ontology for Nutritional Studies pattern: ^\d{7}$ preferred_prefix: ONS publications: - doi: 10.1186/s12263-018-0601-y pmc: PMC5928560 pubmed: '29736190' title: 'ONS: an ontology for a standardized description of interventions and observational studies in nutrition' year: 2018 rdf_uri_format: http://purl.obolibrary.org/obo/ONS_$1 repository: https://github.com/enpadasi/Ontology-for-Nutritional-Studies uri_format: http://purl.obolibrary.org/obo/ONS_$1 version: '2024-07-03' ontie: contact: email: bpeters@lji.org github: bpeters42 name: Bjoern Peters orcid: 0000-0002-8457-6693 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Ontology of Immune Epitopes (ONTIE) is an effort to represent terms in the immunology domain in a formal ontology with the specific goal of representing experiments that identify and characterize immune epitopes. download_owl: https://raw.githubusercontent.com/IEDB/ONTIE/master/ontie.owl example: '0000001' homepage: https://ontology.iedb.org/ keywords: - immunology - infection - life science - major histocompatibility complex - ontology mappings: fairsharing: FAIRsharing.kx2md1 name: Ontology for Immune Epitopes pattern: ^\d{7}$ preferred_prefix: ontie repository: https://github.com/IEDB/ONTIE uri_format: https://ontology.iedb.org/ontology/ONTIE_$1 ontoavida: contact: email: fortuna@ebd.csic.es github: miguelfortuna name: Miguel A. Fortuna orcid: 0000-0002-8374-1941 depends_on: - fbcv - gsso - ncit - ro - stato description: 'The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of the most widely used computational approach for performing experimental evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment). The lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight. OntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA). More information can be found at https://obofoundry.org/ontology/ontoavida.html' download_obo: http://purl.obolibrary.org/obo/ontoavida.obo download_owl: http://purl.obolibrary.org/obo/ontoavida.owl example: '00000001' homepage: https://gitlab.com/fortunalab/ontoavida keywords: - obo - ontology license: CC-BY-4.0 mappings: aberowl: ONTOAVIDA bioportal: ONTOAVIDA obofoundry: ontoavida ols: ontoavida ontobee: ONTOAVIDA name: Ontology for Avida digital evolution platform pattern: ^\d{8}$ preferred_prefix: ONTOAVIDA publications: - doi: 10.1038/s41597-023-02514-3 title: Ontology for the Avida digital evolution platform rdf_uri_format: http://purl.obolibrary.org/obo/ONTOAVIDA_$1 repository: https://gitlab.com/fortunalab/ontoavida uri_format: http://purl.obolibrary.org/obo/ONTOAVIDA_$1 version: '2022-03-15' ontoneo: contact: email: fernanda.farinelli@gmail.com github: FernandaFarinelli name: Fernanda Farinelli orcid: 0000-0003-2338-8872 description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby. download_owl: http://purl.obolibrary.org/obo/ontoneo.owl example: 00000098 homepage: http://ontoneo.com keywords: - electronic health record - obo - obstetrics - ontology license: CC-BY-3.0 mappings: aberowl: ONTONEO biocontext: ONTONEO bioportal: ONTONEO fairsharing: FAIRsharing.5a4y1y obofoundry: ontoneo ols: ontoneo ontobee: ONTONEO name: Obstetric and Neonatal Ontology pattern: ^\d{8}$ preferred_prefix: ONTONEO publications: - doi: 10.1002/asi.23900 title: 'Ontologies for the representation of electronic medical records: The obstetric and neonatal ontology' year: 2017 rdf_uri_format: http://purl.obolibrary.org/obo/ONTONEO_$1 repository: https://github.com/ontoneo-project/Ontoneo uri_format: http://purl.obolibrary.org/obo/ONTONEO_$1 version: '2021-04-29' ontorxn: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: OntoRXN is an ontology for the description of reaction networks as undirected graphs characterized by energies. download_owl: https://gitlab.com/dgarayr/ontorxn/-/raw/prod/OntoRXN.owl example: hasCalculation github_request_issue: 1311 homepage: https://gitlab.com/dgarayr/ontorxn keywords: - ontology license: CC-BY-4.0 name: OntoRXN preferred_prefix: ontorxn publications: - doi: 10.1186/s13321-022-00610-x pmc: PMC9153116 pubmed: '35637523' title: 'Chemical reaction network knowledge graphs: the OntoRXN ontology' year: 2022 oostt: contact: email: mbrochhausen@gmail.com github: mbrochhausen name: Mathias Brochhausen orcid: 0000-0003-1834-3856 description: The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2). download_owl: http://purl.obolibrary.org/obo/oostt.owl example: 00000099 homepage: https://github.com/OOSTT/OOSTT keywords: - obo - ontology - traumatology license: CC-BY-4.0 mappings: aberowl: OOSTT biocontext: OOSTT bioportal: OOSTT fairsharing: FAIRsharing.b4sa0w obofoundry: oostt ols: oostt ontobee: OOSTT name: Ontology of Organizational Structures of Trauma centers and Trauma systems pattern: ^\d{8}$ preferred_prefix: OOSTT rdf_uri_format: http://purl.obolibrary.org/obo/OOSTT_$1 repository: https://github.com/OOSTT/OOSTT uri_format: http://purl.obolibrary.org/obo/OOSTT_$1 version: '2025-01-24' opb: banana: OPB banana_peel: _ contact: email: maxneal@gmail.com name: Maxwell L. Neal orcid: 0000-0002-2390-6572 contributor_extras: - email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms. download_owl: http://aber-owl.net/media/ontologies/OPB/13/opb.owl example: '00573' homepage: http://bioportal.bioontology.org/ontologies/OPB keywords: - concentration - kinetic model - life science - mathematical model - ontology - physics - structure mappings: aberowl: OPB biocontext: OPB bioportal: OPB fairsharing: FAIRsharing.qcceez miriam: opb n2t: opb prefixcommons: opb name: Ontology of Physics for Biology pattern: ^\d+$ preferred_prefix: opb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/opb:$1 publications: - doi: 10.1186/2041-1480-4-41 pmc: PMC3904761 pubmed: '24295137' title: 'Ontology of physics for biology: representing physical dependencies as a basis for biological processes' year: 2013 - doi: 10.1371/journal.pone.0028708 pmc: PMC3246444 pubmed: '22216106' title: 'Physical properties of biological entities: an introduction to the ontology of physics for biology' year: 2011 uri_format: https://bioportal.bioontology.org/ontologies/OPB/?p=classes&conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1 openalex: contact: email: hpiwowar@gmail.com github: hpiwowar name: Heather Piwowar orcid: 0000-0003-1613-5981 contributor: github: dhimmel name: Daniel Himmelstein orcid: 0000-0002-3012-7446 description: OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other. example: W2741809807 github_request_issue: 280 homepage: https://openalex.org/ keywords: - knowledge graph - wikidata name: OpenAlex pattern: ^[WAICV]\d{2,}$ preferred_prefix: openalex reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://openalex.org/$1 openwemi: contact: email: kcoyle@kcoyle.net github: kcoyle name: Karen Coyle orcid: 0000-0002-1085-7089 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: openWEMI is a minimally constrained vocabulary for describing created resources using the concepts of Work, Expression, Manifestation, Item. example: Endeavor homepage: https://dcmi.github.io/openwemi/ license: CC0-1.0 name: openWEMI Vocabulary pattern: ^\w+$ preferred_prefix: openwemi references: - https://journal.code4lib.org/articles/16491 - http://archive.ifla.org/VII/s13/frbr/frbr_2008.pdf repository: https://github.com/dcmi/openwemi uri_format: https://dcmi.github.io/openwemi/ns#$1 opl: banana: OPL contact: email: zhengj2007@gmail.com github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 description: The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. download_owl: http://purl.obolibrary.org/obo/opl.owl example: 0000319 homepage: https://github.com/OPL-ontology/OPL keywords: - anatomy - developmental biology - host - life cycle - life cycle stage - life science - obo - ontology - parasite license: CC-BY-4.0 mappings: aberowl: OPL biocontext: OPL bioportal: OPL fairsharing: FAIRsharing.ez2nhb miriam: opl obofoundry: opl ols: opl ontobee: OPL name: Ontology for Parasite LifeCycle namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: OPL publications: - doi: 10.1186/2041-1480-3-5 pmc: PMC3488002 pubmed: '22621763' title: 'The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms' year: 2012 rdf_uri_format: http://purl.obolibrary.org/obo/OPL_$1 repository: https://github.com/OPL-ontology/OPL uri_format: http://purl.obolibrary.org/obo/OPL_$1 version: '2023-08-28' opm: description: The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization. example: 1h68 homepage: http://opm.phar.umich.edu/ keywords: - computer science - data management mappings: biocontext: OPM fairsharing: FAIRsharing.7c683b miriam: opm n2t: opm name: Orientations of Proteins in Membranes Database pattern: ^[0-9][A-Za-z0-9]{3}$ preferred_prefix: opm uri_format: http://opm.phar.umich.edu/protein.php?pdbid=$1 opmi: appears_in: - labo - scdo contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles. download_owl: http://purl.obolibrary.org/obo/opmi.owl example: '0000101' homepage: https://github.com/OPMI/opmi keywords: - clinical studies - disease - obo - omics - ontology license: CC-BY-4.0 mappings: aberowl: OPMI bioportal: OPMI fairsharing: FAIRsharing.d2d84f obofoundry: opmi ols: opmi ontobee: OPMI name: Ontology of Precision Medicine and Investigation pattern: ^\d{7}$ preferred_prefix: OPMI rdf_uri_format: http://purl.obolibrary.org/obo/OPMI_$1 repository: https://github.com/OPMI/opmi uri_format: http://purl.obolibrary.org/obo/OPMI_$1 version: 1.0.166 orangebook: comment: The web pages on the digital edition can be constructed with some programmatic logic, but not directly contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The first number is the chapter then the remainder are subsections. example: 10.2.1.1.3 github_request_issue: 1311 homepage: https://media.iupac.org/publications/analytical_compendium/ name: IUPAC Compendium of Analytical Nomenclature (Orange Book) preferred_prefix: orangebook references: - https://iupac.org/what-we-do/books/orangebook/ orcid: contact: email: w.simpson@orcid.org github: wjrsimpson name: Will Simpson orcid: 0000-0003-4654-1403 description: ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities. example: 0000-0003-4423-4370 homepage: https://orcid.org keywords: - person - subject agnostic mappings: bartoc: '2021' biocontext: ORCID biolink: ORCID fairsharing: FAIRsharing.nx58jg go: orcid miriam: orcid n2t: orcid wikidata: P496 mastodon: ORCID_Org@scicomm.xyz name: Open Researcher and Contributor pattern: ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$ preferred_prefix: orcid providers: - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/orcid/$1 publications: - doi: 10.23640/07243.16687207.v1 title: 'From Vision to Value: ORCID''s 2022–2025 Strategic Plan' year: 2021 - doi: 10.23640/07243.12009255.v3 title: ORCID's 2025 Vision year: 2020 rdf_uri_format: https://orcid.org/$1 repository: https://github.com/ORCID synonyms: - ORCID - ORCiD twitter: ORCID_Org uri_format: https://orcid.org/$1 ordb: description: The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs). example: '8497' homepage: http://senselab.med.yale.edu/OrDB/ keywords: - gene - life science - protein mappings: biocontext: ORDB fairsharing: FAIRsharing.6375zh miriam: ordb n2t: ordb pathguide: '65' prefixcommons: ordb name: Olfactory Receptor Database pattern: ^\d+$ preferred_prefix: ordb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ordb:$1 publications: - doi: 10.1093/database/baw132 pmc: PMC5045865 pubmed: '27694208' title: ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions year: 2016 - doi: 10.1093/nar/30.1.354 pmc: PMC99065 pubmed: '11752336' title: 'Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences' year: 2002 - doi: 10.1093/nar/28.1.341 pmc: PMC102443 pubmed: '10592268' title: 'Olfactory receptor database: a sensory chemoreceptor resource' year: 2000 uri_format: http://senselab.med.yale.edu/ORDB/Data/$1 oridb.sacch: description: OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae. example: '1' homepage: http://cerevisiae.oridb.org/index.php mappings: biocontext: ORIDB.SACCH miriam: oridb.sacch n2t: oridb.sacch name: OriDB Saccharomyces pattern: ^\d+$ preferred_prefix: oridb.sacch uri_format: http://cerevisiae.oridb.org/details.php?id=$1 oridb.schizo: description: OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe. example: '1' homepage: http://pombe.oridb.org/index.php mappings: biocontext: ORIDB.SCHIZO miriam: oridb.schizo n2t: oridb.schizo name: OriDB Schizosaccharomyces pattern: ^\d+$ preferred_prefix: oridb.schizo uri_format: http://pombe.oridb.org/details.php?id=$1 ornaseq: contact: email: safisher@upenn.edu github: safisher name: Stephen Fisher orcid: 0000-0001-8034-7685 description: An application ontology designed to annotate next-generation sequencing experiments performed on RNA. download_obo: http://purl.obolibrary.org/obo/ornaseq.obo download_owl: http://purl.obolibrary.org/obo/ornaseq.owl example: '0000010' homepage: http://kim.bio.upenn.edu/software/ornaseq.shtml keywords: - obo - ontology - rna sequencing - single cell - single cell rna-seq - transcriptomics license: CC-BY-4.0 mappings: aberowl: ORNASEQ bioportal: ORNASEQ fairsharing: FAIRsharing.e6f303 obofoundry: ornaseq ols: ornaseq ontobee: ORNASEQ name: Ontology of RNA Sequencing pattern: ^\d{7}$ preferred_prefix: ORNASEQ rdf_uri_format: http://purl.obolibrary.org/obo/ORNASEQ_$1 repository: https://github.com/safisher/ornaseq uri_format: http://purl.obolibrary.org/obo/ORNASEQ_$1 version: '2019-07-08' orphanet: contact: email: bliemsl@xs4all.nl name: Spencer L. Liem orcid: 0000-0002-1575-9365 description: Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases. download_owl: http://www.orphadata.org/data/ORDO/ordo_orphanet.owl example: '85163' homepage: http://www.orpha.net/consor/ keywords: - disease - drug - human - life science - ontology - ontology and terminology license: CC-BY-4.0 mappings: biocontext: Orphanet biolink: orphanet fairsharing: FAIRsharing.6bd5k6 integbio: nbdc01422 miriam: orphanet n2t: orphanet prefixcommons: orphanet uniprot: DB-0068 wikidata: P1550 name: Orphanet pattern: ^\d+$ 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 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/orphanet:$1 publications: - pubmed: '19058507' title: '[Orphanet and the Dutch Steering Committee Orphan Drugs. A European and Dutch databank of information on rare diseases]' year: 2008 synonyms: - ORPHA twitter: orphanet uri_format: http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1 orphanet.ordo: banana: Orphanet banana_peel: _ contact: email: ordo.orphanet@inserm.fr name: Ana Rath orcid: 0000-0003-4308-6337 description: 'The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).' download_owl: http://www.orphadata.org/data/ORDO/ordo_orphanet.owl example: C023 example_extras: - '478' homepage: https://www.ebi.ac.uk/ols4/ontologies/ordo keywords: - biomedical science - diagnosis - disease - gene - health science - ontology - phenotype - rare disease license: CC-BY-4.0 mappings: aberowl: ordo biocontext: ORPHANET.ORDO biolink: ORPHA bioportal: ORDO cellosaurus: ORDO fairsharing: FAIRsharing.pbbnwa miriam: orphanet.ordo n2t: orphanet.ordo ols: ordo name: Orphanet Rare Disease Ontology pattern: ^C?\d+$ preferred_prefix: orphanet.ordo providers: - code: legacy description: This link is no longer live homepage: https://www.orpha.net name: Legacy Orphanet Expert uri_format: https://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=en&Expert=$1 publications: - pubmed: '22874158' title: 'Rare diseases knowledge management: the contribution of proximity measurements in OntoOrpha and OMIM' year: 2012 synonyms: - ordo uri_format: http://www.orpha.net/ORDO/Orphanet_$1 version: '4.6' orth: contact: email: jfernand@um.es github: jesualdotomasfernandezbreis name: Jesualdo Tomás Fernández-Breis orcid: 0000-0002-7558-2880 description: 'The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way.' download_owl: https://github.com/qfo/OrthologyOntology/raw/master/orthOntology_RC_v2_A.owl example: HomologyRelation homepage: https://github.com/qfo/OrthologyOntology keywords: - comparative genomics - gene - homologous - ontology - orthologous - paralogous - protein - sequence mappings: aberowl: ORTH bioportal: ORTH fairsharing: FAIRsharing.4877h0 ols: orth name: Orthology Ontology preferred_prefix: orth publications: - doi: 10.1186/s13326-016-0077-x pmc: PMC4893294 pubmed: '27259657' title: 'The Orthology Ontology: development and applications' year: 2016 repository: https://github.com/qfo/OrthologyOntology uri_format: http://purl.org/net/orth#$1 version: '2.0' orthodb: contact: email: evgeny.zdobnov@unige.ch name: Evgeny M Zdobnov orcid: 0000-0002-5178-1498 description: OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups example: Q9P0K8 homepage: https://www.orthodb.org keywords: - dna - eukaryotic - life science - protein mappings: biocontext: ORTHODB fairsharing: FAIRsharing.x989d5 miriam: orthodb n2t: orthodb prefixcommons: orthodb uniprot: DB-0143 name: OrthoDB pattern: ^\w+$ preferred_prefix: orthodb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/orthodb:$1 provides: uniprot publications: - doi: 10.1093/nar/gky1053 pmc: PMC6323947 pubmed: '30395283' title: 'OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs' year: 2019 - doi: 10.1093/nar/gku1220 pmc: PMC4383991 pubmed: '25428351' title: 'OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software' year: 2014 - doi: 10.1093/nar/gkq930 pmc: PMC3013786 pubmed: '20972218' title: 'OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011' year: 2010 uri_format: http://cegg.unige.ch/orthodb/results?searchtext=$1 oryzabase.gene: description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information. example: '117' homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ mappings: biocontext: ORYZABASE.GENE miriam: oryzabase.gene n2t: oryzabase.gene name: Oryzabase Gene pattern: ^\d+$ preferred_prefix: oryzabase.gene uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1 oryzabase.mutant: description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information. example: '21393' homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ mappings: biocontext: ORYZABASE.MUTANT miriam: oryzabase.mutant n2t: oryzabase.mutant name: Oryzabase Mutant pattern: ^\d+$ preferred_prefix: oryzabase.mutant uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1 oryzabase.reference: description: The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan. example: '42840' homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ mappings: miriam: oryzabase.reference n2t: oryzabase.reference name: Oryzabase Reference pattern: ^\d+$ preferred_prefix: oryzabase.reference uri_format: https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1 oryzabase.stage: description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information. example: '34' homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ mappings: biocontext: ORYZABASE.STAGE miriam: oryzabase.stage n2t: oryzabase.stage name: Oryzabase Stage pattern: ^\d+$ preferred_prefix: oryzabase.stage uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1 oryzabase.strain: description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information. example: '1' homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ mappings: biocontext: ORYZABASE.STRAIN miriam: oryzabase.strain n2t: oryzabase.strain name: Oryzabase Strain pattern: ^\d+$ preferred_prefix: oryzabase.strain uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1 osf: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: ID in osf.io example: 2u4tf homepage: https://osf.io keywords: - author - paper - person - researcher - work mappings: wikidata: P7238 name: Open Science Framework ID pattern: ^[a-z0-9]{5}$ preferred_prefix: osf references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://osf.io/$1 oslc: contact: email: jamsden@us.ibm.com name: Jim Amsden contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains. example: Property homepage: http://open-services.net/ns/core keywords: - plm mappings: lov: oslc name: OASIS Open Services for Lifecycle Collaboration Core Vocabulary preferred_prefix: oslc uri_format: http://open-services.net/ns/core#$1 osti.article: comment: Corresponding GitHub linked to software registrations is located at https://github.com/doecode. All related contact information can be found here https://www.osti.gov/contact contributor: email: Lindsey.Anderson@pnnl.gov github: lnanderson name: Lindsey Anderson orcid: 0000-0002-8741-7823 description: 'The U.S. Department of Energy (DOE) Office of Scientific and Technical Information (OSTI) is the main metadata archive for permanent storage of registered [DOE DOI products](https://www.osti.gov/pids/doi-services/doe-data-id-service) (datasets, code, articles, patents, multimedia, etc.). When a DOI is minted a unique OSTI identifier for each record [{osti_id}](https://www.osti.gov/api/v1/docs#endpoints-singlerecord) is provided as the suffix in the DOI schema ([{site-specific-prefix}/{user-supplied-doi-infix}/{osti_id}](https://www.osti.gov/pids/doi-services)) and can be alternatively used as the main product identifier endpoint when [searching OSTI.GOV](https://www.osti.gov/search-tools) registry archive (see example below). OSTI.GOV is the primary registry and search tool for all Department of Energy (DOE) funded science, technology, and engineering research and development (R&D) results and the organizational hub for information about the DOE Office of Scientific and Technical Information (OSTI. **Data Product Type Example:** - https://www.osti.gov/biblio/1668761 - https://www.osti.gov/search/semantic:1668761 - https://www.osti.gov/dataexplorer/biblio/dataset/1668761 - https://www.osti.gov/api/v1/records/1668761 - https://doi.org/10.11578/1668761 **Other Core Product Registry Examples:** - Journal Articles: https://www.osti.gov/pages/biblio - Datasets: https://www.osti.gov/dataexplorer/biblio/dataset/ - Software: https://www.osti.gov/doecode/biblio/ - Patents: https://www.osti.gov/doepatents/biblio/ - Multimedia: https://www.osti.gov/sciencecinema/biblio/' example: '1668761' github_request_issue: 1050 homepage: https://www.osti.gov/ keywords: - article - articles - publication - publications license: https://www.osti.gov/disclaim mappings: wikidata: P3894 name: Office of Scientific and Technical Information (OSTI) pattern: ^\d+$ preferred_prefix: osti.article references: - https://www.energy.gov/doe-public-access-plan reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.osti.gov/biblio/$1 otl: contact: email: guiderdoni@cirad.fr name: Emmanuel Guiderdoni orcid: 0000-0003-2760-2864 description: Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information. example: AADB12 homepage: http://oryzatagline.cirad.fr/ keywords: - dna - life science mappings: biocontext: OTL fairsharing: FAIRsharing.61c2x6 miriam: otl n2t: otl prefixcommons: otl name: Oryza Tag Line pattern: ^A[A-Z]+\d+$ preferred_prefix: otl providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/otl:$1 publications: - doi: 10.1093/nar/gkm762 pmc: PMC2238859 pubmed: '17947330' title: Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library year: 2007 - doi: '17947330' title: Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. uri_format: http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1 otol: contributor: email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 description: Identifier for an entity in open tree of life example: '3905431' github_request_issue: 470 homepage: https://tree.opentreeoflife.org mappings: wikidata: P9157 name: Open Tree of Life pattern: ^[1-9]\d*$ preferred_prefix: otol reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://tree.opentreeoflife.org/taxonomy/browse?id=$1 ovae: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqunh He orcid: 0000-0001-9189-9661 description: OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). download_owl: http://purl.obolibrary.org/obo/ovae.owl example: 0000609 homepage: http://www.violinet.org/ovae/ keywords: - adverse reaction - biomedical science - obo - ontology - vaccine license: CC-BY-3.0 mappings: aberowl: OVAE biocontext: OVAE bioportal: OVAE fairsharing: FAIRsharing.w4x6n4 obofoundry: ovae ols: ovae ontobee: OVAE name: Ontology of Vaccine Adverse Events pattern: ^\d{7}$ preferred_prefix: OVAE publications: - doi: 10.1186/2041-1480-4-40 pmc: PMC4177204 pubmed: '24279920' title: The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines year: 2013 rdf_uri_format: http://purl.obolibrary.org/obo/OVAE_$1 repository: https://github.com/OVAE-Ontology/ovae uri_format: http://purl.obolibrary.org/obo/OVAE_$1 version: 1.0.34 owl: contact: email: rmrich5@gmail.com name: Rafael Richards orcid: 0000-0001-5699-0515 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. ' download_owl: https://triplydb.com/w3c/owl/download.trig.gz example: Ontology homepage: https://www.w3.org/TR/owl-features/ keywords: - computer science - informatics - ontology - ontology and terminology - subject agnostic - w3c rec mappings: biocontext: owl fairsharing: FAIRsharing.atygwy integbio: nbdc00307 lov: owl ols: owl zazuko: owl name: Web Ontology Language preferred_prefix: owl uri_format: http://www.w3.org/2002/07/owl#$1 version: '$Date: 2009/11/15 10:54:12 $' owlstar: contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This proposed vocabulary allows edges in Property Graphs (e.g Neo4j, RDF*) to be augmented with edge properties that specify ontological semantics, including (but not limited) to OWL-DL interpretations. [from GitHub] download_rdf: https://github.com/linkml/owlstar/raw/master/owlstar.ttl example: AllSomeInterpretation homepage: https://linkml.io/owlstar/ license: CC0-1.0 mappings: biolink: os name: Ontological Interpretations for Web Property Graphs pattern: ^\w+$ preferred_prefix: owlstar repository: https://github.com/linkml/owlstar uri_format: http://w3id.org/owlstar/$1 p3db.protein: description: Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites. example: '70' homepage: http://www.p3db.org/ keywords: - protein - small molecule mappings: biocontext: P3DB.PROTEIN miriam: p3db.protein n2t: p3db.protein prefixcommons: p3db name: P3DB Protein pattern: ^\d+$ preferred_prefix: p3db.protein providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/p3db:$1 uri_format: http://www.p3db.org/protein.php?id=$1&ref=0 p3db.site: description: Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins. example: '65' homepage: http://www.p3db.org/ mappings: biocontext: P3DB.SITE miriam: p3db.site n2t: p3db.site name: P3DB Site pattern: ^\d+$ preferred_prefix: p3db.site uri_format: http://www.p3db.org/phosphosite.php?id=$1&ref=0 packagist: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A repository of software packages written in PHP. example: florianv/swap homepage: https://packagist.org name: Packagist preferred_prefix: packagist uri_format: https://packagist.org/packages/$1 pactr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Pan African Clinical Trials Registry (PACTR) is a regional register of clinical trials conducted in Africa. The registry is an African initiative serving the needs of Africans. It provides an open-access platform where clinical trials can be registered free of charge. The PACTR aims to increase clinical trial registration in Africa by developing awareness of the need to register trials and supporting trialists during registration. (from homepage) example: PACTR202304525632216 homepage: https://pactr.samrc.ac.za/ logo: https://pactr.samrc.ac.za/images/Banner_Split.jpg name: Pan African Clinical Trials Registry pattern: ^PACTR\d+$ preferred_prefix: pactr references: - https://pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=25488 paleodb: description: The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data. example: '83088' homepage: http://paleodb.org/ keywords: - taxonomy mappings: biocontext: PALEODB miriam: paleodb n2t: paleodb prefixcommons: paleodb name: Paleobiology Database pattern: ^\d+$ preferred_prefix: paleodb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/paleodb:$1 uri_format: http://fossilworks.org/?a=taxonInfo&taxon_no=$1 pandit: description: PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. example: PF00004 homepage: http://www.ebi.ac.uk/goldman-srv/pandit keywords: - dna - protein - structure mappings: integbio: nbdc00607 prefixcommons: pandit re3data: r3d100011232 name: Protein and Associated NucleotideDomains with Inferred Trees preferred_prefix: pandit providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pandit:$1 provides: pfam reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam=$1 panorama: contact: email: brendanx@uw.edu name: Brendan MacLean orcid: 0000-0002-9575-0255 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow. It makes links to the Proteomics Exchange when possible. example: FxnI151FMs homepage: https://panoramaweb.org keywords: - life science - metabolomics - proteomics mappings: fairsharing: FAIRsharing.uBpQ1q name: Panorama Public preferred_prefix: panorama publications: - doi: 10.1074/mcp.ra117.000543 pmc: PMC5986241 pubmed: '29487113' title: 'Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline' year: 2018 - doi: 10.1021/pr5006636 pmc: PMC4156235 pubmed: '25102069' title: 'Panorama: a targeted proteomics knowledge base' year: 2014 - doi: 10.1074/mcp.RA117.000543 title: 'Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline.' uri_format: https://panoramaweb.org/$1.url panther.family: contact: email: pdthomas@usc.edu name: Paul D Thomas orcid: 0000-0002-9074-3507 description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families. example: PTHR12345 homepage: http://www.pantherdb.org/ keywords: - classification - gene - ontology - pathway - protein mappings: biocontext: PANTHER.FAMILY biolink: PANTHER.FAMILY go: PANTHER miriam: panther.family n2t: panther.family prefixcommons: panther uniprot: DB-0069 name: PANTHER Family part_of: panther pattern: ^PTHR\d{5}(\:SF\d{1,3})?$ preferred_prefix: panther.family providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/panther:$1 publications: - doi: 10.1093/nar/gky1038 pmc: PMC6323939 pubmed: '30407594' title: 'PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools' year: 2019 - doi: 10.1101/gr.772403 pmc: PMC403709 pubmed: '12952881' title: 'PANTHER: a library of protein families and subfamilies indexed by function' year: 2003 uri_format: http://www.pantherdb.org/panther/family.do?clsAccession=$1 panther.node: description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes. example: PTN000000026 homepage: http://pantree.org/ mappings: biocontext: PANTHER.NODE miriam: panther.node n2t: panther.node name: PANTHER Node part_of: panther pattern: ^PTN\d{9}$ preferred_prefix: panther.node uri_format: http://www.pantree.org/node/annotationNode.jsp?id=$1 panther.pathway: description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components. example: P00024 homepage: http://www.pantherdb.org/ mappings: biocontext: PANTHER.PATHWAY edam: '1161' miriam: panther.pathway n2t: panther.pathway name: PANTHER Pathway part_of: panther pattern: ^P\d{5}$ preferred_prefix: panther.pathway uri_format: http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1 panther.pthcmp: description: 'The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway components may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation.' example: P00266 homepage: http://www.pantherdb.org/ mappings: biocontext: PANTHER.PTHCMP miriam: panther.pthcmp n2t: panther.pthcmp name: PANTHER Pathway Component part_of: panther pattern: ^(G|P|U|C|S)\d{5}$ preferred_prefix: panther.pthcmp uri_format: http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1 pao: contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp name: Pankaj Jaiswal orcid: 0000-0002-1005-8383 deprecated: true homepage: http://www.plantontology.org keywords: - obo - ontology mappings: biocontext: PAO obofoundry: pao name: Plant Anatomy Ontology preferred_prefix: PAO rdf_uri_format: http://purl.obolibrary.org/obo/PAO_$1 uri_format: http://purl.obolibrary.org/obo/PAO_$1 pass2: deprecated: true description: The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity. example: '46977' homepage: http://caps.ncbs.res.in/pass2 keywords: - classification - dna - genome - structure mappings: biocontext: PASS2 integbio: nbdc02108 miriam: pass2 n2t: pass2 prefixcommons: pass2 name: Protein Alignment organised as Structural Superfamily pattern: ^\d+$ preferred_prefix: pass2 providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pass2:$1 uri_format: http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1 pathbank: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. example: SMP0000219 homepage: https://pathbank.org keywords: - animal genetics - bioinformatics - biology - cell biology - cheminformatics - database management - drug metabolism - endocrinology - genetics - human genetics - medical informatics - metabolomics - microbiology - molecular biology - molecular microbiology - plant genetics - proteomics - systems biology - transcriptomics license: ODbL-1.0 mappings: fairsharing: FAIRsharing.3xwMon togoid: Pathbank name: PathBank pattern: ^(SMP|PW)\d+$ preferred_prefix: pathbank uri_format: https://pathbank.org/view/$1 pathguide: contact: email: gary.bader@utoronto.ca github: gbader name: Gary Bader orcid: 0000-0003-0185-8861 description: Pathguide contains information about 325 biological related resources and molecular interaction related resources. example: '49' homepage: http://pathguide.org keywords: - gene - interaction - pathway - protein - small molecule mappings: integbio: nbdc00608 prefixcommons: pathguide name: Pathguide pattern: ^\d+$ preferred_prefix: pathguide providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pathguide:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=$1 pathoplant: description: PathoPlant® is a database on plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. PathoPlant® also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon pathogen infection or elicitor treatment. example: MO000027 homepage: http://www.pathoplant.de keywords: - gene expression - interaction - pathway - protein - small molecule mappings: pathguide: '333' prefixcommons: pathoplant name: PathoPlant® preferred_prefix: pathoplant providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pathoplant:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.pathoplant.de/detail.php?accNo=$1 pathwaycommons: contact: email: chris@sanderlab.org github: sanderlab name: Chris Sander orcid: 0000-0001-6059-6270 description: Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language. example: '485991' homepage: http://www.pathwaycommons.org/pc/ keywords: - pathway mappings: biocontext: PATHWAYCOMMONS miriam: pathwaycommons n2t: pathwaycommons prefixcommons: pathwaycommons re3data: r3d100012731 uniprot: DB-0253 name: Pathway Commons pattern: ^\d+$ preferred_prefix: pathwaycommons providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pathwaycommons:$1 publications: - doi: 10.1093/nar/gkz946/5606621 pubmed: '31647099' - doi: 10.1093/nar/gkq1039 pmc: PMC3013659 pubmed: '21071392' title: Pathway Commons, a web resource for biological pathway data year: 2010 uri_format: http://www.pathwaycommons.org/pc/record2.do?id=$1 pato: appears_in: - agro - aism - cdno - cl - colao - ecocore - ecto - fovt - gallont - lepao - mco - ms - pcl - pco - phipo - planp - proco - rbo - uberon - xpo - zp banana: PATO contact: email: g.gkoutos@gmail.com github: gkoutos name: George Gkoutos orcid: 0000-0002-2061-091X description: PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. download_json: http://purl.obolibrary.org/obo/pato.json download_obo: http://purl.obolibrary.org/obo/pato.obo download_owl: http://purl.obolibrary.org/obo/pato.owl example: 0001998 homepage: https://github.com/pato-ontology/pato/ keywords: - biodiversity - biology - obo - ontology - phenotype - quality license: CC-BY-3.0 mappings: aberowl: PATO agroportal: PATO biocontext: PATO bioportal: PATO fairsharing: FAIRsharing.ezwdhz go: PATO miriam: pato n2t: pato obofoundry: pato ols: pato ontobee: PATO prefixcommons: pato name: Phenotype And Trait Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: PATO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pato:$1 - code: purl description: Legacy PURLs found in OAE homepage: http://purl.org/obo/owl/ name: Legacy PURL uri_format: http://purl.org/obo/owl/PATO#PATO_$1 publications: - doi: 10.1093/bib/bbx035 pmc: PMC6169674 pubmed: '28387809' title: 'The anatomy of phenotype ontologies: principles, properties and applications' year: 2018 - doi: 10.1186/gb-2010-11-1-r2 pmc: PMC2847714 pubmed: '20064205' title: Integrating phenotype ontologies across multiple species year: 2010 - doi: 10.1186/gb-2004-6-1-r8 pmc: PMC549069 pubmed: '15642100' title: Using ontologies to describe mouse phenotypes year: 2004 rdf_uri_format: http://purl.obolibrary.org/obo/PATO_$1 repository: https://github.com/pato-ontology/pato uri_format: http://purl.obolibrary.org/obo/PATO_$1 version: '2025-02-01' pav: contact: email: stian@soiland-reyes.com name: Stian Soiland-Reyes orcid: 0000-0001-9842-9718 contributor: email: nicolas.matentzoglu@gmail.com github: matentzn name: Nicolas Matentzoglu orcid: 0000-0002-7356-1779 contributor_extras: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources. download_owl: http://aber-owl.net/media/ontologies/PAV/3/pav.owl example: authoredBy github_request_issue: 186 homepage: https://pav-ontology.github.io/pav/ keywords: - citation - data management - ontology - quality - resource metadata - subject agnostic mappings: aberowl: PAV biocontext: pav biolink: pav bioportal: PAV fairsharing: FAIRsharing.nbfwwv lov: pav name: Provenance, Authoring, and Versioning Vocabulary pattern: ^[a-z][a-zA-Z]+$ preferred_prefix: pav publications: - doi: 10.1186/2041-1480-4-37 pmc: PMC4177195 pubmed: '24267948' title: 'PAV ontology: provenance, authoring and versioning' year: 2013 repository: http://pav-ontology.github.io/pav/ reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://purl.org/pav/$1 paxdb.organism: description: PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species. example: '9606' homepage: http://pax-db.org/ mappings: biocontext: PAXDB.ORGANISM miriam: paxdb.organism n2t: paxdb.organism name: PaxDb Organism pattern: ^\d+$ preferred_prefix: paxdb.organism uri_format: http://pax-db.org/#!species/$1 paxdb.protein: description: PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels. example: '977869' homepage: http://pax-db.org/ mappings: biocontext: PAXDB.PROTEIN miriam: paxdb.protein n2t: paxdb.protein name: PaxDb Protein pattern: ^\d+$ preferred_prefix: paxdb.protein uri_format: http://pax-db.org/#!protein/$1 pazar: contact: email: wyeth@cmmt.ubc.ca name: Wyeth W. Wasserman orcid: 0000-0001-6098-6412 description: The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors. example: TF0001053 homepage: http://www.pazar.info/ keywords: - dna - life science - regulation - rna mappings: biocontext: PAZAR fairsharing: FAIRsharing.33yggg integbio: nbdc00611 miriam: pazar n2t: pazar pathguide: '521' prefixcommons: pazar name: Pazar Transcription Factor pattern: ^TF\w+$ preferred_prefix: pazar providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pazar:$1 publications: - doi: 10.1093/nar/gkn783 pmc: PMC2686574 pubmed: '18971253' title: The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences year: 2008 - doi: 10.1186/gb-2007-8-10-r207 pmc: PMC2246282 pubmed: '17916232' title: 'PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation' year: 2007 uri_format: http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1 pba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A controlled vocabulary to support the study of transcription in the primate brain download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-pba.obo example: '128011350' homepage: https://www.blueprintnhpatlas.org/ keywords: - ontology name: Primate Brain Atlas pattern: ^\d+$ preferred_prefix: PBA uri_format: https://biopragmatics.github.io/providers/pba/$1 pcl: contact: email: davidos@ebi.ac.uk github: dosumis name: David Osumi-Sutherland orcid: 0000-0002-7073-9172 depends_on: - bfo - chebi - cl - go - nbo - ncbitaxon - omo - pato - pr - ro - so - uberon description: Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties. download_json: http://purl.obolibrary.org/obo/pcl.json download_obo: http://purl.obolibrary.org/obo/pcl.obo download_owl: http://purl.obolibrary.org/obo/pcl.owl example: '0011124' homepage: https://github.com/obophenotype/provisional_cell_ontology keywords: - anatomy - annotation - cell - cell biology - life science - obo - ontology license: CC-BY-4.0 mappings: aberowl: PCL bioportal: PCL fairsharing: FAIRsharing.bfcfd0 obofoundry: pcl ols: pcl ontobee: PCL name: Provisional Cell Ontology pattern: ^\d{7}$ preferred_prefix: PCL publications: - doi: 10.1101/2021.10.10.463703 title: Brain Data Standards - A method for building data-driven cell-type ontologies year: 2021 rdf_uri_format: http://purl.obolibrary.org/obo/PCL_$1 repository: https://github.com/obophenotype/provisional_cell_ontology uri_format: http://purl.obolibrary.org/obo/PCL_$1 version: '2025-01-08' pco: appears_in: - ecocore - envo contact: email: rlwalls2008@gmail.com github: ramonawalls name: Ramona Walls orcid: 0000-0001-8815-0078 depends_on: - bfo - caro - envo - go - iao - ncbitaxon - pato - ro description: The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. download_obo: http://purl.obolibrary.org/obo/pco.obo download_owl: http://purl.obolibrary.org/obo/pco.owl example: '0000021' homepage: https://github.com/PopulationAndCommunityOntology/pco keywords: - biodiversity - community care - ecology - evolution - obo - ontology - population genetics - social and behavioural science license: CC0-1.0 mappings: aberowl: PCO agroportal: PCO biocontext: PCO bioportal: PCO ecoportal: PCO fairsharing: FAIRsharing.vq28qp obofoundry: pco ols: pco ontobee: PCO name: Population and Community Ontology pattern: ^\d{7}$ preferred_prefix: PCO publications: - doi: 10.1371/journal.pone.0089606 pubmed: '24595056' title: 'Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies' year: 2014 rdf_uri_format: http://purl.obolibrary.org/obo/PCO_$1 repository: https://github.com/PopulationAndCommunityOntology/pco uri_format: http://purl.obolibrary.org/obo/PCO_$1 version: '2021-05-03' pd_st: contact: email: henrich@embl.de github: ThorstenHen name: Thorsten Henrich orcid: 0000-0002-1548-3290 deprecated: true homepage: http://4dx.embl.de/platy keywords: - obo - ontology mappings: biocontext: PD_ST obofoundry: pd_st name: Platynereis stage ontology preferred_prefix: PD_ST rdf_uri_format: http://purl.obolibrary.org/obo/PD_ST_$1 uri_format: http://purl.obolibrary.org/obo/PD_ST_$1 pdb: contact: email: harukin@protein.osaka-u.ac.jp name: Haruki Nakamura orcid: 0000-0001-6690-5863 description: The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. example: 2gc4 example_extras: - 157d homepage: https://www.wwpdb.org/ keywords: - bioinformatics - epidemiology - protein - proteomics - structural biology - structure - virology mappings: biocontext: PDB edam: '1127' fairsharing: FAIRsharing.rs2815 go: PDB integbio: nbdc00613 miriam: pdb n2t: pdb ncbi: PDB pathguide: '398' prefixcommons: pdbj re3data: r3d100010910 togoid: Pdb uniprot: DB-0172 wikidata: P638 name: PDB Structure pattern: ^[0-9][A-Za-z0-9]{3}$ preferred_prefix: pdb providers: - code: CURATOR_REVIEW description: Proteopedia homepage: http://www.proteopedia.org/ name: Proteopedia uri_format: http://proteopedia.org/wiki/index.php/$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pdbj:$1 - code: dionysus description: DIONYSUS is a database of protein-carbohydrate interfaces, offering annotated data and tools for exploring interaction patterns and annotating proteins. homepage: www.dsimb.inserm.fr/DIONYSUS name: DIONYSUS publications: - doi: 10.1093/nar/gkae890 pubmed: '39436020' title: 'DIONYSUS: a database of protein-carbohydrate interfaces' year: 2024 uri_format: https://www.dsimb.inserm.fr/DIONYSUS/structure/$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: furna description: FURNA (Functions of RNAs) is a database of ligand-RNA interactions and Gene Ontology annotations for RNAs in the Protein Data Bank (PDB). example: 157d homepage: https://seq2fun.dcmb.med.umich.edu/furna/ name: furna publications: - doi: 10.1371/journal.pbio.3002476 pmc: PMC11309384 pubmed: '39074139' title: 'FURNA: A database for functional annotations of RNA structures' year: 2024 uri_format: https://seq2fun.dcmb.med.umich.edu/furna/pdb.cgi?pdbid=$1 - code: pdbe description: Protein Databank in Europe (PDBe) homepage: http://www.pdbe.org/ name: Protein Databank in Europe (PDBe) uri_format: https://www.ebi.ac.uk/pdbe/entry/pdb/$1 - code: pdbj description: Protein Data Bank Japan (PDBj) homepage: http://www.pdbj.org/ name: Protein Data Bank Japan (PDBj) uri_format: https://pdbj.org/mine/summary/$1 - code: rcsb description: RCSB PDB homepage: https://www.rcsb.org/ name: RCSB PDB uri_format: https://www.rcsb.org/structure/$1 publications: - doi: 10.1093/nar/gkae890 pubmed: '39436020' title: 'DIONYSUS: a database of protein-carbohydrate interfaces' year: 2024 - doi: 10.1371/journal.pbio.3002476 pmc: PMC11309384 pubmed: '39074139' title: 'FURNA: A database for functional annotations of RNA structures' year: 2024 - doi: 10.1002/pro.4211 pmc: PMC8740847 pubmed: '34664328' title: 'Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data' year: 2021 - doi: 10.1002/pro.3273 pmc: PMC5734392 pubmed: '28815765' title: New tools and functions in data-out activities at Protein Data Bank Japan (PDBj) year: 2017 - doi: 10.1093/nar/gkw962 pmc: PMC5210648 pubmed: '27789697' title: 'Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures' year: 2016 - doi: 10.1093/nar/gkr811 pmc: PMC3245181 pubmed: '21976737' title: 'Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format' year: 2011 - doi: 10.1007/s10822-011-9460-y pubmed: '21796434' title: 'Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr' year: 2011 - doi: 10.1093/database/baq021 pmc: PMC2997606 pubmed: '20798081' title: 'PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan' year: 2010 - pubmed: '12099029' title: '[Development of PDBj: Advanced database for protein structures]' year: 2002 rdf_uri_format: https://rdf.wwpdb.org/pdb/$1 synonyms: - RCSB_PDB - pdbe - pdbj - wwpdb twitter: PDBj_en uri_format: https://www.wwpdb.org/pdb?id=$1 pdb-ccd: comment: might be same as pdb.ligand, not sure though contact: email: berman@rcsb.rutgers.edu name: Helen Berman orcid: 0000-0002-3337-0660 contributor_extras: - email: bmeldal@ebi.ac.uk github: bmeldal-eg name: Birgit Meldal orcid: 0000-0003-4062-6158 description: The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names. example: AB0 example_extras: - A - PI has_canonical: pdb.ligand homepage: https://www.ebi.ac.uk/pdbe-srv/pdbechem/ keywords: - chemical - classification mappings: biocontext: PDB-CCD miriam: pdb-ccd n2t: pdb-ccd prefixcommons: ccd togoid: PdbCcd name: Chemical Component Dictionary pattern: ^\w{1,3}$ preferred_prefix: pdb-ccd providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ccd:$1 publications: - doi: 10.1038/nsb1203-980 pubmed: '14634627' title: Announcing the worldwide Protein Data Bank year: 2003 synonyms: - pdbechem uri_format: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1 pdb.ligand: description: The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands. example: TRQ homepage: https://www.pdbe.org/ keywords: - interaction - protein - small molecule - structure mappings: biocontext: PDB.LIGAND miriam: pdb.ligand n2t: pdb.ligand pathguide: '169' prefixcommons: pdbligand wikidata: P3636 name: PDB ligand pattern: ^[A-Za-z0-9]+$ preferred_prefix: pdb.ligand providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pdbligand:$1 - code: rcsb description: PDB Ligand at RCSB homepage: http://www.rcsb.org name: PDB Ligand at RCSB uri_format: http://www.rcsb.org/ligand/$1 synonyms: - PDB_CHEM_ID uri_format: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1 pdbsum: contact: email: roman@ebi.ac.uk name: Roman Laskowski orcid: 0000-0001-5528-0087 description: PDBsum provides an overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them. example: 1kfv homepage: http://www.ebi.ac.uk/pdbsum keywords: - interaction - protein - structural biology - structure mappings: fairsharing: FAIRsharing.7vjq5t integbio: nbdc00308 pathguide: '461' prefixcommons: pdbsum uniprot: DB-0119 name: PDBsum; at-a-glance overview of macromolecular structures preferred_prefix: pdbsum providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pdbsum:$1 provides: pdb publications: - doi: 10.1002/pro.3289 pmc: PMC5734310 pubmed: '28875543' title: 'PDBsum: Structural summaries of PDB entries' year: 2017 - doi: 10.1093/nar/gkt940 pmc: PMC3965036 pubmed: '24153109' title: PDBsum additions year: 2013 - doi: 10.1093/nar/gkn860 pmc: PMC2686501 pubmed: '18996896' title: PDBsum new things year: 2008 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.ebi.ac.uk/pdbsum/$1 pdc.study: contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The National Cancer Institute's Proteomic Data Commons (PDC) makes cancer-related proteomic datasets easily accessible to the public. example: PDC000351 github_request_issue: 430 homepage: https://pdc.cancer.gov/pdc name: Proteomic Data Commons pattern: ^PDC\d+$ preferred_prefix: pdc.study reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://pdc.cancer.gov/pdc/study/$1 pdro: contact: email: paul.fabry@usherbrooke.ca github: pfabry name: Paul Fabry orcid: 0000-0002-3336-2476 description: An ontology to describe entities related to prescription of drugs download_owl: http://purl.obolibrary.org/obo/pdro.owl example: 0010039 homepage: https://github.com/OpenLHS/PDRO keywords: - drug - obo - ontology - primary health care license: CC-BY-4.0 mappings: aberowl: PDRO biocontext: PDRO bioportal: PDRO fairsharing: FAIRsharing.9te3ev obofoundry: pdro ols: pdro ontobee: PDRO name: The Prescription of Drugs Ontology pattern: ^\d{7}$ preferred_prefix: PDRO providers: - code: pdro.legacy description: An incorrect encoding of OBO purls homepage: http://purl.obolibrary.org/obo/pdro name: PDRO Hash uri_format: http://purl.obolibrary.org/obo/PDRO/PDRO.owl#PDRO_$1 publications: - doi: 10.3390/ijerph182212025 pmc: PMC8619589 pubmed: '34831777' title: 'The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its Parts' year: 2021 rdf_uri_format: http://purl.obolibrary.org/obo/PDRO_$1 repository: https://github.com/OpenLHS/PDRO uri_format: http://purl.obolibrary.org/obo/PDRO_$1 version: '2021-06-08' pdumdv: contact: email: frederic.bastian@unil.ch github: fbastian name: Frédéric Bastian orcid: 0000-0002-9415-5104 deprecated: true description: Life cycle stages for Platynereis dumerilii download_obo: http://purl.obolibrary.org/obo/pdumdv.obo download_owl: http://purl.obolibrary.org/obo/pdumdv.owl example: '0001410' homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv keywords: - developmental biology - life cycle stage - life science - obo - ontology license: CC-BY-3.0 mappings: aberowl: PDUMDV biocontext: PDUMDV bioportal: PDUMDV fairsharing: FAIRsharing.493qns obofoundry: pdumdv ols: pdumdv ontobee: PdumDv name: Platynereis Developmental Stages pattern: ^\d{7}$ preferred_prefix: PdumDv rdf_uri_format: http://purl.obolibrary.org/obo/PdumDv_$1 repository: https://github.com/obophenotype/developmental-stage-ontologies synonyms: - PdumDv uri_format: http://purl.obolibrary.org/obo/PdumDv_$1 peco: appears_in: - agro - mco contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp name: Pankaj Jaiswal orcid: 0000-0002-1005-8383 description: A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. download_obo: https://raw.githubusercontent.com/Planteome/plant-experimental-conditions-ontology/master/peco.obo download_owl: http://purl.obolibrary.org/obo/peco.owl example: '0007114' homepage: http://planteome.org/ keywords: - botany - experimental condition - experimental measurement - experimentally determined - obo - ontology - study design license: CC-BY-4.0 logo: http://planteome.org/sites/default/files/garland_logo.PNG mappings: aberowl: PECO agroportal: PECO biocontext: PECO bioportal: PECO fairsharing: FAIRsharing.6yNXYK obofoundry: peco ols: peco ontobee: PECO name: Plant Experimental Conditions Ontology pattern: ^\d{7}$ preferred_prefix: PECO publications: - doi: 10.1093/nar/gkx1152 pmc: PMC5753347 pubmed: '29186578' title: 'The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics' year: 2018 rdf_uri_format: http://purl.obolibrary.org/obo/PECO_$1 repository: https://github.com/Planteome/plant-experimental-conditions-ontology uri_format: https://browser.planteome.org/amigo/term/PECO:$1 version: '2023-11-10' ped: contact: email: zhangzhang@big.ac.cn name: Zhang Zhang orcid: 0000-0001-6603-5060 description: The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins. example: PED00037 homepage: https://proteinensemble.org/ keywords: - botany - plant genetics mappings: fairsharing: FAIRsharing.4ef690 integbio: nbdc02490 miriam: ped name: Protein Ensemble Database pattern: ^PED\d{5}$ preferred_prefix: ped publications: - doi: 10.1093/nar/gky1026 pmc: PMC6324055 pubmed: '30364952' title: 'Plant editosome database: a curated database of RNA editosome in plants' year: 2019 uri_format: https://proteinensemble.org/$1 ped.ensemble: description: The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins. example: PED00017e001 homepage: https://proteinensemble.org/ mappings: miriam: ped.ensemble name: Protein Ensemble Database ensemble part_of: ped pattern: ^PED\d{5}e\d{3}$ preferred_prefix: ped.ensemble uri_format: https://proteinensemble.org/$1 peff: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true download_obo: https://github.com/HUPO-PSI/PEFF/raw/master/CV/psi-peff-OBSOLETE-DO_NOT_USE.obo example: '0001011' homepage: https://www.psidev.info/peff keywords: - ontology name: PSI Extended File Format pattern: ^\d{7}$ preferred_prefix: peff uri_format: https://biopragmatics.github.io/providers/peff/$1 pennsieve: description: 'Pennsieve is a publicly accessible Scientific Data Management and publication platform. The platform supports data curation, sharing and publishing complex scientific datasets with a focus on integration between graph-based metadata and file-archival. The platform provides a "peer"-reviewed publication mechanism and public datasets are available through its Discover Web Application and APIs. ' example: N:package:e3243db3-7986-488e-9a10-c7a0bfdcfe8a homepage: https://discover.pennsieve.io mappings: miriam: ps name: Pennsieve pattern: ^N:package:[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$ preferred_prefix: pennsieve uri_format: https://discover.pennsieve.io/package/$1 pepbank: comment: This resource doesn't exist on the web anymore deprecated: true description: PepBank is a database of peptides based on sequence text mining and public peptide data sources. Only peptides that are 20 amino acids or shorter are stored. Only peptides with available sequences are stored. example: '21877' homepage: http://pepbank.mgh.harvard.edu/ keywords: - protein - structure mappings: pathguide: '235' prefixcommons: pepbank name: PepBank Peptide Database preferred_prefix: pepbank providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pepbank:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://pepbank.mgh.harvard.edu/interactions/details/$1 pephub: contact: email: nsheffield@virginia.edu github: nsheff name: Nathan Sheffield orcid: 0000-0001-5643-4068 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: PEPhub is a database, web interface, and API for sharing, retrieving, and validating sample metadata. PEPhub uses Portable Encapsulated Projects (PEP) biological metadata standard to store, edit, and access PEPs in one place. example: geo example_extras: - bedbase/gse198944 - databio/encode_batch_1 - geo/gse185244 github_request_issue: 1194 homepage: https://pephub.databio.org/ name: PEPhub pattern: ^[A-Za-z0-9_\-]+(/[A-Za-z0-9_\-]+)?$ preferred_prefix: pephub publications: - doi: 10.1093/gigascience/giae033 pmc: PMC11238423 pubmed: '38991851' title: 'PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://pephub.databio.org/$1 peptideatlas: contact: email: edeutsch@systemsbiology.org github: edeutsch name: Eric W. Deutsch orcid: 0000-0001-8732-0928 description: The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools. example: PAp00000009 homepage: http://www.peptideatlas.org/ keywords: - mass spectrometry - protein - proteomics - structure mappings: biocontext: PEPTIDEATLAS edam: '2626' fairsharing: FAIRsharing.dvyrsz integbio: nbdc01812 miriam: peptideatlas n2t: peptideatlas prefixcommons: peptideatlas re3data: r3d100010889 uniprot: DB-0071 name: PeptideAtlas pattern: ^PAp[0-9]{8}$ preferred_prefix: peptideatlas providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/peptideatlas:$1 publications: - doi: 10.1038/embor.2008.56 pmc: PMC2373374 pubmed: '18451766' title: 'PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows' year: 2008 - doi: 10.1093/nar/gkj040 pmc: PMC1347403 pubmed: '16381952' title: The PeptideAtlas project year: 2006 - doi: 10.1038/embor.2008.56. title: 'PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows.' 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 (Providers) example: SCC111 homepage: https://www.perkinelmer.com/ mappings: cellosaurus: PerkinElmer name: PerkinElmer cell line collection preferred_prefix: perkinelmer uri_format: https://www.perkinelmer.com/searchresult?searchName=$1 peroxibase: contact: email: dunand@lrsv.ups-tlse.fr name: Christophe Dunand orcid: 0000-0003-1637-4042 description: Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences. example: '5282' homepage: http://peroxibase.toulouse.inra.fr/ keywords: - enzyme - life science - protein - regulation mappings: biocontext: PEROXIBASE fairsharing: FAIRsharing.z1czxj integbio: nbdc01869 miriam: peroxibase n2t: peroxibase prefixcommons: peroxibase uniprot: DB-0072 name: Peroxibase pattern: ^\d+$ preferred_prefix: peroxibase providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/peroxibase:$1 publications: - doi: 10.1093/nar/gks1083 pmc: PMC3531118 pubmed: '23180785' title: 'PeroxiBase: a database for large-scale evolutionary analysis of peroxidases' year: 2012 - doi: 10.1093/jxb/ern317 pubmed: '19112168' title: 'PeroxiBase: a powerful tool to collect and analyse peroxidase sequences from Viridiplantae' year: 2008 uri_format: http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1 pesticideinfo: description: chemical in the database supplied by Pesticide Action Network North America example: PRI10 homepage: https://www.pesticideinfo.org mappings: wikidata: P11949 name: PesticideInfo chemical ID pattern: ^PRI\d*$ preferred_prefix: pesticideinfo uri_format: https://www.pesticideinfo.org/chemical/$1 pesticides: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients. example: derivatives%2Fthiocyclam%20hydrochloride homepage: http://www.alanwood.net/pesticides name: Alan Wood's Pesticides preferred_prefix: pesticides uri_format: http://www.alanwood.net/pesticides/$1.html pfam: contact: email: agb@ebi.ac.uk name: Alex Bateman orcid: 0000-0002-6982-4660 description: The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored. example: PF11779 homepage: https://www.ebi.ac.uk/interpro/ keywords: - biology - domain - protein license: CC0-1.0 mappings: biocontext: PFAM edam: '1138' fairsharing: FAIRsharing.y3scf6 go: Pfam integbio: nbdc00163 miriam: pfam n2t: pfam ncbi: PFAM prefixcommons: pfam re3data: r3d100012850 togoid: Pfam uniprot: DB-0073 wikidata: P3519 name: Pfam pattern: ^PF\d{5}$ preferred_prefix: pfam providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pfam:$1 - code: sanger description: The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored. homepage: http://pfam.sanger.ac.uk/ name: Sanger Pfam Mirror uri_format: http://pfam.sanger.ac.uk/family?entry=$1 - code: xfam description: Pfam's familes in their old home in the xfam.org homepage: https://pfam.xfam.org name: Xfam uri_format: https://pfam.xfam.org/family?acc=$1 publications: - doi: 10.1093/nar/27.1.260 pmc: PMC148151 pubmed: '9847196' title: 'Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins' year: 1999 - doi: 10.1093/nar/26.1.320 pmc: PMC147209 pubmed: '9399864' title: 'Pfam: multiple sequence alignments and HMM-profiles of protein domains' year: 1998 - doi: 10.1002/(sici)1097-0134(199707)28:3<405::aid-prot10>3.0.co;2-l pubmed: '9223186' title: 'Pfam: a comprehensive database of protein domain families based on seed alignments' year: 1997 - doi: 10.1093/nar/gkae997 pubmed: '39540428' title: 'The Pfam protein families database: embracing AI/ML' year: 2024 - doi: 10.1093/nar/gkaa913 pmc: PMC7779014 pubmed: '33125078' title: 'Pfam: The protein families database in 2021' year: 2021 - doi: 10.1093/nar/gky995 pmc: PMC6324024 pubmed: '30357350' title: The Pfam protein families database in 2019 year: 2019 - doi: 10.1093/nar/gkv1344 pmc: PMC4702930 pubmed: '26673716' title: 'The Pfam protein families database: towards a more sustainable future' year: 2015 - doi: 10.1093/nar/gkt1223 pmc: PMC3965110 pubmed: '24288371' title: 'Pfam: the protein families database' year: 2013 - doi: 10.1093/nar/gkr1065 pmc: PMC3245129 pubmed: '22127870' title: The Pfam protein families database year: 2011 - doi: 10.1093/nar/gkp985 pmc: PMC2808889 pubmed: '19920124' title: The Pfam protein families database year: 2009 - doi: 10.1093/nar/gkm960 pmc: PMC2238907 pubmed: '18039703' title: The Pfam protein families database year: 2007 - doi: 10.1093/nar/gkj149 pmc: PMC1347511 pubmed: '16381856' title: 'Pfam: clans, web tools and services' year: 2006 - doi: 10.1093/nar/gkh121 pmc: PMC308855 pubmed: '14681378' title: The Pfam protein families database year: 2004 - doi: 10.1093/nar/30.1.276 pmc: PMC99071 pubmed: '11752314' title: The Pfam protein families database year: 2002 - doi: 10.1093/nar/28.1.263 pmc: PMC102420 pubmed: '10592242' title: The Pfam protein families database year: 2000 references: - https://twitter.com/PfamDB/status/1555149527228813314 synonyms: - PF twitter: Xfam_EBI uri_format: https://www.ebi.ac.uk/interpro/entry/pfam/$1 pfam.clan: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Higher order grouping of Pfam families example: CL0192 homepage: https://pfam.xfam.org license: CC0-1.0 mappings: edam: '2758' name: Pfam Clans pattern: ^CL\d+$ preferred_prefix: pfam.clan providers: - code: xfam description: Pfam's clans in their old home in the xfam.org homepage: https://pfam.xfam.org name: Xfam uri_format: https://pfam.xfam.org/clan/$1 references: - https://twitter.com/PfamDB/status/1555149527228813314 uri_format: https://www.ebi.ac.uk/interpro/set/pfam/$1 pfr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets. example: '1001' homepage: http://repository.topdownproteomics.org/proteoforms keywords: - data management - subject agnostic mappings: fairsharing: FAIRsharing.wqsxtg re3data: r3d100012385 name: Proteoform Atlas pattern: ^\d+$ preferred_prefix: pfr synonyms: - TDR uri_format: http://repository.topdownproteomics.org/proteoforms/$1 pgdso: contact: email: po-discuss@plantontology.org name: Plant Ontology Administrators deprecated: true homepage: http://www.plantontology.org keywords: - obo - ontology mappings: biocontext: PGDSO obofoundry: pgdso name: Plant Growth and Development Stage preferred_prefix: PGDSO rdf_uri_format: http://purl.obolibrary.org/obo/PGDSO_$1 uri_format: http://purl.obolibrary.org/obo/PGDSO_$1 pgs: description: The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation. example: PGS000018 homepage: http://pgscatalog.org mappings: miriam: pgs name: Polygenic Score Catalog pattern: ^PGS[0-9]{6}$ preferred_prefix: pgs uri_format: https://www.pgscatalog.org/pgs/$1 pgx: contact: email: mbaudis@me.com github: mbaudis name: Michael Baudis orcid: 0000-0002-9903-4248 description: The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt "neoplasm" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs. example: pgxbs-kftva5zv homepage: https://progenetix.org/ keywords: - biomedical science - genomics mappings: biocontext: PGX cellosaurus: Progenetix fairsharing: FAIRsharing.65tdnz miriam: pgx n2t: pgx re3data: r3d100012820 name: Progenetix pattern: ^\w{3,15}[-_]\w[\w.-]{3,128}$ preferred_prefix: pgx publications: - doi: 10.1093/nar/gku1123 pmc: PMC4383937 pubmed: '25428357' title: 'arrayMap 2014: an updated cancer genome resource' year: 2014 - doi: 10.1186/1471-2164-15-82 pmc: PMC3909908 pubmed: '24476156' title: Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens year: 2014 - doi: 10.1093/nar/gkt1108 pmc: PMC3965091 pubmed: '24225322' title: 'Progenetix: 12 years of oncogenomic data curation' year: 2013 - doi: 10.1371/journal.pone.0036944 pmc: PMC3356349 pubmed: '22629346' title: 'arrayMap: a reference resource for genomic copy number imbalances in human malignancies' year: 2012 - doi: 10.1186/1471-2407-7-226 pmc: PMC2225423 pubmed: '18088415' title: 'Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data' year: 2007 - doi: 10.2144/000112102 pubmed: '16568815' title: Online database and bioinformatics toolbox to support data mining in cancer cytogenetics year: 2006 - doi: 10.1093/bioinformatics/17.12.1228 pubmed: '11751233' title: 'Progenetix.net: an online repository for molecular cytogenetic aberration data' year: 2001 synonyms: - Progenetix twitter: progenetix uri_format: https://progenetix.org/services/ids/$1 pharmacodb.cell: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by cell line. example: 22RV1_12_2019 homepage: https://pharmacodb.ca/cell_lines mappings: cellosaurus: PharmacoDB name: PharmacoDB Cells preferred_prefix: pharmacodb.cell uri_format: https://pharmacodb.ca/cell_lines/$1 pharmacodb.dataset: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by dataset. example: '1' homepage: https://pharmacodb.ca/datasets name: PharmacoDB Datasets pattern: ^\d+$ preferred_prefix: pharmacodb.dataset uri_format: https://pharmacodb.ca/datasets/$1 pharmacodb.tissue: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by tissue. example: '13' homepage: https://pharmacodb.ca/tissues name: PharmacoDB Tissues pattern: ^\d+$ preferred_prefix: pharmacodb.tissue uri_format: https://pharmacodb.ca/tissues/$1 pharmgkb.disease: contact: email: teri.klein@stanford.edu github: TeriKlein name: Teri E Klein orcid: 0000-0001-5527-6475 description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. example: PA447218 homepage: http://www.pharmgkb.org/ keywords: - pharmacogenomics license: CC-BY-SA-4.0 mappings: biocontext: PHARMGKB.DISEASE biolink: PHARMGKB.DISEASE edam: '2651' miriam: pharmgkb.disease n2t: pharmgkb.disease prefixcommons: pharmgkb.disease wikidata: P7001 name: PharmGKB Disease pattern: ^PA\d+$ preferred_prefix: pharmgkb.disease providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pharmgkb.disease:$1 publications: - doi: 10.2217/bmm.11.94 pmc: PMC3339046 pubmed: '22103613' title: 'From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource' year: 2011 - doi: 10.1038/sj.tpj.6500035 pubmed: '11908751' title: 'Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base' year: 2001 uri_format: http://www.pharmgkb.org/disease/$1 pharmgkb.drug: contact: email: teri.klein@stanford.edu github: TeriKlein name: Teri E Klein orcid: 0000-0001-5527-6475 description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. example: PA448710 homepage: http://www.pharmgkb.org/ keywords: - drug - pharmacogenomics license: CC-BY-SA-4.0 mappings: biocontext: PHARMGKB.DRUG biolink: PHARMGKB.DRUG edam: '2652' miriam: pharmgkb.drug n2t: pharmgkb.drug prefixcommons: pharmgkb.drug wikidata: P7001 name: PharmGKB Drug pattern: ^PA\d+$ preferred_prefix: pharmgkb.drug providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pharmgkb.drug:$1 publications: - doi: 10.2217/bmm.11.94 pmc: PMC3339046 pubmed: '22103613' title: 'From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource' year: 2011 - doi: 10.1038/sj.tpj.6500035 pubmed: '11908751' title: 'Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base' year: 2001 uri_format: http://www.pharmgkb.org/drug/$1 pharmgkb.gene: contact: email: teri.klein@stanford.edu github: TeriKlein name: Teri E Klein orcid: 0000-0001-5527-6475 description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. example: PA131 homepage: http://www.pharmgkb.org/ keywords: - gene - ontology - pharmacogenomics license: CC-BY-SA-4.0 mappings: biocontext: PHARMGKB.GENE biolink: PHARMGKB.GENE bioportal: PHARMGKB go: PharmGKB miriam: pharmgkb.gene n2t: pharmgkb.gene prefixcommons: pharmgkb.gene uniprot: DB-0074 wikidata: P7001 name: PharmGKB Gene pattern: ^PA\w+$ preferred_prefix: pharmgkb.gene providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pharmgkb.gene:$1 publications: - doi: 10.2217/bmm.11.94 pmc: PMC3339046 pubmed: '22103613' title: 'From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource' year: 2011 - doi: 10.1385/1-59259-957-5:179 pubmed: '16100408' title: 'PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base' year: 2005 uri_format: http://www.pharmgkb.org/gene/$1 pharmgkb.pathways: contact: email: teri.klein@stanford.edu github: TeriKlein name: Teri E Klein orcid: 0000-0001-5527-6475 description: "The PharmGKB database is a central repository for genetic, genomic,\ \ molecular and cellular phenotype data and clinical information about people\ \ who have participated in pharmacogenomics research studies. The data includes,\ \ but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic\ \ research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter\ \ domains. \nPharmGKB Pathways are drug centric, gene based, interactive pathways\ \ which focus on candidate genes and gene groups and associated genotype and phenotype\ \ data of relevance for pharmacogenetic and pharmacogenomic studies." example: PA146123006 homepage: http://www.pharmgkb.org/ keywords: - pathway - pharmacogenomics license: CC-BY-SA-4.0 mappings: biocontext: PHARMGKB.PATHWAYS biolink: PHARMGKB.PATHWAYS edam: '2650' miriam: pharmgkb.pathways n2t: pharmgkb.pathways prefixcommons: pharmgkb.pathways wikidata: P7001 name: PharmGKB pattern: ^PA\d+$ preferred_prefix: pharmgkb.pathways providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pharmgkb.pathways:$1 publications: - doi: 10.2217/bmm.11.94 pmc: PMC3339046 pubmed: '22103613' title: 'From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource' year: 2011 - doi: 10.1038/sj.tpj.6500035 pubmed: '11908751' title: 'Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base' year: 2001 uri_format: http://www.pharmgkb.org/pathway/$1 pharmgkb.variant: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: SNPs and other variants that can be mapped to dbSNP. example: PA166156302 github_request_issue: 1368 homepage: https://www.pharmgkb.org license: CC-BY-SA-4.0 mappings: biolink: PHARMGKB.VARIANT name: PharmGKB Variant pattern: ^PA\d+$ preferred_prefix: pharmgkb.variant uri_format: https://www.pharmgkb.org/variant/$1 pharmvar: contact: email: agaedigk@cmh.edu name: Andrea Gaedigk orcid: 0000-0001-6968-1893 description: The Pharmacogene Variation (PharmVar) Consortium is the new home for PGx gene nomenclature serving as a centralized ‘Next-Generation’ Pharmacogene Variation data repository. The major focus of PharmVar is to catalogue allelic variation of genes impacting drug metabolism, disposition and response and provide a unifying designation system (nomenclature) for the global pharmacogenetic/genomic community. Efforts are synchronized between PharmVar, the Pharmacogenomic KnowledgeBase, and the Clinical Pharmacogenetic Implementation Consortium. example: CYP2A6 homepage: https://www.pharmvar.org keywords: - gene - pharmacogenomics - variant mappings: prefixcommons: pharmvar name: Pharmacogene Variation Consortium preferred_prefix: pharmvar providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pharmvar:$1 provides: hgnc.symbol publications: - doi: 10.1002/cpt.910 pmc: PMC5836850 pubmed: '29134625' title: 'The Pharmacogene Variation (PharmVar) Consortium: Incorporation of the Human Cytochrome P450 (CYP) Allele Nomenclature Database' year: 2017 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.pharmvar.org/gene/$1 phenolexplorer: description: Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis. example: '75' homepage: http://www.phenol-explorer.eu/foods/ mappings: biocontext: PHENOLEXPLORER miriam: phenolexplorer n2t: phenolexplorer re3data: r3d100012197 name: Phenol-Explorer pattern: ^\d+$ preferred_prefix: phenolexplorer uri_format: http://phenol-explorer.eu/foods/$1 phenx: contact: email: yingqin@rti.org name: PhenX Admin contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants. download_owl: http://aber-owl.net/media/ontologies/PHENX/16/phenx.owl example: '130502' github_request_issue: 503 homepage: https://www.phenxtoolkit.org/ keywords: - biomedical science - disease - environmental science - exposure - life science - ontology - phenotype mappings: aberowl: PHENX bioportal: PHENX fairsharing: FAIRsharing.y5jcwa integbio: nbdc02244 name: PhenX Toolkit pattern: ^\d+$ preferred_prefix: phenx publications: - doi: 10.1038/gim.2016.199 pmc: PMC5507752 pubmed: '28079902' title: PhenX measures for phenotyping rare genetic conditions year: 2017 - doi: 10.1093/aje/kwr193 pmc: PMC3141081 pubmed: '21749974' title: 'The PhenX Toolkit: get the most from your measures' year: 2011 - doi: 10.1097/mol.0b013e3283377395 pmc: PMC8038872 pubmed: '20154612' title: 'PhenX: a toolkit for interdisciplinary genetics research' year: 2010 synonyms: - phenxtoolkit uri_format: https://www.phenxtoolkit.org/protocols/view/$1 phipo: contact: email: alayne.cuzick@rothamsted.ac.uk github: CuzickA name: Alayne Cuzick orcid: 0000-0001-8941-3984 depends_on: - pato description: Ontology of species-neutral phenotypes observed in pathogen-host interactions. download_obo: http://purl.obolibrary.org/obo/phipo.obo download_owl: http://purl.obolibrary.org/obo/phipo.owl example: '0000001' homepage: https://github.com/PHI-base/phipo keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: PHIPO bioportal: PHIPO obofoundry: phipo ols: phipo ontobee: PHIPO name: Pathogen Host Interaction Phenotype Ontology pattern: ^\d{7}$ preferred_prefix: PHIPO publications: - doi: 10.1093/nar/gkab1037 pmc: PMC8728202 pubmed: '34788826' title: 'PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions' year: 2022 rdf_uri_format: http://purl.obolibrary.org/obo/PHIPO_$1 repository: https://github.com/PHI-base/phipo uri_format: http://purl.obolibrary.org/obo/PHIPO_$1 version: '2024-08-29' phosphopoint.kinase: description: PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information. example: AURKA homepage: http://kinase.bioinformatics.tw/ mappings: biocontext: PHOSPHOPOINT.KINASE miriam: phosphopoint.kinase n2t: phosphopoint.kinase name: PhosphoPoint Kinase pattern: ^\w+$ 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=$1&drawing=0&sorting=0&kinome=0 phosphosite.curation: contributor: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to curation records that collect information extracted from specific publications. example: '34665743' github_request_issue: 1136 homepage: https://www.phosphosite.org name: PhosphoSite Curation pattern: ^\d+$ preferred_prefix: phosphosite.curation reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.phosphosite.org/curatedInfoAction.action?record=$1 phosphosite.protein: description: PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database. example: '12300' homepage: http://www.phosphosite.org/homeAction.do mappings: biocontext: PHOSPHOSITE.PROTEIN miriam: phosphosite.protein n2t: phosphosite.protein name: PhosphoSite Protein pattern: ^\d{5}$ preferred_prefix: phosphosite.protein uri_format: http://www.phosphosite.org/proteinAction.do?id=$1 phosphosite.residue: description: PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence. example: '2842' homepage: http://www.phosphosite.org/homeAction.do mappings: biocontext: PHOSPHOSITE.RESIDUE miriam: phosphosite.residue n2t: phosphosite.residue name: PhosphoSite Residue pattern: ^\d+$ preferred_prefix: phosphosite.residue uri_format: http://www.phosphosite.org/siteAction.do?id=$1 phosphosite.sitegroup: comment: Potentially could use a URI format like https://www.phosphosite.org/siteGroupAction.action?protOrg=1156&id=$1, but it's not obvious what the protOrg does. contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur. example: '447860' github_request_issue: 432 homepage: https://www.phosphosite.org keywords: - biochemistry - grouping - post-translational modification name: PhosphoSite Site Group pattern: ^\d+$ preferred_prefix: phosphosite.sitegroup reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 phrr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Philippine Health Research Registry (PHRR), managed by the Philippine Council for Health Research and Development, is a tool for good governance to promote transparency and accountability in health research. PHRR is a publicly accessible database on newly approved health researches. It includes clinical trials and non-clinical studies conducted in the Philippines. The registry is compliant with the World Health Organization (WHO) standard for clinical trials registry. [from website] example: '4195' homepage: https://registry.healthresearch.ph name: Philippine Health Research Registry preferred_prefix: phrr uri_format: https://registry.healthresearch.ph/index.php/registry?view=research&layout=details&cid=$1 phylomedb: contact: email: toni.gabaldon@crg.eu github: tgabaldon name: Toni Gabaldón orcid: 0000-0003-0019-1735 description: PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins. example: Phy000CLXM_RAT homepage: http://phylomedb.org/ keywords: - genome - life science - phylogenetics - phylogenomics - phylogeny - protein - taxonomy mappings: biocontext: PHYLOMEDB fairsharing: FAIRsharing.7hxxc4 integbio: nbdc01764 miriam: phylomedb n2t: phylomedb prefixcommons: phylomedb uniprot: DB-0144 name: PhylomeDB pattern: ^\w+$ preferred_prefix: phylomedb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/phylomedb:$1 publications: - doi: 10.1093/nar/gkab966 pmc: PMC8728271 pubmed: '34718760' title: 'PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies' year: 2022 - doi: 10.1093/nar/gkt1177 pmc: PMC3964985 pubmed: '24275491' title: 'PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome' year: 2013 - doi: 10.1093/nar/gkq1109 pmc: PMC3013701 pubmed: '21075798' title: 'PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions' year: 2010 - doi: 10.1093/nar/gkm899 pmc: PMC2238872 pubmed: '17962297' title: 'PhylomeDB: a database for genome-wide collections of gene phylogenies' year: 2007 twitter: phylomedb uri_format: http://phylomedb.org/?seqid=$1 phytozome.locus: description: Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information. example: Glyma0021s00410 homepage: http://www.phytozome.net/ mappings: biocontext: PHYTOZOME.LOCUS miriam: phytozome.locus n2t: phytozome.locus ncbi: Phytozome name: Plant Genome Network pattern: ^[A-Za-z0-9]+$ preferred_prefix: phytozome.locus synonyms: - JGI Phytozome uri_format: http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1 pibase: description: PIBASE is a collection of all protein structural interfaces extracted from the Protein Data Bank and PQS structure databases. Both chain-chain and domain-domain (SCOP and CATH definitions) interfaces are detected. example: '21692' homepage: http://salilab.org/pibase keywords: - protein - structure mappings: pathguide: '183' prefixcommons: pibase name: Database of structurally defined protein interfaces preferred_prefix: pibase providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pibase:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id=$1 pictar: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true example: hsa-let-7a homepage: https://pictar.mdc-berlin.de/ name: PicTar preferred_prefix: pictar synonyms: - pictar-vert pid.pathway: contact: email: schaefec@mail.nih.gov name: Carl F. Schaefer orcid: 0000-0002-5941-3390 description: The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information. example: eff796f3-6195-11e5-8ac5-06603eb7f303 homepage: https://www.ndexbio.org/index.html#/networkset/8a2d7ee9-1513-11e9-bb6a-0ac135e8bacf keywords: - gene - life science - pathway - protein - small molecule mappings: biocontext: PID.PATHWAY edam: '2344' fairsharing: FAIRsharing.ncgh1j miriam: pid.pathway n2t: pid.pathway pathguide: '119' prefixcommons: pid name: 'NCI Pathway Interaction Database: Pathway' pattern: ^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$ preferred_prefix: pid.pathway providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pid:$1 publications: - doi: 10.1093/nar/gkn653 pmc: PMC2686461 pubmed: '18832364' title: 'PID: the Pathway Interaction Database' year: 2008 synonyms: - pid uri_format: http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1 pigqtldb: description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs. example: '14' homepage: https://www.animalgenome.org/QTLdb keywords: - dna - genome mappings: biocontext: PIGQTLDB miriam: pigqtldb n2t: pigqtldb prefixcommons: pigqtldb name: Animal Genome Pig QTL part_of: qtldb pattern: ^\d+$ preferred_prefix: pigqtldb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pigqtldb:$1 uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 pii: appears_in: - pubmed contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A combination of an ISBN and local unique identifier for articles and other published works. Please see the [Wikipedia page](https://en.wikipedia.org/wiki/Publisher_Item_Identifier) for a detailed explanation. Some PIIs are used as the local identifiers in DOIs, such as https://doi.org/10.1136/S0003-4967(24)38620-0. example: S0960-9822(11)01319-4 example_extras: - B0-123-12345-1/12345-1 github_request_issue: 1447 homepage: https://en.wikipedia.org/wiki/Publisher_Item_Identifier name: Publisher Item Identifier pattern: ^((S\d{4}-\d{4}\(\d{2}\)\d{5})|(B\d-\d{3}-\d{5}-\d/\d{5}))-[\d|X]$ preferred_prefix: pii pina: contact: email: wujm@bjmu.edu.cn name: Jianmin Wu orcid: 0000-0002-8876-128X description: Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. example: Q13485 homepage: http://cbg.garvan.unsw.edu.au/pina/ keywords: - data visualization - life science mappings: biocontext: PINA fairsharing: FAIRsharing.7q4gsz miriam: pina n2t: pina pathguide: '348' name: Protein Interaction Network Analysis pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ preferred_prefix: pina provides: uniprot publications: - doi: 10.1093/nar/gkaa1075 pmc: PMC7779002 pubmed: '33231689' title: 'PINA 3.0: mining cancer interactome' year: 2021 - doi: 10.1093/nar/gkr967 pmc: PMC3244997 pubmed: '22067443' title: 'PINA v2.0: mining interactome modules' year: 2011 - doi: 10.1038/nmeth.1282 pubmed: '19079255' title: Integrated network analysis platform for protein-protein interactions year: 2008 uri_format: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1 piroplasma: description: PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: TA14985 homepage: http://piroplasmadb.org/ mappings: biocontext: PIROPLASMA miriam: piroplasma n2t: piroplasma name: PiroplasmaDB pattern: ^TA\d+$ preferred_prefix: piroplasma uri_format: http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 pirsf: contact: email: wuc@udel.edu name: Cathy H. Wu orcid: 0000-0001-6379-8601 description: The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. example: PIRSF000100 homepage: https://pir.georgetown.edu/ keywords: - life science - protein - proteomics - structure mappings: biocontext: PIRSF edam: '1136' fairsharing: FAIRsharing.vssch2 go: PIRSF miriam: pirsf n2t: pirsf prefixcommons: pirsf uniprot: DB-0079 name: PIR Superfamily Classification System pattern: ^PIRSF\d{6}$ preferred_prefix: pirsf providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pirsf:$1 publications: - doi: 10.1093/nar/gkh097 pmc: PMC308831 pubmed: '14681371' title: 'PIRSF: family classification system at the Protein Information Resource' year: 2004 uri_format: https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1 pkdb: contact: email: konigmatt@googlemail.com name: Matthias König orcid: 0000-0003-1725-179X description: 'PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. ' example: PKDB00198 homepage: https://www.hu-berlin.de/?set_language=en&cl=en keywords: - clinical studies - clinical veterinary medicine - life science - personalized medicine - pharmacogenomics - pharmacology - preclinical studies mappings: fairsharing: FAIRsharing.AYegqK miriam: pkdb name: PK-DB pattern: ^PKDB[0-9]{5}$ preferred_prefix: pkdb publications: - doi: 10.1093/nar/gkaa990 pmc: PMC7779054 pubmed: '33151297' title: 'PK-DB: pharmacokinetics database for individualized and stratified computational modeling' year: 2021 repository: https://github.com/matthiaskoenig/pkdb/issues uri_format: https://pk-db.com/data/$1 plana: appears_in: - planp contact: email: smr@stowers.org github: srobb1 name: Sofia Robb orcid: 0000-0002-3528-5267 depends_on: - ro - uberon description: PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea. download_obo: http://purl.obolibrary.org/obo/plana.obo download_owl: http://purl.obolibrary.org/obo/plana.owl example: '0000001' homepage: https://github.com/obophenotype/planaria-ontology keywords: - anatomy - developmental biology - life science - obo - ontology - organ - organelle - tissue license: CC-BY-3.0 mappings: aberowl: PLANA biocontext: PLANA bioportal: PLANA fairsharing: FAIRsharing.g1qrqs obofoundry: plana ols: plana ontobee: PLANA name: Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology pattern: ^\d{7}$ preferred_prefix: PLANA publications: - doi: 10.1242/dev.196097 pmc: PMC8353266 pubmed: '34318308' title: 'Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms' year: 2021 rdf_uri_format: http://purl.obolibrary.org/obo/PLANA_$1 repository: https://github.com/obophenotype/planaria-ontology uri_format: http://purl.obolibrary.org/obo/PLANA_$1 version: '2023-03-13' planp: contact: email: smr@stowers.org github: srobb1 name: Sofia Robb orcid: 0000-0002-3528-5267 depends_on: - go - pato - plana - ro description: Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea. download_obo: http://purl.obolibrary.org/obo/planp.obo download_owl: http://purl.obolibrary.org/obo/planp.owl example: '0000001' homepage: https://github.com/obophenotype/planarian-phenotype-ontology keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: PLANP bioportal: PLANP obofoundry: planp ols: planp ontobee: PLANP name: Planarian Phenotype Ontology pattern: ^\d+$ preferred_prefix: PLANP rdf_uri_format: http://purl.obolibrary.org/obo/PLANP_$1 repository: https://github.com/obophenotype/planarian-phenotype-ontology uri_format: http://purl.obolibrary.org/obo/PLANP_$1 version: '2020-03-28' planttfdb: contact: email: gaog@mail.cbi.pku.edu.cn github: gao-ge name: Ge Gao orcid: 0000-0001-6470-8815 description: The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors. example: Ath_AT1G01030.1 homepage: http://planttfdb.cbi.pku.edu.cn keywords: - dna - gene - life science - protein - regulation - rna - small molecule mappings: biocontext: PLANTTFDB fairsharing: FAIRsharing.ex3fqk miriam: planttfdb n2t: planttfdb pathguide: '497' prefixcommons: planttfdb re3data: r3d100011301 name: Plant Transcription Factor Database pattern: ^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\._\-#]*)$ preferred_prefix: planttfdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/planttfdb:$1 publications: - doi: 10.1093/nar/gkw982 pmc: PMC5210657 pubmed: '27924042' title: 'PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants' year: 2016 - doi: 10.1093/molbev/msv058 pmc: PMC4476157 pubmed: '25750178' title: An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors year: 2015 - doi: 10.1093/nar/gkt1016 pmc: PMC3965000 pubmed: '24174544' title: 'PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors' year: 2013 uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1 plasmodb: contact: email: oharb@upenn.edu github: ramobrah name: Omar S. Harb orcid: 0000-0003-4446-6200 description: AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: PF11_0344 homepage: http://plasmodb.org/plasmo/ keywords: - genome - genomics - infectious disease medicine mappings: biocontext: PLASMODB fairsharing: FAIRsharing.g4n8sw go: PlasmoDB integbio: nbdc01783 miriam: plasmodb n2t: plasmodb ncbi: ApiDB_PlasmoDB pathguide: '514' prefixcommons: plasmodb re3data: r3d100011569 name: PlasmoDB pattern: ^\w+$ preferred_prefix: plasmodb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/plasmodb:$1 publications: - doi: 10.1093/nar/gkn814 pmc: PMC2686598 pubmed: '18957442' title: 'PlasmoDB: a functional genomic database for malaria parasites' year: 2008 synonyms: - ApiDB_PlasmoDB twitter: VEuPathDB uri_format: http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 plo: contact: email: mb4@sanger.ac.uk name: Matt Berriman deprecated: true homepage: http://www.sanger.ac.uk/Users/mb4/PLO/ keywords: - obo - ontology mappings: biocontext: PLO obofoundry: plo name: Plasmodium Life Cycle preferred_prefix: PLO rdf_uri_format: http://purl.obolibrary.org/obo/PLO_$1 uri_format: http://purl.obolibrary.org/obo/PLO_$1 plos: contact: email: subjectareas@plos.org name: PLOS Taxonomy Team contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontologization of Public Library of Science (PLOS) journal keywords and topics. It's not clear how the IDs correspond to the actual pages. Appears in ADCAD. example: '1443' github_request_issue: 1318 homepage: http://journals.plos.org keywords: - ontology - publication - subject agnostic mappings: aberowl: PLOSTHES bioportal: PLOSTHES fairsharing: FAIRsharing.2ndf9r name: PLOS Thesaurus pattern: ^\d+$ preferred_prefix: plos synonyms: - PLOSTHES uri_format: http://localhost/plosthes.2017-1#$1 pmap.cutdb: contact: email: adam@burnham.org name: Adam Godzik orcid: 0000-0002-2425-852X description: The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites). example: '25782' homepage: http://cutdb.burnham.org keywords: - enzyme - pathway - protein mappings: biocontext: PMAP.CUTDB miriam: pmap.cutdb n2t: pmap.cutdb prefixcommons: pmap.cutdb name: CutDB pattern: ^\d+$ preferred_prefix: pmap.cutdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pmap.cutdb:$1 publications: - doi: 10.1093/nar/gkl813 pmc: PMC1669773 pubmed: '17142225' title: 'CutDB: a proteolytic event database' year: 2006 uri_format: http://cutdb.burnham.org/relation/show/$1 pmap.substratedb: contact: email: eroshkin@burnham.org name: Alexey M. Eroshkin orcid: 0000-0003-2023-4608 description: The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates. example: '1915' homepage: http://substrate.burnham.org/ keywords: - domain - protein - reaction mappings: biocontext: PMAP.SUBSTRATEDB miriam: pmap.substratedb n2t: pmap.substratedb prefixcommons: pmap.substratedb name: SubstrateDB pattern: ^\d+$ preferred_prefix: pmap.substratedb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pmap.substratedb:$1 publications: - doi: 10.1093/nar/gkn683 pmc: PMC2686432 pubmed: '18842634' title: 'PMAP: databases for analyzing proteolytic events and pathways' year: 2008 uri_format: http://substrate.burnham.org/protein/annotation/$1/html pmc: comment: Note that the Europe PMC instance redirects canonical local unique identifiers from https://europepmc.org/articles/PMC3084216 to https://europepmc.org/article/PMC/3084216. However, this is an implementation detail and does not reflect the official format of a PMC identifier, which indeed does include `PMC` at the beginning of the local unique identifier contact: email: beck@ncbi.nlm.nih.gov github: jeffbeckncbi name: Jeff Beck orcid: 0000-0002-1798-9797 description: PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature. example: PMC3084216 example_extras: - PMC7418728 - PMC7418728.1 - PMC7418728.2 homepage: http://europepmc.org/ keywords: - bibliography - centrally registered identifier - knowledge and information systems mappings: biocontext: PMCID biolink: PMC cellosaurus: PMCID fairsharing: FAIRsharing.2b4316 go: PMCID miriam: pmc n2t: pmc prefixcommons: pmc wikidata: P932 name: PubMed Central pattern: ^PMC\d+(\.\d+)?$ preferred_prefix: pmc providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pmc:$1 - code: ncbi.pmc description: PubMed Central homepage: https://www.ncbi.nlm.nih.gov/pmc/ name: PubMed Central uri_format: https://www.ncbi.nlm.nih.gov/pmc/articles/$1 publications: - doi: 10.1093/nar/gkr1184 pmc: PMC3245031 pubmed: '22140104' title: Database resources of the National Center for Biotechnology Information year: 2011 - doi: 10.1093/nar/gkq1172 pmc: PMC3013733 pubmed: '21097890' title: Database resources of the National Center for Biotechnology Information year: 2010 references: - https://github.com/biopragmatics/bioregistry/issues/965 synonyms: - PMC - PMCID uri_format: http://europepmc.org/articles/$1 pmdb: description: The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques. example: PM0012345 homepage: https://bioinformatics.cineca.it/PMDB/ keywords: - protein - structural biology - structure mappings: biocontext: PMDB fairsharing: FAIRsharing.wkaakq miriam: pmdb n2t: pmdb prefixcommons: pmdb name: Protein Model Database pattern: ^PM\d{7}$ preferred_prefix: pmdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pmdb:$1 publications: - doi: 10.1093/nar/gkj105 pmc: PMC1347467 pubmed: '16381873' title: The PMDB Protein Model Database year: 2006 uri_format: https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1 pmp: contact: email: torsten.schwede@unibas.ch name: Torsten Schwede orcid: 0000-0003-2715-335X deprecated: true description: The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers. example: Q0VCA6 homepage: http://www.proteinmodelportal.org/ keywords: - prediction - protein - structure mappings: biocontext: PMP miriam: pmp n2t: pmp pathguide: '438' prefixcommons: pmp name: Protein Model Portal pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ preferred_prefix: pmp providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pmp:$1 provides: uniprot publications: - doi: 10.1007/s10969-008-9048-5 pmc: PMC2704613 pubmed: '19037750' title: The Protein Model Portal year: 2008 uri_format: http://www.proteinmodelportal.org/query/uniprot/$1 pmr: contact: email: laia.subirats@gmail.com name: Laia Subirats orcid: 0000-0001-8646-5463 description: Resource for the community to store, retrieve, search, reference, and reuse CellML models. download_owl: http://aber-owl.net/media/ontologies/PMR/4/pmr.owl example: ebf69ca24298b28b2361e7d43eb52d6c homepage: https://www.auckland.ac.nz/en.html keywords: - biomedical science - life science - mathematics - ontology - physiology - systems biology mappings: aberowl: PMR bioportal: PMR fairsharing: FAIRsharing.bcjrnq miriam: pmr name: Physical Medicine and Rehabilitation pattern: ^[a-z0-9]{32,32}$ preferred_prefix: pmr publications: - doi: 10.1098/rsfs.2015.0103 pmc: PMC4759754 pubmed: '27051515' title: 'The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable' year: 2016 - doi: 10.1186/1471-2105-12-22 pmc: PMC3033326 pubmed: '21235804' title: Revision history aware repositories of computational models of biological systems year: 2011 - doi: 10.1093/bioinformatics/btq723 pubmed: '21216774' title: The Physiome Model Repository 2 year: 2011 - doi: 10.1098/rsta.2008.0310 pmc: PMC3268215 pubmed: '19380315' title: CellML metadata standards, associated tools and repositories year: 2009 - doi: 10.1093/bioinformatics/btn390 pubmed: '18658182' title: The CellML Model Repository year: 2008 - doi: 10.1109/iembs.2006.260202 pubmed: '17947072' title: Toward a curated CellML model repository year: 2006 - doi: 10.1109/IEMBS.2006.260202 title: Toward a curated CellML model repository. twitter: physiomeproject uri_format: https://models.physiomeproject.org/exposure/$1 pmr.workspace: description: Workspace (Git repository) for modeling projects managed by the Physiome Model Repository example: modularmassactionprimer homepage: https://www.auckland.ac.nz/en.html mappings: miriam: pmr.workspace name: Physiome Model Repository workspace pattern: ^[a-zA-Z0-9_\-]+(/.*?)?$ preferred_prefix: pmr.workspace uri_format: https://models.physiomeproject.org/workspace/$1 po: appears_in: - agro - ecocore - envo - gallont - genepio banana: PO contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp name: Pankaj Jaiswal orcid: 0000-0002-1005-8383 description: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. download_obo: http://purl.obolibrary.org/obo/po.obo download_owl: http://purl.obolibrary.org/obo/po.owl example: 0009089 homepage: http://browser.planteome.org/amigo keywords: - botany - classification - expression data - life cycle - life science - obo - ontology - plant anatomy - plant development stage - structure license: CC-BY-4.0 logo: https://raw.githubusercontent.com/Planteome/plant-ontology/refs/heads/master/Planteome_profile.jpg mappings: aberowl: PO agroportal: PO biocontext: PO bioportal: PO cellosaurus: PO edam: '1180' fairsharing: FAIRsharing.3ngg40 go: PO miriam: po n2t: po obofoundry: po ols: po ontobee: PO prefixcommons: po name: Plant Ontology namespace_in_lui: true pattern: ^\d+$ preferred_prefix: PO providers: - code: amigo description: Plant Ontology through Amigo homepage: http://www.plantontology.org/ name: Plant Ontology through Amigo uri_format: https://browser.planteome.org/amigo/term/PO:$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/po:$1 publications: - doi: 10.1093/nar/gkx1152 pmc: PMC5753347 pubmed: '29186578' title: 'The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics' year: 2018 - doi: 10.1007/978-1-4939-3167-5_5 pubmed: '26519402' title: 'The Plant Ontology: A Tool for Plant Genomics' year: 2016 - doi: 10.1371/journal.pbio.1002033 pmc: PMC4285398 pubmed: '25562316' title: Finding our way through phenotypes year: 2015 - doi: 10.1093/pcp/pcs163 pmc: PMC3583023 pubmed: '23220694' title: The plant ontology as a tool for comparative plant anatomy and genomic analyses year: 2012 - doi: 10.1002/cfg.496 pmc: PMC2447502 pubmed: '18629207' title: 'Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages' year: 2005 - doi: 10.1002/cfg.154 pmc: PMC2447263 pubmed: '18628842' title: The Plant Ontology Consortium and plant ontologies year: 2002 - doi: 10.1093/nar/gkm908 pmc: PMC2238838 pubmed: '18194960' title: 'The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations' year: 2008 rdf_uri_format: http://purl.obolibrary.org/obo/PO_$1 repository: https://github.com/Planteome/plant-ontology twitter: planteome uri_format: http://purl.obolibrary.org/obo/PO_$1 version: '2024-04-17' pocketome: contact: email: ikufareva@ucsd.edu name: Ruben Abagyan orcid: 0000-0001-9309-2976 description: Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries. example: 1433C_TOBAC_1_252 homepage: http://www.pocketome.org/sfSearch.cgi?act=browseall keywords: - life science mappings: biocontext: POCKETOME fairsharing: FAIRsharing.tc6df8 miriam: pocketome n2t: pocketome pathguide: '537' name: Pocketome pattern: ^[A-Za-z_0-9]+$ preferred_prefix: pocketome publications: - doi: 10.1093/nar/gkr825 pmc: PMC3245087 pubmed: '22080553' title: 'Pocketome: an encyclopedia of small-molecule binding sites in 4D' year: 2011 - doi: 10.1007/978-1-60761-274-2_11 pmc: PMC2975493 pubmed: '19727619' title: The flexible pocketome engine for structural chemogenomics year: 2009 uri_format: http://www.pocketome.org/files/$1.html polbase: contact: email: lreha@ualberta.ca name: Linda Reha-Krantz orcid: 0000-0003-4497-423X description: Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity. example: 19-T4 homepage: http://polbase.neb.com/ keywords: - biochemistry - genetics mappings: biocontext: POLBASE fairsharing: FAIRsharing.s9ztmd integbio: nbdc02079 miriam: polbase n2t: polbase name: PolBase pattern: ^[A-Za-z-0-9]+$ preferred_prefix: polbase publications: - doi: 10.1093/nar/gkr847 pmc: PMC3245023 pubmed: '21993301' title: 'Polbase: a repository of biochemical, genetic and structural information about DNA polymerases' year: 2011 uri_format: https://polbase.neb.com/polymerases/$1#sequences polytraits.trait: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Reproductive and behavioural traits of both adult and larval stages, as well as information on environmental preferences and a few morphological traits. example: PRED github_request_issue: 1422 homepage: http://polytraits.lifewatchgreece.eu/terms name: Polytraits Trait Definitions preferred_prefix: polytraits.trait rdf_uri_format: http://polytraits.lifewatchgreece.eu/terms/$1 uri_format: http://polytraits.lifewatchgreece.eu/traitspublic_traitdefinitions.php#$1 pombase: contact: email: vw253@cam.ac.uk github: ValWood name: Valerie Wood orcid: 0000-0001-6330-7526 description: PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets. example: SPCC13B11.01 homepage: https://www.pombase.org/ keywords: - life science license: CC-BY-4.0 mappings: biocontext: PomBase biolink: PomBase fairsharing: FAIRsharing.8jsya3 go: PomBase integbio: nbdc00332 miriam: pombase n2t: pombase ncbi: PomBase prefixcommons: pombase re3data: r3d100011478 uniprot: DB-0031 wikidata: P6245 name: PomBase pattern: ^S\w+(\.)?\w+(\.)?$ preferred_prefix: pombase providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pombase:$1 publications: - doi: 10.1093/nar/gky961 pmc: PMC6324063 pubmed: '30321395' title: 'PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information' year: 2019 - doi: 10.1186/s12915-016-0276-z pmc: PMC4918006 pubmed: '27334346' title: 'Model organism databases: essential resources that need the support of both funders and users' year: 2016 - doi: 10.1093/nar/gku1040 pmc: PMC4383888 pubmed: '25361970' title: 'PomBase 2015: updates to the fission yeast database' year: 2014 - doi: 10.1186/1471-2105-15-155 pmc: PMC4039540 pubmed: '24885854' title: A method for increasing expressivity of Gene Ontology annotations using a compositional approach year: 2014 - doi: 10.1093/bioinformatics/btu103 pmc: PMC4058955 pubmed: '24574118' title: 'Canto: an online tool for community literature curation' year: 2014 - doi: 10.1093/bioinformatics/btt266 pmc: PMC3694669 pubmed: '23658422' title: 'FYPO: the fission yeast phenotype ontology' year: 2013 - doi: 10.1093/nar/gks1050 pmc: PMC3531070 pubmed: '23161678' title: Gene Ontology annotations and resources year: 2012 - doi: 10.1093/nar/gkr1028 pmc: PMC3245151 pubmed: '22102568' title: 'The Gene Ontology: enhancements for 2011' year: 2011 - doi: 10.1093/nar/gkr853 pmc: PMC3245111 pubmed: '22039153' title: 'PomBase: a comprehensive online resource for fission yeast' year: 2011 synonyms: - PomBase uri_format: https://www.pombase.org/gene/$1 poro: appears_in: - gallont contact: email: robert.thacker@stonybrook.edu github: bobthacker name: Bob Thacker orcid: 0000-0002-9654-0073 depends_on: - ro - uberon description: An ontology describing the anatomical structures and characteristics of Porifera (sponges) download_obo: http://purl.obolibrary.org/obo/poro.obo download_owl: http://purl.obolibrary.org/obo/poro.owl example: '0000550' homepage: https://github.com/obophenotype/porifera-ontology keywords: - anatomy - obo - ontology - phylogeny - taxonomic classification - taxonomy license: CC-BY-3.0 mappings: aberowl: PORO biocontext: PORO bioportal: PORO fairsharing: FAIRsharing.93g1th obofoundry: poro ols: poro ontobee: PORO name: Porifera Ontology pattern: ^\d{7}$ preferred_prefix: PORO publications: - doi: 10.1186/2041-1480-5-39 pmc: PMC4177528 pubmed: '25276334' title: 'The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology' year: 2014 rdf_uri_format: http://purl.obolibrary.org/obo/PORO_$1 repository: https://github.com/obophenotype/porifera-ontology uri_format: http://purl.obolibrary.org/obo/PORO_$1 version: '2016-10-06' ppdb: contact: email: ppdb@gifu-u.ac.jp name: Yoshiharu Y. Yamamoto orcid: 0000-0002-9667-0572 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties. ' example: '1484' homepage: https://sitem.herts.ac.uk/aeru/ppdb/ keywords: - life science mappings: fairsharing: FAIRsharing.7k8zh0 integbio: nbdc01041 name: Pesticide Properties DataBase pattern: ^\d+$ preferred_prefix: ppdb publications: - doi: 10.1093/nar/gkt1027 pmc: PMC3965062 pubmed: '24194597' title: 'ppdb: plant promoter database version 3.0' year: 2013 - doi: 10.1093/nar/gkm785 pmc: PMC2238996 pubmed: '17947329' title: 'ppdb: a plant promoter database' year: 2007 uri_format: https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm ppo: contact: email: rlwalls2008@gmail.com github: ramonawalls name: Ramona Walls orcid: 0000-0001-8815-0078 description: An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales. download_owl: http://purl.obolibrary.org/obo/ppo.owl example: 0002058 homepage: https://github.com/PlantPhenoOntology/PPO keywords: - botany - life cycle - obo - ontology - phenology - phenotype license: CC-BY-3.0 mappings: aberowl: PPO agroportal: PPO biocontext: PPO bioportal: PPO fairsharing: FAIRsharing.hakg7c obofoundry: ppo ols: ppo ontobee: PPO name: Plant Phenology Ontology pattern: ^\d{7}$ preferred_prefix: PPO publications: - doi: 10.3389/fpls.2018.00517 pmc: PMC5938398 pubmed: '29765382' title: 'The Plant Phenology Ontology: A New Informatics Resource for Large-Scale Integration of Plant Phenology Data' year: 2018 rdf_uri_format: http://purl.obolibrary.org/obo/PPO_$1 repository: https://github.com/PlantPhenoOntology/PPO uri_format: http://purl.obolibrary.org/obo/PPO_$1 version: '2024-07-09' ppr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - email: egon.willighagen@gmail.com github: egonw name: Egon Willighagen orcid: 0000-0001-7542-0286 - email: javier.millanacosta@maastrichtuniversity.nl github: jmillanacosta name: Javier Millán Acosta orcid: 0000-0002-4166-7093 description: Preprints are articles which have not been peer-reviewed from various preprint servers and open research platforms such as bioRxiv, ChemRxiv, PeerJ Preprints and F1000. example: PPR103739 homepage: https://europepmc.org/Preprints keywords: - bibliometrics - preprints - publishing name: Europe PMC Preprints pattern: ^PPR\d+$ preferred_prefix: ppr references: - https://github.com/bridgedb/tiwid/pull/21 uri_format: https://europepmc.org/article/ppr/$1 pr: appears_in: - chiro - cl - pcl - scdo - uberon banana: PR contact: email: dan5@georgetown.edu github: nataled name: Darren Natale orcid: 0000-0001-5809-9523 contributor_extras: - email: dan5@georgetown.edu github: nataled name: Darren Natale orcid: 0000-0001-5809-9523 description: The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies. download_obo: http://purl.obolibrary.org/obo/pr.obo download_owl: http://purl.obolibrary.org/obo/pr.owl example: '000000024' example_extras: - A0A0G2QC33 - A0A0G2QC33-2 - P0DP23 - Q15796 - Q15796-1 homepage: http://proconsortium.org keywords: - annotation - biocuration - biology - data model - glycosylation - methylation - obo - ontology - phosphorylation - protein - protein acetylation - protein-containing complex - ptm site prediction license: CC-BY-4.0 logo: https://raw.githubusercontent.com/PROconsortium/logo/master/PROlogo_small.png mappings: aberowl: PR agroportal: PR biocontext: PR bioportal: PR fairsharing: FAIRsharing.4ndncv go: PR integbio: nbdc01630 miriam: pr n2t: pr obofoundry: pr ols: pr ontobee: PR prefixcommons: pr uniprot: DB-0181 wikidata: P4926 name: Protein Ontology namespace_in_lui: true pattern: ^(?:\d{9}|[OPQ][0-9][A-Z0-9]{3}[0-9](?:-\d+)?|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2}(?:-\d+)?)$ preferred_prefix: PR providers: - code: CURATOR_REVIEW description: Protein Ontology at Georgetown homepage: https://proconsortium.org/ name: Protein Ontology at Georgetown uri_format: https://proconsortium.org/app/entry/PR:$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pr:$1 - code: ontorat description: Misguided re-labeling of IRIs from ontorat tool homepage: http://purl.obolibrary.org/obo/vo/ontorat name: OntoRat uri_format: http://purl.obolibrary.org/obo/vo/ontorat/PR_$1 publications: - doi: 10.1093/nar/gkw1075 pmc: PMC5210558 pubmed: '27899649' title: 'Protein Ontology (PRO): enhancing and scaling up the representation of protein entities' year: 2016 - doi: 10.1093/nar/gkt1173 pmc: PMC3964965 pubmed: '24270789' title: 'Protein Ontology: a controlled structured network of protein entities' year: 2013 - doi: 10.1186/1471-2105-12-371 pmc: PMC3189193 pubmed: '21929785' title: The representation of protein complexes in the Protein Ontology (PRO) year: 2011 - doi: 10.1093/nar/gkq907 pmc: PMC3013777 pubmed: '20935045' title: 'The Protein Ontology: a structured representation of protein forms and complexes' year: 2010 - doi: 10.1186/1471-2105-8-s9-s1 pmc: PMC2217659 pubmed: '18047702' title: Framework for a protein ontology year: 2007 rdf_uri_format: http://purl.obolibrary.org/obo/PR_$1 references: - https://github.com/biopragmatics/bioregistry/issues/959 repository: https://github.com/PROconsortium/PRoteinOntology synonyms: - PR - PRO uri_format: http://purl.obolibrary.org/obo/PR_$1 version: '70.0' 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/$1 pride: contact: email: yperez@ebi.ac.uk github: ypriverol name: Yasset Perez-Riverol orcid: 0000-0001-6579-6941 deprecated: true description: The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays. download_owl: http://purl.obolibrary.org/obo/pride/releases/2025-02-17/pride.owl example: '0000006' homepage: https://github.com/PRIDE-Utilities/pride-ontology keywords: - ontology - protein - proteomics mappings: aberowl: PRIDE biocontext: PRIDE fairsharing: FAIRsharing.e1byny integbio: nbdc00630 miriam: pride n2t: pride ols: pride prefixcommons: pride re3data: r3d100010137 uniprot: DB-0130 name: Proteomics Identification Database Ontology pattern: ^\d{7}$ preferred_prefix: pride providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pride:$1 publications: - doi: 10.1093/nar/gkab1038 pmc: PMC8728295 pubmed: '34723319' title: 'The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences' year: 2022 - doi: 10.1093/nar/gky1106 pmc: PMC6323896 pubmed: '30395289' title: 'The PRIDE database and related tools and resources in 2019: improving support for quantification data' year: 2019 - doi: 10.1093/nar/gkv1145 pmc: PMC4702828 pubmed: '26527722' title: 2016 update of the PRIDE database and its related tools year: 2015 - doi: 10.1002/pmic.201400120 pubmed: '25047258' title: How to submit MS proteomics data to ProteomeXchange via the PRIDE database year: 2014 - doi: 10.1038/nbt.2839 pmc: PMC3986813 pubmed: '24727771' title: ProteomeXchange provides globally coordinated proteomics data submission and dissemination year: 2014 - doi: 10.1093/nar/gks1262 pmc: PMC3531176 pubmed: '23203882' title: 'The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013' year: 2012 - doi: 10.1002/0471250953.bi1308s21 pubmed: '18428683' title: Using the Proteomics Identifications Database (PRIDE) year: 2008 - doi: 10.1093/nar/gkm1021 pmc: PMC2238846 pubmed: '18033805' title: 'PRIDE: new developments and new datasets' year: 2007 - doi: 10.1093/nar/gkj138 pmc: PMC1347500 pubmed: '16381953' title: 'PRIDE: a public repository of protein and peptide identifications for the proteomics community' year: 2006 - doi: 10.1002/pmic.200401303 pubmed: '16041671' title: 'PRIDE: the proteomics identifications database' year: 2005 repository: https://github.com/PRIDE-Utilities/pride-ontology twitter: pride_ebi uri_format: http://purl.obolibrary.org/obo/PRIDE_$1 version: '2025-02-17' pride.project: description: The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects. example: PXD000440 homepage: https://www.ebi.ac.uk/pride/ mappings: biocontext: PRIDE.PROJECT cellosaurus: PRIDE miriam: pride.project n2t: pride.project name: PRIDE Project pattern: ^P(X|R)D\d{6}$ 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/$1 prints: contact: email: teresa.k.attwood@manchester.ac.uk name: Teresa K. Attwood orcid: 0000-0003-2409-4235 description: PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours. example: PR00001 homepage: http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/ keywords: - biology - domain - protein - structural biology mappings: biocontext: PRINTS fairsharing: FAIRsharing.h8r843 go: PRINTS integbio: nbdc00039 miriam: prints n2t: prints prefixcommons: sprint uniprot: DB-0082 name: PRINTS compendium of protein fingerprints pattern: ^PR\d{5}$ preferred_prefix: prints providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/sprint:$1 - code: prints.alt1 description: Alternative access homepage: http://130.88.97.239/dbbrowser/sprint/ name: PRINTS Alt. 1 uri_format: http://130.88.97.239/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=$1 publications: - doi: 10.1093/database/bas019 pmc: PMC3326521 pubmed: '22508994' title: 'The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012' year: 2012 - doi: 10.1093/nar/gkg030 pmc: PMC165477 pubmed: '12520033' title: PRINTS and its automatic supplement, prePRINTS year: 2003 - doi: 10.1093/bioinformatics/15.10.799 pubmed: '10705433' title: 'FingerPRINTScan: intelligent searching of the PRINTS motif database' year: 1999 - doi: 10.1093/nar/28.1.225 pmc: PMC102408 pubmed: '10592232' title: 'PRINTS-S: the database formerly known as PRINTS' year: 2000 synonyms: - sprint uri_format: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off probesanddrugs: contact: email: ctibor.skuta@img.cas.cz name: Ctibor Škuta orcid: 0000-0001-5325-4934 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Probes & Drugs portal (P&D) is a hub for the integration of high-quality bioactive compound sets enabling their analysis and comparison. Its main focus is on chemical probes and drugs but it also includes additional relevant sets from specialist databases/scientific publications, and vendor sets. Upon these, established bioactive chemistry sources (such as ChEMBL, BindingDB, Guide To Pharmacology, DrugCentral or DrugBank) are utilized for compounds' biological annotation. example: PD000596 homepage: https://www.probes-drugs.org license: CC BY-SA 4.0 mappings: wikidata: P11199 name: Probes and Drugs pattern: ^PD\d{6}$ preferred_prefix: probesanddrugs uri_format: https://www.probes-drugs.org/compound/$1 probonto: banana: PROB banana_peel: _ contact: email: pierre.grenon@ifomis.uni-saarland.de github: pgrenon name: Pierre Grenon orcid: 0000-0003-4614-562X description: ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities. download_rdf: file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/probonto.ttl example: c0000005 example_extras: - k0001285 homepage: http://probonto.org keywords: - computational biology - mathematics - statistics - systems biology mappings: biocontext: PROBONTO fairsharing: FAIRsharing.8zqzm9 miriam: probonto n2t: probonto ols: probonto name: Probability Distribution Ontology pattern: ^(c|k)\d{7}$ preferred_prefix: probonto publications: - doi: 10.1093/bioinformatics/btw170 pmc: PMC5013898 pubmed: '27153608' title: 'ProbOnto: ontology and knowledge base of probability distributions' year: 2016 repository: https://github.com/probonto/ontology uri_format: http://www.probonto.org/ontology#PROB_$1 version: 2.5.0 proco: contact: email: wes_schafer@merck.com github: schaferw name: Wes Schafer orcid: 0000-0002-8786-1756 depends_on: - chebi - cheminf - obi - pato - ro - sbo description: PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry. download_owl: http://purl.obolibrary.org/obo/proco.owl example: '0000001' homepage: https://github.com/proco-ontology/PROCO keywords: - obo - ontology license: CC-BY-4.0 mappings: aberowl: PROCO bioportal: PROCO obofoundry: proco ols: proco ontobee: PROCO name: Process Chemistry Ontology pattern: ^\d{7}$ preferred_prefix: PROCO rdf_uri_format: http://purl.obolibrary.org/obo/PROCO_$1 repository: https://github.com/proco-ontology/PROCO uri_format: http://purl.obolibrary.org/obo/PROCO_$1 version: '2022-04-11' prodom: contact: email: Daniel.Kahn@toulouse.inra.fr name: Daniel Kahn orcid: 0000-0003-1644-0169 description: ProDom is a database of protein domain families generated from the global comparison of all available protein sequences. example: PD10000 homepage: http://prodom.prabi.fr/prodom/current/html/home.php keywords: - classification - life science - protein mappings: biocontext: PRODOM fairsharing: FAIRsharing.a8z6gz integbio: nbdc00174 miriam: prodom n2t: prodom prefixcommons: prodom name: ProDom pattern: ^PD\d+$ preferred_prefix: prodom providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/prodom:$1 publications: - doi: 10.1093/nar/gki034 pmc: PMC539988 pubmed: '15608179' title: 'The ProDom database of protein domain families: more emphasis on 3D' year: 2005 - doi: 10.1093/bib/3.3.246 pubmed: '12230033' title: 'ProDom: automated clustering of homologous domains' year: 2002 uri_format: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1 proglyc: description: ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information. example: AC119 homepage: http://www.proglycprot.org/ mappings: biocontext: PROGLYC miriam: proglyc n2t: proglyc name: ProGlycProt pattern: ^[A-Z]C\d{1,3}$ preferred_prefix: proglyc uri_format: http://www.proglycprot.org/detail.aspx?ProId=$1 propreo: contact: email: satyasahoo@ieee.org name: Satya S. Sahoo orcid: 0000-0001-9190-4256 deprecated: true description: A comprehensive proteomics data and process provenance ontology. download_owl: http://aber-owl.net/media/ontologies/PROPREO/2/propreo.owl example: protein homepage: http://lsdis.cs.uga.edu/projects/glycomics/propreo/ keywords: - obo - ontology - owl - proteomics mappings: aberowl: PROPREO biocontext: PROPREO bioportal: PROPREO obofoundry: propreo prefixcommons: propreo name: Proteomics data and process provenance preferred_prefix: PROPREO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/propreo:$1 rdf_uri_format: http://purl.obolibrary.org/obo/PROPREO_$1 uri_format: http://purl.obolibrary.org/obo/PROPREO_$1 prosite: contact: email: Ioannis.Xenarios@unil.ch name: Ioannis Xenarios orcid: 0000-0002-3413-6841 description: PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. example: PS00001 homepage: https://www.expasy.org/prosite/ keywords: - biology - protein - structure mappings: biocontext: PROSITE fairsharing: FAIRsharing.vwc6bd go: Prosite integbio: nbdc00241 miriam: prosite n2t: prosite prefixcommons: prosite togoid: Prosite uniprot: DB-0084 wikidata: P4355 name: PROSITE pattern: ^PS\d{5}$ preferred_prefix: prosite providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/prosite:$1 publications: - doi: 10.1093/bioinformatics/btt129 pmc: PMC3634184 pubmed: '23505298' title: 'pfsearchV3: a code acceleration and heuristic to search PROSITE profiles' year: 2013 - doi: 10.1093/nar/gks1067 pmc: PMC3531220 pubmed: '23161676' title: New and continuing developments at PROSITE year: 2012 - doi: 10.1093/nar/gkj063 pmc: PMC1347426 pubmed: '16381852' title: The PROSITE database year: 2006 uri_format: https://prosite.expasy.org/$1 protclustdb: contact: email: klimke@ncbi.nlm.nih.gov name: William Klimke description: ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters. example: O80725 homepage: https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters keywords: - genetics - genomics - life science - protein - structure mappings: biocontext: PROTCLUSTDB fairsharing: FAIRsharing.da493y miriam: protclustdb n2t: protclustdb prefixcommons: protclustdb name: ProtClustDB pattern: ^\w+$ preferred_prefix: protclustdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/protclustdb:$1 publications: - doi: 10.1093/nar/gkn734 pmc: PMC2686591 pubmed: '18940865' title: The National Center for Biotechnology Information's Protein Clusters Database year: 2008 uri_format: https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1 protcom: comment: This resource doesn't exist on the web anymore deprecated: true description: This database is a collection of protein-protein homo- and hetero-complexes as well as domain-domain structures. This issue of the database contains 17.024 entries (as of October 2007) of which 1350 are two-chain protein hetero-complexes, 7773 homodimers and 1589 are one-chain proteins parsed into two domains (domain structures). example: 12e8LH homepage: http://www.ces.clemson.edu/compbio/protcom keywords: - protein - structure mappings: pathguide: '242' prefixcommons: protcom name: Database of protein-protein complexes preferred_prefix: protcom providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/protcom:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.ces.clemson.edu/compbio/protcom/print_file.cgi?pdbid=$1 protege: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology of metadata from protege download_rdf: https://protege.stanford.edu/plugins/owl/protege example: defaultLanguage github_request_issue: 1317 homepage: http://protege.stanford.edu name: Protege Ontology preferred_prefix: protege uri_format: http://protege.stanford.edu/plugins/owl/protege#$1 proteomicsdb.peptide: comment: The fact that this has .peptide as a subspace is a bit of a misnomer. Its original registration with MIRIAM uses a subview over the protein to point to peptides, but the identifiers in this semantic space seem to be about proteins. description: ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein. example: '53504' homepage: https://www.proteomicsdb.org/#peptideSearch mappings: biocontext: PROTEOMICSDB.PEPTIDE miriam: proteomicsdb.peptide n2t: proteomicsdb.peptide name: ProteomicsDB Peptide pattern: ^\d+$ preferred_prefix: proteomicsdb.peptide uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1 proteomicsdb.protein: description: ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins. example: '53504' homepage: https://www.proteomicsdb.org/#human mappings: biocontext: PROTEOMICSDB.PROTEIN miriam: proteomicsdb.protein n2t: proteomicsdb.protein name: ProteomicsDB Protein pattern: ^\d+$ preferred_prefix: proteomicsdb.protein uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1/summary protonet.cluster: contact: email: michall@cc.huji.ac.il github: LinialLab name: Michal Linial orcid: 0000-0002-9357-4526 description: ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information. example: '4349895' homepage: http://www.protonet.cs.huji.ac.il/ keywords: - classification - clustering - protein mappings: biocontext: PROTONET.CLUSTER miriam: protonet.cluster n2t: protonet.cluster prefixcommons: protonet.cluster name: ProtoNet Cluster pattern: ^\d+$ preferred_prefix: protonet.cluster providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/protonet.cluster:$1 publications: - doi: 10.1110/ps.062185706 pmc: PMC2242553 pubmed: '16672244' title: 'Functional annotation prediction: all for one and one for all' year: 2006 uri_format: http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1 protonet.proteincard: contact: email: michall@cc.huji.ac.il github: LinialLab name: Michal Linial orcid: 0000-0002-9357-4526 description: ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information. example: '16941567' homepage: http://www.protonet.cs.huji.ac.il/ keywords: - protein mappings: biocontext: PROTONET.PROTEINCARD miriam: protonet.proteincard n2t: protonet.proteincard prefixcommons: protonet.proteincard name: ProtoNet ProteinCard pattern: ^\d+$ preferred_prefix: protonet.proteincard providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/protonet.proteincard:$1 publications: - doi: 10.1110/ps.062185706 pmc: PMC2242553 pubmed: '16672244' title: 'Functional annotation prediction: all for one and one for all' year: 2006 uri_format: http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1 prov: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web. download_owl: http://aber-owl.net/media/ontologies/PROV/1/prov.owl example: Activity homepage: https://www.w3.org/ns/prov keywords: - ontology - w3c rec mappings: aberowl: PROV biocontext: prov biolink: prov lov: prov ols: prov zazuko: prov name: PROV Namespace preferred_prefix: prov uri_format: http://www.w3.org/ns/prov#$1 pscdb: contact: email: mota@i.nagoya-u.ac.jp name: Motonori Ota orcid: 0000-0001-9090-668X description: The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion. example: '051' homepage: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html keywords: - life science mappings: biocontext: PSCDB fairsharing: FAIRsharing.3d4jx0 integbio: nbdc01636 miriam: pscdb n2t: pscdb name: Protein Structural Change Database pattern: ^\d+$ preferred_prefix: pscdb publications: - doi: 10.1093/nar/gkr966 pmc: PMC3245091 pubmed: '22080505' title: 'PSCDB: a database for protein structural change upon ligand binding' year: 2011 - doi: 10.1016/j.jmb.2011.02.058 pubmed: '21376729' title: Classification and annotation of the relationship between protein structural change and ligand binding year: 2011 uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html psdo: contact: email: zachll@umich.edu github: zachll name: Zach Landis-Lewis orcid: 0000-0002-9117-9338 depends_on: - bfo - iao - ro - stato description: 'Performance Summary Display Ontology (PSDO) is an application ontology about motivating information in performance summaries and the visual and textual entities that are used to communicate about performance. Motivating information includes performance comparisons and changes that motivate improvement or sustainment, such as improvement towards a goal, loss of high performer status, or the presence of a performance gap. Visual and textual entities include charts, tables, and graphs that display performance information. PSDO''s domain focus is healthcare organizations that use clinical quality dashboards and feedback interventions for healthcare professionals and teams. Performance information is commonly about the quality of care and health outcomes that have been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is supported by the NIH, National Library of Medicine (1K01LM012528-01, 1R01LM013894-01). Landis-Lewis Z, Stansbury C, Rincón J, Gross C. Performance Summary Display Ontology: Feedback intervention content, delivery, and interpreted information. International Conference on Biomedical Ontology 2022 (ICBO 2022). https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf' download_owl: http://purl.obolibrary.org/obo/psdo.owl example: '0000055' homepage: https://github.com/Display-Lab/psdo keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: PSDO bioportal: PSDO obofoundry: psdo ols: psdo ontobee: PSDO name: Performance Summary Display Ontology pattern: ^\d{7}$ preferred_prefix: PSDO rdf_uri_format: http://purl.obolibrary.org/obo/PSDO_$1 repository: https://github.com/Display-Lab/psdo uri_format: http://purl.obolibrary.org/obo/PSDO_$1 version: 1.0.1 pseudogene: contact: email: mark@gersteinlab.org name: Mark Gerstein orcid: 0000-0002-9746-3719 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase. example: PGOHUM00000289843 homepage: http://www.pseudogene.org keywords: - gene - ontology mappings: bioportal: pseudo integbio: nbdc00178 prefixcommons: pseudogene name: PseudoGene preferred_prefix: pseudogene providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pseudogene:$1 synonyms: - pseudogene.org uri_format: http://tables.pseudogene.org/[?species_name]/$1 pseudomonas: description: The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation. example: PSEEN0001 homepage: http://www.pseudomonas.com/ mappings: biocontext: PSEUDOMONAS miriam: pseudomonas n2t: pseudomonas name: Pseudomonas Genome Database pattern: ^P\w+$ preferred_prefix: pseudomonas uri_format: http://www.pseudomonas.com/feature/show/?locus_tag=$1 psipar: banana: PAR comment: This resource is no longer loaded on XML and the sourceforge link from the HUPO website to the psi-par.obo artifact is dead. deprecated: true description: Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms. example: '0116' homepage: https://www.psidev.info/psi-par mappings: biocontext: PSIPAR miriam: psipar n2t: psipar name: Protein Affinity Reagents pattern: ^\d+$ preferred_prefix: psipar uri_format: https://www.ebi.ac.uk/ontology-lookup/?termId=PAR:$1 pso: contact: email: cooperl@oregonstate.edu github: cooperl09 name: Laurel Cooper orcid: 0000-0002-6379-8932 depends_on: - ro description: The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter. download_obo: http://purl.obolibrary.org/obo/pso.obo download_owl: http://purl.obolibrary.org/obo/pso.owl example: '0000013' homepage: https://github.com/Planteome/plant-stress-ontology keywords: - hospital - medical informatics - monitoring - obo - occupational medicine - ontology license: CC-BY-3.0 mappings: aberowl: PSO agroportal: PSO bioportal: PSO fairsharing: FAIRsharing.dyj433 obofoundry: pso ols: pso ontobee: PSO name: Plant Stress Ontology pattern: ^\d{7}$ preferred_prefix: PSO publications: - doi: 10.1093/nar/gkx1152 pmc: PMC5753347 pubmed: '29186578' title: 'The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics' year: 2018 rdf_uri_format: http://purl.obolibrary.org/obo/PSO_$1 repository: https://github.com/Planteome/plant-stress-ontology uri_format: http://purl.obolibrary.org/obo/PSO_$1 version: '2023-11-14' pspub: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Documentation of the Phenoscape Curation Workflow homepage: https://wiki.phenoscape.org/wiki/Curation_workflow name: Phenoscape Publication preferred_prefix: pspub psskb: contact: email: kaysheva1@gmail.com name: Anna L. Kaysheva orcid: 0000-0003-4472-2016 contributor: email: palayoor.n@northeastern.edu github: nalikapalayoor name: Nalika Palayoor orcid: 0009-0008-8406-631X description: PSSKB allows researchers to model post translational modifications and amino acid substitutions in proteins, providing 3D structural representations. Identifiers represent protein motifs on which PSSKB provides data. example: 2VM6_A55_A135 github_request_issue: 1398 homepage: https://psskb.org/ name: Protein Structure and Stability Knowledge Base pattern: ^[A-Za-z0-9_]+$ preferred_prefix: psskb publications: - doi: 10.1002/jcc.70046 pubmed: '39876062' title: 'PSSKB: A Web Application to Study Protein Structures' year: 2025 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://psskb.org/motif/card/$1 pubchem.bioassay: contact: email: pruitt@ncbi.nlm.nih.gov name: Kim Dixon Pruitt orcid: 0000-0001-7950-1374 description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results. example: '1018' homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay keywords: - small molecule mappings: biocontext: PUBCHEM.BIOASSAY edam: '2638' go: PubChem_BioAssay integbio: nbdc00640 miriam: pubchem.bioassay n2t: pubchem.bioassay prefixcommons: pubchem.bioassay name: NCBI PubChem database of bioassay records part_of: pubchem pattern: ^\d+$ preferred_prefix: pubchem.bioassay providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pubchem.bioassay:$1 publications: - doi: 10.1093/nar/gkl1031 pmc: PMC1781113 pubmed: '17170002' title: Database resources of the National Center for Biotechnology Information year: 2006 synonyms: - pubchem.aid - pubchem.assay twitter: pubchem uri_format: https://pubchem.ncbi.nlm.nih.gov/bioassay/$1 pubchem.cell: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Cell Lines in PubChem example: '31' homepage: https://pubchem.ncbi.nlm.nih.gov keywords: - bioactivities - cell lines - chemistry name: PubChem Cell Line part_of: pubchem pattern: ^\d+$ preferred_prefix: pubchem.cell twitter: pubchem uri_format: https://pubchem.ncbi.nlm.nih.gov/cell/$1 pubchem.classification: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The PubChem Classification Browser allows you to browse the distribution of PubChem data among nodes in the hierarchy of interest, thereby providing an aggregate view of PubChem data. It also allows you to search for PubChem records annotated with the desired hierarchy/term, providing a powerful way to quickly find the subset of PubChem records. example: '87' homepage: https://pubchem.ncbi.nlm.nih.gov/classification/ keywords: - chemistry name: PubChem Classification part_of: pubchem pattern: ^\d+$ preferred_prefix: pubchem.classification twitter: pubchem uri_format: https://pubchem.ncbi.nlm.nih.gov/classification/#hid=$1 pubchem.compound: contact: email: bolton@ncbi.nlm.nih.gov name: Evan E Bolton orcid: 0000-0002-5959-6190 description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records. example: '100101' homepage: https://pubchem.ncbi.nlm.nih.gov/ keywords: - chemical - chemistry - epidemiology - metabolite - structure - virology mappings: biocontext: PUBCHEM.COMPOUND biolink: CID cellosaurus: PubChem cheminf: '000140' edam: '2639' fairsharing: FAIRsharing.qt3w7z go: PubChem_Compound integbio: nbdc02626 miriam: pubchem.compound n2t: pubchem.compound pathguide: '361' prefixcommons: pubchem.compound re3data: r3d100010129 togoid: PubchemCompound wikidata: P662 name: PubChem CID part_of: pubchem pattern: ^\d+$ preferred_prefix: pubchem.compound providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pubchem.compound:$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/pubchem/$1 publications: - doi: 10.1093/nar/gkaa971 pmc: PMC7778930 pubmed: '33151290' title: 'PubChem in 2021: new data content and improved web interfaces' year: 2021 - doi: 10.1093/nar/gky1033 pmc: PMC6324075 pubmed: '30371825' title: 'PubChem 2019 update: improved access to chemical data' year: 2019 - doi: 10.1093/nar/gkw1118 pmc: PMC5210581 pubmed: '27899599' title: 'PubChem BioAssay: 2017 update' year: 2016 - doi: 10.1093/nar/gkt978 pmc: PMC3965008 pubmed: '24198245' title: 'PubChem BioAssay: 2014 update' year: 2013 - doi: 10.1093/nar/gkr1132 pmc: PMC3245056 pubmed: '22140110' title: PubChem's BioAssay Database year: 2011 - doi: 10.1016/j.drudis.2010.10.003 pmc: PMC3010383 pubmed: '20970519' title: PubChem as a public resource for drug discovery year: 2010 - doi: 10.1093/nar/gkp456 pmc: PMC2703903 pubmed: '19498078' title: 'PubChem: a public information system for analyzing bioactivities of small molecules' year: 2009 - doi: 10.1093/nar/gkl1031 pmc: PMC1781113 pubmed: '17170002' title: Database resources of the National Center for Biotechnology Information year: 2006 rdf_uri_format: http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID$1 synonyms: - CID - DSSTox_CID - PUBCHEM_CID - PubChem_Compound_CID - Pubchem - pubchem_id twitter: pubchem uri_format: https://pubchem.ncbi.nlm.nih.gov/compound/$1 pubchem.element: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number. example: '1' homepage: https://pubchem.ncbi.nlm.nih.gov/periodic-table keywords: - chemistry name: PubChem Element part_of: pubchem pattern: ^\d+$ preferred_prefix: pubchem.element twitter: pubchem uri_format: https://pubchem.ncbi.nlm.nih.gov/element/$1 pubchem.substance: description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records. example: '100101' homepage: https://pubchem.ncbi.nlm.nih.gov/ keywords: - protein - small molecule - structure mappings: biocontext: PUBCHEM.SUBSTANCE cheminf: '000141' go: PubChem_Substance integbio: nbdc00642 miriam: pubchem.substance n2t: pubchem.substance prefixcommons: pubchem.substance togoid: PubchemSubstance wikidata: P2153 name: PubChem Substance ID (SID) part_of: pubchem pattern: ^\d+$ preferred_prefix: pubchem.substance providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pubchem.substance:$1 publications: - doi: 10.1093/nar/gkl1031 pmc: PMC1781113 pubmed: '17170002' title: Database resources of the National Center for Biotechnology Information year: 2006 rdf_uri_format: http://rdf.ncbi.nlm.nih.gov/pubchem/substance/SID$1 synonyms: - DSSTox_Generic_SID twitter: pubchem uri_format: https://pubchem.ncbi.nlm.nih.gov/substance/$1 publons.publication: description: identifier for the defunct/merged Publons website; URL redirects to Web of Science's P8372 (WOSID) example: '18466622' homepage: https://publons.com mappings: wikidata: P3431 name: Publons publication preferred_prefix: publons.publication uri_format: https://publons.com/publon/$1 publons.researcher: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Database of researchers to track publications, citation metrics, peer reviews, and journal editing work. example: '1981638' homepage: https://publons.com/researcher mappings: biolink: ResearchID wikidata: P3829 name: Publons Researcher pattern: ^\d+$ preferred_prefix: publons.researcher uri_format: https://publons.com/researcher/$1 pubmed: contact: email: beck@ncbi.nlm.nih.gov github: jeffbeckncbi name: Jeff Beck orcid: 0000-0002-1798-9797 description: PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. example: '16333295' homepage: https://www.ncbi.nlm.nih.gov/PubMed/ keywords: - bibliography - biomedical science - citation - publication mappings: biocontext: PUBMED cellosaurus: PubMed cheminf: '000302' edam: '1187' fairsharing: FAIRsharing.2b9b61 go: PMID integbio: nbdc00179 miriam: pubmed n2t: pubmed prefixcommons: pubmed togoid: Pubmed wikidata: P698 name: PubMed pattern: ^\d+$ preferred_prefix: pubmed providers: - code: CURATOR_REVIEW description: PubMed through Linkedlife data homepage: http://linkedlifedata.com/ name: PubMed through Linkedlife data uri_format: http://linkedlifedata.com/resource/pubmed/id/$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pubmed:$1 - code: epmc description: Europe PMC homepage: http://europepmc.org/ name: Europe PMC uri_format: http://europepmc.org/abstract/MED/$1 - code: hubmed description: HubMed homepage: http://www.hubmed.org/ name: HubMed uri_format: https://www.hubmed.org/?term=$1 - code: pubmed.new description: New-style link for pubmed homepage: https://pubmed.ncbi.nlm.nih.gov name: PubMed (new) uri_format: https://pubmed.ncbi.nlm.nih.gov/$1 - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/pubmed/$1 - code: uniprot.citation description: UniProt mints PURLs for citations identifiers homepage: https://uniprot.org/ name: UniProt uri_format: http://purl.uniprot.org/citations/$1 - code: uniprot.pubmed description: UniProt mints PURLs for PubMed identifiers homepage: https://uniprot.org/ name: UniProt uri_format: http://purl.uniprot.org/pubmed/$1 publications: - doi: 10.1093/nar/gkj158 pmc: PMC1347520 pubmed: '16381840' title: Database resources of the National Center for Biotechnology Information year: 2006 rdf_uri_format: http://rdf.ncbi.nlm.nih.gov/pubchem/reference/$1 synonyms: - MEDLINE - PMID - PubMed - PubMed ID - pmid uri_format: https://pubmed.ncbi.nlm.nih.gov/$1/ puro: contact: email: silvio.peroni@unibo.it github: essepuntato name: Silvio Peroni orcid: 0000-0003-0530-4305 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology for the characterisation of the roles of agents – people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians. example: RoleInTime homepage: http://www.sparontologies.net/ontologies/pro keywords: - bibliography - citation - data model - report - subject agnostic mappings: fairsharing: FAIRsharing.3e88d6 name: Publishing Roles Ontology preferred_prefix: PuRO publications: - doi: 10.1145/2362499.2362502 title: Scholarly publishing and linked data year: 2012 repository: https://github.com/sparontologies/pro twitter: sparontologies uri_format: http://purl.org/spar/pro/$1 pw: banana: PW contact: email: gthayman@mcw.edu github: gthayman name: G. Thomas Hayman orcid: 0000-0002-9553-7227 description: 'The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions.' download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo download_owl: http://purl.obolibrary.org/obo/pw.owl example: '0000423' homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html keywords: - biological regulation - disease - drug - drug metabolism - enzymatic reaction - human - life science - mathematical model - molecular entity - network model - obo - ontology - pathway - pathway model - signaling license: CC-BY-4.0 logo: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif mappings: aberowl: PW biocontext: PW bioportal: PW fairsharing: FAIRsharing.f73xhd miriam: pw n2t: pw obofoundry: pw ols: pw ontobee: PW prefixcommons: pw wikidata: P7333 name: Pathway ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: PW providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pw:$1 - code: miriam_obo_legacy description: An old URI style for MIRIAM homepage: https://identifiers.org/ name: MIRIAM OBO Legacy uri_format: http://identifiers.org/obo.pw/PW:$1 publications: - doi: 10.1186/s40246-014-0017-8 pmc: PMC4191248 pubmed: '25265995' title: 'Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease' year: 2014 - doi: 10.1186/2041-1480-5-7 pmc: PMC3922094 pubmed: '24499703' title: The pathway ontology - updates and applications year: 2014 - doi: 10.1093/database/bar010 pmc: PMC3072770 pubmed: '21478484' title: The Rat Genome Database pathway portal year: 2011 rdf_uri_format: http://purl.obolibrary.org/obo/PW_$1 repository: https://github.com/rat-genome-database/PW-Pathway-Ontology twitter: ratgenome uri_format: http://purl.obolibrary.org/obo/PW_$1 version: '7.86' pwo: contact: email: silvio.peroni@unibo.it github: essepuntato name: Silvio Peroni orcid: 0000-0003-0530-4305 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity. example: Workflow homepage: http://www.sparontologies.net/ontologies/pwo keywords: - bibliography - citation - data model - report - spar - subject agnostic mappings: fairsharing: FAIRsharing.c4e46c lov: pwo name: Publishing Workflow Ontology preferred_prefix: PWO publications: - doi: 10.3233/sw-160230 title: The Publishing Workflow Ontology (PWO) year: 2017 repository: https://github.com/sparontologies/pwo twitter: sparontologies uri_format: http://purl.org/spar/pwo/$1 px: description: The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination. example: PXD000500 homepage: http://www.proteomexchange.org/ mappings: biocontext: PX miriam: px n2t: px name: ProteomeXchange pattern: ^(R)?PXD\d{6}$ preferred_prefix: px uri_format: http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1 pypi: description: The Python Package Index (PyPI) is a repository for Python packages. example: numpy homepage: https://www.python.org/psf/ mappings: miriam: pypi name: PyPI pattern: ^[a-zA-Z_][a-zA-Z0-9\-_]+$ preferred_prefix: pypi uri_format: https://pypi.org/project/$1 qb: contact: email: richard@cyganiak.de github: cygri name: Richard Cyganiak orcid: 0000-0001-9950-5209 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF. It is based on the core information model from SDMX (and thus also DDI). download_rdf: http://purl.org/linked-data/cube# example: Observation homepage: https://www.w3.org/TR/vocab-data-cube keywords: - methods - w3c rec mappings: lov: qb zazuko: qb name: The data cube vocabulary pattern: ^\w+$ preferred_prefix: qb repository: https://github.com/UKGovLD/publishing-statistical-data uri_format: http://purl.org/linked-data/cube#$1 qtldb: description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent. example: '4685' homepage: https://www.animalgenome.org/QTLdb mappings: miriam: qtldb name: Animal Genome QTL pattern: ^\d+$ preferred_prefix: qtldb uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 qudt: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types. download_owl: http://aber-owl.net/media/ontologies/QUDT/4/qudt.owl download_rdf: http://qudt.org/schema/qudt/ example: baseDimensionEnumeration homepage: https://qudt.org keywords: - astrophysics and astronomy - experimental measurement - methods - ontology - unit mappings: aberowl: QUDT bartoc: '18206' biolink: qud bioportal: QUDT fairsharing: FAIRsharing.d3pqw7 lov: qudt zazuko: qudt name: Quantities, Units, Dimensions, and Types Ontology preferred_prefix: qudt providers: - code: v11 description: Version 1.1 provider homepage: http://qudt.org name: Version 1.1 uri_format: http://qudt.org/1.1/schema/qudt#$1 repository: https://github.com/qudt/qudt-public-repo uri_format: http://qudt.org/schema/qudt#$1 radiomics: contact: email: alberto.traverso@maastro.nl name: Alberto Traverso orcid: 0000-0001-6183-4429 description: The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual. [bioportal] example: LK99 homepage: http://www.radiomics.org/RO keywords: - ontology mappings: bioportal: RO name: Radiomics Ontology preferred_prefix: radiomics uri_format: http://www.radiomics.org/RO/$1 radlex: contact: email: radlex-feedback@lists.rsna.org name: Radiological Society of North America contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'A comprehensive set of radiology terms for use in radiology reporting, decision support, data mining, data registries, education and research. RadLex provides the foundation for vital data resources used in radiology: - The LOINC/RSNA Radiology Playbook - RadElement Common Data Elements -RadReport Radiology Reporting Templates The development of RadLex has been supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the cancer Biomedical Informatics Grid (caBIG) project.' download_owl: http://aber-owl.net/media/ontologies/RADLEX/37/radlex.owl example: RID1 homepage: https://radlex.org keywords: - anatomy - biomedical science - clinical studies - diagnosis - medical imaging - medical informatics - ontology - radiology license: http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/RadLex_License_Agreement_and_Terms_of_Use_V2_Final.pdf mappings: aberowl: RADLEX bioportal: RADLEX fairsharing: FAIRsharing.shm2f2 hl7: 2.16.840.1.113883.6.256 name: RSNA Informatics RadLex pattern: ^RID\d+$ preferred_prefix: radlex publications: - doi: 10.1016/j.jvir.2009.04.031 pubmed: '19560008' title: 'The IR Radlex Project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology' year: 2009 - doi: 10.1016/j.jvir.2008.10.022 pubmed: '19081735' title: 'The IR RadLex project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology' year: 2008 - doi: 10.2214/ajr.174.5.1741463 pubmed: '10789815' title: Radiology lexicon year: 2000 uri_format: https://radlex.org/RID/$1 version: '4.1' rapdb.locus: description: Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB. example: Os01g0883800 homepage: https://rapdb.dna.affrc.go.jp/ mappings: miriam: rapdb.locus name: RAP-DB Locus pattern: ^Os\S+g\d{7}$ preferred_prefix: rapdb.locus synonyms: - irgsp uri_format: https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$1 rapdb.transcript: description: Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB. example: Os01t0883800-02 homepage: https://rapdb.dna.affrc.go.jp/ keywords: - dna - genome mappings: go: RAP-DB miriam: rapdb.transcript ncbi: RAP-DB prefixcommons: rapdb name: Rice annotation Project database pattern: ^Os\S+t\d{7}-\d{2}$ preferred_prefix: rapdb.transcript providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/rapdb:$1 uri_format: https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1 ratmap: comment: This resource doesn't exist on the web anymore deprecated: true description: The Rat Genome Database RatMap is focused on presenting rat genes, DNA-markers, QTL:s etc that is localized to chromosome. The database is dedicated to rat gene nomenclature and should be consulted for queries in such matters example: '5' homepage: http://ratmap.org keywords: - dna - gene - genome mappings: ncbi: RATMAP prefixcommons: ratmap name: Rat Genome Database preferred_prefix: ratmap providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ratmap:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://ratmap.org/Showgene.php?gene_stable_id=$1 rbk: contact: email: oxburl@mmc.org name: Leif Oxburgh orcid: 0000-0002-2825-7663 description: (Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function. example: Q-2958 homepage: https://www.rebuildingakidney.org/ keywords: - cell biology - developmental biology - genomics - molecular biology mappings: biocontext: RBK fairsharing: FAIRsharing.78d3ad miriam: rbk n2t: rbk name: Rebuilding a Kidney pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$ preferred_prefix: rbk publications: - doi: 10.1681/asn.2016101077 pmc: PMC5407737 pubmed: '28096308' title: (Re)Building a Kidney year: 2017 - doi: 10.1681/ASN.2016101077 title: (Re)Building a Kidney. repository: https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Create-citable-datasets uri_format: https://www.rebuildingakidney.org/id/$1 rbo: contact: email: daniel.c.berrios@nasa.gov github: DanBerrios name: Daniel C. Berrios orcid: 0000-0003-4312-9552 depends_on: - bfo - chmo - envo - obi - pato - ro - uo description: RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. download_json: http://purl.obolibrary.org/obo/rbo.json download_obo: http://purl.obolibrary.org/obo/rbo.obo download_owl: http://purl.obolibrary.org/obo/rbo.owl example: '00000105' example_extras: - '010007' homepage: https://github.com/Radiobiology-Informatics-Consortium/RBO keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: RBO bioportal: RBO obofoundry: rbo ols: rbo ontobee: RBO name: Radiation Biology Ontology pattern: ^\d{6,8}$ preferred_prefix: RBO rdf_uri_format: http://purl.obolibrary.org/obo/RBO_$1 repository: https://github.com/Radiobiology-Informatics-Consortium/RBO uri_format: http://purl.obolibrary.org/obo/RBO_$1 version: '2025-02-18' rcb: contact: email: atsushi.yoshiki@riken.jp name: Atsushi Yoshiki orcid: 0000-0002-9450-5151 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center. example: RCB0002 homepage: https://cell.brc.riken.jp/en/rcb keywords: - animal - bioresource - cell - cell line - cultured cell - cultured cell line - dna - embryo - experimental animal - experimental plant - faseb list - gene - genetic material - organ - plant - recombinant host - seed - sperm - tissue - virus mappings: cellosaurus: RCB rrid: IMSR_RBRC name: RIKEN Bioresource Center Cell Bank pattern: ^RCB\d+$ preferred_prefix: rcb publications: - pubmed: '34532769' - pubmed: '19448331' uri_format: https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1 rdf: contact: email: rmrich5@gmail.com name: Rafael Richards orcid: 0000-0001-5699-0515 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts example: type homepage: http://www.w3.org/1999/02/22-rdf-syntax-ns keywords: - computer science - subject agnostic - w3c rec mappings: biocontext: rdf fairsharing: FAIRsharing.p77ph9 lov: rdf zazuko: rdf name: Resource Description Framework preferred_prefix: rdf uri_format: http://www.w3.org/1999/02/22-rdf-syntax-ns#$1 rdfa: contact: email: ivan@w3.org github: iherman name: Ivan Herman orcid: 0000-0003-0782-2704 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: RDFa Core is a specification for attributes to express structured data in any markup language. The embedded data already available in the markup language (e.g., HTML) can often be reused by the RDFa markup, so that publishers don't need to repeat significant data in the document content. (from https://www.w3.org/TR/rdfa-core/) download_rdf: http://www.w3.org/ns/rdfa.ttl example: PrefixOrTermMapping homepage: http://www.w3.org/ns/rdfa keywords: - rdf mappings: lov: rdfa zazuko: rdfa name: RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting preferred_prefix: rdfa uri_format: http://www.w3.org/ns/rdfa#$1 rdfs: contact: email: danbri@w3.org name: Dan Brickley orcid: 0000-0002-6450-7041 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary. download_owl: https://triplydb.com/w3c/rdfs/download.trig.gz example: label homepage: https://www.w3.org/TR/rdf-schema/ keywords: - bioinformatics - life science - linguistics - ontology - ontology and terminology - w3c rec mappings: aberowl: RDFS biocontext: rdfs bioportal: RDFS fairsharing: FAIRsharing.v9n3gk lov: rdfs ols: rdfs zazuko: rdfs name: RDF Schema preferred_prefix: rdfs uri_format: http://www.w3.org/2000/01/rdf-schema#$1 rdo: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms. download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.obo download_owl: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.owl example: '9002859' homepage: https://ratmine.mcw.edu/ontology/disease/ keywords: - ontology name: RGD Disease Ontology pattern: ^\d{7}$ preferred_prefix: rdo uri_format: http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1 re3data: description: Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines. example: r3d100010772 homepage: https://datacite.org mappings: bartoc: '822' miriam: re3data name: re3data pattern: ^r3d\d{9,9}$ preferred_prefix: re3data uri_format: https://www.re3data.org/repository/$1 reactome: contact: email: deustp01@med.nyu.edu github: deustp01 name: Peter D'Eustachio orcid: 0000-0002-5494-626X contributor_extras: - email: smoxon@lbl.gov github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 description: The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology. example: R-BTA-418592 homepage: https://www.reactome.org/ keywords: - human - pathway - reaction license: CC0-1.0 mappings: biocontext: REACTOME cheminf: '000411' edam: '1155' go: Reactome integbio: nbdc00185 miriam: reactome n2t: reactome pathguide: '103' prefixcommons: reactome re3data: r3d100010861 togoid: ReactomePathway wikidata: P3937 name: Reactome pattern: ^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$ preferred_prefix: reactome providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/reactome:$1 - code: browser description: An interactive view over pathways. homepage: https://reactome.org/PathwayBrowser/ name: Reactome Pathway Browser uri_format: https://reactome.org/PathwayBrowser/#/$1 - code: pathwaycommons description: Pathway diagram drawn with Cytoscape homepage: https://www.pathwaycommons.org name: Pathway Commons uri_format: https://apps.pathwaycommons.org/pathways?uri=http%3A%2F%2Fidentifiers.org%2Freactome%2F$1 publications: - doi: 10.1093/nar/gki072 pmc: PMC540026 pubmed: '15608231' title: 'Reactome: a knowledgebase of biological pathways' year: 2005 references: - https://github.com/biopragmatics/bioregistry/pull/1086 synonyms: - RE - REACT - reactome.pathway uri_format: https://reactome.org/content/detail/$1 reaxys: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier. example: '1257009' homepage: https://www.reaxys.com mappings: edam: '1003' wikidata: P1579 name: Reaxys pattern: ^\d+$ preferred_prefix: reaxys synonyms: - Beilstein - Reaxys rebase: contact: email: roberts@neb.com name: Richard John Roberts orcid: 0000-0002-4348-0169 description: REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. example: '101' homepage: http://rebase.neb.com/rebase/ keywords: - dna - enzyme - genome - life science - protein - rna - small molecule - structure mappings: biocontext: REBASE edam: '2325' fairsharing: FAIRsharing.9sb9qh go: REBASE integbio: nbdc00648 miriam: rebase n2t: rebase pathguide: '72' prefixcommons: rebase re3data: r3d100012171 uniprot: DB-0089 wikidata: P4866 name: REBASE Enzyme Number pattern: ^\d+$ preferred_prefix: rebase providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/rebase:$1 publications: - doi: 10.1093/nar/gku1046 pmc: PMC4383893 pubmed: '25378308' title: 'REBASE--a database for DNA restriction and modification: enzymes, genes and genomes' year: 2014 - doi: 10.1093/nar/gkp874 pmc: PMC2808884 pubmed: '19846593' title: 'REBASE--a database for DNA restriction and modification: enzymes, genes and genomes' year: 2009 uri_format: http://rebase.neb.com/rebase/enz/$1.html rebec: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Presents the new fast tracks for clinical research and observational studies on INDIGENOUS PEOPLE AND TRADITIONAL COMMUNITIES and on NEGLECTED TROPICAL DISEASES (NTDs). Fast-track can reduce the normal approval period for clinical trials to less than 48 hours, if the documentation, information and any mandatory changes requested are provided by the registrant. example: RBR-6qvdftm homepage: https://ensaiosclinicos.gov.br name: Brazilian Registry of Clinical Trials pattern: ^RBR-\w+$ preferred_prefix: rebec uri_format: https://ensaiosclinicos.gov.br/rg/$1 receptome.family: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database. example: '5.1' homepage: http://www.receptome.org keywords: - protein mappings: prefixcommons: hpmr name: Human Plasma Membrane Receptome Families preferred_prefix: receptome.family providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/hpmr:$1 uri_format: http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1 redfly: comment: This resource doesn't exist on the web anymore deprecated: true description: REDflyis a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). example: '8' homepage: http://redfly.ccr.buffalo.edu keywords: - regulation mappings: pathguide: '265' prefixcommons: redfly name: Regulatory Elements Database for Drosophila preferred_prefix: redfly providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/redfly:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id=$1 refseq: contact: email: pruitt@ncbi.nlm.nih.gov name: Kim Dixon Pruitt orcid: 0000-0001-7950-1374 contributor_extras: - github: slobentanzer name: Sebastian Lobentanzer orcid: 0000-0003-3399-6695 description: The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products. example: NP_012345 example_extras: - WP_029104145.1 has_canonical: ncbiprotein homepage: https://www.ncbi.nlm.nih.gov/projects/RefSeq/ keywords: - computational biology - dna - genetics - life science - protein - rna mappings: biocontext: RefSeq edam: '1098' fairsharing: FAIRsharing.4jg0qw go: RefSeq hl7: 2.16.840.1.113883.6.280 integbio: nbdc00187 miriam: refseq n2t: refseq prefixcommons: refseq re3data: r3d100010285 uniprot: DB-0117 name: Reference Sequence Collection pattern: ^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\d+)|(NZ_[A-Z]{2,4}\d+))(\.\d+)?$ preferred_prefix: refseq providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/refseq:$1 publications: - doi: 10.1093/nar/gkae1038 pubmed: '39526381' title: 'NCBI RefSeq: reference sequence standards through 25 years of curation and annotation' year: 2024 - doi: 10.1093/nar/gkv1189 pmc: PMC4702849 pubmed: '26553804' title: 'Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation' year: 2015 - doi: 10.1093/nar/gkl842 pmc: PMC1716718 pubmed: '17130148' title: 'NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins' year: 2006 references: - https://github.com/biopragmatics/bioregistry/issues/545 synonyms: - REFSEQ_PROT uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 reo: comment: 'From James O.: It was an ontology for "reagents" developed by @Matthew Brush. Since OBI was interested in reagents, Matt developed it in coordination with OBI and had plans to submit it to OBO. I believe that REO was once included in Ontobee, and OBI even started using some REO terms. But REO was never submitted to OBO. I believe it was abandoned.' contact: email: matt@tislab.org github: mbrush name: Matthew Brush orcid: 0000-0002-1048-5019 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs. download_owl: https://github.com/tis-lab/reagent-ontology/raw/master/reo/ontology_files/reo_pre-merged_or_reasoned_files/reo_reasoned_9-6-12.owl example: 0000079 homepage: https://github.com/tis-lab/reagent-ontology keywords: - ontology mappings: ontobee: REO name: Reagent Ontology pattern: ^\d{7}$ preferred_prefix: reo references: - https://github.com/obi-ontology/obi/issues/1015 - https://code.google.com/archive/p/reagent-ontology/ - https://github.com/obi-ontology/obi/issues/1135 repository: https://github.com/tis-lab/reagent-ontology uri_format: http://purl.obolibrary.org/obo/REO_$11 repeatsdb.protein: description: RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database. example: P29894 homepage: https://repeatsdb.org/ mappings: miriam: repeatsdb.protein name: RepeatsDB Protein pattern: ^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$ preferred_prefix: repeatsdb.protein provides: uniprot uri_format: https://repeatsdb.org/protein/$1 repeatsdb.structure: description: RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database. example: 2gc4E homepage: https://repeatsdb.org/ mappings: miriam: repeatsdb.structure name: RepeatsDB Structure pattern: ^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$ preferred_prefix: repeatsdb.structure uri_format: https://repeatsdb.org/structure/$1 repec: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Peruvian Clinical Trials Registry - REPEC is a non-profit online information system developed in 2007 by INS. It is a publicly accessible prospective registry aimed at providing information about clinical trials underway in Peru. REPEC also includes Registries for Trial Sites, Institutional Research Ethics Committees, Sponsors and Contract Research Organizations. REPEC contains records of clinical trials since 1995. Since December 14, 2012, the Peruvian National Institute of Health, by means of the General Office for Research and Technological Transfer (OGITT), has started a process to improve REPEC and to join the WHO International Clinical Trials Registry Platform (ICTRP) and to be acknowledged as a Primary Registry. More information about primary registries is available in ICRTP at http://apps.who.int/trialsearch/. (from website) example: 046-19 homepage: https://ensayosclinicos-repec.ins.gob.pe/en/ logo: https://ensayosclinicos-repec.ins.gob.pe/images/plantilla/img_logo_principal_repec_en.png name: Peruvian Clinical Trial Registry pattern: ^\d+-\d+(-[A-Z])?$ preferred_prefix: repec uri_format: https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC=$1 reproduceme: contact: email: sheeba.samuel@uni-jena.de name: Sheeba Samuel orcid: 0000-0002-7981-8504 description: The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility. download_owl: http://aber-owl.net/media/ontologies/REPRODUCE-ME/7/reproduce-me.owl example: MicrobeamManipulation homepage: https://w3id.org/reproduceme/research keywords: - ontology mappings: aberowl: REPRODUCE-ME bioportal: REPRODUCE-ME ols: reproduceme name: REPRODUCE-ME Ontology preferred_prefix: reproduceme uri_format: https://w3id.org/reproduceme#$1 version: '1.1' researchgate.profile: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier for a person, used by ResearchGate profiles example: Rita-Heuser homepage: https://www.researchgate.net keywords: - person - researcher mappings: wikidata: P2038 name: ResearchGate profile ID pattern: ^[0-9A-Za-z_-]+$ preferred_prefix: researchgate.profile references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://www.researchgate.net/profile/$1 resid: contact: email: john.garavelli@ebi.ac.uk name: John Garavelli orcid: 0000-0002-4131-735X deprecated: true description: The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. example: AA0001 homepage: https://proteininformationresource.org/resid/ keywords: - obo - ontology - protein - small molecule - structure mappings: biocontext: RESID edam: '2619' go: RESID miriam: resid n2t: resid obofoundry: resid prefixcommons: resid name: Protein covalent bond pattern: ^AA\d{4}$ preferred_prefix: RESID providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/resid:$1 publications: - doi: 10.1002/pmic.200300764 pubmed: '15174124' title: Annotation of post-translational modifications in the Swiss-Prot knowledge base year: 2004 rdf_uri_format: http://purl.obolibrary.org/obo/RESID_$1 uri_format: https://proteininformationresource.org/cgi-bin/resid?id=$1 reto: contact: email: vladimir.n.mironov@gmail.com name: Vladimir Mironov description: Regulation of Transcription download_obo: https://www.bio.ntnu.no/ontology/ReTO/reto.obo download_owl: https://www.bio.ntnu.no/ontology/ReTO/reto.owl download_rdf: http://www.bio.ntnu.no/ontology/ReTO/reto.rdf homepage: http://www.semantic-systems-biology.org/apo keywords: - life science - ontology - regulation of gene expression - transcript - transcriptomics mappings: aberowl: RETO bioportal: RETO fairsharing: FAIRsharing.4qyf0f ols: reto name: Regulation of Transcription Ontology no_own_terms: true preferred_prefix: reto rex: contact: email: amalik@ebi.ac.uk github: amalik01 name: Adnan Malik orcid: 0000-0001-8123-5351 deprecated: true description: An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. download_owl: http://purl.obolibrary.org/obo/rex.owl example: '0000512' homepage: https://www.ebi.ac.uk/chebi/ keywords: - biochemistry - chemistry - enzymatic reaction - life science - obo - ontology - reaction data mappings: aberowl: REX biocontext: REX bioportal: REX fairsharing: FAIRsharing.g0a7s0 obofoundry: rex ols: rex ontobee: REX prefixcommons: rex name: Physico-chemical process part_of: chebi pattern: ^\d{7}$ preferred_prefix: REX providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/rex:$1 rdf_uri_format: http://purl.obolibrary.org/obo/REX_$1 uri_format: http://purl.obolibrary.org/obo/REX_$1 version: '2017-11-19' rexo: contact: email: kuiper@bio.ntnu.no github: makuintnu name: Martin Kuiper orcid: 0000-0002-1171-9876 description: Regulation of Gene Expression download_obo: https://www.bio.ntnu.no/ontology/ReXO/rexo.obo download_owl: https://www.bio.ntnu.no/ontology/ReXO/rexo.owl download_rdf: http://www.bio.ntnu.no/ontology/ReXO/rexo.rdf homepage: http://www.semantic-systems-biology.org/apo keywords: - expression data - life science - ontology - orthologous - regulation of gene expression mappings: aberowl: REXO bioportal: REXO fairsharing: FAIRsharing.recas1 ols: rexo name: Regulation of Gene Expression Ontology no_own_terms: true preferred_prefix: rexo publications: - doi: 10.1186/s12859-014-0386-y pmc: PMC4279962 pubmed: '25490885' title: Finding gene regulatory network candidates using the gene expression knowledge base year: 2014 rfam: contact: email: apetrov@ebi.ac.uk github: AntonPetrov name: Anton I Petrov orcid: 0000-0001-7279-2682 description: 'The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion.' example: RF00230 homepage: https://rfam.org/ keywords: - genetics mappings: biocontext: RFAM edam: '2356' fairsharing: FAIRsharing.fex4c8 go: Rfam integbio: nbdc00654 miriam: rfam n2t: rfam ncbi: RFAM name: Rfam database of RNA families pattern: ^RF\d{5}$ preferred_prefix: rfam publications: - doi: 10.1093/nar/gkae1023 pubmed: '39526405' title: 'Rfam 15: RNA families database in 2025' year: 2024 - doi: 10.1093/nar/gkx1038 pmc: PMC5753348 pubmed: '29112718' title: 'Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families' year: 2018 - doi: 10.1093/nar/gku1063 pmc: PMC4383904 pubmed: '25392425' title: 'Rfam 12.0: updates to the RNA families database' year: 2014 twitter: RfamDB uri_format: https://rfam.org/family/$1 rfc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Legacy site for IETF RFC proposals example: '5013' homepage: https://www.ietf.org/ mappings: n2t: rfc name: Internet Standard -- IETF Request for Comments pattern: ^\d+$ preferred_prefix: rfc uri_format: https://tools.ietf.org/rfc/rfc$1 rgap: comment: This resource has been updated as of 19 November, 2024 contact: email: Robin.Buell@uga.edu name: C. Robin Buell orcid: 0000-0002-6727-4677 description: This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and the Genome Browser that provides an integrated display of annotation data. example: LOC_Os02g13300 homepage: https://rice.uga.edu keywords: - dna - genome mappings: prefixcommons: rgap name: Rice Genome Annotation Project preferred_prefix: rgap providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/rgap:$1 publications: - doi: 10.1093/nar/gkae1061 pubmed: '39558187' title: 'The rice genome annotation project: an updated database for mining the rice genome' year: 2024 - doi: 10.1093/nar/gkl976 pmc: PMC1751532 pubmed: '17145706' title: 'The TIGR Rice Genome Annotation Resource: improvements and new features' year: 2006 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://rice.uga.edu/cgi-bin/ORF_infopage.cgi?orf=$1 rgd: contact: email: jrsmith@mcw.edu name: Jennifer R Smith orcid: 0000-0002-6443-9376 description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes. example: '7499841' homepage: http://rgd.mcw.edu/ keywords: - behavior - biomedical science - comparative genomics - congenic rat - data analysis service - disease - dna - est - faseb list - function - gene - genetic - genome - genomic - genomics - genotype - gold standard - human - immunology - inbred rat strain - knockout - map - marker - model organism - molecular medicine - mouse - mutant - ontology - organism supplier - pathway - phenomics - phenotype - physiology - proteomics - qtl - quantitative genetics - rat - recombinant inbred rat - sequence - strain - translational medicine - variation - veterinary medicine license: CC-BY-4.0 mappings: aberowl: RGD biocontext: RGD bioportal: RGD cellosaurus: RGD edam: '2620' fairsharing: FAIRsharing.pfg82t go: RGD integbio: nbdc00188 miriam: rgd n2t: rgd ncbi: RGD pathguide: '267' prefixcommons: rgd re3data: r3d100010417 rrid: RGD togoid: Rgd uniprot: DB-0091 wikidata: P3853 name: Rat Genome Database pattern: ^\d{4,}$ preferred_prefix: rgd providers: - code: agr description: RGD through the Alliance of Genome Resources homepage: https://www.alliancegenome.org name: RGD through the Alliance of Genome Resources uri_format: https://www.alliancegenome.org/gene/RGD:$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/rgd:$1 publications: - doi: 10.1093/database/baae132 pmc: PMC11753291 pubmed: '39841812' title: Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database - doi: 10.1093/genetics/iyac005 pmc: PMC8982048 pubmed: '35380657' title: 'MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses' year: 2022 - doi: 10.1007/s00335-021-09932-x pmc: PMC8570235 pubmed: '34741192' title: The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research year: 2021 - doi: 10.1093/nar/gkz1041 pmc: PMC7145519 pubmed: '31713623' title: 'The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform' year: 2020 - doi: 10.1007/978-1-4939-9581-3_3 pubmed: '31228152' title: Rat Genome Databases, Repositories, and Tools year: 2019 - doi: 10.1007/978-1-4939-9581-3_2 pubmed: '31228151' title: Rat Genome Assemblies, Annotation, and Variant Repository year: 2019 - doi: 10.1007/978-1-4939-9581-3_1 pubmed: '31228150' title: 'The Rat: A Model Used in Biomedical Research' year: 2019 - doi: 10.1093/database/baz037 pmc: PMC6444380 pubmed: '30938777' title: Quantitative phenotype analysis to identify, validate and compare rat disease models year: 2019 - doi: 10.1093/database/baz014 pmc: PMC6369425 pubmed: '30753478' title: Integrated curation and data mining for disease and phenotype models at the Rat Genome Database year: 2019 - doi: 10.1007/978-1-4939-7737-6_8 pmc: PMC6487669 pubmed: '29761460' title: A Primer for the Rat Genome Database (RGD) year: 2018 - doi: 10.1093/ilar/ilw041 pmc: PMC6057551 pubmed: '28838068' title: Rat Genome and Model Resources year: 2017 - doi: 10.1242/dmm.026021 pmc: PMC5087824 pubmed: '27736745' title: Exploring human disease using the Rat Genome Database year: 2016 - doi: 10.1016/j.csbj.2015.11.006 pmc: PMC4700298 pubmed: '27602200' title: Disease, Models, Variants and Altered Pathways-Journeying RGD Through the Magnifying Glass year: 2015 - doi: 10.1152/physiolgenomics.00046.2016 pmc: PMC5005459 pubmed: '27287925' title: Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database year: 2016 - doi: 10.1093/database/baw034 pmc: PMC4805243 pubmed: '27009807' title: The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database year: 2016 - doi: 10.1093/nar/gku1026 pmc: PMC4383884 pubmed: '25355511' title: 'The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease' year: 2014 - doi: 10.1186/s40246-014-0017-8 pmc: PMC4191248 pubmed: '25265995' title: 'Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease' year: 2014 - doi: 10.1093/database/bat015 pmc: PMC3630803 pubmed: '23603846' title: 'PhenoMiner: quantitative phenotype curation at the rat genome database' year: 2013 - pubmed: '23434633' - doi: 10.1371/journal.pcbi.1000582 pmc: PMC2775909 pubmed: '19956751' title: 'The rat genome database curators: who, what, where, why' year: 2009 - pubmed: '18996890' - doi: 10.1093/nar/gkl988 pmc: PMC1761441 pubmed: '17151068' title: The Rat Genome Database, update 2007--easing the path from disease to data and back again year: 2006 - pubmed: '10400928' title: A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat year: 1999 synonyms: - RGD twitter: ratgenome uri_format: http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1 rgd.qtl: description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes. example: '1354581' homepage: http://rgd.mcw.edu/ mappings: biocontext: RGD.QTL miriam: rgd.qtl n2t: rgd.qtl name: Rat Genome Database qTL pattern: ^\d+$ preferred_prefix: rgd.qtl twitter: ratgenome uri_format: http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1 rgd.strain: description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology. example: '5688061' homepage: http://rgd.mcw.edu/ mappings: biocontext: RGD.STRAIN miriam: rgd.strain n2t: rgd.strain name: Rat Genome Database strain pattern: ^\d+$ preferred_prefix: rgd.strain twitter: ratgenome uri_format: http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1 rhea: contact: email: anne.morgat@sib.swiss name: Anne Morgat orcid: 0000-0002-1216-2969 description: ' Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants. Rhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB.' example: '12345' homepage: https://www.rhea-db.org/ keywords: - biochemistry - life science - reaction - small molecule license: CC-BY-4.0 mappings: biocontext: RHEA edam: '2644' fairsharing: FAIRsharing.pn1sr5 go: RHEA integbio: nbdc02083 miriam: rhea n2t: rhea pathguide: '310' prefixcommons: rhea re3data: r3d100010891 togoid: Rhea name: Rhea, the Annotated Reactions Database pattern: ^\d{5}$ preferred_prefix: rhea providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/rhea:$1 publications: - doi: 10.1093/nar/gkab1016 pmc: PMC8728268 pubmed: '34755880' title: Rhea, the reaction knowledgebase in 2022 year: 2022 - doi: 10.1093/bioinformatics/btz817 pmc: PMC7162351 pubmed: '31688925' title: Enzyme annotation in UniProtKB using Rhea year: 2020 - doi: 10.1093/nar/gky876 pmc: PMC6324061 pubmed: '30272209' title: 'Updates in Rhea: SPARQLing biochemical reaction data' year: 2019 - doi: 10.1093/nar/gkw990 pmc: PMC5210663 pubmed: '27789701' title: Updates in Rhea - an expert curated resource of biochemical reactions year: 2016 - doi: 10.1093/nar/gku961 pmc: PMC4384025 pubmed: '25332395' title: Updates in Rhea--a manually curated resource of biochemical reactions year: 2014 - doi: 10.1093/nar/gkr1126 pmc: PMC3245052 pubmed: '22135291' title: Rhea--a manually curated resource of biochemical reactions year: 2011 synonyms: - RHEA twitter: rhea_db uri_format: https://www.rhea-db.org/rhea/$1 ribocentre: contact: email: huanglin36@mail.sysu.edu.cn name: Lin Huang orcid: 0000-0002-2121-365X contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: Ribocentre is designed to contain comprehensive information of all natural ribozymes. example: hammer github_request_issue: 611 homepage: https://www.ribocentre.org/ name: Ribocentre pattern: ^[a-zA-Z0-9-]+$ preferred_prefix: ribocentre publications: - doi: 10.1093/nar/gkac840 pmc: PMC9825448 pubmed: '36177882' title: 'Ribocentre: a database of ribozymes' year: 2023 repository: https://github.com/ribocentre/ribocentre.github.io reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - ribocenter uri_format: https://www.ribocentre.org/docs/$1 ricecyc: description: RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project example: PWY-1042 homepage: http://www.gramene.org/pathway/ricecyc.html keywords: - gene - pathway mappings: pathguide: '227' prefixcommons: ricecyc name: Rice Metabolic Pathways preferred_prefix: ricecyc providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ricecyc:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object=$1 ricegap: description: The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines. example: LOC_Os02g13300 homepage: http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml mappings: biocontext: RICEGAP miriam: ricegap n2t: ricegap name: Rice Genome Annotation Project pattern: ^LOC\_Os\d{1,2}g\d{5}$ preferred_prefix: ricegap uri_format: http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1 ricenetdb.compound: description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' example: OSC1416 homepage: http://bis.zju.edu.cn/ricenetdb mappings: biocontext: RICENETDB.COMPOUND miriam: ricenetdb.compound n2t: ricenetdb.compound name: RiceNetDB Compound pattern: ^OSC\d{4}$ preferred_prefix: ricenetdb.compound uri_format: http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1 ricenetdb.gene: description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' example: LOC_Os01g49190.1 homepage: http://bis.zju.edu.cn/ricenetdb/ mappings: biocontext: RICENETDB.GENE miriam: ricenetdb.gene n2t: ricenetdb.gene name: RiceNetDB Gene pattern: ^LOC\_Os\d{1,2}g\d{5}\.\d$ preferred_prefix: ricenetdb.gene uri_format: http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1 ricenetdb.mirna: description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' example: osa-miR446 homepage: http://bis.zju.edu.cn/ricenetdb mappings: biocontext: RICENETDB.MIRNA miriam: ricenetdb.mirna n2t: ricenetdb.mirna name: RiceNetDB miRNA pattern: ^osa-miR\d{3,5}[a-z]{0,1}$ preferred_prefix: ricenetdb.mirna uri_format: http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1 ricenetdb.protein: description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' example: LOC_Os01g49190 homepage: http://bis.zju.edu.cn/ricenetdb/ mappings: biocontext: RICENETDB.PROTEIN miriam: ricenetdb.protein n2t: ricenetdb.protein name: RiceNetDB Protein pattern: ^LOC\_Os\d{1,2}g\d{5}$ preferred_prefix: ricenetdb.protein uri_format: http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1 ricenetdb.reaction: description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' example: OSR0818 homepage: http://bis.zju.edu.cn/ricenetdb mappings: biocontext: RICENETDB.REACTION miriam: ricenetdb.reaction n2t: ricenetdb.reaction name: RiceNetDB Reaction pattern: ^OSR\d{4}$ preferred_prefix: ricenetdb.reaction uri_format: http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1 rism: description: RISM Online is a new service that will publish the bibliographic and authority data from the catalogue of the Répertoire International des Sources Musicales project. example: people/11035 homepage: https://rism.digital/ mappings: miriam: rism name: RISM Online pattern: ^[a-z]+/[0-9]+$ preferred_prefix: rism uri_format: https://rism.online/$1 rna_sstrand: description: RNA STRAND contains known RNA secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known RNA secondary structures, and to provide the scientific community with simple yet powerful ways of analysing, searching and updating the proposed database. example: CRW_00469 homepage: http://www.rnasoft.ca/sstrand keywords: - rna - structure mappings: prefixcommons: rna_sstrand name: RNA SSTRAND preferred_prefix: rna_sstrand providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/rna_sstrand:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID=$1 rnacentral: contact: email: bsweeney@ebi.ac.uk github: blakesweeney name: Blake A Sweeney orcid: 0000-0002-6497-2883 description: RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases. example: URS0000759CF4 homepage: https://rnacentral.org/ keywords: - bioinformatics - biology mappings: biocontext: RNACENTRAL edam: '3856' fairsharing: FAIRsharing.KcCjL7 go: RNAcentral integbio: nbdc01215 miriam: rnacentral n2t: rnacentral ncbi: RNAcentral wikidata: P8697 name: RNACentral pattern: ^URS[0-9A-F]{10}(\_\d+)?$ preferred_prefix: rnacentral publications: - doi: 10.1093/nar/gky1034 pmc: PMC6324050 pubmed: '30395267' title: 'RNAcentral: a hub of information for non-coding RNA sequences' year: 2019 - doi: 10.1093/nar/gkw1008 pmc: PMC5210518 pubmed: '27794554' title: 'RNAcentral: a comprehensive database of non-coding RNA sequences' year: 2016 repository: https://github.com/RNAcentral/ synonyms: - LNCRNADB twitter: RNAcentral uri_format: https://rnacentral.org/rna/$1 rnajunction: contact: email: ygyingli@ncsu.edu name: Yaroslava G Yingling orcid: 0000-0002-8557-9992 description: 'RNAJunction is a database of RNA junctions and kissing loop structures. It contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions. It allows searching by PDB code, structural classification, sequence, keyword or inter-helix angles. RNAJunction is designed to aid analysis of RNA structures as well as design of novel RNA structures on a nanoscale. ' example: '8668' homepage: http://rnajunction.abcc.ncifcrf.gov keywords: - rna - structural biology - structure mappings: fairsharing: FAIRsharing.zzgvrv prefixcommons: rnajunction name: Database of RNA Junctions and Kissing loop Structures preferred_prefix: rnajunction providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/rnajunction:$1 publications: - doi: 10.1093/nar/gkm842 pmc: PMC2238914 pubmed: '17947325' title: 'RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign' year: 2007 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://rnajunction.ncifcrf.gov/JunctionPage.php?jid=$1 rnaloops: contact: email: Maciej.Antczak@cs.put.poznan.pl github: mantczak name: Maciej Antczak orcid: 0000-0002-5320-2023 contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: Rnaloops stores the information about n-way junctions (where n≥3) found in experimentally determined rna 3d structures deposited in the protein data bank. example: '91792' github_request_issue: 601 homepage: https://rnaloops.cs.put.poznan.pl keywords: - rna - structural bioinformatcs name: RNAloops pattern: ^\d+$ preferred_prefix: rnaloops reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://rnaloops.cs.put.poznan.pl/search/details/$1 rnamod: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A comprehensive listing of post-transcriptionally modified nucleosides from RNA - example: '051' homepage: http://rna.rega.kuleuven.be/rnamods/ keywords: - post-transcriptional modification - rna - structural bioinformatcs name: The RNA Modification Database pattern: ^\d{3}$ preferred_prefix: rnamod uri_format: http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1 rnamods: description: The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. example: '101' homepage: http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm keywords: - rna - structure mappings: biocontext: RNAMODS go: RNAmods miriam: rnamods n2t: rnamods prefixcommons: rnamods name: RNA Modification Database pattern: ^\d{3}$ preferred_prefix: rnamods providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/rnamods:$1 uri_format: http://mods.rna.albany.edu/mods/modifications/view/$1 rnao: contact: email: BatchelorC@rsc.org name: Colin Batchelor orcid: 0000-0001-5985-7429 deprecated: true description: Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures. download_obo: http://purl.obolibrary.org/obo/rnao.obo download_owl: http://purl.obolibrary.org/obo/rnao.owl example: 0000128 homepage: https://github.com/bgsu-rna/rnao keywords: - biochemistry - life science - molecular structure - obo - ontology - ribonucleic acid - rna secondary structure - sequence motif license: CC0-1.0 mappings: aberowl: RNAO biocontext: RNAO bioportal: RNAO fairsharing: FAIRsharing.kqt2h2 obofoundry: rnao ols: rnao ontobee: RNAO prefixcommons: rnao name: RNA ontology pattern: ^\d{7}$ preferred_prefix: RNAO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/rnao:$1 publications: - doi: 10.1261/rna.2343206 pmc: PMC1421088 pubmed: '16484377' title: 'The RNA Ontology Consortium: an open invitation to the RNA community' year: 2006 - doi: 10.3233/ao-2011-0082 title: 'The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data' year: 2011 rdf_uri_format: http://purl.obolibrary.org/obo/RNAO_$1 repository: https://github.com/BGSU-RNA/rnao uri_format: http://purl.obolibrary.org/obo/RNAO_$1 version: '2019-04-15' rnavdb: description: The RNA Virus Database is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments and contains translated genome sequences for all species. example: '164750' homepage: http://virus.zoo.ox.ac.uk/rnavirusdb/ keywords: - genome - rna mappings: prefixcommons: rvd name: RNA Virus Database preferred_prefix: rnavdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/rvd:$1 uri_format: http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id=$1 ro: appears_in: - agro - aism - cdno - cl - clao - clyh - colao - cteno - ecao - ecocore - ecto - envo - foodon - fovt - gallont - genepio - go - hso - lepao - maxo - ons - ontoavida - pcl - pco - plana - planp - poro - proco - psdo - pso - rbo - uberon - upa - xpo - zp banana: RO banana_peel: _ contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies. download_json: http://purl.obolibrary.org/obo/ro.json download_obo: http://purl.obolibrary.org/obo/ro.obo download_owl: http://purl.obolibrary.org/obo/ro.owl example: '0002533' example_extras: - HOM0000022 homepage: https://oborel.github.io/ keywords: - life science - obo - ontology - relations license: CC0-1.0 mappings: aberowl: RO agroportal: RO biocontext: RO biolink: RO bioportal: OBOREL fairsharing: FAIRsharing.9w8ea0 go: RO miriam: ro n2t: ro obofoundry: ro ols: ro ontobee: RO prefixcommons: ro wikidata: P3590 name: Relation Ontology namespace_in_lui: true pattern: ^(HOM)?\d{7}$ preferred_prefix: RO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ro:$1 publications: - doi: 10.1186/2041-1480-5-41 pmc: PMC4177597 pubmed: '25276335' title: 'Structuring research methods and data with the research object model: genomics workflows as a case study' year: 2014 - doi: 10.1186/gb-2005-6-5-r46 pmc: PMC1175958 pubmed: '15892874' title: Relations in biomedical ontologies year: 2005 rdf_uri_format: http://purl.obolibrary.org/obo/RO_$1 repository: https://github.com/oborel/obo-relations synonyms: - RO_proposed_relation - obo_rel - oborel uri_format: http://purl.obolibrary.org/obo/RO_$1 version: '2024-04-24' roleo: banana: RoleO banana_peel: _ comment: This resource doesn't exist on the web anymore contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 deprecated: true description: The Role Ontology (RoleO) is a ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles. download_owl: http://aber-owl.net/media/ontologies/ROLEO/1/roleo.owl example: '0000002' homepage: http://sourceforge.net/projects/roleo keywords: - obo - ontology mappings: aberowl: ROLEO bioportal: ROLEO prefixcommons: roleo name: Role Ontology pattern: ^\d{7}$ preferred_prefix: RoleO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/roleo:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://purl.obolibrary.org/obo/RoleO_$1 ror: contact: email: maria.gould@ucop.edu github: mariagould name: Maria Gould orcid: 0000-0002-2916-3423 description: 'ROR (Research Organization Registry) is a global, community-led registry of open persistent identifiers for research organizations. ROR is jointly operated by California Digital Library, Crossref, and Datacite.' download_owl: https://w3id.org/rorio/rorio.owl example: 03yrm5c26 homepage: https://ror.org keywords: - data management - ontology license: CC0-1.0 mappings: bartoc: '20474' fairsharing: FAIRsharing.1jKfji miriam: ror n2t: ror mastodon: ResearchOrgs@mastodon.social name: Research Organization Registry pattern: ^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$ preferred_prefix: ror repository: https://github.com/ror-community twitter: ResearchOrgs uri_format: https://ror.org/$1 rouge: contact: email: ohara@kazusa.or.jp name: Osamu Ohara orcid: 0000-0002-3328-9571 description: The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. example: mKIAA4200 homepage: http://www.kazusa.or.jp/rouge/ keywords: - dna - life science - protein mappings: biocontext: ROUGE fairsharing: FAIRsharing.vdbagq integbio: nbdc00672 miriam: rouge n2t: rouge prefixcommons: rouge uniprot: DB-0092 name: Rodent Unidentified Gene-Encoded Large Proteins pattern: ^m\w+$ preferred_prefix: rouge providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/rouge:$1 publications: - doi: 10.1093/nar/gkh035 pmc: PMC308769 pubmed: '14681467' title: 'HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE' year: 2004 uri_format: https://www.kazusa.or.jp/rouge/gfpage/$1 rpcec: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Cuban Public Registry of Clinical Trials (RPCEC) is a website with a database of clinical trials, with national coverage. It was established in 2007 under the leadership of the National Coordinating Center of Clinical Trials (CENCEC) and with INFOMED collaboration. (from homepage) example: RPCEC00000423 homepage: https://rpcec.sld.cu/en/home name: Cuban Registry of Clinical Trials pattern: ^RPCEC\d+$ preferred_prefix: rpcec uri_format: https://rpcec.sld.cu/en/trials/$1 rrid: banana: RRID contact: email: bandrow@gmail.com github: bandrow name: Anita Bandrowski orcid: 0000-0002-5497-0243 contributor_extras: - email: bandrow@gmail.com github: bandrow name: Anita Bandrowski orcid: 0000-0002-5497-0243 description: 'The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools. The initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch.' example: AB_262044 homepage: https://rrid.site keywords: - annotation - centrally registered identifier - chemistry - citation - data retrieval - knowledge and information systems - life science - resource metadata mappings: biocontext: RRID fairsharing: FAIRsharing.ATwSZG miriam: rrid n2t: rrid name: Research Resource Identification namespace_in_lui: true pattern: ^[a-zA-Z]+.+$ preferred_prefix: rrid publications: - doi: 10.1093/nar/gkac927 pmc: PMC9825422 pubmed: '36370112' title: 'The Antibody Registry: ten years of registering antibodies' year: 2023 - doi: 10.1093/gigascience/giac058 pmc: PMC9197678 pubmed: '35701373' title: 'A decade of GigaScience: What can be learned from half a million RRIDs in the scientific literature?' year: 2022 - doi: 10.1371/journal.pcbi.1008967 pmc: PMC8189493 pubmed: '34043624' title: 'Antibody Watch: Text mining antibody specificity from the literature' year: 2021 - doi: 10.1002/cnr2.1150 pmc: PMC7941525 pubmed: '32721132' title: Improving transparency and scientific rigor in academic publishing year: 2018 - doi: 10.7554/elife.41676 pmc: PMC6351100 pubmed: '30693867' title: Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines year: 2019 - doi: 10.1038/nmeth.3995 pmc: PMC10335836 pubmed: '27595404' title: A proposal for validation of antibodies year: 2016 - doi: 10.1016/j.neuron.2016.04.030 pmc: PMC5854161 pubmed: '27151636' title: 'RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods' year: 2016 - doi: 10.1002/cne.23913 pmc: PMC4684178 pubmed: '26599696' title: 'The Resource Identification Initiative: A Cultural Shift in Publishing' year: 2016 - doi: 10.12688/f1000research.6555.2 pmc: PMC4648211 pubmed: '26594330' title: 'The Resource Identification Initiative: A cultural shift in publishing' year: 2015 - doi: 10.7717/peerj.148 pmc: PMC3771067 pubmed: '24032093' title: 'On the reproducibility of science: unique identification of research resources in the biomedical literature' year: 2013 uri_format: https://scicrunch.org/resolver/RRID:$1 rrrc: description: Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models. [from RRID] example: '961' homepage: http://www.rrrc.us/ keywords: - animal - biomedical - catalog - cell line - cryopreserved - database - disease - drug - embryo - embryonic stem cell - gamete - genome - genotyping - germplasma - human - hybrid - inbred - infectious - molecular - mutant - nuclear - ovarian - pathogen - protocol - rat - rat model - reagent - research - stem cell - strain - tissue mappings: rrid: RRRC name: Rat Resource and Research Center pattern: ^\d+$ preferred_prefix: rrrc uri_format: https://www.rrrc.us/Strain/?x=$1 rs: contact: email: sjwang@mcw.edu github: shurjenw name: Shur-Jen Wang orcid: 0000-0001-5256-8683 description: Ontology of rat strains download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.obo download_owl: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.owl example: 0001807 homepage: http://rgd.mcw.edu/rgdweb/search/strains.html keywords: - genetic strain - life science - mutation - obo - ontology license: CC-BY-4.0 logo: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif mappings: aberowl: RS biocontext: RS bioportal: RS cellosaurus: RS fairsharing: FAIRsharing.vajn3f obofoundry: rs ols: rs ontobee: RS prefixcommons: rs name: Rat Strain Ontology pattern: ^\d{7}$ preferred_prefix: RS providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/rs:$1 publications: - doi: 10.1186/2041-1480-4-36 pmc: PMC4177145 pubmed: '24267899' title: 'Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD' year: 2013 - doi: 10.1093/database/bat015 pmc: PMC3630803 pubmed: '23603846' title: 'PhenoMiner: quantitative phenotype curation at the rat genome database' year: 2013 rdf_uri_format: http://purl.obolibrary.org/obo/RS_$1 repository: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology twitter: ratgenome uri_format: http://purl.obolibrary.org/obo/RS_$1 version: '6.242' rtecs: contact: email: vep1@cdc.gov name: Vernon Putz-Anderson orcid: 0000-0002-3588-3259 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'RTECS is a compendium of data extracted from the open scientific literature. The data are recorded in the format developed by the RTECS staff and arranged in alphabetical order by prime chemical name. Six types of toxicity data are included in the file: (1) primary irritation; (2) mutagenic effects; (3) reproductive effects; (4) tumorigenic effects; (5) acute toxicity; and (6) other multiple dose toxicity. Specific numeric toxicity values such as LD50, LC50, TDLo, and TCLo are noted as well as species studied and route of administration used. For each citation, the bibliographic source is listed thereby enabling the user to access the actual studies cited. No attempt has been made to evaluate the studies cited in RTECS. The user has the responsibility of making such assessments.' example: AB1925000 homepage: https://www.cdc.gov/niosh/rtecs/ mappings: cheminf: '000566' name: Registry of Toxic Effects of Chemical Substances pattern: ^AB\d+$ preferred_prefix: rtecs proprietary: true publications: - doi: 10.1016/s1074-9098%2899%2900058-1 title: 'An overview of the Registry of Toxic Effects of Chemical Substances (RTECS): Critical information on chemical hazards' year: 1999 references: - https://www.cdc.gov/niosh/docs/97-119/pdfs/97-119.pdf - https://www.cdc.gov/niosh/npg/npgdrtec.html rubygems: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A repository of software packages written in Ruby. example: bel homepage: https://rubygems.org name: RubyGems preferred_prefix: rubygems uri_format: https://rubygems.org/gems/$1 runbiosimulations: description: runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive. example: 5fde96bdc5f1aa9ff0cce18a homepage: https://icahn.mssm.edu/ mappings: miriam: runbiosimulations name: runBioSimulations pattern: ^[0-9a-z]{24,24}$ preferred_prefix: runbiosimulations uri_format: https://run.biosimulations.org/simulations/$1 rxno: contact: email: batchelorc@rsc.org github: batchelorc name: Colin Batchelor orcid: 0000-0001-5985-7429 description: RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization. download_obo: https://github.com/rsc-ontologies/rxno/raw/master/rxno.obo download_owl: http://purl.obolibrary.org/obo/rxno.owl example: '0000253' homepage: https://github.com/rsc-ontologies/rxno keywords: - molecular chemistry - obo - ontology - reaction data license: CC-BY-4.0 mappings: aberowl: RXNO biocontext: RXNO bioportal: RXNO fairsharing: FAIRsharing.w4tncg obofoundry: rxno ols: rxno ontobee: RXNO wikidata: P2106 name: Name Reaction Ontology pattern: ^\d{7}$ preferred_prefix: RXNO rdf_uri_format: http://purl.obolibrary.org/obo/RXNO_$1 repository: https://github.com/rsc-ontologies/rxno uri_format: http://purl.obolibrary.org/obo/RXNO_$1 version: '2021-12-16' rxnorm: contact: email: custserv@nlm.nih.gov name: NLM Customer Service contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary. example: '221058' homepage: https://www.nlm.nih.gov/research/umls/rxnorm/ keywords: - biomedical science - drug - drug name - ontology - preclinical studies license: https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf mappings: aberowl: RXNORM biocontext: RXCUI biolink: RXNORM bioportal: RXNORM fairsharing: FAIRsharing.36pf8q hl7: 2.16.840.1.113883.6.88 wikidata: P3345 name: RxNorm pattern: ^[0-9]{1,7}$ preferred_prefix: rxnorm providers: - code: bp description: RxNorm in BioPortal homepage: http://purl.bioontology.org/ontology/RXNORM name: BioPortal uri_format: http://purl.bioontology.org/ontology/RXNORM/$1 publications: - doi: 10.1136/amiajnl-2011-000116 pmc: PMC3128404 pubmed: '21515544' title: 'Normalized names for clinical drugs: RxNorm at 6 years' year: 2011 - pmc: PMC2655997 pubmed: '18998891' title: RxTerms - a drug interface terminology derived from RxNorm year: 2008 - doi: 10.1109/mitp.2005.122 title: 'RxNorm: prescription for electronic drug information exchange' year: 2005 synonyms: - RXCUI uri_format: https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1 s_mart_db: description: S/MARt DB collects information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix. example: SM0000020 homepage: http://smartdb.bioinf.med.uni-goettingen.de/ keywords: - protein mappings: integbio: nbdc00674 pathguide: '47' prefixcommons: s_mart_db name: The S/MAR transaction DataBase preferred_prefix: s_mart_db providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/s_mart_db:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi?$1 sabiork.compound: description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information. example: '75' homepage: http://sabiork.h-its.org/ mappings: miriam: sabiork.compound n2t: sabiork.compound name: SABIO-RK Compound pattern: ^\d+$ preferred_prefix: sabiork.compound uri_format: http://sabiork.h-its.org/newSearch?q=$1 sabiork.ec: contact: email: ulrike.wittig@h-its.org name: Ulrike Wittig orcid: 0000-0002-9077-5664 description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data. example: 2.7.1.1 homepage: http://sabiork.h-its.org/ keywords: - reaction mappings: biocontext: SABIORK.EC miriam: sabiork.ec n2t: sabiork.ec prefixcommons: sabiork.ec name: SABIO-RK EC Record pattern: ^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$ preferred_prefix: sabiork.ec providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/sabiork.ec:$1 provides: ec publications: - pubmed: '17822389' title: Storing and annotating of kinetic data year: 2007 uri_format: http://sabiork.h-its.org/newSearch?q=ecnumber:$1 sabiork.kineticrecord: contact: email: ulrike.wittig@h-its.org name: Ulrike Wittig orcid: 0000-0002-9077-5664 description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information. example: '5046' homepage: http://sabiork.h-its.org/ keywords: - classification - enzyme - kinetics mappings: biocontext: SABIORK.KINETICRECORD go: SABIO-RK miriam: sabiork.kineticrecord n2t: sabiork.kineticrecord prefixcommons: sabiork.kinetic name: SABIO Reaction Kinetics pattern: ^\d+$ preferred_prefix: sabiork.kineticrecord providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/sabiork.kinetic:$1 publications: - pubmed: '17822389' title: Storing and annotating of kinetic data year: 2007 uri_format: http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1 sabiork.reaction: contact: email: ulrike.wittig@h-its.org name: Ulrike Wittig orcid: 0000-0002-9077-5664 description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information. example: '75' homepage: http://sabiork.h-its.org/ keywords: - biochemistry - kinetics - life science - pathway - reaction mappings: biocontext: SABIORK.REACTION edam: '2309' fairsharing: FAIRsharing.cwx04e miriam: sabiork.reaction n2t: sabiork.reaction pathguide: '226' prefixcommons: sabiork.reaction re3data: r3d100011052 uniprot: DB-0177 name: SABIO-RK Reaction pattern: ^\d+$ preferred_prefix: sabiork.reaction providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/sabiork.reaction:$1 publications: - doi: 10.1093/nar/gkx1065 pubmed: '29092055' - doi: 10.1093/nar/gkr1046 pmc: PMC3245076 pubmed: '22102587' title: SABIO-RK--database for biochemical reaction kinetics year: 2011 synonyms: - SABIO-RK uri_format: http://sabiork.h-its.org/reacdetails.jsp?reactid=$1 sael: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List preferred_prefix: sael publications: - doi: 10.1002/cfg.434 pmc: PMC2447422 pubmed: '18629134' title: 'The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data' year: 2004 salk: appears_in: - efo comment: spider stuff! contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Scientific research institute for neuroscience, genetics, immunology, plant biology and more. example: '037727' homepage: https://www.salk.edu/ name: Salk Institute for Biological Studies pattern: ^\d{6}$ preferred_prefix: salk uri_format: https://abrc.osu.edu/stocks/number/SALK_$1 salmon: contact: email: brycemecum@gmail.com github: amoeba name: Bryce Mecum orcid: 0000-0002-0381-3766 description: An ontology representing knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. This ontology is considered to be in the early stages of development, though it is based upon considerable previous work. Contributions of all kinds are welcome and encouraged, including alignments, updates to existing terms, and new terms. download_owl: http://aber-owl.net/media/ontologies/SALMON/2/salmon.owl example: '00000674' homepage: https://github.com/DataONEorg/sem-prov-ontologies/ keywords: - ontology mappings: aberowl: SALMON bioportal: SALMON name: Salmon Ontology pattern: ^\d+$ preferred_prefix: salmon uri_format: https://purl.dataone.org/odo/SALMON_$1 sao: contact: email: slarson@ncmir.ucsd.edu name: Stephen Larson deprecated: true description: SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules. download_owl: http://aber-owl.net/media/ontologies/SAO/2/sao.owl example: '5277619' homepage: http://ccdb.ucsd.edu/CCDBWebSite/sao.html keywords: - biochemistry - obo - ontology - owl mappings: aberowl: SAO biocontext: SAO bioportal: SAO obofoundry: sao prefixcommons: sao name: Subcellular Anatomy Ontology pattern: ^\d+$ preferred_prefix: SAO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/sao:$1 rdf_uri_format: http://purl.obolibrary.org/obo/SAO_$1 references: - http://www.ontobee.org/ontology/SAO uri_format: http://uri.neuinfo.org/nif/nifstd/sao$1 sasap: contact: email: brycemecum@gmail.com github: amoeba name: Bryce Mecum orcid: 0000-0002-0381-3766 description: An ontology which represents information about the State of Alaska's Salmon and People (SASAP) project, as well as knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. download_owl: http://aber-owl.net/media/ontologies/SASAP/2/sasap.owl example: '00000101' homepage: https://github.com/DataONEorg/sem-prov-ontologies keywords: - ontology mappings: aberowl: SASAP bioportal: SASAP name: The State of Alaska's Salmon and People Ontology pattern: ^\d+$ preferred_prefix: sasap uri_format: https://purl.dataone.org/odo/SASAP_$1 sasbdb: contact: email: a.kikhney@embl-hamburg.de name: Al Kikhney orcid: 0000-0003-1321-3956 description: Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data. example: SASDAX8 homepage: http://www.sasbdb.org/ keywords: - life science - molecular biology mappings: biocontext: SASBDB fairsharing: FAIRsharing.i1F3Hb miriam: sasbdb n2t: sasbdb re3data: r3d100012273 uniprot: DB-0258 name: Small Angle Scattering Biological Data Bank pattern: ^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$ preferred_prefix: sasbdb publications: - doi: 10.1002/pro.3731 pmc: PMC6933840 pubmed: '31576635' title: 'SASBDB: Towards an automatically curated and validated repository for biological scattering data' year: 2019 - doi: 10.1093/nar/gku1047 pmc: PMC4383894 pubmed: '25352555' title: SASBDB, a repository for biological small-angle scattering data year: 2014 uri_format: http://www.sasbdb.org/data/$1 sbo: appears_in: - proco - scdo banana: SBO contact: email: sheriff@ebi.ac.uk github: rsmsheriff name: Rahuman Sheriff orcid: 0000-0003-0705-9809 description: The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort. download_obo: http://purl.obolibrary.org/obo/sbo.obo download_owl: http://purl.obolibrary.org/obo/sbo.owl example: 0000485 homepage: http://www.ebi.ac.uk/sbo/ keywords: - mathematical model - modeling and simulation - molecular interaction - obo - ontology - pathway model - systems biology license: Artistic License 2.0 mappings: aberowl: SBO biocontext: SBO bioportal: SBO fairsharing: FAIRsharing.s19src miriam: sbo n2t: sbo obofoundry: sbo ols: sbo ontobee: SBO prefixcommons: sbo name: Systems Biology Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: SBO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/sbo:$1 - code: biomodels description: Provider for SBO at BioModels homepage: http://biomodels.net name: BioModels uri_format: http://biomodels.net/SBO/SBO_$1 publications: - doi: 10.1038/msb.2011.77 pmc: PMC3261705 pubmed: '22027554' title: Controlled vocabularies and semantics in systems biology year: 2011 - doi: 10.1186/1471-2202-7-s1-s11 pmc: PMC1775041 pubmed: '17118155' title: Model storage, exchange and integration year: 2006 rdf_uri_format: http://purl.obolibrary.org/obo/SBO_$1 repository: https://github.com/EBI-BioModels/SBO twitter: biomodels uri_format: http://purl.obolibrary.org/obo/SBO_$1 version: '2021-08-28' scancerrna: contact: email: zty2009@hit.edu.cn name: Tianyi Zhao orcid: 0000-0001-7352-2959 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: SCancerRNA provides identifiers for non-coding RNA biomarkers, including long ncRNA, microRNA, PIWI-interacting RNA, small nucleolar RNA, and circular RNA, with data on their differential expression at the cellular level in cancer. example: '9530' github_request_issue: 1215 homepage: http://www.scancerrna.com/ name: SCancerRNA pattern: ^\d+$ preferred_prefix: scancerrna publications: - doi: 10.1093/gpbjnl/qzae023 pubmed: '39341795' title: 'SCancerRNA: Expression at the Single-cell Level and Interaction Resource of Non-coding RNA Biomarkers for Cancers' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: http://www.scancerrna.com/toDetail?id=$1 scdo: contact: email: giant.plankton@gmail.com github: JadeHotchkiss name: Jade Hotchkiss orcid: 0000-0002-2193-0704 depends_on: - apollosv - aro - chebi - chmo - cmo - doid - dron - duo - envo - eupath - exo - gaz - gsso - hp - hsapdv - ico - ido - idomal - mp - nbo - ncit - obi - ogms - opmi - pr - sbo - stato - symp - uo - vo - vt description: An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease. download_obo: http://purl.obolibrary.org/obo/scdo.obo download_owl: http://purl.obolibrary.org/obo/scdo.owl example: 0000728 homepage: https://scdontology.h3abionet.org/ keywords: - biomedical science - genetic disorder - obo - ontology - sickle cell disease license: GPL-3.0 logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBbWtCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--69320a8be8ca6a407eaf142714307b4c7e6b5f45/cropped-Screenshot-from-2020-05-23-20-20-32-2.png?disposition=inline mappings: aberowl: SCDO bioportal: SCDO fairsharing: FAIRsharing.kkq6pw obofoundry: scdo ols: scdo ontobee: SCDO name: Sickle Cell Disease Ontology pattern: ^\d{7}$ preferred_prefix: SCDO publications: - doi: 10.1093/database/baac014 pmc: PMC9216550 pubmed: '35363306' title: 'The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation' year: 2022 - doi: 10.1089/omi.2020.0153 pmc: PMC7549008 pubmed: '33021900' title: 'The Sickle Cell Disease Ontology: Enabling Collaborative Research and Co-Designing of New Planetary Health Applications' year: 2020 - doi: 10.1093/database/baz118 pmc: PMC6878945 pubmed: '31769834' title: 'The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation' year: 2019 rdf_uri_format: http://purl.obolibrary.org/obo/SCDO_$1 repository: https://github.com/scdodev/scdo-ontology uri_format: http://purl.obolibrary.org/obo/SCDO_$1 version: '2021-04-15' schem: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Selventa legacy chemical namespace used with the Biological Expression Language example: A0001 homepage: https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-chemical-names.txt keywords: - bel - chemistry - selventa license: Apache-2.0 name: Selventa Chemicals pattern: ^A\d{4}$ preferred_prefix: schem uri_format: https://biopragmatics.github.io/providers/schem/$1 schema: contact: email: johardi@stanford.edu name: Josef Hardi contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond. download_owl: http://aber-owl.net/media/ontologies/SCHEMAORG/2/schemaorg.owl download_rdf: https://schema.org/version/latest/schemaorg-all-http.rdf example: Person homepage: https://schema.org keywords: - computer science - general & upper - ontology - subject agnostic mappings: aberowl: SCHEMAORG biolink: schema bioportal: SCHEMA fairsharing: FAIRsharing.hzdzq8 lov: schema ols: schemaorg_http zazuko: schema name: Schema.org preferred_prefix: schema repository: http://github.com/schemaorg/schemaorg synonyms: - schemaorg uri_format: https://schema.org/$1 scholia.resource: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A frontend to Wikidata example: doi homepage: https://scholia.toolforge.org/ keywords: - registry - wikidata name: Scholia Registry preferred_prefix: scholia.resource uri_format: https://bioregistry.io/metaregistry/scholia/$1 sciflection: description: Sciflection is a public repository for experiments and associated spectra, usually uploaded from Electronic Lab Notebooks, shared under FAIR conditions example: 5ede4273-b26c-4ea4-adb7-3ce294ab3397 homepage: https://sciformation.com/sciflection.html mappings: miriam: sciflection re3data: r3d100013413 name: Sciflection pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$ preferred_prefix: sciflection uri_format: https://sciflection.com/$1 sciprofiles: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: numerical identifier for an author in SciProfiles by MDPI example: '118021' homepage: https://sciprofiles.com/ keywords: - person - researcher mappings: wikidata: P8159 name: SciProfiles ID pattern: ^[1-9]\d*$ preferred_prefix: sciprofiles references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://sciprofiles.com/profile/$1 scomp: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Selventa legacy complex namespace used with the Biological Expression Language example: C0001 homepage: https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-named-complexes.txt keywords: - bel - protein complexes - selventa license: Apache-2.0 name: Selventa Complexes pattern: ^C\d{4}$ preferred_prefix: scomp uri_format: https://biopragmatics.github.io/providers/scomp/$1 scop: contact: email: JMChandonia@lbl.gov github: jmchandonia name: John-Marc Chandonia orcid: 0000-0002-5153-9079 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: SCOP(e) unique identifier. This is simply a number that may be used to reference any entry in the SCOP(e) hierarchy, from root to leaves (Fold, Superfamily, Family, etc.). example: '47419' homepage: https://scop.berkeley.edu keywords: - protein - structure mappings: biocontext: SCOP edam: '1042' miriam: scop n2t: scop prefixcommons: scop name: Structural Classification of Proteins - Unique Identifier pattern: ^\d+$ preferred_prefix: scop providers: - code: CURATOR_REVIEW description: SCOP at Berkeley homepage: http://scop.berkeley.edu/ name: SCOP at Berkeley uri_format: http://scop.berkeley.edu/sunid=$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/scop:$1 - code: mrc description: SCOP at UK Medical Research council (MRC) homepage: https://scop.mrc-lmb.cam.ac.uk name: SCOP at UK Medical Research council (MRC) uri_format: https://scop.mrc-lmb.cam.ac.uk/term/$1 publications: - doi: 10.1093/nar/27.1.254 pmc: PMC148149 pubmed: '9847194' title: 'SCOP: a Structural Classification of Proteins database' year: 1999 - doi: 10.1093/nar/25.1.236 pmc: PMC146380 pubmed: '9016544' title: 'SCOP: a structural classification of proteins database' year: 1997 - doi: 10.1093/nar/28.1.257 pmc: PMC102479 pubmed: '10592240' title: 'SCOP: a structural classification of proteins database' year: 2000 - doi: 10.1107/s0907444998009172 pubmed: '10089491' title: 'SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data' year: 1998 references: - https://scop.berkeley.edu/help/#stableidentifiers synonyms: - scop.sun - scop.sunid uri_format: http://scop.berkeley.edu/sunid=$1 scop.sccs: contact: email: JMChandonia@lbl.gov github: jmchandonia name: John-Marc Chandonia orcid: 0000-0002-5153-9079 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This is a dot notation used to concisely describe a SCOP(e) class, fold, superfamily, and family. For example, a.39.1.1 references the 'Calbindin D9K' family, where 'a' represents the class, '39' represents the fold, '1' represents the superfamily, and the last '1' represents the family. example: a.39.1.1 example_extras: - a - a.39 - a.39.1 homepage: https://scop.berkeley.edu mappings: edam: '1041' name: SCOP(e) concise classification string preferred_prefix: scop.sccs references: - https://scop.berkeley.edu/help/#stableidentifiers uri_format: http://scop.berkeley.edu/sccs=$1 scop.sid: contact: email: JMChandonia@lbl.gov github: jmchandonia name: John-Marc Chandonia orcid: 0000-0002-5153-9079 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: ' A 7-character sid consists of "d" followed by the 4-character PDB ID of the file of origin, the PDB chain ID (''_'' if none, ''.'' if multiple as is the case in genetic domains), and a single character (usually an integer) if needed to specify the domain uniquely (''_'' if not). Sids are currently all lower case, even when the chain letter is upper case. Example sids include d4akea1, d9hvpa_, and d1cph.1.' example: d4akea1 example_extras: - d1cph.1 - d9hvpa_ homepage: https://scop.berkeley.edu mappings: edam: '1039' name: Structural Classification of Protein - Stable Domain Identifier preferred_prefix: scop.sid references: - https://scop.berkeley.edu/help/#stableidentifiers uri_format: http://scop.berkeley.edu/sid=$1 scopus: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: "Scopus is the largest abstract and citation database of peer-reviewed\ \ literature: scientific journals, books and conference proceedings. \nDelivering\ \ a comprehensive overview of the world's research output in the fields of science,\ \ technology, medicine, social sciences, and arts \nand humanities, Scopus features\ \ smart tools to track, analyze and visualize research." example: '56305849200' homepage: https://www.scopus.com keywords: - subject agnostic mappings: biolink: ScopusID fairsharing: FAIRsharing.0a674c wikidata: P1153 name: Scopus Researcher pattern: ^\d+$ preferred_prefix: scopus synonyms: - scopus.author twitter: Scopus uri_format: https://www.scopus.com/authid/detail.uri?authorId=$1 scopus.affiliation: description: identifier for an organisation in author affiliations per Scopus example: '60025709' homepage: http://info.sciencedirect.com/scopus/scopus-in-detail/tools/affiliationidentifier mappings: wikidata: P1155 name: Scopus affiliation ID preferred_prefix: scopus.affiliation uri_format: https://www.scopus.com/affil/profile.uri?afid=$1 scopus.publication: description: identifier for a source/publication venue (journal, conference, etc) in Scopus example: '16129' homepage: https://www.scopus.com/ mappings: wikidata: P1156 name: Scopus Publication pattern: ^[1-9]\d{0,11}$ preferred_prefix: scopus.publication uri_format: https://www.scopus.com/sourceid/$1 scopus.work: description: unique academic work identifier assigned in Scopus bibliographic database example: 2-s2.0-0030770923 homepage: https://www.scopus.com/ mappings: wikidata: P1154 name: Scopus Work pattern: ^2-s2\.0-\d+$ preferred_prefix: scopus.work synonyms: - scopus.eid uri_format: http://www.scopus.com/record/display.url?origin=inward&eid=$1 scoro: contact: email: silvio.peroni@unibo.it github: essepuntato name: Silvio Peroni orcid: 0000-0003-0530-4305 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator). example: IntellectualContribution homepage: http://www.sparontologies.net/ontologies/scoro keywords: - academy - bibliography - citation - data model - report - subject agnostic mappings: fairsharing: FAIRsharing.c86b48 lov: scoro name: Scholarly Contributions and Roles Ontology preferred_prefix: SCoRO publications: - doi: 10.3233/sw-150177 title: The Document Components Ontology (DoCO) year: 2016 repository: https://github.com/sparontologies/scoro twitter: sparontologies uri_format: http://purl.org/spar/scoro/$1 scpd: comment: This resource doesn't exist on the web anymore deprecated: true description: Database containing promotor sequences found in Saccharomyces cerevisiae. example: CDC2 homepage: http://rulai.cshl.edu/SCPD/ keywords: - dna - rna mappings: pathguide: '130' prefixcommons: scpd name: Saccharomyces cerevisiae promoter database preferred_prefix: scpd providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/scpd:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://rulai.cshl.edu/cgi-bin/SCPD/getgene2?$1 scr: contact: email: abandrowski@ncmir.ucsd.edu name: Anita Bandrowski orcid: 0000-0002-5497-0243 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources. example: 022586 github_request_issue: 421 homepage: https://scicrunch.org/browse/resourcedashboard keywords: - interactive portal - life science - neurobiology - nih initiative - rrid mappings: fairsharing: FAIRsharing.kj4pvk integbio: nbdc01937 rrid: SCR name: SciCrunch Registry pattern: ^\d+$ preferred_prefix: scr publications: - doi: 10.1002/cne.23913 pmc: PMC4684178 pubmed: '26599696' title: 'The Resource Identification Initiative: A Cultural Shift in Publishing' year: 2016 - pubmed: '22434839' synonyms: - scicrunch uri_format: http://scicrunch.org/resolver/SCR_$1 scretf: description: ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor. example: RSC3 homepage: http://stormo.wustl.edu/ScerTF/ mappings: biocontext: SCRETF miriam: scretf n2t: scretf name: ScerTF pattern: ^\w+$ preferred_prefix: scretf uri_format: http://stormo.wustl.edu/ScerTF/details/$1 sdap: description: SDAP is a Web server that integrates a database of allergenic proteins with various bioinformatics tools for performing structural studies related to allergens and characterization of their epitopes. example: '610' homepage: http://fermi.utmb.edu/SDAP keywords: - protein - structure mappings: prefixcommons: sdap name: Structural Database of Allergenic Proteins preferred_prefix: sdap providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/sdap:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid=$1 sdbs: description: The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra. example: '4544' homepage: http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi mappings: biocontext: SDBS integbio: nbdc01520 miriam: sdbs n2t: sdbs name: Spectral Database for Organic Compounds pattern: ^\d+$ preferred_prefix: sdbs uri_format: http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1 sdgio: contact: email: pier.buttigieg@awi.de name: Pier Luigi Buttigieg orcid: 0000-0002-4366-3088 description: An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators. download_owl: https://github.com/SDG-InterfaceOntology/sdgio/raw/master/sdgio.owl example: '00020134' homepage: https://github.com/SDG-InterfaceOntology/sdgio keywords: - environmental science - ontology - sustainability mappings: agroportal: SDGIO fairsharing: FAIRsharing.d5ff6e ols: sdgio ontobee: SDGIO name: Sustainable Development Goals Interface Ontology pattern: ^\d{8}$ preferred_prefix: sdgio publications: - doi: 10.1186/s13326-016-0097-6 pmc: PMC5035502 pubmed: '27664130' title: 'The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation' year: 2016 references: - https://github.com/SDG-InterfaceOntology/sdgio/issues/233 repository: https://github.com/SDG-InterfaceOntology/sdgio uri_format: http://purl.unep.org/sdg/SDGIO_$1 sdis: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Selventa legacy disease namespace used with the Biological Expression Language example: D0001 homepage: https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-diseases.txt keywords: - bel - diseases - selventa license: Apache-2.0 name: Selventa Diseases pattern: ^D\d{4}$ preferred_prefix: sdis uri_format: https://biopragmatics.github.io/providers/sdis/$1 sedml.format: description: Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML). example: csv homepage: http://sed-ml.org/ mappings: miriam: sedml.format name: SED-ML data format pattern: ^[a-z]+(\..*?)?$ preferred_prefix: sedml.format uri_format: https://sed-ml.org/urns.html#format:$1 sedml.language: description: Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML). example: sbml.level-3.version-2 homepage: http://sed-ml.org/ mappings: miriam: sedml.language name: SED-ML model format pattern: ^[a-z]+(\..*?)?$ preferred_prefix: sedml.language uri_format: https://sed-ml.org/urns.html#language:$1 seed.compound: description: This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems. example: cpd15380 homepage: http://modelseed.org/ mappings: biocontext: SEED.COMPOUND miriam: seed.compound n2t: seed.compound name: SEED Compound pattern: ^cpd\d+$ preferred_prefix: seed.compound repository: https://github.com/TheSEED uri_format: http://modelseed.org/biochem/compounds/$1 seed.reaction: description: ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions. example: rxn00001 homepage: http://modelseed.org/biochem/reactions/ mappings: biolink: SEED.REACTION miriam: seed.reaction n2t: seed.reaction name: SEED Reactions pattern: ^rxn\d+$ preferred_prefix: seed.reaction uri_format: http://modelseed.org/biochem/reactions/$1 seed.role: contributor: github: samseaver name: Sam Seaver orcid: 0000-0002-7674-5194 description: 'With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [Fellowship for Interpretation of Genomes (FIG)](http://thefig.info/) as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. This prefix provides identifiers for molecular roles that describe the function of one or more proteins in microbes and plants.' example: Histidinol dehydrogenase (EC 1.1.1.23) example_extras: - Archease - Xylan oligosaccharide ABC transporter, substrate-binding component github_request_issue: 1340 homepage: https://theseed.org/ license: MIT name: The SEED preferred_prefix: seed.role publications: - doi: 10.1093/nar/gki866 pmc: PMC1251668 pubmed: '16214803' title: The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes year: 2005 repository: https://github.com/orgs/TheSEED reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://pubseed.theseed.org/SubsysEditor.cgi?page=FunctionalRolePage&fr=$1 seed.subsystem: contributor_extras: - email: aireland@lbl.gov github: ialarmedalien name: AJ Ireland orcid: 0000-0003-1982-9065 - email: seaver@anl.gov github: samseaver name: Sam Seaver orcid: 0000-0002-7674-5194 deprecated: true description: This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems. example: Biotin_biosynthesis homepage: http://seed-viewer.theseed.org/seedviewer.cgi mappings: biocontext: SEED go: SEED miriam: seed n2t: seed ncbi: SEED name: SEED Subsystem pattern: ^\w+$ preferred_prefix: seed.subsystem publications: - doi: 10.1093/nar/gki866 pmc: PMC1251668 pubmed: '16214803' title: The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes year: 2005 repository: https://github.com/TheSEED synonyms: - seed uri_format: https://pubseed.theseed.org/SubsysEditor.cgi?page=ShowSubsystem&subsystem=$1 seinet: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A vocabulary about species to support the environmental research community in Arizona and New Mexico example: '762' github_request_issue: 653 homepage: https://swbiodiversity.org/seinet/index.php mappings: wikidata: P6209 name: Southwestern Environmental Information Network pattern: ^\d+$ preferred_prefix: seinet reviewer: github: callahantiff name: Tiffany J. Callahan orcid: 0000-0002-8169-9049 uri_format: https://swbiodiversity.org/seinet/taxa/index.php?taxon=$1 semapv: contact: email: nicolas.matentzoglu@gmail.com github: matentzn name: Nicolas Matentzoglu orcid: 0000-0002-7356-1779 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Semantic Mapping Vocabulary provides and defines terms used for creating and maintaining semantic mappings, in particular mapping metadata. download_owl: https://raw.githubusercontent.com/mapping-commons/semantic-mapping-vocabulary/main/semapv.owl example: LexicalMatching homepage: https://mapping-commons.github.io/semantic-mapping-vocabulary/ keywords: - ontology license: CC0-1.0 mappings: bartoc: '20428' name: Semantic Mapping Vocabulary owners: - name: Semanticly partnered: true wikidata: Q115518213 preferred_prefix: semapv references: - https://github.com/biopragmatics/bioregistry/pull/714 synonyms: - sempav_voc uri_format: https://w3id.org/semapv/vocab/$1 semion: description: identifier of an author or reviewer, in Semion example: '22132778' homepage: https://www.semion.io mappings: wikidata: P7671 name: Semion author ID pattern: ^\d+$ preferred_prefix: semion uri_format: https://www.semion.io/Author/$1 senso: contact: email: brycemecum@gmail.com github: amoeba name: Bryce Mecum orcid: 0000-0002-0381-3766 description: The SENSO ontology is designed to provide classification terms for labeling sensitive data for data archival and sharing. download_owl: http://aber-owl.net/media/ontologies/SENSO/1/senso.owl download_rdf: https://ontologies.dataone.org/SENSO.ttl example: '00000003' homepage: https://github.com/DataONEorg/sem-prov-ontologies keywords: - ontology mappings: aberowl: SENSO bioportal: SENSO name: Sensitive Data Ontology pattern: ^\d+$ preferred_prefix: senso uri_format: http://purl.dataone.org/odo/SENSO_$1 seo: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: SEO is a reference ontology for modelling data about scientific events such as conferences, symposioums and workshops. download_rdf: https://raw.githubusercontent.com/saidfathalla/SEOontology/master/SEO.ttl example: Symposium homepage: https://w3id.org/seo keywords: - academy - events mappings: lov: seo name: Scientific Event Ontology preferred_prefix: seo uri_format: https://w3id.org/seo#$1 sep: contact: email: psidev-gps-dev@lists.sourceforge.net name: SEP developers via the PSI and MSI mailing lists deprecated: true description: A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments. download_obo: https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo download_owl: http://purl.obolibrary.org/obo/sep.owl example: '00073' homepage: https://psidev.info/sepcv keywords: - obo - ontology - protein mappings: aberowl: SEP biocontext: SEP bioportal: SEP obofoundry: sep ontobee: SEP prefixcommons: sep name: Sample processing and separation techniques pattern: ^\d{5,6}$ preferred_prefix: SEP providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/sep:$1 rdf_uri_format: http://purl.obolibrary.org/obo/SEP_$1 uri_format: http://purl.obolibrary.org/obo/SEP_$1 sepio: contact: email: mhb120@gmail.com github: mbrush name: Matthew Brush orcid: 0000-0002-1048-5019 description: An ontology for representing the provenance of scientific claims and the evidence that supports them. download_owl: http://purl.obolibrary.org/obo/sepio.owl example: 0000048 homepage: https://github.com/monarch-initiative/SEPIO-ontology keywords: - obo - ontology license: CC-BY-3.0 logo: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/SEPIO-LOGOS/sepio_logo_black-banner.png mappings: aberowl: SEPIO biocontext: SEPIO bioportal: SEPIO obofoundry: sepio ols: sepio ontobee: SEPIO name: Scientific Evidence and Provenance Information Ontology pattern: ^\d{7}$ preferred_prefix: SEPIO rdf_uri_format: http://purl.obolibrary.org/obo/SEPIO_$1 repository: https://github.com/monarch-initiative/SEPIO-ontology uri_format: http://purl.obolibrary.org/obo/SEPIO_$1 version: '2023-06-13' sfam: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Selventa legacy protein family namespace used with the Biological Expression Language example: F0001 homepage: https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-protein-families.txt keywords: - bel - protein families - selventa license: Apache-2.0 name: Selventa Families pattern: ^F\d{4}$ preferred_prefix: sfam uri_format: https://biopragmatics.github.io/providers/sfam/$1 sgd: contact: email: cherry@genome.stanford.edu name: J. Michael Cherry orcid: 0000-0001-9163-5180 description: The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae. example: S000002493 homepage: https://www.yeastgenome.org/ keywords: - epigenetics - eukaryotic - genome - life science - nucleotide - proteomics - transcriptomics license: CC-BY-4.0 mappings: biocontext: SGD edam: '2632' fairsharing: FAIRsharing.pzvw40 go: SGD integbio: nbdc00202 miriam: sgd n2t: sgd ncbi: SGD prefixcommons: sgd re3data: r3d100010419 togoid: Sgd uniprot: DB-0095 wikidata: P3406 name: Saccharomyces Genome Database pattern: ^((S\d+$)|(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: 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 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/sgd:$1 publications: - doi: 10.1002/(sici)1097-0061(199812)14:16<1453::aid-yea348>3.0.co;2-g pmc: PMC3037831 pubmed: '9885151' title: Expanding yeast knowledge online year: 1998 - doi: 10.1126/science.282.5396.2022 pmc: PMC3057080 pubmed: '9851918' title: 'Comparison of the complete protein sets of worm and yeast: orthology and divergence' year: 1998 - doi: 10.1093/nar/27.1.74 pmc: PMC148101 pubmed: '9847146' title: Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure year: 1999 - doi: 10.1093/nar/26.1.73 pmc: PMC147204 pubmed: '9399804' title: 'SGD: Saccharomyces Genome Database' year: 1998 - doi: 10.1126/science.277.5330.1259 pmc: PMC3039837 pubmed: '9297238' title: Yeast as a model organism year: 1997 - pmc: PMC3057085 pubmed: '9169866' title: Genetic and physical maps of Saccharomyces cerevisiae year: 1997 - doi: 10.1073/pnas.94.11.5506 pmc: PMC34160 pubmed: '9159100' title: 'Molecular linguistics: extracting information from gene and protein sequences' year: 1997 - pubmed: '7660459' title: Genetic nomenclature guide. Saccharomyces cerevisiae year: 1995 - doi: 10.1101/2024.09.16.613348 pmc: PMC11430078 pubmed: '39345624' title: 'Saccharomyces Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements' year: 2024 - doi: 10.1093/database/baw020 pmc: PMC4795930 pubmed: '26989152' title: 'From one to many: expanding the Saccharomyces cerevisiae reference genome panel' year: 2016 - doi: 10.1101/pdb.top083840 pmc: PMC5673599 pubmed: '26631132' title: 'The Saccharomyces Genome Database: A Tool for Discovery' year: 2015 - doi: 10.1101/pdb.prot088922 pmc: PMC5673602 pubmed: '26631126' title: 'The Saccharomyces Genome Database: Exploring Genome Features and Their Annotations' year: 2015 - doi: 10.1101/pdb.prot088914 pmc: PMC5673600 pubmed: '26631125' title: 'The Saccharomyces Genome Database: Gene Product Annotation of Function, Process, and Component' year: 2015 - doi: 10.1101/pdb.prot088906 pmc: PMC5673598 pubmed: '26631124' title: 'The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining' year: 2015 - doi: 10.1101/pdb.prot088898 pmc: PMC5673601 pubmed: '26631123' title: 'The Saccharomyces Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes' year: 2015 - doi: 10.1093/nar/gkv1250 pmc: PMC4702884 pubmed: '26578556' title: The Saccharomyces Genome Database Variant Viewer year: 2015 - doi: 10.1002/dvg.22862 pmc: PMC4545726 pubmed: '25997651' title: Biocuration at the Saccharomyces genome database year: 2015 - doi: 10.1371/journal.pone.0120671 pmc: PMC4363492 pubmed: '25781462' title: AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae year: 2015 - doi: 10.1093/nar/gku975 pmc: PMC4384031 pubmed: '25313161' title: The complex portal--an encyclopaedia of macromolecular complexes year: 2014 - doi: 10.1093/database/bau075 pmc: PMC4105709 pubmed: '25052702' title: Standardized description of scientific evidence using the Evidence Ontology (ECO) year: 2014 - doi: 10.1534/g3.113.008995 pmc: PMC3962479 pubmed: '24374639' title: 'The reference genome sequence of Saccharomyces cerevisiae: then and now' year: 2014 - doi: 10.1093/nar/gkt1158 pmc: PMC3965049 pubmed: '24265222' title: Saccharomyces genome database provides new regulation data year: 2013 - doi: 10.1093/database/bat054 pmc: PMC3706743 pubmed: '23842463' title: A guide to best practices for Gene Ontology (GO) manual annotation year: 2013 - doi: 10.1093/database/bat012 pmc: PMC3595989 pubmed: '23487186' title: 'The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database' year: 2013 - doi: 10.1093/database/bat004 pmc: PMC3567487 pubmed: '23396302' title: 'The YeastGenome app: the Saccharomyces Genome Database at your fingertips' year: 2013 - doi: 10.1093/database/bas001 pmc: PMC3308158 pubmed: '22434836' title: CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations year: 2012 - doi: 10.1093/database/bar062 pmc: PMC3308152 pubmed: '22434830' title: YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit year: 2012 - doi: 10.1093/database/bar057 pmc: PMC3308148 pubmed: '22434826' title: 'Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report' year: 2012 - doi: 10.1093/nar/gkr1029 pmc: PMC3245034 pubmed: '22110037' title: 'Saccharomyces Genome Database: the genomics resource of budding yeast' year: 2011 - doi: 10.1093/database/bar004 pmc: PMC3067894 pubmed: '21411447' title: 'Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study' year: 2011 - doi: 10.1093/database/bap001 pmc: PMC2790299 pubmed: '20157474' title: New mutant phenotype data curation system in the Saccharomyces Genome Database year: 2009 - doi: 10.1093/nar/gkp917 pmc: PMC2808950 pubmed: '19906697' title: Saccharomyces Genome Database provides mutant phenotype data year: 2009 - doi: 10.1016/j.tim.2009.04.005 pmc: PMC3057094 pubmed: '19577472' title: 'Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns' year: 2009 - doi: 10.1093/nar/gkm909 pmc: PMC2238894 pubmed: '17982175' title: 'Gene Ontology annotations at SGD: new data sources and annotation methods' year: 2007 - doi: 10.1093/nar/gkl931 pmc: PMC1669759 pubmed: '17142221' title: 'Expanded protein information at SGD: new pages and proteome browser' year: 2006 - doi: 10.1002/yea.1400 pmc: PMC3040122 pubmed: '17001629' title: 'Saccharomyces cerevisiae S288C genome annotation: a working hypothesis' year: 2006 - doi: 10.1093/nar/gkj117 pmc: PMC1347479 pubmed: '16381907' title: 'Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome' year: 2006 - doi: 10.1093/nar/gki023 pmc: PMC539977 pubmed: '15608219' title: 'Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD)' year: 2005 - doi: 10.1093/bib/5.1.9 pmc: PMC3037832 pubmed: '15153302' title: 'Saccharomyces genome database: underlying principles and organisation' year: 2004 - doi: 10.1093/nar/gkh033 pmc: PMC308767 pubmed: '14681421' title: Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms year: 2004 - doi: 10.1093/nar/gkg054 pmc: PMC165501 pubmed: '12519985' title: Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins year: 2003 - doi: 10.1016/s0076-6879(02)50972-1 pubmed: '12073322' title: Saccharomyces Genome Database year: 2002 - doi: 10.1093/nar/30.1.69 pmc: PMC99086 pubmed: '11752257' title: Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO) year: 2002 - doi: 10.1093/nar/29.1.80 pmc: PMC29796 pubmed: '11125055' title: Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data year: 2001 - doi: 10.1093/nar/28.1.77 pmc: PMC102447 pubmed: '10592186' title: Integrating functional genomic information into the Saccharomyces genome database year: 2000 - doi: 10.1002/9780470089941.et1104s01 title: Using Model Organism Databases (MODs) year: 2009 - doi: 10.1002/(SICI)1097-0061(199812)14:16<1453::AID-YEA348>3.0.CO;2-G title: Expanding yeast knowledge online. twitter: yeastgenome uri_format: https://www.yeastgenome.org/locus/$1 sgd.pathways: contact: email: Karen.Christie@jax.org github: krchristie name: Karen R. Christie orcid: 0000-0001-5501-853X description: Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD). example: PWY3O-214 homepage: http://pathway.yeastgenome.org/ keywords: - genome - pathway - sequence mappings: biocontext: SGD.PATHWAYS miriam: sgd.pathways n2t: sgd.pathways prefixcommons: sgd.pathways name: Saccharomyces genome database pathways pattern: ^PWY\w{2}\-\d{3}$ preferred_prefix: sgd.pathways providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/sgd.pathways:$1 publications: - doi: 10.1101/2024.09.16.613348 pmc: PMC11430078 pubmed: '39345624' title: 'Saccharomyces Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements' year: 2024 - doi: 10.1093/nar/gkh033 pmc: PMC308767 pubmed: '14681421' title: Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms year: 2004 uri_format: http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1 sgn: contact: email: lam87@cornell.edu github: lukasmueller name: Lukas A. Mueller orcid: 0000-0001-8640-1750 description: The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant. example: '0001' homepage: http://solgenomics.net/ keywords: - agriculture - botany - comparative genomics - genome - genomics - pathway - plant - small molecule mappings: biocontext: SGN fairsharing: FAIRsharing.3zqvaf go: SGN integbio: nbdc02414 miriam: sgn n2t: sgn ncbi: SGN pathguide: '433' prefixcommons: sgn re3data: r3d100012078 name: Sol Genomics Network pattern: ^\d+$ preferred_prefix: sgn providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/sgn:$1 publications: - doi: 10.1093/nar/gku1195 pmc: PMC4383978 pubmed: '25428362' title: The Sol Genomics Network (SGN)--from genotype to phenotype to breeding year: 2014 - doi: 10.1093/nar/gkq866 pmc: PMC3013765 pubmed: '20935049' title: 'The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl' year: 2010 twitter: solgenomics uri_format: http://solgenomics.net/phenome/locus_display.pl?locus_id=$1 sh: contact: email: dr.shorthair@pm.me github: dr-shorthair name: Simon Cox orcid: 0000-0002-3884-3420 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A language for validating RDF graphs against a set of conditions download_owl: https://triplydb.com/w3c/sh/download.trig.gz example: NodeShape homepage: https://www.w3.org/TR/shacl/ keywords: - informatics - knowledge and information systems - ontology - ontology and terminology - quality - w3c rec mappings: fairsharing: FAIRsharing.f1449d lov: sh zazuko: sh name: Shapes Constraint Language preferred_prefix: sh repository: https://github.com/w3c/data-shapes synonyms: - shacl uri_format: http://www.w3.org/ns/shacl#$1 shareloc: description: 'ShareLoc defines terms to annotate data sets from single molecule localization microscopy, including but not limited to: imaging technique, biological structures or molecules of interest, cell types, experimental condition, labeling method, fixation protocol, etc.' download_owl: https://raw.githubusercontent.com/imodpasteur/ShareLoc.XYZ/ontology/shareloc.owl example: '000004' homepage: https://shareloc.xyz keywords: - ontology mappings: ols: shareloc name: ShareLoc pattern: ^\d{6}$ preferred_prefix: shareloc uri_format: https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_$1 sharkipedia.species: contact: email: creeas@gmail.com github: creeas name: Christopher Mull orcid: 0000-0003-1710-8256 contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone. example: '983' github_request_issue: 607 homepage: https://www.sharkipedia.org/ name: Sharkipedia Species part_of: sharkipedia pattern: ^\d+$ preferred_prefix: sharkipedia.species publications: - doi: 10.1038/s41597-022-01655-1 pmc: PMC9464254 pubmed: '36088355' title: 'Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series' year: 2022 repository: https://github.com/sharkipedia/sharkipedia reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.sharkipedia.org/species/$1 sharkipedia.trait: contact: email: creeas@gmail.com github: creeas name: Christopher Mull orcid: 0000-0003-1710-8256 contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone. example: '13' github_request_issue: 607 homepage: https://www.sharkipedia.org/ name: Sharkipedia Trait part_of: sharkipedia pattern: ^\d+$ preferred_prefix: sharkipedia.trait publications: - doi: 10.1038/s41597-022-01655-1 pmc: PMC9464254 pubmed: '36088355' title: 'Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series' year: 2022 repository: https://github.com/sharkipedia/sharkipedia reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.sharkipedia.org/traits/$1 sharkipedia.trend: contact: email: creeas@gmail.com github: creeas name: Christopher Mull orcid: 0000-0003-1710-8256 contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone. example: '3447' github_request_issue: 607 homepage: https://www.sharkipedia.org/ name: Sharkipedia Trend part_of: sharkipedia pattern: ^\d+$ preferred_prefix: sharkipedia.trend publications: - doi: 10.1038/s41597-022-01655-1 pmc: PMC9464254 pubmed: '36088355' title: 'Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series' year: 2022 repository: https://github.com/sharkipedia/sharkipedia reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.sharkipedia.org/trends/$1 sheepqtldb: description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs. example: '19803' homepage: https://www.animalgenome.org/QTLdb keywords: - dna - genome mappings: biocontext: SHEEPQTLDB miriam: sheepqtldb n2t: sheepqtldb prefixcommons: sheepqtldb name: Animal Genome Sheep QTL part_of: qtldb pattern: ^\d+$ preferred_prefix: sheepqtldb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/sheepqtldb:$1 uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 shex: contact: email: gregg@greggkellogg.net github: gkellogg name: Gregg Kellogg contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Shape Expressions (ShEx) language describes RDF nodes and graph structures. A node constraint describes an RDF node (IRI, blank node or literal) and a shape describes the triples involving nodes in an RDF graph. These descriptions identify predicates and their associated cardinalities and datatypes. ShEx shapes can be used to communicate data structures associated with some process or interface, generate or validate data, or drive user interfaces. download_rdf: https://www.w3.org/ns/shex.ttl example: TripleExpression homepage: http://www.w3.org/ns/shex# keywords: - metadata - rdf - semantic web mappings: zazuko: shex name: Shape Expression Vocabulary pattern: ^\w+$ preferred_prefix: shex repository: https://github.com/shexspec/shexspec.github.io uri_format: http://www.w3.org/ns/shex#$1 shibase: comment: This resource doesn't exist on the web anymore deprecated: true description: The database focuses on the comparative genomics of Shigella and provides a way to summarize large volumes of genomic and comparison data in a visually intuitive format. example: SDY2614 homepage: http://www.mgc.ac.cn/ShiBASE/ keywords: - genome mappings: prefixcommons: shibase name: ShiBASE preferred_prefix: shibase providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/shibase:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=$1 sibo: contact: email: cjmungall@lbl.gov name: Chris Mungall orcid: 0000-0002-6601-2165 deprecated: true description: Social Behavior in insects download_obo: http://purl.obolibrary.org/obo/sibo.obo download_owl: http://purl.obolibrary.org/obo/sibo.owl example: 0000509 homepage: https://github.com/obophenotype/sibo keywords: - biology - obo - ontology license: CC-BY-3.0 mappings: aberowl: SIBO biocontext: SIBO bioportal: SIBO fairsharing: FAIRsharing.q09hck obofoundry: sibo ols: sibo ontobee: SIBO name: Social Insect Behavior Ontology pattern: ^\d{7}$ preferred_prefix: SIBO rdf_uri_format: http://purl.obolibrary.org/obo/SIBO_$1 repository: https://github.com/obophenotype/sibo uri_format: http://purl.obolibrary.org/obo/SIBO_$1 sider.drug: description: SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER. example: '2244' homepage: http://sideeffects.embl.de/ mappings: biocontext: SIDER.DRUG miriam: sider.drug n2t: sider.drug name: SIDER Drug pattern: ^\d+$ preferred_prefix: sider.drug uri_format: http://sideeffects.embl.de/drugs/$1 sider.effect: description: SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER. example: C0017565 homepage: http://sideeffects.embl.de/ mappings: biocontext: SIDER.EFFECT miriam: sider.effect n2t: sider.effect name: SIDER Side Effect pattern: ^C\d+$ preferred_prefix: sider.effect provides: umls uri_format: http://sideeffects.embl.de/se/$1 sigmaaldrich: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Sigma Aldrich is a life sciences supply vendor. example: HPA000698 github_request_issue: 216 homepage: https://www.sigmaaldrich.com keywords: - biology - chemistry - life sciences - vendor mappings: cellosaurus: Sigma-Aldrich pathguide: '236' name: Sigma Aldrich preferred_prefix: sigmaaldrich uri_format: https://www.sigmaaldrich.com/US/en/product/sigma/$1 signaling-gateway: contact: email: kenan@ucsd.edu name: Kenan Azam orcid: 0000-0001-7016-8624 description: The Signaling Gateway provides information on mammalian proteins involved in cellular signaling. example: A001094 homepage: http://www.signaling-gateway.org/molecule keywords: - pathway - protein - small molecule mappings: biocontext: SIGNALING-GATEWAY miriam: signaling-gateway n2t: signaling-gateway pathguide: '87' prefixcommons: signaling-gateway name: Signaling Gateway pattern: ^A\d{6}$ preferred_prefix: signaling-gateway providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/signaling-gateway:$1 publications: - doi: 10.1093/bioinformatics/btr190 pmc: PMC3106186 pubmed: '21505029' title: Signaling gateway molecule pages--a data model perspective year: 2011 - doi: 10.1093/nar/gkm907 pmc: PMC2238911 pubmed: '17965093' title: The Molecule Pages database year: 2007 - doi: 10.1038/nature01307 pubmed: '12478304' title: The Molecule Pages database year: 2002 uri_format: http://www.signaling-gateway.org/molecule/query?afcsid=$1 signor: contact: email: gianni.cesareni@torvergata.it name: Gianni Cesareni orcid: 0000-0002-9528-6018 description: SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. example: SIGNOR-C41 homepage: https://signor.uniroma2.it/ keywords: - biology license: CC-BY-NC-4.0 mappings: fairsharing: FAIRsharing.ss78t4 miriam: signor pathguide: '599' uniprot: DB-0206 name: Signaling Network Open Resource pattern: ^SIGNOR\-[A-Z]+\d+$ preferred_prefix: signor publications: - doi: 10.1093/nar/gkac883 pmc: PMC9825604 pubmed: '36243968' title: 'SIGNOR 3.0, the SIGnaling network open resource 3.0: 2022 update' year: 2022 - doi: 10.1093/nar/gkv1048 pmc: PMC4702784 pubmed: '26467481' title: 'SIGNOR: a database of causal relationships between biological entities' year: 2015 synonyms: - SIGNOR uri_format: https://signor.uniroma2.it/relation_result.php?id=$1 signor.relation: comment: Currently, you can put a SIGNOR relation ID into the main page search box and it will resolve, but there is not currently a way to resolve them via a URL pattern contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: Identifiers for relationships between proteins and complexes, along with their type and provenance example: SIGNOR-252737 github_request_issue: 604 homepage: https://signor.uniroma2.it keywords: - protein-protein interactions name: SIGNOR Relation part_of: signor pattern: ^SIGNOR-\d+$ preferred_prefix: signor.relation reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 silva.taxon: contact: email: lorenz.reimer@dsmz.de name: Lorenz Reimer orcid: 0000-0002-7805-0660 contributor: email: jplfaria@anl.gov github: jplfaria name: Jose P. Faria orcid: 0000-0001-9302-7250 description: 'SILVA is a resource of aligned ribosomal RNA (rRNA) gene sequences for Bacteria, Archaea, and Eukaryotes. It assigns internal, auto-incremented integer identifiers to taxa. However, these identifiers are not persistent nor unique - if the label for a taxon is changed, it assigned a new identifier and the old identifier is removed.' example: '11084' github_request_issue: 1306 homepage: https://www.arb-silva.de license: CC-BY-SA-4.0 logo: https://www.arb-silva.de/fileadmin/graphics_general/main/dissemination/silva-sticker-1_2_ext_33.png name: SILVA Taxon pattern: ^\d+$ preferred_prefix: silva.taxon publications: - doi: 10.1093/nar/gkt1209 pmc: PMC3965112 pubmed: '24293649' title: The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks year: 2014 - doi: 10.1093/nar/gks1219 pmc: PMC3531112 pubmed: '23193283' title: 'The SILVA ribosomal RNA gene database project: improved data processing and web-based tools' year: 2012 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 sio: banana: SIO banana_peel: _ contact: email: michel.dumontier@gmail.com github: micheldumontier name: Michel Dumontier orcid: 0000-0003-4727-9435 description: The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. download_owl: http://semanticscience.org/ontology/sio/v1.59/sio-release.owl example: 000912 homepage: https://github.com/micheldumontier/semanticscience keywords: - biology - knowledge representation - natural science - ontology - subject agnostic mappings: aberowl: SIO agroportal: SIO biocontext: SIO biolink: SIO bioportal: SIO fairsharing: FAIRsharing.dpkb5f lov: sio miriam: sio ols: sio ontobee: SIO name: Semanticscience Integrated Ontology pattern: ^\d{6}$ preferred_prefix: sio publications: - doi: 10.1186/2041-1480-5-14 pmc: PMC4015691 pubmed: '24602174' title: The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery year: 2014 repository: https://github.com/micheldumontier/semanticscience uri_format: https://semanticscience.org/resource/SIO_$1 version: '1.59' siren: comment: appears in FOODON, there is no website other than the spreadsheet referenced below on langual's site contact: email: patrice.buche@inrae.fr name: Patrice Buche orcid: 0000-0002-9134-5404 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A modern method of records management and an automated cross-referenced subject index for accurate and comprehensive information retrieval developed by the US FDA's Bureau of Foods example: F11903 homepage: https://www.langual.org/langual_indexed_datasets.asp mappings: agroportal: SIREN name: Scientific Information Retrieval and Exchange Network pattern: ^F\d+$ preferred_prefix: siren publications: - doi: 10.1093/jaoac/65.5.1268 title: 'SIREN: Data Base Approach to Scientific Information Handling in the Bureau of Foods, Food and Drug Administration' year: 1982 references: - https://github.com/FoodOntology/foodon/issues/267 - https://www.langual.org/download/IndexedDatasets/FDA/SIREN%20(updated).TXT synonyms: - SUBSET_SIREN sisu: contact: email: hannele.laivuori@helsinki.fi name: Hannele Laivuori orcid: 0000-0003-3212-7826 description: The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies. example: 17:41223048 homepage: http://www.sisuproject.fi/ keywords: - biomedical science - epidemiology - genomics - medicine - preclinical studies mappings: biocontext: SISU fairsharing: FAIRsharing.t1a232 miriam: sisu n2t: sisu name: Sequencing Initiative Suomi pattern: ^[0-9]+:[0-9]+$ preferred_prefix: sisu publications: - doi: 10.1371/journal.pone.0128524 pmc: PMC4452275 pubmed: '26030606' title: Targeted resequencing of the pericentromere of chromosome 2 linked to constitutional delay of growth and puberty year: 2015 - doi: 10.1371/journal.pgen.1004494 pmc: PMC4117444 pubmed: '25078778' title: Distribution and medical impact of loss-of-function variants in the Finnish founder population year: 2014 uri_format: http://search.sisuproject.fi/#/variant/$1 sitex: contact: email: imedvedeva@celgene.com github: imedvedeva-celgene name: Irina Medvedeva orcid: 0000-0003-2802-8198 description: SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments. example: '1000' homepage: http://www-bionet.sscc.ru/sitex/ keywords: - domain - eukaryotic - life science - sequence - structure mappings: biocontext: SITEX fairsharing: FAIRsharing.5mr9c5 miriam: sitex n2t: sitex prefixcommons: sitex name: SitEx pattern: ^\d+$ preferred_prefix: sitex providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/sitex:$1 publications: - doi: 10.1093/nar/gkr1187 pmc: PMC3245165 pubmed: '22139920' title: 'SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes' year: 2011 uri_format: http://www-bionet.sscc.ru/sitex/index.php?siteid=$1 skip: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine. example: SKIP001214 homepage: https://skip.stemcellinformatics.org/en/ mappings: cellosaurus: SKIP name: Stemcell Knowledge and Information Portal pattern: ^SKIP\d+$ preferred_prefix: skip uri_format: https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1 skm: description: 'Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors. ' example: rx00408 homepage: http://www.nib.si/eng/ mappings: miriam: skm name: Stress Knowledge Map pattern: ^rx[0-9]{5}$ preferred_prefix: skm uri_format: https://skm.nib.si/api/pss/reactions?reaction_id=$1&return_field=summary skos: contact: email: alistair.miles@linacre.ox.ac.uk github: alimanfoo name: Alistair Miles orcid: 0000-0001-9018-4680 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web download_owl: http://aber-owl.net/media/ontologies/skos/1/skos.owl download_rdf: http://www.w3.org/TR/skos-reference/skos.rdf example: prefLabel homepage: https://www.w3.org/2004/02/skos/ keywords: - ontology - subject agnostic - w3c rec mappings: aberowl: skos bartoc: '18274' biocontext: skos fairsharing: FAIRsharing.48e326 lov: skos ols: skos zazuko: skos name: Simple Knowledge Organization System preferred_prefix: skos uri_format: http://www.w3.org/2004/02/skos/core#$1 skosxl: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Simple Knowledge Organization System (SKOS) is a common data model for sharing and linking knowledge organization systems via the Semantic Web. SKOS-XL defines an extension for the Simple Knowledge Organization System, providing additional support for describing and linking lexical entities.This document provides a brief description of the SKOS-XL vocabulary. example: literalForm homepage: http://www.w3.org/2008/05/skos-xl# keywords: - data model - metadata - semantic web - skos - w3c rec mappings: lov: skosxl zazuko: skosxl name: Simple Knowledge Organization System eXtension for Labels preferred_prefix: skosxl uri_format: http://www.w3.org/2008/05/skos-xl#$1 slctr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Sri Lanka Clinical Trials Registry (SLCTR) is a Registry for clinical trials involving human subjects, conducted in Sri Lanka or overseas. The SLCTR is a Primary Registry linked to the Registry Network of the International Clinical Trials Registry Platform of the WHO (WHO-ICTRP). It is a not-for-profit Registry, with free and open access to researchers, clinicians, and the general public. (from homepage) example: SLCTR/2023/010 homepage: https://slctr.lk/ logo: https://slctr.lk/images/logo.png name: Sri Lanka Clinical Trials Registry pattern: ^SLCTR/\d{4}/\d+$ preferred_prefix: slctr references: - https://slctr.lk/trials/slctr-2023-010 slkbase: description: Cell line databases/resources example: '3618' homepage: https://sumlineknowledgebase.com/ mappings: cellosaurus: SLKBase name: SUM Breast Cancer Cell Line Knowledge Base pattern: ^\d+$ preferred_prefix: slkbase uri_format: https://sumlineknowledgebase.com/?page_id=$1 slm: banana: SLM contact: email: swisslipids@isb-sib.ch name: Alan Bridge orcid: 0000-0003-2148-9135 description: SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions. download_rdf: file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/swisslipids.ttl example: '000000341' homepage: http://www.swisslipids.org/#/ keywords: - life science - metabolomics license: CC-BY-4.0 mappings: biocontext: SWISSLIPID fairsharing: FAIRsharing.pxr7x2 integbio: nbdc02026 miriam: slm n2t: swisslipid ols: slm pathguide: '687' re3data: r3d100012603 togoid: Swisslipids uniprot: DB-0197 wikidata: P8691 name: SwissLipid namespace_in_lui: true pattern: ^\d+$ preferred_prefix: SLM publications: - doi: 10.1093/bioinformatics/btv285 pmc: PMC4547616 pubmed: '25943471' title: The SwissLipids knowledgebase for lipid biology year: 2015 synonyms: - swisslipid - swisslipids uri_format: https://www.swisslipids.org/#/entity/SLM:$1 slso: contact: email: daniel.c.berrios@nasa.gov github: DanBerrios name: Dan Berrios orcid: 0000-0003-4312-9552 description: The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive and other systems that contain space life science research data. download_json: http://purl.obolibrary.org/obo/slso.json download_obo: http://purl.obolibrary.org/obo/slso.obo download_owl: http://purl.obolibrary.org/obo/slso.owl example: '0000000' homepage: https://github.com/nasa/LSDAO keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: SLSO bioportal: SLSO obofoundry: slso ontobee: SLSO name: Space Life Sciences Ontology preferred_prefix: SLSO rdf_uri_format: http://purl.obolibrary.org/obo/SLSO_$1 repository: https://github.com/nasa/LSDAO uri_format: http://purl.obolibrary.org/obo/SLSO_$1 smart: contact: email: chris.ponting@ed.ac.uk name: Chris P. Ponting orcid: 0000-0003-0202-7816 description: The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures. example: SM00015 homepage: http://smart.embl-heidelberg.de/ keywords: - domain - life science - protein - structure mappings: biocontext: SMART fairsharing: FAIRsharing.hsbpq3 go: SMART integbio: nbdc00682 miriam: smart n2t: smart prefixcommons: smart togoid: Smart uniprot: DB-0097 name: Simple Modular Architecture Research Tool pattern: ^SM\d{5}$ preferred_prefix: smart providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/smart:$1 publications: - doi: 10.1093/nar/27.1.229 pmc: PMC148142 pubmed: '9847187' title: 'SMART: identification and annotation of domains from signalling and extracellular protein sequences' year: 1999 - doi: 10.1093/nar/gkx922 pmc: PMC5753352 pubmed: '29040681' title: 20 years of the SMART protein domain annotation resource year: 2018 - doi: 10.1093/nar/gku949 pmc: PMC4384020 pubmed: '25300481' title: 'SMART: recent updates, new developments and status in 2015' year: 2014 - doi: 10.1093/nar/gkr931 pmc: PMC3245027 pubmed: '22053084' title: 'SMART 7: recent updates to the protein domain annotation resource' year: 2011 - doi: 10.1093/nar/gkn808 pmc: PMC2686533 pubmed: '18978020' title: 'SMART 6: recent updates and new developments' year: 2008 - doi: 10.1093/nar/gkj079 pmc: PMC1347442 pubmed: '16381859' title: 'SMART 5: domains in the context of genomes and networks' year: 2006 - doi: 10.1093/nar/gkh088 pmc: PMC308822 pubmed: '14681379' title: 'SMART 4.0: towards genomic data integration' year: 2004 - doi: 10.1093/nar/30.1.242 pmc: PMC99073 pubmed: '11752305' title: Recent improvements to the SMART domain-based sequence annotation resource year: 2002 - doi: 10.1093/nar/28.1.231 pmc: PMC102444 pubmed: '10592234' title: 'SMART: a web-based tool for the study of genetically mobile domains' year: 2000 - doi: 10.1016/s0959-440x(99)80055-4 pubmed: '10361098' title: Protein families in multicellular organisms year: 1999 - doi: 10.1016/S0959-440X(99)80055-4 title: Protein families in multicellular organisms. uri_format: http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1 smc.bgc: contact: email: dwudwary@lbl.gov name: Daniel W Udwary orcid: 0000-0002-3491-0198 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: The secondary metabolism collaboratory is a database for secondary metabolite biosynthetic gene clusters. This prefix represents identifiers for individual biosynthetic gene clusters (BGCs) linked to their corresponding bacterial or archaeal source. example: '12039302' github_request_issue: 1301 homepage: https://smc.jgi.doe.gov name: Secondary Metabolism Collaboratory pattern: ^\d+$ preferred_prefix: smc.bgc publications: - doi: 10.1093/nar/gkae1060 pubmed: '39540430' title: 'The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://smc.jgi.doe.gov/bgc/$1 smc.source: contact: email: dwudwary@lbl.gov name: Daniel W Udwary orcid: 0000-0002-3491-0198 contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: The secondary metabolism collaboratory is a database for secondary metabolite biosynthetic gene clusters. This prefix represents identifiers for bacteria and archaea sources linked to their associated set of biosynthetic gene clusters (BGCs). example: '1' github_request_issue: 1301 homepage: https://smc.jgi.doe.gov name: Secondary Metabolism Collaboratory pattern: ^\d+$ preferred_prefix: smc.source publications: - doi: 10.1093/nar/gkae1060 pubmed: '39540430' title: 'The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: https://smc.jgi.doe.gov/sources/$1 smid: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C. elegans and other nematodes. SMIDs aim to make life easier for describing biogenic small molecules in metabolomic and genomic applications. ' example: '137' homepage: https://smid-db.org/ name: C. elegans Small Molecule Identifier Database pattern: ^\d+$ preferred_prefix: smid synonyms: - SMID-DB uri_format: https://smid-db.org/smid/$1 smiles: contact: email: tim.vandermeersch@gmail.com github: timvdm name: Tim Vandermeersch contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - github: NishaSharma14 name: Nisha Sharma orcid: 0009-0006-4755-1039 description: Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions. example: CC2(C)C\1CCC(C)/C=C/12 homepage: https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html keywords: - chemistry - life science mappings: fairsharing: FAIRsharing.qv4b3c wikidata: P233 name: Simplified molecular-input line-entry system pattern: ^[A-Za-z0-9+\-\*=#$:().>/\\\[\]%]+$ preferred_prefix: smiles providers: - code: cms.canonicalize description: Canonicalizes a given SMILES string according to the allowed toolkits. homepage: https://api.naturalproducts.net/latest/docs#/convert/SMILES_Canonicalise_convert_canonicalsmiles_get name: Canonicalizes a SMILES via the Cheminformatics Microservice uri_format: https://api.naturalproducts.net/latest/convert/canonicalsmiles?smiles=$1 - code: cms.convert description: Convert SMILES to various molecular formats using different toolkits. homepage: https://api.naturalproducts.net/latest/docs#/convert/SMILES_convert_to_Formats_convert_formats_get name: Convert SMILES to various molecular formats via the Cheminformatics Microservice uri_format: https://api.naturalproducts.net/latest/convert/formats?smiles=$1 - code: cms.coordinates2d description: Generates 2D Coordinates using the CDK Structure diagram generator/RDKit/Open Babel and returns the mol block. homepage: https://api.naturalproducts.net/latest/docs#/convert/Create2D_Coordinates_convert_mol2D_get name: Generate 2D coordinates via the Cheminformatics Microservice uri_format: https://api.naturalproducts.net/latest/convert/mol2D?smiles=$1 - code: cms.coordinates3d description: Generates a random 3D conformer from SMILES using the specified molecule toolkit. homepage: https://api.naturalproducts.net/latest/docs#/convert/Create3D_Coordinates_convert_mol3D_get name: Generate 3D conformer via the Cheminformatics Microservice uri_format: https://api.naturalproducts.net/latest/convert/mol3D?smiles=$1 - code: cms.cxsmiles description: Convert SMILES to CXSMILES. For more informations. homepage: https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_CXSMILES_convert_cxsmiles_get name: Convert SMILES to CXSMILES via the Cheminformatics Microservice uri_format: https://api.naturalproducts.net/latest/convert/cxsmiles?smiles=$1 - code: cms.depict2d description: Generates a 2D depiction of a molecule using CDK or RDKit with the given parameters. homepage: https://api.naturalproducts.net/latest/docs#/depict/Depict2D_molecule_depict_2D_get name: Depict 2D via the Cheminformatics Microservice uri_format: https://api.naturalproducts.net/latest/depict/2D?smiles=$1 - code: cms.depict3d description: Generate 3D depictions of molecules using OpenBabel or RDKit. homepage: https://api.naturalproducts.net/latest/docs#/depict/Depict3D_Molecule_depict_3D_get name: Depict 3D via the Cheminformatics Microservice uri_format: https://api.naturalproducts.net/latest/depict/3D?smiles=$1 - code: cms.descriptor description: Returns descriptors calculated from the molecule with RDKit homepage: https://api.naturalproducts.net/latest/docs#/chem/get_descriptors_chem_descriptors_get name: RDKit Descriptor via the Cheminformatics Microservice uri_format: https://api.naturalproducts.net/latest/chem/descriptors?smiles=$1 - code: cms.inchi description: Convert SMILES to InChI. homepage: https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_InChI_convert_inchi_get name: Convert SMILES to InChI via the Cheminformatics Microservice uri_format: https://api.naturalproducts.net/latest/convert/inchi?smiles=$1 - code: cms.inchikey description: Convert SMILES to InChIKey. homepage: https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_InChIKey_convert_inchikey_get name: Convert SMILES to InChIKey via the Cheminformatics Microservice uri_format: https://api.naturalproducts.net/latest/convert/inchikey?smiles=$1 - code: cms.iupac description: Generates IUPAC name for given SMILES using [STOUT](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00512-4) package. homepage: https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_IUPACname_convert_iupac_get name: Generate IUPAC name from SMILES via the Cheminformatics Microservice uri_format: https://api.naturalproducts.net/latest/convert/iupac?smiles=$1 - code: cms.selfies description: Generates SELFIES string for a given SMILES string. homepage: https://api.naturalproducts.net/latest/docs#/convert/encode_SELFIES_convert_selfies_get name: Generates SELFIES for a SMILES via the Cheminformatics Microservice uri_format: https://api.naturalproducts.net/latest/convert/selfies?smiles=$1 publications: - doi: 10.1186/1758-2946-4-24 pmc: PMC3551648 pubmed: '23031664' title: mol2chemfig, a tool for rendering chemical structures from molfile or SMILES format to LATE X code year: 2012 - doi: 10.1021/ci00067a005 title: SMILES. 3. DEPICT. Graphical depiction of chemical structures year: 1990 - doi: 10.1021/ci00062a008 title: SMILES. 2. Algorithm for generation of unique SMILES notation year: 1989 - doi: 10.1021/ci00057a005 title: SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules year: 1988 references: - https://github.com/biopragmatics/bioregistry/issues/931 repository: https://github.com/timvdm/OpenSMILES/blob/master/discussion_summary.txt uri_format: https://www.simolecule.com/cdkdepict/depict/bow/svg?smi=$1&zoom=2.0&annotate=cip smpdb: contact: email: david.wishart@ualberta.ca github: DavidWishartLab name: David S. Wishart orcid: 0000-0002-3207-2434 description: The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. example: SMP0000219 homepage: https://smpdb.ca/ keywords: - chemical - human - life science - metabolite - pathway mappings: biocontext: SMPDB biolink: PathWhiz edam: '2659' fairsharing: FAIRsharing.y1zyaq integbio: nbdc00908 miriam: smpdb n2t: smpdb pathguide: '311' prefixcommons: smpdb name: Small Molecule Pathway Database pattern: ^SMP\d+$ preferred_prefix: smpdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/smpdb:$1 publications: - doi: 10.1093/nar/gkt1067 pmc: PMC3965088 pubmed: '24203708' title: 'SMPDB 2.0: big improvements to the Small Molecule Pathway Database' year: 2013 - doi: 10.1093/nar/gkp1002 pmc: PMC2808928 pubmed: '19948758' title: 'SMPDB: The Small Molecule Pathway Database' year: 2009 - doi: doi:10.1093/nar/gkp1002 title: 'SMPDB: The Small Molecule Pathway Database.' synonyms: - SMP twitter: WishartLab uri_format: https://smpdb.ca/view/$1 snap: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality. example: Quality homepage: http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf keywords: - gene - interaction - pathway - protein mappings: pathguide: '494' prefixcommons: snap name: Snapshot preferred_prefix: snap providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/snap:$1 synonyms: - bfo11snap uri_format: http://www.ifomis.org/bfo/1.1/snap#$1 snctp: comment: it appears they cede information into WHO contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The SNCTP (Swiss National Clinical Trials Portal) is the portal where clinical trials in Switzerland are published. It contains data from two sources: from BASEC, the national platform for submitting applications for research projects to ethics committees, and from the ICTRP (the WHO International Clinical Trials Registry Platform), which covers the 17 primary registries worldwide. The ICTRP clinical trials shown on the SNCTP are limited to those conducted in Switzerland; there is also an option to display trials conducted in one of Switzerland''s neighbouring countries. [from homepage]' example: SNCTP000005580 homepage: https://kofam.ch/en/snctp-portal name: Swiss National Clinical Trials Portal preferred_prefix: snctp snomedct: contact: email: custserv@nlm.nih.gov name: NLM Customer Service contributor_extras: - email: nicolas.matentzoglu@gmail.com github: matentzn name: Nicolas Matentzoglu orcid: 0000-0002-7356-1779 description: SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc. download_owl: http://snomed.info/sct/900000000000207008/version/20200131 example: '284196006' homepage: http://www.snomedbrowser.com/ keywords: - biomedical science - health science - medicine - ontology - preclinical studies license: https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf mappings: aberowl: SNOMEDCT biocontext: SNOMEDCT biolink: SNOMEDCT bioportal: SNOMEDCT fairsharing: FAIRsharing.d88s6e hl7: 2.16.840.1.113883.6.96 miriam: snomedct n2t: snomedct ols: snomed prefixcommons: snomedct wikidata: P5806 name: SNOMED CT (International Edition) pattern: ^(\w+)?\d+$ preferred_prefix: snomedct providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/snomedct:$1 - code: bioportal.purl description: BioPortal PURL homepage: https://bioontology.org name: BioPortal PURL uri_format: http://purl.bioontology.org/ontology/SNOMEDCT/$1 publications: - doi: 10.1097/00024665-200609000-00011 pubmed: '16980782' title: 'Standardized nursing language in the systematized nomenclature of medicine clinical terms: A cross-mapping validation method' year: 2006 rdf_uri_format: http://snomed.info/id/$1 synonyms: - SCTID - SCTID_2010_1_31 - SNOMECT - SNOMED - SNOMEDCT - SNOMEDCTCT - SNOMEDCTCT_2018_03_01 - SNOMEDCTCT_2019_03_01 - SNOMEDCT_2005_07_31 - SNOMEDCT_2010_1_31 - SNOMEDCT_2020_03_01 - SNOMEDCT_US - SNOMEDCT_US_2015_03_01 - SNOMEDCT_US_2016_03_01 - SNOMEDCT_US_2018_03_01 - SNOMEDCT_US_2018_09_01 - SNOMEDCT_US_2019_03_01 - SNOMEDCT_US_2019_09_01 - SNOMEDCT_US_2020_03_01 - SNOMEDCT_US_2020_09_01 - SNOMEDCT_US_2021_03_01 - SNOMEDCT_US_2021_07_31 - SNOMEDCT_US_2021_09_01 - SNOMEDCT_US_2022_07_31 - SNOMEDCT_US_2022_09_01 - SNOMEDCT_US_2022_12_31 - SNOMEDCT_US_2023_02_28 - SNOMEDCT_US_2023_03_01 - SNOMEDCT_US_2023_09_01 - SNOMEDCT_US_2023_10_01 - SNOMEDCT_US_2023_11_01 - SNOMEDCT_US_2024_03_01 - SNOMED_CT - SNOMED_CT_US_2018_03_01 - SNOWMEDCT - SNOWMEDCT_US - SNOWMEDCT_US_2018_03_01 uri_format: http://snomed.info/id/$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/ keywords: - rna mappings: integbio: nbdc00323 prefixcommons: snornalbmedb name: snoRNABase preferred_prefix: snornabase providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/snornalbmedb:$1 uri_format: http://www-snorna.biotoul.fr/plus.php?id=$1 snp2tfbs: description: SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome. example: rs11603840 homepage: https://ccg.epfl.ch/snp2tfbs/ mappings: miriam: snp2tfbs name: SNP to Transcription Factor Binding Sites pattern: ^rs[0-9]+$ preferred_prefix: snp2tfbs provides: dbsnp uri_format: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1 snp500cancer: comment: This resource doesn't exist on the web anymore deprecated: true description: The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer. example: TP53-47 homepage: http://snp500cancer.nci.nih.gov keywords: - dna mappings: prefixcommons: snp500cancer name: SNP500Cancer preferred_prefix: snp500cancer providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/snp500cancer:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id=$1 so: appears_in: - pcl banana: SO contact: email: keilbeck@genetics.utah.edu github: keilbeck name: Karen Eilbeck orcid: 0000-0002-0831-6427 description: The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data. download_obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/master/Ontology_Files/so.obo download_owl: http://purl.obolibrary.org/obo/so.owl example: '0001157' homepage: http://www.sequenceontology.org/ keywords: - bioinformatics - biology - deoxyribonucleic acid - dna - gene - genome - life science - obo - ontology - ribonucleic acid - rna - sequence - sequence annotation - sequence feature - structure license: CC-BY-4.0 logo: https://obofoundry.org/images/so_logo.png mappings: aberowl: SO agroportal: SO biocontext: SO bioportal: SO fairsharing: FAIRsharing.6bc7h9 go: SO miriam: so n2t: so obofoundry: so ols: so ontobee: SO prefixcommons: so name: Sequence types and features ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: SO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/so:$1 publications: - doi: 10.1186/gb-2010-11-8-r88 pmc: PMC2945790 pubmed: '20796305' title: A standard variation file format for human genome sequences year: 2010 - doi: 10.1016/j.jbi.2010.03.002 pmc: PMC3052763 pubmed: '20226267' title: Evolution of the Sequence Ontology terms and relationships year: 2010 - doi: 10.1186/gb-2005-6-5-r44 pmc: PMC1175956 pubmed: '15892872' title: 'The Sequence Ontology: a tool for the unification of genome annotations' year: 2005 rdf_uri_format: http://purl.obolibrary.org/obo/SO_$1 repository: https://github.com/The-Sequence-Ontology/SO-Ontologies uri_format: http://purl.obolibrary.org/obo/SO_$1 version: '2024-11-18' sopharm: contact: email: adrien.coulet@loria.fr name: Adrien Coulet orcid: 0000-0002-1466-062X deprecated: true description: SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. SO-Pharm articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables to represent pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables to represent patient and more largely panel included in trials, and populations. SO-Pharm enables the representation of measured items on this patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains. download_owl: http://aber-owl.net/media/ontologies/SOPHARM/18/sopharm.owl homepage: http://www.loria.fr/~coulet/sopharm2.0_description.php keywords: - obo - ontology mappings: aberowl: SOPHARM biocontext: SOPHARM bioportal: SOPHARM obofoundry: sopharm name: Suggested Ontology for Pharmacogenomics preferred_prefix: SOPHARM rdf_uri_format: http://purl.obolibrary.org/obo/SOPHARM_$1 uri_format: http://purl.obolibrary.org/obo/SOPHARM_$1 sosa: contact: email: dr.shorthair@pm.me github: dr-shorthair name: Simon Cox orcid: 0000-0002-3884-3420 contributor: github: StroemPhi name: Philip Strömert orcid: 0000-0002-1595-3213 description: This ontology is based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group. download_rdf: https://www.w3.org/ns/sosa/ example: FeatureOfInterest github_request_issue: 1274 homepage: https://www.w3.org/TR/vocab-ssn/ keywords: - environment - iot license: http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document mappings: agroportal: SOSA lov: sosa zazuko: sosa name: Sensor, Observation, Sample, and Actuator Ontology preferred_prefix: sosa publications: - doi: 10.1016/j.websem.2018.06.003 title: 'SOSA: A lightweight ontology for sensors, observations, samples, and actuators' year: 2019 repository: https://github.com/w3c/sdw reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.w3.org/ns/sosa/$1 soybase: contact: email: Jacqueline.Campbell@usda.gov name: Jacqueline Campbell orcid: 0000-0003-2787-3955 description: SoyBase is a repository for curated genetics, genomics and related data resources for soybean. example: BARC-013845-01256 homepage: http://soybase.org/ keywords: - agriculture - comparative genomics - development - life science - obo - phenotype - plant breeding - spider mappings: biocontext: SOYBASE fairsharing: FAIRsharing.z4agsr integbio: nbdc01817 miriam: soybase n2t: soybase ncbi: SoyBase pathguide: '44' prefixcommons: soy re3data: r3d100010846 name: SoyBase pattern: ^\w+(\-)?\w+(\-)?\w+$ preferred_prefix: soybase providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/soy:$1 publications: - doi: 10.1093/nar/gkp798 pmc: PMC2808871 pubmed: '20008513' title: SoyBase, the USDA-ARS soybean genetics and genomics database year: 2009 twitter: SoyBaseDatabase uri_format: 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 keywords: - ontology - upper-level ontology name: Span preferred_prefix: span synonyms: - bfo11span spbase: comment: This resource doesn't exist on the web anymore deprecated: true description: SpBase, is designed to present the results of the genome sequencing project for the purple sea urchin. THe sequences and annotations emerging from this effort are organized in a database that provides the research community access to those data not normally presented through NCBI and other large databases. example: SPU_000001 homepage: http://spbase.org keywords: - dna - genome - rna mappings: integbio: nbdc00686 prefixcommons: spbase name: SpBase preferred_prefix: spbase providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/spbase:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id=$1 spd: contact: email: ramirez@macn.gov.ar github: martinjramirez name: Martin Ramirez orcid: 0000-0002-0358-0130 description: An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). download_obo: http://purl.obolibrary.org/obo/spd.obo download_owl: http://purl.obolibrary.org/obo/spd.owl example: '0000001' homepage: http://research.amnh.org/atol/files/ keywords: - anatomy - behavior - life science - obo - ontology - spider license: CC-BY-3.0 mappings: aberowl: SPD biocontext: SPD bioportal: SPD fairsharing: FAIRsharing.yecp83 obofoundry: spd ols: spd ontobee: SPD prefixcommons: spdo wikidata: P4537 name: Spider Ontology pattern: ^\d{7}$ preferred_prefix: SPD providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/spdo:$1 publications: - doi: 10.3390/d11100202 title: The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data year: 2019 rdf_uri_format: http://purl.obolibrary.org/obo/SPD_$1 repository: https://github.com/obophenotype/spider-ontology uri_format: http://purl.obolibrary.org/obo/SPD_$1 spdx: description: The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception. example: CC-BY-1.0 homepage: https://spdx.org/licenses mappings: miriam: spdx n2t: spdx name: Software Package Data Exchange License pattern: ^[0-9A-Za-z\-.]+$ preferred_prefix: spdx uri_format: https://spdx.org/licenses/$1 sphn: contact: email: Sabine.Oesterle@sib.swiss name: Sabine Oesterle orcid: 0000-0003-3248-7899 contributor: email: deepak.unni3@gmail.com github: deepakunni3 name: Deepak Unni orcid: 0000-0002-3583-7340 description: The Swiss Personalized Health Network is a national infrastructure initiative with the aim to develop, implement, and validate coordinated data infrastructures in order to make health-relevant data interoperable and shareable for research in Switzerland. The sphn RDF schema builds the foundation for all data exchanges within the sphn by integrating semantic information defined in the [sphn dataset](https://sphn.ch/document/sphn-dataset/). download_owl: https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology/-/raw/master/rdf_schema/sphn_rdf_schema.owl download_rdf: https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology/-/raw/master/rdf_schema/sphn_rdf_schema.ttl example: Allergy github_request_issue: 535 homepage: https://www.sphn.ch keywords: - ontology license: CC-BY-4.0 name: Swiss Personalized Health Network Schema pattern: ^\S+$ preferred_prefix: sphn repository: https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://biomedit.ch/rdf/sphn-ontology/sphn#$1 spike.map: contact: email: Yossih@tauex.tau.ac.il name: Yosef Shiloh orcid: 0000-0002-1538-6060 description: SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps. example: spike00001 homepage: http://www.cs.tau.ac.il/~spike/ keywords: - dna - gene expression - pathway mappings: biocontext: SPIKE.MAP miriam: spike.map n2t: spike.map prefixcommons: spike name: SPIKE Map pattern: ^spike\d{5}$ preferred_prefix: spike.map providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/spike:$1 publications: - doi: 10.1093/nar/gkq1167 pmc: PMC3014840 pubmed: '21097778' title: 'SPIKE: a database of highly curated human signaling pathways' year: 2010 - doi: 10.1186/1471-2105-9-110 pmc: PMC2263022 pubmed: '18289391' title: SPIKE--a database, visualization and analysis tool of cellular signaling pathways year: 2008 uri_format: http://www.cs.tau.ac.il/~spike/maps/$1.html splash: description: The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance. example: splash10-0zq2000000-77302b0326a418630a84 homepage: http://mona.fiehnlab.ucdavis.edu/ mappings: biocontext: SPLASH miriam: splash n2t: splash name: Spectra Hash Code pattern: ^splash\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$ preferred_prefix: splash uri_format: http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1 splicenest: comment: This resource doesn't exist on the web anymore deprecated: true description: SpliceNest [1] is a web based graphical tool to explore gene structure, including alternative splicing, based on a mapping on the EST consensus sequences (contigs) from GeneNest [2] to the complete human genome. example: Hs635 homepage: http://splicenest.molgen.mpg.de/ keywords: - dna - gene - genome mappings: prefixcommons: splicenest name: SpliceNest preferred_prefix: splicenest providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/splicenest:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster=$1 spp: contact: email: nmckenna@bcm.edu name: Neil McKenna orcid: 0000-0001-6689-0104 description: The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways. example: 10.1621/vwN2g2HaX3 homepage: https://www.signalingpathways.org/index.jsf keywords: - omics - transcriptomics mappings: fairsharing: FAIRsharing.WxI96O miriam: spp re3data: r3d100013650 name: Signaling Pathways Project pattern: ^10.\w{4}/\w{10}$ preferred_prefix: spp publications: - doi: 10.1038/s41597-019-0193-4 pmc: PMC6823428 pubmed: '31672983' title: The Signaling Pathways Project, an integrated 'omics knowledgebase for mammalian cellular signaling pathways year: 2019 twitter: sigpathproject uri_format: https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1 srao: contact: email: allyson.lister@oerc.ox.ac.uk github: allysonlister name: Allyson Lister orcid: 0000-0002-7702-4495 description: The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies. download_obo: https://github.com/FAIRsharing/subject-ontology/raw/refs/heads/master/SRAO.obo download_owl: https://github.com/FAIRsharing/subject-ontology/raw/refs/heads/master/SRAO.owl example: '0000400' homepage: https://github.com/FAIRsharing/subject-ontology keywords: - agriculture - biomedical science - classification - computer science - earth science - environmental science - fair - humanities - life science - metadata standardization - metascience - natural science - ontology - resource metadata - topics mappings: fairsharing: FAIRsharing.b1xD9f ols: srao name: FAIRsharing Subject Ontology part_of: fairsharing pattern: ^\d{7}$ preferred_prefix: srao repository: https://github.com/FAIRsharing/subject-ontology twitter: FAIRsharing_org uri_format: http://www.fairsharing.org/ontology/subject/SRAO_$1 version: '2025-02-23' ssbd.dataset: contact: email: sonami@riken.jp name: Shuichi Onami orcid: 0000-0002-8255-1724 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations. example: '1' homepage: https://ssbd.riken.jp keywords: - cell biology - developmental biology - molecular dynamics mappings: fairsharing: FAIRsharing.we2r5a name: System Science of Biological Dynamics dataset pattern: ^\d+$ preferred_prefix: ssbd.dataset publications: - doi: 10.1093/bioinformatics/btw417 pmc: PMC5181557 pubmed: '27412095' title: 'SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena' year: 2016 uri_format: https://ssbd.riken.jp/database/dataset/$1 ssbd.project: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations. example: '1' homepage: https://ssbd.riken.jp name: System Science of Biological Dynamics project pattern: ^\d+$ preferred_prefix: ssbd.project uri_format: https://ssbd.riken.jp/database/project/$1 ssn: contact: email: dr.shorthair@pm.me github: dr-shorthair name: Simon Cox orcid: 0000-0002-3884-3420 contributor: github: StroemPhi name: Philip Strömert orcid: 0000-0002-1595-3213 description: This ontology describes sensors, actuators and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports. download_owl: http://aber-owl.net/media/ontologies/SSN/2/ssn.owl download_rdf: https://www.w3.org/ns/ssn/ example: hasProperty github_request_issue: 1272 homepage: https://www.w3.org/TR/vocab-ssn keywords: - imaging - iot - methods - monitoring - ontology - remote sensing - resource metadata - sensor data - w3c rec - web of things license: http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document mappings: aberowl: SSN agroportal: SSN bioportal: SSN fairsharing: FAIRsharing.c0bvcy lov: ssn zazuko: ssn name: Semantic Sensor Network Ontology preferred_prefix: ssn publications: - doi: 10.3233/sw-180320 title: 'The Modular SSN Ontology: A Joint W3C and OGC Standard Specifying the Semantics of Sensors, Observations, Sampling, and Actuation' year: 2019 - doi: 10.1016/j.websem.2018.06.003 title: 'SOSA: A lightweight ontology for sensors, observations, samples, and actuators' year: 2018 - doi: 10.1016/j.websem.2012.05.003 title: The SSN ontology of the W3C semantic sensor network incubator group year: 2012 repository: https://github.com/w3c/sdw-sosa-ssn reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.w3.org/ns/ssn/$1 ssn.system: contact: email: dr.shorthair@pm.me github: dr-shorthair name: Simon Cox orcid: 0000-0002-3884-3420 contributor: email: philip.stroemert@tib.eu github: StroemPhi name: Philip Strömert orcid: 0000-0002-1595-3213 description: This ontology describes system capabilities, operating ranges, and survival ranges. Please report any errors to the W3C Spatial Data on the Web Working Group via the SDW WG Public List public-sdw-wg@w3.org download_rdf: http://www.w3.org/ns/ssn/systems example: qualityOfObservation github_request_issue: 1270 homepage: https://www.w3.org/TR/vocab-ssn/ license: http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document name: System capabilities, operating ranges, and survival ranges ontology preferred_prefix: ssn.system reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.w3.org/ns/ssn/systems/$1 ssrn.article: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier for an article/paper at the SSRN example: '1667659' homepage: https://ssrn.com mappings: wikidata: P893 name: Social Science Research Network Article preferred_prefix: ssrn.article references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://ssrn.com/abstract=$1 ssrn.author: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier for an author at the Social Science Research Network example: '112517' homepage: https://ssrn.com keywords: - person - researcher mappings: wikidata: P3747 name: Social Science Research Network Author pattern: ^[1-9]\d{0,6}$ preferred_prefix: ssrn.author references: - https://github.com/biopragmatics/bioregistry/pull/1171 uri_format: https://ssrn.com/author=$1 sssom: contact: email: nicolas.matentzoglu@gmail.com github: matentzn name: Nicolas Matentzoglu orcid: 0000-0002-7356-1779 contributor: email: nicolas.matentzoglu@gmail.com github: matentzn name: Nicolas Matentzoglu orcid: 0000-0002-7356-1779 description: SSSOM is a Simple Standard for Sharing Ontological Mappings, providing - a TSV-based representation for ontology term mappings - a comprehensive set of standard metadata elements to describe mappings and - a standard translation between the TSV and the Web Ontology Language (OWL). Most metadata elements, such as "sssom:mapping_justification" are defined in the sssom namespace. example: mapping_justification example_extras: - superClassOf github_request_issue: 759 homepage: https://w3id.org/sssom license: BSD-3-Clause name: Simple Standard for Sharing Ontological Mappings pattern: ^[A-Za-z_]+$ preferred_prefix: sssom repository: https://github.com/mapping-commons/sssom reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://w3id.org/sssom/$1 sstoss: comment: This resource doesn't exist on the web anymore deprecated: true description: SSToSS is a database which provides sequence-structural templates of single member protein domain superfamilies like PASS2. Sequence-structural templates are recognized by considering the content and overlap of sequence similarity and structural parameters like, solvent inaccessibility, secondary structural content, hydrogen bonding and spatial packing of the residues among the protein of single member superfamilies. example: 01.01.005 homepage: http://caps.ncbs.res.in/SSTOSS/index.htm keywords: - protein - structure mappings: prefixcommons: sstoss name: Sequence-Structural Templates of Single-member Superfamilies preferred_prefix: sstoss providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/sstoss:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code=$1 stap: contact: email: bhsung@kribb.re.kr name: Bong Hyun Sung orcid: 0000-0002-8992-1118 description: STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB). example: 1a24 homepage: http://psb.kobic.re.kr/STAP/refinement/ keywords: - life science - statistics mappings: biocontext: STAP fairsharing: FAIRsharing.ja9cdq miriam: stap n2t: stap name: Statistical Torsional Angles Potentials pattern: ^[0-9][A-Za-z0-9]{3}$ preferred_prefix: stap publications: - doi: 10.1093/bioinformatics/btv595 pubmed: '26504145' title: 'NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores' year: 2015 - doi: 10.1371/journal.pone.0108888 pmc: PMC4184813 pubmed: '25279564' title: Protein NMR structures refined without NOE data year: 2014 - doi: 10.1002/prot.24265 pubmed: '23408564' title: 'Statistical torsion angle potential energy functions for protein structure modeling: a bicubic interpolation approach' year: 2013 - doi: 10.1093/nar/gkr1021 pmc: PMC3245188 pubmed: '22102572' title: 'STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures' year: 2011 uri_format: http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1 stato: appears_in: - ontoavida - psdo - scdo banana: STATO contact: email: proccaserra@gmail.com github: proccaserra name: Philippe Rocca-Serra orcid: 0000-0001-9853-5668 description: STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots. download_owl: http://purl.obolibrary.org/obo/stato.owl example: 0000288 homepage: http://stato-ontology.org/ keywords: - data visualization - experimental measurement - graph - obo - ontology - protocol - statistics - study design license: CC-BY-3.0 logo: https://raw.githubusercontent.com/ISA-tools/stato/dev/images/stato-logo-3.png mappings: aberowl: STATO biocontext: STATO bioportal: STATO fairsharing: FAIRsharing.na5xp miriam: stato obofoundry: stato ols: stato ontobee: STATO name: The Statistical Methods Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: STATO publications: - pubmed: '32109232' title: Semantic concept schema of the linear mixed model of experimental observations - pubmed: '31831744' title: Experiment design driven FAIRification of omics data matrices, an exemplar rdf_uri_format: http://purl.obolibrary.org/obo/STATO_$1 repository: https://github.com/ISA-tools/stato uri_format: http://purl.obolibrary.org/obo/STATO_$1 version: '2025-02-22' stitch: contact: email: bork@embl.de name: Peer Bork orcid: 0000-0002-2627-833X description: STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. example: BQJCRHHNABKAKU homepage: http://stitch.embl.de/ keywords: - interaction - life science - protein - small molecule mappings: biocontext: STITCH fairsharing: FAIRsharing.zhwa8x miriam: stitch n2t: stitch pathguide: '313' prefixcommons: stitch re3data: r3d100012165 name: Search Tool for Interactions of Chemicals pattern: ^\w{14}$ preferred_prefix: stitch providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/stitch:$1 publications: - doi: 10.1093/nar/gkt1207 pmc: PMC3964996 pubmed: '24293645' title: 'STITCH 4: integration of protein-chemical interactions with user data' year: 2013 - doi: 10.1093/nar/gkr1011 pmc: PMC3245073 pubmed: '22075997' title: 'STITCH 3: zooming in on protein-chemical interactions' year: 2011 - doi: 10.1093/nar/gkp937 pmc: PMC2808890 pubmed: '19897548' title: 'STITCH 2: an interaction network database for small molecules and proteins' year: 2009 - doi: 10.1093/nar/gkm795 pmc: PMC2238848 pubmed: '18084021' title: 'STITCH: interaction networks of chemicals and proteins' year: 2007 uri_format: http://stitch.embl.de/interactions/$1 stn: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The pre-IND tracking number for submissions to the FDA example: '125768' homepage: https://www.fda.gov/media/128698/download name: FDA Submission Tracking Number preferred_prefix: stn storedb: banana: STOREDB contact: email: PNS12@cam.ac.uk name: Dr Paul Schofield orcid: 0000-0002-5111-7263 description: STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons. example: STUDY1040 homepage: https://www.storedb.org/ keywords: - biomedical science - ecology - epidemiology - life science - preclinical studies mappings: biocontext: STOREDB fairsharing: FAIRsharing.6h8d2r integbio: nbdc02191 miriam: storedb n2t: storedb re3data: r3d100011049 name: Store DB namespace_in_lui: true pattern: ^(STUDY|FILE|DATASET)\d+$ preferred_prefix: storedb uri_format: https://www.storedb.org/?$1 storedb.dataset: comment: Unfortunately, the resolver itself doesn't work since datasets are actually hierarchically assigned within studies. contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: Datasets inside StoreDB example: '1251' homepage: https://www.storedb.org/ name: STOREDB at University of Cambridge part_of: storedb pattern: ^\d+$ preferred_prefix: storedb.dataset uri_format: https://www.storedb.org/?STOREDB:DATASET$1 storedb.file: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: File inside StoreDB example: '12929' homepage: https://www.storedb.org/ name: STOREDB at University of Cambridge part_of: storedb pattern: ^\d+$ preferred_prefix: storedb.file uri_format: https://www.storedb.org/store_v3/download.jsp?fileId=$1 storedb.study: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Study inside StoreDB example: '1174' homepage: https://www.storedb.org/ name: STOREDB at University of Cambridge part_of: storedb pattern: ^\d+$ preferred_prefix: storedb.study providers: - code: doi description: DOIs for studies homepage: https://www.storedb.org/ name: StoreDB DOI uri_format: http://dx.doi.org/doi:10.20348/STOREDB/$1 uri_format: https://www.storedb.org/store_v3/study.jsp?studyId=$1 streptomedb: contact: email: stefan.guenther@pharmazie.uni-freiburg.de name: Stefan Günther orcid: 0000-0003-3744-189X contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifers for natural products isolated or mutasynthesized by bacteria of the genus Streptomyces. example: '15753' github_request_issue: 1287 homepage: http://streptomedb.vm.uni-freiburg.de:8000/streptomedb name: StreptomeDB pattern: ^\d+$ preferred_prefix: streptomedb publications: - doi: 10.1093/nar/gkae1030 pubmed: '39498494' title: 'StreptomeDB 4.0: a comprehensive database of streptomycetes natural products enriched with protein interactions and interactive spectral visualization' year: 2024 - doi: 10.1093/nar/gkaa868 pmc: PMC7779017 pubmed: '33051671' title: 'StreptomeDB 3.0: an updated compendium of streptomycetes natural products' year: 2020 - doi: 10.1093/nar/gkv1319 pmc: PMC4702922 pubmed: '26615197' title: StreptomeDB 2.0--an extended resource of natural products produced by streptomycetes year: 2015 - doi: 10.1093/nar/gks1253 pmc: PMC3531085 pubmed: '23193280' title: 'StreptomeDB: a resource for natural compounds isolated from Streptomyces species' year: 2012 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: http://streptomedb.vm.uni-freiburg.de:8000/streptomedb/get_drugcard/$1 string: contact: email: bork@embl.de name: Peer Bork orcid: 0000-0002-2627-833X description: 'STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.' example: P53350 homepage: http://string-db.org/ keywords: - biology - interaction - life science - protein mappings: biocontext: STRING edam: '2302' fairsharing: FAIRsharing.9b7wvk integbio: nbdc00690 miriam: string n2t: string pathguide: '93' prefixcommons: string re3data: r3d100010604 uniprot: DB-0141 name: Search Tool for Retrieval of Interacting Genes/Proteins pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$ preferred_prefix: string providers: - code: CURATOR_REVIEW description: STRING at Heidelberg homepage: http://string.embl.de/ name: STRING at Heidelberg uri_format: https://string.embl.de/cgi/network?identifier=$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/string:$1 provides: uniprot publications: - doi: 10.1093/nar/gkae1113 pubmed: '39558183' title: 'The STRING database in 2025: protein networks with directionality of regulation' year: 2024 - doi: 10.1093/nar/gky1131 pmc: PMC6323986 pubmed: '30476243' title: 'STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets' year: 2019 - doi: 10.1093/nar/gkw937 pmc: PMC5210637 pubmed: '27924014' title: 'The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible' year: 2016 - doi: 10.1093/bioinformatics/btv696 pmc: PMC4896368 pubmed: '26614125' title: 'SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles' year: 2015 - doi: 10.1093/nar/gku1003 pmc: PMC4383874 pubmed: '25352553' title: 'STRING v10: protein-protein interaction networks, integrated over the tree of life' year: 2014 - doi: 10.1093/nar/gks1094 pmc: PMC3531103 pubmed: '23203871' title: 'STRING v9.1: protein-protein interaction networks, with increased coverage and integration' year: 2012 - doi: 10.1093/nar/gkn760 pmc: PMC2686466 pubmed: '18940858' title: STRING 8--a global view on proteins and their functional interactions in 630 organisms year: 2008 uri_format: https://string-db.org/cgi/network?identifier=$1 sty: contact: email: olivier@nlm.nih.gov name: Olivier Bodenreider orcid: 0000-0003-4769-4217 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - email: tiago.lubiana.alves@usp.br github: lubianat name: Tiago Lubiana orcid: 0000-0003-2473-2313 description: UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types. example: T039 homepage: https://lhncbc.nlm.nih.gov/semanticnetwork/ keywords: - ontology mappings: aberowl: STY agroportal: STY biolink: UMLSSG bioportal: STY ecoportal: STY wikidata: P11955 name: UMLS Semantic Types Ontology pattern: ^T\d{3}$ preferred_prefix: sty providers: - code: bioportal.purl description: BioPortal PURL homepage: http://purl.bioontology.org/ontology/STY name: BioPortal PURL uri_format: http://purl.bioontology.org/ontology/STY/$1 synonyms: - UMLSSG - umls.st - umls.sty uri_format: https://uts.nlm.nih.gov/uts/umls/semantic-network/$1 subtilist: contact: email: antoine.danchin@normalesup.org name: Antoine Danchin orcid: 0000-0002-6350-5001 description: 'SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments.' example: BG11523 homepage: http://genolist.pasteur.fr/SubtiList/ keywords: - dna - genome - protein mappings: biocontext: SUBTILIST fairsharing: FAIRsharing.40j2vd miriam: subtilist n2t: subtilist ncbi: SubtiList prefixcommons: subtilist name: Bacillus subtilis genome sequencing project pattern: ^BG\d+$ preferred_prefix: subtilist providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/subtilist:$1 publications: - doi: 10.1093/nar/30.1.62 pmc: PMC99059 pubmed: '11752255' title: 'SubtiList: the reference database for the Bacillus subtilis genome' year: 2002 uri_format: http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1 subtiwiki: contact: email: jstuelk@gwdg.de name: Jörg Stülke orcid: 0000-0001-5881-5390 description: "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis.\ \ It provides comprehensive information on all genes and their proteins and RNA\ \ products, as well as information related to the current investigation of the\ \ gene/protein. \nNote: Currently, direct access to RNA products is restricted.\ \ This is expected to be rectified soon." example: BSU29180 homepage: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page keywords: - dna - gene - life science - protein - rna mappings: biocontext: SUBTIWIKI fairsharing: FAIRsharing.2ck3st integbio: nbdc00693 miriam: subtiwiki n2t: subtiwiki prefixcommons: subtiwiki name: SubtiWiki pattern: ^BSU\d{5}$ preferred_prefix: subtiwiki providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/subtiwiki:$1 publications: - doi: 10.1093/nar/gkv1006 pmc: PMC4702770 pubmed: '26433225' title: SubtiWiki 2.0--an integrated database for the model organism Bacillus subtilis year: 2015 - doi: 10.1093/database/bap012 pmc: PMC2790307 pubmed: '20157485' title: 'A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki' year: 2009 - doi: 10.1099/mic.0.035790-0 pubmed: '19959575' title: 'Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis' year: 2009 uri_format: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1 sugarbind: contact: email: frederique.lisacek@isb-sib.ch name: Frederique Lisacek orcid: 0000-0002-0948-4537 description: The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands. download_owl: http://aber-owl.net/media/ontologies/SUGARBIND/1/sugarbind.owl example: lectins/172 homepage: http://sugarbind.expasy.org/ keywords: - biomedical science - glycomics - ontology mappings: aberowl: SUGARBIND biocontext: SUGARBIND bioportal: SUGARBIND fairsharing: FAIRsharing.d064y6 integbio: nbdc02224 miriam: sugarbind n2t: sugarbind name: SugarBind pattern: ^[A-Za-z]+\/[0-9]+$ preferred_prefix: sugarbind publications: - doi: 10.1093/nar/gkv1247 pmc: PMC4702881 pubmed: '26578555' title: SugarBindDB, a resource of glycan-mediated host-pathogen interactions year: 2015 - doi: 10.1007/978-4-431-56454-6_13 title: SugarBindDB year: 2016 twitter: ISBSIB uri_format: http://sugarbind.expasy.org/$1 sulo: contact: email: michel.dumontier@gmail.com github: micheldumontier name: Michel Dumontier orcid: 0000-0003-4727-9435 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Simplified Upper Level Ontology (SULO) is ontology with a minimal set of classes and relations to guide the development of a personal health knowledge graph. [from homepage] download_rdf: https://w3id.org/sulo/sulo.ttl example: Capability github_request_issue: 1446 homepage: https://aidava-dev.github.io/sulo/ license: CC0-1.0 name: Simplified Upper Level Ontology preferred_prefix: sulo rdf_uri_format: https://w3id.org/sulo/$1 repository: https://github.com/aidava-dev/sulo/ uri_format: https://w3id.org/sulo/$1 supfam: contact: email: pandura@mrc-lmb.cam.ac.uk name: Arun Prasad Pandurangan orcid: 0000-0001-7168-7143 description: SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. example: SSF57615 homepage: http://supfam.org/SUPERFAMILY/ keywords: - classification - genome - protein - structure mappings: biocontext: SUPFAM miriam: supfam n2t: supfam prefixcommons: superfamily uniprot: DB-0155 name: SUPERFAMILY pattern: ^\w+$ preferred_prefix: supfam providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/superfamily:$1 publications: - doi: 10.1093/nar/gky1130 pubmed: '30445555' - doi: 10.1006/jmbi.2001.5080 pubmed: '11697912' title: Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure year: 2001 uri_format: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1 sweetrealm: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 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://raw.githubusercontent.com/EnvironmentOntology/envo/master/src/envo/sources/sweetrealm.obo example: ANOVA homepage: https://bioportal.bioontology.org/ontologies/SWEET keywords: - ontology mappings: bioportal: SWEET name: Semantic Web for Earth and Environment Technology Ontology preferred_prefix: sweetrealm uri_format: http://sweetontology.net/matrMineral/$1 swh: banana: swh description: Software Heritage is the universal archive of software source code. example: 1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d homepage: https://archive.softwareheritage.org mappings: biocontext: SWH miriam: swh n2t: swh name: Software Heritage namespace_in_lui: true pattern: ^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\S+)*$ preferred_prefix: swh uri_format: https://archive.softwareheritage.org/browse/swh:$1 swiss-model: contact: email: torsten.schwede@unibas.ch name: Torsten Schwede orcid: 0000-0003-2715-335X description: The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences. example: P23298 homepage: https://swissmodel.expasy.org keywords: - life science - protein - proteomics - structure mappings: biocontext: SWISS-MODEL fairsharing: FAIRsharing.vxz9pn miriam: swiss-model n2t: swiss-model prefixcommons: swissmodel re3data: r3d100010605 name: SWISS-MODEL Repository pattern: ^\w+$ preferred_prefix: swiss-model providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/swissmodel:$1 provides: uniprot publications: - doi: 10.1093/nar/gkw1132 pmc: PMC5210589 pubmed: '27899672' title: The SWISS-MODEL Repository-new features and functionality year: 2016 - doi: 10.1093/nar/gku340 pmc: PMC4086089 pubmed: '24782522' title: 'SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information' year: 2014 - doi: 10.1093/nar/gkn750 pmc: PMC2686475 pubmed: '18931379' title: The SWISS-MODEL Repository and associated resources year: 2008 twitter: SWISS_MODEL uri_format: https://swissmodel.expasy.org/repository/uniprot/$1 swissregulon: contact: email: erik.vannimwegen@unibas.ch name: Erik van Nimwegen orcid: 0000-0001-6338-1312 description: A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form. example: AHR homepage: http://swissregulon.unibas.ch keywords: - life science mappings: biocontext: SWISSREGULON fairsharing: FAIRsharing.7fnx38 integbio: nbdc02225 miriam: swissregulon n2t: swissregulon name: SwissRegulon pattern: ^[A-Za-z0-9]+$ preferred_prefix: swissregulon publications: - doi: 10.1093/nar/gks1145 pmc: PMC3531101 pubmed: '23180783' title: 'SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates' year: 2012 - doi: 10.1093/nar/gkl857 pmc: PMC1716717 pubmed: '17130146' title: 'SwissRegulon: a database of genome-wide annotations of regulatory sites' year: 2006 uri_format: http://swissregulon.unibas.ch/query/$1 swo: appears_in: - mcro contact: email: allyson.lister@oerc.ox.ac.uk github: allysonlister name: Allyson Lister orcid: 0000-0002-7702-4495 description: The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community. download_json: https://raw.githubusercontent.com/allysonlister/swo/master/swo.json download_obo: https://raw.githubusercontent.com/allysonlister/swo/master/swo.obo download_owl: https://raw.githubusercontent.com/allysonlister/swo/master/swo.owl example: '0000144' homepage: https://github.com/allysonlister/swo keywords: - algorithm - bioinformatics - computer science - obo - ontology - software - workflow license: CC-BY-4.0 mappings: aberowl: SWO biocontext: SWO bioportal: SWO fairsharing: FAIRsharing.sp3szt obofoundry: swo ols: swo ontobee: SWO prefixcommons: swo name: Software ontology pattern: ^\d{7}$ preferred_prefix: SWO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/swo:$1 - code: ebi description: The EBI's old SWO URIs before switching over to OBO PURLs homepage: http://www.ebi.ac.uk/swo/license name: Legacy EBI SWO uri_format: http://www.ebi.ac.uk/swo/SWO_$1 - code: ebi.data description: The EBI's old SWO URIs before switching over to OBO PURLs homepage: http://www.ebi.ac.uk/swo/data name: Legacy EBI SWO uri_format: http://www.ebi.ac.uk/swo/data/SWO_$1 - code: ebi.efo description: The EBI's old SWO URIs before switching over to OBO PURLs homepage: http://www.ebi.ac.uk/efo/swo/ name: Legacy EBI SWO uri_format: http://www.ebi.ac.uk/efo/swo/SWO_$1 - code: ebi.license description: The EBI's old SWO URIs before switching over to OBO PURLs homepage: http://www.ebi.ac.uk/swo/license name: Legacy EBI SWO uri_format: http://www.ebi.ac.uk/swo/license/SWO_$1 - code: ebi.maturity description: The EBI's old SWO URIs before switching over to OBO PURLs homepage: http://www.ebi.ac.uk/swo/maturity name: Legacy EBI SWO uri_format: http://www.ebi.ac.uk/swo/maturity/SWO_$1 publications: - doi: 10.1186/2041-1480-5-25 pmc: PMC4098953 pubmed: '25068035' title: 'The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation' year: 2014 rdf_uri_format: http://purl.obolibrary.org/obo/SWO_$1 repository: https://github.com/allysonlister/swo uri_format: http://purl.obolibrary.org/obo/SWO_$1 version: '2023-03-05' swrl: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: SWRL enables Horn-like rules to be combined with an OWL knowledge base. example: Variable homepage: https://www.w3.org/2003/11/swrl# keywords: - vocabularies mappings: lov: swrl name: A Semantic Web Rule Language Combining OWL and RuleML preferred_prefix: swrl uri_format: http://www.w3.org/2003/11/swrl#$1 symp: appears_in: - scdo contact: email: lynn.schriml@gmail.com github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 description: The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases. download_json: http://purl.obolibrary.org/obo/symp.json download_obo: http://purl.obolibrary.org/obo/symp.obo download_owl: http://purl.obolibrary.org/obo/symp.owl example: 0019171 homepage: http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page keywords: - biomedical science - diagnosis - disease - life science - obo - ontology - pain medicine - patient care license: CC0-1.0 mappings: aberowl: SYMP biocontext: SYMP bioportal: SYMP fairsharing: FAIRsharing.ay74mj obofoundry: symp ols: symp ontobee: SYMP prefixcommons: symptom wikidata: P8656 name: Symptom Ontology pattern: ^\d{7}$ preferred_prefix: SYMP providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/symptom:$1 publications: - doi: 10.1093/nar/gkad1051 pubmed: '37953304' title: 'The DO-KB Knowledgebase: a 20-year journey developing the disease open science ecosystem' year: 2023 - doi: 10.1093/nar/gkab1063 pmc: PMC8728220 pubmed: '34755882' title: The Human Disease Ontology 2022 update year: 2022 - doi: 10.1093/nar/gkp832 pmc: PMC2808878 pubmed: '19850722' title: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database year: 2009 rdf_uri_format: http://purl.obolibrary.org/obo/SYMP_$1 repository: https://github.com/DiseaseOntology/SymptomOntology synonyms: - SYMP uri_format: http://purl.obolibrary.org/obo/SYMP_$1 version: '2024-05-17' synapse: description: Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate. example: '41455251.1' homepage: https://sagebionetworks.org mappings: integbio: nbdc02162 miriam: synapse re3data: r3d100011894 name: Synapse Data Repository pattern: ^[0-9]*\.*[0-9]*$ preferred_prefix: synapse uri_format: https://repo-prod.prod.sagebase.org/ga4gh/drs/v1/objects/syn$1 synbip.bts: contact: email: lifengcheng@zju.edu.cn name: Fengcheng Li orcid: 0000-0002-1846-639X contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for the binding targets of synthetic binding proteins (SBP), describing the specific molecules or complexes that SBPs interact with for their intended applications example: st00576 github_request_issue: 1268 homepage: http://synbip.idrblab.net name: Synthetic Binding Proteins Binding Target pattern: ^st\d+$ preferred_prefix: synbip.bts publications: - doi: 10.1093/nar/gkae893 pubmed: '39413165' title: 'SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery for synthetic binding protein innovation' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: http://synbip.idrblab.net/data/bts/details/$1 synbip.epitope: contact: email: lifengcheng@zju.edu.cn name: Fengcheng Li orcid: 0000-0002-1846-639X contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for synthetic binding protein-target complexes, detailing their components, 3D structures and docking statistics example: mt002305 github_request_issue: 1268 homepage: http://synbip.idrblab.net name: Synthetic Binding Protein Epitope pattern: ^mt\d+$ preferred_prefix: synbip.epitope publications: - doi: 10.1093/nar/gkae893 pubmed: '39413165' title: 'SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery for synthetic binding protein innovation' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: http://synbip.idrblab.net/data/sbp-target-complex/details/$1 synbip.pss: contact: email: lifengcheng@zju.edu.cn name: Fengcheng Li orcid: 0000-0002-1846-639X contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for the protein scaffolds of synthetic binding proteins (SBP), detailing their structural frameworks and roles in facilitating SBP function. example: ps048 github_request_issue: 1268 homepage: http://synbip.idrblab.net name: Synthetic Binding Protein Protein Scaffold pattern: ^ps\d+$ preferred_prefix: synbip.pss publications: - doi: 10.1093/nar/gkae893 pubmed: '39413165' title: 'SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery for synthetic binding protein innovation' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: http://synbip.idrblab.net/data/scaffold/details/$1 synbip.sbp: contact: email: lifengcheng@zju.edu.cn name: Fengcheng Li orcid: 0000-0002-1846-639X contributor: email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: Identifiers for synthetic binding proteins, providing detailed information on their sequences, structures, targets, and functional properties for research, diagnostic, and therapeutic applications. example: sbp000002 github_request_issue: 1268 homepage: http://synbip.idrblab.net name: Synthetic Binding Protein pattern: ^sbp\d+$ preferred_prefix: synbip.sbp publications: - doi: 10.1093/nar/gkae893 pubmed: '39413165' title: 'SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery for synthetic binding protein innovation' year: 2024 reviewer: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 uri_format: http://synbip.idrblab.net/data/sbp/details/$1 syoid: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: Gemina Symptom Ontology preferred_prefix: syoid references: - https://github.com/DiseaseOntology/SymptomOntology/issues/7#event-4223716562 t3db: contact: email: david.wishart@ualberta.ca name: David Wishart orcid: 0000-0002-3207-2434 description: Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. example: T3D0001 homepage: http://www.t3db.org/ keywords: - biomedical science - life science - molecule - protein mappings: biocontext: T3DB edam: '2662' fairsharing: FAIRsharing.psn0h2 miriam: t3db n2t: t3db pathguide: '326' prefixcommons: t3db re3data: r3d100012189 name: Toxin and Toxin Target Database pattern: ^T3D\d+$ preferred_prefix: t3db providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/t3db:$1 publications: - doi: 10.1093/nar/gku1004 pmc: PMC4383875 pubmed: '25378312' title: 'T3DB: the toxic exposome database' year: 2014 - doi: 10.1093/nar/gkp934 pmc: PMC2808899 pubmed: '19897546' title: 'T3DB: a comprehensively annotated database of common toxins and their targets' year: 2009 uri_format: http://www.t3db.org/toxins/$1 t4fs: contact: email: allyson.lister@oerc.ox.ac.uk github: allysonlister name: Allyson Lister orcid: 0000-0002-7702-4495 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A terminology for the skills necessary to make data FAIR and to keep it FAIR. download_json: http://purl.obolibrary.org/obo/t4fs.json download_obo: http://purl.obolibrary.org/obo/t4fs.obo download_owl: http://purl.obolibrary.org/obo/t4fs.owl example: '0000127' homepage: https://github.com/terms4fairskills/FAIRterminology keywords: - curated information - digital curation - fair - obo - ontology - subject agnostic license: CC-BY-4.0 logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBZ1VDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--692c3b4cc5ea2f7aa8cc80267dad833f16dcccbb/terms4FAIRskills.png?disposition=inline mappings: aberowl: T4FS bioportal: T4FS fairsharing: FAIRsharing.fb99fa obofoundry: t4fs ols: t4fs ontobee: T4FS name: terms4FAIRskills pattern: ^\d{7}$ preferred_prefix: T4FS publications: - doi: 10.5281/zenodo.4772741 title: 'EOSC Co-creation funded project 074: Delivery of a proof of concept for terms4FAIRskills: Technical report' year: 2021 - doi: 10.5281/zenodo.4705219 title: 'EOSC Co-creation funded project 074: Delivery of a proof of concept for terms4FAIRskills: Technical report' year: 2021 rdf_uri_format: http://purl.obolibrary.org/obo/T4FS_$1 repository: https://github.com/terms4fairskills/FAIRterminology uri_format: http://purl.obolibrary.org/obo/T4FS_$1 version: '2025-02-09' tads: contact: email: dsonensh@odu.edu name: Daniel Sonenshine orcid: 0000-0001-9370-918X deprecated: true description: 'The anatomy of the Tick, Families: Ixodidae, Argassidae' download_obo: http://purl.obolibrary.org/obo/tads.obo download_owl: http://purl.obolibrary.org/obo/tads.owl example: '0000547' homepage: https://www.vectorbase.org/ontology-browser keywords: - anatomy - life science - obo - ontology license: CC-BY-4.0 mappings: aberowl: TADS biocontext: TADS bioportal: TADS fairsharing: FAIRsharing.8wm364 obofoundry: tads ols: tads ontobee: TADS name: Tick Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: TADS publications: - doi: 10.1111/j.1365-2583.2008.00781.x pubmed: '18237287' title: Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase year: 2008 rdf_uri_format: http://purl.obolibrary.org/obo/TADS_$1 repository: https://github.com/VEuPathDB-ontology/TADS uri_format: http://purl.obolibrary.org/obo/TADS_$1 version: '2015-08-20' tahe: contact: email: pierre.sprumont@unifr.ch name: Pierre Sprumont deprecated: true keywords: - obo - ontology mappings: biocontext: TAHE obofoundry: tahe name: Terminology of Anatomy of Human Embryology preferred_prefix: TAHE rdf_uri_format: http://purl.obolibrary.org/obo/TAHE_$1 uri_format: http://purl.obolibrary.org/obo/TAHE_$1 tahh: contact: email: pierre.sprumont@unifr.ch name: Pierre Sprumont deprecated: true keywords: - obo - ontology mappings: biocontext: TAHH obofoundry: tahh name: Terminology of Anatomy of Human Histology preferred_prefix: TAHH rdf_uri_format: http://purl.obolibrary.org/obo/TAHH_$1 uri_format: http://purl.obolibrary.org/obo/TAHH_$1 tair.gene: banana: Gene banana_peel: ':' contact: email: aisling.doyle9@gmail.com name: Aisling Doyle orcid: 0000-0003-3871-858X description: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus. example: '2200934' homepage: http://arabidopsis.org/index.jsp keywords: - gene mappings: biocontext: TAIR.GENE miriam: tair.gene n2t: tair.gene prefixcommons: tair.gene name: TAIR Gene part_of: tair pattern: ^\d{7}$ preferred_prefix: tair.gene providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/tair.gene:$1 publications: - doi: 10.1007/s10142-002-0077-z pubmed: '12444417' title: 'TAIR: a resource for integrated Arabidopsis data' year: 2002 uri_format: http://arabidopsis.org/servlets/TairObject?accession=Gene:$1 tair.locus: contact: email: aisling.doyle9@gmail.com name: Aisling Doyle orcid: 0000-0003-3871-858X contributor_extras: - email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS. example: '2200950' homepage: http://arabidopsis.org/index.jsp keywords: - genome mappings: biocontext: TAIR.LOCUS go: TAIR miriam: tair.locus n2t: tair.locus ncbi: TAIR prefixcommons: tair.locus name: The Arabidopsis Information Resource pattern: ^\d+$ preferred_prefix: tair.locus providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/tair.locus:$1 - code: thalemine description: Data mining on aradopsis homepage: https://bar.utoronto.ca/thalemine name: ThaleMine uri_format: https://bar.utoronto.ca/thalemine/portal.do?externalids=$1 publications: - doi: 10.1007/s10142-002-0077-z pubmed: '12444417' title: 'TAIR: a resource for integrated Arabidopsis data' year: 2002 uri_format: https://www.arabidopsis.org/locus?accession=$1 tair.protein: banana: AASequence banana_peel: ':' contact: email: aisling.doyle9@gmail.com name: Aisling Doyle orcid: 0000-0003-3871-858X contributor_extras: - email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept example: '1009107926' homepage: http://arabidopsis.org/index.jsp keywords: - protein mappings: biocontext: TAIR.PROTEIN miriam: tair.protein n2t: tair.protein prefixcommons: tair.protein name: TAIR Protein pattern: ^\d{10}$ preferred_prefix: tair.protein providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/tair.protein:$1 - code: legacy description: This was the old URI for TAIR proteins homepage: https://www.arabidopsis.org name: Legacy uri_format: http://arabidopsis.org/servlets/TairObject?accession=AASequence:$1 publications: - doi: 10.1007/s10142-002-0077-z pubmed: '12444417' title: 'TAIR: a resource for integrated Arabidopsis data' year: 2002 uri_format: https://www.arabidopsis.org/protein?key=$1 tao: contact: email: wasila.dahdul@usd.edu name: Wasila Dahdul orcid: 0000-0003-3162-7490 deprecated: true description: Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa download_obo: http://aber-owl.net/media/ontologies/TAO/135/tao.obo download_owl: http://purl.obolibrary.org/obo/tao.owl example: 0000086 homepage: http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology keywords: - anatomy - classification - obo - ontology license: CC0-1.0 mappings: aberowl: TAO biocontext: TAO bioportal: TAO obofoundry: tao ols: tao prefixcommons: tao name: Teleost Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: TAO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/tao:$1 publications: - doi: 10.1093/sysbio/syq013 pmc: PMC2885267 pubmed: '20547776' title: 'The teleost anatomy ontology: anatomical representation for the genomics age' year: 2010 rdf_uri_format: http://purl.obolibrary.org/obo/TAO_$1 synonyms: - TAO_RETIRED uri_format: http://purl.obolibrary.org/obo/TAO_$1 version: '2012-08-10' tarbase: description: TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used. example: hsa-let-7a-2-3p homepage: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index keywords: - biomedical science - life science mappings: biocontext: TARBASE fairsharing: FAIRsharing.a0k4cd integbio: nbdc02102 miriam: tarbase n2t: tarbase pathguide: '283' name: TarBase pattern: ^[a-z]{3}\-(mir|let|lin)\-\w+(\-\w+\-\w+)$ preferred_prefix: tarbase publications: - doi: 10.1093/nar/gkx1141 pmc: PMC5753203 pubmed: '29156006' title: 'DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions' year: 2018 - doi: 10.1093/nar/gku1215 pmc: PMC4383989 pubmed: '25416803' title: 'DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions' year: 2014 - doi: 10.1093/nar/gkn809 pmc: PMC2686456 pubmed: '18957447' title: 'The database of experimentally supported targets: a functional update of TarBase' year: 2008 - doi: 10.1261/rna.2239606 pmc: PMC1370898 pubmed: '16373484' title: 'TarBase: A comprehensive database of experimentally supported animal microRNA targets' year: 2005 uri_format: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1 taxrank: contact: email: balhoff@renci.org github: balhoff name: Jim Balhoff orcid: 0000-0002-8688-6599 description: A vocabulary of taxonomic ranks (species, family, phylum, etc) download_obo: http://purl.obolibrary.org/obo/taxrank.obo download_owl: http://purl.obolibrary.org/obo/taxrank.owl example: '0000001' homepage: https://github.com/phenoscape/taxrank keywords: - life science - obo - ontology - taxonomic classification - taxonomy license: CC0-1.0 mappings: aberowl: TAXRANK agroportal: TAXRANK biocontext: TAXRANK bioportal: TAXRANK fairsharing: FAIRsharing.p1sejz obofoundry: taxrank ols: taxrank ontobee: TAXRANK prefixcommons: taxrank name: Taxonomic rank vocabulary pattern: ^\d{7}$ preferred_prefix: TAXRANK providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/taxrank:$1 publications: - doi: 10.1186/2041-1480-4-34 pmc: PMC4177199 pubmed: '24267744' title: 'The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes' year: 2013 rdf_uri_format: http://purl.obolibrary.org/obo/TAXRANK_$1 repository: https://github.com/phenoscape/taxrank uri_format: http://purl.obolibrary.org/obo/TAXRANK_$1 version: '2024-11-28' tcb: description: Cell line collections example: '2966' homepage: https://www.pirbright.ac.uk/tick-cell-lines-views-page mappings: cellosaurus: TCB name: Tick Cell Biobank pattern: ^\d+$ preferred_prefix: tcb uri_format: https://www.pirbright.ac.uk/node/$1 tccd: comment: This resource doesn't exist on the web anymore deprecated: true description: Cell Cycle Database is a collection of genes and proteins involved in human and yeast cell cycle example: TP53 homepage: http://www.itb.cnr.it/cellcycle keywords: - gene - pathway - protein mappings: prefixcommons: tccd name: The Cell Cycle DB preferred_prefix: tccd providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/tccd:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name=$1 tcdb: contact: email: msaier@ucsd.edu name: Milton H. Saier, Jr. orcid: 0000-0001-5530-0017 description: The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally. example: 5.A.1.1.1 homepage: https://www.tcdb.org keywords: - cell biology - computational biology - knowledge and information systems - life science - phylogenetics - protein - structure mappings: biocontext: TCDB edam: '2756' fairsharing: FAIRsharing.p3bzqb go: TC miriam: tcdb n2t: tcdb pathguide: '104' prefixcommons: tcdb uniprot: DB-0135 wikidata: P7260 name: Transporter Classification Database pattern: ^\d+(\.[A-Z])?(\.\d+)?(\.\d+)?(\.\d+)?$ preferred_prefix: tcdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/tcdb:$1 publications: - doi: 10.1093/nar/gkaa1004 pmc: PMC7778945 pubmed: '33170213' title: 'The Transporter Classification Database (TCDB): 2021 update' year: 2021 - doi: 10.1093/nar/gkv1103 pmc: PMC4702804 pubmed: '26546518' title: 'The Transporter Classification Database (TCDB): recent advances' year: 2015 - doi: 10.1093/nar/gkt1097 pmc: PMC3964967 pubmed: '24225317' title: The transporter classification database year: 2013 - doi: 10.1093/nar/gkn862 pmc: PMC2686586 pubmed: '19022853' title: 'The Transporter Classification Database: recent advances' year: 2008 - doi: 10.1093/nar/gkj001 pmc: PMC1334385 pubmed: '16381841' title: 'TCDB: the Transporter Classification Database for membrane transport protein analyses and information' year: 2006 synonyms: - TC uri_format: http://www.tcdb.org/search/result.php?tc=$1 tctr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The TCTR was estabished in 2009 and has been operated by Clinical Research Collaboration Network (CRCN), an organization under the Medical Research Foundation, which is a non-profit organization, and financially supported by Thailand Center of Excellence for Life Sciences (TCELS). CRCN has been retitled the Medical Research Network (MedResNet) since June 15, 2012. (from homepage) example: TCTR20230429001 homepage: https://www.thaiclinicaltrials.org name: Thai Clinical Trials Registry pattern: ^TCTR\d+$ preferred_prefix: tctr uri_format: https://www.thaiclinicaltrials.org/show/$1 tdwg.taxonrank: contact: email: rhyam@rbge.org.uk name: Roger Hyam orcid: 0000-0003-4581-1379 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Ontology describing a controlled vocabulary for taxon ranks. download_rdf: https://tdwg.github.io/ontology/ontology/voc/TaxonRank.rdf example: InfragenericTaxon github_request_issue: 1321 homepage: https://github.com/tdwg/ontology name: TDWG Taxon Rank LSID Ontology preferred_prefix: tdwg.taxonrank repository: https://github.com/tdwg/ontology uri_format: http://rs.tdwg.org/ontology/voc/TaxonRank#$1 te: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 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: contact: email: edgar.wingender@edgar-wingender.de name: Edgar Wingender orcid: 0000-0002-7729-8453 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 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 keywords: - binding - binding site - bioinformatics - expression data - phylogenetics - transcription factor - transcription factor binding site prediction - transcriptomics mappings: fairsharing: FAIRsharing.XykycZ go: TFClass pathguide: '666' name: Classification of Transcription Factors in Mammalia preferred_prefix: tfclass publications: - doi: 10.1093/nar/gkx987 pmc: PMC5753292 pubmed: '29087517' title: 'TFClass: expanding the classification of human transcription factors to their mammalian orthologs' year: 2018 uri_format: http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1 tgd: description: The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature. example: TTHERM_00648910 homepage: http://ciliate.org/index.php/ keywords: - genome mappings: biocontext: TGD go: TGD miriam: tgd n2t: tgd prefixcommons: tgd name: Tetrahymena Genome Database pattern: ^TTHERM\_\d+$ preferred_prefix: tgd providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/tgd:$1 uri_format: http://ciliate.org/index.php/feature/details/$1 tgma: contact: email: topalis@imbb.forth.gr name: Pantelis Topalis orcid: 0000-0002-1635-4810 deprecated: true description: A structured controlled vocabulary of the anatomy of mosquitoes. download_obo: http://purl.obolibrary.org/obo/tgma.obo download_owl: http://purl.obolibrary.org/obo/tgma.owl example: 0000984 homepage: https://www.vectorbase.org/ontology-browser keywords: - anatomy - life science - mosquito - obo - ontology license: CC0-1.0 mappings: aberowl: TGMA biocontext: TGMA bioportal: TGMA fairsharing: FAIRsharing.dqnfkg obofoundry: tgma ols: tgma ontobee: TGMA prefixcommons: tgma name: Mosquito gross anatomy ontology pattern: ^\d{7}$ preferred_prefix: TGMA providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/tgma:$1 publications: - doi: 10.1111/j.1365-2583.2008.00781.x pubmed: '18237287' title: Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase year: 2008 rdf_uri_format: http://purl.obolibrary.org/obo/TGMA_$1 repository: https://github.com/VEuPathDB-ontology/TGMA uri_format: http://purl.obolibrary.org/obo/TGMA_$1 version: '2013-06-03' tgn: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: 'TGN is a structured vocabulary currently containing around 1,106,000 names and other information about places. Names for a place may include names in the vernacular language, English, other languages, historical names, names and in natural order and inverted order. Among these names, one is flagged as the preferred name. TGN is a thesaurus, compliant with ISO and NISO standards for thesaurus construction; it contains hierarchical, equivalence, and associative relationships. Note that TGN is not a GIS (Geographic Information System). While many records in TGN include coordinates, these coordinates are approximate and are intended for reference only. The focus of each TGN record is a place. There are around 912,000 places in the TGN. In the database, each place record (also called a subject) is identified by a unique numeric ID. Linked to the record for the place are names, the place''s parent or position in the hierarchy, other relationships, geographic coordinates, notes, sources for the data, and place types, which are terms describing the role of the place (e.g., inhabited place and state capital). The temporal coverage of the TGN ranges from prehistory to the present and the scope is global. The TGN is a hierarchical database; its trees branch from a root called Top of the TGN hierarchies (Subject_ID: 1000000). Currently there are two TGN facets, World and Extraterrestrial Places. Under the facet World, places are arranged in hierarchies generally representing the current political and physical world, although some historical nations and empires are also included. There may be multiple broader contexts, making the TGN polyhierarchical. The primary users of the Getty vocabularies include museums, art libraries, archives, visual resource collection catalogers, bibliographic projects concerned with art, researchers in art and art history, and the information specialists who are dealing with the needs of these users. In addition, a significant number of users of the Getty vocabularies are students or members of the general public.' example: '1023371' homepage: https://www.getty.edu/research/tools/vocabularies/tgn/ mappings: bartoc: '109' 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/$1 th: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia] example: H3.03.00.0.00007 homepage: https://ifaa.unifr.ch/ keywords: - biology - cytology - histology - life sciences mappings: wikidata: P1694 name: Terminologia Histologica pattern: ^H\d\.\d{2}\.\d{2}\.\d\.\d{5}$ preferred_prefix: th references: - https://en.wikipedia.org/wiki/Terminologia_Histologica theiler: appears_in: - mmusdv contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Stages 1-28 of mouse embryo development example: '10' example_decoys: - 10e example_extras: - 10b homepage: https://embryology.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages name: Theiler Stage pattern: ^\d+[a-d]?$ preferred_prefix: theiler providers: - code: legacy description: Legacy URL at UNSW homepage: https://embryology.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages name: Legacy URL at UNSW uri_format: https://embryology.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages#Theiler_Stage_$1 synonyms: - thielerstage uri_format: http://php.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages#Theiler_Stage_$1 thermofisher: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: ThermoFisher is a life sciences supply vendor. example: OSR00185W homepage: https://www.thermofisher.com keywords: - biology - chemistry - life sciences - vendor name: Thermo Fisher Scientific pattern: ^\w+$ preferred_prefix: thermofisher uri_format: https://www.thermofisher.com/antibody/product/$1 tigrfam: contributor_extras: - email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. example: TIGR00010 homepage: http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi keywords: - protein mappings: biocontext: TIGRFAM edam: '1141' miriam: tigrfam n2t: tigrfam ncbi: TIGRFAM prefixcommons: tigrfams name: TIGR protein families pattern: ^TIGR\d+$ preferred_prefix: tigrfam providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/tigrfams:$1 references: - https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/license_and_availability.txt - https://github.com/biopragmatics/bioregistry/issues/366 uri_format: https://www.ncbi.nlm.nih.gov/cdd?term=$1 time: contact: email: dr.shorthair@pm.me github: dr-shorthair name: Simon Cox orcid: 0000-0002-3884-3420 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Owl-time is an owl-2 dl ontology of temporal concepts, for describing the temporal properties of resources in the world or described in web pages. the ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. time positions and durations may be expressed using either the conventional (gregorian) calendar and clock, or using another temporal reference system such as unix-time, geologic time, or different calendars. download_owl: http://aber-owl.net/media/ontologies/TIME/2/time.owl example: DateTimeDescription github_request_issue: 505 homepage: https://www.w3.org/TR/owl-time/ keywords: - data coordination - data model - metadata standardization - ontology - resource metadata - subject agnostic - time mappings: aberowl: TIME bioportal: TIME fairsharing: FAIRsharing.hw3bh2 lov: time zazuko: time name: Time Ontology in OWL preferred_prefix: time repository: https://github.com/w3c/sdw/ uri_format: http://www.w3.org/2006/time#$1 tkg: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells. example: '0221' homepage: http://www2.idac.tohoku.ac.jp/dep/ccr/ mappings: cellosaurus: TKG name: Tohoku University cell line catalog pattern: ^\d+$ preferred_prefix: tkg uri_format: http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html tngb: description: Cell line collections (Providers) example: '67035' homepage: http://biobanknetwork.telethon.it/ mappings: cellosaurus: TNGB name: Telethon Network of Genetic Biobanks pattern: ^\d+$ preferred_prefix: tngb uri_format: http://biobanknetwork.telethon.it/Sample/View?sampleId=$1 to: appears_in: - agro contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp name: Pankaj Jaiswal orcid: 0000-0002-1005-8383 description: A controlled vocabulary to describe phenotypic traits in plants. download_obo: http://purl.obolibrary.org/obo/to.obo download_owl: http://purl.obolibrary.org/obo/to.owl example: '0000630' homepage: http://browser.planteome.org/amigo keywords: - botany - life cycle - obo - ontology - phenotype - plant - structure - trait license: CC-BY-4.0 logo: http://planteome.org/sites/default/files/garland_logo.PNG mappings: aberowl: TO agroportal: TO biocontext: TO bioportal: PTO fairsharing: FAIRsharing.w69t6r obofoundry: to ols: to ontobee: TO prefixcommons: pto name: Plant Trait Ontology pattern: ^\d{7}$ preferred_prefix: TO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pto:$1 publications: - doi: 10.1093/nar/gkx1152 pmc: PMC5753347 pubmed: '29186578' title: 'The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics' year: 2018 rdf_uri_format: http://purl.obolibrary.org/obo/TO_$1 repository: https://github.com/Planteome/plant-trait-ontology uri_format: http://purl.obolibrary.org/obo/TO_$1 version: '2023-07-17' togoid: contact: email: ktym@dbcls.jp github: ktym name: Toshiaki Katayama orcid: 0000-0003-2391-0384 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: TogoID is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. TogoID supports datasets from various biological categories such as gene, protein, chemical compound, pathway, disease, etc. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations. (from https://togoid.dbcls.jp/) download_rdf: https://raw.githubusercontent.com/togoid/togoid-config/main/ontology/togoid-ontology.ttl example: AffyProbeset homepage: https://togoid.dbcls.jp/ontology name: TogoID Ontology preferred_prefix: togoid publications: - doi: 10.1093/bioinformatics/btac491 pmc: PMC9438948 pubmed: '35801937' title: 'TogoID: an exploratory ID converter to bridge biological datasets' year: 2022 rdf_uri_format: https://togoid.dbcls.jp/ontology#$1 repository: https://github.com/dbcls/togoid/togoid-config uri_format: https://togoid.dbcls.jp/#$1 togovar: description: TogoVar (A comprehensive Japanese genetic variation database) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them. example: tgv139393198 homepage: https://grch38.togovar.org/ mappings: integbio: nbdc02359 miriam: togovar togoid: Togovar name: TogoVar pattern: ^tgv[0-9]+$ preferred_prefix: togovar uri_format: https://grch38.togovar.org/variant/$1 tokue: deprecated: true description: Cell line databases/resources homepage: http://cell-lines.toku-e.com mappings: cellosaurus: TOKU-E name: TOKU-E Cell-culture Database preferred_prefix: tokue uri_format: http://cell-lines.toku-e.com/Cell-Lines_$1.html tol: contributor_extras: - email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 description: "The Tree of Life Web Project (ToL) is a collaborative effort of biologists\ \ and nature enthusiasts from around the world. On more than 10,000 World Wide\ \ Web pages, the project provides information about biodiversity, the characteristics\ \ of different groups of organisms, and their evolutionary history (phylogeny).\ \ \n\nEach page contains information about a particular group, with pages linked\ \ one to another hierarchically, in the form of the evolutionary tree of life.\ \ Starting with the root of all Life on Earth and moving out along diverging branches\ \ to individual species, the structure of the ToL project thus illustrates the\ \ genetic connections between all living things." example: '98034' homepage: http://tolweb.org/tree/ mappings: bartoc: '400' biocontext: TOL miriam: tol n2t: tol wikidata: P5221 name: Tree of Life Web Project pattern: ^\d+$ preferred_prefix: tol synonyms: - tol.webproj uri_format: http://tolweb.org/$1 topdb: description: The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases. example: AP00378 homepage: http://topdb.enzim.hu/ keywords: - protein mappings: biocontext: TOPDB edam: '2789' miriam: topdb n2t: topdb prefixcommons: topdb name: Topology Data Bank of Transmembrane Proteins pattern: ^[A-Z0-9]+$ preferred_prefix: topdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/topdb:$1 uri_format: http://topdb.enzim.hu/?m=show&id=$1 topfind: contact: email: chris.overall@ubc.ca name: Christopher M. Overall orcid: 0000-0001-5844-2731 description: 'TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.' example: Q9UKQ2 homepage: https://topfind.clip.msl.ubc.ca keywords: - life science mappings: biocontext: TOPFIND fairsharing: FAIRsharing.rkpmhn miriam: topfind n2t: topfind re3data: r3d100012721 name: TopFind pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ preferred_prefix: topfind provides: uniprot publications: - doi: 10.1093/nar/gku1012 pmc: PMC4383881 pubmed: '25332401' title: 'Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events' year: 2014 - doi: 10.1093/nar/gkr1025 pmc: PMC3244998 pubmed: '22102574' title: TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function year: 2011 - doi: 10.1038/nmeth.1669 pubmed: '21822272' title: TopFIND, a knowledgebase linking protein termini with function year: 2011 uri_format: http://clipserve.clip.ubc.ca/topfind/proteins/$1 toxoplasma: description: ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: TGME49_053730 homepage: http://toxodb.org/toxo/ mappings: biocontext: TOXOPLASMA miriam: toxoplasma n2t: toxoplasma name: ToxoDB pattern: ^\w+$ preferred_prefix: toxoplasma uri_format: http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 trans: contact: email: lynn.schriml@gmail.com github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 description: The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles. download_obo: http://purl.obolibrary.org/obo/trans.obo download_owl: http://purl.obolibrary.org/obo/trans.owl example: '0000024' homepage: https://github.com/DiseaseOntology/PathogenTransmissionOntology keywords: - health science - obo - ontology - pathogen license: CC0-1.0 mappings: aberowl: TRANS biocontext: TRANS bioportal: TRANS fairsharing: FAIRsharing.nygmp7 obofoundry: trans ols: trans ontobee: TRANS prefixcommons: pt name: Pathogen Transmission Ontology pattern: ^\d{7}$ preferred_prefix: TRANS providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/pt:$1 publications: - doi: 10.1093/nar/gkab1063 pmc: PMC8728220 pubmed: '34755882' title: The Human Disease Ontology 2022 update year: 2022 - doi: 10.1093/nar/gkp832 pmc: PMC2808878 pubmed: '19850722' title: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database year: 2009 rdf_uri_format: http://purl.obolibrary.org/obo/TRANS_$1 repository: https://github.com/DiseaseOntology/PathogenTransmissionOntology uri_format: http://purl.obolibrary.org/obo/TRANS_$1 version: '2022-10-10' transportdb: description: TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available. example: MMP0523 homepage: http://www.membranetransport.org keywords: - protein mappings: pathguide: '105' prefixcommons: transportdb name: TransportDB preferred_prefix: transportdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/transportdb:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.membranetransport.org/protein.php?pOID=mmar1&pSynonym=$1 transyt: description: The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes. example: TR0000001 homepage: https://www.bio.di.uminho.pt/ mappings: miriam: transyt name: Transport Systems Tracker pattern: ^T[A-Z]\d{7}$ preferred_prefix: transyt uri_format: https://transyt.bio.di.uminho.pt/reactions/$1 tred: comment: This resource doesn't exist on the web anymore deprecated: true description: Transcriptional Regulatory Element Database (TRED) has been built in response to increasing needs of an integrated repository for both cis- and trans- regulatory elements in mammals, and the lack of such resources at present. example: '21552' homepage: http://rulai.cshl.edu/TRED keywords: - dna - regulation mappings: pathguide: '167' prefixcommons: tred name: Transcriptional Regulatory Element Database preferred_prefix: tred providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/tred:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid=$1 treebase: contact: email: rutgeraldo@gmail.com github: rvosa name: Rutger Vos orcid: 0000-0001-9254-7318 description: TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc. example: TB2:S1000 homepage: http://treebase.org/ keywords: - classification - phylogenetics - phylogenomics mappings: biocontext: TREEBASE fairsharing: FAIRsharing.zcn4w4 integbio: nbdc01882 miriam: treebase n2t: treebase prefixcommons: treebase re3data: r3d100010170 name: TreeBASE pattern: ^TB[1,2]?:[A-Z][a-z]?\d+$ preferred_prefix: treebase providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/treebase:$1 publications: - doi: 10.1186/1471-2148-9-93 pmc: PMC2685121 pubmed: '19426482' title: Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment year: 2009 repository: https://github.com/TreeBASE/treebase/issues twitter: treebase uri_format: http://purl.org/phylo/treebase/phylows/study/$1?format=html treefam: contact: email: Fab.Schreiber@gmail.com github: fabsta name: Fabian Schreiber orcid: 0000-0001-9150-5706 description: TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. example: TF101014 homepage: http://www.treefam.org/ keywords: - classification - gene mappings: biocontext: TREEFAM integbio: nbdc01596 miriam: treefam n2t: treefam prefixcommons: treefam uniprot: DB-0185 name: TreeFam pattern: ^\w{1,2}\d+$ preferred_prefix: treefam providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/treefam:$1 publications: - doi: 10.1093/nar/gkt1055 pmc: PMC3965059 pubmed: '24194607' title: 'TreeFam v9: a new website, more species and orthology-on-the-fly' year: 2013 uri_format: http://www.treefam.org/family/$1 tricdb: description: Tri©DB is a newly developed integrated platform functioning as a knowledge base and reporting system for cancer precision medicine. This platform harmonizes and mines cancer-related data from various aspects, presenting them on a centralized platform with enhanced accessibility, rich annotations, and robust analysis capabilities. The development of Tri©DB is aimed at meeting the needs of a broad range of researchers, thereby propelling both foundational and translational research in cancer precision medicine. example: 1eec8393-e598-41ed-9d8b-6d5b0db94470 homepage: http://www.biomeddb.org/ mappings: miriam: tricdb name: tricdb pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$ preferred_prefix: tricdb uri_format: http://biomeddb.org/Disease/Details?DISEASEID=$1 trichdb: contact: email: oharb@pcbi.upenn.edu name: Omar Harb orcid: 0000-0003-4446-6200 description: TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: TVAG_386080 homepage: http://trichdb.org/trichdb/ keywords: - genomics mappings: biocontext: TRICHDB fairsharing: FAIRsharing.pv0ezt integbio: nbdc01785 miriam: trichdb n2t: trichdb re3data: r3d100012461 name: TrichDB pattern: ^\w+$ preferred_prefix: trichdb publications: - doi: 10.1093/nar/gkn631 pmc: PMC2686445 pubmed: '18824479' title: 'GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis' year: 2008 twitter: eupathdb uri_format: http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 tritrypdb: contact: email: oharb@pcbi.upenn.edu name: Omar Harb orcid: 0000-0003-4446-6200 description: TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: Tb927.8.620 homepage: http://tritrypdb.org/tritrypdb/ keywords: - comparative genomics - genomics - infectious disease medicine mappings: biocontext: TRITRYPDB fairsharing: FAIRsharing.fs1z27 go: TriTrypDB integbio: nbdc01786 miriam: tritrypdb n2t: tritrypdb re3data: r3d100011479 name: TriTrypDB pattern: ^\w+(\.)?\w+(\.)?\w+$ preferred_prefix: tritrypdb publications: - doi: 10.1093/nar/gkp851 pmc: PMC2808979 pubmed: '19843604' title: 'TriTrypDB: a functional genomic resource for the Trypanosomatidae' year: 2009 twitter: VEuPathDB uri_format: http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 trnadbce: comment: requires authentication to access description: The tRNA Gene DataBase Curated by Experts "tRNADB-CE" was constructed by analyzing 927 complete and 1301 draft genomes of Bacteria and Archaea, 171 complete virus genomes, 121 complete chloroplast genomes, 12 complete eukaryote (Plant and Fungi) genomes and approximately 230 million DNA sequence entries that originated from environmental metagenomic clones. example: '265912' homepage: http://trna.nagahama-i-bio.ac.jp keywords: - dna - gene - genome - rna mappings: integbio: nbdc00720 prefixcommons: trnadbce name: tRNA Gene Database preferred_prefix: trnadbce proprietary: true providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/trnadbce:$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID=$1 tsc: description: Centralized repository and distribution site for variety of Tetrahymena strains and species. Maintains diverse array of wild type, mutant, and genetically engineered strains of T. thermophila, the most commonly used laboratory species, and variety of other species derived from both laboratory maintained stocks and wild isolates. All stocks are stored in liquid nitrogen to maintain genetic integrity and prevent senescence. In addition to providing worldwide access to strains currently in collection, TSC continually upgrades collection by accepting deposition of newly developed laboratory strains and well characterized wild isolates collected from clearly defined natural sites. [from RRID] example: SD00043 homepage: https://tetrahymena.vet.cornell.edu/ keywords: - biology - cell - cellular - culture - eukaryota - genetics - model - molecular - protozoan - repository - research - tetrahymena thermophila mappings: rrid: TSC name: Tetrahymena Stock Center pattern: ^SD\d+$ preferred_prefix: tsc uri_format: https://tetrahymena.vet.cornell.edu/display.php?stockid=$1 ttd.drug: description: The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target. example: DAP000773 homepage: http://bidd.nus.edu.sg/group/ttd/ttd.asp mappings: biocontext: TTD.DRUG edam: '2653' miriam: ttd.drug n2t: ttd.drug name: TTD Drug pattern: ^DAP\d+$ preferred_prefix: ttd.drug uri_format: http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1 ttd.target: description: The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target. example: TTDS00056 homepage: http://bidd.nus.edu.sg/group/ttd/ttd.asp mappings: biocontext: TTD.TARGET edam: '2654' miriam: ttd.target n2t: ttd.target name: TTD Target pattern: ^TTDS\d+$ preferred_prefix: ttd.target uri_format: http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1 tto: contact: email: balhoff@renci.org github: balhoff name: Jim Balhoff orcid: 0000-0002-8688-6599 description: An ontology covering the taxonomy of teleosts (bony fish) download_obo: http://purl.obolibrary.org/obo/tto.obo download_owl: http://purl.obolibrary.org/obo/tto.owl example: '1058367' homepage: https://github.com/phenoscape/teleost-taxonomy-ontology keywords: - fish - life science - obo - ontology - phenotype - taxonomic classification license: CC0-1.0 mappings: aberowl: TTO biocontext: TTO bioportal: TTO fairsharing: FAIRsharing.1rj558 obofoundry: tto ols: tto ontobee: TTO prefixcommons: tto name: Teleost taxonomy ontology pattern: ^\d+$ preferred_prefix: TTO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/tto:$1 publications: - doi: 10.1038/npre.2010.4629.1 title: The Teleost Taxonomy Ontology year: 2010 rdf_uri_format: http://purl.obolibrary.org/obo/TTO_$1 repository: https://github.com/phenoscape/teleost-taxonomy-ontology uri_format: http://purl.obolibrary.org/obo/TTO_$1 txpo: contact: email: yuki.yamagata@riken.jp github: yuki-yamagata name: Yuki Yamagata orcid: 0000-0002-9673-1283 description: 'Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity. The TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms. In applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp' download_owl: http://purl.obolibrary.org/obo/txpo.owl example: '0002066' homepage: https://toxpilot.nibiohn.go.jp/ keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: TXPO bioportal: TXPO obofoundry: txpo ols: txpo ontobee: TXPO name: Toxic Process Ontology pattern: ^\d{7}$ preferred_prefix: TXPO publications: - doi: 10.1038/s41598-020-71370-7 pmc: PMC7471325 pubmed: '32883995' title: Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management year: 2020 rdf_uri_format: http://purl.obolibrary.org/obo/TXPO_$1 repository: https://github.com/txpo-ontology/TXPO uri_format: http://purl.obolibrary.org/obo/TXPO_$1 version: '2022-12-07' uberon: appears_in: - aism - amphx - chiro - cl - clo - clyh - colao - cteno - ecao - ecocore - ecto - envo - foodon - fovt - genepio - go - hso - lepao - maxo - mco - mfmo - ons - pcl - plana - poro - zp banana: UBERON contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 depends_on: - bfo - bspo - chebi - cl - envo - go - nbo - ncbitaxon - omo - pato - pr - ro description: Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. download_json: http://purl.obolibrary.org/obo/uberon.json download_obo: http://purl.obolibrary.org/obo/uberon/basic.obo download_owl: http://purl.obolibrary.org/obo/uberon.owl example: '2005080' homepage: http://uberon.org keywords: - anatomy - developmental biology - life science - obo - ontology - taxonomy license: CC-BY-3.0 logo: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/uberon-logos/uberon_logo_black-banner.png mappings: aberowl: UBERON biocontext: UBERON bioportal: UBERON cellosaurus: UBERON fairsharing: FAIRsharing.4c0b6b go: UBERON miriam: uberon n2t: uberon obofoundry: uberon ols: uberon ontobee: UBERON togoid: Uberon wikidata: P1554 name: Uber Anatomy Ontology namespace_in_lui: true pattern: ^\d+$ preferred_prefix: UBERON providers: - code: cellguide description: CellGuide is a comprehensive resource for knowledge about cell types. homepage: https://cellxgene.cziscience.com/cellguide name: Cell Guide uri_format: https://cellxgene.cziscience.com/cellguide/tissues/UBERON_$1 - code: cellxgene description: Explore single cell data through the CZ CELLxGENE portal homepage: https://onto.cellxgene-labs.prod.si.czi.technology name: CELLxGENE uri_format: https://onto.cellxgene-labs.prod.si.czi.technology/a/ontology/UBERON/UBERON:$1 publications: - doi: 10.1186/2041-1480-5-21 pmc: PMC4089931 pubmed: '25009735' title: Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon year: 2014 - doi: 10.1186/gb-2012-13-1-r5 pmc: PMC3334586 pubmed: '22293552' title: Uberon, an integrative multi-species anatomy ontology year: 2012 rdf_uri_format: http://purl.obolibrary.org/obo/UBERON_$1 repository: https://github.com/obophenotype/uberon synonyms: - UBERON - Uber-anatomy ontology - Uberon twitter: uberanat uri_format: http://purl.obolibrary.org/obo/UBERON_$1 version: '2025-01-15' ubio.namebank: description: NameBank is a "biological name server" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context. example: '2555646' homepage: http://www.ubio.org mappings: biocontext: UBIO.NAMEBANK miriam: ubio.namebank n2t: ubio.namebank name: uBio NameBank pattern: ^\d+$ preferred_prefix: ubio.namebank uri_format: http://www.ubio.org/browser/details.php?namebankID=$1 ubprop: comment: All of these are typedefs in uberon now contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: Uberon Property preferred_prefix: ubprop synonyms: - UBPROP - UBREL ucas: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An identifier for institutions in the United Kingdom, used in GRID and ROR. example: N21 homepage: https://www.ucas.com keywords: - bibliometrics - institution name: UK Universities and Colleges Admissions Service pattern: ^\w\d+$ preferred_prefix: ucas ucsc: contact: email: max@soe.ucsc.edu github: maximilianh name: Maximilian Haeussler orcid: 0000-0001-8721-8253 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. example: uc001rvw.5 homepage: https://genome.ucsc.edu/ mappings: biocontext: UCSC uniprot: DB-0139 wikidata: P2576 name: UCSC Genome Browser preferred_prefix: ucsc publications: - doi: 10.1093/nar/gky1095 pmc: PMC6323953 pubmed: '30407534' title: 'The UCSC Genome Browser database: 2019 update' year: 2019 uri_format: ftp://hgdownload.cse.ucsc.edu/goldenPath/$1 ucum: contact: email: dr.shorthair@pm.me github: dr-shorthair name: Simon Cox orcid: 0000-0002-3884-3420 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Unified Code for Units of Measure (UCUM) is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business. example: aBq example_extras: - '%' - /A/s3/cg3/T3 - /g - /m3 - Cel.d-1 - Em.s-2 - K2 - Wb - dL/g - dlm - dlx - g.cm-3 - kW/h - m.s-2 - m/s - m/s/d - mmol.mL-1 - mol.L-1 - mol.um - ng-1 - pA - ug.mL-1 - umol.L-1 - us homepage: https://ucum.org keywords: - data identity and mapping - general & upper - measurement - subject agnostic - unit mappings: bartoc: '1895' fairsharing: FAIRsharing.27w8k0 hl7: 2.16.840.1.113883.6.8 lov: ucum name: Unified Code for Units of Measure preferred_prefix: ucum publications: - doi: 10.1136/jamia.1999.0060151 pmc: PMC61354 pubmed: '10094068' title: Units of measure in clinical information systems year: 1999 references: - https://units-of-measurement.org/ repository: https://github.com/ucum-org/ucum uri_format: https://units-of-measurement.org/$1 ukprn: comment: Added because of appearance in ROR contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier for an educational organization issued by the UK Register of Learning Providers example: '10007835' homepage: https://www.ukrlp.co.uk mappings: wikidata: P4971 name: UK Provider Reference Number pattern: ^[1-9]\d*$ preferred_prefix: ukprn synonyms: - ukprns uri_format: https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails?x=&pn_p_id=$1&pv_status=VERIFIED&pv_vis_code=L umbbd.compound: description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information. example: c0001 homepage: http://umbbd.ethz.ch/ mappings: biocontext: UMBBD.COMPOUND miriam: umbbd.compound n2t: umbbd.compound wikidata: P8121 name: UM-BBD compound part_of: umbbd pattern: ^c\d+$ 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 providers: - code: eawag description: Graphical depiction of pathway homepage: http://eawag-bbd.ethz.ch name: Pathway map diagram uri_format: http://eawag-bbd.ethz.ch/$1/$1_map.html synonyms: - UM-BBD_pathwayID uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1 umbbd.reaction: description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information. example: r0001 homepage: http://umbbd.ethz.ch/ mappings: biocontext: UMBBD.REACTION go: UM-BBD_reactionID miriam: umbbd.reaction n2t: umbbd.reaction name: EAWAG Biocatalysis/Biodegradation Database part_of: umbbd pattern: ^r\d+$ 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=$1 uminctr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An additional Japanese clinical trial registry example: UMIN000049383 homepage: https://www.umin.ac.jp/ctr/index.htm mappings: integbio: nbdc01470 name: University hospital Medical Information Network Clinical Trial Registry pattern: ^UMIN\d+$|^C\d+$ preferred_prefix: uminctr references: - https://center6.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000056224 umls: 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 license: https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/license_agreement.html logo: https://uts.nlm.nih.gov/uts/assets/images/umls_tree_sm.jpg mappings: bartoc: '20052' biocontext: UMLS edam: '1181' hl7: 2.16.840.1.113883.6.86 miriam: umls n2t: umls wikidata: P2892 name: Unified Medical Language System Concept Unique Identifier pattern: ^C\d+$ preferred_prefix: umls synonyms: - UMLS - UMLS CUI - UMLS_CUI - umls.cui uri_format: https://uts.nlm.nih.gov/uts/umls/concept/$1 umls.aui: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An identifier for an atom; the smallest unit of naming in a source, viz, a specific string with specific code values and identifiers from a specific source. As such, they can be thought of as representing a single meaning with a source Atoms are the units of terminology that come from sources and form the building blocks of the concepts in the Metathesaurus. example: A0118748 homepage: https://www.nlm.nih.gov/research/umls name: Unified Medical Language System Atomic Unique Identifier pattern: ^A\d+$ preferred_prefix: umls.aui synonyms: - UMLS_ICD9CM_2005_AUI unichem: description: identifier of a compound in the UniChem database example: '161671' homepage: https://chembl.gitbook.io/unichem/downloads mappings: wikidata: P11089 name: UniChem compound pattern: ^\d+$ preferred_prefix: unichem uri_format: https://www.ebi.ac.uk/unichem/compoundsources?type=uci&compound=$1 unigene: deprecated: true description: A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. example: '4900' homepage: http://www.ncbi.nlm.nih.gov/unigene keywords: - dna - gene - gene expression - life science - protein mappings: biocontext: UNIGENE fairsharing: FAIRsharing.ge1c3p integbio: nbdc00220 miriam: unigene n2t: unigene prefixcommons: unigene re3data: r3d100010774 name: UniGene pattern: ^\d+$ preferred_prefix: unigene providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/unigene:$1 publications: - doi: 10.1093/nar/gkg033 pmc: PMC165480 pubmed: '12519941' title: Database resources of the National Center for Biotechnology year: 2003 uri_format: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1 unii: description: The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information. example: 3G6A5W338E homepage: https://precision.fda.gov/uniisearch mappings: biocontext: UNII cheminf: '000563' miriam: unii n2t: unii wikidata: P652 name: Unique Ingredient Identifier pattern: ^[A-Z0-9]+$ preferred_prefix: unii uri_format: https://precision.fda.gov/uniisearch/srs/unii/$1 unimod: contact: email: jcottrell@matrixscience.com name: John Cottrell orcid: 0000-0003-3843-0818 description: Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide). download_owl: https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/unimod.owl example: '1200' homepage: http://www.unimod.org/ keywords: - bioinformatics - ontology mappings: biocontext: UNIMOD edam: '3757' fairsharing: FAIRsharing.zZHCUQ miriam: unimod n2t: unimod ols: unimod name: Unimod protein modification database for mass spectrometry pattern: ^\d+$ preferred_prefix: unimod publications: - doi: 10.1002/pmic.200300744 pubmed: '15174123' title: 'Unimod: Protein modifications for mass spectrometry' year: 2004 uri_format: http://www.unimod.org/modifications_view.php?editid1=$1 uniparc: contact: email: agb@ebi.ac.uk github: bateman-research name: Alex Bateman orcid: 0000-0002-6982-4660 description: The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases. example: UPI000000000A homepage: http://www.uniprot.org/uniparc/ keywords: - protein - structure mappings: biocontext: UNIPARC edam: '2392' go: UniParc miriam: uniparc n2t: uniparc prefixcommons: uniparc re3data: r3d100011519 name: UniProt Archive pattern: ^UPI[A-F0-9]{10}$ preferred_prefix: uniparc providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/uniparc:$1 publications: - doi: 10.1093/nar/gkh131 pmc: PMC308865 pubmed: '14681372' title: 'UniProt: the Universal Protein knowledgebase' year: 2004 uri_format: https://www.uniprot.org/uniparc/$1 unipathway.compound: description: UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds. example: UPC04349 homepage: http://www.grenoble.prabi.fr/obiwarehouse/unipathway mappings: biocontext: UNIPATHWAY.COMPOUND miriam: unipathway.compound n2t: unipathway.compound name: UniPathway Compound pattern: ^UPC\d{5}$ preferred_prefix: unipathway.compound uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1 unipathway.reaction: description: UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions. example: UCR00226 homepage: http://www.grenoble.prabi.fr/obiwarehouse/unipathway mappings: biocontext: UNIPATHWAY.REACTION miriam: unipathway.reaction n2t: unipathway.reaction name: UniPathway Reaction pattern: ^UCR\d{5}$ preferred_prefix: unipathway.reaction uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1 uniprot: contact: email: agb@ebi.ac.uk github: bateman-research name: Alex Bateman orcid: 0000-0002-6982-4660 contributor_extras: - email: m.naguthana@hotmail.com github: nagutm name: Mufaddal Naguthanawala orcid: 0009-0009-5240-7463 description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information. example: P0DP23 homepage: http://www.uniprot.org keywords: - biology - protein - taxonomic classification license: CC-BY-4.0 mappings: aberowl: UP biocontext: UniProtKB biolink: UniProtKB cellosaurus: UniProtKB edam: '3021' fairsharing: FAIRsharing.wf28wm go: UniProtKB integbio: nbdc00221 miriam: uniprot n2t: uniprot ncbi: UniProt prefixcommons: uniprot re3data: r3d100011521 togoid: Uniprot wikidata: P352 name: UniProt Protein pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ preferred_prefix: uniprot providers: - code: aipd description: A curated database standardizing information on autoinhibited proteins. homepage: http://ssbio.cau.ac.kr/databases/AiPD/ name: Autoinhibited Protein Database publications: - doi: 10.1093/database/baae085 pmc: PMC11349611 pubmed: '39192607' title: 'Autoinhibited Protein Database: a curated database of autoinhibitory domains and their autoinhibition mechanisms' year: 2024 uri_format: http://165.194.60.211:9006/detail/$1 - code: bfvd description: Predicted protein structures for viral sequences homepage: https://bfvd.foldseek.com name: Big Fantastic Virus Database publications: - doi: 10.1093/nar/gkae1119 pubmed: '39574394' title: BFVD-a large repository of predicted viral protein structures year: 2024 uri_format: https://bfvd.foldseek.com/cluster/$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/uniprot:$1 - code: describeprot description: Structural and functional descriptors for proteins at the amino acid level homepage: http://biomine.cs.vcu.edu/servers/DESCRIBEPROT name: DescribePROT publications: - doi: 10.1007/978-1-0716-4196-5_10 pubmed: '39576581' title: DescribePROT Database of Residue-Level Protein Structure and Function Annotations year: 2024 uri_format: http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/result_v2.php?uniprot=$1 - code: drugbank description: DrugBank PolyPeptide. homepage: https://go.drugbank.com name: DrugBank Polypeptide uri_format: https://go.drugbank.com/polypeptides/$1 - code: iedb.antigen description: A comprehensive collection of data on immune epitopes, covering experimental data and resources, including antigens homepage: https://www.iedb.org/ name: Immune Epitope Database uri_format: https://www.iedb.org/antigen/UNIPROT:$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: 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: 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 - code: oglcnac description: A comprehensive catalog of O-GlcNAcylated proteins homepage: https://www.oglcnac.mcw.edu name: The O-GlcNAc Database publications: - doi: 10.1007/s00216-024-05571-8 pubmed: '39379619' title: 'The O-GlcNAc database: introducing new features and tools developed from community feedback' year: 2024 uri_format: https://www.oglcnac.mcw.edu/search/?query_protein=$1 - code: oma description: The OMA project is a method and database for the inference of orthologs among complete genomes. homepage: https://omabrowser.org/oma/home/ name: Orthologous Matrix Browser uri_format: http://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p2=orthologs&p1=$1 - 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: pharos description: Part of the Illuminating the Druggable Genome project homepage: https://pharos.nih.gov/idg name: Pharos uri_format: https://pharos.nih.gov/idg/targets/$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/uniprot/$1 publications: - doi: 10.1007/978-1-0716-4196-5_10 pubmed: '39576581' title: DescribePROT Database of Residue-Level Protein Structure and Function Annotations year: 2024 - doi: 10.1093/nar/gkae1119 pubmed: '39574394' title: BFVD-a large repository of predicted viral protein structures year: 2024 - doi: 10.1093/nar/gkae1010 pubmed: '39552041' title: 'UniProt: the Universal Protein Knowledgebase in 2025' year: 2024 - doi: 10.1007/s00216-024-05571-8 pubmed: '39379619' title: 'The O-GlcNAc database: introducing new features and tools developed from community feedback' year: 2024 - doi: 10.1093/database/baae085 pmc: PMC11349611 pubmed: '39192607' title: 'Autoinhibited Protein Database: a curated database of autoinhibitory domains and their autoinhibition mechanisms' year: 2024 - doi: 10.1093/nar/gkj161 pmc: PMC1347523 pubmed: '16381842' title: 'The Universal Protein Resource (UniProt): an expanding universe of protein information' year: 2006 rdf_uri_format: http://purl.uniprot.org/uniprot/$1 synonyms: - SwissProt - UP - UniProt - UniProtKB - Uniprot ID - uniprot/swiss-prot uri_format: http://purl.uniprot.org/uniprot/$1 uniprot.arba: contributor: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: Association-Rule-Based Annotator (ARBA), a multiclass, self-training annotation system for automatic classification and annotation of UniProtKB proteins. This replaces the previous rule-based SAAS system. example: ARBA00000001 github_request_issue: 620 homepage: https://www.uniprot.org/arba mappings: go: ARBA name: Association-Rule-Based Annotator pattern: ^ARBA\d+$ preferred_prefix: uniprot.arba reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - arba uri_format: https://www.uniprot.org/arba/$1 uniprot.chain: description: This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein. example: PRO_0000016681 homepage: https://www.uniprot.org mappings: miriam: uniprot.chain name: UniProt Chain part_of: uniprot pattern: ^PRO_[0-9]{10}$ preferred_prefix: uniprot.chain synonyms: - UPPRO uri_format: http://purl.uniprot.org/annotation/$1 uniprot.core: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Properties and classes used for protein annotation download_owl: https://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/core.owl example: certain homepage: http://purl.uniprot.org/core/ keywords: - biology - ontology mappings: lov: uniprot name: Uniprot Core Ontology preferred_prefix: uniprot.core uri_format: http://purl.uniprot.org/core/$1 uniprot.disease: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary. download_obo: https://rest.uniprot.org/diseases/stream?compressed=false&format=obo&query=%28%2A%29 example: DI-04240 homepage: https://www.uniprot.org/diseases/ keywords: - ontology mappings: biolink: SPDI wikidata: P11430 name: UniProt Diseases part_of: uniprot pattern: ^DI-\d{5}$ preferred_prefix: uniprot.disease synonyms: - DI - SP_DI uri_format: https://www.uniprot.org/diseases/$1 uniprot.isoform: description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information. example: Q5BJF6-3 homepage: http://www.uniprot.org/ mappings: biocontext: UNIPROT.ISOFORM biolink: UNIPROT.ISOFORM miriam: uniprot.isoform n2t: uniprot.isoform name: UniProt Isoform part_of: uniprot pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\-\d+)$ 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 - code: obo.1 description: This incorrect encoding was found inside IDO-COVID-19 homepage: http://purl.obolibrary.org name: Nonstandard OBO PURL uri_format: http://purl.obolibrary.org/obo/UniProtKB_$1 synonyms: - UPISO uri_format: http://purl.uniprot.org/isoforms/$1 uniprot.journal: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier for a scientific journal, in the UniProt database example: '3546' homepage: https://www.uniprot.org/journals mappings: wikidata: P4616 name: UniProt journal pattern: ^\d{4}$ preferred_prefix: uniprot.journal rdf_uri_format: http://purl.uniprot.org/journals/$1 uri_format: https://www.uniprot.org/journals/$1 uniprot.keyword: description: UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries. download_obo: https://rest.uniprot.org/keywords/stream?compressed=false&fields=id%2Cname%2Ccategory%2Cgene_ontologies&format=tsv&query=%28%2A%29 example: KW-1273 homepage: http://www.uniprot.org/keywords/ keywords: - classification - ontology mappings: go: UniProtKB-KW prefixcommons: uniprot.kw name: UniProt Keywords part_of: uniprot pattern: ^KW-\d{4}$ preferred_prefix: uniprot.keyword providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/uniprot.kw:$1 synonyms: - SP_KW - UniProtKB-KW - uniprot.keyword - uniprot.kw uri_format: https://www.uniprot.org/keywords/$1 uniprot.location: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms. download_obo: https://rest.uniprot.org/locations/stream?compressed=false&format=obo&query=%28%2A%29 example: SL-0002 homepage: https://www.uniprot.org/locations/ keywords: - ontology mappings: go: UniProtKB-SubCell name: UniProt Subcellular Locations part_of: uniprot pattern: ^SL-\d+$ preferred_prefix: uniprot.location synonyms: - SP_SL - UPLOC - UniProtKB-SubCell uri_format: https://www.uniprot.org/locations/$1 uniprot.mnemonic: contributor: email: b.gyori@northeastern.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information. This entry represents UniProt mnemonics which combine an alphanumeric representation the protein name and a species identification code representing the biological source of the protein. example: BRAF_HUMAN github_request_issue: 1110 homepage: https://www.uniprot.org/ mappings: togoid: UniprotMnemonic name: UniProt pattern: ^[A-Z0-9]{1,10}_[A-Z0-9]{1,5}$ preferred_prefix: uniprot.mnemonic publications: - doi: 10.1093/nar/gkj161 pmc: PMC1347523 pubmed: '16381842' title: 'The Universal Protein Resource (UniProt): an expanding universe of protein information' year: 2006 reviewer: email: tiago.lubiana.alves@usp.br github: lubianat name: Tiago Lubiana orcid: 0000-0003-2473-2313 uri_format: https://www.uniprot.org/uniprotkb/$1 uniprot.proteome: contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: UniProt provides proteome sets of proteins whose genomes have been completely sequenced. example: UP000005640 github_request_issue: 604 homepage: https://www.uniprot.org/proteomes name: UniProt Proteomes part_of: uniprot pattern: ^UP\d{9}$ preferred_prefix: uniprot.proteome reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.uniprot.org/proteomes/$1 uniprot.ptm: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The post-translational modifications used in the UniProt knowledgebase (Swiss-Prot and TrEMBL). The definition of the post-translational modifications usage as well as other information is provided in the following format example: PTM-0450 homepage: https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs/ptmlist keywords: - biochemistry - post-translational modification - structural biology license: CC-BY-4.0 name: UniProt Post-Translational Modification part_of: uniprot pattern: ^PTM-\d{4}$ preferred_prefix: uniprot.ptm references: - https://twitter.com/cthoyt/status/1510570256619778053 - https://www.uniprot.org/docs/ptmlist.txt synonyms: - PTM uri_format: https://biopragmatics.github.io/providers/uniprot.ptm/$1 uniprot.resource: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources. example: DB-0174 homepage: https://www.uniprot.org/database/ name: UniProt Resource part_of: uniprot pattern: ^DB-\d{4}$ preferred_prefix: uniprot.resource synonyms: - uniprot.database - uniprot.db uri_format: https://www.uniprot.org/database/$1 uniprot.tissue: description: The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified. example: TS-0285 homepage: https://www.uniprot.org/docs/tisslist.txt mappings: biocontext: TISSUELIST miriam: tissuelist n2t: tissuelist name: Tissue List part_of: uniprot pattern: ^TS-\d{4}$ preferred_prefix: uniprot.tissue uri_format: https://www.uniprot.org/tissues/$1 uniprot.var: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species.' example: 068078 homepage: https://web.expasy.org/variant_pages name: UniProt Variants part_of: uniprot pattern: ^\d+$ preferred_prefix: uniprot.var providers: - code: expasy description: Expasy external page for protein variant homepage: https://web.expasy.org/variant_pages name: ExPaSy uri_format: https://web.expasy.org/variant_pages/VAR_$1.html synonyms: - SP_VAR - UPVAR - UniProtKB_VAR uri_format: http://purl.uniprot.org/annotation/VAR_$1 uniref: description: The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view. example: UniRef90_P00750 homepage: https://www.uniprot.org/ mappings: edam: '2346' miriam: uniref re3data: r3d100011518 name: UniRef pattern: ^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$ preferred_prefix: uniref uri_format: https://www.uniprot.org/uniref/$1 unirule: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates. UniRule rules can annotate protein properties such as the protein name, function, catalytic activity, pathway membership, and subcellular location, along with sequence specific information, such as the positions of post-translational modifications and active sites. example: UR000124451 homepage: https://www.uniprot.org/unirule/ mappings: go: UniRule name: UniRule preferred_prefix: unirule uri_format: https://www.uniprot.org/unirule/$1 unists: description: UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences. example: '456789' homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists keywords: - gene - protein mappings: biocontext: UNISTS edam: '2389' miriam: unists n2t: unists ncbi: UniSTS prefixcommons: unists name: Database of Sequence Tagged Sites pattern: ^\d+$ preferred_prefix: unists providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/unists:$1 uri_format: https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1 unite: contact: email: urmas.koljalg@ut.ee name: Urmas Kõljalg orcid: 0000-0002-5171-1668 description: UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa. example: UDB000691 homepage: http://unite.ut.ee/ keywords: - biodiversity - bioinformatics - dna - ecology - genomics - metagenomics - taxonomy mappings: biocontext: UNITE edam: '2390' fairsharing: FAIRsharing.cnwx8c integbio: nbdc01905 miriam: unite n2t: unite ncbi: UNITE prefixcommons: unite re3data: r3d100011316 name: Molecular database for the identification of fungi pattern: ^UDB\d{6}$ preferred_prefix: unite providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/unite:$1 publications: - doi: 10.1111/j.1469-8137.2009.03160.x pubmed: '20409185' title: The UNITE database for molecular identification of fungi--recent updates and future perspectives year: 2010 uri_format: http://unite.ut.ee/bl_forw.php?nimi=$1 unpd: comment: The website is dead, there are no places to get the source information except inside https://oolonek.github.io/ISDB/. contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true homepage: http://pkuxxj.pku.edu.cn/UNPD/ name: Universal Natural Products Database preferred_prefix: unpd publications: - doi: 10.1021/acs.jnatprod.6b01093 pubmed: '28616931' title: Database for Rapid Dereplication of Known Natural Products Using Data from MS and Fast NMR Experiments year: 2017 - doi: 10.1371/journal.pone.0062839 pmc: PMC3636197 pubmed: '23638153' title: Use of natural products as chemical library for drug discovery and network pharmacology year: 2013 references: - http://bioinf-applied.charite.de/supernatural_new/index.php?site=vendor_info&id=Universal%20Natural%20Products%20Database - https://pharmacognosy.in/the-universal-natural-products-database-unpd/ - https://oolonek.github.io/ISDB/ uo: appears_in: - agro - ms - rbo - scdo banana: UO contact: email: g.gkoutos@gmail.com github: gkoutos name: George Gkoutos orcid: 0000-0002-2061-091X description: Ontology of standardized units download_obo: http://purl.obolibrary.org/obo/uo.obo download_owl: http://purl.obolibrary.org/obo/uo.owl example: 0000080 homepage: https://github.com/bio-ontology-research-group/unit-ontology keywords: - life science - mathematics - measurement - obo - ontology - unit license: CC-BY-3.0 mappings: aberowl: UO agroportal: UO biocontext: UO bioportal: UO fairsharing: FAIRsharing.mjnypw miriam: uo n2t: uo obofoundry: uo ols: uo ontobee: UO prefixcommons: uo name: Units of measurement ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: UO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/uo:$1 publications: - doi: 10.1093/database/bas033 pmc: PMC3468815 pubmed: '23060432' title: 'The Units Ontology: a tool for integrating units of measurement in science' year: 2012 rdf_uri_format: http://purl.obolibrary.org/obo/UO_$1 repository: https://github.com/bio-ontology-research-group/unit-ontology uri_format: http://purl.obolibrary.org/obo/UO_$1 version: '2023-05-25' upa: contact: email: Anne.Morgat@sib.swiss github: amorgat name: Anne Morgat orcid: 0000-0002-1216-2969 depends_on: - ro deprecated: true description: A manually curated resource for the representation and annotation of metabolic pathways download_obo: https://raw.githubusercontent.com/geneontology/unipathway/master/upa.obo download_owl: http://purl.obolibrary.org/obo/upa.owl example: UCR00513 homepage: https://github.com/geneontology/unipathway keywords: - obo - ontology - pathway license: CC-BY-3.0 mappings: aberowl: UPA biocontext: UNIPATHWAY bioportal: UPA edam: '2645' go: UniPathway obofoundry: upa ols: upa ontobee: UPA pathguide: '414' prefixcommons: unipathway name: Unipathway pattern: ^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$ preferred_prefix: UPA providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/unipathway:$1 publications: - doi: 10.1093/nar/gkr1023 pmc: PMC3245108 pubmed: '22102589' title: 'UniPathway: a resource for the exploration and annotation of metabolic pathways' year: 2011 rdf_uri_format: http://purl.obolibrary.org/obo/UPA_$1 repository: https://github.com/geneontology/unipathway synonyms: - UPa - unipathway - unipathway.pathway uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1 version: '2024-03-06' upheno: contact: email: jmcl@ebi.ac.uk github: jamesamcl name: James McLaughlin orcid: 0000-0002-8361-2795 description: The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology. download_owl: http://purl.obolibrary.org/obo/upheno.owl homepage: https://github.com/obophenotype/upheno keywords: - evolutionary biology - obo - ontology - phenomics - phenotype license: CC0-1.0 logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBa01CIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--3f5258d2bcf30a7e127b5a9fe209b27e25e88883/up.png?disposition=inline mappings: aberowl: UPHENO biocontext: UPHENO bioportal: UPHENO fairsharing: FAIRsharing.r41qhx obofoundry: upheno ols: upheno ontobee: UPHENO name: Unified Phenotype Ontology no_own_terms: true preferred_prefix: UPHENO publications: - doi: 10.1101/2024.09.18.613276 title: 'The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics' rdf_uri_format: http://purl.obolibrary.org/obo/UPHENO_$1 repository: https://github.com/obophenotype/upheno uri_format: http://purl.obolibrary.org/obo/UPHENO_$1 version: '2025-01-11' urdbms.syndromefinder: appears_in: - nando contact: email: naritomi@med.u-ryukyu.ac.jp name: Kenji Naritomi contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true example: '3567' github_request_issue: 1320 mappings: integbio: nbdc00728 name: UR-DBMS Syndrome Finder pattern: ^\d+$ preferred_prefix: urdbms.syndromefinder publications: - doi: 10.1038/s10038-024-01277-y pubmed: '39085458' title: An application supporting diagnosis for rare genetic diseases - UR-DBMS and Syndrome Finder year: 2024 uri_format: http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php?winid=1&recid=$1 uspto: comment: Information about the regular expression was derived from examples at https://patft.uspto.gov/netahtml/PTO/srchnum.htm. TODO, make the regular expression work for '100000000' contributor_extras: - github: dhimmel name: Daniel Himmelstein orcid: 0000-0002-3012-7446 description: The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement. example: '4145692' example_extras: - '0000001' - 10,000,000 - '6923014' - AI00007 - D000152 - H001234 - PP07514 - RE12345 - RX00001 - T855019 - X000001 homepage: http://patft.uspto.gov/netahtml/PTO/index.html mappings: biocontext: USPTO miriam: uspto n2t: uspto name: United States Patent and Trademark Office pattern: ^(\d{1,2},?\d{3},?\d{3}|(PP|RE|AI|RX)\d{2},?\d{3}|(D|T|H|X)\d{3},?\d{3})$ preferred_prefix: uspto references: - https://github.com/biopragmatics/bioregistry/issues/253 uri_format: http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1 utrdb: description: 'A curated database of 5'' and 3'' untranslated sequences of eukaryotic mRNAs. In the current update, the UTR entries are organized in a gene-centric structure to better visualize and retrieve 5'' and 3''UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets. ' example: 5UTR_107_ENST00000517291.2 homepage: https://utrdb.cloud.ba.infn.it/utrdb/index_107.html mappings: integbio: nbdc00730 miriam: utrdb name: UTRdb pattern: ^([3-5][A-Z])\w+[^A-Z][0-9]$ preferred_prefix: utrdb uri_format: https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e=$1 vac: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Vaccine Adjuvant Compendium (VAC) was established in 2020 by the NIAID Division of Allergy, Immunology, and Transplantation to foster collaborations between NIAID-supported adjuvant researchers and the broader scientific community. The VAC displays adjuvant characteristics or metadata defined through NIAID-supported adjuvant studies to help vaccine developers identify suitable adjuvants for various vaccine indications, including immune-mediated and infectious diseases. In addition, the VAC welcomes the inclusion of adjuvant metadata generated by other research programs. example: '15' homepage: https://vac.niaid.nih.gov keywords: - biology - immunology - vaccines name: Vaccine Adjuvant Compendium pattern: ^\d+$ preferred_prefix: vac uri_format: https://vac.niaid.nih.gov/view?id=$1 validatordb: contact: email: david.sehnal@gmail.com name: David Sehnal orcid: 0000-0002-0682-3089 description: Database of validation results for ligands and non-standard residues in the Protein Data Bank. example: 2h6o homepage: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ keywords: - life science mappings: biocontext: VALIDATORDB fairsharing: FAIRsharing.c9psgb integbio: nbdc02174 miriam: validatordb n2t: validatordb name: ValidatorDB pattern: ^[A-Za-z0-9\/]+$ preferred_prefix: validatordb provides: pdb publications: - doi: 10.1093/nar/gku1118 pmc: PMC4383933 pubmed: '25392418' title: 'ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank' year: 2014 uri_format: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1 vandf: contact: email: michael.lincoln@med.va.gov name: Michael Lincoln contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes. ' example: '4019477' homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF keywords: - biomedical science - drug - drug interaction - ontology - pharmacology mappings: aberowl: VANDF biolink: VANDF bioportal: VANDF fairsharing: FAIRsharing.xn3pb3 hl7: 2.16.840.1.113883.6.229 name: Veterans Administration National Drug File pattern: ^\d+$ preferred_prefix: vandf publications: - pmc: PMC2244318 pubmed: '12463886' title: 'A semantic normal form for clinical drugs in the UMLS: early experiences with the VANDF' year: 2002 uri_format: http://purl.bioontology.org/ontology/VANDF/$1 vann: contact: email: nospam@iandavis.com github: iand name: Ian Davis contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This document describes a vocabulary for annotating descriptions of vocabularies with examples and usage notes. example: usageNote homepage: https://vocab.org/vann/ keywords: - metadata mappings: lov: vann zazuko: vann name: A vocabulary for annotating vocabulary descriptions preferred_prefix: vann uri_format: https://vocab.org/vann/#$1 vario: banana: VariO contact: email: mauno.vihinen@med.lu.se github: maunov name: Mauno Vihinen orcid: 0000-0002-9614-7976 deprecated: true description: The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level. download_obo: http://purl.obolibrary.org/obo/vario.obo download_owl: http://purl.obolibrary.org/obo/vario.owl example: '0376' homepage: http://variationontology.org keywords: - deoxyribonucleic acid - dna structural variation - genetics - obo - ontology - protein - ribonucleic acid - sequence variant license: CC-BY-4.0 mappings: aberowl: VARIO agroportal: VARIO biocontext: VARIO bioportal: VARIO fairsharing: FAIRsharing.65xkbs miriam: vario n2t: vario obofoundry: vario ols: vario ontobee: VariO name: Variation Ontology namespace_in_lui: true pattern: ^\d+$ 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 publications: - doi: 10.1186/s12864-018-5262-0 pmc: PMC6309100 pubmed: '30591019' title: Systematics for types and effects of DNA variations year: 2018 - doi: 10.1002/humu.22954 pubmed: '26773573' title: VariOtator, a Software Tool for Variation Annotation with the Variation Ontology year: 2016 - doi: 10.1007/s00439-015-1529-6 pubmed: '25616435' title: Types and effects of protein variations year: 2015 - doi: 10.1186/2041-1480-5-9 pmc: PMC3931275 pubmed: '24533660' title: 'Variation ontology: annotator guide' year: 2014 - doi: 10.1101/gr.157495.113 pmc: PMC3912426 pubmed: '24162187' title: Variation Ontology for annotation of variation effects and mechanisms year: 2013 rdf_uri_format: http://purl.obolibrary.org/obo/VariO_$1 uri_format: http://purl.obolibrary.org/obo/VariO_$1 version: '2018-11-09' vbase2: contact: email: wmueller@gbf.de name: Werner Müller orcid: 0000-0002-1297-9725 description: The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes. example: humIGHV025 homepage: http://www.vbase2.org/vbase2.php keywords: - gene - life science mappings: biocontext: VBASE2 fairsharing: FAIRsharing.qvxhb1 integbio: nbdc01897 miriam: vbase2 n2t: vbase2 ncbi: VBASE2 prefixcommons: vbase2 name: Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse pattern: ^\w+$ preferred_prefix: vbase2 providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/vbase2:$1 publications: - doi: 10.1093/nar/gki088 pmc: PMC540042 pubmed: '15608286' title: VBASE2, an integrative V gene database year: 2005 uri_format: http://www.vbase2.org/vgene.php?id=$1 vbo: contact: email: Sabrina@tislab.org github: sabrinatoro name: Sabrina Toro orcid: 0000-0002-4142-7153 depends_on: - ncbitaxon description: Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names. download_json: http://purl.obolibrary.org/obo/vbo.json download_obo: http://purl.obolibrary.org/obo/vbo.obo download_owl: http://purl.obolibrary.org/obo/vbo.owl example: 0000038 homepage: https://github.com/monarch-initiative/vertebrate-breed-ontology keywords: - obo - ontology license: CC-BY-4.0 mappings: aberowl: VBO bioportal: VBO cellosaurus: VBO obofoundry: vbo ols: vbo ontobee: VBO name: Vertebrate Breed Ontology pattern: ^\d{7}$ preferred_prefix: VBO rdf_uri_format: http://purl.obolibrary.org/obo/VBO_$1 repository: https://github.com/monarch-initiative/vertebrate-breed-ontology uri_format: http://purl.obolibrary.org/obo/VBO_$1 version: '2025-02-12' vbrc: description: The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis. example: '35742' homepage: http://vbrc.org/ mappings: biocontext: VBRC miriam: vbrc n2t: vbrc prefixcommons: vbrc name: Viral Bioinformatics Resource Center pattern: ^\d+$ preferred_prefix: vbrc providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/vbrc:$1 uri_format: http://vbrc.org/gene_detail.asp?gene_id=$1 vcard: contact: email: r@iannel.la github: riannella name: Renato Iannella orcid: 0000-0001-5547-3508 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: vCard is a specification developed by the Internet Engineering Task Force (IETF) for the description of people and organisations download_rdf: https://www.w3.org/2006/vcard/ns example: Agent github_request_issue: 1317 homepage: https://www.w3.org/TR/vcard-rdf/ keywords: - people mappings: lov: vcard zazuko: vcard name: Virtual Contact File preferred_prefix: vcard uri_format: http://www.w3.org/2006/vcard/ns#$1 vcell: description: Models developed with the Virtual Cell (VCell) software prorgam. example: '201022999' homepage: https://health.uconn.edu/ mappings: miriam: vcell name: VCell Published Models pattern: ^\d{5,}$ preferred_prefix: vcell uri_format: https://vcell.org/biomodel-$1 vdrc: description: Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID. [from RRID] example: '100291' homepage: http://stockcenter.vdrc.at/control/main keywords: - biomaterial supply resource - drosophila - fly lines mappings: rrid: VDRC name: Vienna Drosophila Resource Center pattern: ^\d+$ preferred_prefix: vdrc uri_format: https://shop.vbc.ac.at/vdrc_store/$1.html vectorbase: contact: email: d.e.starns@liv.ac.uk github: obsidian83 name: David Starns orcid: 0000-0001-6583-9067 description: 'VectorBase is part of the VEuPathDB, a NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens and related species of interest. Currently, VectorBase contains genome information for approximately 80 organisms: mosquitoes, bed bugs, biting midges, ticks, tsetse flies, mites, sand flies, house flies, body lice, stable flies, kissing bugs, and a snail which is an intermediate host.' example: ISCW007415 homepage: https://www.vectorbase.org/ keywords: - comparative genomics - functional genomics - gene - genome - genomics - population dynamics - population genetics - protein mappings: biocontext: VECTORBASE fairsharing: FAIRsharing.3etvdn integbio: nbdc01909 miriam: vectorbase n2t: vectorbase ncbi: VectorBase prefixcommons: vectorbase re3data: r3d100010880 name: Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens pattern: ^\D{4}\d{6}(\-\D{2})?$ preferred_prefix: vectorbase providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/vectorbase:$1 - code: vectorbase.alt1 description: An alternate provider based on the search functionality homepage: https://www.vectorbase.org name: Vectorbase Alt. 1 uri_format: https://www.vectorbase.org/search/site/$1?&site="Genome" - code: vectorbase.alt2 description: An alternate provider based on the app structure homepage: https://www.vectorbase.org name: Vectorbase Alt. 2 uri_format: https://vectorbase.org/vectorbase/app/record/gene/$1 publications: - doi: 10.1093/nar/gku1117 pmc: PMC4383932 pubmed: '25510499' title: 'VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases' year: 2014 - doi: 10.1093/nar/gkn857 pmc: PMC2686483 pubmed: '19028744' title: 'VectorBase: a data resource for invertebrate vector genomics' year: 2008 twitter: VectorBase uri_format: https://vectorbase.org/gene/$1 vega: contact: email: jla1@sanger.ac.uk name: Jennifer L Harrow orcid: 0000-0003-0338-3070 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A repository for high-quality gene models produced by the manual annotation of vertebrate genomes. example: OTTHUMG00000169812 homepage: https://vega.archive.ensembl.org/index.html keywords: - genome - life science mappings: fairsharing: FAIRsharing.mr293q prefixcommons: vega re3data: r3d100012575 name: Vertebrate Genome Annotation Database preferred_prefix: vega providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/vega:$1 publications: - doi: 10.1093/nar/gkt1241 pmc: PMC3964964 pubmed: '24316575' title: The Vertebrate Genome Annotation browser 10 years on year: 2013 - doi: 10.1093/nar/gkm987 pmc: PMC2238886 pubmed: '18003653' title: The vertebrate genome annotation (Vega) database year: 2007 synonyms: - VEGA uri_format: http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1 vegbank: description: 'VegBank is the vegetation plot database of the Ecological Society of America''s Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. ' example: VB.Ob.3736.GRSM125 homepage: http://vegbank.org/ mappings: miriam: vegbank re3data: r3d100010153 name: VegBank pattern: ^VB\.[A-Za-z][A-Za-z]\..*$ preferred_prefix: vegbank uri_format: http://vegbank.org/cite/$1 venom: appears_in: - vbo contact: email: DBrodbelt@RVC.AC.UK name: David Brodbelt orcid: 0000-0001-5628-4194 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Veterinary Nomenclature (VeNom) is a standard set of clinical veterinary terms for use in referral veterinary hospital electronic patient records and first opinion veterinary practice management systems. example: '12969' homepage: https://venomcoding.org/ name: Veterinary Nomenclature pattern: ^\d+$ preferred_prefix: VeNom proprietary: true references: - https://github.com/biopragmatics/bioregistry/pull/724 vfb: contact: email: r.court@ed.ac.uk name: Robert Court orcid: 0000-0002-0173-9080 description: An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster. example: '00000001' homepage: https://VirtualFlyBrain.org keywords: - life science - neurobiology mappings: fairsharing: FAIRsharing.nzaz6z miriam: vfb n2t: vfb re3data: r3d100011373 name: Virtual Fly Brain pattern: ^[0-9a-zA-Z]{8}$ preferred_prefix: vfb publications: - doi: 10.1186/1471-2105-13-122 pmc: PMC3412715 pubmed: '22676296' title: Web tools for large-scale 3D biological images and atlases year: 2012 - doi: 10.1093/bioinformatics/bts113 pubmed: '22402613' title: A strategy for building neuroanatomy ontologies year: 2012 - doi: 10.1093/bioinformatics/btr677 pubmed: '22180411' title: The Virtual Fly Brain browser and query interface year: 2011 - doi: doi:10.1186/1471-2105-13-122 title: Web tools for large-scale 3D biological images and atlases uri_format: http://virtualflybrain.org/reports/$1 vfdb.gene: description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes. example: VFG2154 homepage: http://www.mgc.ac.cn/VFs/ mappings: biocontext: VFDB.GENE miriam: vfdb.gene n2t: vfdb.gene name: VFDB Gene pattern: ^\w+$ preferred_prefix: vfdb.gene uri_format: http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1 vfdb.genus: description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus. example: Chlamydia homepage: http://www.mgc.ac.cn/VFs/ mappings: biocontext: VFDB.GENUS miriam: vfdb.genus n2t: vfdb.genus name: VFDB Genus pattern: ^\w+$ preferred_prefix: vfdb.genus uri_format: http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1 vgnc: contact: email: stweedie@ebi.ac.uk name: Susan Tweedie orcid: 0000-0003-1818-8243 description: The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee. example: '3792' homepage: https://vertebrate.genenames.org keywords: - life science mappings: cellosaurus: VGNC fairsharing: FAIRsharing.5NhJFK integbio: nbdc02624 miriam: vgnc ncbi: VGNC togoid: Vgnc uniprot: DB-0226 name: Vertebrate Gene Nomenclature Committee pattern: ^\d{1,9}$ preferred_prefix: vgnc publications: - doi: 10.1093/nar/gkaa980 pmc: PMC7779007 pubmed: '33152070' title: 'Genenames.org: the HGNC and VGNC resources in 2021' year: 2021 uri_format: https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1 vhog: contact: email: bgee@isb-sib.ch name: Bgee team deprecated: true description: 'vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 "historical homology". Each mapping has been manually reviewed, and we provide confidence codes and references when available.' download_obo: ftp://ftp.bgee.org/general/ontologies/vHOG.obo download_owl: http://purl.obolibrary.org/obo/vhog.owl example: '0000411' homepage: http://bgee.unil.ch keywords: - anatomy - development - obo - ontology logo: http://bgee.org/img/logo/bgee13_logo.png mappings: aberowl: VHOG biocontext: VHOG bioportal: VHOG obofoundry: vhog prefixcommons: vhog name: Vertebrate Homologous Organ Group Ontology pattern: ^\d{7}$ preferred_prefix: VHOG providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/vhog:$1 rdf_uri_format: http://purl.obolibrary.org/obo/VHOG_$1 synonyms: - VHOG_RETIRED uri_format: http://purl.obolibrary.org/obo/VHOG_$1 viaf: description: The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web. example: '75121530' homepage: http://viaf.org keywords: - centrally registered identifier - knowledge and information systems mappings: bartoc: '2053' fairsharing: FAIRsharing.a15ac6 miriam: viaf n2t: viaf wikidata: P214 name: VIAF ID pattern: ^\d+$ preferred_prefix: viaf providers: - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/viaf/$1 - code: viaf.https description: A duplicate endpoint over HTTPS first_party: true homepage: http://viaf.org name: VIAF (https) uri_format: https://viaf.org/$1 rdf_uri_format: http://viaf.org/viaf/$1 uri_format: http://viaf.org/viaf/$1 vibso: contact: email: philip.stroemert@tib.eu github: StroemPhi name: Philip Strömert orcid: 0000-0002-1595-3213 contributor: email: philip.stroemert@tib.eu github: StroemPhi name: Philip Strömert orcid: 0000-0002-1595-3213 description: The Vibration Spectroscopy Ontology defines technical terms with which research data produced in vibrational spectroscopy experiments can be semantically enriched, made machine readable and FAIR. example: 0000008 github_request_issue: 1278 homepage: https://nfdi4chem.github.io/VibrationalSpectroscopyOntology/ license: CC-BY-4.0 name: Vibrational Spectroscopy Ontology pattern: ^\d{7}$ preferred_prefix: vibso repository: https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://purl.obolibrary.org/obo/VIBSO_$1 vido: contact: email: johnbeverley2021@u.northwestern.edu github: johnbeve name: John Beverly orcid: 0000-0002-1118-1738 description: The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc. download_owl: https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-virus/master/ontology/vido.owl example: '0001114' homepage: https://github.com/infectious-disease-ontology-extensions/ido-virus keywords: - ontology mappings: aberowl: VIDO bioportal: VIDO ols: vido ontobee: VIDO name: The Virus Infectious Disease Ontology pattern: ^\d{7}$ preferred_prefix: vido providers: - code: obo.1 description: This incorrect encoding was found inside IDO-COVID-19 homepage: http://purl.obolibrary.org name: Nonstandard OBO PURL uri_format: http://purl.obolibrary.org/VIDO_$1 repository: https://github.com/infectious-disease-ontology-extensions/ido-virus uri_format: http://purl.obolibrary.org/obo/VIDO_$1 version: '2020-08-25' violinnet: appears_in: - oae contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: Defunct vaccine information source from the He Lab example: '4140' mappings: wikidata: P1925 name: ViolinNet pattern: ^\d+$ preferred_prefix: violinnet synonyms: - violinID - violinId uri_format: http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=$1 viperdb: description: VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. example: 2c6s homepage: http://viperdb.scripps.edu/ keywords: - small molecule - structure mappings: integbio: nbdc00835 prefixcommons: viperdb re3data: r3d100012362 name: VIPERdb preferred_prefix: viperdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/viperdb:$1 provides: pdb uri_format: https://viperdb.org/Info_Page.php?VDB=$1 vipr: contact: email: rscheuermann@jcvi.org name: Richard Scheuermann orcid: 0000-0003-1355-892X description: The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information. example: BeAn 70563 homepage: http://www.viprbrc.org/brc/home.do?decorator=vipr keywords: - biomedical science - epidemiology - genomics - immunology - life science - proteomics - virology mappings: biocontext: VIPR fairsharing: FAIRsharing.2qx8n8 miriam: vipr n2t: vipr ncbi: ViPR re3data: r3d100011931 name: Virus Pathogen Resource pattern: ^[A-Za-z 0-9]+$ preferred_prefix: vipr publications: - doi: 10.3390/v4113209 pmc: PMC3509690 pubmed: '23202522' title: 'Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community' year: 2012 - doi: 10.1093/nar/gkr859 pmc: PMC3245011 pubmed: '22006842' title: 'ViPR: an open bioinformatics database and analysis resource for virology research' year: 2011 - doi: 10.1016/b978-0-12-809633-8.20995-3 pmc: PMC7173540 title: Database and Analytical Resources for Viral Research Community year: 2021 - doi: 10.1016/b978-0-12-801238-3.95728-3 pmc: PMC7157461 title: Virus Databases ☆ year: 2017 repository: https://github.com/VirusBRC uri_format: http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena viralzone: contact: email: Philippe.Lemercier@sib.swiss name: Philippe Le Mercier orcid: 0000-0001-8528-090X description: ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures. example: '992' homepage: http://www.expasy.org/viralzone/ keywords: - epidemiology - life science - molecular biology - virology - virus mappings: biocontext: VIRALZONE fairsharing: FAIRsharing.tppk10 go: VZ integbio: nbdc02226 miriam: viralzone n2t: viralzone prefixcommons: vz re3data: r3d100013314 name: ViralZone pattern: ^\d+$ preferred_prefix: viralzone providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/vz:$1 - code: viralzone.alt1 description: Alternate view homepage: http://viralzone.expasy.org name: Viralzone Alt 1. uri_format: http://viralzone.expasy.org/all_by_protein/$1 publications: - doi: 10.1093/nar/gks1220 pmc: PMC3531065 pubmed: '23193299' title: 'ViralZone: recent updates to the virus knowledge resource' year: 2012 - doi: 10.1093/nar/gkq901 pmc: PMC3013774 pubmed: '20947564' title: 'ViralZone: a knowledge resource to understand virus diversity' year: 2010 synonyms: - vz uri_format: https://viralzone.expasy.org/$1 virgen: description: VirGen a comprehensive viral genome resource, which organizes the ‘sequence space’ of viral genomes in a structured fashion. It has been developed with an objective to serve as an annotated and curated database for complete viral genome sequences. example: AY321118 homepage: http://bioinfo.ernet.in/virgen/virgen.html keywords: - genome mappings: prefixcommons: virgen name: VirGen preferred_prefix: virgen providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/virgen:$1 virmirdb: description: A database containing predicted viral miRNA candidate hairpins. example: '11002' homepage: http://alk.ibms.sinica.edu.tw keywords: - rna - structure mappings: prefixcommons: virmirdb name: Vir-Mir db preferred_prefix: virmirdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/virmirdb:$1 provides: ncbitaxon reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id=$1 viroligo: description: The VirOligo database (1) is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place. example: BM0456 homepage: http://viroligo.okstate.edu keywords: - small molecule mappings: prefixcommons: viroligo name: VirOligo preferred_prefix: viroligo providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/viroligo:$1 uri_format: http://viroligo.okstate.edu/main.php?vid=$1 virsirna: description: The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region. example: virsi1909 homepage: http://crdd.osdd.net/servers/virsirnadb mappings: biocontext: VIRSIRNA miriam: virsirna n2t: virsirna name: VIRsiRNA pattern: ^virsi\d+$ preferred_prefix: virsirna uri_format: http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1 virushostdb: contact: email: ogata@kuicr.kyoto-u.ac.jp name: Hiroyuki Ogata orcid: 0000-0001-6594-377X description: Virus-Host DB organizes data about the relationships between viruses and their hosts, represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts. Virus-Host DB covers viruses with complete genomes stored in 1) NCBI/RefSeq and 2) GenBank whose accession numbers are listed in EBI Genomes. The host information is collected from RefSeq, GenBank (in free text format), UniProt, ViralZone, and manually curated with additional information obtained by literature surveys. example: '438782' homepage: https://www.genome.jp/virushostdb/ keywords: - virus mappings: integbio: nbdc02395 prefixcommons: virushostdb name: Virus-HostDB preferred_prefix: virushostdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/virushostdb:$1 provides: ncbitaxon publications: - doi: 10.3390/v8030066 pmc: PMC4810256 pubmed: '26938550' title: Linking Virus Genomes with Host Taxonomy year: 2016 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.genome.jp/virushostdb/$1 vita: description: ViTa is a database which collects virus data from miRBase and ICTV, VirGne, VBRC.., etc, including known miRNAs on virus and supporting predicted host miRNA targets by miRanda and TargetScan. ViTa also rovide effective annotations, including human miRNA expression, virus infected tissues, annotation of virus and comparisons. example: AB016785 homepage: http://vita.mbc.nctu.edu.tw/ keywords: - gene expression - rna - structure mappings: prefixcommons: vita name: Virus' miRNA target preferred_prefix: vita providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/vita:$1 uri_format: http://vita.mbc.nctu.edu.tw/search.php?acc=$1 vitro: appears_in: - fabio - foaf contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Vitro is a full stack framework for building semantic web applications. It is not domain specific. download_owl: https://raw.githubusercontent.com/vivo-archive/Linked-Data-Indexer/refs/heads/master/src/main/resources/vitro-0.7.owl example: descriptionAnnot github_request_issue: 1317 homepage: https://github.com/vivo-project/Vitro keywords: - ontology name: Vitro Application Ontology preferred_prefix: vitro repository: https://github.com/vivo-project/Vitro uri_format: http://vitro.mannlib.cornell.edu/ns/vitro/0.7#$1 vivo: contact: email: christian.hauschke@tib.eu github: hauschke name: Christian Hauschke orcid: 0000-0003-2499-7741 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology about scholarship download_owl: https://raw.githubusercontent.com/vivo-ontologies/vivo-ontology/master/vivo.owl example: Laboratory github_request_issue: 1317 homepage: https://vivoweb.org keywords: - academy - natural science - ontology - protocol - researcher data - resource metadata - study design license: unlicense mappings: aberowl: VIVO biocontext: VIVO bioportal: VIVO fairsharing: FAIRsharing.6xfgaq lov: vivo name: VIVO Ontology preferred_prefix: vivo repository: https://github.com/vivo-ontologies/vivo-ontology uri_format: http://vivoweb.org/ontology/core#$1 vmc: deprecated: true mappings: biolink: VMC name: Variation Modelling Collaboration preferred_prefix: vmc references: - https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.67hbe76b6a4z - https://github.com/ga4gh/vr-spec vmhgene: description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. example: '8639.1' homepage: https://www.vmh.life/ mappings: miriam: vmhgene name: VMH Gene pattern: ^[0-9]+\.[0-9]+$ preferred_prefix: vmhgene uri_format: https://www.vmh.life/#gene/$1 vmhmetabolite: description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. example: h2o homepage: https://www.vmh.life/ mappings: biocontext: VMHMETABOLITE miriam: vmhmetabolite n2t: vmhmetabolite name: VMH metabolite pattern: ^[a-zA-Z0-9_\(\_\)\[\]]+$ preferred_prefix: vmhmetabolite uri_format: https://www.vmh.life/#metabolite/$1 vmhreaction: description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. example: HEX1 homepage: https://www.vmh.life/ mappings: biocontext: VMHREACTION miriam: vmhreaction n2t: vmhreaction name: VMH reaction pattern: ^[a-zA-Z0-9_\(\_\)\[\]]+$ preferred_prefix: vmhreaction uri_format: https://www.vmh.life/#reaction/$1 vo: appears_in: - scdo contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqunh He orcid: 0000-0001-9189-9661 description: The Vaccine Ontology (VO) is a community-based biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine types and annotations, integrate various vaccine data, and support computer-assisted reasoning. The VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities. download_owl: http://purl.obolibrary.org/obo/vo.owl example: 0000093 homepage: https://violinet.org/vaccineontology keywords: - biological process - biomedical science - immunology - obo - ontology - pathobiochemistry - pathogen - small molecule - vaccination - vaccine license: CC-BY-4.0 logo: https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaUFDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--0d3898a5618b34c0bc948bb0d101e906f212f05f/vo_banner.png?disposition=inline mappings: aberowl: VO biocontext: VO bioportal: VO fairsharing: FAIRsharing.zwtww5 obofoundry: vo ols: vo ontobee: VO prefixcommons: vo wikidata: P1928 name: Vaccine Ontology pattern: ^\d{7}$ preferred_prefix: VO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/vo:$1 publications: - doi: 10.2174/1381612826666201125112131 pubmed: '33238868' title: Ontology-based Precision Vaccinology for Deep Mechanism Understanding and Precision Vaccine Development year: 2021 - doi: 10.1186/2041-1480-3-17 pmc: PMC3639077 pubmed: '23256535' title: Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses year: 2012 - doi: 10.1186/2041-1480-2-s2-s8 pmc: PMC3102897 pubmed: '21624163' title: Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology year: 2011 - doi: 10.1186/1745-7580-6-s1-s5 pmc: PMC2946783 pubmed: '20875156' title: Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN year: 2010 rdf_uri_format: http://purl.obolibrary.org/obo/VO_$1 repository: https://github.com/vaccineontology/VO uri_format: http://purl.obolibrary.org/obo/VO_$1 version: '2024-12-29' voc4cat: comment: The most current version of a concept can be accessed so * https://w3id.org/nfdi4cat/voc4cat_0000123 other/older versions from releases like so * https://w3id.org/nfdi4cat/voc4cat/v2023-08-17/voc4cat_0000123. This is pretty unique and isn't tracked by the Bioregistry currently. contact: email: nikolaos.moustakas@catalysis.de github: nmoust name: Nikolaos Moustakas orcid: 0000-0002-6242-2167 contributor: email: David.Linke@catalysis.de github: dalito name: David Linke orcid: 0000-0002-5898-1820 description: Voc4Cat is a [SKOS](https://www.w3.org/TR/2009/REC-skos-reference-20090818/) vocabulary for the catalysis disciplines. The vocabulary was created in the [NFDI4Cat](http://www.nfdi4cat.org/) initiative. The first collection of terms was published in June 2023 with a focus on photo catalysis. Our goal is to continuously extend the vocabulary to other areas of catalysis and related disciplines like chemical engineering or materials science. example: '0000123' github_request_issue: 957 homepage: https://nfdi4cat.github.io/voc4cat/ license: CC0-1.0 name: A vocabulary for the catalysis disciplines pattern: ^\d{7,}$ preferred_prefix: voc4cat repository: https://github.com/nfdi4cat/voc4cat reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://w3id.org/nfdi4cat/voc4cat_$1 void: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary. example: feature homepage: http://vocab.deri.ie/void keywords: - metadata mappings: biocontext: void lov: void zazuko: void name: Vocabulary of Interlinked Datasets preferred_prefix: void uri_format: http://rdfs.org/ns/void#$1 vsao: contact: email: wasila.dahdul@usd.edu name: Wasila Dahdul orcid: 0000-0003-3162-7490 deprecated: true description: Vertebrate skeletal anatomy ontology. download_obo: http://aber-owl.net/media/ontologies/VSAO/20/vsao.obo download_owl: http://purl.obolibrary.org/obo/vsao.owl example: 0000183 homepage: https://www.nescent.org/phenoscape/Main_Page keywords: - anatomy - obo - ontology - vertebrate mappings: aberowl: VSAO biocontext: VSAO bioportal: VSAO obofoundry: vsao ols: vsao prefixcommons: vao name: Vertebrate Skeletal Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: VSAO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/vao:$1 rdf_uri_format: http://purl.obolibrary.org/obo/VSAO_$1 synonyms: - VSAO_RETIRED uri_format: http://purl.obolibrary.org/obo/VSAO_$1 version: '2012-11-06' vsdb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source. example: '1868' homepage: https://sitem.herts.ac.uk/aeru/vsdb name: Veterinary Substances DataBase pattern: ^\d+$ preferred_prefix: vsdb uri_format: https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm vsmo: contact: email: lars.eisen@colostate.edu name: Lars Eisen orcid: 0000-0002-0094-3186 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems. download_json: https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.json download_obo: https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.obo download_owl: https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.owl example: '0000000' homepage: https://code.google.com/archive/p/vector-surveillance-and-management-ontology/ keywords: - ontology license: New BSD License name: Ontology for vector surveillance and management preferred_prefix: vsmo publications: - doi: 10.1603/me12169 pmc: PMC3695545 pubmed: '23427646' title: Ontology for vector surveillance and management year: 2013 uri_format: http://purl.obolibrary.org/obo/VSMO_$1 vso: contact: email: albertgoldfain@gmail.com name: Albert Goldfain description: 'The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. ' download_owl: http://aber-owl.net/media/ontologies/VSO/1/vso.owl example: '0000041' homepage: https://bioportal.bioontology.org/ontologies/VSO keywords: - biomedical science - blood - experimental measurement - health - health science - ontology - owl mappings: aberowl: VSO bioportal: VSO fairsharing: FAIRsharing.jjb2p2 prefixcommons: vso zazuko: vso name: Vital Sign Ontology pattern: ^\d{7}$ preferred_prefix: vso providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/vso:$1 uri_format: https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1 vt: appears_in: - scdo contact: email: caripark@iastate.edu github: caripark name: Carissa Park orcid: 0000-0002-2346-5201 description: The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms. download_obo: https://github.com/AnimalGenome/vertebrate-trait-ontology/raw/master/current_release/vt.obo download_owl: http://purl.obolibrary.org/obo/vt.owl example: 0000685 homepage: https://github.com/AnimalGenome/vertebrate-trait-ontology keywords: - animal physiology - biology - developmental biology - morphology - obo - ontology - phenotype - physiology - trait - vertebrate license: CC-BY-4.0 mappings: aberowl: VT agroportal: VT biocontext: VT bioportal: VT fairsharing: FAIRsharing.10gr18 obofoundry: vt ols: vt ontobee: VT prefixcommons: vt name: Vertebrate trait ontology pattern: ^\d{7}$ preferred_prefix: VT providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/vt:$1 publications: - doi: 10.1186/2041-1480-4-13 pmc: PMC3851175 pubmed: '23937709' title: 'The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species' year: 2013 rdf_uri_format: http://purl.obolibrary.org/obo/VT_$1 repository: https://github.com/AnimalGenome/vertebrate-trait-ontology uri_format: http://purl.obolibrary.org/obo/VT_$1 version: '2025-02-11' vto: contact: email: balhoff@renci.org github: balhoff name: Jim Balhoff orcid: 0000-0002-8688-6599 description: Comprehensive hierarchy of extinct and extant vertebrate taxa. download_obo: http://purl.obolibrary.org/obo/vto.obo download_owl: http://purl.obolibrary.org/obo/vto.owl example: '9008500' homepage: https://github.com/phenoscape/vertebrate-taxonomy-ontology keywords: - bone - obo - ontology - taxonomy license: CC0-1.0 mappings: aberowl: VTO biocontext: VTO bioportal: VTO fairsharing: FAIRsharing.akmeb9 obofoundry: vto ols: vto ontobee: VTO name: Vertebrate Taxonomy Ontology pattern: ^\d{7}$ preferred_prefix: VTO publications: - doi: 10.1186/2041-1480-4-34 pmc: PMC4177199 pubmed: '24267744' title: 'The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes' year: 2013 rdf_uri_format: http://purl.obolibrary.org/obo/VTO_$1 repository: https://github.com/phenoscape/vertebrate-taxonomy-ontology uri_format: http://purl.obolibrary.org/obo/VTO_$1 version: '2020-11-13' vuid: comment: The example corresponds to acetaminophen contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Veterans Health Administration is America’s largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year. example: '4007166' homepage: https://www.va.gov/health name: Veterans Health Administration (VHA) unique identifier pattern: ^\d+$ preferred_prefix: vuid references: - https://academic.oup.com/jamia/article/17/4/432/866953 wb.rnai: description: WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes. example: WBRNAi00086878 homepage: https://www.wormbase.org/ mappings: biocontext: WB.RNAI miriam: wb.rnai n2t: wb.rnai name: WormBase RNAi pattern: ^WBRNAi\d{8}$ preferred_prefix: wb.rnai uri_format: https://www.wormbase.org/species/c_elegans/rnai/$1 wbbt: contact: email: raymond@caltech.edu github: raymond91125 name: Raymond Lee orcid: 0000-0002-8151-7479 description: Ontology about the gross anatomy of the C. elegans download_obo: http://purl.obolibrary.org/obo/wbbt.obo download_owl: http://purl.obolibrary.org/obo/wbbt.owl example: 0001290 homepage: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology keywords: - anatomy - cell - life science - obo - ontology - worm license: CC-BY-4.0 mappings: aberowl: WBBT biocontext: WBbt biolink: WBbt bioportal: WB-BT fairsharing: FAIRsharing.phk7dd go: WBbt obofoundry: wbbt ols: wbbt ontobee: WBbt prefixcommons: wbbt name: C. elegans Gross Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: WBbt providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/wbbt:$1 publications: - doi: 10.1002/cfg.248 pmc: PMC2447384 pubmed: '18629098' title: Building a cell and anatomy ontology of Caenorhabditis elegans year: 2003 rdf_uri_format: http://purl.obolibrary.org/obo/WBbt_$1 repository: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology synonyms: - WBbt uri_format: http://purl.obolibrary.org/obo/WBbt_$1 version: '2025-01-02' wbls: contact: email: cgrove@caltech.edu github: chris-grove name: Chris Grove orcid: 0000-0001-9076-6015 description: Ontology about the development and life stages of the C. elegans download_obo: http://purl.obolibrary.org/obo/wbls.obo download_owl: http://purl.obolibrary.org/obo/wbls.owl example: 0000690 homepage: https://github.com/obophenotype/c-elegans-development-ontology keywords: - development - developmental biology - life cycle - life cycle stage - life science - obo - ontology - worm license: CC-BY-4.0 mappings: aberowl: WBLS biocontext: WBLS biolink: WBls bioportal: WB-LS fairsharing: FAIRsharing.sm90nh go: WBls obofoundry: wbls ols: wbls ontobee: WBls prefixcommons: wbls name: C. elegans development ontology pattern: ^\d{7}$ preferred_prefix: WBls providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/wbls:$1 publications: - doi: 10.1093/nar/gkz920 pmc: PMC7145598 pubmed: '31642470' title: 'WormBase: a modern Model Organism Information Resource' year: 2020 rdf_uri_format: http://purl.obolibrary.org/obo/WBls_$1 repository: https://github.com/obophenotype/c-elegans-development-ontology synonyms: - WBls uri_format: http://purl.obolibrary.org/obo/WBls_$1 version: '2025-01-04' wbphenotype: contact: email: cgrove@caltech.edu github: chris-grove name: Chris Grove orcid: 0000-0001-9076-6015 description: Ontology about C. elegans and other nematode phenotypes download_obo: http://purl.obolibrary.org/obo/wbphenotype.obo download_owl: http://purl.obolibrary.org/obo/wbphenotype.owl example: 0000983 homepage: https://github.com/obophenotype/c-elegans-phenotype-ontology keywords: - anatomy - life science - obo - ontology - phenotype - worm license: CC-BY-4.0 mappings: aberowl: WBPHENOTYPE biocontext: WBPhenotype bioportal: WB-PHENOTYPE fairsharing: FAIRsharing.agvc7y go: WBPhenotype obofoundry: wbphenotype ols: wbphenotype ontobee: WBPhenotype prefixcommons: wbphenotype name: C. elegans phenotype pattern: ^\d{7}$ preferred_prefix: WBPhenotype providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/wbphenotype:$1 publications: - doi: 10.1186/1471-2105-12-32 pmc: PMC3039574 pubmed: '21261995' title: 'Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community' year: 2011 rdf_uri_format: http://purl.obolibrary.org/obo/WBPhenotype_$1 repository: https://github.com/obophenotype/c-elegans-phenotype-ontology synonyms: - WBPhenotype uri_format: http://purl.obolibrary.org/obo/WBPhenotype_$1 version: '2025-01-02' webelements: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Browser for the periodic table of the elements example: chromium homepage: https://www.webelements.com/ keywords: - chemistry name: Web Elements pattern: ^\w+$ preferred_prefix: webelements uri_format: https://www.webelements.com/$1 wgs84: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum example: latitude homepage: https://www.w3.org/2003/01/geo/wgs84_pos keywords: - geography mappings: biolink: wgs lov: geo name: WGS84 Geo Positioning preferred_prefix: wgs84 uri_format: http://www.w3.org/2003/01/geo/wgs84_pos#$1 wicell: description: Cell line collections (Providers) example: ai10e-kctd13b homepage: https://www.wicell.org mappings: cellosaurus: WiCell name: WiCell Research Institute Cell Collection preferred_prefix: wicell uri_format: https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true wikidata: contact: email: vrandecic@gmail.com github: vrandezo name: Denny Vrandečić orcid: 0000-0002-9593-2294 description: Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic. example: Q47475003 homepage: https://www.wikidata.org/ keywords: - chemistry - genomics - metabolomics - proteomics - subject agnostic license: CC0-1.0 mappings: bartoc: '1940' biocontext: WIKIDATA biolink: WIKIDATA cellosaurus: Wikidata cheminf: '000567' fairsharing: FAIRsharing.6s749p miriam: wikidata n2t: wikidata name: Wikidata pattern: ^(Q|P|E)\d+$ preferred_prefix: wikidata providers: - code: scholia description: Scholia can generally resolve many Wikidata entries in the biomedical and bibliometric domains homepage: https://scholia.toolforge.org name: Scholia uri_format: https://scholia.toolforge.org/$1 publications: - doi: 10.1145/2187980.2188242 title: Wikidata year: 2012 synonyms: - WD_Entity - wd - wdeschema twitter: wikidata uri_format: http://www.wikidata.org/entity/$1 wikidata.property: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Wikidata is a free and open knowledge base that can be read and edited by both humans and machines. Wikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. ' example: P4355 homepage: https://www.wikidata.org license: CC0-1.0 mappings: biocontext: WD_Prop biolink: WIKIDATA_PROPERTY name: Wikidata Property part_of: wikidata pattern: ^P\d+$ preferred_prefix: wikidata.property providers: - code: scholia description: Scholia can generally resolve many Wikidata entries in the biomedical and bibliometric domains homepage: https://scholia.toolforge.org name: Scholia uri_format: https://scholia.toolforge.org/$1 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/$1.html wikipathways: contact: email: egon.willighagen@gmail.com github: egonw name: Egon Willighagen orcid: 0000-0001-7542-0286 contributor_extras: - email: egon.willighagen@gmail.com github: egonw name: Egon Willighagen orcid: 0000-0001-7542-0286 description: WikiPathways is a database of biological pathways maintained by and for the scientific community. example: WP732 homepage: http://www.wikipathways.org/ keywords: - biological regulation - drug interaction - epidemiology - genetic interaction - molecular interaction - pathway - pathway model - protein interaction - reaction data - signaling - virology license: CC0-1.0 logo: https://www.wikipathways.org/assets/img/wikipathways-logo-horizontal.svg mappings: biocontext: WIKIPATHWAYS edam: '3952' fairsharing: FAIRsharing.g7b4rj integbio: nbdc02116 miriam: wikipathways n2t: wikipathways pathguide: '237' prefixcommons: wikipathways re3data: r3d100013316 togoid: Wikipathways wikidata: P2410 mastodon: wikipathways@fosstodon.org name: WikiPathways pattern: ^WP\d{1,5}(\_r\d+)?$ preferred_prefix: wikipathways providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/wikipathways:$1 - code: scholia description: 'Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. ' homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/wikipathways/$1 publications: - doi: 10.1093/nar/gkad960 pmc: PMC10767877 pubmed: '37941138' title: 'WikiPathways 2024: next generation pathway database' year: 2024 - doi: 10.1093/nar/gkaa1024 pmc: PMC7779061 pubmed: '33211851' title: 'WikiPathways: connecting communities' year: 2021 - doi: 10.1093/nar/gkx1064 pmc: PMC5753270 pubmed: '29136241' title: 'WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research' year: 2018 - doi: 10.1093/nar/gkv1024 pmc: PMC4702772 pubmed: '26481357' title: 'WikiPathways: capturing the full diversity of pathway knowledge' year: 2015 - doi: 10.1093/nar/gkr1074 pmc: PMC3245032 pubmed: '22096230' title: 'WikiPathways: building research communities on biological pathways' year: 2011 - doi: 10.1371/journal.pbio.0060184 pmc: PMC2475545 pubmed: '18651794' title: 'WikiPathways: pathway editing for the people' year: 2008 rdf_uri_format: http://identifiers.org/wikipathways/$1 twitter: WikiPathways uri_format: http://www.wikipathways.org/instance/$1 wikipathways.vocab: contact: email: egon.willighagen@gmail.com github: egonw name: Egon Willighagen orcid: 0000-0001-7542-0286 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology supporting data modeling in WikiPathways download_owl: http://aber-owl.net/media/ontologies/WIKIPATHWAYS/225/wikipathways.owl example: DataNode homepage: http://www.wikipathways.org keywords: - ontology mappings: aberowl: WIKIPATHWAYS bioportal: WIKIPATHWAYS mastodon: wikipathways@fosstodon.org name: WikiPathways Ontology preferred_prefix: wikipathways.vocab references: - https://github.com/biopragmatics/bioregistry/issues/818 uri_format: https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/?p=classes&conceptid=http%3A%2F%2Fvocabularies.wikipathways.org%2Fwp%23$1 wikipedia.en: contributor_extras: - email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay. example: SM_UB-81 example_extras: - Pharyngeal_pouch_(embryology) homepage: http://en.wikipedia.org/wiki/Main_Page mappings: biocontext: WIKIPEDIA.EN go: Wikipedia miriam: wikipedia.en n2t: wikipedia.en prefixcommons: wikipedia name: Wikipedia pattern: ^\S+$ preferred_prefix: wikipedia.en providers: - code: 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 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/wikipedia:$1 - code: volupedia description: A mix of wikipedia and 3d homepage: http://en.volupedia.org name: Volupedia uri_format: http://en.volupedia.org/wiki/$1 references: - https://github.com/biopragmatics/bioregistry/issues/794 synonyms: - wikipedia uri_format: http://en.wikipedia.org/wiki/$1 wiktionary: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A free dictionary example: pharmacist github_request_issue: 1310 homepage: https://wiktionary.org license: CC BY SA 4.0 name: Wiktionary preferred_prefix: wiktionary uri_format: https://en.wiktionary.org/wiki/$1 worfdb: description: WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends). example: T01B6.1 homepage: http://worfdb.dfci.harvard.edu/ keywords: - dna mappings: biocontext: WORFDB integbio: nbdc00738 miriam: worfdb n2t: worfdb ncbi: WorfDB prefixcommons: worfdb name: C. elegans ORFeome cloning project pattern: ^\w+(\.\d+)$ preferred_prefix: worfdb providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/worfdb:$1 uri_format: http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1 world2dpage: comment: This resource doesn't exist on the web anymore deprecated: true description: A public repository, standards compliant, for proteomics image data published in the literature. This repository currently contains data from 16 published articles, putting together 22 reference maps for 15 species, totalizing nearly 4'400 identified spots. example: '0020' homepage: http://world-2dpage.expasy.org/repository/ keywords: - 2d-page - protein - structure mappings: prefixcommons: world2dpage uniprot: DB-0121 name: The World-2DPAGE database preferred_prefix: world2dpage providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/world2dpage:$1 publications: - doi: 10.1016/j.jprot.2008.02.005 pubmed: '18617148' title: The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server year: 2008 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://world-2dpage.expasy.org/repository/$1 worldavatar.compchem: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Linked-data framework for connecting species in chemical kinetic reaction mechanisms with quantum calculations. A mechanism can be constructed from thermodynamic, reaction rate, and transport data that has been obtained either experimentally, computationally, or by a combination of both. In order to implement this approach, two existing ontologies, namely OntoKin, for representing chemical kinetic reaction mechanisms, and OntoCompChem, for representing quantum chemistry calculations, are extended. (from https://nfdi4cat.org/services/ontologie-sammlung/) download_owl: http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl homepage: https://como.ceb.cam.ac.uk/preprints/223/ keywords: - ontology name: Computational Chemistry Ontology no_own_terms: true preferred_prefix: worldavatar.compchem worldavatar.kin: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Represents chemical kinetic reaction mechanisms. download_owl: http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl example: ElementNumber homepage: http://www.theworldavatar.com/ontokin/ keywords: - ontology name: Ontology for Chemical Kinetic Reaction Mechanisms preferred_prefix: worldavatar.kin uri_format: http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#$1 wormbase: contact: email: todd@wormbase.org github: tharris name: Todd W Harris orcid: 0000-0003-3406-163X contributor_extras: - email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities. example: WBGene00000001 homepage: https://www.wormbase.org/ keywords: - anatomy - blast - c elegans - catalog - database - faseb list - gene - gene expression - gene function - gene mapping - gene prediction - geneotype - genome - genomic sequence - genomics - life science - ortholog - orthology assignment - phenotype - roundworm - transposon family - wormmart license: CC0-1.0 mappings: biocontext: WormBase biolink: WBVocab edam: '1805' fairsharing: FAIRsharing.zx1td8 go: WB_REF integbio: nbdc00740 miriam: wb n2t: wb ncbi: WormBase pathguide: '426' prefixcommons: wormbase re3data: r3d100010424 rrid: WB-STRAIN:WBStrain uniprot: DB-0110 wikidata: P3860 name: WormBase pattern: ^(CE[0-9]{5}|WB[A-Z][a-z]+\d+)$ preferred_prefix: WormBase providers: - code: agr description: WormBase through the Alliance of Genome Resources homepage: https://www.alliancegenome.org name: WormBase through the Alliance of Genome Resources uri_format: https://www.alliancegenome.org/gene/WB:$1 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/wormbase:$1 - code: wormbase.c_elegans description: Pages describing C. Elegans genes. homepage: http://www.wormbase.org name: WormBase C. Elegans Gene Portal uri_format: http://www.wormbase.org/species/c_elegans/gene/$1 publications: - doi: 10.1093/nar/gkz920 pmc: PMC7145598 pubmed: '31642470' title: 'WormBase: a modern Model Organism Information Resource' year: 2020 - doi: 10.1093/nar/gkx998 pmc: PMC5753391 pubmed: '29069413' title: 'WormBase 2017: molting into a new stage' year: 2018 - pubmed: '24194605' - doi: 10.1186/1471-2105-12-175 pmc: PMC3213741 pubmed: '21595960' title: 'Toward an interactive article: integrating journals and biological databases' year: 2011 - doi: 10.1093/nar/gkq1116 pmc: PMC3013707 pubmed: '21071413' title: 'The BioGRID Interaction Database: 2011 update' year: 2010 - doi: 10.1186/1471-2105-11-550 pmc: PMC2992068 pubmed: '21059240' title: Localizing triplet periodicity in DNA and cDNA sequences year: 2010 - doi: 10.1002/mrd.21130 pmc: PMC2830379 pubmed: '19921742' title: 'Representing ontogeny through ontology: a developmental biologist''s guide to the gene ontology' year: 2010 - doi: 10.1093/nar/gkp1018 pmc: PMC2808930 pubmed: '19920128' title: 'The Gene Ontology in 2010: extensions and refinements' year: 2009 - doi: 10.1093/nar/gkp952 pmc: PMC2808986 pubmed: '19910365' title: 'WormBase: a comprehensive resource for nematode research' year: 2009 - doi: 10.1186/1471-2105-10-228 pmc: PMC2719631 pubmed: '19622167' title: 'Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation' year: 2009 - doi: 10.1371/journal.pcbi.1000431 pmc: PMC2699109 pubmed: '19578431' title: 'The Gene Ontology''s Reference Genome Project: a unified framework for functional annotation across species' year: 2009 - doi: 10.1186/1471-2105-9-549 pmc: PMC2651883 pubmed: '19099578' title: nGASP--the nematode genome annotation assessment project year: 2008 - pubmed: '17991679' - pubmed: '15608221' - doi: 10.1093/nar/29.1.82 pmc: PMC29781 pubmed: '11125056' title: 'WormBase: network access to the genome and biology of Caenorhabditis elegans' year: 2001 synonyms: - WB - WB_REF - wb - wormbase twitter: wormbase uri_format: https://www.wormbase.org/get?name=$1 wormpep: description: Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project. example: CE28239 homepage: https://www.wormbase.org/db/seq/protein keywords: - protein - structure mappings: biocontext: WORMPEP miriam: wormpep n2t: wormpep prefixcommons: wormpep name: Wormpep pattern: ^CE\d{5}$ preferred_prefix: wormpep providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/wormpep:$1 uri_format: https://www.wormbase.org/db/seq/protein?name=$1 worms: contact: email: leen.vandepitte@vliz.be name: Leen Vandepitte orcid: 0000-0002-8160-7941 contributor_extras: - email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 description: The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts. example: '146421' homepage: http://www.marinespecies.org/ keywords: - biodiversity - environmental science - taxonomy mappings: bartoc: '720' biocontext: WORMS fairsharing: FAIRsharing.7g1bzj miriam: worms n2t: worms wikidata: P850 name: WoRMS-ID for taxa pattern: ^\d+$ preferred_prefix: worms publications: - doi: 10.1371/journal.pone.0194599 pmc: PMC5889062 pubmed: '29624577' title: 'A decade of the World Register of Marine Species - General insights and experiences from the Data Management Team: Where are we, what have we learned and how can we continue?' year: 2018 twitter: WRMarineSpecies uri_format: http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1 wos: description: 'unique academic work identifier assigned in Web of Science bibliographic database (Web of Science Core Collection only and do not include WOS: prefix)' example: 000177759000002 homepage: https://www.webofscience.com mappings: wikidata: P8372 name: Web of Science ID (work) preferred_prefix: wos references: - https://github.com/biopragmatics/bioregistry/issues/805 synonyms: - wosid - wosuid uri_format: https://www.webofscience.com/wos/woscc/full-record/WOS:$1 wos.researcher: description: identifier for a researcher in a system for scientific authors, redirects to a Web of Science ID, along with P3829 example: B-5720-2018 homepage: https://access.clarivate.com/login?app=wos mappings: wikidata: P1053 name: ResearcherID pattern: ^[A-Z]{1,3}-\d{4}-(19|20)\d\d$ preferred_prefix: wos.researcher uri_format: https://www.webofscience.com/wos/author/record/$1 wwf.ecoregion: comment: ENVO includes xrefs to this resource. See EnvironmentOntology/envo#658 contributor: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions. example: AT1402 github_request_issue: 153 homepage: https://www.worldwildlife.org/biomes mappings: wikidata: P1294 name: World Wildlife Fund Ecoregion pattern: ^AT\d+$ preferred_prefix: wwf.ecoregion reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - WWF uri_format: https://www.worldwildlife.org/ecoregions/$1 xao: appears_in: - xpo contact: email: Erik.Segerdell@cchmc.org github: seger name: Erik Segerdell orcid: 0000-0002-9611-1279 description: XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis. download_obo: http://purl.obolibrary.org/obo/xao.obo download_owl: http://purl.obolibrary.org/obo/xao.owl example: 0004486 homepage: http://www.xenbase.org/anatomy/xao.do?method=display keywords: - anatomy - developmental biology - life cycle - life cycle stage - life science - morphology - obo - ontology - structure license: CC-BY-3.0 mappings: aberowl: XAO bartoc: '581' biocontext: XAO bioportal: XAO fairsharing: FAIRsharing.17zapb obofoundry: xao ols: xao ontobee: XAO wikidata: P4495 name: Xenopus Anatomy Ontology pattern: ^\d{7}$ preferred_prefix: XAO publications: - doi: 10.1186/2041-1480-4-31 pmc: PMC3816597 pubmed: '24139024' title: 'Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase' year: 2013 - doi: 10.1186/1471-213x-8-92 pmc: PMC2561031 pubmed: '18817563' title: An ontology for Xenopus anatomy and development year: 2008 rdf_uri_format: http://purl.obolibrary.org/obo/XAO_$1 repository: https://github.com/xenopus-anatomy/xao uri_format: http://purl.obolibrary.org/obo/XAO_$1 version: '2024-09-03' xco: appears_in: - agro - ecto contact: email: jrsmith@mcw.edu github: jrsjrs name: Jennifer Smith orcid: 0000-0002-6443-9376 description: Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. download_obo: http://purl.obolibrary.org/obo/xco.obo download_owl: http://purl.obolibrary.org/obo/xco.owl example: 0000780 homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000 keywords: - assay - biomedical science - experimental condition - experimental measurement - experimentally determined - life science - measurement - obo - ontology - protocol - study design license: CC0-1.0 logo: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif mappings: aberowl: XCO biocontext: XCO bioportal: XCO fairsharing: FAIRsharing.x39h5y obofoundry: xco ols: xco ontobee: XCO prefixcommons: xco name: Experimental condition ontology pattern: ^\d{7}$ preferred_prefix: XCO providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/xco:$1 publications: - doi: 10.1186/2041-1480-4-26 pmc: PMC3882879 pubmed: '24103152' title: 'The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications' year: 2013 - doi: 10.3389/fgene.2012.00087 pmc: PMC3361058 pubmed: '22654893' title: Three ontologies to define phenotype measurement data year: 2012 rdf_uri_format: http://purl.obolibrary.org/obo/XCO_$1 repository: https://github.com/rat-genome-database/XCO-experimental-condition-ontology twitter: ratgenome uri_format: http://purl.obolibrary.org/obo/XCO_$1 version: '4.195' xenbase: contact: email: troy_pells@yahoo.ca github: pellst name: Troy Pells orcid: 0000-0002-2340-5356 description: Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions. example: XB-GENE-922462 homepage: https://www.xenbase.org/ keywords: - anatomy - cell biology - developmental biology - expression - functional genomics - genetics - genome - genomics - proteomics mappings: biocontext: Xenbase biolink: Xenbase edam: '2738' fairsharing: FAIRsharing.jrv6wj go: Xenbase miriam: xenbase n2t: xenbase ncbi: Xenbase prefixcommons: xenbase re3data: r3d100011331 uniprot: DB-0129 name: Xenbase pattern: ^XB\-\w+\-\d+$ preferred_prefix: xenbase providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/xenbase:$1 publications: - doi: 10.1186/s12859-022-04636-8 pmc: PMC8939077 pubmed: '35317743' title: 'The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development' year: 2022 - doi: 10.1093/nar/gkz933 pmc: PMC7145613 pubmed: '31733057' title: 'Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database' year: 2020 - doi: 10.3389/fphys.2019.00154 pmc: PMC6399412 pubmed: '30863320' title: 'Xenbase: Facilitating the Use of' year: 2019 - doi: 10.1007/978-1-4939-7737-6_10 pmc: PMC6853059 pubmed: '29761462' title: 'Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database' year: 2018 - doi: 10.1093/nar/gkx936 pmc: PMC5753396 pubmed: '29059324' title: 'Xenbase: a genomic, epigenomic and transcriptomic model organism database' year: 2018 - doi: 10.1016/j.ydbio.2016.03.030 pmc: PMC5045824 pubmed: '27039265' title: Xenopus genomic data and browser resources year: 2016 - doi: 10.1093/database/bau108 pmc: PMC4224262 pubmed: '25380782' title: 'The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud' year: 2014 - doi: 10.1093/nar/gku956 pmc: PMC4384024 pubmed: '25313157' title: Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes year: 2014 - doi: 10.1186/2041-1480-4-31 pmc: PMC3816597 pubmed: '24139024' title: 'Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase' year: 2013 - doi: 10.1093/nar/gkp953 pmc: PMC2808955 pubmed: '19884130' title: 'Xenbase: gene expression and improved integration' year: 2009 - doi: doi:10.3389/fphys.2019.00154 title: 'Xenbase: Facilitating the Use of Xenopus to Model Human Disease.' - doi: doi:10.1007/978-1-4939-7737-6_10. title: 'Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.' synonyms: - Xenbase twitter: Xenbase uri_format: https://www.xenbase.org/entry/$1 ximbio: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Cell line collections (Providers) example: '151022' homepage: https://ximbio.com mappings: cellosaurus: Ximbio name: Ximbio pattern: ^\d+$ preferred_prefix: ximbio uri_format: https://ximbio.com/reagent/$1 xl: deprecated: true description: A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry. homepage: http://www.psidev.info/groups/controlled-vocabularies mappings: aberowl: XL biocontext: XL ols: xl ontobee: XL name: Cross-linker reagents ontology preferred_prefix: xl xlmod: contact: email: gerhard.mayer@rub.de github: germa name: Gerhard Mayer orcid: 0000-0002-1767-2343 description: A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry. download_obo: http://purl.obolibrary.org/obo/xlmod.obo download_owl: http://purl.obolibrary.org/obo/xlmod.owl example: '00050' homepage: http://www.psidev.info/groups/controlled-vocabularies keywords: - chemical biology - experimental measurement - mass spectrometry assay - mass spectrum - metabolomics - obo - omics - ontology license: CC-BY-3.0 mappings: aberowl: XLMOD bioportal: XLMOD fairsharing: FAIRsharing.6ccbe6 obofoundry: xlmod ols: xlmod ontobee: XLMOD name: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary pattern: ^\d{5}$ preferred_prefix: XLMOD rdf_uri_format: http://purl.obolibrary.org/obo/XLMOD_$1 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/ keywords: - subject agnostic mappings: biocontext: xml fairsharing: FAIRsharing.b5cc91 name: Extensible Markup Language preferred_prefix: xml uri_format: http://www.w3.org/XML/1998/namespace#$1 xpo: contact: email: Erik.Segerdell@cchmc.org github: seger name: Erik Segerdell orcid: 0000-0002-9611-1279 depends_on: - bfo - chebi - cl - go - iao - pato - ro - xao description: XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis. download_obo: http://purl.obolibrary.org/obo/xpo.obo download_owl: http://purl.obolibrary.org/obo/xpo.owl example: '0100002' homepage: https://github.com/obophenotype/xenopus-phenotype-ontology keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: XPO biolink: XPO bioportal: XPO obofoundry: xpo ols: xpo ontobee: XPO name: Xenopus Phenotype Ontology pattern: ^\d+$ preferred_prefix: XPO publications: - doi: 10.1186/s12859-022-04636-8 pmc: PMC8939077 pubmed: '35317743' title: 'The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development' year: 2022 rdf_uri_format: http://purl.obolibrary.org/obo/XPO_$1 repository: https://github.com/obophenotype/xenopus-phenotype-ontology uri_format: http://purl.obolibrary.org/obo/XPO_$1 version: '2024-04-18' xsd: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 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 keywords: - w3c rec mappings: biocontext: xsd lov: xsd zazuko: xsd name: XML Schema Definition preferred_prefix: xsd uri_format: http://www.w3.org/2001/XMLSchema#$1 xuo: appears_in: - hsapdv contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: XUO preferred_prefix: xuo ydpm: description: The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition. example: YAL001C homepage: http://www-deletion.stanford.edu/YDPM/ keywords: - protein mappings: biocontext: YDPM miriam: ydpm n2t: ydpm prefixcommons: ydpm name: Yeast Deletion and the Mitochondrial Proteomics Project pattern: ^Y[A-Z]{2}\d+[CW]$ preferred_prefix: ydpm providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ydpm:$1 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 yeastract: contact: email: isacorreia@tecnico.ulisboa.pt name: Isabel Sá-Correia orcid: 0000-0003-2208-5183 description: YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references. example: YBR125c homepage: http://www.yeastract.com keywords: - dna - gene - life science - regulation - small molecule mappings: fairsharing: FAIRsharing.mphj4z pathguide: '205' prefixcommons: yeastract name: Yeast Searching for Transcriptional Regulators and Consensus Tracking preferred_prefix: yeastract providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/yeastract:$1 publications: - doi: 10.1093/nar/gkt1015 pmc: PMC3965121 pubmed: '24170807' title: 'The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae' year: 2013 - doi: 10.1093/nar/gkq964 pmc: PMC3013800 pubmed: '20972212' title: 'YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface' year: 2010 - doi: 10.1093/nar/gkm976 pmc: PMC2238916 pubmed: '18032429' title: 'YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae' year: 2007 - doi: 10.1093/nar/gkj013 pmc: PMC1347376 pubmed: '16381908' title: 'The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae' year: 2006 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://www.yeastract.com/view.php?existing=locus&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 ygob: comment: This resource doesn't exist on the web anymore deprecated: true description: YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes. example: ADH1 homepage: http://wolfe.gen.tcd.ie/ygob keywords: - gene - genome mappings: prefixcommons: ygob name: Yeast Genome Order Browser preferred_prefix: ygob providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/ygob:$1 provides: hgnc.symbol reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene=$1 yid: description: The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521]. example: SNR17A homepage: http://compbio.soe.ucsc.edu/yeast_introns.html mappings: biocontext: YID miriam: yid n2t: yid name: Yeast Intron Database v3 pattern: ^[A-Z0-9]+$ preferred_prefix: yid uri_format: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1 ymdb: contact: email: david.wishart@ualberta.ca github: DavidWishartLab name: David S. Wishart orcid: 0000-0002-3207-2434 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast). example: YMDB00001 homepage: http://www.ymdb.ca keywords: - life science - metabolomics mappings: fairsharing: FAIRsharing.tawpg2 pathguide: '388' re3data: r3d100012733 name: Yeast Metabolome Database pattern: ^YMDB\d+$ preferred_prefix: ymdb publications: - doi: 10.1093/nar/gkr916 pmc: PMC3245085 pubmed: '22064855' title: 'YMDB: the Yeast Metabolome Database' year: 2011 twitter: WishartLab uri_format: http://www.ymdb.ca/compounds/$1 ypo: contact: email: cherry@genome.stanford.edu name: Mike Cherry orcid: 0000-0001-9163-5180 deprecated: true homepage: http://www.yeastgenome.org/ keywords: - obo - ontology mappings: biocontext: YPO obofoundry: ypo name: Yeast Phenotype Ontology preferred_prefix: YPO rdf_uri_format: http://purl.obolibrary.org/obo/YPO_$1 uri_format: http://purl.obolibrary.org/obo/YPO_$1 yrcpdr: contact: email: mriffle@u.washington.edu name: Michael Riffle orcid: 0000-0003-1633-8607 description: The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions. example: '2673500' homepage: http://www.yeastrc.org/pdr/ keywords: - computational biology - life science - protein mappings: biocontext: YRCPDR fairsharing: FAIRsharing.karvzj miriam: yrcpdr n2t: yrcpdr prefixcommons: yrc re3data: r3d100010975 name: YRC PDR pattern: ^\d+$ preferred_prefix: yrcpdr providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/yrc:$1 uri_format: http://yeastrc.org/pdr/viewProtein.do?id=$1 zazuko: contact: email: ktk@netlabs.org github: ktk name: Adrian Gschwend orcid: 0000-0002-2079-9636 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This service fills a gap between services like prefix.cc and LOV or looking up the original vocabulary specification. Not all vocabularies (or schema or ontology, whatever you want to call them) provide an HTML view. If you resolve some of the common prefixes all you get back is some RDF serialization which is not ideal. (from ) example: frbr homepage: https://prefix.zazuko.com/ license: MIT name: Zazuko Prefix Server preferred_prefix: zazuko uri_format: 'https://prefix.zazuko.com/prefix/$1:' zea: contact: email: Leszek@missouri.edu name: Leszek Vincent orcid: 0000-0002-9316-2919 deprecated: true description: Maize gross anatomy download_obo: http://aber-owl.net/media/ontologies/ZEA/2/zea.obo example: '0015177' homepage: http://www.maizemap.org/ keywords: - anatomy - maize - obo - ontology mappings: aberowl: ZEA biocontext: ZEA bioportal: ZEA obofoundry: zea prefixcommons: zea name: Maize gross anatomy pattern: ^\d{7}$ preferred_prefix: ZEA providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/zea:$1 rdf_uri_format: http://purl.obolibrary.org/obo/ZEA_$1 uri_format: http://purl.obolibrary.org/obo/ZEA_$1 zeco: appears_in: - mco contact: email: ybradford@zfin.org github: ybradford name: Yvonne Bradford orcid: 0000-0002-9900-7880 description: Ontology of Zebrafish Experimental Conditions download_json: http://purl.obolibrary.org/obo/zeco.json download_obo: http://purl.obolibrary.org/obo/zeco.obo download_owl: http://purl.obolibrary.org/obo/zeco.owl example: '0000171' homepage: https://github.com/ybradford/zebrafish-experimental-conditions-ontology keywords: - allele - animal physiology - bibliography - developmental biology - disease process modeling - expression data - gene - genetics - genome - genomics - model organism - mutation - obo - ontology - phenotype license: CC-BY-3.0 mappings: aberowl: ZECO biocontext: ZECO bioportal: ZECO fairsharing: FAIRsharing.np2wfz obofoundry: zeco ols: zeco ontobee: ZECO name: Zebrafish Experimental Conditions Ontology pattern: ^\d{7}$ preferred_prefix: ZECO rdf_uri_format: http://purl.obolibrary.org/obo/ZECO_$1 repository: https://github.com/ybradford/zebrafish-experimental-conditions-ontology uri_format: http://purl.obolibrary.org/obo/ZECO_$1 version: '2022-02-14' zenodo.record: contact: email: lars.holm.nielsen@cern.ch name: Lars Holm Nielsen orcid: 0000-0001-8135-3489 contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: Zenodo is an open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts. example: '4390079' github_request_issue: 454 homepage: https://zenodo.org keywords: - data management - subject agnostic mappings: fairsharing: FAIRsharing.wy4egf integbio: nbdc02187 re3data: r3d100010468 wikidata: P4901 name: Zenodo pattern: ^\d+$ preferred_prefix: zenodo.record reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - zenodo twitter: zenodo_org uri_format: https://zenodo.org/record/$1 zfa: appears_in: - zp contact: email: van_slyke@zfin.org github: cerivs name: Ceri Van Slyke orcid: 0000-0002-2244-7917 description: ZFA description. download_json: http://purl.obolibrary.org/obo/zfa.json download_obo: http://purl.obolibrary.org/obo/zfa.obo download_owl: http://purl.obolibrary.org/obo/zfa.owl example: 0005926 homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources keywords: - anatomy - developmental biology - life cycle - life cycle stage - life science - morphology - obo - ontology - structure - zebrafish license: CC-BY-3.0 mappings: aberowl: ZFA biocontext: ZFA bioportal: ZFA fairsharing: FAIRsharing.s3r6sk obofoundry: zfa ols: zfa ontobee: ZFA prefixcommons: zfa name: Zebrafish anatomy and development ontology pattern: ^\d{7}$ preferred_prefix: ZFA providers: - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/zfa:$1 publications: - doi: 10.1186/2041-1480-5-12 pmc: PMC3944782 pubmed: '24568621' title: 'The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio' year: 2014 rdf_uri_format: http://purl.obolibrary.org/obo/ZFA_$1 repository: https://github.com/cerivs/zebrafish-anatomical-ontology synonyms: - ZFA_RETIRED uri_format: http://purl.obolibrary.org/obo/ZFA_$1 version: '2025-01-28' zfin: contact: email: dhowe@zfin.org name: Doug Howe orcid: 0000-0001-5831-7439 description: ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN. example: ZDB-GENE-041118-11 homepage: http://zfin.org keywords: - adult - animal physiology - antibody - cdna - developmental biology - embryo - expressed sequence tag - fish - gene - genetics - genome - genomics - pathology - research - zebrafish - zebrafish line license: CC-BY-4.0 mappings: biocontext: ZFIN fairsharing: FAIRsharing.ybxnhg go: ZFIN integbio: nbdc00746 miriam: zfin n2t: zfin ncbi: ZFIN prefixcommons: zfin re3data: r3d100010421 rrid: ZIRC uniprot: DB-0113 wikidata: P3870 name: Zebrafish Information Network Gene pattern: ^ZDB\-\w+\-\d+\-\d+$ preferred_prefix: zfin providers: - 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 - code: bio2rdf description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. homepage: https://bio2rdf.org name: Bio2RDF uri_format: http://bio2rdf.org/zfin:$1 publications: - doi: 10.1093/nar/gky1090 pmc: PMC6323962 pubmed: '30407545' title: 'The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources' year: 2019 - doi: 10.1093/nar/gks938 pubmed: '23074187' title: 'ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics' - doi: 10.1016/b978-0-12-374814-0.00017-3 pubmed: '21924170' title: Data extraction, transformation, and dissemination through ZFIN - doi: 10.1093/nar/gkq1077 pubmed: '21036866' title: 'ZFIN: enhancements and updates to the Zebrafish Model Organism Database' - doi: 10.1002/0471250953.bi0118s31. pubmed: '20836073' title: Exploring zebrafish genomic, functional and phenotypic data using ZFIN - doi: 10.1093/nar/gkm956 pmc: PMC2238839 pubmed: '17991680' title: 'The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes' year: 2007 - doi: 10.1093/nar/gkj086 pubmed: '16381936' title: 'The Zebrafish Information Network: the zebrafish model organism database' - doi: 10.1093/nar/gkg027 pubmed: '12519991' title: 'The Zebrafish Information Network (ZFIN): the zebrafish model organism database' - doi: 10.1016/s0168-9525(99)01741-2 pubmed: '10354586' title: Zebrafish in the Net - doi: 10.1016/B978-0-12-374814-0.00017-3 title: Data extraction, transformation, and dissemination through ZFIN. synonyms: - ZFIN twitter: zfinmod uri_format: http://zfin.org/$1 zfs: contact: email: van_slyke@zfin.org github: cerivs name: Ceri Van Slyke orcid: 0000-0002-2244-7917 description: Developmental stages of the Zebrafish download_obo: http://purl.obolibrary.org/obo/zfs.obo download_owl: http://purl.obolibrary.org/obo/zfs.owl example: '0000050' homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources keywords: - aging - anatomy - developmental biology - life cycle - marine biology - obo - ontology - zoology license: CC-BY-3.0 mappings: aberowl: ZFS biocontext: ZFS bioportal: ZFS fairsharing: FAIRsharing.bc8ayj obofoundry: zfs ols: zfs ontobee: ZFS name: Zebrafish developmental stages ontology pattern: ^\d{7}$ preferred_prefix: ZFS rdf_uri_format: http://purl.obolibrary.org/obo/ZFS_$1 repository: https://github.com/cerivs/zebrafish-anatomical-ontology uri_format: http://purl.obolibrary.org/obo/ZFS_$1 version: '2020-03-10' zinc: description: ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. example: ZINC1084 homepage: http://zinc15.docking.org/ mappings: biocontext: ZINC miriam: zinc n2t: zinc re3data: r3d100010372 wikidata: P2084 name: ZINC is not Commercial pattern: ^(ZINC)?\d+$ preferred_prefix: zinc uri_format: http://zinc15.docking.org/substances/$1 zp: contact: email: ybradford@zfin.org github: ybradford name: Yvonne Bradford orcid: 0000-0002-9900-7880 depends_on: - bfo - bspo - go - pato - ro - uberon - zfa description: The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism. download_obo: http://purl.obolibrary.org/obo/zp.obo download_owl: http://purl.obolibrary.org/obo/zp.owl example: 0019030 homepage: https://github.com/obophenotype/zebrafish-phenotype-ontology keywords: - obo - ontology license: CC-BY-3.0 mappings: aberowl: ZP biocontext: ZP bioportal: ZP obofoundry: zp ols: zp ontobee: ZP name: Zebrafish Phenotype Ontology pattern: ^\d+$ preferred_prefix: ZP rdf_uri_format: http://purl.obolibrary.org/obo/ZP_$1 repository: https://github.com/obophenotype/zebrafish-phenotype-ontology uri_format: http://purl.obolibrary.org/obo/ZP_$1 version: '2024-04-18'