3dmet: fairsharing: abbreviation: 3DMET description: 3DMET is a database of three-dimensional structures of natural metabolites. id: '1999' name: Three-Dimensional Structure Database of Natural Metabolites prefix: FAIRsharing.5ab0n7 subjects: - Life Science - Metabolomics mappings: fairsharing: FAIRsharing.5ab0n7 miriam: 3dmet n2t: 3dmet prefixcommons: 3DMET miriam: deprecated: false description: 3DMET is a database collecting three-dimensional structures of natural metabolites. homepage: http://www.3dmet.dna.affrc.go.jp/ id: '00000066' name: 3DMET namespaceEmbeddedInLui: false pattern: ^B\d{5}$ prefix: 3dmet sampleId: B00162 uri_format: http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1 n2t: description: 3DMET is a database collecting three-dimensional structures of natural metabolites. example: B00162 homepage: http://www.3dmet.dna.affrc.go.jp/ name: 3DMET database namespaceEmbeddedInLui: false pattern: ^B\d{5}$ prefix: 3dmet uri_format: http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1 name: 3D Metabolites prefixcommons: is_identifiers: true is_obo: false prefix: 3DMET uri_format: http://identifiers.org/3dmet/$1 wikidata: database: Q23948774 prefix: P2796 4dn.biosource: cellosaurus: category: Biological sample resources homepage: https://data.4dnucleome.org/ name: 4D Nucleome Data Portal prefix: 4DN uri_format: https://data.4dnucleome.org/biosources/$1 example: 4DNSR73BT2A2 fairsharing: abbreviation: 4DN description: The 4D Nucleome Data Portal (4DN) hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization. It is a platform to search, visualize, and download nucleomics data. id: '2771' name: 4DNucleome Data Portal prefix: FAIRsharing.CugtbQ subjects: - Life Science homepage: https://data.4dnucleome.org/biosources mappings: cellosaurus: 4DN fairsharing: FAIRsharing.CugtbQ miriam: 4dn miriam: deprecated: false description: The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases. homepage: https://data.4dnucleome.org/ id: 00000833 name: 4D Nucleome namespaceEmbeddedInLui: false pattern: ^4DN[A-Z]{2}[A-Z0-9]{7}$ prefix: 4dn sampleId: 4DNES265ETYQ uri_format: https://data.4dnucleome.org/$1 name: 4D Nucleome Data Portal Biosource synonyms: - 4DN uri_format: https://data.4dnucleome.org/biosources/$1 wikidata: database: Q110613621 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 Mich\xE1n Aguirre" orcid: 0000-0002-5798-662X - email: mineromero2901@ciencias.unam.mx github: MinRo60 name: "Minerva Mar\xEDa Romero P\xE9rez" orcid: 0000-0002-6240-9325 - email: victorinolavida@ciencias.unam.mx github: Victorinolavida name: "Jos\xE9 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 uri_format: https://data.4dnucleome.org/experiment-set-replicates/$1 wikidata: database: Q110613797 aao: description: A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon. fairsharing: abbreviation: AAO description: A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO has been integrated into Uberon. id: '876' name: Amphibian gross Anatomy Ontology prefix: FAIRsharing.mxx5rp mappings: fairsharing: FAIRsharing.mxx5rp obofoundry: aao prefixcommons: AAO no_own_terms: true obofoundry: contact: david.c.blackburn@gmail.com contact.label: David Blackburn deprecated: true homepage: http://github.com/seger/aao inactive: true name: Amphibian gross anatomy prefix: aao prefixcommons: is_identifiers: false is_obo: true prefix: AAO uri_format: http://purl.obolibrary.org/obo/AAO_$1 abcd: cellosaurus: category: Biological sample resources homepage: https://web.expasy.org/abcd/ name: AntiBodies Chemically Defined database prefix: ABCD uri_format: https://web.expasy.org/abcd/$1 description: The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies example: AD834 fairsharing: abbreviation: ABCD description: The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies. id: '2969' name: ABCD database prefix: FAIRsharing.Z8OKi5 subjects: - Molecular biology - Immunology homepage: https://web.expasy.org/abcd/ mappings: cellosaurus: ABCD fairsharing: FAIRsharing.Z8OKi5 uniprot: ABCD name: AntiBodies Chemically Defined database uniprot: category: Protocols and materials databases identifier: '236' link_is_explicit: 'true' name: ABCD curated depository of sequenced antibodies prefix: ABCD uri_format: https://web.expasy.org/cgi-bin/abcd/search_abcd.pl?input=$1 uri_format: https://web.expasy.org/abcd/ABCD_$1 abm: cellosaurus: category: Cell line collections homepage: https://www.abmgood.com/Cell-Biology.html name: Applied Biological Materials cell line products prefix: ABM uri_format: https://www.abmgood.com/catalogsearch/result/?cat=&q=$1 example: T0599 mappings: cellosaurus: ABM abs: fairsharing: abbreviation: ABS description: ABS is a database of Annotated regulatory Binding Sites from known binding sites identified in promoters of orthologous vertebrate genes. id: '1899' name: Annotated regulatory Binding Sites from Orthologous Promoters prefix: FAIRsharing.7mnebr subjects: - Biology mappings: fairsharing: FAIRsharing.7mnebr miriam: abs n2t: abs prefixcommons: ABS miriam: deprecated: false description: The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. homepage: http://genome.crg.es/datasets/abs2005/ id: '00000277' name: ABS namespaceEmbeddedInLui: false pattern: ^A\d+$ prefix: abs sampleId: A0014 uri_format: http://genome.crg.es/datasets/abs2005/entries/$1.html n2t: description: The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. example: A0014 homepage: http://genome.crg.es/datasets/abs2005/ name: ABS at IMIM namespaceEmbeddedInLui: false pattern: ^A\d+$ prefix: abs uri_format: http://genome.crg.es/datasets/abs2005/entries/$1.html name: Annotated Regulatory Binding Sites prefixcommons: is_identifiers: true is_obo: false prefix: ABS uri_format: http://identifiers.org/abs/$1 wikidata: database: Q111134507 ac: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Activity Streams is an open format specification for activity stream protocols, which are used to syndicate activities taken in social web applications and services, similar to those in Facebook's, Instagram's, and Twitter's. The standard provides a general way to represent activities. example: Add homepage: http://www.w3.org/ns/activitystreams name: Activity Streams uri_format: http://www.w3.org/ns/activitystreams#$1 aceview.worm: mappings: miriam: aceview.worm n2t: aceview.worm prefixcommons: ACEVIEW.WORM miriam: deprecated: false description: AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression. homepage: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm id: 00000282 name: Aceview Worm namespaceEmbeddedInLui: false pattern: ^[a-z0-9-]+$ prefix: aceview.worm sampleId: aap-1 uri_format: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1 n2t: description: AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression. example: aap-1 homepage: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm name: AceView Worm at NCBI namespaceEmbeddedInLui: false pattern: ^[a-z0-9-]+$ prefix: aceview.worm uri_format: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1 prefixcommons: is_identifiers: true is_obo: false prefix: ACEVIEW.WORM uri_format: http://identifiers.org/aceview.worm/$1 addexbio: cellosaurus: category: Cell line collections homepage: https://www.addexbio.com/productshow?id=4 name: AddexBio cell line products prefix: AddexBio uri_format: https://www.addexbio.com/productdetail?pid=$1 example: C0020004/4992 mappings: cellosaurus: AddexBio addgene: fairsharing: abbreviation: Addgene description: Addgene is a non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Addgene are working with thousands of laboratories to assemble a high-quality library of published plasmids for use in research and discovery. By linking plasmids with articles, scientists can always find data related to the materials they request. id: '1738' name: Addgene prefix: FAIRsharing.8hcczk subjects: - Life Science mappings: fairsharing: FAIRsharing.8hcczk miriam: addgene n2t: addgene miriam: deprecated: false description: Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world. homepage: http://addgene.org/ id: '00000675' name: Addgene Plasmid Repository namespaceEmbeddedInLui: false pattern: ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$ prefix: addgene sampleId: '50943' uri_format: http://addgene.org/$1 n2t: description: Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world. example: '50943' homepage: http://addgene.org/ name: Addgene Plasmid Repository namespaceEmbeddedInLui: false pattern: ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$ prefix: addgene uri_format: http://addgene.org/$1 adw: bioportal: name: Animal Natural History and Life History Ontology prefix: ADW fairsharing: abbreviation: ADW description: An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities. id: '1038' name: Animal natural history and life history prefix: FAIRsharing.t9fvdn mappings: bioportal: ADW fairsharing: FAIRsharing.t9fvdn miriam: adw n2t: adw obofoundry: adw prefixcommons: ADW miriam: deprecated: false description: Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology. homepage: https://animaldiversity.org/ id: 00000492 name: Animal Diversity Web namespaceEmbeddedInLui: false pattern: ^[A-Z_a-z]+$ prefix: adw sampleId: Lycalopex_vetulus uri_format: https://animaldiversity.org/accounts/$1/ n2t: description: Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology. example: Lycalopex_vetulus homepage: https://animaldiversity.org/ name: Animal Diversity Web at University of Michigan namespaceEmbeddedInLui: false pattern: ^[A-Z_a-z]+$ prefix: adw uri_format: https://animaldiversity.org/accounts/$1/ obofoundry: contact: adw_geeks@umich.edu contact.label: Animal Diversity Web technical staff deprecated: true homepage: http://www.animaldiversity.org inactive: true name: Animal natural history and life history prefix: adw prefixcommons: is_identifiers: false is_obo: true prefix: ADW uri_format: http://purl.obolibrary.org/obo/ADW_$1 uri_format: https://animaldiversity.org/accounts/$1 aeo: bioportal: name: Anatomical Entity Ontology prefix: AEO download_obo: https://raw.githubusercontent.com/obophenotype/human-developmental-anatomy-ontology/master/src/ontology/aeo.obo example: '0001017' fairsharing: abbreviation: AEO description: The AEO ontology of anatomical structures is a resource to facilitate the increase in knowledge in anatomy ontologies, supporting annotation and enabling compatibility with other anatomy ontologies. The ontology can be used to classify most organisms as its terms are appropriate for most plant and fungal tissues. It is envisaged that in future the ontology will include more non-animal anatomical terms. id: '1175' name: Anatomical Entity Ontology prefix: FAIRsharing.93ee19 subjects: - Anatomy - Life Science mappings: bioportal: AEO fairsharing: FAIRsharing.93ee19 obofoundry: aeo ols: aeo ontobee: AEO prefixcommons: AEO obofoundry: appears_in: - ehdaa2 contact: J.Bard@ed.ac.uk contact.label: Jonathan Bard deprecated: false description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology download.owl: http://purl.obolibrary.org/obo/aeo.owl homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/ inactive: true license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Anatomical Entity Ontology preferredPrefix: AEO prefix: aeo repository: https://github.com/obophenotype/human-developmental-anatomy-ontology ols: description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology download: http://purl.obolibrary.org/obo/aeo.owl homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/ name: Anatomical Entity Ontology prefix: aeo version: '2014-12-05' version.iri: http://purl.obolibrary.org/obo/aeo/releases/2014-12-05/aeo.owl ontobee: library: Library name: Anatomical Entity Ontology prefix: AEO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: AEO uri_format: http://purl.obolibrary.org/obo/AEO_$1 synonyms: - AEO_RETIRED aero: bioportal: name: Adverse Event Reporting Ontology prefix: AERO example: '0000125' fairsharing: abbreviation: AERO description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events. id: '221' name: Adverse Event Reporting ontology prefix: FAIRsharing.rycy2x mappings: bioportal: AERO fairsharing: FAIRsharing.rycy2x obofoundry: aero prefixcommons: AERO obofoundry: contact: mcourtot@gmail.com contact.label: Melanie Courtot contact.orcid: 0000-0002-9551-6370 deprecated: true description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events download.owl: http://purl.obolibrary.org/obo/aero.owl homepage: http://purl.obolibrary.org/obo/aero inactive: true license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Adverse Event Reporting Ontology prefix: aero pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: AERO uri_format: http://purl.obolibrary.org/obo/AERO_$1 affy.probeset: mappings: miriam: affy.probeset n2t: affy.probeset prefixcommons: AFFY.PROBESET miriam: deprecated: false 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. homepage: http://www.affymetrix.com/ id: 00000394 name: Affymetrix Probeset namespaceEmbeddedInLui: false pattern: \d{4,}((_[asx])?_at)? 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 sampleId: 243002_at uri_format: https://www.affymetrix.com/LinkServlet?probeset=$1 n2t: 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/ name: Affymetrix ProbeSet in Santa Clara namespaceEmbeddedInLui: false pattern: \d{4,}((_[asx])?_at)? prefix: affy.probeset uri_format: https://www.affymetrix.com/LinkServlet?probeset=$1 prefixcommons: is_identifiers: true is_obo: false prefix: AFFY.PROBESET uri_format: http://identifiers.org/affy.probeset/$1 afo: bioportal: name: Allotrope Merged Ontology Suite prefix: AFO fairsharing: abbreviation: AFO description: The Agriculture and Forestry Ontology (AFO), also known as the Agriforest Ontology, combines the concepts of the Agriforest Thesaurus with The Finnish General Upper Ontology (YSO). This combination of ontologies can be used for describing resources especially in domain of agriculture, forestry, veterinary medicine, food science, environmental science and biology. id: '924' name: Agriculture and Forestry Ontology prefix: FAIRsharing.595710 subjects: - Environmental Science - Forest Management - Agricultural Engineering - Agriculture - Veterinary Medicine - Food Chemistry - Biology homepage: https://www.allotrope.org/ mappings: bioportal: AFO fairsharing: FAIRsharing.595710 ols: afo no_own_terms: true ols: description: Allotrope Merged Ontology Suite download: http://afo-ols.semanticsfirst.com/ontologies/afo name: Allotrope Merged Ontology Suite prefix: afo version: '2019-05-10' version.iri: http://purl.allotrope.org/voc/afo/merged-OLS/REC/2019/05/10 aftol.taxonomy: contributor_extras: - email: laylamichan@ciencias.unam.mx github: lmichan name: "Layla Mich\xE1n Aguirre" orcid: 0000-0002-5798-662X homepage: https://aftol.umn.edu mappings: miriam: aftol.taxonomy n2t: aftol.taxonomy prefixcommons: AFTOL.TAXONOMY miriam: deprecated: false description: The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species. homepage: http://aftol.org/data.php id: '00000411' name: AFTOL namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: aftol.taxonomy sampleId: '959' uri_format: http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1 n2t: description: The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species. example: '959' homepage: http://aftol.org/data.php name: AFTOL at University of Minnesota namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: aftol.taxonomy uri_format: http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1 name: Assembling the Fungal Tree of Life - Taxonomy prefixcommons: is_identifiers: true is_obo: false prefix: AFTOL.TAXONOMY uri_format: http://identifiers.org/aftol.taxonomy/$1 agricola: contributor_extras: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 - email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 go: homepage: http://agricola.nal.usda.gov/ name: AGRICultural OnLine Access prefix: AGRICOLA_ID mappings: go: AGRICOLA_ID miriam: agricola n2t: agricola prefixcommons: AGRICOLA miriam: deprecated: false description: AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century. homepage: http://agricola.nal.usda.gov/ id: 00000589 name: AGRICOLA namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: agricola sampleId: '50018' uri_format: http://ddr.nal.usda.gov/dspace/handle/10113/$1 n2t: description: AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century. example: '50018' homepage: http://agricola.nal.usda.gov/ name: AGRICOLA at National Agricultural Library namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: agricola uri_format: http://ddr.nal.usda.gov/dspace/handle/10113/$1 name: Agricultural Online Access prefixcommons: is_identifiers: true is_obo: false prefix: AGRICOLA uri_format: http://identifiers.org/agricola/$1 synonyms: - AGR - AGRICOLA_ID uri_format: https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1 agro: bioportal: name: AGRonomy Ontology prefix: AGRO download_obo: https://raw.githubusercontent.com/KrishnaTO/agro/master/agro.obo example: '00020007' fairsharing: abbreviation: AgrO description: AgrO, the Agronomy Ontology, describes agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments. AgrO is being built by CGIAR using traits identified by agronomists, the ICASA variables, and other existing ontologies such as ENVO, UO, and PATO. It will complement existing crop, livestock, and fish ontologies to enable harmonized approaches to data collection, facilitating easier data sharing and reuse. A key use case for AgrO is the Agronomy Field Information Management System (AgroFIMS). AgroFIMS enables digital collection of agronomic data that is semantically described a priori with agronomic terms from AgrO. id: '714' name: Agronomy Ontology prefix: FAIRsharing.m40bhw subjects: - Farming Systems Research - Plant Breeding - Agronomy - Agriculture mappings: bioportal: AGRO fairsharing: FAIRsharing.m40bhw obofoundry: agro ols: agro ontobee: AGRO prefixcommons: AGRO obofoundry: contact: m.a.laporte@cgiar.org contact.github: marieALaporte contact.label: "Marie-Ang\xE9lique Laporte" contact.orcid: 0000-0002-8461-9745 depends_on: - bfo - envo - foodon - go - iao - ncbitaxon - obi - pato - peco - po - ro - to - uo - xco deprecated: false description: Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments download.owl: http://purl.obolibrary.org/obo/agro.owl homepage: https://github.com/AgriculturalSemantics/agro inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Agronomy Ontology preferredPrefix: AGRO prefix: agro publications: - id: http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf title: 'Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics.' repository: https://github.com/AgriculturalSemantics/agro ols: description: AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities download: http://purl.obolibrary.org/obo/agro.owl homepage: https://github.com/AgriculturalSemantics/agro name: Agronomy Ontology prefix: agro version: '2021-11-05' version.iri: http://purl.obolibrary.org/obo/agro/releases/2021-11-05/agro.owl ontobee: library: Library name: Agronomy Ontology prefix: AGRO pattern: ^\d{8}$ prefixcommons: is_identifiers: false is_obo: true prefix: AGRO uri_format: http://purl.obolibrary.org/obo/AGRO_$1 agrovoc: description: AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages. example: '2842' fairsharing: abbreviation: AGROVOC description: AGROVOC is a controlled vocabulary covering all areas of interest of the Food and Agriculture Organization (FAO) of the United Nations, including food, nutrition, agriculture, fisheries, forestry, environment etc. It is published by FAO and edited by a community of experts. AGROVOC consists of over 40,100 concepts available in up to 41 languages. AGROVOC uses semantic web technologies, linking to other multilingual knowledge organization systems and building bridges between datasets. Your library can use AGROVOC to index its documents or datasets, or you can use it from inside your content management system (e.g., Drupal) to organize your documents or web site. You can also use AGROVOC as an hub to access many other vocabularies available on the web. To date, AGROVOC is used by researchers, librarians and information managers for indexing, retrieving and organizing data in agricultural information systems and Web pages. Currently, AGROVOC is an SKOS-XL concept scheme and a Linked Open Data (LOD*) set aligned with over 20 other multilingual knowledge organization systems related to agriculture. You may browse AGROVOC, access its Web Services or SPARQL endpoint. id: '399' name: AGROVOC prefix: FAIRsharing.anpj91 subjects: - Botany - Fisheries Science - Environmental Science - Forest Management - Data Management - Agriculture - Nutritional Science homepage: https://data.apps.fao.org/catalog/organization/agrovoc mappings: fairsharing: FAIRsharing.anpj91 name: Agronomy Vocabulary pattern: ^[a-z0-9]+$ references: - http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_core.nt.zip - http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_lod.nt.zip - https://en.wikipedia.org/wiki/AGROVOC uri_format: http://aims.fao.org/aos/agrovoc/c_$1 aism: bioportal: name: Ontology for the Anatomy of the Insect SkeletoMuscular system prefix: AISM example: '0000027' mappings: bioportal: AISM obofoundry: aism ols: aism ontobee: AISM name: Ontology for the Anatomy of the Insect SkeletoMuscular system obofoundry: appears_in: - colao - lepao contact: entiminae@gmail.com contact.github: JCGiron contact.label: "Jennifer C. Gir\xF3n" contact.orcid: 0000-0002-0851-6883 depends_on: - bfo - bspo - caro - pato - ro - uberon deprecated: false description: The AISM contains terms used in insect biodiversity research for describing structures of the exoskeleton and the skeletomuscular system. It aims to serve as the basic backbone of generalized terms to be expanded with order-specific terminology. download.json: http://purl.obolibrary.org/obo/aism.json download.obo: http://purl.obolibrary.org/obo/aism.obo download.owl: http://purl.obolibrary.org/obo/aism.owl homepage: https://github.com/insect-morphology/aism inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) preferredPrefix: AISM prefix: aism repository: https://github.com/insect-morphology/aism ols: description: The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research. download: http://purl.obolibrary.org/obo/aism.owl homepage: https://github.com/insect-morphology/aism name: Ontology for the Anatomy of the Insect SkeletoMuscular system prefix: aism version: '2022-03-17' version.iri: http://purl.obolibrary.org/obo/aism/releases/2022-03-17/aism.owl ontobee: library: Library name: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) prefix: AISM pattern: ^\d{7}$ allergome: fairsharing: abbreviation: Allergome description: Allergome aims to supply information on Allergenic Molecules (Allergens) causing an IgE-mediated (allergic, atopic) disease (anaphylaxis, asthma, atopic dermatitis, conjunctivitis, rhinitis, urticaria). The resource is funded through the Allergen Data Laboratories via unrestricted grants from companies and institutions. id: '1746' name: Allergome prefix: FAIRsharing.w6cxgb subjects: - Medicine - Health Science - Life Science - Biomedical Science mappings: fairsharing: FAIRsharing.w6cxgb miriam: allergome n2t: allergome prefixcommons: ALLERGOME uniprot: Allergome miriam: deprecated: false 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. homepage: http://www.allergome.org/ id: '00000334' name: Allergome namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: allergome sampleId: '1948' uri_format: http://www.allergome.org/script/dettaglio.php?id_molecule=$1 n2t: description: Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources. example: '1948' homepage: http://www.allergome.org/ name: Allergome at Rome namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: allergome uri_format: http://www.allergome.org/script/dettaglio.php?id_molecule=$1 prefixcommons: is_identifiers: true is_obo: false prefix: ALLERGOME uri_format: http://identifiers.org/allergome/$1 uniprot: category: Protein family/group databases identifier: '160' link_is_explicit: 'true' name: Allergome; a platform for allergen knowledge prefix: Allergome uri_format: http://www.allergome.org/script/dettaglio.php?id_molecule=$1 alzforum.mutation: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease. example: app-d678n-tottori homepage: https://www.alzforum.org/mutations name: Alzforum Mutations synonyms: - Alzforum_mut uri_format: https://www.alzforum.org/mutations/$1 amoebadb: fairsharing: abbreviation: AmoebaDB description: AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first released, AmoebaDB contained the genomes of three Entamoeba species. AmoebaDB integrates whole genome sequence and annotation and will rapidly expand to include experimental data and environmental isolate sequences provided by community researchers . The database includes supplemental bioinformatics analyses and a web interface for data-mining. id: '2095' name: AmoebaDB prefix: FAIRsharing.swbypy subjects: - Genomics - Life Science mappings: fairsharing: FAIRsharing.swbypy miriam: amoebadb n2t: amoebadb prefixcommons: AMOEBADB miriam: deprecated: false description: AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. homepage: http://amoebadb.org/amoeba/ id: 00000148 name: AmoebaDB namespaceEmbeddedInLui: false pattern: ^EDI_\d+$ prefix: amoebadb sampleId: EDI_244000 uri_format: https://amoebadb.org/amoeba/app/record/gene/$1 n2t: description: AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: EDI_244000 homepage: http://amoebadb.org/amoeba/ name: AmoebaDB at EuPathDB namespaceEmbeddedInLui: false pattern: ^EDI_\d+$ prefix: amoebadb uri_format: https://amoebadb.org/amoeba/app/record/gene/$1 prefixcommons: is_identifiers: true is_obo: false prefix: AMOEBADB uri_format: http://identifiers.org/amoebadb/$1 amphx: bioportal: name: The Amphioxus Development and Anatomy Ontology prefix: AMPHX example: '1000160' mappings: bioportal: AMPHX obofoundry: amphx ols: amphx ontobee: AMPHX obofoundry: contact: hescriva@obs-banyuls.fr contact.github: hescriva contact.label: Hector Escriva contact.orcid: 0000-0001-7577-5028 depends_on: - uberon deprecated: false description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). download.obo: http://purl.obolibrary.org/obo/amphx.obo download.owl: http://purl.obolibrary.org/obo/amphx.owl homepage: https://github.com/EBISPOT/amphx_ontology inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: The Amphioxus Development and Anatomy Ontology preferredPrefix: AMPHX prefix: amphx repository: https://github.com/EBISPOT/amphx_ontology ols: description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). download: https://raw.githubusercontent.com/EBISPOT/amphx_ontology/master/amphx.owl homepage: https://github.com/EBISPOT/amphx_ontology name: Amphioxus Development and Anatomy Ontology (AMPHX) prefix: amphx version: '2020-12-18' version.iri: http://purl.obolibrary.org/obo/amphx/releases/2020-12-18/amphx.owl ontobee: library: Library name: The Amphioxus Development and Anatomy Ontology prefix: AMPHX pattern: ^\d+$ antibodyregistry: mappings: miriam: antibodyregistry n2t: antibodyregistry prefixcommons: ANTIBODYREGISTRY miriam: deprecated: false 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. homepage: http://antibodyregistry.org/ id: '00000516' name: Antibody Registry namespaceEmbeddedInLui: false pattern: ^\d{6}$ prefix: antibodyregistry sampleId: '493771' uri_format: http://antibodyregistry.org/AB_$1 n2t: description: The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information. example: '493771' homepage: http://antibodyregistry.org/ name: Antibody Registry at University of California namespaceEmbeddedInLui: false pattern: ^\d{6}$ prefix: antibodyregistry uri_format: http://antibodyregistry.org/AB_$1 prefixcommons: is_identifiers: true is_obo: false prefix: ANTIBODYREGISTRY uri_format: http://identifiers.org/antibodyregistry/$1 antweb: fairsharing: abbreviation: AntWeb description: AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures. id: '1749' name: AntWeb prefix: FAIRsharing.yk38tw subjects: - Anatomy - Life Science mappings: fairsharing: FAIRsharing.yk38tw miriam: antweb n2t: antweb ncbi: AntWeb prefixcommons: ANTWEB miriam: deprecated: false description: AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures. homepage: http://www.antweb.org/ id: '00000146' name: AntWeb namespaceEmbeddedInLui: false pattern: ^casent\d+(\-D\d+)?$ prefix: antweb sampleId: casent0106247 uri_format: http://www.antweb.org/specimen.do?name=$1 n2t: description: AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures. example: casent0106247 homepage: http://www.antweb.org/ name: AntWeb at California Academy of Sciences namespaceEmbeddedInLui: false pattern: ^casent\d+(\-D\d+)?$ prefix: antweb uri_format: http://www.antweb.org/specimen.do?name=$1 ncbi: example: CASENT0058943-D01 homepage: http://www.antweb.org name: Ant Database prefix: AntWeb prefixcommons: is_identifiers: true is_obo: false prefix: ANTWEB uri_format: http://identifiers.org/antweb/$1 aop: mappings: miriam: aop n2t: aop prefixcommons: AOP miriam: deprecated: false description: International repository of Adverse Outcome Pathways. homepage: https://aopwiki.org/ id: '00000617' name: AOPWiki namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: aop sampleId: '98' uri_format: https://aopwiki.org/aops/$1 n2t: description: International repository of Adverse Outcome Pathways. example: '98' homepage: https://aopwiki.org/ name: AOPWiki namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: aop uri_format: https://aopwiki.org/aops/$1 prefixcommons: is_identifiers: true is_obo: false prefix: AOP uri_format: http://identifiers.org/aop/$1 aop.events: mappings: miriam: aop.events n2t: aop.events prefixcommons: AOP.EVENTS miriam: deprecated: false description: International repository of Adverse Outcome Pathways. homepage: https://aopwiki.org/ id: '00000652' name: AOPWiki (Key Event) namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: aop.events sampleId: '3' uri_format: https://aopwiki.org/events/$1 n2t: description: International repository of Adverse Outcome Pathways. example: '3' homepage: https://aopwiki.org/ name: AOPWiki (Key Event) namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: aop.events uri_format: https://aopwiki.org/events/$1 prefixcommons: is_identifiers: true is_obo: false prefix: AOP.EVENTS uri_format: http://identifiers.org/aop.events/$1 aop.relationships: mappings: miriam: aop.relationships n2t: aop.relationships prefixcommons: AOP.RELATIONSHIPS miriam: deprecated: false description: International repository of Adverse Outcome Pathways. homepage: https://aopwiki.org/ id: '00000653' name: AOPWiki (Key Event Relationship) namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: aop.relationships sampleId: '5' uri_format: https://aopwiki.org/relationships/$1 n2t: description: International repository of Adverse Outcome Pathways. example: '5' homepage: https://aopwiki.org/ name: AOPWiki (Key Event Relationship) namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: aop.relationships uri_format: https://aopwiki.org/relationships/$1 prefixcommons: is_identifiers: true is_obo: false prefix: AOP.RELATIONSHIPS uri_format: http://identifiers.org/aop.relationships/$1 aop.stressor: mappings: miriam: aop.stressor n2t: aop.stressor prefixcommons: AOP.STRESSOR miriam: deprecated: false description: International repository of Adverse Outcome Pathways. homepage: https://aopwiki.org/ id: '00000654' name: AOPWiki (Stressor) namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: aop.stressor sampleId: '9' uri_format: https://aopwiki.org/stressors/$1 n2t: description: International repository of Adverse Outcome Pathways. example: '9' homepage: https://aopwiki.org/ name: AOPWiki (Stressor) namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: aop.stressor uri_format: https://aopwiki.org/stressors/$1 prefixcommons: is_identifiers: true is_obo: false prefix: AOP.STRESSOR uri_format: http://identifiers.org/aop.stressor/$1 apaonto: bioportal: name: Psychology Ontology prefix: APAONTO description: Ontology from the APA example: Abdomen fairsharing: abbreviation: APAONTO description: APA thesaurus . Flat ontology file id: '567' name: Psychology Ontology prefix: FAIRsharing.gkw1w8 subjects: [] homepage: https://bioportal.bioontology.org/ontologies/APAONTO mappings: bioportal: APAONTO fairsharing: FAIRsharing.gkw1w8 uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1 apd: fairsharing: abbreviation: APD description: The Antimicrobial Peptide Database (APD) contains information on antimicrobial peptides from across a wide taxonomic range. It includes a glossary, nomenclature, classification, information search, prediction, design, and statistics of AMPs. The antimicrobial peptides in this database contain less than 100 amino acid residues, are in the mature and active form, and primarily from natural sources, ranging from bacteria, fungi, plants, to animals. id: '2105' name: Antimicrobial Peptide Database prefix: FAIRsharing.ctwd7b subjects: - Biology mappings: fairsharing: FAIRsharing.ctwd7b miriam: apd n2t: apd prefixcommons: APD miriam: deprecated: false description: The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides. homepage: http://aps.unmc.edu/AP/ id: 00000278 name: APD namespaceEmbeddedInLui: false pattern: ^\d{5}$ prefix: apd sampleId: '01001' uri_format: http://aps.unmc.edu/AP/database/query_output.php?ID=$1 n2t: description: The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides. example: '01001' homepage: http://aps.unmc.edu/AP/ name: APD at Nebraska namespaceEmbeddedInLui: false pattern: ^\d{5}$ prefix: apd uri_format: http://aps.unmc.edu/AP/database/query_output.php?ID=$1 name: Antimicrobial Peptide Database prefixcommons: is_identifiers: true is_obo: false prefix: APD uri_format: http://identifiers.org/apd/$1 aphidbase.transcript: mappings: miriam: aphidbase.transcript n2t: aphidbase.transcript prefixcommons: APHIDBASE.TRANSCRIPT miriam: deprecated: false description: AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information. homepage: http://www.aphidbase.com/aphidbase id: 00000393 name: AphidBase Transcript namespaceEmbeddedInLui: false pattern: ^ACYPI\d{6}(-RA)?$ prefix: aphidbase.transcript sampleId: ACYPI000159 uri_format: http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1 n2t: description: AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information. example: ACYPI000159 homepage: http://www.aphidbase.com/aphidbase name: AphidBase at INRA namespaceEmbeddedInLui: false pattern: ^ACYPI\d{6}(-RA)?$ prefix: aphidbase.transcript uri_format: http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1 prefixcommons: is_identifiers: true is_obo: false prefix: APHIDBASE.TRANSCRIPT uri_format: http://identifiers.org/aphidbase.transcript/$1 apid.interactions: mappings: miriam: apid.interactions n2t: apid.interactions prefixcommons: APID.INTERACTIONS miriam: deprecated: false description: APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier. homepage: http://cicblade.dep.usal.es:8080/APID/ id: '00000576' name: APID Interactomes namespaceEmbeddedInLui: false pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ prefix: apid.interactions sampleId: P01116 uri_format: http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1 n2t: description: APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier. example: P01116 homepage: http://cicblade.dep.usal.es:8080/APID/ name: APID at Salamanca namespaceEmbeddedInLui: false pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ prefix: apid.interactions uri_format: http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1 prefixcommons: is_identifiers: true is_obo: false prefix: APID.INTERACTIONS uri_format: http://identifiers.org/apid.interactions/$1 provides: uniprot apo: bioportal: name: Ascomycete Phenotype Ontology prefix: APO example: 0000184 fairsharing: abbreviation: APO description: Ascomycete Phenotype Ontology is a structured controlled vocabulary for the phenotypes of Ascomycete fungi. id: '113' name: Ascomycete Phenotype Ontology prefix: FAIRsharing.dyqz3y subjects: - Life Science - Cell Biology mappings: bioportal: APO fairsharing: FAIRsharing.dyqz3y obofoundry: apo ols: apo ontobee: APO prefixcommons: YPO obofoundry: contact: stacia@stanford.edu contact.github: srengel contact.label: Stacia R Engel contact.orcid: 0000-0001-5472-917X deprecated: false description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi download.obo: http://purl.obolibrary.org/obo/apo.obo download.owl: http://purl.obolibrary.org/obo/apo.owl homepage: http://www.yeastgenome.org/ inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Ascomycete phenotype ontology preferredPrefix: APO prefix: apo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/20157474 title: New mutant phenotype data curation system in the Saccharomyces Genome Database repository: https://github.com/obophenotype/ascomycete-phenotype-ontology ols: description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi. download: http://purl.obolibrary.org/obo/apo.owl homepage: http://www.yeastgenome.org/ name: Ascomycete Phenotype Ontology (APO) prefix: apo version: '2022-04-19' version.iri: http://purl.obolibrary.org/obo/apo/releases/2022-04-19/apo.owl ontobee: library: Library name: Ascomycete phenotype ontology prefix: APO pattern: ^\d{7}$ preferred_prefix: APO prefixcommons: is_identifiers: false is_obo: true prefix: YPO uri_format: http://purl.obolibrary.org/obo/YPO_$1 uri_format: https://www.yeastgenome.org/observable/APO:$1 apollosv: bioportal: name: Apollo Structured Vocabulary prefix: APOLLO-SV example: '00000443' fairsharing: abbreviation: Apollo-SV description: An ontology of infectious disease epidemiology and ecology (a.k.a. population biology). id: '88' name: Apollo-SV prefix: FAIRsharing.ngv2xx subjects: - Ecology - Biomedical Science - Epidemiology - Population Genetics mappings: bioportal: APOLLO-SV fairsharing: FAIRsharing.ngv2xx obofoundry: apollo_sv ols: apollo_sv ontobee: APOLLO_SV obofoundry: appears_in: - scdo contact: hoganwr@ufl.edu contact.github: hoganwr contact.label: William Hogan contact.orcid: 0000-0002-9881-1017 deprecated: false description: Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models download.owl: http://purl.obolibrary.org/obo/apollo_sv.owl homepage: https://github.com/ApolloDev/apollo-sv inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Apollo Structured Vocabulary preferredPrefix: APOLLO_SV prefix: apollo_sv publications: - id: https://doi.org/10.1186/s13326-016-0092-y title: 'The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation' repository: https://github.com/ApolloDev/apollo-sv ols: description: Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models download: http://purl.obolibrary.org/obo/apollo_sv.owl homepage: https://github.com/ApolloDev/apollo-sv name: Apollo Structured Vocabulary (Apollo-SV) prefix: apollo_sv version: 4.1.1 version.iri: http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl ontobee: library: Library name: Apollo Structured Vocabulary prefix: APOLLO_SV pattern: ^\d{8}$ arachnoserver: fairsharing: abbreviation: ArachnoServer description: ArachnoServer is a manually curated database containing information on the sequence, three-dimensional structure, and biological activity of protein toxins derived from spider venom. id: '2037' name: 'ArachnoServer: Spider toxin database' prefix: FAIRsharing.c54ywe subjects: - Life Science mappings: fairsharing: FAIRsharing.c54ywe miriam: arachnoserver n2t: arachnoserver prefixcommons: ARACHNOSERVER uniprot: ArachnoServer miriam: deprecated: false 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. homepage: http://www.arachnoserver.org/ id: 00000193 name: ArachnoServer namespaceEmbeddedInLui: false pattern: ^AS\d{6}$ prefix: arachnoserver sampleId: AS000060 uri_format: http://www.arachnoserver.org/toxincard.html?id=$1 n2t: description: ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information. example: AS000060 homepage: http://www.arachnoserver.org/ name: ArachnoServer at Brisbane namespaceEmbeddedInLui: false pattern: ^AS\d{6}$ prefix: arachnoserver uri_format: http://www.arachnoserver.org/toxincard.html?id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: ARACHNOSERVER uri_format: http://identifiers.org/arachnoserver/$1 uniprot: category: Organism-specific databases identifier: '145' link_is_explicit: 'true' name: 'ArachnoServer: Spider toxin database' prefix: ArachnoServer uri_format: http://www.arachnoserver.org araport: description: Website with general information about Arabidopsis and functionalities such as a genomic viewer homepage: https://www.araport.org/ mappings: ncbi: Araport uniprot: Araport name: Arabidopsis Information Portal ncbi: example: AT1G01010 homepage: https://www.araport.org/ name: Arabidopsis Information Portal prefix: Araport uniprot: category: Organism-specific databases identifier: '221' link_is_explicit: 'true' name: Arabidopsis Information Portal prefix: Araport uri_format: https://bar.utoronto.ca/thalemine/portal.do?externalids=$1 uri_format: https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1 ardb: mappings: miriam: ardb n2t: ardb prefixcommons: ARDB miriam: deprecated: false description: The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes. homepage: http://ardb.cbcb.umd.edu/ id: '00000522' name: Antibiotic Resistance Genes Database namespaceEmbeddedInLui: false pattern: ^[A-Z_]{3}[0-9]{4,}$ prefix: ardb sampleId: CAE46076 uri_format: http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1 n2t: description: The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes. example: CAE46076 homepage: http://ardb.cbcb.umd.edu/ name: ARDB at University of Maryland namespaceEmbeddedInLui: false pattern: ^[A-Z_]{3}[0-9]{4,}$ prefix: ardb uri_format: http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1 prefixcommons: is_identifiers: true is_obo: false prefix: ARDB uri_format: http://identifiers.org/ardb/$1 ark: banana: ark mappings: miriam: ark n2t: ark prefixcommons: ARK miriam: deprecated: false description: An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type. homepage: http://n2t.net/ id: 00000592 name: ARK namespaceEmbeddedInLui: true pattern: ^(ark\:)/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$ prefix: ark sampleId: /12345/fk1234 uri_format: http://n2t.net/ark:$1 n2t: example: /88435/hq37vq534 homepage: https://wiki.ucop.edu/display/Curation/ARK name: Archival Resource Key namespaceEmbeddedInLui: false prefix: ark uri_format: n2t.net/ark:$1 name: Archival Resource Key pattern: ^/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$ prefixcommons: is_identifiers: true is_obo: false prefix: ARK uri_format: http://identifiers.org/ark/$1 uri_format: http://n2t.net/ark:$1 aro: bioportal: name: Antibiotic Resistance Ontology prefix: ARO example: '1000001' mappings: bioportal: ARO obofoundry: aro ols: aro ontobee: ARO prefixcommons: ARO obofoundry: appears_in: - scdo contact: mcarthua@mcmaster.ca contact.github: agmcarthur contact.label: Andrew G. McArthur contact.orcid: 0000-0002-1142-3063 deprecated: false description: Antibiotic resistance genes and mutations download.owl: http://purl.obolibrary.org/obo/aro.owl homepage: https://github.com/arpcard/aro inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Antibiotic Resistance Ontology preferredPrefix: ARO prefix: aro publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31665441 title: 'CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.' repository: https://github.com/arpcard/aro ols: description: Antibiotic resistance genes and mutations download: http://purl.obolibrary.org/obo/aro.owl homepage: https://github.com/arpcard/aro name: Antibiotic Resistance Ontology prefix: aro ontobee: library: Library name: Antibiotic Resistance Ontology prefix: ARO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: ARO uri_format: http://purl.obolibrary.org/obo/ARO_$1 arrayexpress: cellosaurus: category: Gene expression databases homepage: https://www.ebi.ac.uk/arrayexpress/ name: ArrayExpress Archive of Functional Genomics prefix: ArrayExpress uri_format: https://www.ebi.ac.uk/arrayexpress/experiments/$1 fairsharing: abbreviation: ArrayExpress description: ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Experiments are submitted directly to ArrayExpress or are imported from the NCBI GEO database. id: '1845' name: ArrayExpress prefix: FAIRsharing.6k0kwd subjects: - Functional Genomics mappings: cellosaurus: ArrayExpress fairsharing: FAIRsharing.6k0kwd miriam: arrayexpress n2t: arrayexpress prefixcommons: ARRAYEXPRESS miriam: deprecated: false description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations. homepage: https://www.ebi.ac.uk/arrayexpress/ id: '00000036' name: ArrayExpress namespaceEmbeddedInLui: false pattern: ^[AEP]-\w{4}-\d+$ prefix: arrayexpress providers: - code: omicsdi description: ArrayExpress through OmicsDI homepage: https://www.omicsdi.org/ name: ArrayExpress through OmicsDI uri_format: https://www.omicsdi.org/dataset/arrayexpress-repository/$1 sampleId: E-MEXP-1712 uri_format: https://www.ebi.ac.uk/arrayexpress/experiments/$1 n2t: description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations. example: E-MEXP-1712 homepage: https://www.ebi.ac.uk/arrayexpress/ name: ArrayExpress namespaceEmbeddedInLui: false pattern: ^[AEP]-\w{4}-\d+$ prefix: arrayexpress uri_format: https://www.ebi.ac.uk/arrayexpress/experiments/$1 prefixcommons: is_identifiers: true is_obo: false prefix: ARRAYEXPRESS uri_format: http://identifiers.org/arrayexpress/$1 arrayexpress.platform: mappings: miriam: arrayexpress.platform n2t: arrayexpress.platform prefixcommons: ARRAYEXPRESS.PLATFORM miriam: deprecated: false description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results. homepage: https://www.ebi.ac.uk/arrayexpress/ id: 00000294 name: ArrayExpress Platform namespaceEmbeddedInLui: false pattern: ^[AEP]-\w{4}-\d+$ prefix: arrayexpress.platform sampleId: A-GEOD-50 uri_format: https://www.ebi.ac.uk/arrayexpress/arrays/$1 n2t: description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results. example: A-GEOD-50 homepage: https://www.ebi.ac.uk/arrayexpress/ name: ArrayExpress Platform at EBI namespaceEmbeddedInLui: false pattern: ^[AEP]-\w{4}-\d+$ prefix: arrayexpress.platform uri_format: https://www.ebi.ac.uk/arrayexpress/arrays/$1 prefixcommons: is_identifiers: true is_obo: false prefix: ARRAYEXPRESS.PLATFORM uri_format: http://identifiers.org/arrayexpress.platform/$1 arraymap: fairsharing: abbreviation: arrayMap description: Part of the Progenetix project, the arrayMap database facilitates the study of the genetics of human cancer. The Progenetix project provides the data customisation and visualization tools to mine the available data. The arrayMap database is developed by the group "Theoretical Cytogenetics and Oncogenomics" at the Department of Molecular Life Sciences of the University of Zurich. id: '2135' name: arrayMap - Genomic Array Data for Cancer CNV Profiles prefix: FAIRsharing.1fbc5y subjects: - Genomics - Bioinformatics - Life Science - Biomedical Science mappings: fairsharing: FAIRsharing.1fbc5y miriam: arraymap n2t: arraymap prefixcommons: ARRAYMAP miriam: deprecated: false description: arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome. homepage: https://www.arraymap.org id: '00000621' name: ArrayMap namespaceEmbeddedInLui: false pattern: ^[\w\-:,]{3,64}$ prefix: arraymap sampleId: icdom:8500_3 uri_format: https://www.arraymap.org/pgx:$1 n2t: description: arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome. example: icdom:8500_3 homepage: https://www.arraymap.org name: ArrayMap namespaceEmbeddedInLui: false pattern: ^[\w\-:,]{3,64}$ prefix: arraymap uri_format: https://www.arraymap.org/pgx:$1 prefixcommons: is_identifiers: true is_obo: false prefix: ARRAYMAP uri_format: http://identifiers.org/arraymap/$1 arxiv: mappings: miriam: arxiv n2t: arxiv prefixcommons: ARXIV scholia: arxiv miriam: deprecated: false description: arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology. homepage: https://arxiv.org/ id: '00000035' name: arXiv namespaceEmbeddedInLui: false pattern: ^(\w+(\-\w+)?(\.\w+)?)?\d{4,7}(\.\d+(v\d+)?)?$ prefix: arxiv sampleId: 0807.4956v1 uri_format: https://arxiv.org/abs/$1 n2t: description: arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology. example: 0807.4956v1 homepage: https://arxiv.org/ name: Cornell University arXiv namespaceEmbeddedInLui: false pattern: ^(\w+(\-\w+)?(\.\w+)?)?\d{4,7}(\.\d+(v\d+)?)?$ prefix: arxiv uri_format: https://arxiv.org/abs/$1 prefixcommons: is_identifiers: true is_obo: false prefix: ARXIV uri_format: http://identifiers.org/arxiv/$1 asap: fairsharing: abbreviation: ASAP description: ASAP is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data. It was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. id: '2115' name: A Systematic Annotation Package prefix: FAIRsharing.anpa6 subjects: - Developmental Biology - Life Science - Comparative Genomics go: homepage: https://asap.genetics.wisc.edu/asap/ASAP1.htm name: A Systematic Annotation Package for Community Analysis of Genomes prefix: ASAP uri_format: https://asap.genetics.wisc.edu/asap/feature_info.php?FeatureID=$1 mappings: fairsharing: FAIRsharing.anpa6 go: ASAP miriam: asap n2t: asap ncbi: ASAP prefixcommons: ASAP miriam: deprecated: false description: ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. homepage: http://asap.ahabs.wisc.edu/asap/home.php id: 00000283 name: ASAP namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9-]+$ prefix: asap sampleId: ABE-0009634 uri_format: http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1 n2t: description: ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. example: ABE-0009634 homepage: http://asap.ahabs.wisc.edu/asap/home.php name: ASAP at University of Wisconsin namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9-]+$ prefix: asap uri_format: http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1 name: A Systematic Annotation Package for Community Analysis of Genomes ncbi: example: ABE-0000006 homepage: https://asap.genetics.wisc.edu/asap/logon.php name: A Systematic Annotation Package for Community Analysis of Genomes prefix: ASAP prefixcommons: is_identifiers: true is_obo: false prefix: ASAP uri_format: http://identifiers.org/asap/$1 ascl: fairsharing: abbreviation: ASCL description: The Astrophysics Source Code Library (ASCL) is a free online registry for source code of interest to astronomers and astrophysicists. It provides code that has been used in research that has appeared in, or been submitted to, peer-reviewed publications.Peer-reviewed papers that describe methods or experiments involving the development or use of source code are added by the ASCL team. id: '2546' name: Astrophysics Source Code Library prefix: FAIRsharing.wb0txg subjects: - Astrophysics and Astronomy mappings: fairsharing: FAIRsharing.wb0txg miriam: ascl n2t: ascl prefixcommons: ASCL miriam: deprecated: false description: The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001). homepage: http://ascl.net/ id: '00000641' name: Astrophysics Source Code Library namespaceEmbeddedInLui: false pattern: ^[0-9\.]+$ prefix: ascl sampleId: '1801.012' uri_format: http://ascl.net/$1 n2t: description: The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001). example: '1801.012' homepage: http://ascl.net/ name: Astrophysics Source Code Library namespaceEmbeddedInLui: false pattern: ^[0-9\.]+$ prefix: ascl uri_format: http://ascl.net/$1 prefixcommons: is_identifiers: true is_obo: false prefix: ASCL uri_format: http://identifiers.org/ascl/$1 asin: mappings: miriam: asin n2t: asin prefixcommons: ASIN miriam: deprecated: false description: Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue. homepage: https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182 id: '00000670' name: Amazon Standard Identification Number (ASIN) namespaceEmbeddedInLui: false pattern: ^[0-9]{10}$ prefix: asin sampleId: 0471491039 uri_format: https://amzn.com/$1 n2t: description: Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue. example: 0471491039 homepage: https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182 name: Amazon Standard Identification Number (ASIN) namespaceEmbeddedInLui: false pattern: ^[0-9]{10}$ prefix: asin uri_format: https://amzn.com/$1 name: Amazon Standard Identification Number prefixcommons: is_identifiers: true is_obo: false prefix: ASIN uri_format: http://identifiers.org/asin/$1 aspgd.locus: go: homepage: http://www.aspergillusgenome.org/ name: Aspergillus Genome Database prefix: AspGD_LOCUS uri_format: http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=$1 mappings: go: AspGD_LOCUS miriam: aspgd.locus n2t: aspgd.locus prefixcommons: ASPGD.LOCUS miriam: deprecated: false description: The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information. homepage: http://www.aspgd.org/ id: '00000412' name: AspGD Locus namespaceEmbeddedInLui: false pattern: ^[A-Za-z_0-9]+$ prefix: aspgd.locus sampleId: ASPL0000349247 uri_format: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1 n2t: description: The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information. example: ASPL0000349247 homepage: http://www.aspgd.org/ name: AspGD at Stanford Medical School namespaceEmbeddedInLui: false pattern: ^[A-Za-z_0-9]+$ prefix: aspgd.locus uri_format: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1 prefixcommons: is_identifiers: true is_obo: false prefix: ASPGD.LOCUS uri_format: http://identifiers.org/aspgd.locus/$1 aspgd.protein: mappings: miriam: aspgd.protein n2t: aspgd.protein prefixcommons: ASPGD.PROTEIN miriam: deprecated: false description: The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information. homepage: http://www.aspgd.org/ id: '00000413' name: AspGD Protein namespaceEmbeddedInLui: false pattern: ^[A-Za-z_0-9]+$ prefix: aspgd.protein sampleId: ASPL0000349247 uri_format: http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1 n2t: description: The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information. example: ASPL0000349247 homepage: http://www.aspgd.org/ name: AspGD Protein at Stanford Medical School namespaceEmbeddedInLui: false pattern: ^[A-Za-z_0-9]+$ prefix: aspgd.protein uri_format: http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1 prefixcommons: is_identifiers: true is_obo: false prefix: ASPGD.PROTEIN uri_format: http://identifiers.org/aspgd.protein/$1 asrp: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes. example: ASRP1423 homepage: https://asrp.danforthcenter.org/ name: Arabidopsis Small RNA Project assembly: mappings: miriam: assembly miriam: deprecated: false description: A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. homepage: https://www.ncbi.nlm.nih.gov/ id: 00000884 name: Assembly namespaceEmbeddedInLui: false pattern: ^[a-zA-Z0-9_\.]+$ prefix: assembly sampleId: GCF_000005845.2 uri_format: https://www.ncbi.nlm.nih.gov/assembly/$1 atc: bioportal: name: Anatomical Therapeutic Chemical Classification prefix: ATC fairsharing: abbreviation: ATC description: The Anatomical Therapeutic Chemical (ATC) Classification System is used for the classification of active ingredients of drugs according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. It is controlled by the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC), and was first published in 1976. id: '1152' name: Anatomical Therapeutic Chemical Classification prefix: FAIRsharing.1a27h8 subjects: - Chemical Biology - Pharmacology - Biomedical Science mappings: bioportal: ATC fairsharing: FAIRsharing.1a27h8 miriam: atc n2t: atc prefixcommons: ATC miriam: deprecated: false description: The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels. homepage: http://www.whocc.no/atc_ddd_index/ id: 00000088 name: Anatomical Therapeutic Chemical namespaceEmbeddedInLui: false pattern: ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$ prefix: atc sampleId: A10BA02 uri_format: http://www.whocc.no/atc_ddd_index/?code=$1 n2t: description: The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels. example: A10BA02 homepage: http://www.whocc.no/atc_ddd_index/ name: Anatomical Therapeutic Chemical Index at WHO namespaceEmbeddedInLui: false pattern: ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$ prefix: atc uri_format: http://www.whocc.no/atc_ddd_index/?code=$1 name: Anatomical Therapeutic Chemical Classification System prefixcommons: is_identifiers: true is_obo: false prefix: ATC uri_format: http://identifiers.org/atc/$1 synonyms: - ATC_code - ATTC wikidata: prefix: P267 atcc: cellosaurus: category: Cell line collections homepage: https://www.atcc.org/ name: American Type Culture Collection prefix: ATCC uri_format: https://www.atcc.org/Products/$1 fairsharing: abbreviation: ATCC description: ATCC authenticates microorganisms and cell lines and manages logistics of long-term preservation and distribution of cultures for the scientific community. ATCC supports the cultures it acquires and authenticates with expert technical support, intellectual property management and characterization data. id: '1752' name: American Type Culture Collection database prefix: FAIRsharing.j0ezpm subjects: - Virology - Life Science - Epidemiology homepage: https://www.lgcstandards-atcc.org mappings: cellosaurus: ATCC fairsharing: FAIRsharing.j0ezpm miriam: atcc n2t: atcc ncbi: ATCC prefixcommons: ATCC miriam: deprecated: false description: The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences. homepage: http://www.atcc.org/ id: 00000284 name: ATCC namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: atcc sampleId: '11303' uri_format: http://www.lgcstandards-atcc.org/Products/All/$1.aspx n2t: description: The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences. example: '11303' homepage: http://www.atcc.org/ name: ATCC in Virginia namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: atcc uri_format: http://www.lgcstandards-atcc.org/Products/All/$1.aspx name: American Type Culture Collection ncbi: example: '123456' homepage: http://www.atcc.org/ name: American Type Culture Collection database prefix: ATCC pattern: ^([A-Z]+-)?\d+$ prefixcommons: is_identifiers: true is_obo: false prefix: ATCC uri_format: http://identifiers.org/atcc/$1 synonyms: - ATCC - ATCC number - ATCC(dna) - ATCC(in host) uri_format: https://www.atcc.org/products/$1 atcvet: mappings: miriam: atcvet n2t: atcvet prefixcommons: ATCVET miriam: deprecated: false description: The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use. homepage: http://www.whocc.no/atcvet/atcvet_index/ id: '00000267' name: Anatomical Therapeutic Chemical Vetinary namespaceEmbeddedInLui: false pattern: ^Q[A-Z0-9]+$ prefix: atcvet sampleId: QJ51RV02 uri_format: http://www.whocc.no/atcvet/atcvet_index/?code=$1 n2t: description: The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use. example: QJ51RV02 homepage: http://www.whocc.no/atcvet/atcvet_index/ name: Anatomical Therapeutic Chemical Vet Index at WHO namespaceEmbeddedInLui: false pattern: ^Q[A-Z0-9]+$ prefix: atcvet uri_format: http://www.whocc.no/atcvet/atcvet_index/?code=$1 prefixcommons: is_identifiers: true is_obo: false prefix: ATCVET uri_format: http://identifiers.org/atcvet/$1 atfdb.family: mappings: miriam: atfdb.family n2t: atfdb.family prefixcommons: ATFDB.FAMILY miriam: deprecated: false description: The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found. homepage: http://www.bioguo.org/AnimalTFDB/family_index.php id: '00000316' name: Animal TFDB Family namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: atfdb.family sampleId: CUT uri_format: http://www.bioguo.org/AnimalTFDB/family.php?fam=$1 n2t: description: The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found. example: CUT homepage: http://www.bioguo.org/AnimalTFDB/family_index.php name: Animal TFDB at Hubei Bioinformatics & Molecular Imaging Key Laboratory namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: atfdb.family uri_format: http://www.bioguo.org/AnimalTFDB/family.php?fam=$1 prefixcommons: is_identifiers: true is_obo: false prefix: ATFDB.FAMILY uri_format: http://identifiers.org/atfdb.family/$1 ato: bioportal: name: Amphibian Taxonomy Ontology prefix: ATO example: '0000000' fairsharing: abbreviation: ATO description: Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource id: '583' name: Amphibian Taxonomy Ontology prefix: FAIRsharing.ayjdsm mappings: bioportal: ATO fairsharing: FAIRsharing.ayjdsm obofoundry: ato prefixcommons: ATO obofoundry: contact: david.c.blackburn@gmail.com contact.label: David Blackburn deprecated: true homepage: http://www.amphibanat.org inactive: true name: Amphibian taxonomy prefix: ato pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: ATO uri_format: http://purl.obolibrary.org/obo/ATO_$1 atol: bioportal: name: Animal Trait Ontology for Livestock prefix: ATOL download_owl: https://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=atol.owl example: '0002233' fairsharing: abbreviation: ATOL description: 'ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment. ATOL aims to: provide a reference ontology of phenotypic traits of farm animals for the international scientific and 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; and structure the ontology in relation to animal production.' id: '1535' name: Animal Trait Ontology for Livestock prefix: FAIRsharing.wsfk5z subjects: - Animal Husbandry - Agriculture - Life Science mappings: bioportal: ATOL fairsharing: FAIRsharing.wsfk5z ols: atol ols: contact: pylebail@rennes.inra.fr 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: http://www.atol-ontology.com/public/telechargement/atol.owl homepage: http://www.atol-ontology.com name: Animal Trait Ontology for Livestock prefix: atol version: '2018-09-13' pattern: ^\d{7}$ autdb: mappings: miriam: autdb n2t: autdb prefixcommons: AUTDB miriam: deprecated: false 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. homepage: http://autism.mindspec.org/autdb/ id: '00000415' name: AutDB namespaceEmbeddedInLui: false pattern: ^[A-Z]+[A-Z-0-9]{2,}$ prefix: autdb sampleId: ADA uri_format: http://autism.mindspec.org/GeneDetail/$1 n2t: description: AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder. example: ADA homepage: http://autism.mindspec.org/autdb/ name: AutDB at MindSpec namespaceEmbeddedInLui: false pattern: ^[A-Z]+[A-Z-0-9]{2,}$ prefix: autdb uri_format: http://autism.mindspec.org/GeneDetail/$1 prefixcommons: is_identifiers: true is_obo: false prefix: AUTDB uri_format: http://identifiers.org/autdb/$1 bacdive: fairsharing: abbreviation: BacDive description: "BacDive\u2014the Bacterial Diversity Metadatabase merges detailed\ \ strain-linked information on the different aspects of bacterial and archaeal\ \ biodiversity. BacDive contains entries for over 63,000 strains and provides\ \ information on their taxonomy, morphology, physiology, sampling and concomitant\ \ environmental conditions as well as molecular biology." id: '2674' name: Bacterial Diversity Metadatabase prefix: FAIRsharing.aSszvY subjects: - Biodiversity - Life Science - Microbiology mappings: fairsharing: FAIRsharing.aSszvY miriam: bacdive n2t: bacdive miriam: deprecated: false description: "BacDive\u2014the Bacterial Diversity Metadatabase merges detailed\ \ strain-linked information on the different aspects of bacterial and archaeal\ \ biodiversity." homepage: https://bacdive.dsmz.de/ id: '00000676' name: Bacterial Diversity Metadatabase namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: bacdive sampleId: '131392' uri_format: https://bacdive.dsmz.de/strain/$1 n2t: description: BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. example: '131392' homepage: https://bacdive.dsmz.de/ name: Bacterial Diversity Metadatabase namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: bacdive uri_format: https://bacdive.dsmz.de/strain/$1 bacmap.biog: mappings: miriam: bacmap.biog n2t: bacmap.biog prefixcommons: BACMAP.BIOG miriam: deprecated: false description: BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information. homepage: http://bacmap.wishartlab.com/ id: '00000361' name: BacMap Biography namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bacmap.biog sampleId: '1050' uri_format: http://bacmap.wishartlab.com/organisms/$1 n2t: description: BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information. example: '1050' homepage: http://bacmap.wishartlab.com/ name: BacMap Biography at University of Alberta namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bacmap.biog uri_format: http://bacmap.wishartlab.com/organisms/$1 prefixcommons: is_identifiers: true is_obo: false prefix: BACMAP.BIOG uri_format: http://identifiers.org/bacmap.biog/$1 bacmap.map: mappings: miriam: bacmap.map n2t: bacmap.map prefixcommons: BACMAP.MAP miriam: deprecated: false description: BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information. homepage: http://bacmap.wishartlab.com/ id: '00000416' name: BacMap Map namespaceEmbeddedInLui: false pattern: ^\w+(\_)?\d+(\.\d+)?$ prefix: bacmap.map sampleId: AP011135 uri_format: http://bacmap.wishartlab.com/maps/$1/index.html n2t: description: BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information. example: AP011135 homepage: http://bacmap.wishartlab.com/ name: BacMap Genome Map at University of Alberta namespaceEmbeddedInLui: false pattern: ^\w+(\_)?\d+(\.\d+)?$ prefix: bacmap.map uri_format: http://bacmap.wishartlab.com/maps/$1/index.html prefixcommons: is_identifiers: true is_obo: false prefix: BACMAP.MAP uri_format: http://identifiers.org/bacmap.map/$1 bactibase: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria. example: BAC045 fairsharing: abbreviation: BACTIBASE description: BACTIBASE contains calculated or predicted physicochemical properties of bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships structure/function and target organisms of these peptides and therefore better exploitation of their biological activity in both the medical and food sectors. id: '1928' name: 'Bactibase: database dedicated to bacteriocins' prefix: FAIRsharing.5f5mfm subjects: - Life Science homepage: http://bactibase.hammamilab.org mappings: fairsharing: FAIRsharing.5f5mfm name: Bactibase uri_format: http://bactibase.hammamilab.org/$1 bams: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: 'BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions.' homepage: https://bams1.org name: Brain Architecture Knowledge Management System Neuroanatomical Ontology references: - https://www.frontiersin.org/articles/10.3389/neuro.11.002.2008/full bao: bioportal: name: BioAssay Ontology prefix: BAO fairsharing: abbreviation: BAO description: The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. id: '874' name: BioAssay Ontology prefix: FAIRsharing.mye76w subjects: - Biochemistry - Life Science - Biomedical Science mappings: bioportal: BAO fairsharing: FAIRsharing.mye76w miriam: bao n2t: bao ols: bao ontobee: BAO prefixcommons: BAO miriam: deprecated: false description: The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. homepage: http://bioportal.bioontology.org/ontologies/BAO/ id: 00000597 name: BioAssay Ontology namespaceEmbeddedInLui: false pattern: ^\d{7}$ prefix: bao sampleId: 0002989 uri_format: http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1 n2t: description: The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. example: 0002989 homepage: http://bioportal.bioontology.org/ontologies/BAO/ name: BioAssay Ontology through BioPortal namespaceEmbeddedInLui: false pattern: ^\d{7}$ prefix: bao uri_format: http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1 ols: description: The BioAssay Ontology (BAO) describes biological screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 700 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation. download: http://www.bioassayontology.org/bao/ homepage: http://bioassayontology.org name: BioAssay Ontology prefix: bao version: 2.7.2 version.iri: http://www.bioassayontology.org/bao/bao_complete.owl ontobee: library: Not Specified/No name: BioAssay Ontology prefix: BAO prefixcommons: is_identifiers: true is_obo: false prefix: BAO uri_format: http://identifiers.org/bao/$1 synonyms: - BAO bbkg: mappings: miriam: bbkg miriam: deprecated: false description: Blue Brain Project's published data as knowledge graphs and Web Studios. homepage: https://portal.bluebrain.epfl.ch id: 00000903 name: Blue Brain Project Knowledge Graph namespaceEmbeddedInLui: false pattern: ^[-\w]+(?:\/[-\w]+)(?:\/\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b)$ prefix: bbkg sampleId: topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a uri_format: https://bbp.epfl.ch/nexus/web/studios/public/$1 bbtp: mappings: miriam: bbtp miriam: deprecated: false 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 ). homepage: https://portal.bluebrain.epfl.ch id: 00000889 name: Blue Brain Project Topological sampling Knowledge Graph namespaceEmbeddedInLui: false 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 prefix: bbtp sampleId: f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a uri_format: https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1 bcgo: bioportal: name: Breast Cancer Grading Ontology prefix: BCGO cellosaurus: category: Anatomy/cell type resources homepage: https://github.com/obi-bcgo/bcgo name: Beta Cell Genomics Ontology prefix: BCGO uri_format: http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/$1 download_owl: https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl mappings: bioportal: BCGO cellosaurus: BCGO obofoundry: bcgo ontobee: BCGO prefixcommons: BCGO obofoundry: contact: jiezheng@pennmedicine.upenn.edu contact.github: zhengj2007 contact.label: Jie Zheng contact.orcid: 0000-0002-2999-0103 deprecated: true description: An application ontology built for beta cell genomics studies. download.owl: http://purl.obolibrary.org/obo/bcgo.owl homepage: https://github.com/obi-bcgo/bcgo inactive: true license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Beta Cell Genomics Ontology prefix: bcgo repository: https://github.com/obi-bcgo/bcgo ontobee: library: Library name: Beta Cell Genomics Ontology prefix: BCGO prefixcommons: is_identifiers: false is_obo: true prefix: BCGO uri_format: http://purl.obolibrary.org/obo/BCGO_$1 bcio: bioportal: name: Brain-Computer Interaction (BCI) Ontology prefix: BCI-O download_owl: http://humanbehaviourchange.org/ontology/bcio.owl example: '040000' mappings: bioportal: BCI-O ols: bcio ols: description: The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation. download: http://humanbehaviourchange.org/ontology/bcio.owl homepage: https://www.humanbehaviourchange.org/ name: The Behaviour Change Intervention Ontology prefix: bcio version.iri: http://humanbehaviourchange.org/ontology/bcio.owl/2022-04-30 pattern: ^\d{6}$ bco: bioportal: name: Biological Collections Ontology prefix: BCO example: 0000081 fairsharing: abbreviation: BCO description: The Biological Collections Ontology (BCO) supports the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. The BCO covers distinctions between individuals, organisms, voucher specimens, lots, samples, the relations between these entities, and the processes governing the creation and use of "samples". Also within scope are properties including collector, location, time, storage environment, containers, institution, and collection identifiers. id: '1080' name: Biological Collections Ontology prefix: FAIRsharing.8ktkqy subjects: - Metagenomics - Taxonomy - Ecology - Biodiversity mappings: bioportal: BCO fairsharing: FAIRsharing.8ktkqy obofoundry: bco ols: bco ontobee: BCO prefixcommons: BCO obofoundry: appears_in: - fovt contact: rlwalls2008@gmail.com contact.github: ramonawalls contact.label: Ramona Walls contact.orcid: 0000-0001-8815-0078 deprecated: false 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 homepage: https://github.com/BiodiversityOntologies/bco inactive: false license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Biological Collections Ontology preferredPrefix: BCO prefix: bco repository: https://github.com/BiodiversityOntologies/bco ols: description: An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. download: http://purl.obolibrary.org/obo/bco.owl homepage: https://github.com/BiodiversityOntologies/bco name: Biological Collections Ontology prefix: bco version: '2021-11-14' version.iri: http://purl.obolibrary.org/obo/bco/releases/2021-11-14/bco.owl ontobee: library: Library name: Biological Collections Ontology prefix: BCO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: BCO uri_format: http://purl.obolibrary.org/obo/BCO_$1 bcrc: cellosaurus: category: Cell line collections homepage: https://catalog.bcrc.firdi.org.tw/ name: Taiwan Bioresource Collection and Research Center prefix: BCRC uri_format: https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 example: '60316' homepage: https://catalog.bcrc.firdi.org.tw mappings: cellosaurus: BCRC name: BCRC Strain Collection Catalog pattern: ^\d+$ uri_format: https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1 bcrj: cellosaurus: category: Cell line collections homepage: http://bcrj.org.br/celula/bcrj name: Banco de Celulas do Rio de Janeiro prefix: BCRJ uri_format: http://bcrj.org.br/celula/$1 example: 0278 mappings: cellosaurus: BCRJ pattern: ^\d{4}$ bdgp.est: has_canonical: dbest mappings: miriam: bdgp.est n2t: bdgp.est ncbi: BDGP_EST prefixcommons: BDGP.EST miriam: deprecated: false 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). homepage: https://www.ncbi.nlm.nih.gov/dbEST/index.html id: 00000285 name: BDGP EST namespaceEmbeddedInLui: false pattern: ^\w+(\.)?(\d+)?$ prefix: bdgp.est sampleId: EY223054.1 uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1 n2t: description: The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI). example: EY223054.1 homepage: https://www.ncbi.nlm.nih.gov/dbEST/index.html name: BDGP EST at NCBI namespaceEmbeddedInLui: false pattern: ^\w+(\.)?(\d+)?$ prefix: bdgp.est uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1 ncbi: example: '123456' homepage: http://www.fruitfly.org/EST/index.shtml name: Berkeley Drosophila Genome Project EST database prefix: BDGP_EST prefixcommons: is_identifiers: true is_obo: false prefix: BDGP.EST uri_format: http://identifiers.org/bdgp.est/$1 bdgp.insertion: mappings: miriam: bdgp.insertion n2t: bdgp.insertion prefixcommons: BDGP.INSERTION miriam: deprecated: false description: BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element. homepage: http://flypush.imgen.bcm.tmc.edu/pscreen/ id: '00000156' name: BDGP insertion DB namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: bdgp.insertion sampleId: KG09531 uri_format: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1 n2t: description: BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element. example: KG09531 homepage: http://flypush.imgen.bcm.tmc.edu/pscreen/ name: BDGP Gene Disruption Project namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: bdgp.insertion uri_format: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1 prefixcommons: is_identifiers: true is_obo: false prefix: BDGP.INSERTION uri_format: http://identifiers.org/bdgp.insertion/$1 bdsc: mappings: miriam: bdsc n2t: bdsc miriam: deprecated: false description: The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research. homepage: https://bdsc.indiana.edu/about/mission.html id: '00000332' name: Bloomington Drosophila Stock Center namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bdsc sampleId: '33607' uri_format: https://bdsc.indiana.edu/stocks/$1 n2t: description: The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research. example: '33607' homepage: https://bdsc.indiana.edu/about/mission.html name: BDSC at Indiana University namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bdsc uri_format: https://bdsc.indiana.edu/stocks/$1 beetlebase: fairsharing: abbreviation: BeetleBase description: BeetleBase is a community resource for Tribolium genetics, genomics and developmental biology. The database is built on the Chado generic data model, and is able to store various types of data, ranging from genome sequences to mutant phenotypes. id: '1940' name: BeetleBase prefix: FAIRsharing.h5f091 subjects: - Computational Biology - Life Science mappings: fairsharing: FAIRsharing.h5f091 miriam: beetlebase n2t: beetlebase ncbi: BEETLEBASE prefixcommons: BEETLEBASE miriam: deprecated: false description: BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications. homepage: http://beetlebase.org/ id: '00000157' name: BeetleBase namespaceEmbeddedInLui: false pattern: ^TC\d+$ prefix: beetlebase sampleId: TC010103 uri_format: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1 n2t: description: BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications. example: TC010103 homepage: http://beetlebase.org/ name: BeetleBase at Kansas State University namespaceEmbeddedInLui: false pattern: ^TC\d+$ prefix: beetlebase uri_format: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1 ncbi: example: TC030551 homepage: http://www.beetlebase.org/ name: Tribolium Genome Database -- Insertion prefix: BEETLEBASE prefixcommons: is_identifiers: true is_obo: false prefix: BEETLEBASE uri_format: http://identifiers.org/beetlebase/$1 begdb: fairsharing: abbreviation: BEGDB description: The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate QM calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods. id: '2365' name: The Benchmark Energy & Geometry Database prefix: FAIRsharing.nbe4fq subjects: - Life Science mappings: fairsharing: FAIRsharing.nbe4fq miriam: begdb n2t: begdb prefixcommons: BEGDB miriam: deprecated: false description: The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods. homepage: http://www.begdb.com id: '00000622' name: Benchmark Energy & Geometry Database namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: begdb sampleId: '4214' uri_format: http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1 n2t: description: The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods. example: '4214' homepage: http://www.begdb.com name: Benchmark Energy & Geometry Database namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: begdb uri_format: http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: BEGDB uri_format: http://identifiers.org/begdb/$1 beiresources: cellosaurus: category: Cell line collections homepage: https://www.beiresources.org/Home.aspx name: BEI Resources prefix: BEI_Resources uri_format: https://www.beiresources.org/Catalog/cellBanks/$1.aspx contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 example: MRA-253 homepage: https://www.beiresources.org mappings: cellosaurus: BEI_Resources name: BEI Resources synonyms: - BEI_Resources uri_format: https://www.beiresources.org/Catalog/cellBanks/$1.aspx bel: comment: INDRA uses bel as a catch-all for scomp/sfam contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents. example: 9-1-1 Complex fairsharing: abbreviation: BEL description: BEL is a language for representing scientific findings in the life sciences in a reusable, shareable, and computable form. BEL is designed to represent scientific findings by capturing causal and correlative relationships in context, where context can include information about the biological and experimental system in which the relationships were observed, the supporting publications cited and the process of curation. BEL is intended as a knowledge capture and interchange medium, supporting the operation of systems that integrate knowledge derived from independent efforts. The language is designed to be use-neutral, facilitating the storage and use of structured knowledge for inference by applications through a knowledge assembly process that can create computable biological networks. While BEL does not prescribe any particular assembly process or any particular knowledge format for the output of an assembly process, a suite of software components called the BEL Framework provides everything necessary to create, compile, assemble, and deliver computable knowledge models to BEL-aware applications. The current version of BEL provides the means to describe biological interactions qualitatively but not to quantify the magnitude or rate of these interactions. This limitation is by design because this quantitative information has significant variability and is not consistently reported in the literature. It is our hope that future versions of BEL can accommodate these additional data. id: '1243' name: Biological Expression Language prefix: FAIRsharing.dp0jvd subjects: - Biology homepage: https://biological-expression-language.github.io/ mappings: fairsharing: FAIRsharing.dp0jvd name: Biological Expression Language bfo: bioportal: name: Basic Formal Ontology prefix: BFO example: '0000001' fairsharing: abbreviation: ISO/IEC 21838-2:2021 BFO description: "ISO/IEC 21838-2:2021 describes Basic Formal Ontology (BFO), which\ \ is an ontology that is conformant to the requirements specified for top-level\ \ ontologies in ISO/IEC 21838\u20111." id: '1248' name: "ISO/IEC 21838-2:2021 Information technology \u2014 Top-level ontologies\ \ (TLO) \u2014 Part 2: Basic Formal Ontology (BFO)" prefix: FAIRsharing.wcpd6f subjects: - Subject Agnostic go: description: An upper ontology used by Open Bio Ontologies (OBO) Foundry. BFO contains upper-level classes as well as core relations such as part_of (BFO_0000050) name: Basic Formal Ontology prefix: BFO mappings: bioportal: BFO fairsharing: FAIRsharing.wcpd6f go: BFO obofoundry: bfo ols: bfo ontobee: BFO prefixcommons: BFO obofoundry: appears_in: - agro - aism - cdno - colao - duo - ecocore - epio - foodon - fovt - hso - lepao - mco - ons - pcl - pco - pco - psdo - rbo - xpo - zp contact: phismith@buffalo.edu contact.github: phismith contact.label: Barry Smith contact.orcid: 0000-0003-1384-116X deprecated: false 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 homepage: http://ifomis.org/bfo/ inactive: false license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Basic Formal Ontology preferredPrefix: BFO prefix: bfo repository: https://github.com/BFO-ontology/BFO ols: description: The upper level ontology upon which OBO Foundry ontologies are built. download: http://purl.obolibrary.org/obo/bfo.owl homepage: https://github.com/BFO-ontology/BFO name: Basic Formal Ontology prefix: bfo version: '2019-08-26' version.iri: http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl ontobee: library: Foundry name: Basic Formal Ontology prefix: BFO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: BFO uri_format: http://purl.obolibrary.org/obo/BFO_$1 bgee.family: mappings: miriam: bgee.family n2t: bgee.family prefixcommons: BGEE.FAMILY miriam: deprecated: false description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species. homepage: http://bgee.unil.ch/bgee/bgee id: '00000417' name: Bgee family namespaceEmbeddedInLui: false pattern: ^(ENSFM|ENSGTV:)\d+$ prefix: bgee.family sampleId: ENSFM00500000270089 uri_format: http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1 n2t: description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species. example: ENSFM00500000270089 homepage: http://bgee.unil.ch/bgee/bgee name: Bgee at Lausanne namespaceEmbeddedInLui: false pattern: ^(ENSFM|ENSGTV:)\d+$ prefix: bgee.family uri_format: http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: BGEE.FAMILY uri_format: http://identifiers.org/bgee.family/$1 bgee.gene: mappings: miriam: bgee.gene n2t: bgee.gene prefixcommons: BGEE.GENE miriam: deprecated: false description: Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee. homepage: https://bgee.org/ id: 00000418 name: Bgee gene namespaceEmbeddedInLui: false pattern: ^[A-Za-z]+\d+$ prefix: bgee.gene sampleId: FBgn0000015 uri_format: https://bgee.org/?page=gene&gene_id=$1 n2t: description: Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee. example: FBgn0000015 homepage: https://bgee.org/ name: Bgee gene namespaceEmbeddedInLui: false pattern: ^[A-Za-z]+\d+$ prefix: bgee.gene uri_format: https://bgee.org/?page=gene&gene_id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: BGEE.GENE uri_format: http://identifiers.org/bgee.gene/$1 bgee.organ: mappings: miriam: bgee.organ n2t: bgee.organ prefixcommons: BGEE.ORGAN miriam: deprecated: false description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures. homepage: http://bgee.unil.ch/bgee/bgee id: '00000420' name: Bgee organ namespaceEmbeddedInLui: false pattern: ^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\:\d+$ prefix: bgee.organ sampleId: EHDAA:2185 uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_id=$1&organ_children=on n2t: description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures. example: EHDAA:2185 homepage: http://bgee.unil.ch/bgee/bgee name: Bgee at Lausanne namespaceEmbeddedInLui: false pattern: ^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\:\d+$ prefix: bgee.organ uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_id=$1&organ_children=on prefixcommons: is_identifiers: true is_obo: false prefix: BGEE.ORGAN uri_format: http://identifiers.org/bgee.organ/$1 uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1 bgee.stage: mappings: miriam: bgee.stage n2t: bgee.stage prefixcommons: BGEE.STAGE miriam: deprecated: false description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages. homepage: http://bgee.unil.ch/bgee/bgee id: 00000419 name: Bgee stage namespaceEmbeddedInLui: false pattern: ^(FBvd|XtroDO|HsapDO|MmusDO)\:\d+$ prefix: bgee.stage sampleId: HsapDO:0000004 uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_id=$1&stage_children=on n2t: description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages. example: HsapDO:0000004 homepage: http://bgee.unil.ch/bgee/bgee name: Bgee at Lausanne namespaceEmbeddedInLui: false pattern: ^(FBvd|XtroDO|HsapDO|MmusDO)\:\d+$ prefix: bgee.stage uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_id=$1&stage_children=on prefixcommons: is_identifiers: true is_obo: false prefix: BGEE.STAGE uri_format: http://identifiers.org/bgee.stage/$1 uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1 bigg.compartment: mappings: miriam: bigg.compartment n2t: bigg.compartment prefixcommons: BIGG.COMPARTMENT miriam: deprecated: false description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments. homepage: http://bigg.ucsd.edu/compartments/ id: '00000555' name: BiGG Compartment namespaceEmbeddedInLui: false pattern: ^[a-z_A-Z]+$ prefix: bigg.compartment sampleId: c uri_format: http://bigg.ucsd.edu/compartments/$1 n2t: description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments. example: c homepage: http://bigg.ucsd.edu/compartments/ name: BiGG Compartment at University of California namespaceEmbeddedInLui: false pattern: ^[a-z_A-Z]+$ prefix: bigg.compartment uri_format: http://bigg.ucsd.edu/compartments/$1 prefixcommons: is_identifiers: true is_obo: false prefix: BIGG.COMPARTMENT uri_format: http://identifiers.org/bigg.compartment/$1 bigg.metabolite: mappings: miriam: bigg.metabolite n2t: bigg.metabolite prefixcommons: BIGG.METABOLITE miriam: deprecated: false description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes. homepage: http://bigg.ucsd.edu/universal/metabolites id: '00000556' name: BiGG Metabolite namespaceEmbeddedInLui: false pattern: ^[a-z_A-Z0-9]+$ prefix: bigg.metabolite sampleId: 12dgr161 uri_format: http://bigg.ucsd.edu/models/universal/metabolites/$1 n2t: description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes. example: 12dgr161 homepage: http://bigg.ucsd.edu/universal/metabolites name: BiGG Metabolite at University of Cakifornia namespaceEmbeddedInLui: false pattern: ^[a-z_A-Z0-9]+$ prefix: bigg.metabolite uri_format: http://bigg.ucsd.edu/models/universal/metabolites/$1 prefixcommons: is_identifiers: true is_obo: false prefix: BIGG.METABOLITE uri_format: http://identifiers.org/bigg.metabolite/$1 bigg.model: mappings: miriam: bigg.model n2t: bigg.model prefixcommons: BIGG.MODEL miriam: deprecated: false description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models. homepage: http://bigg.ucsd.edu/models id: '00000554' name: BiGG Model namespaceEmbeddedInLui: false pattern: ^[a-z_A-Z0-9]+$ prefix: bigg.model sampleId: iECABU_c1320 uri_format: http://bigg.ucsd.edu/models/$1 n2t: description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models. example: iECABU_c1320 homepage: http://bigg.ucsd.edu/models name: BiGG Model at University of California namespaceEmbeddedInLui: false pattern: ^[a-z_A-Z0-9]+$ prefix: bigg.model uri_format: http://bigg.ucsd.edu/models/$1 prefixcommons: is_identifiers: true is_obo: false prefix: BIGG.MODEL uri_format: http://identifiers.org/bigg.model/$1 bigg.reaction: mappings: miriam: bigg.reaction n2t: bigg.reaction prefixcommons: BIGG.REACTION miriam: deprecated: false description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions. homepage: http://bigg.ucsd.edu/universal/reactions id: '00000557' name: BiGG Reaction namespaceEmbeddedInLui: false pattern: ^[a-z_A-Z0-9]+$ prefix: bigg.reaction sampleId: 13GS uri_format: http://bigg.ucsd.edu/models/universal/reactions/$1 n2t: description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions. example: 13GS homepage: http://bigg.ucsd.edu/universal/reactions name: BiGG Reaction at University of California namespaceEmbeddedInLui: false pattern: ^[a-z_A-Z0-9]+$ prefix: bigg.reaction uri_format: http://bigg.ucsd.edu/models/universal/reactions/$1 prefixcommons: is_identifiers: true is_obo: false prefix: BIGG.REACTION uri_format: http://identifiers.org/bigg.reaction/$1 bila: deprecated: true fairsharing: abbreviation: BILA description: This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource. id: '1035' name: Bilateria anatomy prefix: FAIRsharing.eqgjeq mappings: fairsharing: FAIRsharing.eqgjeq prefixcommons: BILA obofoundry: name: Bilateria anatomy prefix: bila prefixcommons: is_identifiers: false is_obo: true prefix: BILA uri_format: http://purl.obolibrary.org/obo/BILA_$1 bindingdb: fairsharing: abbreviation: BindingDB description: BindingDB enables research by making a growing collection of high-quality, quantitative, protein-ligand binding data findable and usable. Funded by NIGMS/NIH. id: '1772' name: BindingDB database of measured binding affinities prefix: FAIRsharing.3b36hk subjects: - Drug Discovery - Chemistry - Life Science - Computational Chemistry - Medicinal Chemistry mappings: fairsharing: FAIRsharing.3b36hk miriam: bindingdb n2t: bindingdb prefixcommons: BINDINGDB uniprot: BindingDB miriam: deprecated: false description: BindingDB is the first public database of protein-small molecule affinity data. homepage: https://www.bindingdb.org id: '00000264' name: BindingDB namespaceEmbeddedInLui: false pattern: ^\w\d+$ prefix: bindingdb sampleId: e999 uri_format: http://www.bindingdb.org/compact/$1 n2t: description: BindingDB is the first public database of protein-small molecule affinity data. example: e999 homepage: https://www.bindingdb.org name: BindingDB namespaceEmbeddedInLui: false pattern: ^\w\d+$ prefix: bindingdb uri_format: http://www.bindingdb.org/compact/$1 prefixcommons: is_identifiers: true is_obo: false prefix: BINDINGDB uri_format: http://identifiers.org/bindingDB/$1 uniprot: category: Chemistry databases identifier: '127' link_is_explicit: 'true' name: BindingDB database of measured binding affinities prefix: BindingDB uri_format: https://www.bindingdb.org/uniprot/$1 biocarta.pathway: mappings: miriam: biocarta.pathway n2t: biocarta.pathway prefixcommons: BIOCARTA.PATHWAY miriam: deprecated: false description: BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps. homepage: https://www.biocarta.com/ id: '00000421' name: BioCarta Pathway namespaceEmbeddedInLui: false pattern: ^([hm]\_)?\w+Pathway$ prefix: biocarta.pathway sampleId: h_aktPathway uri_format: https://cgap.nci.nih.gov/Pathways/BioCarta/$1 n2t: description: BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps. example: h_aktPathway homepage: https://www.biocarta.com/ name: BioCarta Pathway at NCI namespaceEmbeddedInLui: false pattern: ^([hm]\_)?\w+Pathway$ prefix: biocarta.pathway uri_format: https://cgap.nci.nih.gov/Pathways/BioCarta/$1 prefixcommons: is_identifiers: true is_obo: false prefix: BIOCARTA.PATHWAY uri_format: http://identifiers.org/biocarta.pathway/$1 biocatalogue.service: mappings: miriam: biocatalogue.service n2t: biocatalogue.service prefixcommons: BIOCATALOGUE.SERVICE miriam: deprecated: false description: The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all. homepage: https://www.biocatalogue.org/ id: '00000140' name: BioCatalogue namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: biocatalogue.service sampleId: '614' uri_format: https://www.biocatalogue.org/services/$1 n2t: description: The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all. example: '614' homepage: https://www.biocatalogue.org/ name: BioCatalogue at EMBL-EBI namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: biocatalogue.service uri_format: https://www.biocatalogue.org/services/$1 name: BioCatalogue Service prefixcommons: is_identifiers: true is_obo: false prefix: BIOCATALOGUE.SERVICE uri_format: http://identifiers.org/biocatalogue.service/$1 biocyc: go: homepage: http://biocyc.org/ name: BioCyc collection of metabolic pathway databases prefix: BioCyc uri_format: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=$1 mappings: go: BioCyc miriam: biocyc n2t: biocyc prefixcommons: BIOCYC uniprot: BioCyc miriam: deprecated: false description: BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. homepage: http://biocyc.org id: 00000194 name: BioCyc namespaceEmbeddedInLui: false pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$ prefix: biocyc sampleId: ECOLI:CYT-D-UBIOX-CPLX uri_format: http://biocyc.org/getid?id=$1 n2t: description: BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. example: ECOLI:CYT-D-UBIOX-CPLX homepage: http://biocyc.org name: BioCyc at SRI International namespaceEmbeddedInLui: false pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$ prefix: biocyc uri_format: http://biocyc.org/getid?id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: BIOCYC uri_format: http://identifiers.org/biocyc/$1 uniprot: category: Enzyme and pathway databases identifier: '5' link_is_explicit: 'true' name: BioCyc Collection of Pathway/Genome Databases prefix: BioCyc uri_format: https://biocyc.org/getid?id=$1 biogrid: fairsharing: abbreviation: BioGRID description: "The Biological General Repository for Interaction Datasets (BioGRID)\ \ is a public database that archives and disseminates genetic and protein interaction\ \ data from model organisms and humans. BioGRID currently holds over\_1,740,000\ \ interactions\_curated from both high-throughput datasets and individual focused\ \ studies, as derived from over 70,000+ publications in the primary literature.\ \ Complete coverage of the entire literature is maintained for budding yeast\ \ (S. cerevisiae), fission yeast (S. pombe) and thale cress (A. thaliana), and\ \ efforts to expand curation across multiple metazoan species are underway.\ \ All data are freely provided via our search index and available for download\ \ in many standardized formats." id: '2028' name: Biological General Repository for Interaction Datasets prefix: FAIRsharing.9d5f5r subjects: - Cheminformatics - Biochemistry - Bioinformatics - Chemical Biology - Proteomics - Life Science - Systems Biology mappings: fairsharing: FAIRsharing.9d5f5r miriam: biogrid n2t: biogrid prefixcommons: BIOGRID uniprot: BioGRID miriam: deprecated: false description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. homepage: http://thebiogrid.org/ id: 00000058 name: BioGRID namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: biogrid sampleId: '31623' uri_format: http://thebiogrid.org/$1 n2t: description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. example: '31623' homepage: http://thebiogrid.org/ name: BioGRID database of physical and genetic interactions namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: biogrid uri_format: http://thebiogrid.org/$1 prefixcommons: is_identifiers: false is_obo: false prefix: BIOGRID uri_format: http://thebiogrid.org/$1 twitter: biogrid uniprot: category: Protein-protein interaction databases identifier: '184' link_is_explicit: 'true' name: The Biological General Repository for Interaction Datasets (BioGRID) prefix: BioGRID uri_format: https://thebiogrid.org/$1 biogrid.interaction: contact: email: md.tyers@umontreal.ca github: null name: Mike Tyers orcid: 0000-0002-9713-9994 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. example: '2649230' homepage: https://thebiogrid.org/ name: BioGRID Interactions part_of: biogrid pattern: ^\d+$ twitter: biogrid uri_format: https://thebiogrid.org/interaction/$1 biolegend: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: BioLegend is a life sciences supply vendor. example: '3403' homepage: https://www.biolegend.com name: BioLegend pattern: ^\d+$ uri_format: https://www.biolegend.com/Default.aspx?ID=6664&productid=$1 biolink: biolink: is_identifiers: false is_obo: false prefix: biolink uri_format: https://w3id.org/biolink/vocab/$1 bioportal: name: Biolink Model prefix: BIOLINK fairsharing: abbreviation: biolink description: 'A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations. Biolink Model is designed as a way of standardizing types and relational structures in knowledge graphs (KGs), where the KG may be either a property graph or RDF triple store. The schema is expressed as a YAML, which may be translated into a number of different representations including OWL, Python dataclasses, GraphQL and more. The schema assumes a property graph, where nodes represent individual entities, and edges represent relationship between entities. Biolink Model provides a schema for representing both nodes and edges. The model itself can be divided into a few parts: Entities (subjects and objects), Predicates (relationships between core concepts), Associations (statements including evidence and provenance), Entity Slots (node properties), and Edge Slots (edge properties).' id: '3649' name: Biolink Model prefix: FAIRsharing.ad9d85 subjects: - Functional Genomics - Medical Biotechnology - Biomedical Science - Translational Medicine - Medical Informatics homepage: https://biolink.github.io/biolink-model/ mappings: biolink: biolink bioportal: BIOLINK fairsharing: FAIRsharing.ad9d85 miriam: biolink miriam: deprecated: false description: A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations. homepage: https://biolink.github.io/biolink-model id: 00000782 name: BioLink Model namespaceEmbeddedInLui: false pattern: ^\S+$ prefix: biolink sampleId: Gene uri_format: https://w3id.org/biolink/vocab/$1 biominder: mappings: miriam: biominder n2t: biominder prefixcommons: BIOMINDER miriam: deprecated: false description: Database of the dielectric properties of biological tissues. homepage: https://datalab.rwth-aachen.de/MINDER id: '00000634' name: Bio-MINDER Tissue Database namespaceEmbeddedInLui: false pattern: ^[a-z0-9\-]+$ prefix: biominder sampleId: aef4c195-9cf9-46db-a12a-7cfd1ff3eec3 uri_format: https://datalab.rwth-aachen.de/MINDER/resource/$1 n2t: description: Database of the dielectric properties of biological tissues. example: aef4c195-9cf9-46db-a12a-7cfd1ff3eec3 homepage: https://datalab.rwth-aachen.de/MINDER name: Bio-MINDER Tissue Database namespaceEmbeddedInLui: false pattern: ^[a-z0-9\-]+$ prefix: biominder uri_format: https://datalab.rwth-aachen.de/MINDER/resource/$1 prefixcommons: is_identifiers: true is_obo: false prefix: BIOMINDER uri_format: http://identifiers.org/biominder/$1 biomodels.db: go: homepage: https://www.ebi.ac.uk/biomodels/ name: BioModels Database prefix: BIOMD synonyms: - BIOMDID uri_format: https://www.ebi.ac.uk/biomodels/$1 mappings: go: BIOMD miriam: biomodels.db n2t: biomodels.db prefixcommons: BIOMODELS.DB miriam: deprecated: false description: BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. homepage: https://www.ebi.ac.uk/biomodels/ id: '00000007' name: BioModels Database namespaceEmbeddedInLui: false pattern: ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ prefix: biomodels.db providers: - code: CURATOR_REVIEW description: Caltech mirror homepage: http://biomodels.caltech.edu/ name: Caltech mirror uri_format: http://biomodels.caltech.edu/$1 - code: omicsdi description: BioModels through OmicsDI homepage: https://www.omicsdi.org/ name: BioModels through OmicsDI uri_format: https://www.omicsdi.org/dataset/biomodels/$1 sampleId: BIOMD0000000048 uri_format: https://www.ebi.ac.uk/biomodels/$1 n2t: description: BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. example: BIOMD0000000048 homepage: https://www.ebi.ac.uk/biomodels/ name: BioModels Database namespaceEmbeddedInLui: false pattern: ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ prefix: biomodels.db uri_format: https://www.ebi.ac.uk/biomodels/$1 prefixcommons: is_identifiers: true is_obo: false prefix: BIOMODELS.DB uri_format: http://identifiers.org/biomodels.db/$1 synonyms: - BIOMD biomodels.kisao: bioportal: name: Kinetic Simulation Algorithm Ontology prefix: KISAO fairsharing: abbreviation: KiSAO description: The Kinetic Simulation Algorithm Ontology aims at providing support in unambiguously referring to simulation algorithms when describing a simulation experiment. It describes and classifies existing algorithms and their inter-relationships through the algorithm characteristics and parameters. id: '974' name: Kinetic Simulation Algorithm Ontology prefix: FAIRsharing.jcg19w subjects: - Bioinformatics - Computer Science mappings: bioportal: KISAO fairsharing: FAIRsharing.jcg19w miriam: biomodels.kisao n2t: biomodels.kisao obofoundry: kisao ols: kisao ontobee: KISAO prefixcommons: KISAO miriam: deprecated: false description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment. homepage: http://bioportal.bioontology.org/ontologies/KISAO id: 00000108 name: KiSAO namespaceEmbeddedInLui: false pattern: ^KISAO_\d+$ prefix: biomodels.kisao sampleId: KISAO_0000057 uri_format: http://purl.bioontology.org/ontology/KISAO/kisao:$1 n2t: description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment. example: KISAO_0000057 homepage: http://bioportal.bioontology.org/ontologies/KISAO name: KiSAO via NCBO's Bioportal namespaceEmbeddedInLui: false pattern: ^KISAO_\d+$ prefix: biomodels.kisao uri_format: http://purl.bioontology.org/ontology/KISAO/kisao:$1 obofoundry: contact: jonrkarr@gmail.com contact.github: jonrkarr contact.label: Jonathan Karr contact.orcid: 0000-0002-2605-5080 deprecated: false description: A classification of algorithms for simulating biology, their parameters, and their outputs download.owl: http://purl.obolibrary.org/obo/kisao.owl homepage: https://github.com/SED-ML/KiSAO inactive: false license: Artistic License 2.0 license.url: http://opensource.org/licenses/Artistic-2.0 name: Kinetic Simulation Algorithm Ontology preferredPrefix: KISAO prefix: kisao publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/22027554 title: Controlled vocabularies and semantics in systems biology repository: https://github.com/SED-ML/KiSAO ols: description: A classification of algorithms for simulating biology and their outputs download: http://purl.obolibrary.org/obo/kisao.owl homepage: http://co.mbine.org/standards/kisao name: Kinetic Simulation Algorithm Ontology prefix: kisao version: '2.30' ontobee: library: Library name: Kinetic Simulation Algorithm Ontology prefix: KISAO preferred_prefix: biomodels.kisao prefixcommons: is_identifiers: false is_obo: true prefix: KISAO uri_format: http://purl.obolibrary.org/obo/KISAO_$1 synonyms: - kisao biomodels.teddy: bioportal: name: Terminology for the Description of Dynamics prefix: TEDDY download_owl: http://svn.code.sf.net/p/teddyontology/code/teddy/tags/current/teddy-inferred.owl example: '0000066' fairsharing: abbreviation: TEDDY description: The TErminology for the Description of DYnamics (TEDDY) project aims to provide an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. id: '923' name: TErminology for the Description of DYnamics prefix: FAIRsharing.w9jvbt subjects: - Neurophysiology - Synthetic Biology - Systems Biology mappings: bioportal: TEDDY fairsharing: FAIRsharing.w9jvbt miriam: biomodels.teddy n2t: biomodels.teddy ols: teddy prefixcommons: BIOMODELS.TEDDY miriam: deprecated: false description: The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. homepage: http://teddyontology.sourceforge.net/ id: '00000107' name: TEDDY namespaceEmbeddedInLui: false pattern: ^TEDDY_\d{7}$ prefix: biomodels.teddy sampleId: TEDDY_0000066 uri_format: http://purl.bioontology.org/ontology/TEDDY/$1 n2t: description: The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. example: TEDDY_0000066 homepage: http://teddyontology.sourceforge.net/ name: TEDDY through BioPortal namespaceEmbeddedInLui: false pattern: ^TEDDY_\d{7}$ prefix: biomodels.teddy uri_format: http://purl.bioontology.org/ontology/TEDDY/$1 ols: description: TEDDY is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems and Synthetic Biology. download: http://www.biomodels.net/teddy/TEDDY name: Terminology for Description of Dynamics prefix: teddy version: '2014-04-24' version.iri: http://identifiers.org/combine.specifications/teddy.rel-2014-04-24 pattern: ^\d+$ prefixcommons: is_identifiers: true is_obo: false prefix: BIOMODELS.TEDDY uri_format: http://identifiers.org/biomodels.teddy/$1 synonyms: - teddy uri_format: https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1 biomodels.vocabulary: mappings: miriam: biomodels.vocabulary n2t: biomodels.vocabulary prefixcommons: BIOMODELS.VOCABULARY miriam: deprecated: false description: Vocabulary used in the RDF representation of SBML models. homepage: http://biomodels.net/rdf/vocabulary.rdf id: '00000514' name: SBML RDF Vocabulary namespaceEmbeddedInLui: false pattern: ^[A-Za-z]+$ prefix: biomodels.vocabulary sampleId: rateRule uri_format: http://biomodels.net/rdf/vocabulary.rdf#$1 n2t: description: Vocabulary used in the RDF representation of SBML models. example: rateRule homepage: http://biomodels.net/rdf/vocabulary.rdf name: Vocabulary via BioModels.net namespaceEmbeddedInLui: false pattern: ^[A-Za-z]+$ prefix: biomodels.vocabulary uri_format: http://biomodels.net/rdf/vocabulary.rdf#$1 prefixcommons: is_identifiers: true is_obo: false prefix: BIOMODELS.VOCABULARY uri_format: http://identifiers.org/biomodels.vocabulary/$1 bionumbers: mappings: miriam: bionumbers n2t: bionumbers prefixcommons: BIONUMBERS miriam: deprecated: false description: BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data. homepage: https://bionumbers.hms.harvard.edu id: '00000101' name: BioNumbers namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bionumbers sampleId: '104674' uri_format: https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1 n2t: description: BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data. example: '104674' homepage: https://bionumbers.hms.harvard.edu name: BioNumbers database namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bionumbers uri_format: https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: BIONUMBERS uri_format: http://identifiers.org/bionumbers/$1 bioportal: fairsharing: abbreviation: BioPortal description: "BioPortal is a library of biomedical ontologies and terminologies\ \ developed in Web Ontology Language (OWL), Resource Description Framework (RDF)(S),\ \ Open Biological and Biomedical Ontologies (OBO) format, and Prot\xE9g\xE9\ \ frames and Rich Release Format. BioPortal groups ontologies by domain to aid\ \ discoverability and allows users to browse, search and visualize the content\ \ of ontologies. BioPortal also provides ontology recommendation, text annotation,\ \ ontology mapping, and a reference index to resources like PubMed." id: '2290' name: BioPortal prefix: FAIRsharing.4m97ah subjects: - Life Science - Ontology and Terminology mappings: fairsharing: FAIRsharing.4m97ah miriam: bioportal n2t: bioportal prefixcommons: BIOPORTAL miriam: deprecated: false description: "BioPortal is an open repository of biomedical ontologies that provides\ \ access via Web services and Web browsers to ontologies developed in OWL, RDF,\ \ OBO format and Prot\xE9g\xE9 frames. BioPortal functionality includes the\ \ ability to browse, search and visualize ontologies." homepage: http://bioportal.bioontology.org/ id: 00000187 name: BioPortal namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bioportal sampleId: '1046' uri_format: http://bioportal.bioontology.org/ontologies/$1 n2t: description: BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. example: '1046' homepage: http://bioportal.bioontology.org/ name: BioPortal at National Center for Biomedical Ontology namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bioportal uri_format: http://bioportal.bioontology.org/ontologies/$1 prefixcommons: is_identifiers: true is_obo: false prefix: BIOPORTAL uri_format: http://identifiers.org/bioportal/$1 bioproject: fairsharing: abbreviation: BioProject description: A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. The BioProject database is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. id: '2210' name: NCBI BioProject prefix: FAIRsharing.aqhv1y subjects: - Life Science mappings: fairsharing: FAIRsharing.aqhv1y miriam: bioproject n2t: bioproject prefixcommons: BIOPROJECT miriam: deprecated: false description: "BioProject provides an organizational framework to access metadata\ \ about research projects and the data from the projects that are deposited\ \ into different databases. It provides information about a project\u2019s scope,\ \ material, objectives, funding source and general relevance categories." homepage: http://trace.ddbj.nig.ac.jp/bioproject/ id: 00000349 name: BioProject namespaceEmbeddedInLui: false pattern: ^PRJ[DEN][A-Z]\d+$ prefix: bioproject providers: - code: ncbi description: BioProject at NCBI homepage: https://www.ncbi.nlm.nih.gov/bioproject name: BioProject at NCBI uri_format: https://www.ncbi.nlm.nih.gov/bioproject?term=$1 - code: ebi description: BioProject at European Nucleotide Archive (ENA) homepage: https://www.ebi.ac.uk/ena/ name: BioProject at European Nucleotide Archive (ENA) uri_format: https://www.ebi.ac.uk/ena/browser/view/$1 sampleId: PRJDB3 uri_format: http://trace.ddbj.nig.ac.jp/BPSearch/bioproject?acc=$1 n2t: description: BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories. example: PRJDB3 homepage: https://www.ncbi.nlm.nih.gov/bioproject name: BioProject at NCBI namespaceEmbeddedInLui: false pattern: ^PRJ[DEN][A-Z]\d+$ prefix: bioproject uri_format: https://www.ncbi.nlm.nih.gov/bioproject?term=$1 prefixcommons: is_identifiers: true is_obo: false prefix: BIOPROJECT uri_format: http://identifiers.org/bioproject/$1 uri_format: https://www.ncbi.nlm.nih.gov/bioproject/?term=$1 bioregistry: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database. example: bioregistry homepage: https://bioregistry.io name: Bioregistry uri_format: https://bioregistry.io/registry/$1 bioregistry.collection: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Manually curated collections of resources stored in the bioregistry example: '0000001' homepage: https://bioregistry.io/collection name: Bioregistry Collections pattern: ^\d{7}$ uri_format: https://bioregistry.io/collection/$1 bioregistry.registry: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Bioregistry's meta-registry example: miriam homepage: https://bioregistry.io/metaregistry/ name: Bioregistry Metaregistry uri_format: https://bioregistry.io/metaregistry/$1 bioregistry.schema: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Schema for the export of the Bioregistry as RDF example: '0000001' homepage: https://bioregistry.io/schema name: Bioregistry Schema pattern: ^\d{7}$ uri_format: https://bioregistry.io/schema/#$1 biorxiv: description: The bioRxiv is a preprint server for biology example: 2021.07.23.453588 example_extras: - 000091 - 000091v1 - 2022.01.24.477526v1 go: homepage: https://www.biorxiv.org/ name: bioRxiv prefix: bioRxiv synonyms: - BIORXIV uri_format: https://www.biorxiv.org/content/$1 homepage: https://biorxiv.org mappings: go: bioRxiv scholia: biorxiv name: bioRxiv pattern: ^(\d{4}\.\d{2}\.\d{2}\.)?\d{6,8}(v\d{1,3})?$ uri_format: https://www.biorxiv.org/content/10.1101/$1 biosample: cellosaurus: category: Biological sample resources homepage: https://www.ebi.ac.uk/biosamples/ name: BioSamples database prefix: BioSamples uri_format: https://www.ebi.ac.uk/biosamples/samples/$1 fairsharing: abbreviation: BioSample description: "The NCBI BioSample database stores submitter-supplied descriptive\ \ information, or metadata, about the biological materials from which data stored\ \ in NCBI\u2019s primary data archives are derived. NCBI\u2019s archives host\ \ data from diverse types of samples from any species, so the BioSample database\ \ is similarly diverse; typical examples of a BioSample include a cell line,\ \ a primary tissue biopsy, an individual organism or an environmental isolate.\ \ The BioSample database promotes the use of structured and consistent attribute\ \ names and values that describe what the samples are as well as information\ \ about their provenance, where appropriate." id: '2211' name: NCBI BioSample prefix: FAIRsharing.qr6pqk subjects: - Biology mappings: cellosaurus: BioSamples fairsharing: FAIRsharing.qr6pqk miriam: biosample n2t: biosample prefixcommons: BIOSAMPLE miriam: deprecated: false description: The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation. homepage: https://www.ebi.ac.uk/biosamples/ id: '00000350' name: BioSample namespaceEmbeddedInLui: false pattern: ^SAM[NED](\w)?\d+$ prefix: biosample providers: - code: ncbi description: BioSample at NCBI homepage: http://www.ncbi.nlm.nih.gov/biosample name: BioSample at NCBI uri_format: http://www.ncbi.nlm.nih.gov/biosample?term=$1 - code: CURATOR_REVIEW description: BioSample at DNA Data Bank of Japan homepage: http://trace.ddbj.nig.ac.jp/biosample/ name: BioSample at DNA Data Bank of Japan uri_format: http://trace.ddbj.nig.ac.jp/BSSearch/biosample?acc=$1 sampleId: SAMEA2397676 uri_format: https://www.ebi.ac.uk/biosamples/sample/$1 n2t: description: The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation. example: SAMEA2397676 homepage: https://www.ebi.ac.uk/biosamples/ name: BioSamples Database at EBI namespaceEmbeddedInLui: false pattern: ^SAM[NED](\w)?\d+$ prefix: biosample uri_format: https://www.ebi.ac.uk/biosamples/sample/$1 prefixcommons: is_identifiers: true is_obo: false prefix: BIOSAMPLE uri_format: http://identifiers.org/biosample/$1 synonyms: - biosamples biosimulations: mappings: miriam: biosimulations miriam: deprecated: false description: BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools. homepage: https://icahn.mssm.edu/ id: 00000880 name: biosimulations namespaceEmbeddedInLui: false pattern: ^[a-zA-Z0-9_-]{3,}$ prefix: biosimulations sampleId: Yeast-cell-cycle-Irons-J-Theor-Biol-2009 uri_format: https://biosimulations.org/projects/$1 biosimulators: fairsharing: abbreviation: BioSimulators description: BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms, and modeling formats) needed for specific modeling projects. id: '3207' name: BioSimulators prefix: FAIRsharing.pwEima subjects: - Computational Biology - Systems Biology mappings: fairsharing: FAIRsharing.pwEima miriam: biosimulators miriam: deprecated: false 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). homepage: https://biosimulators.org/ id: '00000767' name: BioSimulators namespaceEmbeddedInLui: false pattern: '[a-zA-Z0-9-_]+' prefix: biosimulators sampleId: vcell uri_format: https://biosimulators.org/simulators/$1 biostudies: fairsharing: abbreviation: BioStudies description: The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication. id: '2507' name: BioStudies prefix: FAIRsharing.mtjvme subjects: - Life Science - Biomedical Science mappings: fairsharing: FAIRsharing.mtjvme miriam: biostudies n2t: biostudies miriam: deprecated: false description: The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication. homepage: https://www.ebi.ac.uk/biostudies/ id: 00000694 name: BioStudies database namespaceEmbeddedInLui: false pattern: ^S-[A-Z]{4}[A-Z\d\-]+$ prefix: biostudies sampleId: S-EPMC6266652 uri_format: https://www.ebi.ac.uk/biostudies/studies/$1 n2t: description: The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication. example: S-EPMC6266652 homepage: https://www.ebi.ac.uk/biostudies/ name: BioStudies database namespaceEmbeddedInLui: false pattern: ^S-[A-Z]{4}[A-Z\d\-]+$ prefix: biostudies uri_format: https://www.ebi.ac.uk/biostudies/studies/$1 biosystems: fairsharing: abbreviation: BioSystems description: The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. The resource provides categorical information on genes, proteins and small molecules of biosystems. id: '1964' name: NCBI BioSystems Database prefix: FAIRsharing.w2eeqr subjects: - Biology - Systems Biology mappings: fairsharing: FAIRsharing.w2eeqr miriam: biosystems n2t: biosystems prefixcommons: BIOSYSTEMS miriam: deprecated: false description: The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. homepage: https://www.ncbi.nlm.nih.gov/biosystems/ id: 00000097 name: BioSystems namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: biosystems sampleId: '001' uri_format: https://www.ncbi.nlm.nih.gov/biosystems/$1 n2t: description: The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. example: '001' homepage: https://www.ncbi.nlm.nih.gov/biosystems/ name: BioSystems database at NCBI namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: biosystems uri_format: https://www.ncbi.nlm.nih.gov/biosystems/$1 prefixcommons: is_identifiers: true is_obo: false prefix: BIOSYSTEMS uri_format: http://identifiers.org/biosystems/$1 biotools: description: BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research. fairsharing: abbreviation: bio.tools description: bio.tools is a registry of information about bioinformatics software and data services. It was created to help researchers in biological and biomedical science to find and use such resources. id: '3300' name: bio.tools prefix: FAIRsharing.63520c subjects: - Bioinformatics - Biomedical Science - Biology mappings: fairsharing: FAIRsharing.63520c miriam: biotools n2t: biotools prefixcommons: BIOTOOLS miriam: deprecated: false description: Tool and data services registry. homepage: https://bio.tools/ id: '00000616' name: BioTools namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9\_]*$ prefix: biotools sampleId: uniprotkb uri_format: https://bio.tools/$1 n2t: description: Tool and data services registry. example: uniprotkb homepage: https://bio.tools/ name: BioTools namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9\_]*$ prefix: biotools uri_format: https://bio.tools/$1 pattern: ^[-A-Za-z0-9\_]*$ prefixcommons: is_identifiers: true is_obo: false prefix: BIOTOOLS uri_format: http://identifiers.org/biotools/$1 biozil: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Redistributor of bilogics and biomedical supplies example: ls-c35719-120 homepage: https://www.biozol.de/en name: BIOZIL uri_format: https://www.biozol.de/en/product/$1 birnlex: bioportal: name: Biomedical Informatics Research Network Project Lexicon prefix: BIRNLEX comment: Part of the NeuroLex namespace now description: The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. example: birnlex_2023 fairsharing: abbreviation: BIRNLEX description: The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. id: '522' name: Biomedical Informatics Research Network Project Lexicon prefix: FAIRsharing.jedbbt subjects: [] homepage: https://bioportal.bioontology.org/ontologies/BIRNLEX mappings: bioportal: BIRNLEX fairsharing: FAIRsharing.jedbbt name: Biomedical Informatics Research Network Lexicon bitbucket: fairsharing: abbreviation: Bitbucket description: Bitbucket is a Git-based source code repository hosting service owned by Atlassian. It provides a number of different access levels, from free through to premium paid services. Users can create public or private repositories, the latter of which is restricted to 5 users under the free plan. id: '3275' name: Bitbucket prefix: FAIRsharing.fc3431 subjects: - Knowledge and Information Systems - Subject Agnostic - Software Engineering mappings: fairsharing: FAIRsharing.fc3431 miriam: bitbucket miriam: deprecated: false description: Bitbucket is a Git-based source code repository hosting service owned by Atlassian. homepage: https://www.atlassian.com/ id: 00000899 name: Bitbucket namespaceEmbeddedInLui: false pattern: ^[0-9A-Za-z-_\.]+/[0-9A-Za-z-_\.]+$ prefix: bitbucket sampleId: andreadega/systems-biology-compiler uri_format: https://bitbucket.org/$1 bitterdb.cpd: mappings: miriam: bitterdb.cpd n2t: bitterdb.cpd prefixcommons: BITTERDB.CPD miriam: deprecated: false description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds. homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php id: 00000348 name: BitterDB Compound namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bitterdb.cpd sampleId: '46' uri_format: http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1 n2t: description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds. example: '46' homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php name: BitterDB Compound at The Hebrew University of Jerusalem namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bitterdb.cpd uri_format: http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: BITTERDB.CPD uri_format: http://identifiers.org/bitterdb.cpd/$1 bitterdb.rec: mappings: miriam: bitterdb.rec n2t: bitterdb.rec prefixcommons: BITTERDB.REC miriam: deprecated: false description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors. homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php id: '00000347' name: BitterDB Receptor namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bitterdb.rec sampleId: '1' uri_format: http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1 n2t: description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors. example: '1' homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php name: BitterDB Receptor at The Hebrew University of Jerusalem namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bitterdb.rec uri_format: http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: BITTERDB.REC uri_format: http://identifiers.org/bitterdb.rec/$1 bko: bioportal: name: Bricks ontology prefix: BKO comment: This resource also uses SBO terms and resolves them, e.g., http://www.sbgnbricks.org/BKO/full/entry/all/SBO:0000177/. contact: email: adrienrougny@gmail.com github: adrienrougny name: Adrien Rougny orcid: 0000-0002-2118-035X contributor: email: null github: bgyori name: Benjamin Gyori orcid: 0000-0001-9439-5346 description: SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way. example: '0000204' homepage: http://www.sbgnbricks.org/ mappings: bioportal: BKO name: SBGN Bricks data and ontology pattern: ^\d+$ 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:$1 bmrb: fairsharing: abbreviation: BMRB description: BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy. id: '2114' name: Biological Magnetic Resonance Data Bank prefix: FAIRsharing.p06nme subjects: - Structural Biology mappings: fairsharing: FAIRsharing.p06nme miriam: bmrb uniprot: BMRB miriam: deprecated: false description: BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy. homepage: http://www.bmrb.wisc.edu/ id: '00000716' name: Biological Magnetic Resonance Data Bank namespaceEmbeddedInLui: false pattern: ^(bmr|bmse|bmst)?[0-9]{1,6}$ prefix: bmrb sampleId: '15000' uri_format: http://rest.bmrb.wisc.edu/bmrb/$1/html uniprot: category: 3D structure databases identifier: '256' link_is_explicit: 'true' name: Biological Magnetic Resonance Data Bank prefix: BMRB uri_format: https://bmrb.io/data_library/summary/protein.php?uniprot=$1 bmrb.restraint: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively. example: '28789' homepage: https://restraintsgrid.bmrb.io/NRG/MRGridServlet name: NMR Restraints Grid pattern: ^\d+$ 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=$1 bold.taxonomy: mappings: miriam: bold.taxonomy n2t: bold.taxonomy ncbi: BOLD prefixcommons: BOLD.TAXONOMY miriam: deprecated: false description: The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information. homepage: http://www.boldsystems.org/ id: 00000158 name: BOLD Taxonomy namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bold.taxonomy sampleId: '27267' uri_format: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1 n2t: description: The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information. example: '27267' homepage: http://www.boldsystems.org/ name: BOLD taxonomy browser namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bold.taxonomy uri_format: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1 ncbi: example: EPAF263 homepage: http://www.barcodinglife.com name: Barcode of Life database prefix: BOLD prefixcommons: is_identifiers: true is_obo: false prefix: BOLD.TAXONOMY uri_format: http://identifiers.org/bold.taxonomy/$1 bootstrep: mappings: obofoundry: bootstrep prefixcommons: BOOTSTREP obofoundry: contact: vlee@ebi.ac.uk contact.label: Vivian Lee deprecated: true homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html inactive: true name: Gene Regulation Ontology prefix: bootstrep prefixcommons: is_identifiers: false is_obo: true prefix: BOOTSTREP uri_format: http://purl.obolibrary.org/obo/BOOTSTREP_$1 bpdb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Database of biopesticides maintained by the University of Hertfordshire ' example: '2404' homepage: https://sitem.herts.ac.uk/aeru/bpdb/index.htm name: Bio-Pesticides DataBase pattern: ^\d+$ uri_format: https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm brenda: fairsharing: abbreviation: BRENDA description: BRENDA is the main collection of enzyme functional data available to the scientific community. id: '1789' name: BRENDA Enzyme Database prefix: FAIRsharing.etp533 subjects: - Life Science go: homepage: http://www.brenda-enzymes.info name: BRENDA, The Comprehensive Enzyme Information System prefix: BRENDA uri_format: https://www.brenda-enzymes.info/enzyme.php?ecno=$1 mappings: fairsharing: FAIRsharing.etp533 go: BRENDA miriam: brenda n2t: brenda prefixcommons: BRENDA uniprot: BRENDA miriam: deprecated: false description: BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. homepage: https://www.brenda-enzymes.org/ id: '00000071' name: BRENDA namespaceEmbeddedInLui: false pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ prefix: brenda sampleId: 1.1.1.1 uri_format: https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1 n2t: description: BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. example: 1.1.1.1 homepage: https://www.brenda-enzymes.org/ name: Brenda enzyme database namespaceEmbeddedInLui: false pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ prefix: brenda uri_format: https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1 prefixcommons: is_identifiers: true is_obo: false prefix: BRENDA uri_format: http://identifiers.org/brenda/$1 uniprot: category: Enzyme and pathway databases identifier: '131' link_is_explicit: 'true' name: BRENDA Comprehensive Enzyme Information System prefix: BRENDA uri_format: https://www.brenda-enzymes.org/enzyme.php?ecno=%s&UniProtAcc=%u&OrganismID=%d broad: mappings: miriam: broad n2t: broad prefixcommons: BROAD miriam: deprecated: false description: Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae. homepage: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/ id: 00000438 name: Broad Fungal Genome Initiative namespaceEmbeddedInLui: false pattern: ^S\d+$ prefix: broad sampleId: S7000002168151102 uri_format: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1 n2t: description: Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae. example: S7000002168151102 homepage: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/ name: Broad Fungal Genome Initiative at Broad Institute namespaceEmbeddedInLui: false pattern: ^S\d+$ prefix: broad uri_format: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1 prefixcommons: is_identifiers: true is_obo: false prefix: BROAD uri_format: http://identifiers.org/broad/$1 bs: comment: An alernative vocabulary that has been aligned and integrated in Sequence Ontology (SO). contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library. download_obo: https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/subsets/biosapiens.obo example: '00042' homepage: https://github.com/The-Sequence-Ontology/SO-Ontologies name: Biosapiens Protein Feature Ontology pattern: ^\d+$ repository: https://github.com/The-Sequence-Ontology/SO-Ontologies bspo: bioportal: name: Spatial Ontology prefix: BSPO download_obo: https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo example: 0000029 fairsharing: abbreviation: BSPO description: This ontology represents 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. id: '1034' name: Biological SPatial Ontology prefix: FAIRsharing.newa3z subjects: - Anatomy - Life Science mappings: bioportal: BSPO fairsharing: FAIRsharing.newa3z obofoundry: bspo ols: bspo ontobee: BSPO prefixcommons: BSPO obofoundry: appears_in: - aism - colao - fovt - lepao - zp contact: cjmungall@lbl.gov contact.github: cmungall contact.label: Chris Mungall contact.orcid: 0000-0002-6601-2165 deprecated: false description: An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces download.obo: http://purl.obolibrary.org/obo/bspo.obo download.owl: http://purl.obolibrary.org/obo/bspo.owl homepage: https://github.com/obophenotype/biological-spatial-ontology inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Biological Spatial Ontology preferredPrefix: BSPO prefix: bspo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/25140222 title: 'Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.' repository: https://github.com/obophenotype/biological-spatial-ontology ols: 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: http://purl.obolibrary.org/obo/bspo.owl homepage: https://github.com/obophenotype/biological-spatial-ontology name: Biological Spatial Ontology prefix: bspo version: '2021-10-13' version.iri: http://purl.obolibrary.org/obo/bspo/releases/2021-10-13/bspo.owl ontobee: library: Library name: Biological Spatial Ontology prefix: BSPO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: BSPO uri_format: http://purl.obolibrary.org/obo/BSPO_$1 bto: bioportal: name: BRENDA Tissue and Enzyme Source Ontology prefix: BTO cellosaurus: category: Anatomy/cell type resources homepage: https://bioportal.bioontology.org/ontologies/BTO name: BRENDA Tissue Ontology prefix: BTO uri_format: https://bioportal.bioontology.org/ontologies/BTO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_$1 example: 0000590 fairsharing: abbreviation: BTO description: A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. id: '1' name: BRENDA tissue / enzyme source prefix: FAIRsharing.1414v8 subjects: - Enzymology - Life Science go: description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. name: BRENDA tissue / enzyme ontology prefix: BTO mappings: bioportal: BTO cellosaurus: BTO fairsharing: FAIRsharing.1414v8 go: BTO miriam: bto n2t: bto obofoundry: bto ols: bto ontobee: BTO prefixcommons: BTO wikidata: P5501 miriam: deprecated: false description: The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. homepage: https://www.ebi.ac.uk/ols/ontologies/bto id: '00000111' name: Brenda Tissue Ontology namespaceEmbeddedInLui: true pattern: ^BTO:\d{7}$ prefix: bto sampleId: '0000146' uri_format: https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=BTO:$1 n2t: description: The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. example: '0000146' homepage: http://bioportal.bioontology.org/ontologies/BTO name: Brenda Tissue Ontology through BioPortal namespaceEmbeddedInLui: true pattern: ^BTO:\d{7}$ prefix: bto uri_format: http://purl.bioontology.org/ontology/BTO/BTO:$1 obofoundry: contact: c.dudek@tu-braunschweig.de contact.github: chdudek contact.label: Christian-Alexander Dudek contact.orcid: 0000-0001-9117-7909 deprecated: false description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. download.json: http://purl.obolibrary.org/obo/bto.json download.obo: http://purl.obolibrary.org/obo/bto.obo download.owl: http://purl.obolibrary.org/obo/bto.owl homepage: http://www.brenda-enzymes.org inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: BRENDA tissue / enzyme source preferredPrefix: BTO prefix: bto publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/21030441 title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources' repository: https://github.com/BRENDA-Enzymes/BTO ols: description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. download: http://purl.obolibrary.org/obo/bto.owl homepage: http://www.brenda-enzymes.org name: The BRENDA Tissue Ontology (BTO) prefix: bto version: '2021-10-26' version.iri: http://purl.obolibrary.org/obo/bto/releases/2021-10-26/bto.owl ontobee: library: Library name: BRENDA tissue / enzyme source prefix: BTO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: BTO uri_format: http://purl.obolibrary.org/obo/BTO_$1 synonyms: - BTO wikidata: database: Q4836352 database.homepage: https://www.brenda-enzymes.org/ontology.php?ontology_id=3 database.label: BRENDA tissue ontology homepage: https://www.brenda-enzymes.org/ontology.php?ontology_id=3 name: Brenda Tissue Ontology ID pattern: BTO:\d+ prefix: P5501 uri_format: https://www.brenda-enzymes.org/ontology.php?ontology_id=3&id_go=$1 bugbase.expt: mappings: miriam: bugbase.expt n2t: bugbase.expt prefixcommons: BUGBASE.EXPT miriam: deprecated: false description: BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments. homepage: http://bugs.sgul.ac.uk/E-BUGS id: '00000404' name: BugBase Expt namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bugbase.expt sampleId: '288' uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view n2t: description: BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments. example: '288' homepage: http://bugs.sgul.ac.uk/E-BUGS name: BugBase Expt at University of London namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bugbase.expt uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view prefixcommons: is_identifiers: true is_obo: false prefix: BUGBASE.EXPT uri_format: http://identifiers.org/bugbase.expt/$1 bugbase.protocol: mappings: miriam: bugbase.protocol n2t: bugbase.protocol prefixcommons: BUGBASE.PROTOCOL miriam: deprecated: false description: BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols. homepage: http://bugs.sgul.ac.uk/E-BUGS id: '00000403' name: BugBase Protocol namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bugbase.protocol sampleId: '67' uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$1&action=view n2t: description: BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols. example: '67' homepage: http://bugs.sgul.ac.uk/E-BUGS name: BugBase Protocol at University of London namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bugbase.protocol uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$1&action=view prefixcommons: is_identifiers: true is_obo: false prefix: BUGBASE.PROTOCOL uri_format: http://identifiers.org/bugbase.protocol/$1 bykdb: fairsharing: abbreviation: BYKdb description: The Bacterial protein tYrosine Kinase database (BYKdb) contains computer-annotated BY-kinase sequences. The database web interface allows static and dynamic queries and provides integrated analysis tools including sequence annotation. id: '1557' name: Bacterial protein tYrosine Kinase database prefix: FAIRsharing.jr30xc subjects: - Life Science mappings: fairsharing: FAIRsharing.jr30xc miriam: bykdb n2t: bykdb prefixcommons: BYKDB miriam: deprecated: false description: The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information. homepage: https://bykdb.ibcp.fr/BYKdb/ id: '00000253' name: BYKdb namespaceEmbeddedInLui: false pattern: ^[A-Z0-9]+$ prefix: bykdb sampleId: A0A009E7X8 uri_format: https://bykdb.ibcp.fr/data/html/annotated/$1.html n2t: description: The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information. example: A0A009E7X8 homepage: https://bykdb.ibcp.fr/BYKdb/ name: BYKdb at CNRS namespaceEmbeddedInLui: false pattern: ^[A-Z0-9]+$ prefix: bykdb uri_format: https://bykdb.ibcp.fr/data/html/annotated/$1.html name: Bacterial Tyrosine Kinase Database prefixcommons: is_identifiers: true is_obo: false prefix: BYKDB uri_format: http://identifiers.org/bykdb/$1 provides: uniprot cabri: fairsharing: abbreviation: CABRI description: CABRI provides an integrated resource including catalogues of strains of different organism types, genetic materials and other biologicals resources of European culture collections so that the user world-wide can access these relevant data during one searching session through a common entry point and get in touch with collections for ordering products to be delivered to their place of work. id: '1815' name: Common Access to Biological Resources and Information prefix: FAIRsharing.qx2rvz subjects: - Molecular biology - Medical Microbiology - Applied Microbiology - Virology - Molecular Microbiology - Microbiology mappings: fairsharing: FAIRsharing.qx2rvz miriam: cabri n2t: cabri ncbi: CABRI prefixcommons: CABRI miriam: deprecated: false description: CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it. homepage: http://www.cabri.org/ id: '00000261' name: CABRI namespaceEmbeddedInLui: false pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$ 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] sampleId: dsmz_mutz-id:ACC 291 uri_format: http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1] n2t: description: CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it. example: dsmz_mutz-id:ACC 291 homepage: http://www.cabri.org/ name: CABRI Cell Lines catalogue in Genova (SRS) namespaceEmbeddedInLui: false pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$ prefix: cabri uri_format: http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1] ncbi: example: ACC 424 name: Common Access to Biological Resources and Information Project prefix: CABRI prefixcommons: is_identifiers: true is_obo: false prefix: CABRI uri_format: http://identifiers.org/cabri/$1 cadsr: mappings: miriam: cadsr n2t: cadsr miriam: deprecated: false description: The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR. homepage: https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki id: 00000695 name: Cancer Data Standards Registry and Repository namespaceEmbeddedInLui: false pattern: ^[0-9]*$ prefix: cadsr sampleId: '3771992' uri_format: https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1] n2t: description: The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR. example: '3771992' homepage: https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki name: Cancer Data Standards Registry and Repository namespaceEmbeddedInLui: false pattern: ^[0-9]*$ prefix: cadsr uri_format: https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1] caloha: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins. download_obo: https://download.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo example: TS-0001 homepage: https://github.com/calipho-sib/controlled-vocabulary name: CALIPHO Group Ontology of Human Anatomy pattern: ^TS-\d+$ references: - https://twitter.com/neXtProt_news/status/1350105997633867781 repository: https://github.com/calipho-sib/controlled-vocabulary twitter: neXtProt_news cameo: fairsharing: abbreviation: CAMEO description: Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB. Benchmarking results are made available as reference data for methods development. id: '2382' name: Continuously Automated Model Evaluation prefix: FAIRsharing.dq34p2 subjects: - Life Science mappings: fairsharing: FAIRsharing.dq34p2 miriam: cameo n2t: cameo prefixcommons: CAMEO miriam: deprecated: false 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. homepage: https://cameo3d.org id: '00000623' name: CAMEO namespaceEmbeddedInLui: false pattern: ^[0-9\-_]+$ prefix: cameo sampleId: 2019-08-03_00000089_1 uri_format: https://www.cameo3d.org/sp/targets/target/$1 n2t: description: The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB. example: 2018-03-24_00000030_1 homepage: https://cameo3d.org name: CAMEO namespaceEmbeddedInLui: false pattern: ^[0-9\-_]+$ prefix: cameo uri_format: https://www.cameo3d.org/sp/targets/target/$1 name: Continuous Automated Model Evaluation prefixcommons: is_identifiers: true is_obo: false prefix: CAMEO uri_format: http://identifiers.org/cameo/$1 caps: mappings: miriam: caps n2t: caps prefixcommons: CAPS miriam: deprecated: false description: CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. homepage: http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home id: 00000396 name: CAPS-DB namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: caps sampleId: '434' uri_format: http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1 n2t: description: CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. example: '434' homepage: http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home name: CAPS-DB at Leeds Institute of Molecular Medicine namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: caps uri_format: http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1 prefixcommons: is_identifiers: true is_obo: false prefix: CAPS uri_format: http://identifiers.org/caps/$1 caro: bioportal: name: Common Anatomy Reference Ontology prefix: CARO example: '0000000' fairsharing: abbreviation: CARO description: The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. id: '551' name: Common Anatomy Reference Ontology prefix: FAIRsharing.3kcgmr subjects: - Anatomy - Life Science go: description: An upper ontology for anatomy used by OBO Foundry ontologies. Used to facilitate interoperability between existing anatomy ontologies for different species name: Common Anatomy Reference Ontology prefix: CARO mappings: bioportal: CARO fairsharing: FAIRsharing.3kcgmr go: CARO obofoundry: caro ols: caro ontobee: CARO prefixcommons: CARO obofoundry: appears_in: - aism - colao - lepao - pco - ehdaa2 contact: haendel@ohsu.edu contact.github: mellybelly contact.label: Melissa Haendel contact.orcid: 0000-0001-9114-8737 deprecated: false description: An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species download.owl: http://purl.obolibrary.org/obo/caro.owl homepage: https://github.com/obophenotype/caro/ inactive: false license: CC BY 3.0 license.url: https://creativecommons.org/licenses/by/3.0/ name: Common Anatomy Reference Ontology preferredPrefix: CARO prefix: caro repository: https://github.com/obophenotype/caro ols: description: None download: http://purl.obolibrary.org/obo/caro.owl homepage: https://github.com/obophenotype/caro/ name: Common Anatomy Reference Ontology prefix: caro version: '2022-02-18' version.iri: http://purl.obolibrary.org/obo/caro/releases/2022-02-18/caro.owl ontobee: library: Library name: Common Anatomy Reference Ontology prefix: CARO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: CARO uri_format: http://purl.obolibrary.org/obo/CARO_$1 cas: cheminf: description: Identifier used by the Chemical Abstracts Service database. name: CAS registry number obsolete: false prefix: '000446' fairsharing: abbreviation: CAS RN description: Identifier used by the Chemical Abstracts Service Registry. A CAS Registry Number is a numeric identifier that can contain up to 10 digits, divided by hyphens into three parts. The right-most digit is a check digit used to verify the validity and uniqueness of the entire number. id: '381' name: CAS Registry Number prefix: FAIRsharing.r7Kwy7 subjects: - Cheminformatics go: description: CAS REGISTRY is the most authoritative collection of disclosed chemical substance information, containing more than 54 million organic and inorganic substances and 62 million sequences. CAS REGISTRY covers substances identified from the scientific literature from 1957 to the present, with additional substances going back to the early 1900s. homepage: http://www.cas.org/expertise/cascontent/registry/index.html name: CAS Chemical Registry prefix: CAS mappings: cheminf: '000446' fairsharing: FAIRsharing.r7Kwy7 go: CAS miriam: cas n2t: cas prefixcommons: CAS scholia: cas miriam: deprecated: false description: CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information. homepage: https://commonchemistry.cas.org/ id: '00000237' name: CAS namespaceEmbeddedInLui: false pattern: ^\d{1,7}\-\d{2}\-\d$ prefix: cas providers: - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/cas/$1 sampleId: 50-00-0 uri_format: https://commonchemistry.cas.org/detail?ref=$1 n2t: description: CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information. example: 50-00-0 homepage: http://commonchemistry.org name: CAS through Common Chemistry namespaceEmbeddedInLui: false pattern: ^\d{1,7}\-\d{2}\-\d$ prefix: cas uri_format: http://commonchemistry.org/ChemicalDetail.aspx?ref=$1 prefixcommons: is_identifiers: true is_obo: false prefix: CAS uri_format: http://identifiers.org/cas/$1 synonyms: - CASID - CAS_RN - SECONDARY_CAS_RN - cas_id wikidata: prefix: P231 casspc: comment: Jim Balhoff said that Catalog of Fishes does not publish their data in a machine readable format, but a long time ago they sent a CSV dump to help in the development of TTO and VTO. These ontologies are effectively retired and CASSPC terms are only also used in Phenoscape. contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 contributor_extras: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true example: '5359' go: homepage: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp name: Catalog of Fishes species database prefix: CASSPC synonyms: - CAS_SPC uri_format: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1 homepage: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp mappings: go: CASSPC name: Eschmeyer's Catalog of Fishes pattern: ^\d+$ cath: fairsharing: abbreviation: CATH description: The CATH database is a free, publicly available online resource that provides information on the evolutionary relationships of protein domains. It provides 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). id: '2082' name: CATH prefix: FAIRsharing.xgcyyn subjects: - Evolutionary Biology - Biology mappings: fairsharing: FAIRsharing.xgcyyn miriam: cath n2t: cath prefixcommons: CATH miriam: deprecated: false 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. homepage: http://www.cathdb.info id: '00000612' name: CATH Protein Structural Domain Superfamily namespaceEmbeddedInLui: false pattern: ^[1-6]\.[0-9]+\.[0-9]+\.[0-9]+$ prefix: cath sampleId: 1.10.8.10 uri_format: http://www.cathdb.info/cathnode/$1 n2t: description: CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence. example: 1.10.8.10 homepage: http://www.cathdb.info name: CATH Node through UCL namespaceEmbeddedInLui: false pattern: ^[1-4]\.[0-9]+\.[0-9]+\.[0-9]+$ prefix: cath uri_format: http://www.cathdb.info/cathnode/$1 prefixcommons: is_identifiers: true is_obo: false prefix: CATH uri_format: http://identifiers.org/cath/$1 cath.domain: mappings: miriam: cath.domain n2t: cath.domain prefixcommons: CATH.DOMAIN miriam: deprecated: false description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains. homepage: http://www.cathdb.info/ id: '00000210' name: CATH domain namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: cath.domain sampleId: 1cukA01 uri_format: http://www.cathdb.info/domain/$1 n2t: description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains. example: 1cukA01 homepage: http://www.cathdb.info/ name: CATH domain at UCL namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: cath.domain uri_format: http://www.cathdb.info/domain/$1 prefixcommons: is_identifiers: true is_obo: false prefix: CATH.DOMAIN uri_format: http://identifiers.org/cath.domain/$1 cath.superfamily: mappings: miriam: cath.superfamily n2t: cath.superfamily prefixcommons: CATH.SUPERFAMILY miriam: deprecated: false description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification. homepage: http://www.cathdb.info/ id: 00000209 name: CATH superfamily namespaceEmbeddedInLui: false pattern: ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$ prefix: cath.superfamily sampleId: 1.10.10.200 uri_format: http://www.cathdb.info/cathnode/$1 n2t: description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification. example: 1.10.10.200 homepage: http://www.cathdb.info/ name: CATH superfamily at UCL namespaceEmbeddedInLui: false pattern: ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$ prefix: cath.superfamily uri_format: http://www.cathdb.info/cathnode/$1 part_of: cath prefixcommons: is_identifiers: true is_obo: false prefix: CATH.SUPERFAMILY uri_format: http://identifiers.org/cath.superfamily/$1 cattleqtldb: mappings: miriam: cattleqtldb n2t: cattleqtldb prefixcommons: CATTLEQTLDB miriam: deprecated: false description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs. homepage: https://www.animalgenome.org/QTLdb id: '00000504' name: Animal Genome Cattle QTL namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: cattleqtldb sampleId: '4685' uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 n2t: description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs. example: '4685' homepage: http://www.animalgenome.org/cgi-bin/QTLdb/BT/index name: Animal QTL Cattle at Iowa State University namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: cattleqtldb uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_ID=$1 part_of: qtldb prefixcommons: is_identifiers: true is_obo: false prefix: CATTLEQTLDB uri_format: http://identifiers.org/cattleqtldb/$1 cazy: fairsharing: abbreviation: CAZy description: The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. id: '1834' name: The Carbohydrate-Active enZYmes Database prefix: FAIRsharing.ntyq70 subjects: - Life Science - Glycomics go: description: The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. homepage: http://www.cazy.org/ name: Carbohydrate Active EnZYmes prefix: CAZY uri_format: http://www.cazy.org/$1.html mappings: fairsharing: FAIRsharing.ntyq70 go: CAZY miriam: cazy n2t: cazy prefixcommons: CAZY uniprot: CAZy miriam: deprecated: false description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features. homepage: http://www.cazy.org/ id: 00000195 name: CAZy namespaceEmbeddedInLui: false pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$ prefix: cazy sampleId: GT10 uri_format: http://www.cazy.org/$1.html n2t: description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features. example: GT10 homepage: http://www.cazy.org/ name: CAZy at CNRS namespaceEmbeddedInLui: false pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$ prefix: cazy uri_format: http://www.cazy.org/$1.html prefixcommons: is_identifiers: true is_obo: false prefix: CAZY uri_format: http://identifiers.org/cazy/$1 uniprot: category: Protein family/group databases identifier: '136' link_is_explicit: 'true' name: Carbohydrate-Active enZymes prefix: CAZy uri_format: http://www.cazy.org/fam/$1.html cba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE.' example: '375364' homepage: http://www.cba.ac.cn name: Chinese Biological Abstracts pattern: ^\d+$ uri_format: https://europepmc.org/article/CBA/$1 cbioportal: fairsharing: abbreviation: cBioPortal description: The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. id: '2605' name: cBioPortal for Cancer Genomics prefix: FAIRsharing.6L6MjA subjects: - Genomics - Proteomics - Biomedical Science - Preclinical Studies mappings: fairsharing: FAIRsharing.6L6MjA miriam: cbioportal n2t: cbioportal miriam: deprecated: false description: The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. homepage: http://www.cbioportal.org id: 00000679 name: The cBioPortal for Cancer Genomics namespaceEmbeddedInLui: false pattern: ^[a-z0-9\_]+$ prefix: cbioportal sampleId: laml_tcga_pub uri_format: http://www.cbioportal.org/study?id=$1#summary n2t: description: The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. example: laml_tcga_pub homepage: http://www.cbioportal.org name: The cBioPortal for Cancer Genomics namespaceEmbeddedInLui: false pattern: ^[a-z0-9\_]+$ prefix: cbioportal uri_format: http://www.cbioportal.org/study?id=$1#summary uri_format: https://www.cbioportal.org/study/summary?id=$1 ccdc: mappings: miriam: ccdc miriam: deprecated: false description: The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC. homepage: https://www.ccdc.cam.ac.uk/ id: 00000818 name: CCDC Number namespaceEmbeddedInLui: false pattern: ^\d{6,7}$ prefix: ccdc sampleId: '1829126' uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG ccds: fairsharing: abbreviation: CCDS description: The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations. id: '1966' name: The Consensus CDS prefix: FAIRsharing.46s4nt subjects: - Life Science mappings: fairsharing: FAIRsharing.46s4nt miriam: ccds n2t: ccds prefixcommons: CCDS uniprot: CCDS miriam: deprecated: false description: The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations. homepage: http://www.ncbi.nlm.nih.gov/CCDS/ id: '00000375' name: Consensus CDS namespaceEmbeddedInLui: false pattern: ^CCDS\d+\.\d+$ prefix: ccds sampleId: CCDS13573.1 uri_format: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1 n2t: description: The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations. example: CCDS13573.1 homepage: http://www.ncbi.nlm.nih.gov/CCDS/ name: Consensus CDS at NCBI namespaceEmbeddedInLui: false pattern: ^CCDS\d+\.\d+$ prefix: ccds uri_format: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1 prefixcommons: is_identifiers: false is_obo: false prefix: CCDS uri_format: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1 uniprot: category: Sequence databases identifier: '187' link_is_explicit: 'true' name: The Consensus CDS (CCDS) project prefix: CCDS uri_format: https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=$1 ccle: cellosaurus: category: Cell line databases/resources homepage: https://portals.broadinstitute.org/ccle name: Cancer Cell Line Encyclopedia prefix: CCLE uri_format: https://portals.broadinstitute.org/ccle/page?cell_line=$1 description: Datasets around different cancer cell lines generated by the Broad Institute and Novartis example: BT20_BREAST homepage: https://www.cbioportal.org/study/summary?id=ccle_broad_2019 mappings: cellosaurus: CCLE name: Cancer Cell Line Encyclopedia Cells synonyms: - ccle.cell uri_format: https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1 cco: banana: CCO bioportal: name: Cell Cycle Ontology prefix: CCO download_obo: https://www.bio.ntnu.no/ontology/CCO/cco.obo download_owl: https://www.bio.ntnu.no/ontology/CCO/cco.owl fairsharing: abbreviation: CCO description: CCO contains genes, proteins, interactions (comprising genes or proteins that participate in them), processes from the cell cycle subtree of GO, molecular functions (GO), taxa, and ontological constructs (like an upper level ontology and relationships) to stick everything together. id: '1237' name: Cell Cycle Ontology prefix: FAIRsharing.xhwrnr subjects: - Functional Genomics - Genomics - Proteomics - Life Science mappings: bioportal: CCO fairsharing: FAIRsharing.xhwrnr miriam: cco n2t: cco ols: cco prefixcommons: CCO miriam: deprecated: false description: The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process. homepage: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CCO id: '00000234' name: Cell Cycle Ontology namespaceEmbeddedInLui: true pattern: ^CCO\:\w+$ prefix: cco sampleId: '0000003' uri_format: https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1 n2t: description: The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process. example: '0000003' homepage: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CCO name: Cell Cycle Ontology through OLS namespaceEmbeddedInLui: true pattern: ^CCO\:\w+$ prefix: cco uri_format: https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1 ols: contact: vladimir.n.mironov@gmail.com description: The Cell Cycle Ontology extends existing ontologies for cell cycle knowledge building a resource that integrates and manages knowledge about the cell cycle components and regulatory aspects. download: http://www.bio.ntnu.no/ontology/CCO/cco.owl homepage: http://www.semantic-systems-biology.org/apo name: Cell Cycle Ontology prefix: cco version: '2016-03-23' pattern: ^\w+$ prefixcommons: is_identifiers: true is_obo: false prefix: CCO uri_format: http://identifiers.org/cco/$1 ccrid: cellosaurus: category: Cell line databases/resources homepage: http://cellresource.cn/ name: Chinese Cell Resource Information Database prefix: CCRID uri_format: http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 example: 4201PAT-CCTCC00348 homepage: http://www.cellresource.cn mappings: cellosaurus: CCRID name: National Experimental Cell Resource Sharing Platform uri_format: http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1 cdao: bioportal: name: Comparative Data Analysis Ontology prefix: CDAO example: '0000072' fairsharing: abbreviation: CDAO description: Comparative Data Analysis Ontology (CDAO) is a formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). id: '1155' name: Comparative Data Analysis Ontology prefix: FAIRsharing.kay31r subjects: - Molecular biology - Bioinformatics - Taxonomy - Phylogenetics - Evolutionary Biology - Life Science - Biomedical Science mappings: bioportal: CDAO fairsharing: FAIRsharing.kay31r obofoundry: cdao ols: cdao ontobee: CDAO prefixcommons: CDAO obofoundry: contact: balhoff@renci.org contact.github: balhoff contact.label: Jim Balhoff contact.orcid: 0000-0002-8688-6599 deprecated: false description: a formalization of concepts and relations relevant to evolutionary comparative analysis download.owl: http://purl.obolibrary.org/obo/cdao.owl homepage: https://github.com/evoinfo/cdao inactive: false license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Comparative Data Analysis Ontology preferredPrefix: CDAO prefix: cdao publications: - id: https://doi.org/10.4137/EBO.S2320 title: Initial Implementation of a Comparative Data Analysis Ontology repository: https://github.com/evoinfo/cdao ols: description: The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character. download: http://purl.obolibrary.org/obo/cdao.owl homepage: https://github.com/evoinfo/cdao name: Comparative Data Analysis Ontology prefix: cdao version: '2019-06-26' version.iri: http://purl.obolibrary.org/obo/cdao/2019-06-26/cdao.owl ontobee: library: Library name: Comparative Data Analysis Ontology prefix: CDAO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: CDAO uri_format: http://purl.obolibrary.org/obo/CDAO_$1 cdd: fairsharing: abbreviation: CDD description: The Canadian Disaster Database (CDD) contains detailed disaster information on more than 1000 natural, technological and conflict events (excluding war) that have happened since 1900 at home or abroad and that have directly affected Canadians. The database describes where and when a disaster occurred, the number of injuries, evacuations, and fatalities, as well as a rough estimate of the costs. As much as possible, the CDD contains primary data that is valid, current and supported by reliable and traceable sources, including federal institutions, provincial/territorial governments, non-governmental organizations and media sources. Data is updated and reviewed on a semi-annual basis. id: '2804' name: Canadian Disaster Database prefix: FAIRsharing.ea287c subjects: - Geology - Earth Science go: homepage: https://www.ncbi.nlm.nih.gov/cdd name: Conserved Domain Database at NCBI prefix: CDD uri_format: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 mappings: fairsharing: FAIRsharing.ea287c go: CDD miriam: cdd n2t: cdd ncbi: CDD prefixcommons: CDD uniprot: CDD miriam: deprecated: false description: The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd id: 00000119 name: Conserved Domain Database namespaceEmbeddedInLui: false pattern: ^(cd)?\d{5}$ prefix: cdd sampleId: cd00400 uri_format: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 n2t: description: The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. example: cd00400 homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd name: Conserved Domain Database at NCBI namespaceEmbeddedInLui: false pattern: ^(cd)?\d{5}$ prefix: cdd uri_format: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 ncbi: example: 02194 homepage: https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml name: Conserved Domain Database prefix: CDD prefixcommons: is_identifiers: true is_obo: false prefix: CDD uri_format: http://identifiers.org/cdd/$1 uniprot: category: Family and domain databases identifier: '214' link_is_explicit: 'true' name: Conserved Domains Database prefix: CDD uri_format: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 cdno: bioportal: name: Compositional Dietary Nutrition Ontology prefix: CDNO example: '0000013' mappings: bioportal: CDNO obofoundry: cdno ols: cdno ontobee: CDNO obofoundry: contact: l.andres.hernandez.18@student.scu.edu.au contact.github: LilyAndres contact.label: Liliana Andres Hernandez contact.orcid: 0000-0002-7696-731X depends_on: - bfo - chebi - envo - pato - ro deprecated: false description: CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. download.obo: http://purl.obolibrary.org/obo/cdno.obo download.owl: http://purl.obolibrary.org/obo/cdno.owl homepage: https://cdno.info/ inactive: false license: CC BY 3.0 license.url: https://creativecommons.org/licenses/by/3.0/ name: Compositional Dietary Nutrition Ontology preferredPrefix: CDNO prefix: cdno publications: - id: https://doi.org/10.1002/csc2.20092 title: Knowledge representation and data sharing to unlock crop variation for nutritional food security repository: https://github.com/Southern-Cross-Plant-Science/cdno ols: description: None download: http://purl.obolibrary.org/obo/cdno.owl homepage: https://github.com/Southern-Cross-Plant-Science/cdno name: Compositional Dietary Nutrition Ontology prefix: cdno version: '2022-04-06' version.iri: http://purl.obolibrary.org/obo/cdno/releases/2022-04-06/cdno.owl ontobee: library: Library name: Compositional Dietary Nutrition Ontology prefix: CDNO pattern: ^\d{7}$ cdpd: mappings: miriam: cdpd n2t: cdpd prefixcommons: CDPD miriam: deprecated: false 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). homepage: http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp id: '00000272' name: Canadian Drug Product Database namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: cdpd sampleId: '63250' uri_format: http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1 n2t: description: The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN). example: '63250' homepage: http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp name: Canadian Drug Identification Number at Health Canada namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: cdpd uri_format: http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1 prefixcommons: is_identifiers: true is_obo: false prefix: CDPD uri_format: http://identifiers.org/cdpd/$1 cell_biolabs: cellosaurus: category: Cell line collections homepage: https://www.cellbiolabs.com name: Cell Biolabs cell line products prefix: Cell_Biolabs uri_format: https://www.cellbiolabs.com/search?keywords=$1 example: AKR-270 mappings: cellosaurus: Cell_Biolabs cell_model_passport: cellosaurus: category: Cell line databases/resources homepage: https://cellmodelpassports.sanger.ac.uk/ name: Sanger Cell Model Passports prefix: Cell_Model_Passport uri_format: https://cellmodelpassports.sanger.ac.uk/passports/$1 example: SIDM01262 mappings: cellosaurus: Cell_Model_Passport cellbank.australia: cellosaurus: category: Cell line collections homepage: http://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/ name: CellBank Australia prefix: CBA uri_format: http://www.cellbankaustralia.com/$1 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 mappings: cellosaurus: CBA uri_format: https://www.cellbankaustralia.com/$1.html cellimage: fairsharing: abbreviation: null description: This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The purpose of this database is to advance research on cellular activity, with the ultimate goal of improving human health. It is a repository for images, movies, and animations of cells from a variety of organisms that demonstrate cellular architecture and functions. This comprehensive library is designed as a public resource first and foremost for research, and secondarily as a tool for education. The long-term goal is the construction of a library of images that will serve as primary data for research. id: '1723' name: Cell Image Library prefix: FAIRsharing.8t18te subjects: - Life Science - Cell Biology mappings: fairsharing: FAIRsharing.8t18te miriam: cellimage n2t: cellimage prefixcommons: CELLIMAGE miriam: deprecated: false description: "The Cell: An Image Library\u2122 is a freely accessible, public\ \ repository of reviewed and annotated images, videos, and animations of cells\ \ from a variety of organisms, showcasing cell architecture, intracellular functionalities,\ \ and both normal and abnormal processes." homepage: http://cellimagelibrary.org/ id: '00000257' name: Cell Image Library namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: cellimage sampleId: '24801' uri_format: http://cellimagelibrary.org/images/$1 n2t: description: 'The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.' example: '24801' homepage: http://cellimagelibrary.org/ name: Cell Image Library at American Society for Cell Biology namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: cellimage uri_format: http://cellimagelibrary.org/images/$1 prefixcommons: is_identifiers: true is_obo: false prefix: CELLIMAGE uri_format: http://identifiers.org/cellimage/$1 cellopub: cellosaurus: category: Reference resources homepage: https://web.expasy.org/cellosaurus/ name: Cellosaurus Publication prefix: CelloPub uri_format: https://web.expasy.org/cellosaurus/cellopub/$1 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 uri_format: https://web.expasy.org/cellosaurus/cellopub/$1 cellosaurus: cellosaurus: category: Cell line databases/resources homepage: https://web.expasy.org/cellosaurus/ name: Cellosaurus - a knowledge resource on cell lines prefix: Cellosaurus uri_format: https://web.expasy.org/cellosaurus/$1 download_obo: https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo example: CVCL_0440 fairsharing: abbreviation: Cellosaurus description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.' id: '2348' name: Cellosaurus prefix: FAIRsharing.hkk309 subjects: - Life Science mappings: cellosaurus: Cellosaurus fairsharing: FAIRsharing.hkk309 miriam: cellosaurus n2t: cellosaurus prefixcommons: CELLOSAURUS wikidata: P3289 miriam: deprecated: false description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.' homepage: https://web.expasy.org/cellosaurus/ id: 00000598 name: Cellosaurus namespaceEmbeddedInLui: false pattern: ^CVCL_[A-Z0-9]{4}$ prefix: cellosaurus sampleId: CVCL_0030 uri_format: https://web.expasy.org/cellosaurus/$1 n2t: 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.' example: CVCL_0030 homepage: https://web.expasy.org/cellosaurus/ name: Cellosaurus through SIB namespaceEmbeddedInLui: false pattern: CVCL_[A-Z0-9]{4} prefix: cellosaurus uri_format: https://web.expasy.org/cellosaurus/$1 name: Cellosaurus pattern: ^CVCL_[A-Z0-9]{4}$ prefixcommons: is_identifiers: true is_obo: false prefix: CELLOSAURUS uri_format: http://identifiers.org/cellosaurus/$1 synonyms: - CVCL wikidata: database: Q24691710 database.homepage: https://web.expasy.org/cellosaurus/ database.label: Cellosaurus name: Cellosaurus ID pattern: CVCL_[A-Z\d][A-Z\d][A-Z\d][A-Z\d] prefix: P3289 uri_format: https://web.expasy.org/cellosaurus/$1 cellosaurus.resource: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The set of prefixes used in the Cellosaurus resource example: 4DN homepage: https://web.expasy.org/cellosaurus/ name: Cellosaurus Registry uri_format: https://bioregistry.io/metaregistry/cellosaurus/$1 cellrepo: mappings: miriam: cellrepo miriam: deprecated: false description: The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines homepage: https://cellrepo.ico2s.org/ id: 00000829 name: Cell Version Control Repository namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: cellrepo sampleId: '82' uri_format: https://cellrepo.ico2s.org/repositories/$1 ceph: bioportal: name: Cephalopod Ontology prefix: CEPH download_obo: https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo example: 0000109 fairsharing: abbreviation: CEPH description: An anatomical and developmental ontology for cephalopods id: '668' name: Cephalopod Ontology prefix: FAIRsharing.p58bm4 subjects: [] mappings: bioportal: CEPH fairsharing: FAIRsharing.p58bm4 obofoundry: ceph ols: ceph ontobee: CEPH prefixcommons: CEPH obofoundry: contact: cjmungall@lbl.gov contact.github: cmungall contact.label: Chris Mungall contact.orcid: 0000-0002-6601-2165 deprecated: false description: An anatomical and developmental ontology for cephalopods download.obo: http://purl.obolibrary.org/obo/ceph.obo download.owl: http://purl.obolibrary.org/obo/ceph.owl homepage: https://github.com/obophenotype/cephalopod-ontology inactive: true license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Cephalopod Ontology prefix: ceph repository: https://github.com/obophenotype/cephalopod-ontology ols: description: An anatomical and developmental ontology for cephalopods download: http://purl.obolibrary.org/obo/ceph.owl homepage: https://github.com/obophenotype/cephalopod-ontology name: Cephalopod Ontology prefix: ceph version: '2016-01-12' version.iri: http://purl.obolibrary.org/obo/ceph/releases/2016-01-12/ceph.owl ontobee: library: Library name: Cephalopod Ontology prefix: CEPH pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: CEPH uri_format: http://purl.obolibrary.org/obo/CEPH_$1 cgd: fairsharing: abbreviation: CGD description: The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products. id: '1816' name: Candida Genome Database prefix: FAIRsharing.j7j53 subjects: - Life Science go: homepage: http://www.candidagenome.org/ name: Candida Genome Database prefix: CGD synonyms: - CGDID uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 mappings: fairsharing: FAIRsharing.j7j53 go: CGD miriam: cgd n2t: cgd ncbi: CGD prefixcommons: CGD uniprot: CGD miriam: deprecated: false description: The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products. homepage: http://www.candidagenome.org/ id: '00000145' name: Candida Genome Database namespaceEmbeddedInLui: false pattern: ^CAL\d{7}$ prefix: cgd sampleId: CAL0003079 uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 n2t: description: The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products. example: CAL0003079 homepage: http://www.candidagenome.org/ name: Candida Genome Database at Stanford University namespaceEmbeddedInLui: false pattern: ^CAL\d{7}$ prefix: cgd uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 ncbi: example: CAL0005934 homepage: http://www.candidagenome.org/ name: Candida Genome Database prefix: CGD prefixcommons: is_identifiers: true is_obo: false prefix: CGD uri_format: http://identifiers.org/cgd/$1 uniprot: category: Organism-specific databases identifier: '126' link_is_explicit: 'true' name: Candida Genome Database prefix: CGD uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 cghdb: cellosaurus: category: Cell line databases/resources homepage: http://www.cghtmd.jp/CGHDatabase/index_e.jsp name: CGH Data Base prefix: CGH-DB uri_format: http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en example: 300165/p13898_2106T mappings: cellosaurus: CGH-DB cgnc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans) example: '10087' homepage: http://birdgenenames.org/cgnc/ name: Chicken Gene Nomenclature Consortium pattern: ^\d+$ synonyms: - BirdBase - CGNC uri_format: http://birdgenenames.org/cgnc/GeneReport?id=$1 cgsc: fairsharing: abbreviation: CGSC description: The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. id: '1818' name: Coli Genetic Stock Center prefix: FAIRsharing.1tbrdz subjects: - Life Science go: homepage: http://cgsc.biology.yale.edu/ name: CGSC prefix: CGSC mappings: fairsharing: FAIRsharing.1tbrdz go: CGSC miriam: cgsc n2t: cgsc prefixcommons: CGSC miriam: deprecated: false description: The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. homepage: http://cgsc.biology.yale.edu/index.php id: 00000295 name: CGSC Strain namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: cgsc sampleId: '74' uri_format: http://cgsc.biology.yale.edu/Site.php?ID=$1 n2t: description: The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. example: '74' homepage: http://cgsc.biology.yale.edu/index.php name: CGSC at Yale university namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: cgsc uri_format: http://cgsc.biology.yale.edu/Site.php?ID=$1 name: Coli Genetic Stock Center prefixcommons: is_identifiers: true is_obo: false prefix: CGSC uri_format: http://identifiers.org/cgsc/$1 charprot: mappings: miriam: charprot n2t: charprot prefixcommons: CHARPROT miriam: deprecated: false description: CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession. homepage: http://www.jcvi.org/charprotdb id: '00000341' name: CharProt namespaceEmbeddedInLui: false pattern: ^CH_\d+$ prefix: charprot sampleId: CH_001923 uri_format: http://www.jcvi.org/charprotdb/index.cgi/view/$1 n2t: description: CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession. example: CH_001923 homepage: http://www.jcvi.org/charprotdb name: CharProt at JCVI namespaceEmbeddedInLui: false pattern: ^CH_\d+$ prefix: charprot uri_format: http://www.jcvi.org/charprotdb/index.cgi/view/$1 prefixcommons: is_identifiers: true is_obo: false prefix: CHARPROT uri_format: http://identifiers.org/charprot/$1 chebi: bioportal: name: Chemical Entities of Biological Interest Ontology prefix: CHEBI cellosaurus: category: Chemistry resources homepage: https://www.ebi.ac.uk/chebi/ name: Chemical Entities of Biological Interest prefix: ChEBI uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=$1 cheminf: description: Database identifier used by ChEBI. name: ChEBI obsolete: false prefix: '000407' example: '24867' fairsharing: abbreviation: ChEBI description: "Chemical Entities of Biological Interest (ChEBI) is a free dictionary\ \ that describes 'small\u2019 chemical compounds. These compound includes distinct\ \ synthetic or natural atoms, molecules, ions, ion pair, radicals, radical ions,\ \ complexes, conformers, etc.. These molecular entities can interact with or\ \ affect the processes of living organisms." id: '1036' name: Chemical Entities of Biological Interest prefix: FAIRsharing.62qk8w subjects: - Biochemistry - Chemistry go: homepage: http://www.ebi.ac.uk/chebi/ name: Chemical Entities of Biological Interest prefix: CHEBI synonyms: - ChEBI uri_format: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1 mappings: bioportal: CHEBI cellosaurus: ChEBI cheminf: '000407' fairsharing: FAIRsharing.62qk8w go: CHEBI miriam: chebi n2t: chebi obofoundry: chebi ols: chebi ontobee: CHEBI prefixcommons: CHEBI wikidata: P683 miriam: deprecated: false description: Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. homepage: https://www.ebi.ac.uk/chebi/ id: '00000002' name: ChEBI namespaceEmbeddedInLui: true pattern: ^CHEBI:\d+$ prefix: chebi sampleId: '36927' uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1 n2t: description: Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. example: '36927' homepage: https://www.ebi.ac.uk/chebi/ name: ChEBI (Chemical Entities of Biological Interest) namespaceEmbeddedInLui: true pattern: ^CHEBI:\d+$ prefix: chebi uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1 name: Chemical Entities of Biological Interest obofoundry: appears_in: - cdno - chiro - cl - ecocore - ecto - envo - fobi - foodon - genepio - maxo - mco - ons - pcl - uberon - xpo - scdo contact: amalik@ebi.ac.uk contact.github: amalik01 contact.label: Adnan Malik contact.orcid: 0000-0001-8123-5351 deprecated: false description: A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds. download.obo: http://purl.obolibrary.org/obo/chebi.obo download.owl: http://purl.obolibrary.org/obo/chebi.owl homepage: http://www.ebi.ac.uk/chebi inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Chemical Entities of Biological Interest preferredPrefix: CHEBI prefix: chebi publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/26467479 title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites.' repository: https://github.com/ebi-chebi/ChEBI twitter: chebit ols: description: A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds. download: http://purl.obolibrary.org/obo/chebi.owl homepage: http://www.ebi.ac.uk/chebi name: Chemical Entities of Biological Interest prefix: chebi version: '210' version.iri: http://purl.obolibrary.org/obo/chebi/210/chebi.owl ontobee: library: Foundry name: Chemical Entities of Biological Interest prefix: CHEBI pattern: ^\d+$ prefixcommons: is_identifiers: false is_obo: true prefix: CHEBI uri_format: http://purl.obolibrary.org/obo/CHEBI_$1 providers: - code: chebi-img description: Image server from chebi homepage: https://www.ebi.ac.uk/chebi/ name: ChEBI uri_format: https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=$1 synonyms: - CHEBI - CHEBIID - ChEBI uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1 wikidata: database: Q902623 database.homepage: http://www.ebi.ac.uk/chebi database.label: ChEBI format.rdf: http://purl.obolibrary.org/obo/CHEBI_$1 homepage: https://www.ebi.ac.uk/chebi name: ChEBI ID pattern: \d+ prefix: P683 uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1 chembl: cheminf: description: Identifier used by the ChEMBL database for compounds, assays, target, etc. name: ChEMBL obsolete: false prefix: '000412' fairsharing: abbreviation: ChEMBL description: ChEMBL is an open, manually-curated, large-scale bioactivity database containing information from medicinal chemistry literature. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. Information regarding the compounds tested (including their structures), the biological or physicochemical assays performed on these and the targets of these assays are recorded in a structured form, allowing users to address a broad range of drug discovery questions. id: '1561' name: ChEMBL prefix: FAIRsharing.m3jtpg subjects: - Drug Discovery - Biochemistry - Genomics - Medicinal Chemistry homepage: https://www.ebi.ac.uk/chembl mappings: cheminf: '000412' fairsharing: FAIRsharing.m3jtpg miriam: chembl uniprot: ChEMBL miriam: deprecated: false description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. homepage: https://www.ebi.ac.uk/chembl id: 00000799 name: ChEMBL namespaceEmbeddedInLui: false pattern: ^CHEMBL\d+$ prefix: chembl sampleId: CHEMBL4303805 uri_format: https://www.ebi.ac.uk/chembl/entity/$1 synonyms: - ChEMBL - ChEMBL_ID - chembl uniprot: category: Chemistry databases identifier: '174' link_is_explicit: 'true' name: ChEMBL database of bioactive drug-like small molecules prefix: ChEMBL uri_format: https://www.ebi.ac.uk/chembldb/target/inspect/$1 chembl.cell: cellosaurus: category: Chemistry resources homepage: https://www.ebi.ac.uk/chembldb name: ChEMBL database of bioactive drug-like small molecules - Cell lines section prefix: ChEMBL-Cells uri_format: https://www.ebi.ac.uk/chembldb/cell/inspect/$1 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 example: CHEMBL3307800 mappings: cellosaurus: ChEMBL-Cells part_of: chembl synonyms: - ChEMBL-Cells uri_format: https://www.ebi.ac.uk/chembl/cell_line_report_card/$1 chembl.compound: example: CHEMBL465070 mappings: miriam: chembl.compound n2t: chembl.compound prefixcommons: CHEMBL.COMPOUND wikidata: P592 miriam: deprecated: false description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. homepage: https://www.ebi.ac.uk/chembldb/ id: 00000084 name: ChEMBL compound namespaceEmbeddedInLui: false pattern: ^CHEMBL\d+$ prefix: chembl.compound providers: - code: CURATOR_REVIEW description: ChEMBL compound RDF homepage: https://github.com/egonw/chembl.rdf name: ChEMBL compound RDF uri_format: http://linkedchemistry.info/chembl/chemblid/$1 - code: CURATOR_REVIEW description: ChEMBL compound RDF through EBI RDF Platform homepage: https://www.ebi.ac.uk/rdf/services/chembl/ name: ChEMBL compound RDF through EBI RDF Platform uri_format: https://rdf.ebi.ac.uk/resource/chembl/molecule/$1 sampleId: CHEMBL308052 uri_format: https://www.ebi.ac.uk/chembl/compound/inspect/$1 n2t: description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. example: CHEMBL308052 homepage: https://www.ebi.ac.uk/chembldb/ name: ChEMBL compound database at EBI namespaceEmbeddedInLui: false pattern: ^CHEMBL\d+$ prefix: chembl.compound uri_format: https://www.ebi.ac.uk/chembl/compound/inspect/$1 name: ChEMBL part_of: chembl pattern: ^CHEMBL\d+$ prefixcommons: is_identifiers: true is_obo: false prefix: CHEMBL.COMPOUND uri_format: http://identifiers.org/chembl.compound/$1 wikidata: database: Q6120337 database.homepage: http://www.ebi.ac.uk/chembl database.label: ChEMBL format.rdf: http://rdf.ebi.ac.uk/resource/chembl/molecule/$1 homepage: https://www.ebi.ac.uk/chembl name: ChEMBL ID pattern: CHEMBL\d+ prefix: P592 uri_format: https://www.ebi.ac.uk/chembl/compound_report_card/$1/ chembl.target: cellosaurus: category: Chemistry resources homepage: https://www.ebi.ac.uk/chembldb name: ChEMBL database of bioactive drug-like small molecules - Targets section prefix: ChEMBL-Targets uri_format: https://www.ebi.ac.uk/chembldb/target/inspect/$1 mappings: cellosaurus: ChEMBL-Targets miriam: chembl.target n2t: chembl.target prefixcommons: CHEMBL.TARGET miriam: deprecated: false description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. homepage: https://www.ebi.ac.uk/chembldb/ id: 00000085 name: ChEMBL target namespaceEmbeddedInLui: false pattern: ^CHEMBL\d+$ prefix: chembl.target providers: - code: CURATOR_REVIEW description: ChEMBL target RDF homepage: https://github.com/egonw/chembl.rdf name: ChEMBL target RDF uri_format: http://linkedchemistry.info/chembl/chemblid/$1 - code: CURATOR_REVIEW description: ChEMBL target RDF through EBI RDF Platform homepage: https://rdf.ebi.ac.uk/resource/chembl/ name: ChEMBL target RDF through EBI RDF Platform uri_format: https://rdf.ebi.ac.uk/resource/chembl/target/$1 sampleId: CHEMBL3467 uri_format: https://www.ebi.ac.uk/chembl/target/inspect/$1 n2t: description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. example: CHEMBL3467 homepage: https://www.ebi.ac.uk/chembldb/ name: ChEMBL targets database at EBI namespaceEmbeddedInLui: false pattern: ^CHEMBL\d+$ prefix: chembl.target uri_format: https://www.ebi.ac.uk/chembl/target/inspect/$1 part_of: chembl prefixcommons: is_identifiers: true is_obo: false prefix: CHEMBL.TARGET uri_format: http://identifiers.org/chembl.target/$1 synonyms: - ChEMBL-Targets chemdb: fairsharing: abbreviation: ChemDB description: ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. id: '2088' name: The UC Irvine ChemDB prefix: FAIRsharing.dstf7h subjects: - Biochemistry - Life Science - Biomedical Science - Systems Biology - Preclinical Studies mappings: fairsharing: FAIRsharing.dstf7h miriam: chemdb n2t: chemdb prefixcommons: CHEMDB miriam: deprecated: false description: ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. homepage: http://cdb.ics.uci.edu/ id: 00000279 name: ChemDB namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: chemdb sampleId: '3966782' uri_format: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1 n2t: description: ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. example: '3966782' homepage: http://cdb.ics.uci.edu/ name: ChemDB at UC Irvine namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: chemdb uri_format: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: CHEMDB uri_format: http://identifiers.org/chemdb/$1 chemidplus: fairsharing: abbreviation: ChemIDplus description: ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. id: '2003' name: ChemIDplus prefix: FAIRsharing.5949vn subjects: - Chemistry - Biomedical Science mappings: fairsharing: FAIRsharing.5949vn miriam: chemidplus n2t: chemidplus prefixcommons: CHEMIDPLUS miriam: deprecated: false description: ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. homepage: https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp id: 00000096 name: ChemIDplus namespaceEmbeddedInLui: false pattern: ^\d+\-\d+\-\d+$ prefix: chemidplus sampleId: 57-27-2 uri_format: https://chem.nlm.nih.gov/chemidplus/rn/$1 n2t: description: ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. example: 57-27-2 homepage: https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp name: ChemIDplus at National Library of Medicine namespaceEmbeddedInLui: false pattern: ^\d+\-\d+\-\d+$ prefix: chemidplus uri_format: https://chem.nlm.nih.gov/chemidplus/rn/$1 prefixcommons: is_identifiers: true is_obo: false prefix: CHEMIDPLUS uri_format: http://identifiers.org/chemidplus/$1 synonyms: - ChemIDplus cheminf: bioportal: name: Chemical Information Ontology prefix: CHEMINF download_owl: https://github.com/semanticchemistry/semanticchemistry/raw/master/ontology/cheminf.owl example: '000410' fairsharing: abbreviation: CHEMINF description: The Chemical Information Ontology (CHEMINF) aims to establish a standard in representing chemical information. In particular, it aims to produce an ontology to represent chemical structure and to richly describe chemical properties, whether intrinsic or computed. id: '1056' name: CHEMical INFormation Ontology prefix: FAIRsharing.sjhvyy subjects: - Biochemistry - Chemistry - Life Science mappings: bioportal: CHEMINF fairsharing: FAIRsharing.sjhvyy obofoundry: cheminf ols: cheminf ontobee: CHEMINF prefixcommons: CHEMINF name: Chemical Information Ontology obofoundry: contact: egon.willighagen@gmail.com contact.github: egonw contact.label: Egon Willighagen contact.orcid: 0000-0001-7542-0286 deprecated: false description: Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. download.owl: http://purl.obolibrary.org/obo/cheminf.owl homepage: https://github.com/semanticchemistry/semanticchemistry inactive: false license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Chemical Information Ontology preferredPrefix: CHEMINF prefix: cheminf publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/21991315 title: 'The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web' repository: https://github.com/semanticchemistry/semanticchemistry ols: description: Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. download: http://purl.obolibrary.org/obo/cheminf.owl homepage: https://github.com/semanticchemistry/semanticchemistry name: chemical information ontology (cheminf) - information entities about chemical entities prefix: cheminf version: '2.0' ontobee: library: Library name: Chemical Information Ontology prefix: CHEMINF pattern: ^\d{6}$ prefixcommons: is_identifiers: false is_obo: true prefix: CHEMINF uri_format: http://purl.obolibrary.org/obo/CHEMINF_$1 chemspider: cheminf: description: Database identifier used by ChemSpider. name: ChemSpider obsolete: false prefix: '000405' fairsharing: abbreviation: ChemSpider description: ChemSpider is a freely available collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources. id: '2042' name: ChemSpider prefix: FAIRsharing.96f3gm subjects: - Chemistry - Life Science mappings: cheminf: '000405' fairsharing: FAIRsharing.96f3gm miriam: chemspider n2t: chemspider prefixcommons: CHEMSPIDER wikidata: P661 miriam: deprecated: false description: ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources. homepage: http://www.chemspider.com/ id: 00000138 name: ChemSpider namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: chemspider sampleId: '56586' uri_format: http://www.chemspider.com/Chemical-Structure.$1.html n2t: description: ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources. example: '56586' homepage: http://www.chemspider.com/ name: ChemSpider at RSC namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: chemspider uri_format: http://www.chemspider.com/Chemical-Structure.$1.html name: ChemSpider prefixcommons: is_identifiers: true is_obo: false prefix: CHEMSPIDER uri_format: http://identifiers.org/chemspider/$1 synonyms: - ChemSpiderID - Chemspider wikidata: database: Q2311683 database.homepage: https://www.chemspider.com/ database.label: ChemSpider format.rdf: http://rdf.chemspider.com/$1 homepage: https://www.chemspider.com/ name: ChemSpider ID pattern: '[1-9]\d*' prefix: P661 uri_format: https://www.chemspider.com/Chemical-Structure.$1.html chickenqtldb: mappings: miriam: chickenqtldb n2t: chickenqtldb prefixcommons: CHICKENQTLDB miriam: deprecated: false description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs. homepage: https://www.animalgenome.org/QTLdb id: '00000505' name: Animal Genome Chicken QTL namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: chickenqtldb sampleId: '14362' uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 n2t: description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs. example: '14362' homepage: http://www.animalgenome.org/cgi-bin/QTLdb/GG/index name: Animal QTL Chicken at Iowa State University namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: chickenqtldb uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/GG/qdetails?QTL_ID=$1 part_of: qtldb prefixcommons: is_identifiers: true is_obo: false prefix: CHICKENQTLDB uri_format: http://identifiers.org/chickenqtldb/$1 chiro: bioportal: name: CHEBI Integrated Role Ontology prefix: CHIRO mappings: bioportal: CHIRO obofoundry: chiro ols: chiro ontobee: CHIRO name: ChEBI Integrated Role Ontology no_own_terms: true obofoundry: contact: vasilevs@ohsu.edu contact.github: nicolevasilevsky contact.label: Nicole Vasilevsky contact.orcid: 0000-0001-5208-3432 depends_on: - chebi - go - hp - mp - ncbitaxon - pr - uberon deprecated: false 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 inactive: false license: CC0 1.0 license.url: http://creativecommons.org/publicdomain/zero/1.0/ name: CHEBI Integrated Role Ontology preferredPrefix: CHIRO prefix: chiro publications: - id: https://doi.org/10.26434/chemrxiv.12591221 title: Extension of Roles in the ChEBI Ontology repository: https://github.com/obophenotype/chiro ols: 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: http://purl.obolibrary.org/obo/chiro.owl homepage: https://github.com/obophenotype/chiro name: CHEBI Integrated Role Ontology prefix: chiro version: '2015-11-23' version.iri: http://purl.obolibrary.org/obo/chiro/releases/2015-11-23/chiro.owl ontobee: library: Library name: CHEBI Integrated Role Ontology prefix: CHIRO chmo: bioportal: name: Chemical Methods Ontology prefix: CHMO example: 0002902 fairsharing: abbreviation: CHMO 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; and 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). id: '1424' name: Chemical Methods Ontology prefix: FAIRsharing.9j4wh2 subjects: - Chemistry mappings: bioportal: CHMO fairsharing: FAIRsharing.9j4wh2 obofoundry: chmo ols: chmo ontobee: CHMO prefixcommons: CHMO obofoundry: appears_in: - rbo - scdo contact: batchelorc@rsc.org contact.github: batchelorc contact.label: Colin Batchelor contact.orcid: 0000-0001-5985-7429 deprecated: false description: CHMO, the chemical methods ontology, describes methods used to download.owl: http://purl.obolibrary.org/obo/chmo.owl homepage: https://github.com/rsc-ontologies/rsc-cmo inactive: false license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Chemical Methods Ontology preferredPrefix: CHMO prefix: chmo repository: https://github.com/rsc-ontologies/rsc-cmo ols: contact: chemistry-ontologies@googlegroups.com 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: http://purl.obolibrary.org/obo/chmo.owl homepage: https://github.com/rsc-ontologies/rsc-cmo name: Chemical Methods Ontology prefix: chmo version: '2022-04-19' version.iri: http://purl.obolibrary.org/obo/chmo/releases/2022-04-19/chmo.owl ontobee: library: Library name: Chemical Methods Ontology prefix: CHMO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: CHMO uri_format: http://purl.obolibrary.org/obo/CHMO_$1 cido: bioportal: name: Coronavirus Infectious Disease Ontology prefix: CIDO example: '0000005' fairsharing: abbreviation: CIDO 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, epidemiology, pathogenesis, diagnosis, prevention, and treatment. Its development follows the OBO Foundry Principles. id: '1401' name: Coronavirus Infectious Disease Ontology prefix: FAIRsharing.aVmpKl subjects: - Drug Discovery - Bioinformatics - Drug Repositioning - Virology - Epidemiology mappings: bioportal: CIDO fairsharing: FAIRsharing.aVmpKl obofoundry: cido ols: cido ontobee: CIDO obofoundry: contact: yongqunh@med.umich.edu contact.github: yongqunh contact.label: Yongqun Oliver He contact.orcid: 0000-0001-9189-9661 deprecated: false description: The Coronavirus Infectious Disease Ontology (CIDO) aims to ontologically represent and standardize various aspects of coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment. download.owl: http://purl.obolibrary.org/obo/cido.owl homepage: https://github.com/cido-ontology/cido inactive: false license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Coronavirus Infectious Disease Ontology preferredPrefix: CIDO prefix: cido repository: https://github.com/cido-ontology/cido ols: contact: cido-discuss@googlegroups.com 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: http://purl.obolibrary.org/obo/cido.owl homepage: https://github.com/cido-ontology/cido name: 'CIDO: Ontology of Coronavirus Infectious Disease' prefix: cido version: 1.0.281 ontobee: library: Library name: Coronavirus Infectious Disease Ontology prefix: CIDO pattern: ^\d{7}$ cio: bioportal: name: Confidence Information Ontology prefix: CIO example: '0000040' fairsharing: abbreviation: CIO description: An ontology to capture confidence information about annotations id: '644' name: Confidence Information Ontology prefix: FAIRsharing.e3t0yw subjects: [] mappings: bioportal: CIO fairsharing: FAIRsharing.e3t0yw obofoundry: cio ols: cio ontobee: CIO prefixcommons: CIO obofoundry: contact: frederic.bastian@unil.ch contact.github: fbastian contact.label: "Fr\xE9d\xE9ric Bastian" contact.orcid: 0000-0002-9415-5104 deprecated: false 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 homepage: https://github.com/BgeeDB/confidence-information-ontology inactive: false license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Confidence Information Ontology preferredPrefix: CIO prefix: cio repository: https://github.com/BgeeDB/confidence-information-ontology ols: description: An ontology to capture confidence information about annotations. download: http://purl.obolibrary.org/obo/cio.owl homepage: https://github.com/BgeeDB/confidence-information-ontology name: Confidence Information Ontology prefix: cio version: '2015-03-10' version.iri: http://purl.obolibrary.org/obo/cio/releases/2015-03-10/cio.owl ontobee: library: Library name: Confidence Information Ontology prefix: CIO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: CIO uri_format: http://purl.obolibrary.org/obo/CIO_$1 citexplore: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes. example: C6155 fairsharing: abbreviation: CTX description: The ontology represents CTX phenotypes, genetic variants, and bidirectional relationships between them though a patient model. The CTX ontology was build reusing the Human Phenotype Ontology (HPO) and the Snomed ct ontologies. A set of temporal clinical manifestations are semantically annotated with a domain phenotype ontology and registered with a time-stamped value. id: '936' name: Cerebrotendinous Xanthomatosis Ontology prefix: FAIRsharing.619eqr subjects: - Genetics - Biomedical Science - Preclinical Studies homepage: https://www.ebi.ac.uk/citexplore/ mappings: fairsharing: FAIRsharing.619eqr name: CiteXplore references: - https://www.embl.de/aboutus/communication_outreach/media_relations/2006/061127_hinxton/ synonyms: - CTX uri_format: https://europepmc.org/article/CTX/$1 civic.aid: mappings: miriam: civic.aid miriam: deprecated: false description: 'A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC.' homepage: https://civicdb.org/ id: 00000835 name: CIViC Assertion namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: civic.aid sampleId: '3' uri_format: https://civicdb.org/links/assertions/$1 civic.eid: mappings: miriam: civic.eid miriam: deprecated: false description: "Evidence Items are the central building block of the Clinical Interpretation\ \ of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is\ \ a piece of information that has been manually curated from trustable medical\ \ literature about a Variant or genomic \u2018event\u2019 that has implications\ \ in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis,\ \ Predictive response to therapy, Oncogenicity or protein Function. For example,\ \ an Evidence Item might describe a line of evidence supporting the notion that\ \ tumors with a somatic BRAF V600 mutation generally respond well to the drug\ \ dabrafenib. A Variant may be a single nucleotide substitution, a small insertion\ \ or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression\ \ pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds\ \ to a single citable Source (a publication or conference abstract)." homepage: https://civicdb.org/ id: 00000839 name: CIViC Evidence namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: civic.eid sampleId: '1199' uri_format: https://civicdb.org/links/evidence/$1 cl: bioportal: name: Cell Ontology prefix: CL cellosaurus: category: Anatomy/cell type resources homepage: https://obophenotype.github.io/cell-ontology/ name: Cell Ontology prefix: CL uri_format: https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http://purl.obolibrary.org/obo/$1 download_obo: https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-full.obo example: '0000062' fairsharing: abbreviation: CL description: The Cell Ontology (CL) is a candidate OBO Foundry ontology for the representation of cell types. First described in 2005, the CL integrates cell types from the prokaryotic, fungal, and eukaryotic organisms. As a core component of the OBO Foundry, the CL merges information contained in species-specific anatomical ontologies as well as referencing other OBO Foundry ontologies such as the Protein Ontology (PR) for uniquely expressed biomarkers and the Gene Ontology (GO) for the biological processes a cell type participates in. The CL is under continuous revision to expand representation of cell types and to better integrate with other biomedical ontologies. id: '1004' name: Cell Ontology prefix: FAIRsharing.j9y503 subjects: - Anatomy - Life Science - Cell Biology go: homepage: http://cellontology.org name: Cell Type Ontology prefix: CL mappings: bioportal: CL cellosaurus: CL fairsharing: FAIRsharing.j9y503 go: CL miriam: cl n2t: cl obofoundry: cl ols: cl ontobee: CL prefixcommons: CL miriam: deprecated: false description: The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi. homepage: https://www.ebi.ac.uk/ols/ontologies/cl id: '00000110' name: Cell Type Ontology namespaceEmbeddedInLui: true pattern: ^CL:\d{7}$ prefix: cl sampleId: '0000232' uri_format: https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:$1 n2t: description: The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi. example: '0000232' homepage: http://bioportal.bioontology.org/ontologies/CL name: Cell Type Ontology through BioPortal namespaceEmbeddedInLui: true pattern: ^CL:\d{7}$ prefix: cl uri_format: http://purl.bioontology.org/ontology/CL/CL:$1 obofoundry: appears_in: - go - clo - ecao - mco - pcl - uberon - xpo - ehdaa2 contact: addiehl@buffalo.edu contact.github: addiehl contact.label: Alexander Diehl contact.orcid: 0000-0001-9990-8331 depends_on: - chebi - go - pato - ro - uberon deprecated: false description: The Cell Ontology is a structured controlled vocabulary for cell types in animals. download.obo: http://purl.obolibrary.org/obo/cl.obo download.owl: http://purl.obolibrary.org/obo/cl.owl homepage: https://obophenotype.github.io/cell-ontology/ inactive: false license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Cell Ontology preferredPrefix: CL prefix: cl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27377652 title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.' repository: https://github.com/obophenotype/cell-ontology ols: description: An ontology of cell types. download: http://purl.obolibrary.org/obo/cl.owl homepage: https://obophenotype.github.io/cell-ontology/ name: Cell Ontology prefix: cl version: '2022-02-16' version.iri: http://purl.obolibrary.org/obo/cl/releases/2022-02-16/cl.owl ontobee: library: Library name: Cell Ontology prefix: CL pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: CL uri_format: http://purl.obolibrary.org/obo/CL_$1 wikidata: database: Q55118285 database.label: Cell Ontology homepage: http://www.ontobee.org/ontology/CL name: Cell Ontology ID pattern: CL_[0-9]{7} prefix: P7963 uri_format: http://purl.obolibrary.org/obo/$1 clao: bioportal: name: Collembola Anatomy Ontology prefix: CLAO example: 0000088 mappings: bioportal: CLAO obofoundry: clao ols: clao ontobee: CLAO obofoundry: contact: lagonzalezmo@unal.edu.co contact.github: luis-gonzalez-m contact.label: "Luis Gonz\xE1lez-Monta\xF1a" contact.orcid: 0000-0002-9136-9932 depends_on: - ro deprecated: false description: 'CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).' download.obo: http://purl.obolibrary.org/obo/clao.obo download.owl: http://purl.obolibrary.org/obo/clao.owl homepage: https://github.com/luis-gonzalez-m/Collembola inactive: false license: CC0 1.0 license.url: http://creativecommons.org/publicdomain/zero/1.0/ name: Collembola Anatomy Ontology preferredPrefix: CLAO prefix: clao repository: https://github.com/luis-gonzalez-m/Collembola ols: description: 'CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).' download: http://purl.obolibrary.org/obo/clao.owl homepage: https://github.com/luis-gonzalez-m/Collembola name: Collembola Anatomy Ontology prefix: clao version: '2021-09-27' version.iri: http://purl.obolibrary.org/obo/clao/releases/2021-09-27/clao.owl ontobee: library: Library name: Collembola Anatomy Ontology prefix: CLAO pattern: ^\d{7}$ classyfire: mappings: miriam: classyfire miriam: deprecated: false 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. homepage: http://classyfire.wishartlab.com/ id: '00000770' name: ClassyFire namespaceEmbeddedInLui: false pattern: ^C[0-9]{7}$ prefix: classyfire sampleId: C0004828 uri_format: http://classyfire.wishartlab.com/tax_nodes/$1 cldb: cellosaurus: category: Cell line databases/resources homepage: http://bioinformatics.hsanmartino.it/cldb/ name: Cell Line Data Base prefix: CLDB uri_format: http://bioinformatics.hsanmartino.it/cldb/$1.html mappings: cellosaurus: CLDB miriam: cldb n2t: cldb prefixcommons: CLDB miriam: deprecated: false description: The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories. homepage: http://bioinformatics.hsanmartino.it/hypercldb/indexes.html id: 00000390 name: CLDB namespaceEmbeddedInLui: false pattern: ^(cl|tum)\d+$ prefix: cldb sampleId: cl3603 uri_format: http://bioinformatics.hsanmartino.it/hypercldb/$1.html n2t: description: The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories. example: cl3603 homepage: http://bioinformatics.hsanmartino.it/hypercldb/indexes.html name: CLDB at Genova namespaceEmbeddedInLui: false pattern: ^(cl|tum)\d+$ prefix: cldb uri_format: http://bioinformatics.hsanmartino.it/hypercldb/$1.html name: Cell Line Database prefixcommons: is_identifiers: true is_obo: false prefix: CLDB uri_format: http://identifiers.org/cldb/$1 clingene: biolink: is_identifiers: false is_obo: false prefix: CAID uri_format: http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1 description: The allele registry provides and maintains identifiers for genetic variants example: CA981206459 homepage: https://reg.clinicalgenome.org mappings: biolink: CAID name: ClinGen Allele Registry uri_format: https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1 clinicaltrials: mappings: miriam: clinicaltrials n2t: clinicaltrials prefixcommons: CLINICALTRIALS miriam: deprecated: false description: ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries homepage: https://clinicaltrials.gov/ id: '00000137' name: ClinicalTrials.gov namespaceEmbeddedInLui: false pattern: ^NCT\d{8}$ prefix: clinicaltrials sampleId: NCT00222573 uri_format: https://clinicaltrials.gov/ct2/show/$1 n2t: description: ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries example: NCT00222573 homepage: https://clinicaltrials.gov/ name: ClinicalTrials.gov at NIH namespaceEmbeddedInLui: false pattern: ^NCT\d{8}$ prefix: clinicaltrials uri_format: https://clinicaltrials.gov/ct2/show/$1 prefixcommons: is_identifiers: true is_obo: false prefix: CLINICALTRIALS uri_format: http://identifiers.org/clinicaltrials/$1 clinvar: biolink: is_identifiers: true is_obo: false prefix: CLINVAR uri_format: http://identifiers.org/clinvar$1 cellosaurus: category: Polymorphism and mutation databases homepage: https://www.ncbi.nlm.nih.gov/clinvar/ name: ClinVar prefix: ClinVar uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1 fairsharing: abbreviation: ClinVar description: ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works in collaboration with interested organizations to meet the needs of the medical genetics community as efficiently and effectively as possible. id: '2265' name: ClinVar prefix: FAIRsharing.wx5r6f subjects: - Genomics - Clinical Studies - Biomedical Science - Preclinical Studies mappings: biolink: CLINVAR cellosaurus: ClinVar fairsharing: FAIRsharing.wx5r6f miriam: clinvar n2t: clinvar prefixcommons: ClinVar wikidata: P1929 miriam: deprecated: false description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier. homepage: http://www.ncbi.nlm.nih.gov/clinvar/ id: 00000596 name: ClinVar Variant namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: clinvar sampleId: '12345' uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1 n2t: description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier. example: '12345' homepage: http://www.ncbi.nlm.nih.gov/clinvar/ name: ClinVar Variant at NCBI namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: clinvar uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1 name: ClinVar Variation prefixcommons: is_identifiers: false is_obo: false prefix: ClinVar uri_format: http://www.ncbi.nlm.nih.gov/clinvar/$1 wikidata: database: Q20023123 database.homepage: http://www.ncbi.nlm.nih.gov/clinvar/ database.label: ClinVar homepage: http://www.ncbi.nlm.nih.gov/clinvar/ name: ClinVar Variation ID prefix: P1929 uri_format: http://www.ncbi.nlm.nih.gov/clinvar/variation/$1/ clinvar.record: mappings: miriam: clinvar.record n2t: clinvar.record prefixcommons: CLINVAR.RECORD miriam: deprecated: false description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession. homepage: http://www.ncbi.nlm.nih.gov/clinvar/ id: '00000534' name: ClinVar Record namespaceEmbeddedInLui: false pattern: ^RCV\d+(\.\d+)?$ prefix: clinvar.record sampleId: RCV000033555.3 uri_format: http://www.ncbi.nlm.nih.gov/clinvar/$1/ n2t: description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession. example: RCV000033555.3 homepage: http://www.ncbi.nlm.nih.gov/clinvar/ name: ClinVar Record at NCBI namespaceEmbeddedInLui: false pattern: ^RCV\d+(\.\d+)?$ prefix: clinvar.record uri_format: http://www.ncbi.nlm.nih.gov/clinvar/$1/ prefixcommons: is_identifiers: true is_obo: false prefix: CLINVAR.RECORD uri_format: http://identifiers.org/clinvar.record/$1 uri_format: http://www.ncbi.nlm.nih.gov/clinvar/$1 clinvar.submission: mappings: miriam: clinvar.submission n2t: clinvar.submission prefixcommons: CLINVAR.SUBMISSION miriam: deprecated: false description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession. homepage: http://www.ncbi.nlm.nih.gov/clinvar/ id: 00000595 name: ClinVar Submission namespaceEmbeddedInLui: false pattern: ^SCV\d+(\.\d+)?$ prefix: clinvar.submission sampleId: SCV000151292 uri_format: http://www.ncbi.nlm.nih.gov/clinvar?term=$1 n2t: description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession. example: SCV000151292 homepage: http://www.ncbi.nlm.nih.gov/clinvar/ name: ClinVar Submission at NCBI namespaceEmbeddedInLui: false pattern: ^SCV\d+(\.\d+)?$ prefix: clinvar.submission uri_format: http://www.ncbi.nlm.nih.gov/clinvar?term=$1 prefixcommons: is_identifiers: true is_obo: false prefix: CLINVAR.SUBMISSION uri_format: http://identifiers.org/clinvar.submission/$1 clinvar.submitter: mappings: miriam: clinvar.submitter miriam: deprecated: false description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs). homepage: https://www.ncbi.nlm.nih.gov/clinvar/ id: 00000769 name: ClinVar Submitter namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: clinvar.submitter sampleId: '26957' uri_format: https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1 clo: bioportal: name: Cell Line Ontology prefix: CLO cellosaurus: category: Cell line databases/resources homepage: http://www.clo-ontology.org name: Cell Line Ontology prefix: CLO uri_format: https://www.ebi.ac.uk/ols/ontologies/clo/terms?iri=http://purl.obolibrary.org/obo/$1 example: 0000091 fairsharing: abbreviation: CLO description: The Cell Line Ontology (CLO) is a community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. Thousands of cell lines have been artificially developed and used for different applications. Integration of data from multiple sources is a challenge, confounded by lack of consistent naming conventions, contamination of cell lines, and provision of the same cell lines by multiple commercial sources but with different biological attributes. CLO is a community-based effort to represent all cell lines in a standard ontology approach. id: '1012' name: Cell Line Ontology prefix: FAIRsharing.4dvtcz subjects: - Life Science - Cell Biology mappings: bioportal: CLO cellosaurus: CLO fairsharing: FAIRsharing.4dvtcz obofoundry: clo ols: clo ontobee: CLO prefixcommons: CLO obofoundry: appears_in: - mco contact: siiraa@umich.edu contact.github: siiraa contact.label: Sirarat Sarntivijai contact.orcid: 0000-0002-2548-641X depends_on: - cl - doid - ncbitaxon - uberon deprecated: false description: An ontology to standardize and integrate cell line information and to support computer-assisted reasoning. download.owl: http://purl.obolibrary.org/obo/clo.owl homepage: http://www.clo-ontology.org inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Cell Line Ontology preferredPrefix: CLO prefix: clo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/25852852 title: 'CLO: The Cell Line Ontology' repository: https://github.com/CLO-Ontology/CLO ols: description: The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns. download: http://purl.obolibrary.org/obo/clo.owl homepage: http://www.clo-ontology.org name: 'CLO: Cell Line Ontology' prefix: clo version: 2.1.178 ontobee: library: Library name: Cell Line Ontology prefix: CLO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: CLO uri_format: http://purl.obolibrary.org/obo/CLO_$1 synonyms: - CLO wikidata: prefix: P2158 cls: cellosaurus: category: Cell line collections homepage: https://cls.shop/ name: Cell Lines Service prefix: CLS uri_format: https://www.clsgmbh.de/$1.html example: 300108/p3934_A-172 mappings: cellosaurus: CLS clyh: bioportal: name: Clytia hemisphaerica Development and Anatomy Ontology prefix: CLYH example: '1000100' mappings: bioportal: CLYH obofoundry: clyh ols: clyh ontobee: CLYH obofoundry: contact: lucas.leclere@obs-vlfr.fr contact.github: L-Leclere contact.label: Lucas Leclere contact.orcid: 0000-0002-7440-0467 depends_on: - iao - ro - uberon deprecated: false description: The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle. download.obo: http://purl.obolibrary.org/obo/clyh.obo download.owl: http://purl.obolibrary.org/obo/clyh.owl homepage: https://github.com/EBISPOT/clyh_ontology inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Clytia hemisphaerica Development and Anatomy Ontology preferredPrefix: CLYH prefix: clyh repository: https://github.com/EBISPOT/clyh_ontology ols: description: Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica. download: https://raw.githubusercontent.com/EBISPOT/clyh_ontology/master/clyh.owl homepage: https://github.com/EBISPOT/clyh_ontology name: Clytia hemisphaerica Development and Anatomy Ontology (CLYH) prefix: clyh version: '2020-05-29' version.iri: http://purl.obolibrary.org/obo/clyh/releases/2020-05-29/clyh.owl ontobee: library: Library name: Clytia hemisphaerica Development and Anatomy Ontology prefix: CLYH pattern: ^\d+$ cmecs: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard. example: '595' homepage: https://cmecscatalog.org/cmecs name: Costal and Marine Ecological Classification Standard pattern: ^\d+$ 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: deprecated: true description: This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain mappings: obofoundry: cmf ontobee: CMF prefixcommons: CMF obofoundry: contact: engelsta@ohsu.edu contact.label: Mark Engelstad contact.orcid: 0000-0001-5889-4463 deprecated: true homepage: https://code.google.com/p/craniomaxillofacial-ontology/ inactive: true name: CranioMaxilloFacial ontology prefix: cmf ontobee: library: Library name: CranioMaxilloFacial ontology prefix: CMF prefixcommons: is_identifiers: false is_obo: true prefix: CMF uri_format: http://purl.obolibrary.org/obo/CMF_$1 cmo: bioportal: name: Clinical Measurement Ontology prefix: CMO example: '0001350' fairsharing: abbreviation: CMO description: The Clinical Measurement Ontology is designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs. id: '885' name: Clinical Measurement Ontology prefix: FAIRsharing.dq78pn subjects: - Life Science - Biomedical Science - Preclinical Studies mappings: bioportal: CMO fairsharing: FAIRsharing.dq78pn obofoundry: cmo ols: cmo ontobee: CMO prefixcommons: CMO obofoundry: appears_in: - scdo contact: jrsmith@mcw.edu contact.github: jrsjrs contact.label: Jennifer Smith contact.orcid: 0000-0002-6443-9376 deprecated: false 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 homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html inactive: false license: CC0 1.0 license.url: http://creativecommons.org/publicdomain/zero/1.0/ name: Clinical measurement ontology preferredPrefix: CMO prefix: cmo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/22654893 title: Three ontologies to define phenotype measurement data. - id: https://www.ncbi.nlm.nih.gov/pubmed/24103152 title: 'The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.' repository: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology ols: description: Morphological and physiological measurement records generated from clinical and model organism research and health programs. download: http://purl.obolibrary.org/obo/cmo.owl homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html name: Clinical measurement ontology prefix: cmo version: '2019-02-19' version.iri: http://purl.obolibrary.org/obo/cmo/releases/2019-02-19/cmo.owl ontobee: library: Library name: Clinical measurement ontology prefix: CMO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: CMO uri_format: http://purl.obolibrary.org/obo/CMO_$1 cmpo: bioportal: name: Cellular microscopy phenotype ontology prefix: CMPO example: '0000435' fairsharing: abbreviation: CMPO description: Cellular Microscopy Phenotype Ontology (CMPO) is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations id: '157' name: Cellular Microscopy Phenotype Ontology prefix: FAIRsharing.knp11s subjects: - Cell Biology mappings: bioportal: CMPO fairsharing: FAIRsharing.knp11s ols: cmpo ols: contact: jupp@ebi.ac.uk description: CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. download: http://www.ebi.ac.uk/cmpo/cmpo.owl homepage: http://www.ebi.ac.uk/cmpo name: Cellular Microscopy Phenotype Ontology prefix: cmpo version: '2017-12-19' version.iri: http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl pattern: ^\d{7}$ co_320: example: 0000618 fairsharing: abbreviation: CO_320 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The IBP Rice Trait Ontology is one\ \ of these reference plant ontologies integrated within the Crop Ontology. Based\ \ on SES, Rice Descriptor and IRIS DB." id: '832' name: Rice Ontology prefix: FAIRsharing.2jkxp5 subjects: - Botany - Agriculture - Life Science mappings: fairsharing: FAIRsharing.2jkxp5 ols: co_320 ols: contact: helpdesk@cropontology-curationtool.org description: Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables download: https://cropontology.org/ontology/CO_320/Rice/owl homepage: https://cropontology.org/ontology/CO_320/Rice name: Rice ontology prefix: co_320 version: '2019-10-09' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_320:$1 co_321: example: 0000449 fairsharing: abbreviation: CO_321 description: This ontology defines traits of the International Wheat Information System (IWIS) database and wheat descriptor. The Wheat Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. id: '728' name: Wheat Ontology prefix: FAIRsharing.czzmpg subjects: - Agriculture - Life Science mappings: fairsharing: FAIRsharing.czzmpg ols: co_321 ols: contact: helpdesk@cropontology-curationtool.org description: July 2018 download: https://cropontology.org/ontology/CO_321/Wheat/owl homepage: https://cropontology.org/ontology/CO_321/Wheat name: Wheat ontology prefix: co_321 version: '2019-10-09' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_321:$1 co_322: example: '0000773' fairsharing: abbreviation: CO_322 description: The Maize Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. id: '925' name: Maize Ontology prefix: FAIRsharing.eeyne8 subjects: - Botany - Agriculture - Life Science mappings: fairsharing: FAIRsharing.eeyne8 ols: co_322 ols: contact: helpdesk@cropontology-curationtool.org description: Maize Trait Dictionary in template 5 - CIMMYT- September 2016 download: https://cropontology.org/ontology/CO_322/Maize/owl homepage: https://cropontology.org/ontology/CO_322/Maize name: Maize ontology prefix: co_322 version: '2019-10-09' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_322:$1 co_323: example: '0000252' fairsharing: abbreviation: CO_323 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Barley Ontology is one of these\ \ reference plant ontologies integrated within the Crop Ontology. Its focus\ \ is on traits and variable used in field trials for breeding." id: '872' name: Barley Ontology prefix: FAIRsharing.f69084 subjects: - Botany - Agriculture mappings: fairsharing: FAIRsharing.f69084 ols: co_323 ols: contact: helpdesk@cropontology-curationtool.org description: ICARDA - TDv5 - Sept 2018 download: https://cropontology.org/ontology/CO_323/Barley/owl homepage: https://cropontology.org/ontology/CO_323/Barley name: Barley ontology prefix: co_323 version: '2019-11-20' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_323:$1 co_324: example: '0000111' fairsharing: abbreviation: CO_324 description: The Sorghum Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. id: '1077' name: Sorghum Ontology prefix: FAIRsharing.dxx0c subjects: - Botany - Agriculture mappings: fairsharing: FAIRsharing.dxx0c ols: co_324 ols: contact: helpdesk@cropontology-curationtool.org description: Sorghum TDv5 - Oct 2019 download: https://cropontology.org/ontology/CO_324/Sorghum/owl homepage: https://cropontology.org/ontology/CO_324/Sorghum name: Sorghum ontology prefix: co_324 version: '2019-10-09' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_324:$1 co_325: example: 0000519 fairsharing: abbreviation: CO_325 description: The Banana Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. id: '642' name: Banana Ontology prefix: FAIRsharing.gdszhh subjects: - Agriculture - Life Science mappings: fairsharing: FAIRsharing.gdszhh ols: co_325 ols: contact: helpdesk@cropontology-curationtool.org description: Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019 download: https://cropontology.org/ontology/CO_325/Banana/owl homepage: https://cropontology.org/ontology/CO_325/Banana name: Banana ontology prefix: co_325 version: '2019-10-09' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_325:$1 co_326: example: '0000254' mappings: ols: co_326 ols: contact: helpdesk@cropontology-curationtool.org description: Draft version download: https://cropontology.org/ontology/CO_326/Coconut/owl homepage: https://cropontology.org/ontology/CO_326/Coconut name: Coconut ontology prefix: co_326 pattern: ^\d{7}$ co_327: example: 0000095 fairsharing: abbreviation: CO_327 description: The goal of the CGIAR Pearl Millet Ontology is to help improve food security for subsistence smallholder farmers in East and West Africa with productive and nutritious pearl millet food and fodder production technologies. id: '495' name: Pearl Millet Ontology prefix: FAIRsharing.4e3qh9 subjects: - Botany - Agriculture mappings: fairsharing: FAIRsharing.4e3qh9 ols: co_327 ols: contact: helpdesk@cropontology-curationtool.org description: Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016 download: http://www.cropontology.org/ontology/CO_327/Pearl%20millet/owl homepage: http://www.cropontology.org/ontology/CO_327/Pearl%20millet name: Pearl millet ontology prefix: co_327 pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_327:$1 co_330: example: '0000106' fairsharing: abbreviation: CO_330 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Potato Ontology is one of these\ \ reference plant ontologies integrated within the Crop Ontology." id: '1307' name: Potato Ontology prefix: FAIRsharing.4fa657 subjects: - Botany - Agriculture - Life Science mappings: fairsharing: FAIRsharing.4fa657 ols: co_330 ols: contact: helpdesk@cropontology-curationtool.org description: CIP - potato ontology - december 2018 download: https://cropontology.org/ontology/CO_330/Potato/owl homepage: https://cropontology.org/ontology/CO_330/Potato name: Potato ontology prefix: co_330 version: '2019-10-09' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_330:$1 co_331: example: 0000088 fairsharing: abbreviation: CO_331 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Sweet Potato Ontology is one of\ \ these reference plant ontologies integrated within the Crop Ontology." id: '496' name: Sweet Potato Ontology prefix: FAIRsharing.4g5qcw subjects: - Botany - Agriculture - Life Science mappings: fairsharing: FAIRsharing.4g5qcw ols: co_331 ols: contact: helpdesk@cropontology-curationtool.org description: Sweet Potato Trait Dictionary in template v5 - CIP - November 2019 download: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato/owl homepage: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato name: Sweet Potato ontology prefix: co_331 pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_331:$1 co_333: example: '3000045' fairsharing: abbreviation: CO_333 description: "This ontology was built as part of the AKER project. It describes\ \ variables used in beet phenotyping (experimental properties and measurement\ \ scale) for each institution and breeding company within the project. Reference\ \ Plant Ontologies are being developed in the context of the Planteome project\ \ and are being integrated with the Crop Ontology, which provides harmonized\ \ breeders\u2019 trait names, measurement methods, scales and standard variables\ \ for many crops. The Beet Ontology is one of these reference plant ontologies\ \ integrated within the Crop Ontology." id: '1079' name: Beet Ontology prefix: FAIRsharing.af5655 subjects: - Botany - Plant Breeding - Agriculture - Life Science mappings: fairsharing: FAIRsharing.af5655 ols: co_333 ols: contact: helpdesk@cropontology-curationtool.org description: 'This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017.' download: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology/owl homepage: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology name: Beet Ontology ontology prefix: co_333 pattern: ^\d+$ uri_format: https://www.cropontology.org/rdf/CO_333:$1 co_334: example: '0000070' fairsharing: abbreviation: CO_334 description: Crop-specific trait ontologies enhance the interoperability and effectiveness of data exchange between the data sources which adopt it, by providing standard concepts that are use to describe phenotypes stored in those sources. As one of them, the Cassava Ontology is actively used and shared in different databases such as the BMS (Breeding Management system) of the IBP or the CassavaBase. Cassava, a major staple crop, is the main source of calories for 500 million people across the globe. A perennial woody shrub native to Latin America, cassava is primarily grown as an annual crop in the humid tropics. A cash crop as well as a subsistence crop, cassava's large edible starchy roots are a source of low-cost carbohydrates for millions. Cassava end products range from fresh roots cooked, boiled, baked or fried at the household level, to highly processed starch as a food additive. id: '1099' name: IBP Cassava Trait Ontology prefix: FAIRsharing.v06c4q subjects: - Botany - Agriculture - Nutritional Science mappings: fairsharing: FAIRsharing.v06c4q ols: co_334 ols: contact: helpdesk@cropontology-curationtool.org description: Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016 download: https://cropontology.org/ontology/CO_334/Cassava/owl homepage: https://cropontology.org/ontology/CO_334/Cassava name: Cassava ontology prefix: co_334 version: '2019-10-09' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_334:$1 co_335: example: 0000189 fairsharing: abbreviation: CO_335 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Common Bean Ontology is one of\ \ these reference plant ontologies integrated within the Crop Ontology." id: '1096' name: Common Bean Ontology prefix: FAIRsharing.a14123 subjects: - Botany - Agriculture mappings: fairsharing: FAIRsharing.a14123 ols: co_335 ols: contact: helpdesk@cropontology-curationtool.org description: CIAT Common bean trait dictionary - version August 2014 download: http://www.cropontology.org/ontology/CO_335/Common%20Bean/owl homepage: http://www.cropontology.org/ontology/CO_335/Common%20Bean name: Common Bean ontology prefix: co_335 pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_335:$1 co_336: example: 0000339 fairsharing: abbreviation: CO_336 description: The Soybean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. id: '669' name: Soybean Ontology prefix: FAIRsharing.j75srj subjects: - Agriculture - Life Science mappings: fairsharing: FAIRsharing.j75srj ols: co_336 ols: contact: helpdesk@cropontology-curationtool.org description: Soybean Trait Dictionary in template v5 - IITA - July 2015 download: https://cropontology.org/ontology/CO_336/Soybean/owl homepage: https://cropontology.org/ontology/CO_336/Soybean name: Soybean ontology prefix: co_336 pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_336:$1 co_337: example: '0000054' fairsharing: abbreviation: CO_337 description: The Groundnut Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. id: '40' name: Groundnut Ontology prefix: FAIRsharing.ge8y23 subjects: - Botany - Agriculture - Life Science mappings: fairsharing: FAIRsharing.ge8y23 ols: co_337 ols: contact: helpdesk@cropontology-curationtool.org description: Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015 download: https://cropontology.org/ontology/CO_337/Groundnut/owl homepage: https://cropontology.org/ontology/CO_337/Groundnut name: Groundnut ontology prefix: co_337 version: '2019-10-09' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_337:$1 co_338: example: 0000138 fairsharing: abbreviation: CO_338 description: Development of crop-specific trait ontologies including the Chickpea Ontology began in 2008 as part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. id: '1321' name: Chickpea Ontology prefix: FAIRsharing.js20q3 subjects: - Botany - Agriculture mappings: fairsharing: FAIRsharing.js20q3 ols: co_338 ols: contact: helpdesk@cropontology-curationtool.org description: Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015 download: https://cropontology.org/ontology/CO_338/Chickpea/owl homepage: https://cropontology.org/ontology/CO_338/Chickpea name: Chickpea ontology prefix: co_338 version: '2019-10-09' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_338:$1 co_339: example: '0000032' fairsharing: abbreviation: CO_339 description: The Lentil Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. id: '1352' name: Lentil Ontology prefix: FAIRsharing.ry1ezg subjects: - Botany - Agriculture - Life Science mappings: fairsharing: FAIRsharing.ry1ezg ols: co_339 ols: contact: helpdesk@cropontology-curationtool.org description: Lentil Trait Dictionary in template v5 - ICARDA - July 2015 download: https://cropontology.org/ontology/CO_339/Lentil/owl homepage: https://cropontology.org/ontology/CO_339/Lentil name: Lentil ontology prefix: co_339 version: '2019-10-09' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_339:$1 co_340: example: 0000639 fairsharing: abbreviation: CO_340 description: The Cowpea Trait Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. id: '1302' name: IBP Cowpea Trait Ontology prefix: FAIRsharing.31apg2 subjects: - Botany - Agriculture mappings: fairsharing: FAIRsharing.31apg2 ols: co_340 ols: contact: helpdesk@cropontology-curationtool.org description: Cowpea Trait Dictionary in template v5 - IITA - August 2015 download: https://cropontology.org/ontology/CO_340/Cowpea/owl homepage: https://cropontology.org/ontology/CO_340/Cowpea name: Cowpea ontology prefix: co_340 version: '2019-10-09' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_340:$1 co_341: example: '0000140' fairsharing: abbreviation: CO_341 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Pigeon Pea Ontology is one of these\ \ reference plant ontologies integrated within the Crop Ontology." id: '1078' name: Pigeon Pea Ontology prefix: FAIRsharing.ehe3yp subjects: - Botany - Agriculture - Life Science mappings: fairsharing: FAIRsharing.ehe3yp ols: co_341 ols: contact: helpdesk@cropontology-curationtool.org description: Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015 download: https://cropontology.org/ontology/CO_341/Pigeonpea/owl homepage: https://cropontology.org/ontology/CO_341/Pigeonpea name: Pigeonpea ontology prefix: co_341 version: '2019-11-18' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_341:$1 co_343: example: '0100010' fairsharing: abbreviation: CO_343 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Yam Ontology is one of these reference\ \ plant ontologies integrated within the Crop Ontology." id: '838' name: Yam Ontology prefix: FAIRsharing.7e9cff subjects: - Botany - Agriculture - Life Science mappings: fairsharing: FAIRsharing.7e9cff ols: co_343 ols: contact: helpdesk@cropontology-curationtool.org description: version 2019 - pvs download: https://cropontology.org/ontology/CO_343/Yam/owl homepage: https://cropontology.org/ontology/CO_343/Yam name: Yam ontology prefix: co_343 version: '2019-10-09' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_343:$1 co_345: example: '0000127' fairsharing: abbreviation: CO_345 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Brachiaria Ontology is one of these\ \ reference plant ontologies integrated within the Crop Ontology." id: '494' name: Brachiaria Ontology prefix: FAIRsharing.9e9683 subjects: - Botany - Agriculture - Life Science mappings: fairsharing: FAIRsharing.9e9683 ols: co_345 ols: contact: helpdesk@cropontology-curationtool.org description: Brachiaria (forages) ontology TD v5 - Version Oct 2016 download: https://cropontology.org/ontology/CO_345/Brachiaria/owl homepage: https://cropontology.org/ontology/CO_345/Brachiaria name: Brachiaria ontology prefix: co_345 version: '2019-10-09' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_345:$1 co_346: example: 0000199 fairsharing: abbreviation: CO_346 description: The Mungbean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe data. id: '1100' name: Mungbean Ontology prefix: FAIRsharing.fgd5gq subjects: - Agriculture - Life Science mappings: fairsharing: FAIRsharing.fgd5gq ols: co_346 ols: contact: helpdesk@cropontology-curationtool.org description: oct 2016 download: https://cropontology.org/ontology/CO_346/Mungbean/owl homepage: https://cropontology.org/ontology/CO_346/Mungbean name: Mungbean ontology prefix: co_346 version: '2019-10-09' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_346:$1 co_347: example: 0000108 fairsharing: abbreviation: CO_347 description: The Castor Bean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe data. id: '1070' name: Castor Bean Ontology prefix: FAIRsharing.qrrvyk subjects: - Botany - Agriculture - Life Science mappings: fairsharing: FAIRsharing.qrrvyk ols: co_347 ols: contact: helpdesk@cropontology-curationtool.org description: 'March 2017 version ' download: http://www.cropontology.org/ontology/CO_347/Castor%20bean/owl homepage: http://www.cropontology.org/ontology/CO_347/Castor%20bean name: Castor bean ontology prefix: co_347 pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_347:$1 co_348: example: '1100107' fairsharing: abbreviation: CO_348 description: "Brassica Trait Ontology (BRaTO) hosts trait information to describe\ \ brassica crop data. Terms are collected from various projects including OREGIN,\ \ RIPR (UK) and Rapsodyn (France). Reference Plant Ontologies are being developed\ \ in the context of the Planteome project and are being integrated with the\ \ Crop Ontology, which provides harmonized breeders\u2019 trait names, measurement\ \ methods, scales and standard variables for many crops. The Brassica Ontology\ \ is one of these reference plant ontologies integrated within the Crop Ontology." id: '1019' name: Brassica Ontology prefix: FAIRsharing.af7a2d subjects: - Botany - Agriculture - Life Science mappings: fairsharing: FAIRsharing.af7a2d ols: co_348 ols: contact: helpdesk@cropontology-curationtool.org description: Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France). download: https://cropontology.org/ontology/CO_348/Brassica/owl homepage: https://cropontology.org/ontology/CO_348/Brassica name: Brassica ontology prefix: co_348 version: '2019-11-29' pattern: ^\d+$ uri_format: https://www.cropontology.org/rdf/CO_348:$1 co_350: example: '0000215' fairsharing: abbreviation: CO_350 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Oat Trait Ontology is one of these\ \ reference plant ontologies integrated within the Crop Ontology. The Oat Trait\ \ Dictionary was commissioned by Oat Global (http://oatglobal.org/) to hold\ \ the traits used in the T3/Oat database (http://triticeaetoolbox.org/oat/)." id: '652' name: Oat Trait Ontology prefix: FAIRsharing.35e1c3 subjects: - Botany - Agriculture - Life Science mappings: fairsharing: FAIRsharing.35e1c3 ols: co_350 ols: contact: helpdesk@cropontology-curationtool.org description: Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo download: https://cropontology.org/ontology/CO_350/Oat/owl homepage: https://cropontology.org/ontology/CO_350/Oat name: Oat ontology prefix: co_350 version: '2019-10-09' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_350:$1 co_356: example: '4000027' fairsharing: abbreviation: CO_356 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Vitis Ontology is one of these\ \ reference plant ontologies integrated within the Crop Ontology." id: '1092' name: Vitis Ontology prefix: FAIRsharing.c7f4d7 subjects: - Botany - Agriculture - Life Science mappings: fairsharing: FAIRsharing.c7f4d7 ols: co_356 ols: contact: helpdesk@cropontology-curationtool.org description: Grape Ontology including OIV and bioversity descriptors. INRA July 2017 download: https://cropontology.org/ontology/CO_356/Vitis/owl homepage: https://cropontology.org/ontology/CO_356/Vitis name: Vitis ontology prefix: co_356 version: '2019-11-29' pattern: ^\d+$ uri_format: https://www.cropontology.org/rdf/CO_356:$1 co_357: example: '1000290' fairsharing: abbreviation: CO_357 description: "The Woody Plant Ontology lists all variables used for woody plant\ \ observations. Terms are collected from various sources (past and ongoing projects\ \ at national and international levels). Reference Plant Ontologies are being\ \ developed in the context of the Planteome project and are being integrated\ \ with the Crop Ontology, which provides harmonized breeders\u2019 trait names,\ \ measurement methods, scales and standard variables for many crops. The Woody\ \ Plant Ontology is one of these reference plant ontologies integrated within\ \ the Crop Ontology." id: '1103' name: Woody Plant Ontology prefix: FAIRsharing.2b04ae subjects: - Botany - Life Science mappings: fairsharing: FAIRsharing.2b04ae ols: co_357 ols: contact: helpdesk@cropontology-curationtool.org description: 'This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE.' download: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology/owl homepage: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology name: Woody Plant Ontology ontology prefix: co_357 pattern: ^\d+$ uri_format: https://www.cropontology.org/rdf/CO_357:$1 co_358: example: 0000139 mappings: ols: co_358 ols: contact: helpdesk@cropontology-curationtool.org description: Cotton ontology from CottonGen database - June 2019 download: https://cropontology.org/ontology/CO_358/Cotton/owl homepage: https://cropontology.org/ontology/CO_358/Cotton name: Cotton ontology prefix: co_358 version: '2020-01-03' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_358:$1 co_359: example: 0000947 mappings: ols: co_359 ols: contact: helpdesk@cropontology-curationtool.org description: December 2019 download: https://cropontology.org/ontology/CO_359/Sunflower/owl homepage: https://cropontology.org/ontology/CO_359/Sunflower name: Sunflower ontology prefix: co_359 pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_359:$1 co_360: example: '0000071' fairsharing: abbreviation: CO_360 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Sugar Kelp Trait Ontology is one\ \ of these reference plant ontologies integrated within the Crop Ontology." id: '1093' name: Sugar Kelp Trait Ontology prefix: FAIRsharing.1c1738 subjects: - Botany - Life Science mappings: fairsharing: FAIRsharing.1c1738 ols: co_360 ols: contact: helpdesk@cropontology-curationtool.org description: Sugar Kelp trait ontology download: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait/owl homepage: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait name: Sugar Kelp trait ontology prefix: co_360 pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_360:$1 co_365: example: '0000205' mappings: ols: co_365 ols: contact: helpdesk@cropontology-curationtool.org description: developed by ICARDA - Dec 2018 download: https://cropontology.org/ontology/CO_365/Fababean/owl homepage: https://cropontology.org/ontology/CO_365/Fababean name: Fababean ontology prefix: co_365 version: '2019-10-15' pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_365:$1 co_366: example: '0000072' mappings: ols: co_366 ols: contact: helpdesk@cropontology-curationtool.org description: version Dec 2019 download: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut/owl homepage: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut name: Bambara groundnut ontology prefix: co_366 pattern: ^\d{7}$ uri_format: https://www.cropontology.org/rdf/CO_366:$1 cob: bioportal: name: Core Ontology for Biology and Biomedicine prefix: COB example: 0000080 mappings: bioportal: COB obofoundry: cob ols: cob ontobee: COB obofoundry: contact: bpeters@lji.org contact.github: bpeters42 contact.label: Bjoern Peters contact.orcid: 0000-0002-8457-6693 deprecated: false description: COB brings together key terms from a wide range of OBO projects to improve interoperability. download.owl: http://purl.obolibrary.org/obo/cob.owl homepage: https://github.com/OBOFoundry/COB inactive: false license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Core Ontology for Biology and Biomedicine preferredPrefix: COB prefix: cob repository: https://github.com/OBOFoundry/COB ols: description: COB brings together key terms from a wide range of OBO projects to improve interoperability. download: http://purl.obolibrary.org/obo/cob.owl homepage: https://github.com/OBOFoundry/COB name: Core Ontology for Biology and Biomedicine prefix: cob version: '2022-05-02' version.iri: http://purl.obolibrary.org/obo/cob/releases/2022-05-02/cob.owl ontobee: library: Library name: Core Ontology for Biology and Biomedicine prefix: COB pattern: ^\d{7}$ coconut: comment: '@mSorok is the dev of the resource, hope I got it right!' contributor: email: null github: adafede name: Adriano Rutz orcid: 0000-0003-0443-9902 description: COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a "flat" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties. example: CNP0171505 homepage: https://coconut.naturalproducts.net name: COlleCtion of Open Natural ProdUcTs pattern: ^CNP\d{7}$ 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 cog: biolink: is_identifiers: false is_obo: false prefix: COG uri_format: https://www.ncbi.nlm.nih.gov/research/cog-project/$1 contact: email: cogs@ncbi.nlm.nih.gov github: null name: Michael Y Galperin orcid: 0000-0002-2265-5572 description: 'COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems.' example: COG0001 fairsharing: abbreviation: COG description: Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. id: '1968' name: 'Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes' prefix: FAIRsharing.djsbw2 subjects: - Life Science go: homepage: http://www.ncbi.nlm.nih.gov/COG/ name: NCBI COG cluster prefix: COG_Cluster uri_format: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=$1 homepage: https://www.ncbi.nlm.nih.gov/research/cog/ mappings: biolink: COG fairsharing: FAIRsharing.djsbw2 go: COG_Cluster name: Cluster of orthologous genes pattern: ^COG\d+$ synonyms: - COG_Cluster uri_format: https://www.ncbi.nlm.nih.gov/research/cog/cog/$1 cog.category: contact: email: cogs@ncbi.nlm.nih.gov github: null name: Michael Y Galperin orcid: 0000-0002-2265-5572 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Higher-level classifications of COG Pathways example: K homepage: https://www.ncbi.nlm.nih.gov/research/cog/ name: COG Categories part_of: cog uri_format: https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1 cog.pathway: contact: email: cogs@ncbi.nlm.nih.gov github: null name: Michael Y Galperin orcid: 0000-0002-2265-5572 description: Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. example: NAD%20biosynthesis go: homepage: http://www.ncbi.nlm.nih.gov/COG/ name: NCBI COG pathway prefix: COG_Pathway uri_format: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=$1 homepage: https://www.ncbi.nlm.nih.gov/research/cog/pathways mappings: go: COG_Pathway name: COG Pathways part_of: cog uri_format: https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1 cohd: comment: not really sure where the source is. this also links to a system called athena. I was not able to figure out what COHD stands for. contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012 homepage: https://github.com/MIT-LCP/mimic-omop name: MIMIC III Database no_own_terms: true repository: https://github.com/MIT-LCP/mimic-omop colao: bioportal: name: Coleoptera Anatomy Ontology prefix: COLAO example: '0000000' mappings: bioportal: COLAO obofoundry: colao ols: colao ontobee: COLAO name: Coleoptera Anatomy Ontology obofoundry: contact: entiminae@gmail.com contact.github: JCGiron contact.label: Jennifer C. Giron contact.orcid: 0000-0002-0851-6883 depends_on: - aism - bfo - bspo - caro - pato - ro - uberon deprecated: false description: The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. It has been built using the Ontology Develoment Kit, with the Ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM) as a backbone. download.obo: http://purl.obolibrary.org/obo/colao.obo download.owl: http://purl.obolibrary.org/obo/colao.owl homepage: https://github.com/insect-morphology/colao inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Coleoptera Anatomy Ontology (COLAO) preferredPrefix: COLAO prefix: colao repository: https://github.com/insect-morphology/colao ols: description: The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. download: http://purl.obolibrary.org/obo/colao.owl homepage: https://github.com/insect-morphology/colao name: Coleoptera Anatomy Ontology prefix: colao version: '2021-12-14' version.iri: http://purl.obolibrary.org/obo/colao/releases/2021-12-14/colao.owl ontobee: library: Library name: Coleoptera Anatomy Ontology prefix: COLAO pattern: ^\d{7}$ colonatlas: cellosaurus: category: Cell line databases/resources homepage: http://www.coloncanceratlas.org name: Colorectal Cancer Atlas prefix: ColonAtlas uri_format: http://www.coloncanceratlas.org/search_cell_line?cell_line=$1 example: ALA mappings: cellosaurus: ColonAtlas combine.specifications: mappings: miriam: combine.specifications n2t: combine.specifications prefixcommons: COMBINE.SPECIFICATIONS miriam: deprecated: false description: The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network. homepage: https://co.mbine.org/standards/ id: 00000258 name: COMBINE specifications namespaceEmbeddedInLui: false pattern: ^\w+(\-|\.|\w)*$ prefix: combine.specifications sampleId: sbgn.er.level-1.version-1.2 uri_format: https://co.mbine.org/specifications/$1 n2t: description: The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network. example: sbgn.er.level-1.version-1.2 homepage: https://co.mbine.org/standards/ name: COMBINE at EBI namespaceEmbeddedInLui: false pattern: ^\w+(\-|\.|\w)*$ prefix: combine.specifications uri_format: https://co.mbine.org/specifications/$1 prefixcommons: is_identifiers: true is_obo: false prefix: COMBINE.SPECIFICATIONS uri_format: http://identifiers.org/combine.specifications/$1 come: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif. example: MOL000160 homepage: https://www.flymine.org/come name: The Bioinorganic Motif Database uri_format: https://www.flymine.org/come/entry?gn=$1 complexportal: example: CPX-263 go: homepage: https://www.ebi.ac.uk/complexportal name: Complex Portal database of macromolecular complexes prefix: ComplexPortal uri_format: https://www.ebi.ac.uk/complexportal/complex/$1 mappings: go: ComplexPortal miriam: complexportal n2t: complexportal prefixcommons: COMPLEXPORTAL uniprot: ComplexPortal wikidata: P7718 miriam: deprecated: false description: A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases. homepage: https://www.ebi.ac.uk/complexportal id: '00000657' name: Complex Portal namespaceEmbeddedInLui: false pattern: ^CPX-[0-9]+$ prefix: complexportal sampleId: CPX-2158 uri_format: https://www.ebi.ac.uk/complexportal/complex/$1 n2t: description: A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases. example: CPX-2158 homepage: https://www.ebi.ac.uk/complexportal name: Complex Portal namespaceEmbeddedInLui: false pattern: ^CPX-[0-9]+$ prefix: complexportal uri_format: https://www.ebi.ac.uk/complexportal/complex/$1 name: Complex Portal prefixcommons: is_identifiers: true is_obo: false prefix: COMPLEXPORTAL uri_format: http://identifiers.org/complexportal/$1 synonyms: - ComplexPortal uniprot: category: Protein-protein interaction databases identifier: '228' link_is_explicit: 'true' name: 'ComplexPortal: manually curated resource of macromolecular complexes' prefix: ComplexPortal uri_format: https://www.ebi.ac.uk/complexportal/complex/$1 wikidata: database: Q47196990 database.homepage: https://www.ebi.ac.uk/complexportal/home database.label: Complex Portal homepage: https://www.ebi.ac.uk/complexportal/home name: Complex Portal accession ID pattern: ^CPX-[0-9]+$ prefix: P7718 uri_format: https://www.ebi.ac.uk/complexportal/complex/$1 comptox: mappings: miriam: comptox n2t: comptox prefixcommons: COMPTOX miriam: deprecated: false description: The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks. homepage: https://comptox.epa.gov/dashboard id: 00000658 name: CompTox Chemistry Dashboard namespaceEmbeddedInLui: false pattern: ^DTXSID\d+$ prefix: comptox sampleId: DTXSID2021028 uri_format: https://comptox.epa.gov/dashboard/$1 n2t: description: The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks. example: DTXSID2021028 homepage: https://comptox.epa.gov/dashboard name: CompTox Chemistry Dashboard namespaceEmbeddedInLui: false pattern: ^DTXSID\d+$ prefix: comptox uri_format: https://comptox.epa.gov/dashboard/$1 prefixcommons: is_identifiers: true is_obo: false prefix: COMPTOX uri_format: http://identifiers.org/comptox/$1 compulyeast: fairsharing: abbreviation: Compulyeast description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record. id: '2079' name: Compulyeast prefix: FAIRsharing.rbjs3e subjects: [] mappings: fairsharing: FAIRsharing.rbjs3e miriam: compulyeast n2t: compulyeast prefixcommons: COMPULYEAST miriam: deprecated: false description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record. homepage: http://compluyeast2dpage.dacya.ucm.es/ id: 00000198 name: Compulyeast namespaceEmbeddedInLui: false pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ prefix: compulyeast sampleId: O08709 uri_format: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1 n2t: description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record. example: O08709 homepage: http://compluyeast2dpage.dacya.ucm.es/ name: Compluyeast database at Universidad Complutense Madrid namespaceEmbeddedInLui: false pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ prefix: compulyeast uri_format: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1 name: Compluyeast-2D-DB prefixcommons: is_identifiers: true is_obo: false prefix: COMPULYEAST uri_format: http://identifiers.org/compulyeast/$1 provides: uniprot conoserver: fairsharing: abbreviation: ConoServer description: ConoServer is a database specializing in sequences and structures of peptides expressed by marine cone snails. The database gives access to protein sequences, nucleic acid sequences and structural information on conopeptides. ConoServer's data are first collected from the peer reviewed literature and from publicly available databases, including UniProtKB/Swiss-Prot, NCBI nucleotide (nt), and the World Wide Protein Data Bank. The data are then curated manually, which include the addition of references, the analysis of sequence regions, the identification of cysteine frameworks and gene superfamilies, and the identification of mature peptides in the precusor sequences. id: '1563' name: ConoServer prefix: FAIRsharing.y00hz4 subjects: - Neurophysiology - Statistics - Life Science - Synthetic Biology mappings: fairsharing: FAIRsharing.y00hz4 miriam: conoserver n2t: conoserver prefixcommons: CONOSERVER uniprot: ConoServer miriam: deprecated: false description: ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails. homepage: http://www.conoserver.org/ id: '00000254' name: Conoserver namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: conoserver sampleId: '2639' uri_format: http://www.conoserver.org/?page=card&table=protein&id=$1 n2t: description: ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails. example: '2639' homepage: http://www.conoserver.org/ name: ConoServer at University of Queensland namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: conoserver uri_format: http://www.conoserver.org/?page=card&table=protein&id=$1 name: ConoServer prefixcommons: is_identifiers: true is_obo: false prefix: CONOSERVER uri_format: http://identifiers.org/conoserver/$1 uniprot: category: Organism-specific databases identifier: '156' link_is_explicit: 'true' name: 'ConoServer: Cone snail toxin database' prefix: ConoServer uri_format: http://www.conoserver.org/?page=card&table=protein&id=$1 conso: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases. example: CONSO00010 homepage: https://pharmacome.github.io/conso/ name: Curation of Neurodegeneration Supporting Ontology pattern: ^CONSO\d{5}$ uri_format: https://pharmacome.github.io/conso/$1 coriell: cellosaurus: category: Cell line collections homepage: https://catalog.coriell.org name: Coriell Institute Biorepositories prefix: Coriell uri_format: https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=$1&Product=CC go: 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. homepage: http://ccr.coriell.org/ name: Coriell Institute for Medical Research prefix: CORIELL uri_format: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1 mappings: cellosaurus: Coriell go: CORIELL miriam: coriell n2t: coriell prefixcommons: Coriell miriam: deprecated: false description: The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world. homepage: http://ccr.coriell.org/ id: 00000439 name: Coriell Cell Repositories namespaceEmbeddedInLui: false pattern: ^[A-Z]{2}\d+$ prefix: coriell sampleId: GM17027 uri_format: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1 n2t: description: The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world. example: GM17027 homepage: http://ccr.coriell.org/ name: Coriell Cell Repositories at Coriell Institute namespaceEmbeddedInLui: false pattern: ^[A-Z]{2}\d+$ prefix: coriell uri_format: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1 prefixcommons: is_identifiers: false is_obo: false prefix: Coriell uri_format: https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=$1 corrdb: fairsharing: abbreviation: CorrDB description: A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies id: '2591' name: Animal Trait Correlation Database prefix: FAIRsharing.IziuCK subjects: - Animal Genetics - Genetics - Life Science - Systems Biology mappings: fairsharing: FAIRsharing.IziuCK miriam: corrdb miriam: deprecated: false description: A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies. homepage: https://www.animalgenome.org id: 00000831 name: CorrDB namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: corrdb sampleId: '37232' uri_format: https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1 corum: fairsharing: abbreviation: CORUM description: CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). Each protein complex is described by a protein complex name, subunit composition, function as well as the literature reference that characterizes the respective protein complex. id: '2839' name: ' Comprehensive Resource of Mammalian protein complexes' prefix: FAIRsharing.ohbpNw subjects: - Bioinformatics - Biology go: homepage: https://mips.helmholtz-muenchen.de/corum/ name: CORUM - the Comprehensive Resource of Mammalian protein complexes prefix: CORUM uri_format: https://mips.helmholtz-muenchen.de/corum/?id=$1 mappings: fairsharing: FAIRsharing.ohbpNw go: CORUM miriam: corum n2t: corum prefixcommons: CORUM uniprot: CORUM miriam: deprecated: false description: The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded. homepage: https://mips.helmholtz-muenchen.de/genre/proj/corum/ id: '00000440' name: CORUM namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: corum sampleId: '100' uri_format: https://mips.helmholtz-muenchen.de/corum/?id=$1 n2t: description: The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded. example: '100' homepage: https://mips.helmholtz-muenchen.de/genre/proj/corum/ name: CORUM at Institute for Bioinformatics and Systems Biology (Germany) namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: corum uri_format: https://mips.helmholtz-muenchen.de/corum/?id=$1 name: Comprehensive Resource of Mammalian protein complexes prefixcommons: is_identifiers: true is_obo: false prefix: CORUM uri_format: http://identifiers.org/corum/$1 uniprot: category: Protein-protein interaction databases identifier: '224' link_is_explicit: 'true' name: CORUM comprehensive resource of mammalian protein complexes prefix: CORUM uri_format: http://mips.helmholtz-muenchen.de/corum/#?uniprotID=$1 cosmic: cellosaurus: category: Polymorphism and mutation databases homepage: https://cancer.sanger.ac.uk/cosmic name: Catalogue of somatic mutations in cancer prefix: Cosmic uri_format: https://cancer.sanger.ac.uk/cosmic/sample/overview?id=$1 fairsharing: abbreviation: COSMIC description: The Catalogue of Somatic Mutations in Cancer (COSMIC) is a database of manually-curated somatic mutation information relating to human cancers. The COSMIC database combines manually-curated data and genome-wide screen data. id: '2204' name: Catalogue of Somatic Mutations in Cancer prefix: FAIRsharing.s5zmbp subjects: - Genetics - Biomedical Science mappings: cellosaurus: Cosmic fairsharing: FAIRsharing.s5zmbp miriam: cosmic n2t: cosmic prefixcommons: COSMIC miriam: deprecated: false description: COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes. homepage: http://cancer.sanger.ac.uk/cosmic/ id: '00000601' name: COSMIC Gene namespaceEmbeddedInLui: false pattern: ^[A-Z0-9]+$ prefix: cosmic sampleId: BRAF uri_format: http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1 n2t: description: COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes. example: BRAF homepage: http://cancer.sanger.ac.uk/cosmic/ name: COSMIC Gene at Sanger namespaceEmbeddedInLui: false pattern: ^[A-Z0-9]+$ prefix: cosmic uri_format: http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1 prefixcommons: is_identifiers: false is_obo: false prefix: COSMIC uri_format: http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=$1 cosmic.cell: cellosaurus: category: Cell line databases/resources homepage: https://cancer.sanger.ac.uk/cell_lines name: COSMIC Cell lines Project prefix: Cosmic-CLP uri_format: https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer example: '906801' homepage: https://cancer.sanger.ac.uk/cell_lines/ mappings: cellosaurus: Cosmic-CLP name: COSMIC Cell Lines pattern: ^\d+$ uri_format: https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1 covid19: bioportal: name: COVID-19 Ontology prefix: COVID-19 mappings: bioportal: COVID-19 miriam: covid19 miriam: deprecated: false description: Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease. homepage: https://covid19.sfb.uit.no id: 00000789 name: SARS-CoV-2 namespaceEmbeddedInLui: false pattern: ^\w+_COVID19_[-\w]+$ prefix: covid19 sampleId: SFB_COVID19_MW286762 uri_format: https://covid19.sfb.uit.no/api/records/$1 covoc: contact: email: zmp@ebi.ac.uk github: zoependlington name: "Zo\xEB May Pendlington" orcid: 0000-0002-4071-8397 example: '0010034' homepage: https://github.com/EBISPOT/covoc mappings: ols: covoc ols: description: The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more. download: https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl homepage: https://github.com/EBISPOT/covoc name: CoVoc Coronavirus Vocabulary prefix: covoc version: '2020-08-28' version.iri: http://purl.obolibrary.org/obo/covoc/releases/2020-08-28/covoc.owl pattern: ^\d{7}$ repository: https://github.com/EBISPOT/covoc 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 cpc: fairsharing: abbreviation: CPC description: The Climate Prediction Center (CPC) produces operational predictions of climate variability, real-time monitoring of climate and the required data bases, and assessments of the origins of major climate anomalies. These cover time scales from a week to seasons, extending into the future as far as technically feasible, and cover the land, the ocean, and the atmosphere, extending into the stratosphere. id: '2998' name: Climate Prediction Center prefix: FAIRsharing.e08886 subjects: - Hydrogeology - Geography - Meteorology - Geodesy - Earth Science - Atmospheric Science mappings: fairsharing: FAIRsharing.e08886 miriam: cpc n2t: cpc prefixcommons: CPC miriam: deprecated: false 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. homepage: https://worldwide.espacenet.com/classification id: 00000539 name: Cooperative Patent Classification namespaceEmbeddedInLui: false 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,})$ prefix: cpc sampleId: A01M1/026 uri_format: https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1 n2t: description: The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013. example: A01M1/026 homepage: https://worldwide.espacenet.com/classification name: Cooperative Patent Classification at Espace namespaceEmbeddedInLui: false pattern: ^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H, Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$ prefix: cpc uri_format: https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1 prefixcommons: is_identifiers: true is_obo: false prefix: CPC uri_format: http://identifiers.org/cpc/$1 cpga: bioportal: name: Cereal Plant Gross Anatomy Ontology prefix: GRO-CPGA deprecated: true mappings: bioportal: GRO-CPGA obofoundry: gro prefixcommons: gro.cpga obofoundry: contact: po-discuss@plantontology.org contact.label: Plant Ontology Administrators deprecated: true homepage: http://www.gramene.org/plant_ontology/ inactive: true name: Cereal Plant Gross Anatomy prefix: gro cpt: biolink: is_identifiers: false is_obo: false prefix: CPT uri_format: https://www.ama-assn.org/practice-management/cpt/$1 bioportal: name: CPT - Current Procedural Terminology prefix: CPT contributor: email: null github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 contributor_extras: - email: null github: colleenXu name: Colleen Xu orcid: 0000-0003-2975-882X description: "Current Procedural Terminology, more commonly known as CPT\xAE, refers\ \ to a medical code set created and maintained by the American Medical Association\ \ \u2014 and used by physicians, allied health professionals, nonphysician practitioners,\ \ hospitals, outpatient facilities, and laboratories to represent the services\ \ and procedures they perform. No provider of outpatient services gets paid without\ \ reporting the proper CPT\xAE codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]" example: '00103' fairsharing: abbreviation: CPT description: Current Procedural Terminology is a medical nomenclature used to report medical procedures and services under public and private health insurance programs. id: '198' name: Current Procedural Terminology prefix: FAIRsharing.wpxab1 subjects: - Medicine - Health Science - Biomedical Science homepage: https://www.aapc.com mappings: biolink: CPT bioportal: CPT fairsharing: FAIRsharing.wpxab1 name: Current Procedural Terminology pattern: ^\d+$ references: - https://github.com/biopragmatics/bioregistry/issues/357 - https://github.com/biopragmatics/bioregistry/pull/358 - https://github.com/biolink/biolink-model/pull/993 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.aapc.com/codes/cpt-codes/$1 credit: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: "CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including\ \ 14 roles, that can be used to represent the roles typically played by contributors\ \ to scientific scholarly output. The roles describe each contributor\u2019s specific\ \ contribution to the scholarly output." example: Software homepage: https://casrai.org/credit/ name: CASRAI Contributor Roles Taxonomy crisprdb: fairsharing: abbreviation: CRISPRdb description: CRISPRdb acts as a gateway to a publicly accessible database and software. It enables the easy detection of CRISPR sequences in locally-produced data and the consultation of CRISPR sequence data present in the database. It also gives information on the presence of CRISPR-associated (cas) genes when they have been annotated as such. id: '2384' name: CRISPRdb prefix: FAIRsharing.7sfedh subjects: - Life Science mappings: fairsharing: FAIRsharing.7sfedh miriam: crisprdb n2t: crisprdb prefixcommons: CRISPRDB miriam: deprecated: false description: Repeated CRISPR ("clustered regularly interspaced short palindromic repeats") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data. homepage: http://crispr.i2bc.paris-saclay.fr/ id: '00000626' name: CRISPRdb namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: crisprdb sampleId: '551115' uri_format: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1 n2t: description: Repeated CRISPR ("clustered regularly interspaced short palindromic repeats") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data. example: '551115' homepage: http://crispr.i2bc.paris-saclay.fr/ name: CRISPRdb namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: crisprdb uri_format: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1 prefixcommons: is_identifiers: true is_obo: false prefix: CRISPRDB uri_format: http://identifiers.org/crisprdb/$1 cro: bioportal: name: Contributor Role Ontology prefix: CRO download_obo: https://raw.githubusercontent.com/data2health/contributor-role-ontology/master/cro.obo example: 0000038 mappings: bioportal: CRO obofoundry: cro ols: cro ontobee: CRO prefixcommons: CRO obofoundry: contact: whimar@ohsu.edu contact.github: marijane contact.label: Marijane White contact.orcid: 0000-0001-5059-4132 deprecated: false description: A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. download.owl: http://purl.obolibrary.org/obo/cro.owl homepage: https://github.com/data2health/contributor-role-ontology inactive: false license: CC BY 2.0 license.url: https://creativecommons.org/licenses/by/2.0/ name: Contributor Role Ontology preferredPrefix: CRO prefix: cro repository: https://github.com/data2health/contributor-role-ontology ols: description: A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. download: http://purl.obolibrary.org/obo/cro.owl homepage: https://github.com/data2health/contributor-role-ontology name: Contributor Role Ontology prefix: cro version: '2019-12-11' version.iri: http://purl.obolibrary.org/obo/cro/releases/2019-12-11/cro.owl ontobee: library: Library name: Contributor Role Ontology prefix: CRO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: CRO uri_format: http://purl.obolibrary.org/obo/CRO_$1 cryoem: bioportal: name: Cryo Electron Microscopy prefix: CRYOEM example: '0000052' mappings: bioportal: CRYOEM ols: cryoem ols: contact: isanchez@cnb.csic.es description: Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles download: http://scipion.i2pc.es/ontology/cryoem.owl homepage: http://scipion.i2pc.es/ontology/cryoem name: Cryo Electron Microscopy ontology prefix: cryoem version: '2021-03-09' version.iri: http://scipion.i2pc.es/ontology/cryoem/releases/2021-03-09/cryoem.owl pattern: ^\d{7}$ cryptodb: fairsharing: abbreviation: CryptoDB description: CryptoDB serves as the functional genomics database for Cryptosporidium and related species. CryptoDB is a free, online resource for accessing and exploring genome sequence and annotation, functional genomics data, isolate sequences, and orthology profiles across organisms. It also includes supplemental bioinformatics analyses and a web interface for data-mining. id: '1878' name: CryptoDB prefix: FAIRsharing.t3nprm subjects: - Functional Genomics - Genomics - Parasitology mappings: fairsharing: FAIRsharing.t3nprm miriam: cryptodb n2t: cryptodb prefixcommons: CRYPTODB miriam: deprecated: false 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. homepage: https://cryptodb.org/cryptodb/ id: 00000149 name: CryptoDB namespaceEmbeddedInLui: false pattern: ^\w+ prefix: cryptodb sampleId: cgd7_230 uri_format: https://cryptodb.org/cryptodb/app/record/gene/$1 n2t: 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/ name: CryptoDB at EuPathDB namespaceEmbeddedInLui: false pattern: ^\w+ prefix: cryptodb uri_format: https://cryptodb.org/cryptodb/app/record/gene/$1 prefixcommons: is_identifiers: true is_obo: false prefix: CRYPTODB uri_format: http://identifiers.org/cryptodb/$1 csa: fairsharing: abbreviation: CSA description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme. id: '1849' name: Catalytic Site Atlas prefix: FAIRsharing.2ajtcf subjects: - Life Science mappings: fairsharing: FAIRsharing.2ajtcf miriam: csa n2t: csa prefixcommons: CSA miriam: deprecated: false description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme. homepage: https://www.ebi.ac.uk/thornton-srv/databases/CSA/ id: '00000144' name: CSA namespaceEmbeddedInLui: false pattern: ^[0-9][A-Za-z0-9]{3}$ prefix: csa sampleId: 1a05 uri_format: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1 n2t: description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme. example: 1a05 homepage: https://www.ebi.ac.uk/thornton-srv/databases/CSA/ name: CSA at EBI namespaceEmbeddedInLui: false pattern: ^[0-9][A-Za-z0-9]{3}$ prefix: csa uri_format: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1 name: Catalytic Site Atlas prefixcommons: is_identifiers: true is_obo: false prefix: CSA uri_format: http://identifiers.org/csa/$1 csd: fairsharing: abbreviation: CSD description: Established in 1965, the Cambridge Structural Database (CSD) is the a repository for small-molecule organic and metal-organic crystal 3D structures. Database records are automatically checked and manually curated by one of our expert in-house scientific editors. Every structure is enriched with chemical representations, as well as bibliographic, chemical and physical property information, adding further value to the raw structural data. id: '1796' name: The Cambridge Structural Database prefix: FAIRsharing.vs7865 subjects: - Organic Chemistry - Biochemistry - Organic Molecular Chemistry - Chemistry mappings: fairsharing: FAIRsharing.vs7865 miriam: csd miriam: deprecated: false description: The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode. homepage: https://www.ccdc.cam.ac.uk/ id: 00000820 name: Cambridge Structural Database namespaceEmbeddedInLui: false pattern: ^[A-Z]{6}(\d{2})?$ prefix: csd sampleId: PELNAW uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG csp: bioportal: name: Computer Retrieval of Information on Scientific Projects Thesaurus prefix: CRISP deprecated: true example: 2004-2820 homepage: https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm mappings: bioportal: CRISP name: Computer Retrieval of Information on Science Projects Thesaurus synonyms: - CRISP - CRISP Thesaurus - CRISP Thesaurus, 2006 - CSP2005 cst: bioportal: name: Cancer Staging Terms prefix: CST fairsharing: abbreviation: CST description: A small pathway portal for showcasing Cell Signaling Technology phospho-antibody products. Contains pathway diagrams that are clickable and link to more information about each protein and the commercial products that are available for that protein. id: '1800' name: Cell Signaling Technology Pathway Database prefix: FAIRsharing.n8pxvx subjects: - Life Science - Biomedical Science mappings: bioportal: CST fairsharing: FAIRsharing.n8pxvx miriam: cst n2t: cst prefixcommons: CST miriam: deprecated: false description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways. homepage: http://www.cellsignal.com/pathways/index.html id: 00000429 name: Cell Signaling Technology Pathways namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9_-]+$ prefix: cst sampleId: Akt_PKB uri_format: http://www.cellsignal.com/reference/pathway/$1.html n2t: description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways. example: Akt_PKB homepage: http://www.cellsignal.com/pathways/index.html name: CST Pathways at Cell Signaling Technology namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9_-]+$ prefix: cst uri_format: http://www.cellsignal.com/reference/pathway/$1.html prefixcommons: is_identifiers: true is_obo: false prefix: CST uri_format: http://identifiers.org/cst/$1 cst.ab: mappings: miriam: cst.ab n2t: cst.ab prefixcommons: CST.AB miriam: deprecated: false description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products. homepage: http://www.cellsignal.com/catalog/index.html id: '00000430' name: Cell Signaling Technology Antibody namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: cst.ab sampleId: '3305' uri_format: http://www.cellsignal.com/products/$1.html n2t: description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products. example: '3305' homepage: http://www.cellsignal.com/catalog/index.html name: CST Antibody at Cell Signaling Technology namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: cst.ab uri_format: http://www.cellsignal.com/products/$1.html prefixcommons: is_identifiers: true is_obo: false prefix: CST.AB uri_format: http://identifiers.org/cst.ab/$1 ctd.chemical: biolink: is_identifiers: false is_obo: false prefix: CTD.CHEMICAL uri_format: http://ctdbase.org/detail.go?type=chem&acc=$1 mappings: biolink: CTD.CHEMICAL miriam: ctd.chemical n2t: ctd.chemical prefixcommons: CTD.CHEMICAL miriam: deprecated: false description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. homepage: http://ctdbase.org/ id: 00000098 name: CTD Chemical namespaceEmbeddedInLui: false pattern: ^[CD]\d+$ prefix: ctd.chemical sampleId: D001151 uri_format: http://ctdbase.org/detail.go?type=chem&acc=$1 n2t: description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. example: D001151 homepage: http://ctdbase.org/ name: Comparative Toxicogenomics Database (Chemical) namespaceEmbeddedInLui: false pattern: ^[CD]\d+$ prefix: ctd.chemical uri_format: http://ctdbase.org/detail.go?type=chem&acc=$1 part_of: ctd prefixcommons: is_identifiers: true is_obo: false prefix: CTD.CHEMICAL uri_format: http://identifiers.org/ctd.chemical/$1 provides: mesh ctd.disease: biolink: is_identifiers: false is_obo: false prefix: CTD.DISEASE uri_format: http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1 mappings: biolink: CTD.DISEASE miriam: ctd.disease n2t: ctd.disease prefixcommons: CTD.DISEASE miriam: deprecated: false description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. homepage: http://ctdbase.org/ id: 00000099 name: CTD Disease namespaceEmbeddedInLui: false pattern: ^D\d+$ prefix: ctd.disease sampleId: D053716 uri_format: http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1 n2t: description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. example: D053716 homepage: http://ctdbase.org/ name: Comparative Toxicogenomics Database (Disease) namespaceEmbeddedInLui: false pattern: ^D\d+$ prefix: ctd.disease uri_format: http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1 part_of: ctd prefixcommons: is_identifiers: true is_obo: false prefix: CTD.DISEASE uri_format: http://identifiers.org/ctd.disease/$1 provides: mesh ctd.gene: biolink: is_identifiers: false is_obo: false prefix: CTD.GENE uri_format: http://ctdbase.org/detail.go?type=gene&acc=$1 mappings: biolink: CTD.GENE miriam: ctd.gene n2t: ctd.gene prefixcommons: CTD.GENE miriam: deprecated: false description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. homepage: http://ctdbase.org/ id: '00000100' name: CTD Gene namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: ctd.gene sampleId: '101' uri_format: http://ctdbase.org/detail.go?type=gene&acc=$1 n2t: description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. example: '101' homepage: http://ctdbase.org/ name: Comparative Toxicogenomics Database (Gene) namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: ctd.gene uri_format: http://ctdbase.org/detail.go?type=gene&acc=$1 part_of: ctd prefixcommons: is_identifiers: true is_obo: false prefix: CTD.GENE uri_format: http://identifiers.org/ctd.gene/$1 provides: ncbigene cteno: bioportal: name: Ctenophore Ontology prefix: CTENO download_obo: https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo example: '0000047' fairsharing: abbreviation: CTENO description: An anatomical and developmental ontology for ctenophores (Comb Jellies) id: '529' name: Ctenophore Ontology prefix: FAIRsharing.mgxgza subjects: [] mappings: bioportal: CTENO fairsharing: FAIRsharing.mgxgza obofoundry: cteno ols: cteno ontobee: CTENO prefixcommons: CTENO obofoundry: contact: cjmungall@lbl.gov contact.github: cmungall contact.label: Chris Mungall contact.orcid: 0000-0002-6601-2165 depends_on: - ro - uberon deprecated: false description: An anatomical and developmental ontology for ctenophores (Comb Jellies) download.owl: http://purl.obolibrary.org/obo/cteno.owl homepage: https://github.com/obophenotype/ctenophore-ontology inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Ctenophore Ontology preferredPrefix: CTENO prefix: cteno repository: https://github.com/obophenotype/ctenophore-ontology ols: description: An anatomical and developmental ontology for ctenophores (Comb Jellies) download: http://purl.obolibrary.org/obo/cteno.owl homepage: https://github.com/obophenotype/ctenophore-ontology name: Ctenophore Ontology prefix: cteno version: '2016-10-19' version.iri: http://purl.obolibrary.org/obo/cteno/releases/2016-10-19/cteno.owl ontobee: library: Library name: Ctenophore Ontology prefix: CTENO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: CTENO uri_format: http://purl.obolibrary.org/obo/CTENO_$1 cto: bioportal: name: Clinical Trials Ontology prefix: CTO example: '0000022' fairsharing: abbreviation: CTO description: The Clinical Trials Ontology (CTO) is also known as the Clinical Trial Ontology-Neurodegenerative Diseases (CTO-NDD), and describes clinical trials in the field of neurodegeneration. This resource has been created for use in the IMI-funded AETIONOMY project (www.aetionomy.org). id: '421' name: Clinical Trials Ontology prefix: FAIRsharing.qp211a subjects: - Neurobiology - Biomedical Science - Preclinical Studies mappings: bioportal: CTO fairsharing: FAIRsharing.qp211a obofoundry: cto ols: cto ontobee: CTO name: Clinical Trials Ontology obofoundry: contact: alpha.tom.kodamullil@scai.fraunhofer.de contact.github: akodamullil contact.label: Dr. Alpha Tom Kodamullil contact.orcid: 0000-0001-9896-3531 deprecated: false 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 homepage: https://github.com/ClinicalTrialOntology/CTO/ inactive: false license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: 'CTO: Core Ontology of Clinical Trials' preferredPrefix: CTO prefix: cto repository: https://github.com/ClinicalTrialOntology/CTO ols: 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: http://purl.obolibrary.org/obo/cto.owl homepage: https://github.com/BFO-ontology/BFO name: 'CTO: Core Ontology of Clinical Trials' prefix: cto version: 1.0.0 ontobee: library: Library name: 'CTO: Core Ontology of Clinical Trials' prefix: CTO pattern: ^\d{7}$ cubedb: comment: website down as of 2021-10-04 deprecated: true mappings: miriam: cubedb n2t: cubedb prefixcommons: CUBEDB miriam: deprecated: false 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. homepage: http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html id: 00000397 name: Cube db namespaceEmbeddedInLui: false pattern: ^[A-Za-z_0-9]+$ prefix: cubedb sampleId: AKR uri_format: http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/ n2t: description: Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available. example: AKR homepage: http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html name: Cube db at Bioinformatics Institute (Singapore) namespaceEmbeddedInLui: false pattern: ^[A-Za-z_0-9]+$ prefix: cubedb uri_format: http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/ prefixcommons: is_identifiers: true is_obo: false prefix: CUBEDB uri_format: http://identifiers.org/cubedb/$1 cvdo: bioportal: name: Cardiovascular Disease Ontology prefix: CVDO example: '0000546' fairsharing: abbreviation: CVDO description: CVDO is an ontology based on the OGMS model of disease, designed to describe entities related to cardiovascular diseases (including the diseases themselves, the underlying disorders, and the related pathological processes). id: '371' name: Cardiovascular Disease Ontology prefix: FAIRsharing.2basyz subjects: - Cardiology mappings: bioportal: CVDO fairsharing: FAIRsharing.2basyz obofoundry: cvdo ols: cvdo ontobee: CVDO prefixcommons: CVDO obofoundry: contact: paul.fabry@usherbrooke.ca contact.github: pfabry contact.label: Paul Fabry contact.orcid: 0000-0002-3336-2476 deprecated: false description: An ontology to describe entities related to cardiovascular diseases download.owl: http://purl.obolibrary.org/obo/cvdo.owl homepage: https://github.com/OpenLHS/CVDO inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Cardiovascular Disease Ontology preferredPrefix: CVDO prefix: cvdo repository: https://github.com/OpenLHS/CVDO ols: description: An ontology to describe entities related to cardiovascular diseases download: http://purl.obolibrary.org/obo/cvdo.owl homepage: https://github.com/OpenLHS/CVDO name: Cardiovascular Disease Ontology prefix: cvdo version: '2020-03-05' version.iri: http://purl.obolibrary.org/obo/2020-03-05/cvdo.owl ontobee: library: Library name: Cardiovascular Disease Ontology prefix: CVDO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: CVDO uri_format: http://purl.obolibrary.org/obo/CVDO_$1 d1id: mappings: miriam: d1id n2t: d1id prefixcommons: D1ID miriam: deprecated: false description: DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences. homepage: https://www.dataone.org id: '00000611' name: DataONE namespaceEmbeddedInLui: false pattern: \S+ prefix: d1id sampleId: 00030692-0FE1-4A1B-955E-A2E55D659267 uri_format: https://cn.dataone.org/cn/v2/resolve/{$1} n2t: 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 name: DataONE namespaceEmbeddedInLui: false pattern: \S+ prefix: d1id uri_format: https://cn.dataone.org/cn/v2/resolve/{$1} prefixcommons: is_identifiers: true is_obo: false prefix: D1ID uri_format: http://identifiers.org/d1id/$1 dailymed: mappings: miriam: dailymed n2t: dailymed prefixcommons: DAILYMED miriam: deprecated: false 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. homepage: https://dailymed.nlm.nih.gov/dailymed/ id: '00000434' name: DailyMed namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9-]+ prefix: dailymed sampleId: 973a9333-fec7-46dd-8eb5-25738f06ee54 uri_format: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1 n2t: 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/ name: DailyMed at NLM namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9-]+ prefix: dailymed uri_format: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1 prefixcommons: is_identifiers: true is_obo: false prefix: DAILYMED uri_format: http://identifiers.org/dailymed/$1 dandi: mappings: miriam: dandi miriam: deprecated: false description: 'DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable). DANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data. These data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.' homepage: https://dandiarchive.org/ id: 00000786 name: 'DANDI: Distributed Archives for Neurophysiology Data Integration' namespaceEmbeddedInLui: false pattern: ^\d{6}(\/\d+\.\d+\.\d+)?$ prefix: dandi sampleId: '000017' uri_format: https://dandiarchive.org/dandiset/$1 name: Distributed Archives for Neurophysiology Data Integration darc: fairsharing: abbreviation: DARC description: The Database for Aligned Ribosomal Complexes (DARC) site provides a resource for directly comparing the structures of available ribosomal complexes. id: '1566' name: Database of Aligned Ribosomal Complexes prefix: FAIRsharing.evfe2s subjects: - Life Science mappings: fairsharing: FAIRsharing.evfe2s miriam: darc n2t: darc prefixcommons: DARC miriam: deprecated: false description: DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors. homepage: http://darcsite.genzentrum.lmu.de/darc/index.php id: '00000366' name: DARC namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: darc sampleId: '1250' uri_format: http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1 n2t: description: DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors. example: '1250' homepage: http://darcsite.genzentrum.lmu.de/darc/index.php name: DARC at University of Munich namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: darc uri_format: http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1 name: Database of Aligned Ribosomal Complexes prefixcommons: is_identifiers: true is_obo: false prefix: DARC uri_format: http://identifiers.org/darc/$1 dashr: fairsharing: abbreviation: DASHR description: Integrated annotation and sequencing-based expression data for all major classes of human small non-coding RNAs (sncRNAs) for both full sncRNA transcripts and mature sncRNA products derived from these larger RNAs. id: '2248' name: Database of small human non-coding RNAs prefix: FAIRsharing.ztvs34 subjects: - Life Science mappings: fairsharing: FAIRsharing.ztvs34 miriam: dashr n2t: dashr prefixcommons: DASHR miriam: deprecated: false description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records. homepage: http://lisanwanglab.org/DASHR/ id: '00000564' name: DASHR namespaceEmbeddedInLui: false pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ prefix: dashr sampleId: hsa-mir-200a uri_format: http://lisanwanglab.org/DASHR/entry/$1 n2t: description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records. example: hsa-mir-200a homepage: http://lisanwanglab.org/DASHR/ name: DASHR at University of Pennsylvania namespaceEmbeddedInLui: false pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ prefix: dashr uri_format: http://lisanwanglab.org/DASHR/entry/$1 name: Database of small human noncoding RNAs prefixcommons: is_identifiers: true is_obo: false prefix: DASHR uri_format: http://identifiers.org/dashr/$1 dashr.expression: mappings: miriam: dashr.expression n2t: dashr.expression prefixcommons: DASHR.EXPRESSION miriam: deprecated: false description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression. homepage: https://dashr1.lisanwanglab.org/show-expression-table.php?start=0 id: '00000565' name: DASHR expression namespaceEmbeddedInLui: false pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ prefix: dashr.expression sampleId: hsa-mir-200a uri_format: https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable n2t: description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression. example: hsa-mir-200a homepage: https://dashr1.lisanwanglab.org/show-expression-table.php?start=0 name: DASHR expression at University of Pennsylvania namespaceEmbeddedInLui: false pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ prefix: dashr.expression uri_format: https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable prefixcommons: is_identifiers: true is_obo: false prefix: DASHR.EXPRESSION uri_format: http://identifiers.org/dashr.expression/$1 datanator.gene: mappings: miriam: datanator.gene miriam: deprecated: false description: Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. homepage: https://datanator.info/ id: '00000720' name: Datanator Gene namespaceEmbeddedInLui: false pattern: ^K[0-9]+$ prefix: datanator.gene sampleId: K00973 uri_format: https://www.datanator.info/gene/$1 part_of: datanator datanator.metabolite: mappings: miriam: datanator.metabolite miriam: deprecated: false description: Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. homepage: https://datanator.info/ id: 00000718 name: Datanator Metabolite namespaceEmbeddedInLui: false pattern: ^[A-Z\-]+$ prefix: datanator.metabolite sampleId: OUYCCCASQSFEME-MRVPVSSYSA-N uri_format: https://www.datanator.info/metabolite/$1 part_of: datanator datanator.reaction: mappings: miriam: datanator.reaction miriam: deprecated: false description: "\tDatanator is an integrated database of genomic and biochemical\ \ data designed to help investigators find data about specific molecules and\ \ reactions in specific organisms and specific environments for meta-analyses\ \ and mechanistic models. Datanator currently includes metabolite concentrations,\ \ RNA modifications and half-lives, protein abundances and modifications, and\ \ reaction kinetics integrated from several databases and numerous publications.\ \ The Datanator website and REST API provide tools for extracting clouds of\ \ data about specific molecules and reactions in specific organisms and specific\ \ environments, as well as data about similar molecules and reactions in taxonomically\ \ similar organisms." homepage: https://icahn.mssm.edu/ id: 00000855 name: Datanator Reaction namespaceEmbeddedInLui: false pattern: ^.*?--%3E.*?$ prefix: datanator.reaction sampleId: XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N uri_format: https://datanator.info/reaction/$1 datf: deprecated: true mappings: miriam: datf n2t: datf prefixcommons: DATF miriam: deprecated: false description: DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals. homepage: http://datf.cbi.pku.edu.cn/ id: '00000456' name: DATF namespaceEmbeddedInLui: false pattern: ^AT[1-5]G\d{5}(\.\d+)?$ prefix: datf sampleId: AT1G01030.1 uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1 n2t: description: DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals. example: AT1G01030.1 homepage: http://datf.cbi.pku.edu.cn/ name: DATF through PlantTFDB namespaceEmbeddedInLui: false pattern: ^AT[1-5]G\d{5}(\.\d+)?$ prefix: datf uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1 name: Database of Arabidopsis Transcription Factors prefixcommons: is_identifiers: true is_obo: false prefix: DATF uri_format: http://identifiers.org/datf/$1 dbd: mappings: miriam: dbd n2t: dbd prefixcommons: DBD miriam: deprecated: false description: The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins. homepage: http://www.transcriptionfactor.org/ id: '00000455' name: DBD namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: dbd sampleId: '0045310' uri_format: http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD n2t: description: The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins. example: '0045310' homepage: http://www.transcriptionfactor.org/ name: DBD at MRC Laboratory of Molecular Biology namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: dbd uri_format: http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD name: Transcription Factor Database prefixcommons: is_identifiers: true is_obo: false prefix: DBD uri_format: http://identifiers.org/dbd/$1 dbest: fairsharing: abbreviation: dbEST description: The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. NCBI is in the process of merging EST and GSS records into the Nucleotide database, and the process is expected to be completed 2019. Accession.version and GI identifiers will not change during this process. For more information please see https://ncbiinsights.ncbi.nlm.nih.gov/2018/07/30/upcoming-changes-est-gss-databases/ id: '1969' name: Expressed Sequence Tags database prefix: FAIRsharing.v9fya8 subjects: - Bioinformatics - Life Science mappings: fairsharing: FAIRsharing.v9fya8 miriam: dbest n2t: dbest ncbi: dbEST prefixcommons: DBEST miriam: deprecated: false description: The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. homepage: https://www.ncbi.nlm.nih.gov/nucest id: 00000159 name: dbEST namespaceEmbeddedInLui: false pattern: ^([A-Z]+)?\d+(\.\d+)?$ prefix: dbest providers: - code: ebi description: dbEST through European Nucleotide Archive (ENA) homepage: https://www.ebi.ac.uk/ena name: dbEST through European Nucleotide Archive (ENA) uri_format: https://www.ebi.ac.uk/ena/data/view/$1 - code: CURATOR_REVIEW description: dbEST through DNA Data Bank of Japan (DDBJ) homepage: http://www.ddbj.nig.ac.jp/ name: dbEST through DNA Data Bank of Japan (DDBJ) uri_format: http://getentry.ddbj.nig.ac.jp/getentry/na/$1 sampleId: BP100000 uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1 n2t: description: The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. example: BP100000 homepage: https://www.ncbi.nlm.nih.gov/nucest name: dbEST at NCBI namespaceEmbeddedInLui: false pattern: ^([A-Z]+)?\d+(\.\d+)?$ prefix: dbest uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1 ncbi: example: '123456' homepage: https://www.ncbi.nlm.nih.gov/genbank/dbest name: EST database maintained at the NCBI. prefix: dbEST prefixcommons: is_identifiers: true is_obo: false prefix: DBEST uri_format: http://identifiers.org/dbest/$1 dbg2introns: mappings: miriam: dbg2introns n2t: dbg2introns prefixcommons: DBG2INTRONS miriam: deprecated: false description: The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. homepage: http://webapps2.ucalgary.ca/~groupii/ id: 00000318 name: DBG2 Introns namespaceEmbeddedInLui: false pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$ prefix: dbg2introns sampleId: Cu.me.I1 uri_format: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1 n2t: description: The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. example: Cu.me.I1 homepage: http://webapps2.ucalgary.ca/~groupii/ name: Bacterial Group II Introns at University of Calgary namespaceEmbeddedInLui: false pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$ prefix: dbg2introns uri_format: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1 prefixcommons: is_identifiers: true is_obo: false prefix: DBG2INTRONS uri_format: http://identifiers.org/dbg2introns/$1 dbgap: fairsharing: abbreviation: dbGaP description: The Database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits. id: '1996' name: Database of Genotypes and Phenotypes prefix: FAIRsharing.88v2k0 subjects: - Epigenetics - Genetics - Biomedical Science mappings: fairsharing: FAIRsharing.88v2k0 miriam: dbgap n2t: dbgap prefixcommons: DBGAP miriam: deprecated: false description: The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. homepage: https://www.ncbi.nlm.nih.gov/projects/gap id: '00000602' name: dbGaP namespaceEmbeddedInLui: false pattern: ^phs[0-9]{6}(.v\d+.p\d+)?$ prefix: dbgap sampleId: phs000768.v2.p1 uri_format: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1 n2t: description: The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. example: phs000768.v2.p1 homepage: https://www.ncbi.nlm.nih.gov/projects/gap name: dbGaP through NCBI namespaceEmbeddedInLui: false pattern: ^phs[0-9]{6}(.v\d+.p\d+)?$ prefix: dbgap uri_format: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1 name: Database of Genotypes and Phenotypes prefixcommons: is_identifiers: true is_obo: false prefix: DBGAP uri_format: http://identifiers.org/dbgap/$1 dbmhc: appears_in: - cellosaurus cellosaurus: category: Cell line databases/resources homepage: https://www.ncbi.nlm.nih.gov/gv/mhc/ name: dbMHC database prefix: dbMHC deprecated: true example: '48439' mappings: cellosaurus: dbMHC name: Database of human Major Histocompatibility Complex pattern: ^\d+$ dbprobe: mappings: miriam: dbprobe n2t: dbprobe ncbi: dbProbe prefixcommons: DBPROBE miriam: deprecated: false 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. homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe id: '00000160' name: dbProbe namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: dbprobe sampleId: '1000000' uri_format: https://www.ncbi.nlm.nih.gov/probe/?term=$1 n2t: description: The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities. example: '1000000' homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe name: dbProbe at NCBI namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: dbprobe uri_format: https://www.ncbi.nlm.nih.gov/probe/?term=$1 ncbi: example: '38' homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe name: NCBI Probe database Public registry of nucleic acid reagents prefix: dbProbe prefixcommons: is_identifiers: true is_obo: false prefix: DBPROBE uri_format: http://identifiers.org/dbprobe/$1 dbsnp: cellosaurus: category: Polymorphism and mutation databases homepage: https://www.ncbi.nlm.nih.gov/snp/ name: Single Nucleotide Polymorphism database prefix: dbSNP uri_format: https://www.ncbi.nlm.nih.gov/snp/$1 fairsharing: abbreviation: dbSNP description: dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations. id: '1972' name: Database of Single Nucleotide Polymorphism prefix: FAIRsharing.edxb58 subjects: - Life Science go: homepage: http://www.ncbi.nlm.nih.gov/projects/SNP name: NCBI dbSNP prefix: dbSNP uri_format: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$1 mappings: cellosaurus: dbSNP fairsharing: FAIRsharing.edxb58 go: dbSNP miriam: dbsnp n2t: dbsnp ncbi: dbSNP prefixcommons: dbSNP uniprot: dbSNP miriam: deprecated: false description: The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. homepage: https://www.ncbi.nlm.nih.gov/snp/ id: '00000161' name: dbSNP namespaceEmbeddedInLui: false pattern: ^rs\d+$ prefix: dbsnp providers: - code: sib description: SNP2TFBS homepage: https://ccg.epfl.ch/snp2tfbs/ name: SNP2TFBS uri_format: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1 sampleId: rs121909098 uri_format: https://www.ncbi.nlm.nih.gov/snp/$1 n2t: description: The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. example: rs121909098 homepage: https://www.ncbi.nlm.nih.gov/snp/ name: dbSNP at NCBI namespaceEmbeddedInLui: false pattern: ^rs\d+$ prefix: dbsnp uri_format: https://www.ncbi.nlm.nih.gov/snp/$1 ncbi: example: '4647' homepage: https://www.ncbi.nlm.nih.gov/snp name: Variation database maintained at the NCBI. prefix: dbSNP prefixcommons: is_identifiers: false is_obo: false prefix: dbSNP uri_format: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$1 uniprot: category: Genetic variation databases identifier: '13' link_is_explicit: 'true' name: Database of single nucleotide polymorphism prefix: dbSNP uri_format: https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$1 dc: bioportal: name: Dublin Core prefix: DC description: Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. example: contributor fairsharing: abbreviation: DC description: The Dublin Metadata Element Set, which is often called Dublin Core (DC), is a standardized metadata scheme for description of any kind of resource such as documents in electronic and non-electronic form, digital materials (such as video, sound, images, etc) and composite media like web pages. Dublin Core Metadata may be used for multiple purposes, from simple resource description, to combining metadata vocabularies of different metadata standards, to providing interoperability for metadata vocabularies in the Linked Data cloud and Semantic Web implementations. Please note that this version of the specification for the Dublin Core Element Set 1.1 is somewhat out of date, although it is not officially deprecated. The DCMI Metadata Terms specification is linked to this record and is the current documentation that should be used for the Dublin Core Element Set 1.1. id: '1245' name: Dublin Core Metadata Element Set prefix: FAIRsharing.3nx7t subjects: - Life Science - Subject Agnostic - Biomedical Science has_canonical: dcterms homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ mappings: bioportal: DC fairsharing: FAIRsharing.3nx7t prefixcommons: dc name: Dublin Core prefixcommons: is_identifiers: false is_obo: false prefix: dc uri_format: http://purl.org/dc/elements/1.1/$1 uri_format: http://purl.org/dc/terms/$1 dc_cl: example: '0000003' mappings: obofoundry: dc_cl prefixcommons: DC_CL obofoundry: contact: Lindsay.Cowell@utsouthwestern.edu contact.label: Lindsay Cowell contact.orcid: 0000-0003-1617-8244 deprecated: true homepage: http://www.dukeontologygroup.org/Projects.html inactive: true name: Dendritic cell prefix: dc_cl pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: DC_CL uri_format: http://purl.obolibrary.org/obo/DC_CL_$1 dcat: biolink: is_identifiers: false is_obo: false prefix: dcat uri_format: http://www.w3.org/ns/dcat#$1 bioportal: name: Data Catalog Vocabulary prefix: DCAT description: DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web example: Dataset fairsharing: abbreviation: DCAT description: An RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web. By using DCAT to describe datasets in data catalogs, publishers increase discoverability and enable applications easily to consume metadata from multiple catalogs. It further enables decentralized publishing of catalogs and facilitates federated dataset search across sites. Aggregated DCAT metadata can serve as a manifest file to facilitate digital preservation. id: '747' name: Data Catalog Vocabulary prefix: FAIRsharing.h4j3qm subjects: - Data Management - Subject Agnostic homepage: https://www.w3.org/ns/dcat mappings: biolink: dcat bioportal: DCAT fairsharing: FAIRsharing.h4j3qm prefixcommons: dcat name: Data Catalog prefixcommons: is_identifiers: false is_obo: false prefix: dcat uri_format: http://www.w3.org/ns/dcat#$1 uri_format: http://www.w3.org/ns/dcat#$1 dcterms: biolink: is_identifiers: false is_obo: false prefix: dct uri_format: http://purl.org/dc/terms/$1 bioportal: name: 'DCMI Metadata Terms: properties in /terms/ namespace' prefix: DCTERMS description: This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. example: title fairsharing: abbreviation: DCTERMS description: This document is an up-to-date, authoritative specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. Included are the fifteen terms of the Dublin Core Metadata Element Set, which have also been published as a separate specification. id: '905' name: Dublin Core Metadata Initiative (DCMI) Metadata Terms prefix: FAIRsharing.9vtwjs subjects: - Subject Agnostic homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ mappings: biolink: dct bioportal: DCTERMS fairsharing: FAIRsharing.9vtwjs prefixcommons: dcterms name: Dublin Core Metadata Vocabulary prefixcommons: is_identifiers: false is_obo: false prefix: dcterms uri_format: http://purl.org/dc/terms/$1 synonyms: - dc.terms uri_format: http://purl.org/dc/terms/$1 dctypes: description: This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. example: Collection homepage: https://dublincore.org/specifications/dublin-core/dcmi-terms/ mappings: prefixcommons: dctypes name: Dublin Core Types prefixcommons: is_identifiers: false is_obo: false prefix: dctypes uri_format: http://purl.org/dc/dcmitype/$1 uri_format: http://purl.org/dc/dcmitype/$1 ddanat: bioportal: name: Dictyostelium Discoideum Anatomy Ontology prefix: DDANAT example: '0000006' fairsharing: abbreviation: DDANAT description: 'The Dictyostelium Anatomy Ontology ontology describes the anatomy of the slime mold. It defines the structural makeup of Dictyostelium and its composing parts including the different cell types, throughout its life cycle. It has two main goals: (1) promote the consistent annotation of Dictyostelium-specific events, such as phenotypes and gene expression information; and (2) encourage researchers to use the same terms with the same intended meaning.' id: '928' name: Dictyostelium Anatomy Ontology prefix: FAIRsharing.z656ab subjects: - Anatomy - Life Science go: homepage: http://dictybase.org/Dicty_Info/dicty_anatomy_ontology.html name: Dictyostelium discoideum anatomy prefix: DDANAT mappings: bioportal: DDANAT fairsharing: FAIRsharing.z656ab go: DDANAT obofoundry: ddanat ols: ddanat ontobee: DDANAT prefixcommons: DDANAT obofoundry: contact: pfey@northwestern.edu contact.github: pfey03 contact.label: Petra Fey contact.orcid: 0000-0002-4532-2703 deprecated: false description: A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum download.obo: http://purl.obolibrary.org/obo/ddanat.obo download.owl: http://purl.obolibrary.org/obo/ddanat.owl homepage: http://dictybase.org/ inactive: false license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Dictyostelium discoideum anatomy preferredPrefix: DDANAT prefix: ddanat publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/18366659 title: An anatomy ontology to represent biological knowledge in Dictyostelium discoideum repository: https://github.com/dictyBase/migration-data twitter: dictybase ols: description: A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum download: http://purl.obolibrary.org/obo/ddanat.owl homepage: http://dictybase.org/ name: Dictyostelium discoideum anatomy prefix: ddanat version: '2020-04-13' version.iri: http://purl.obolibrary.org/obo/ddanat/releases/2020-04-13/ddanat.owl ontobee: library: Library name: Dictyostelium discoideum anatomy prefix: DDANAT pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: DDANAT uri_format: http://purl.obolibrary.org/obo/DDANAT_$1 ddpheno: bioportal: name: Dictyostelium Discoideum Phenotype Ontology prefix: DDPHENO download_obo: https://raw.githubusercontent.com/obophenotype/dicty-phenotype-ontology/master/ddpheno.obo example: '0001417' fairsharing: abbreviation: DDPHENO description: "A structured controlled vocabulary of phenotypes of the social amoeba\ \ Dictyostelium discoideum. The Dicty Phenotype Ontology is a hierarchical controlled\ \ vocabulary used for annotating strains with phenotypes. Terms from the Dicty\ \ Phenotype Ontology are required when annotating phenotypes within dictyBase.\ \ The phenotype ontology consists of two composite terms: (1) the anatomical\ \ part or the biological process changed in the mutant, and (2) a quality describing\ \ that modification. For example, a \u2018delayed aggregation\u2019 phenotype\ \ qualifies the \u2018aggregation\u2019 (biological process) as being \u2018\ delayed\u2019, or the \u2018decreased spore size\u2019 qualifies the \u2018\ spore\u2019 to be of \u2018decreased size\u2019." id: '867' name: Dictyostelium Phenotype Ontology prefix: FAIRsharing.9c1p18 subjects: - Life Science mappings: bioportal: DDPHENO fairsharing: FAIRsharing.9c1p18 obofoundry: ddpheno ols: ddpheno ontobee: DDPHENO prefixcommons: DDPHENO obofoundry: contact: pfey@northwestern.edu contact.github: pfey03 contact.label: Petra Fey contact.orcid: 0000-0002-4532-2703 deprecated: false description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. download.obo: http://purl.obolibrary.org/obo/ddpheno.obo download.owl: http://purl.obolibrary.org/obo/ddpheno.owl homepage: http://dictybase.org/ inactive: false license: CC0 1.0 license.url: http://creativecommons.org/publicdomain/zero/1.0/ name: Dictyostelium discoideum phenotype ontology preferredPrefix: DDPHENO prefix: ddpheno publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31840793 title: dictyBase and the Dicty Stock Center (version 2.0) - a progress report repository: https://github.com/obophenotype/dicty-phenotype-ontology twitter: dictybase ols: description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. download: http://purl.obolibrary.org/obo/ddpheno.owl homepage: http://dictybase.org/ name: Dicty Phenotype Ontology (DDPHENO) prefix: ddpheno version: '2020-06-19' version.iri: http://purl.obolibrary.org/obo/ddpheno/releases/2020-06-19/ddpheno.owl ontobee: library: Library name: Dictyostelium discoideum phenotype ontology prefix: DDPHENO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: DDPHENO uri_format: http://purl.obolibrary.org/obo/DDPHENO_$1 decipher: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms example: '1' fairsharing: abbreviation: DECIPHER description: DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources) is an interactive web-based resource that incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance, inversions, and translocations. id: '2636' name: DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources prefix: FAIRsharing.l8Sf5x subjects: - Life Science - Biomedical Science homepage: https://www.deciphergenomics.org/ mappings: fairsharing: FAIRsharing.l8Sf5x prefixcommons: DECIPHER name: DECIPHER CNV Syndromes pattern: ^\d+$ prefixcommons: is_identifiers: false is_obo: true prefix: DECIPHER uri_format: http://purl.obolibrary.org/obo/DECIPHER_$1 references: - https://www.deciphergenomics.org/redirect?to=https%3A%2F%2Fdx.doi.org%2F10.1016%2Fj.ajhg.2009.03.010 uri_format: https://www.deciphergenomics.org/syndrome/$1 degradome: mappings: miriam: degradome n2t: degradome prefixcommons: DEGRADOME miriam: deprecated: false description: The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced. homepage: http://degradome.uniovi.es/ id: '00000454' name: Degradome Database namespaceEmbeddedInLui: false pattern: ^[AMCST][0-9x][0-9]$ prefix: degradome sampleId: Ax1 uri_format: http://degradome.uniovi.es/cgi-bin/protease/$1 n2t: description: The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced. example: Ax1 homepage: http://degradome.uniovi.es/ name: Degradome Database at namespaceEmbeddedInLui: false pattern: ^[AMCST][0-9x][0-9]$ prefix: degradome uri_format: http://degradome.uniovi.es/cgi-bin/protease/$1 prefixcommons: is_identifiers: true is_obo: false prefix: DEGRADOME uri_format: http://identifiers.org/degradome/$1 depmap: cellosaurus: category: Cell line databases/resources homepage: https://depmap.org/portal/ name: Cancer Dependency Map prefix: DepMap uri_format: https://depmap.org/portal/cell_line/$1 description: Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells. example: ACH-000001 homepage: https://depmap.org/portal mappings: cellosaurus: DepMap name: DepMap Cell Lines pattern: ^ACH-\d+$ uri_format: https://depmap.org/portal/cell_line/$1 depod: fairsharing: abbreviation: DEPOD description: DEPOD - the human DEPhOsphorylation Database is a manually curated database collecting human active and inactive phosphatases, their experimentally verified protein and non-protein substrates, and dephosphorylation site information, and pathways in which they are involved. It also provides links to popular kinase databases and protein-protein interaction databases for these phosphatases and substrates. id: '2178' name: The human DEPhOsphorylation Database prefix: FAIRsharing.q9j2e3 subjects: - Life Science mappings: fairsharing: FAIRsharing.q9j2e3 miriam: depod n2t: depod prefixcommons: DEPOD uniprot: DEPOD miriam: deprecated: false description: The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources. homepage: http://www.depod.bioss.uni-freiburg.de id: 00000428 name: DEPOD namespaceEmbeddedInLui: false pattern: ^[A-Z0-9]+$ prefix: depod sampleId: PTPN1 uri_format: http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1 n2t: description: The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources. example: PTPN1 homepage: http://www.depod.bioss.uni-freiburg.de name: DEPOD at EMBL namespaceEmbeddedInLui: false pattern: ^[A-Z0-9]+$ prefix: depod uri_format: http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1 name: Human Dephosphorylation Database prefixcommons: is_identifiers: true is_obo: false prefix: DEPOD uri_format: http://identifiers.org/depod/$1 provides: hgnc.symbol uniprot: category: PTM databases identifier: '190' link_is_explicit: 'true' name: DEPOD human dephosphorylation database prefix: DEPOD uri_format: http://depod.bioss.uni-freiburg.de/showp.php?name=$1 dermo: bioportal: name: Human Dermatological Disease Ontology prefix: DERMO description: DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders example: '0000000' fairsharing: abbreviation: DERMO description: Ontology of human dermatologic disease id: '808' name: Human Dermatological Disease Ontology prefix: FAIRsharing.k008w7 subjects: [] homepage: https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x mappings: bioportal: DERMO fairsharing: FAIRsharing.k008w7 name: Human Dermatological Disease Ontology pattern: ^\d{7}$ dev.ga4ghdos: mappings: miriam: dev.ga4ghdos n2t: dev.ga4ghdos prefixcommons: DEV.GA4GHDOS miriam: deprecated: false description: Assists in resolving data across cloud resources. homepage: http://github.com/ga4gh/data-object-service-schemas id: '00000656' name: Development Data Object Service namespaceEmbeddedInLui: false pattern: ^[a-zA-Z0-9\-:#\.]+$ prefix: dev.ga4ghdos sampleId: 23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00 uri_format: https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1 n2t: description: Assists in resolving data across cloud resources. example: 23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00 homepage: http://github.com/ga4gh/data-object-service-schemas name: Data Object Service namespaceEmbeddedInLui: false pattern: ^[a-zA-Z0-9\-:#\.]+$ prefix: dev.ga4ghdos uri_format: https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1 prefixcommons: is_identifiers: true is_obo: false prefix: DEV.GA4GHDOS uri_format: http://identifiers.org/dev.ga4ghdos/$1 dg.4503: mappings: miriam: dg.4503 miriam: deprecated: false 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 homepage: https://gen3.biodatacatalyst.nhlbi.nih.gov id: 00000869 name: BioData Catalyst namespaceEmbeddedInLui: false 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}' prefix: dg.4503 sampleId: 0000ffeb-36e0-4a29-b21d-84423bda979d uri_format: https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/$1 dg.4dfc: mappings: miriam: dg.4dfc miriam: deprecated: false 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 homepage: https://nci-crdc.datacommons.io/ id: 00000857 name: NCI Data Commons Framework Services namespaceEmbeddedInLui: false 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}' prefix: dg.4dfc sampleId: 81944ba1-81d0-436e-8552-33d77a27834b uri_format: https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1 dg.6vts: mappings: miriam: dg.6vts miriam: deprecated: false 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 homepage: https://jcoin.datacommons.io id: 00000876 name: JCOIN namespaceEmbeddedInLui: false 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}' prefix: dg.6vts sampleId: 2afacf00-9a1d-4d80-8c32-69d3923d3913 uri_format: https://jcoin.datacommons.io/ga4gh/drs/v1/objects/$1 dg.anv0: mappings: miriam: dg.anv0 miriam: deprecated: false 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 homepage: https://gen3.theanvil.io id: 00000871 name: Anvil namespaceEmbeddedInLui: false 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}' prefix: dg.anv0 sampleId: 00077f1c-c45a-47ba-8e6c-1bf6b6b43fce uri_format: https://gen3.theanvil.io/ga4gh/drs/v1/objects/$1 dg.f82a1a: mappings: miriam: dg.f82a1a miriam: deprecated: false 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 homepage: https://kidsfirstdrc.org id: 00000887 name: Kids First namespaceEmbeddedInLui: false 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}' prefix: dg.f82a1a sampleId: 00026f50-858a-446b-8ed9-b0e3ecd7b20e uri_format: https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/$1 dg5b0d: mappings: miriam: dg.5b0d miriam: deprecated: false 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. homepage: https://data.bloodpac.org/. id: 00000895 name: BloodPAC namespaceEmbeddedInLui: false 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}' prefix: dg.5b0d sampleId: 00000d53-99bc-4d3e-8ed7-6dc358baccb7 uri_format: https://data.bloodpac.org/ga4gh/drs/v1/objects/$1 dgrc: cellosaurus: category: Cell line collections homepage: https://dgrc.bio.indiana.edu/cells/Catalog name: Drosophila Genomics Resource Center prefix: DGRC uri_format: https://dgrc.bio.indiana.edu/product/View?product=$1 example: '215' mappings: cellosaurus: DGRC pattern: ^\d+$ dhba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A controlled vocabulary to support the study of transcription in the developing human brain download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dhba.obo example: '10153' homepage: https://www.brainspan.org/ name: Developing Human Brain Atlas pattern: ^\d+$ preferred_prefix: DHBA dicom: bioportal: name: DICOM Controlled Terminology prefix: DCM example: '109082' fairsharing: abbreviation: DICOM description: "DICOM \u2014 Digital Imaging and Communications in Medicine \u2014\ \ is the international standard for medical images and related information (ISO\ \ 12052). It defines the formats for medical images that can be exchanged with\ \ the data and quality necessary for clinical use. DICOM is implemented in almost\ \ every radiology, cardiology imaging, and radiotherapy device (X-ray, CT, MRI,\ \ ultrasound, etc.), and increasingly in devices in other medical domains such\ \ as ophthalmology and dentistry. With tens of thousands of imaging devices\ \ in use, DICOM is one of the most widely deployed healthcare messaging standards\ \ in the world. There are literally billions of DICOM images currently in use\ \ for clinical care. Since its first publication in 1993, DICOM has revolutionized\ \ the practice of radiology, allowing the replacement of X-ray film with a fully\ \ digital workflow. Much as the Internet has become the platform for new consumer\ \ information applications, DICOM has enabled advanced medical imaging applications\ \ that have \u201Cchanged the face of clinical medicine\u201D. From the emergency\ \ department, to cardiac stress testing, to breast cancer detection, DICOM is\ \ the standard that makes medical imaging work \u2014 for doctors and for patients." id: '84' name: Digital Imaging and COmmunications in Medicine prefix: FAIRsharing.b7z8by subjects: - Anatomy - Medicine - Biomedical Science mappings: bioportal: DCM fairsharing: FAIRsharing.b7z8by ols: dicom ols: contact: dclunie@dclunie.com description: DICOM Controlled Terminology download: ftp://medical.nema.org/MEDICAL/Dicom/Resources/Ontology/DCM/dcm.owl homepage: http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html name: DICOM Controlled Terminology prefix: dicom version: 2021e_20211122 pattern: ^\d+$ dictybase: description: A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics fairsharing: abbreviation: dictyBase description: dictyBase is a single-access database for the complete genome sequence and expression data of four Dictyostelid species providing information on research, genome and annotations. There is also a repository of plasmids and strains held at the Dicty Stock Centre. Relevant literature is integrated into the database, and gene models and functional annotation are manually curated from experimental results and comparative multigenome analyses. id: '2293' name: dictyBase prefix: FAIRsharing.4shj9c subjects: - Anatomy - Life Science - Comparative Genomics go: homepage: http://dictybase.org name: dictyBase prefix: dictyBase synonyms: - DDB - DictyBase uri_format: http://dictybase.org/gene/$1 mappings: fairsharing: FAIRsharing.4shj9c go: dictyBase ncbi: dictyBase prefixcommons: dictyBase uniprot: dictyBase name: dictyBase ncbi: example: DDB0191090 homepage: http://dictybase.org/ name: Dictyostelium genome database prefix: dictyBase prefixcommons: is_identifiers: false is_obo: false prefix: dictyBase uri_format: http://dictybase.org/gene/$1 synonyms: - dictyBase uniprot: category: Organism-specific databases comment: Replacement for DictyBase identifier: '15' link_is_explicit: 'true' name: Dictyostelium discoideum online informatics resource prefix: dictyBase uri_format: http://dictybase.org/db/cgi-bin/gene_page.pl?primary_id=$1 dictybase.est: mappings: miriam: dictybase.est n2t: dictybase.est prefixcommons: DICTYBASE.EST miriam: deprecated: false description: The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information. homepage: http://dictybase.org/ id: '00000330' name: Dictybase EST namespaceEmbeddedInLui: false pattern: ^DDB\d+$ prefix: dictybase.est sampleId: DDB0016567 uri_format: http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1 n2t: description: The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information. example: DDB0016567 homepage: http://dictybase.org/ name: Dictybase Gene at Northwestern University namespaceEmbeddedInLui: false pattern: ^DDB\d+$ prefix: dictybase.est uri_format: http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1 name: dictyBase Expressed Sequence Tag part_of: dictybase prefixcommons: is_identifiers: true is_obo: false prefix: DICTYBASE.EST uri_format: http://identifiers.org/dictybase.est/$1 dictybase.gene: mappings: miriam: dictybase.gene n2t: dictybase.gene prefixcommons: DICTYBASE.GENE miriam: deprecated: false description: The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information. homepage: http://dictybase.org/ id: 00000286 name: Dictybase Gene namespaceEmbeddedInLui: false pattern: ^DDB_G\d+$ prefix: dictybase.gene sampleId: DDB_G0267522 uri_format: http://dictybase.org/gene/$1 n2t: description: The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information. example: DDB_G0267522 homepage: http://dictybase.org/ name: Dictybase Gene at Northwestern University namespaceEmbeddedInLui: false pattern: ^DDB_G\d+$ prefix: dictybase.gene uri_format: http://dictybase.org/gene/$1 part_of: dictybase prefixcommons: is_identifiers: true is_obo: false prefix: DICTYBASE.GENE uri_format: http://identifiers.org/dictybase.gene/$1 did: banana: did mappings: miriam: did n2t: did miriam: deprecated: false description: DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary. homepage: https://w3c-ccg.github.io/did-spec/ id: 00000691 name: Decentralized Identifiers (DIDs) namespaceEmbeddedInLui: true pattern: ^did:[a-z0-9]+:[A-Za-z0-9.\-:]+$ prefix: did sampleId: sov:WRfXPg8dantKVubE3HX8pw uri_format: https://uniresolver.io/#did:$1 n2t: description: DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary. example: sov:WRfXPg8dantKVubE3HX8pw homepage: https://w3c-ccg.github.io/did-spec/ name: Decentralized Identifiers (DIDs) namespaceEmbeddedInLui: true pattern: ^did:[a-z0-9]+:[A-Za-z0-9.\-:]+$ prefix: did uri_format: https://uniresolver.io/#did:$1 name: Decentralized Identifier pattern: ^[a-z0-9]+:[A-Za-z0-9.\-:]+$ dideo: bioportal: name: Drug Interaction and Evidence Ontology prefix: DIDEO example: 00000180 fairsharing: abbreviation: DIDEO description: 'A domain ontology for potential drug-drug interactions (PDDIs) that covers the material entities and processes in the domain of discourse for PDDI evidence and knowledge claims. The representation enables the integration of drug interaction mechanisms, effects, risk factors, severity, and management options with the chemical and pharmacological properties (e.g., chemical structure, function, pharmacokinetic and pharmacodynamic properties) of the interacting drugs. It also has a rich and detailed set evidence entities related to pharmacology. See below for publications about DIDEO. A description of the goals of the project can be found in the following workshop paper located in the docs/DIDEO-discussion-ICBO-Brochhausen-2014.pdf: Brochhausen, M., Schneider, J., Malone, D., Empey, PE., Hogan WR., and Boyce, RD. Towards a foundational representation of potential drug-drug interaction knowledge. The 1st International Drug-Drug Interaction Knowledge Representation Workshop (DIKR 2014). Collocated with the 2014 International Conference on Biomedical Ontology (ICBO 2014). October 6th, Houston, Texas. United States.' id: '295' name: The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology prefix: FAIRsharing.9y8f0n subjects: [] mappings: bioportal: DIDEO fairsharing: FAIRsharing.9y8f0n obofoundry: dideo ols: dideo ontobee: DIDEO prefixcommons: DIDEO obofoundry: contact: mbrochhausen@gmail.com contact.github: mbrochhausen contact.label: Mathias Brochhausen contact.orcid: 0000-0003-1834-3856 deprecated: false description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology download.owl: http://purl.obolibrary.org/obo/dideo.owl homepage: https://github.com/DIDEO/DIDEO inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology preferredPrefix: DIDEO prefix: dideo repository: https://github.com/DIDEO/DIDEO ols: description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology download: http://purl.obolibrary.org/obo/dideo.owl homepage: https://github.com/DIDEO/DIDEO name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology prefix: dideo version: '2021-06-11' version.iri: http://purl.obolibrary.org/obo/dideo/release/2021-06-11/dideo.owl ontobee: library: Library name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology prefix: DIDEO pattern: ^\d{8}$ prefixcommons: is_identifiers: false is_obo: true prefix: DIDEO uri_format: http://purl.obolibrary.org/obo/DIDEO_$1 dinto: bioportal: name: The Drug-Drug Interactions Ontology prefix: DINTO mappings: bioportal: DINTO obofoundry: dinto ontobee: DINTO prefixcommons: DINTO obofoundry: contact: maria.herrero@kcl.ac.uk contact.label: 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 inactive: true license: CC BY 3.0 license.url: https://creativecommons.org/licenses/by/3.0/ name: The Drug-Drug Interactions Ontology prefix: dinto publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/26147071 title: "DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug\u2013Drug Interactions\ \ and Their Mechanisms." repository: https://github.com/labda/DINTO ontobee: library: Library name: The Drug-Drug Interactions Ontology prefix: DINTO prefixcommons: is_identifiers: false is_obo: true prefix: DINTO uri_format: http://purl.obolibrary.org/obo/DINTO_$1 dip: fairsharing: abbreviation: DIP description: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both manually by expert curators and automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the core DIP data. id: '2089' name: Database of Interacting Proteins prefix: FAIRsharing.qje0v8 subjects: - Biology mappings: fairsharing: FAIRsharing.qje0v8 miriam: dip n2t: dip prefixcommons: DIP uniprot: DIP miriam: deprecated: false description: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions homepage: https://dip.doe-mbi.ucla.edu/ id: '00000044' name: Database of Interacting Proteins namespaceEmbeddedInLui: false pattern: ^DIP(\:)?\-\d{1,}[ENXS]$ prefix: dip sampleId: DIP-743N uri_format: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1 n2t: description: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions example: DIP-743N homepage: https://dip.doe-mbi.ucla.edu/ name: Database of interacting proteins namespaceEmbeddedInLui: false pattern: ^DIP(\:)?\-\d{1,}[ENXS]$ prefix: dip uri_format: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1 prefixcommons: is_identifiers: true is_obo: false prefix: DIP uri_format: http://identifiers.org/dip/$1 uniprot: category: Protein-protein interaction databases identifier: '16' link_is_explicit: 'true' name: Database of interacting proteins prefix: DIP uri_format: https://dip.doe-mbi.ucla.edu/dip/Browse.cgi?ID=$1 discoverx: cellosaurus: category: Cell line collections homepage: https://www.discoverx.com/products-applications/cell-lines name: DiscoverX cell line products prefix: DiscoverX uri_format: https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact example: 95-0166C6 mappings: cellosaurus: DiscoverX disdriv: bioportal: name: Disease Drivers Ontology prefix: DISDRIV example: '0000000' mappings: bioportal: DISDRIV obofoundry: disdriv ols: disdriv obofoundry: contact: lynn.schriml@gmail.com contact.github: lschriml contact.label: Lynn Schriml contact.orcid: 0000-0001-8910-9851 deprecated: false description: Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. Built in collaboration with EnvO, ExO, ECTO and ChEBI. download.owl: http://purl.obolibrary.org/obo/disdriv.owl homepage: http://www.disease-ontology.org inactive: false license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Disease Drivers Ontology preferredPrefix: DISDRIV prefix: disdriv repository: https://github.com/DiseaseOntology/DiseaseDriversOntology twitter: diseaseontology ols: description: Drivers of human diseases including environmental, maternal and social exposures. download: http://purl.obolibrary.org/obo/disdriv.owl homepage: http://www.disease-ontology.org name: Disease Drivers prefix: disdriv pattern: ^\d+$ diseaseclass: appears_in: - efo contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: Legacy disease classes that later became MONDO download_obo: https://github.com/obophenotype/human-disease-ontology/raw/master/src/experimental/missing-omc.obo example: 0000598 name: Disease Class pattern: ^\d{7}$ diseasesdb: description: 'The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities.' example: '1784' homepage: http://www.diseasesdatabase.com/ name: Diseases Database pattern: ^\d+$ wikidata: database: Q213103 prefix: P557 disprot: fairsharing: abbreviation: DisProt description: The Database of Protein Disorder (DisProt) is a curated database that provides information about intrinsically disordered proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. Disordered regions are manually curated from literature. DisProt annotations cover both structural and functional aspects of disorder detected by specific experimental methods. id: '1904' name: Database of Protein Disorder prefix: FAIRsharing.dt9z89 subjects: - Biomedical Science mappings: fairsharing: FAIRsharing.dt9z89 miriam: disprot n2t: disprot prefixcommons: DISPROT uniprot: DisProt miriam: deprecated: false description: DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature. homepage: https://disprot.org/ id: 00000199 name: DisProt namespaceEmbeddedInLui: false pattern: ^DP\d{5}$ prefix: disprot sampleId: DP00003 uri_format: https://disprot.org/$1 n2t: description: The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. example: DP00003 homepage: http://www.disprot.org/ name: DisProt at Indiana University namespaceEmbeddedInLui: false pattern: ^DP\d{5}$ prefix: disprot uri_format: http://www.disprot.org/$1 prefixcommons: is_identifiers: true is_obo: false prefix: DISPROT uri_format: http://identifiers.org/disprot/$1 uniprot: category: Family and domain databases identifier: '17' link_is_explicit: 'true' name: Database of protein disorder prefix: DisProt uri_format: https://disprot.org/$1 disprot.region: mappings: miriam: disprot.region miriam: deprecated: false description: DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature. homepage: https://www.disprot.org id: '00000745' name: DisProt region namespaceEmbeddedInLui: false pattern: ^DP\d{5}r\d{3}$ prefix: disprot.region sampleId: DP00086r013 uri_format: https://www.disprot.org/$1 dlxb: mappings: miriam: dlxb miriam: deprecated: false description: DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences. homepage: https://doulix.com id: '00000747' name: Linear double stranded DNA sequences namespaceEmbeddedInLui: false pattern: ^[A-Z0-9]{6,7}$ prefix: dlxb sampleId: 6VDC956 uri_format: https://doulix.com/biomodules/$1/ part_of: dlx uri_format: https://doulix.com/biomodules/$1 dlxc: mappings: miriam: dlxc miriam: deprecated: false description: DOULIX lab-tested standard biological parts, in this case, full length constructs. homepage: https://doulix.com id: '00000742' name: Circular double stranded DNA sequences composed namespaceEmbeddedInLui: false pattern: ^[A-Z0-9]{6,7}$ prefix: dlxc sampleId: M77F7JM uri_format: https://doulix.com/constructs/$1/ part_of: dlx uri_format: https://doulix.com/constructs/$1 dmba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A controlled vocabulary to support the study of transcription in the developing mouse brain download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dmba.obo example: '688' homepage: https://developingmouse.brain-map.org/ name: Developing Mouse Brain Atlas pattern: ^\d+$ preferred_prefix: DMBA doi: biolink: is_identifiers: false is_obo: false prefix: doi uri_format: https://doi.org/$1 cellosaurus: category: Reference resources homepage: https://dx.doi.org name: Digital Object Identifier prefix: DOI uri_format: https://dx.doi.org/$1 comment: 'The [DOI resolution factsheet](https://www.doi.org/factsheets/DOIProxy.html) specifies that `https://doi.org/DOI` is the preferred format: > Users may resolve DOI names that are structured to use the DOI system Proxy Server (https://doi.org (preferred)). The resolution of the DOI name in this case depends on the use of URL syntax: the example DOI name doi:10.10.123/456 would be resolved from the address: "https://doi.org/10.123/456". Any standard browser encountering a DOI name in this form will be able to resolve it. The proxy service (both doi.org and the **earlier but no longer preferred** dx.doi.org) is accessible over IPv6, and supports DNSSEC. The proxy servers respond to HTTPS (**preferred**) as well as HTTP requests.' contributor_extras: - email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 - email: null github: dhimmel name: Daniel Himmelstein orcid: 0000-0002-3012-7446 fairsharing: abbreviation: DOI description: "The digital object identifier (DOI) system originated in a joint\ \ initiative of three trade associations in the publishing industry (International\ \ Publishers Association; International Association of Scientific, Technical\ \ and Medical Publishers; Association of American Publishers). The system was\ \ announced at the Frankfurt Book Fair 1997. The International DOI\xAE Foundation\ \ (IDF) was created to develop and manage the DOI system, also in 1997. The\ \ DOI system was adopted as International Standard ISO 26324 in 2012. The DOI\ \ system implements the Handle System and adds a number of new features. The\ \ DOI system provides an infrastructure for persistent unique identification\ \ of objects of any type. The DOI system is designed to work over the Internet.\ \ A DOI name is permanently assigned to an object to provide a resolvable persistent\ \ network link to current information about that object, including where the\ \ object, or information about it, can be found on the Internet. While information\ \ about an object can change over time, its DOI name will not change. A DOI\ \ name can be resolved within the DOI system to values of one or more types\ \ of data relating to the object identified by that DOI name, such as a URL,\ \ an e-mail address, other identifiers and descriptive metadata. The DOI system\ \ enables the construction of automated services and transactions. Applications\ \ of the DOI system include but are not limited to managing information and\ \ documentation location and access; managing metadata; facilitating electronic\ \ transactions; persistent unique identification of any form of any data; and\ \ commercial and non-commercial transactions. The content of an object associated\ \ with a DOI name is described unambiguously by DOI metadata, based on a structured\ \ extensible data model that enables the object to be associated with metadata\ \ of any desired degree of precision and granularity to support description\ \ and services. The data model supports interoperability between DOI applications.\ \ The scope of the DOI system is not defined by reference to the type of content\ \ (format, etc.) of the referent, but by reference to the functionalities it\ \ provides and the context of use. The DOI system provides, within networks\ \ of DOI applications, for unique identification, persistence, resolution, metadata\ \ and semantic interoperability." id: '1332' name: Digital Object Identifier prefix: FAIRsharing.hFLKCn subjects: - Knowledge and Information Systems go: homepage: http://dx.doi.org/ name: Digital Object Identifier prefix: DOI uri_format: http://dx.doi.org/$1 mappings: biolink: doi cellosaurus: DOI fairsharing: FAIRsharing.hFLKCn go: DOI miriam: doi n2t: doi prefixcommons: DOI scholia: doi miriam: deprecated: false description: The Digital Object Identifier System is for identifying content objects in the digital environment. homepage: https://www.doi.org/ id: 00000019 name: DOI namespaceEmbeddedInLui: false pattern: ^(doi\:)?\d{2}\.\d{4}.*$ prefix: doi 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/doi/$1 sampleId: 10.1038/nbt1156 uri_format: https://doi.org/$1 n2t: description: The Digital Object Identifier System is for identifying content objects in the digital environment. example: 10.1038/nbt1156 homepage: https://www.doi.org/ name: Digital Object Identifier namespaceEmbeddedInLui: false pattern: ^(doi\:)?\d{2}\.\d{4}.*$ prefix: doi uri_format: https://doi.org/$1 prefixcommons: is_identifiers: false is_obo: false prefix: DOI uri_format: http://dx.doi.org/$1 providers: - code: dx_doi_http description: An alternate provider from the DOI website using HTTP homepage: https://www.doi.org name: Digital Object Identifier uri_format: http://dx.doi.org/$1 - code: dx_doi_https description: An alternate provider from the DOI website using HTTPS homepage: https://www.doi.org name: Digital Object Identifier uri_format: https://dx.doi.org/$1 - code: doi_http description: An alternate provider from the DOI website using HTTP homepage: https://www.doi.org name: Digital Object Identifier uri_format: http://doi.org/$1 references: - https://github.com/biopragmatics/bioregistry/issues/287 - https://github.com/biopragmatics/bioregistry/pull/316 uri_format: https://doi.org/$1 doid: bioportal: name: Human Disease Ontology prefix: DOID download_obo: https://github.com/DiseaseOntology/HumanDiseaseOntology/raw/main/src/ontology/doid.obo example: 0110974 fairsharing: abbreviation: DOID description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics, underlying mechanisms and related medical vocabulary disease concepts. id: '870' name: Disease Ontology prefix: FAIRsharing.8b6wfq subjects: - Life Science - Biomedical Science mappings: bioportal: DOID fairsharing: FAIRsharing.8b6wfq miriam: doid n2t: doid obofoundry: doid ols: doid ontobee: DOID prefixcommons: DOID wikidata: P699 miriam: deprecated: false description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. homepage: https://www.ebi.ac.uk/ols/ontologies/doid id: '00000233' name: Human Disease Ontology namespaceEmbeddedInLui: true pattern: ^DOID:\d+$ prefix: doid providers: - code: hdo description: Human Disease Ontology at Northwestern University homepage: http://disease-ontology.org/ name: Human Disease Ontology at Northwestern University uri_format: http://disease-ontology.org/term/DOID:$1 sampleId: '11337' uri_format: https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:$1 n2t: description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. example: '11337' homepage: http://disease-ontology.org/ name: Human Disease Ontology at Northwestern University namespaceEmbeddedInLui: true pattern: ^DOID\:\d+$ prefix: doid uri_format: http://disease-ontology.org/term/DOID:$1 obofoundry: appears_in: - clo - scdo contact: lynn.schriml@gmail.com contact.github: lschriml contact.label: Lynn Schriml contact.orcid: 0000-0001-8910-9851 deprecated: false description: An ontology for describing the classification of human diseases organized by etiology. download.obo: http://purl.obolibrary.org/obo/doid.obo download.owl: http://purl.obolibrary.org/obo/doid.owl homepage: http://www.disease-ontology.org inactive: false license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Human Disease Ontology preferredPrefix: DOID prefix: doid publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/25348409 title: 'Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data' - id: https://www.ncbi.nlm.nih.gov/pubmed/34755882 title: The Human Disease Ontology 2022 update repository: https://github.com/DiseaseOntology/HumanDiseaseOntology twitter: diseaseontology ols: description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. download: http://purl.obolibrary.org/obo/doid.owl homepage: http://www.disease-ontology.org name: Human Disease Ontology prefix: doid version: '2022-04-28' version.iri: http://purl.obolibrary.org/obo/doid/releases/2022-04-28/doid.owl ontobee: library: Foundry name: Human Disease Ontology prefix: DOID pattern: ^\d+$ prefixcommons: is_identifiers: false is_obo: true prefix: DOID uri_format: http://purl.obolibrary.org/obo/DOID_$1 synonyms: - do wikidata: database: Q5282129 database.homepage: http://disease-ontology.org/ database.label: Disease Ontology homepage: http://disease-ontology.org name: Disease Ontology ID pattern: DOID:([0-9]{7}|[1-9][0-9]{0,4}) prefix: P699 uri_format: http://www.disease-ontology.org/?id=$1 dommino: homepage: http://korkinlab.org/dommino mappings: miriam: dommino n2t: dommino prefixcommons: DOMMINO miriam: deprecated: false description: DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides. homepage: http://dommino.org/ id: '00000373' name: DOMMINO namespaceEmbeddedInLui: false pattern: ^[0-9][A-Za-z0-9]{3}$ prefix: dommino sampleId: 2GC4 uri_format: http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1 n2t: description: DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides. example: 2GC4 homepage: http://dommino.org/ name: DOMMINO at University of Missouri namespaceEmbeddedInLui: false pattern: ^[0-9][A-Za-z0-9]{3}$ prefix: dommino uri_format: http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1 name: Database of Macromolecular Interactions prefixcommons: is_identifiers: true is_obo: false prefix: DOMMINO uri_format: http://identifiers.org/dommino/$1 door: mappings: miriam: door n2t: door prefixcommons: DOOR miriam: deprecated: false description: DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes. homepage: http://csbl.bmb.uga.edu/DOOR/operon.php id: '00000453' name: DOOR namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: door sampleId: '1398574' uri_format: http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1 n2t: description: DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes. example: '1398574' homepage: http://csbl.bmb.uga.edu/DOOR/operon.php name: DOOR v1 at University of Georgia namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: door uri_format: http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1 name: Database for Prokaryotic Operons prefixcommons: is_identifiers: true is_obo: false prefix: DOOR uri_format: http://identifiers.org/door/$1 doqcs.model: mappings: miriam: doqcs.model n2t: doqcs.model prefixcommons: DOQCS.MODEL miriam: deprecated: false description: The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models. homepage: http://doqcs.ncbs.res.in/ id: '00000134' name: 'Database of Quantitative Cellular Signaling: Model' namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: doqcs.model sampleId: '57' uri_format: http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1 n2t: description: The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models. example: '57' homepage: http://doqcs.ncbs.res.in/ name: Database of Quantitative Cellular Signaling (DOQCS) - Model Access namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: doqcs.model uri_format: http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1 part_of: doqcs prefixcommons: is_identifiers: true is_obo: false prefix: DOQCS.MODEL uri_format: http://identifiers.org/doqcs.model/$1 doqcs.pathway: mappings: miriam: doqcs.pathway n2t: doqcs.pathway prefixcommons: DOQCS.PATHWAY miriam: deprecated: false description: The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways. homepage: http://doqcs.ncbs.res.in/ id: '00000135' name: 'Database of Quantitative Cellular Signaling: Pathway' namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: doqcs.pathway sampleId: '131' uri_format: http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1 n2t: description: The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways. example: '131' homepage: http://doqcs.ncbs.res.in/ name: Database of Quantitative Cellular Signaling (DOQCS) - Pathway Access namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: doqcs.pathway uri_format: http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1 part_of: doqcs prefixcommons: is_identifiers: true is_obo: false prefix: DOQCS.PATHWAY uri_format: http://identifiers.org/doqcs.pathway/$1 dpo: bioportal: name: Drosophila Phenotype Ontology prefix: DPO comment: DPO is a subset of terms from FBcv mappings: bioportal: DPO obofoundry: dpo ols: dpo ontobee: DPO no_own_terms: true obofoundry: contact: cp390@cam.ac.uk contact.github: Clare72 contact.label: Clare Pilgrim contact.orcid: 0000-0002-1373-1705 deprecated: false 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 inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Drosophila Phenotype Ontology preferredPrefix: FBcv prefix: dpo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/24138933 title: The Drosophila phenotype ontology. repository: https://github.com/FlyBase/drosophila-phenotype-ontology ols: description: An ontology for the description of Drosophila melanogaster phenotypes. download: http://purl.obolibrary.org/obo/dpo.owl homepage: http://purl.obolibrary.org/obo/fbcv name: Drosophila Phenotype Ontology (DPO) prefix: dpo version: '2022-04-13' version.iri: http://purl.obolibrary.org/obo/dpo/releases/2022-04-13/dpo.owl ontobee: library: Library name: Drosophila Phenotype Ontology prefix: DPO part_of: fbcv preferred_prefix: DPO dpv: mappings: miriam: dpv n2t: dpv prefixcommons: DPV miriam: deprecated: false 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. homepage: http://www.dpvweb.net/ id: 00000280 name: DPV namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: dpv sampleId: '100' uri_format: http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1 n2t: description: Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. example: '100' homepage: http://www.dpvweb.net/ name: DPV at Rothamsted namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: dpv uri_format: http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1 name: Description of Plant Viruses prefixcommons: is_identifiers: true is_obo: false prefix: DPV uri_format: http://identifiers.org/dpv/$1 dragondb.allele: comment: Deprecated because the website is dead deprecated: true mappings: miriam: dragondb.allele n2t: dragondb.allele prefixcommons: DRAGONDB.ALLELE miriam: deprecated: false description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information. homepage: http://www.antirrhinum.net/ id: '00000300' name: DragonDB Allele namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: dragondb.allele sampleId: cho uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele n2t: description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information. example: cho homepage: http://www.antirrhinum.net/ name: DragonDB Allele at University of British Columbia namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: dragondb.allele uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele part_of: dragondb prefixcommons: is_identifiers: true is_obo: false prefix: DRAGONDB.ALLELE uri_format: http://identifiers.org/dragondb.allele/$1 dragondb.dna: comment: Deprecated because the website is dead deprecated: true mappings: miriam: dragondb.dna n2t: dragondb.dna prefixcommons: DRAGONDB.DNA miriam: deprecated: false description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information. homepage: http://www.antirrhinum.net/ id: 00000297 name: DragonDB DNA namespaceEmbeddedInLui: false pattern: ^\d\w+$ prefix: dragondb.dna sampleId: 3hB06 uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA n2t: description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information. example: 3hB06 homepage: http://www.antirrhinum.net/ name: DragonDB DNA at University of British Columbia namespaceEmbeddedInLui: false pattern: ^\d\w+$ prefix: dragondb.dna uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA part_of: dragondb prefixcommons: is_identifiers: true is_obo: false prefix: DRAGONDB.DNA uri_format: http://identifiers.org/dragondb.dna/$1 dragondb.locus: comment: Deprecated because the website is dead deprecated: true mappings: miriam: dragondb.locus n2t: dragondb.locus prefixcommons: DRAGONDB.LOCUS miriam: deprecated: false description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information. homepage: http://www.antirrhinum.net/ id: 00000299 name: DragonDB Locus namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: dragondb.locus sampleId: DEF uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus n2t: description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information. example: DEF homepage: http://www.antirrhinum.net/ name: DragonDB Locus at University of British Columbia namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: dragondb.locus uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus part_of: dragondb prefixcommons: is_identifiers: true is_obo: false prefix: DRAGONDB.LOCUS uri_format: http://identifiers.org/dragondb.locus/$1 dragondb.protein: comment: Deprecated because the website is dead deprecated: true mappings: miriam: dragondb.protein n2t: dragondb.protein prefixcommons: DRAGONDB.PROTEIN miriam: deprecated: false description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information. homepage: http://www.antirrhinum.net/ id: 00000298 name: DragonDB Protein namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: dragondb.protein sampleId: AMDEFA uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide n2t: description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information. example: AMDEFA homepage: http://www.antirrhinum.net/ name: DragonDB Protein at University of British Columbia namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: dragondb.protein uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide part_of: dragondb prefixcommons: is_identifiers: true is_obo: false prefix: DRAGONDB.PROTEIN uri_format: http://identifiers.org/dragondb.protein/$1 dron: bioportal: name: The Drug Ontology prefix: DRON example: '00023232' fairsharing: abbreviation: DrOn description: An ontology of drug products and packaged drug products. id: '641' name: The Drug Ontology prefix: FAIRsharing.w5ntfd subjects: - Biomedical Science mappings: bioportal: DRON fairsharing: FAIRsharing.w5ntfd obofoundry: dron ols: dron ontobee: DRON prefixcommons: DRON obofoundry: appears_in: - scdo contact: hoganwr@gmail.com contact.github: hoganwr contact.label: William Hogan contact.orcid: 0000-0002-9881-1017 deprecated: false description: An ontology to support comparative effectiveness researchers studying claims data. download.owl: http://purl.obolibrary.org/obo/dron.owl homepage: https://github.com/ufbmi/dron inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: The Drug Ontology preferredPrefix: DRON prefix: dron publications: - id: https://doi.org/10.1186/s13326-017-0121-5 title: 'Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request' repository: https://github.com/ufbmi/dron ols: description: We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive). download: http://purl.obolibrary.org/obo/dron.owl homepage: https://github.com/ufbmi/dron name: The Drug Ontology prefix: dron version: '2022-04-22' version.iri: http://purl.obolibrary.org/obo/dron/releases/2022-04-22/dron.owl ontobee: library: Library name: The Drug Ontology prefix: DRON pattern: ^\d{8}$ prefixcommons: is_identifiers: false is_obo: true prefix: DRON uri_format: http://purl.obolibrary.org/obo/DRON_$1 drsc: mappings: miriam: drsc n2t: drsc prefixcommons: DRSC miriam: deprecated: false description: The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene. homepage: http://flyrnai.org/ id: '00000367' name: DRSC namespaceEmbeddedInLui: false pattern: ^DRSC\d+$ prefix: drsc sampleId: DRSC05221 uri_format: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1 n2t: description: The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene. example: DRSC05221 homepage: http://flyrnai.org/ name: DRSC at Harvard Medical School namespaceEmbeddedInLui: false pattern: ^DRSC\d+$ prefix: drsc uri_format: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1 name: Drosophila RNAi Screening Center prefixcommons: is_identifiers: true is_obo: false prefix: DRSC uri_format: http://identifiers.org/drsc/$1 drugbank: cellosaurus: category: Chemistry resources homepage: https://go.drugbank.com/ name: DrugBank database prefix: DrugBank uri_format: https://go.drugbank.com/drugs/$1 cheminf: description: Database identifier used by DrugBank. name: DrugBank obsolete: false prefix: '000406' example: DB14938 fairsharing: abbreviation: DrugBank description: The DrugBank database is a freely available bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. id: '1844' name: DrugBank prefix: FAIRsharing.353yat subjects: - Life Science - Biomedical Science homepage: http://www.drugbank.ca mappings: cellosaurus: DrugBank cheminf: '000406' fairsharing: FAIRsharing.353yat miriam: drugbank n2t: drugbank prefixcommons: DrugBank uniprot: DrugBank wikidata: P715 miriam: deprecated: false description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information. homepage: http://www.drugbank.ca/ id: '00000102' name: DrugBank namespaceEmbeddedInLui: false pattern: ^DB\d{5}$ prefix: drugbank sampleId: DB00001 uri_format: http://www.drugbank.ca/drugs/$1 n2t: description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information. example: DB00001 homepage: http://www.drugbank.ca/ name: DrugBank drug information namespaceEmbeddedInLui: false pattern: ^DB\d{5}$ prefix: drugbank uri_format: http://www.drugbank.ca/drugs/$1 name: DrugBank prefixcommons: is_identifiers: false is_obo: false prefix: DrugBank uri_format: http://www.drugbank.ca/drugs/$1 synonyms: - DRUGBANK_ID - DrugBank uniprot: category: Chemistry databases identifier: '19' link_is_explicit: 'true' name: Drug and drug target database prefix: DrugBank uri_format: https://www.drugbank.ca/drugs/$1 wikidata: database: Q1122544 database.homepage: http://www.drugbank.ca/ database.label: DrugBank homepage: https://www.drugbank.ca name: DrugBank ID pattern: (SALT\d{1}|CAT\d{1})?\d{5} prefix: P715 uri_format: https://go.drugbank.com/drugs/DB$1 drugbank.salt: description: DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets. example: DBSALT001211 homepage: http://www.drugbank.ca mappings: prefixcommons: DRUGBANK.TARGET name: DrugBank Salts part_of: drugbank pattern: ^DBSALT\d{6}$ prefixcommons: is_identifiers: true is_obo: false prefix: DRUGBANK.TARGET uri_format: http://identifiers.org/drugbank.target/$1 synonyms: - drugbank.target uri_format: https://go.drugbank.com/salts/$1 drugbankv4.target: mappings: miriam: drugbankv4.target n2t: drugbankv4.target prefixcommons: DRUGBANKV4.TARGET miriam: deprecated: false description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database. homepage: http://www.drugbank.ca/targets id: 00000528 name: DrugBank Target v4 namespaceEmbeddedInLui: false pattern: ^BE\d{7}$ prefix: drugbankv4.target sampleId: BE0000048 uri_format: http://www.drugbank.ca/biodb/bio_entities/$1 n2t: description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database. example: BE0000048 homepage: http://www.drugbank.ca/targets name: DrugBank Target information version 4 namespaceEmbeddedInLui: false pattern: ^BE\d{7}$ prefix: drugbankv4.target uri_format: http://www.drugbank.ca/biodb/bio_entities/$1 part_of: drugbank prefixcommons: is_identifiers: true is_obo: false prefix: DRUGBANKV4.TARGET uri_format: http://identifiers.org/drugbankv4.target/$1 drugcentral: biolink: is_identifiers: false is_obo: false prefix: DrugCentral uri_format: http://drugcentral.org/drugcard/$1 description: DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action. example: '307' fairsharing: abbreviation: DrugCentral description: DrugCentral is online drug information that provides information on active ingredients, chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic mode of action. DrugCentral monitors FDA, EMA, and PMDA for new drug approval on regular basis to ensure currency of the resource. This resource was created and is maintained by the Division of Translational Informatics at the University of New Mexico School of Medicine. id: '2363' name: DrugCentral prefix: FAIRsharing.3me82d subjects: - Drug Discovery - Drug Repositioning - Drug Development - Pharmacy - Pharmacology - Biomedical Science homepage: http://drugcentral.org mappings: biolink: DrugCentral fairsharing: FAIRsharing.3me82d uniprot: DrugCentral name: Drug Central pattern: ^\d+$ synonyms: - Drug_Central uniprot: category: Chemistry databases identifier: '239' link_is_explicit: 'true' name: DrugCentral prefix: DrugCentral uri_format: https://drugcentral.org/target/$1 uri_format: http://drugcentral.org/drugcard/$1 dsmz: cellosaurus: category: Cell line collections homepage: https://www.dsmz.de/collection/catalogue/human-and-animal-cell-lines/catalogue name: Deutsche Sammlung von Mikroorganismen und Zellkulturen prefix: DSMZ uri_format: https://www.dsmz.de/collection/catalogue/details/culture/$1 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). example: ACC-1 homepage: https://www.dsmz.de mappings: cellosaurus: DSMZ name: Deutsche Sammlung von Mikroorganismen und Zellkulturen uri_format: https://www.dsmz.de/collection/catalogue/details/culture/$1 dto: appears_in: - pr bioportal: name: Drug Target Ontology prefix: DTO description: 'DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.' example: '90000018' fairsharing: abbreviation: DTO description: Drug Target Ontology (DTO) is developed as a reference for drug targets with the longer-term goal to create a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The first version of the DTO consists of asserted class hierarchies of the four IDG protein families, GPCRs, kinases, ion channels, and nuclear hormone receptors. Protein classes are linked to tissue and disease via different levels of confidence. DTO also contains drug target development classifications, a large collection of cell lines from the LINCS project and relevant cell-disease and cell-tissue relations. DTO is modeled in OWL2-DL to enable further classification by inference reasoning and SPARQL queries. DTO is implemented following a modularization approach. DTO will serve as the organizational framework for drug targets in the IDG PHAROS User Interface Portal (https://pharos.nih.gov). id: '1469' name: Drug Target Ontology prefix: FAIRsharing.tke3y2 subjects: - Drug Discovery - Biomedical Science homepage: https://github.com/DrugTargetOntology/DTO mappings: bioportal: DTO fairsharing: FAIRsharing.tke3y2 name: Drug Target Ontology pattern: ^\d+$ repository: https://github.com/DrugTargetOntology/DTO duo: bioportal: name: The Data Use Ontology prefix: DUO example: '0000046' fairsharing: abbreviation: DUO description: The Data Use Ontology (DUO) describes data use requirements and limitations. DUO allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage. This resource is based on the OBO Foundry principles, and developed using the W3C Web Ontology Language. It is used in production by the European Genome-phenome Archive (EGA) at EMBL-EBI and CRG as well as the Broad Institute for the Data Use Oversight System (DUOS). id: '256' name: The Data Use Ontology prefix: FAIRsharing.5dnjs2 subjects: - Data Management - Subject Agnostic mappings: bioportal: DUO fairsharing: FAIRsharing.5dnjs2 obofoundry: duo ols: duo ontobee: DUO prefixcommons: DUO obofoundry: appears_in: - scdo contact: mcourtot@gmail.com contact.github: mcourtot contact.label: Melanie Courtot contact.orcid: 0000-0002-9551-6370 depends_on: - bfo - iao deprecated: false description: DUO is an ontology which represent data use conditions. download.owl: http://purl.obolibrary.org/obo/duo.owl homepage: https://github.com/EBISPOT/DUO inactive: false license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Data Use Ontology preferredPrefix: DUO prefix: duo repository: https://github.com/EBISPOT/DUO ols: description: DUO is an ontology which represent data use conditions. download: http://purl.obolibrary.org/obo/duo.owl homepage: https://github.com/EBISPOT/DUO name: Data Use Ontology prefix: duo version: '2021-02-23' version.iri: http://purl.obolibrary.org/obo/duo/releases/2021-02-23/duo.owl ontobee: library: Library name: Data Use Ontology prefix: DUO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: DUO uri_format: http://purl.obolibrary.org/obo/DUO_$1 eaglei: cellosaurus: category: Biological sample resources homepage: https://www.eagle-i.net/ name: eagle-i resource discovery tool prefix: eagle-i contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Discovery tool for biomedical research resources available at institutions throughout the U.S. example: 0000012b-5661-2f63-2f73-b43980000000 homepage: https://hawaii.eagle-i.net mappings: cellosaurus: eagle-i name: eagle-i uri_format: http://hawaii.eagle-i.net/i/$1 ebisc: cellosaurus: category: Cell line collections homepage: https://www.ebisc.org name: European Bank for induced pluripotent Stem Cells prefix: EBiSC uri_format: https://cells.ebisc.org/$1 example: ESi007-A mappings: cellosaurus: EBiSC ecacc: cellosaurus: category: Cell line collections homepage: https://www.phe-culturecollections.org.uk/products/celllines/index.aspx name: European Collection of Cell Cultures prefix: ECACC uri_format: https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?refId=$1&collection=ecacc_gc description: The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs). example: '90062901' homepage: https://www.phe-culturecollections.org.uk/collections/ecacc.aspx mappings: cellosaurus: ECACC name: European Collection of Authenticated Cell Culture pattern: ^\d+$ uri_format: https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1 ecao: bioportal: name: The Echinoderm Anatomy and Development Ontology prefix: ECAO example: 0107180 mappings: bioportal: ECAO obofoundry: ecao ols: ecao ontobee: ECAO obofoundry: contact: ettensohn@cmu.edu contact.github: ettensohn contact.label: Charles Ettensohn contact.orcid: 0000-0002-3625-0955 depends_on: - cl - ro - uberon deprecated: false description: An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586). download.obo: http://purl.obolibrary.org/obo/ecao.obo download.owl: http://purl.obolibrary.org/obo/ecao.owl homepage: https://github.com/echinoderm-ontology/ecao_ontology inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: The Echinoderm Anatomy and Development Ontology preferredPrefix: ECAO prefix: ecao repository: https://github.com/echinoderm-ontology/ecao_ontology ols: description: None download: http://purl.obolibrary.org/obo/ecao.owl homepage: https://github.com/echinoderm-ontology/ecao_ontology name: Echinoderm Anatomy and Development Ontology prefix: ecao version: '2020-05-22' version.iri: http://purl.obolibrary.org/obo/ecao/releases/2020-05-22/ecao.owl ontobee: library: Library name: The Echinoderm Anatomy and Development Ontology prefix: ECAO pattern: ^\d{7}$ eccode: example_decoys: - '100' - '2.' - 2.n1 - 2.3. - 2.3.n1 - 2.3.1. - 2.3.1.n - 2.3.4.1. example_extras: - '2' - '2.3' - 2.3.1 - 2.3.1.n12 - 3.1.26.n2 fairsharing: abbreviation: IntEnz description: IntEnz is a freely available resource focused on enzyme nomenclature. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. id: '1853' name: Integrated relational Enzyme database prefix: FAIRsharing.q1fdkc subjects: - Bioinformatics - Enzymology go: homepage: http://enzyme.expasy.org/ name: Enzyme Commission prefix: EC uri_format: https://enzyme.expasy.org/EC/$1 mappings: fairsharing: FAIRsharing.q1fdkc go: EC miriam: ec-code n2t: ec-code prefixcommons: EC miriam: deprecated: false description: The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions. homepage: https://www.ebi.ac.uk/intenz/ id: '00000004' name: Enzyme Nomenclature namespaceEmbeddedInLui: false pattern: ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$ prefix: ec-code providers: - code: CURATOR_REVIEW description: KEGG Ligand Database for Enzyme Nomenclature homepage: https://www.genome.jp/dbget-bin/www_bfind?enzyme name: KEGG Ligand Database for Enzyme Nomenclature uri_format: https://www.genome.jp/dbget-bin/www_bget?ec:$1 - code: expenz description: ExploreEnz at Trinity College homepage: http://www.enzyme-database.org/ name: ExploreEnz at Trinity College uri_format: http://www.enzyme-database.org/query.php?ec=$1 - code: enzymeportal description: Enzyme Portal through EMBL-EBI homepage: https://www.ebi.ac.uk/enzymeportal name: Enzyme Portal through EMBL-EBI uri_format: https://www.ebi.ac.uk/enzymeportal/ec/$1 - code: expasy description: Enzyme nomenclature database, ExPASy (Expert Protein Analysis System) homepage: https://enzyme.expasy.org/ name: Enzyme nomenclature database, ExPASy (Expert Protein Analysis System) uri_format: https://enzyme.expasy.org/EC/$1 sampleId: 1.1.1.1 uri_format: https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1 n2t: description: The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions. example: 1.1.1.1 homepage: https://www.ebi.ac.uk/intenz/ name: IntEnZ (Integrated relational Enzyme database) namespaceEmbeddedInLui: false pattern: ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$ prefix: ec-code uri_format: https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1 name: Enzyme Nomenclature pattern: ^\d{1,2}(((\.\d{1,3}){1,3})|(\.\d+){2}\.n\d{1,3})?$ prefixcommons: is_identifiers: false is_obo: false prefix: EC uri_format: http://www.enzyme-database.org/query.php?ec=$1 synonyms: - EC - EC-CODE - ECCODE - EC_CODE - ec-code - intenz uri_format: https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1 wikidata: prefix: P591 ecg: bioportal: name: Electrocardiography Ontology prefix: ECG description: The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms. example: 000000159 fairsharing: abbreviation: ECG description: The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms. This ontology was developed and is being maintained by the CardioVascular Research Grid (www.cvrg.org). id: '19' name: ElectroCardioGraphy Ontology prefix: FAIRsharing.azr389 subjects: - Biomedical Science homepage: https://bioportal.bioontology.org/ontologies/ECG mappings: bioportal: ECG fairsharing: FAIRsharing.azr389 name: Electrocardiogram Ontology pattern: ^\d+$ synonyms: - ECGOntology echobase: go: homepage: https://www.york.ac.uk/res/thomas/ name: EchoBASE post-genomic database for Escherichia coli prefix: EchoBASE uri_format: https://www.york.ac.uk/res/thomas/Gene.cfm?&recordID=$1 mappings: go: EchoBASE miriam: echobase n2t: echobase prefixcommons: ECHOBASE uniprot: EchoBASE miriam: deprecated: false description: EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products. homepage: http://www.york.ac.uk/ id: '00000200' name: EchoBASE namespaceEmbeddedInLui: false pattern: ^EB\d+$ prefix: echobase sampleId: EB0170 uri_format: http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1 n2t: description: EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products. example: EB0170 homepage: http://www.york.ac.uk/ name: EchoBASE at the University of York namespaceEmbeddedInLui: false pattern: ^EB\d+$ prefix: echobase uri_format: http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1 prefixcommons: is_identifiers: true is_obo: false prefix: ECHOBASE uri_format: http://identifiers.org/echobase/$1 uniprot: category: Organism-specific databases identifier: '20' link_is_explicit: 'true' name: EchoBASE - an integrated post-genomic database for E. coli prefix: EchoBASE uri_format: https://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1 ecmdb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: "The ECMDB is an expertly curated database containing extensive metabolomic\ \ data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655).\ \ This database includes significant quantities of \u201Coriginal\u201D data compiled\ \ by members of the Wishart laboratory as well as additional material derived\ \ from hundreds of textbooks, scientific journals, metabolic reconstructions and\ \ other electronic databases. Each metabolite is linked to more than 100 data\ \ fields describing the compound, its ontology, physical properties, reactions,\ \ pathways, references, external links and associated proteins or enzymes." example: ECMDB00005 homepage: https://ecmdb.ca name: E. coli Metabolite Database pattern: ^ECMDB\d+$ synonyms: - ECMDB uri_format: http://ecmdb.ca/compounds/$1 wikidata: database: Q17052437 eco: bioportal: name: Evidence and Conclusion Ontology prefix: ECO example: 0007807 fairsharing: abbreviation: ECO description: The Evidence and Conclusion Ontology (ECO) contains terms that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has function Y as supported by evidence Z). Capture of this information allows tracking of annotation provenance, establishment of quality control measures, and query of eviden id: '1483' name: Evidence and Conclusion Ontology prefix: FAIRsharing.wvpgwn subjects: - Computational Biology - Life Science go: homepage: http://www.evidenceontology.org/ name: Evidence Code Ontology prefix: ECO uri_format: http://www.evidenceontology.org/browse/#ECO_$1 mappings: bioportal: ECO fairsharing: FAIRsharing.wvpgwn go: ECO miriam: eco n2t: eco obofoundry: eco ols: eco ontobee: ECO prefixcommons: ECO miriam: deprecated: false description: Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity. homepage: https://www.ebi.ac.uk/ols/ontologies/eco id: '00000055' name: Evidence Code Ontology namespaceEmbeddedInLui: true pattern: ECO:\d{7}$ prefix: eco sampleId: '0000006' uri_format: https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1 n2t: description: Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity. example: '0000006' homepage: http://bioportal.bioontology.org/ontologies/ECO name: Evidence Code Ontology through BioPortal namespaceEmbeddedInLui: true pattern: ECO:\d{7}$ prefix: eco uri_format: http://purl.bioontology.org/ontology/ECO/ECO:$1 obofoundry: contact: mgiglio@som.umaryland.edu contact.github: mgiglio99 contact.label: Michelle Giglio contact.orcid: 0000-0001-7628-5565 deprecated: false description: An ontology for experimental and other evidence statements. download.obo: http://purl.obolibrary.org/obo/eco.obo download.owl: http://purl.obolibrary.org/obo/eco.owl homepage: https://github.com/evidenceontology/evidenceontology/ inactive: false license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Evidence ontology preferredPrefix: ECO prefix: eco publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/30407590 title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence information.' - id: https://www.ncbi.nlm.nih.gov/pubmed/25052702 title: Standardized description of scientific evidence using the Evidence Ontology (ECO) repository: https://github.com/evidenceontology/evidenceontology ols: description: The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the biological research domain that arise from laboratory experiments, computational methods, literature curation, or other means. download: http://purl.obolibrary.org/obo/eco.owl homepage: https://github.com/evidenceontology/evidenceontology/ name: Evidence & Conclusion Ontology (ECO) prefix: eco version: '2022-04-11' version.iri: http://purl.obolibrary.org/obo/eco/releases/2022-04-11/eco.owl ontobee: library: Library name: Evidence ontology prefix: ECO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: ECO uri_format: http://purl.obolibrary.org/obo/ECO_$1 ecocore: bioportal: name: An ontology of core ecological entities prefix: ECOCORE example: '00000001' mappings: bioportal: ECOCORE obofoundry: ecocore ols: ecocore ontobee: ECOCORE prefixcommons: ECOCORE obofoundry: contact: p.buttigieg@gmail.com contact.github: pbuttigieg contact.label: Pier Luigi Buttigieg contact.orcid: 0000-0002-4366-3088 depends_on: - bfo - chebi - envo - go - iao - pato - pco - po - ro - uberon deprecated: false description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. download.obo: http://purl.obolibrary.org/obo/ecocore.obo download.owl: http://purl.obolibrary.org/obo/ecocore.owl homepage: https://github.com/EcologicalSemantics/ecocore inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: An ontology of core ecological entities preferredPrefix: ECOCORE prefix: ecocore repository: https://github.com/EcologicalSemantics/ecocore ols: description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. download: http://purl.obolibrary.org/obo/ecocore.owl homepage: https://github.com/EcologicalSemantics/ecocore name: An ontology of core ecological entities prefix: ecocore version: '2022-03-09' version.iri: http://purl.obolibrary.org/obo/ecocore/releases/2022-03-09/ecocore.owl ontobee: library: Library name: An ontology of core ecological entities prefix: ECOCORE pattern: ^\d+$ prefixcommons: is_identifiers: false is_obo: true prefix: ECOCORE uri_format: http://purl.obolibrary.org/obo/ECOCORE_$1 ecocyc: description: EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways. example: AICARTRANSIMPCYCLO-CPLX fairsharing: abbreviation: EcoCyc description: EcoCyc is a model organism database for Escherichia coli K-12 MG1655. EcoCyc curation captures literature-based information on the functions of individual E. coli gene products, metabolic pathways, and regulation of E. coli gene expression. EcoCyc has been curated from 37,000 publications as of 2019. Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc. id: '2054' name: EcoCyc E. coli Database prefix: FAIRsharing.65dmtr subjects: - Biology go: homepage: http://ecocyc.org/ name: Encyclopedia of E. coli metabolism prefix: EcoCyc uri_format: http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=$1 mappings: fairsharing: FAIRsharing.65dmtr go: EcoCyc ncbi: ECOCYC name: EcoCyc ncbi: example: sroC homepage: https://ecocyc.org/ name: E. coli database prefix: ECOCYC uri_format: https://biocyc.org/gene?id=$1 ecogene: fairsharing: abbreviation: EcoGene description: The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. id: '1869' name: Escherichia coli strain K12 genome database prefix: FAIRsharing.3q3kvn subjects: [] mappings: fairsharing: FAIRsharing.3q3kvn miriam: ecogene n2t: ecogene ncbi: EcoGene prefixcommons: EcoGene miriam: deprecated: false description: The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. homepage: http://ecogene.org/ id: '00000163' name: EcoGene namespaceEmbeddedInLui: false pattern: ^EG\d+$ prefix: ecogene sampleId: EG10173 uri_format: http://www.ecogene.org/gene/$1 n2t: description: The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. example: EG10173 homepage: http://ecogene.org/ name: EcoGene at University of Miami namespaceEmbeddedInLui: false pattern: ^EG\d+$ prefix: ecogene uri_format: http://www.ecogene.org/gene/$1 ncbi: example: EG11277 homepage: http://ecogene.org name: Database of Escherichia coli Sequence and Function prefix: EcoGene prefixcommons: is_identifiers: false is_obo: false prefix: EcoGene uri_format: http://ecogene.org/gene/$1 ecolexicon: comment: No resolution - everything is in a single page app contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology. example: canal homepage: http://ecolexicon.ugr.es/en/index.htm name: EcoLexicon ecoliwiki: fairsharing: abbreviation: EcoliWiki description: EcoliWiki is a community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. id: '1576' name: EcoliWiki prefix: FAIRsharing.tx95wa subjects: - Genomics - Bioinformatics - Life Science - Ontology and Terminology go: description: EcoliHub\'s subsystem for community annotation of E. coli K-12 homepage: http://ecoliwiki.net/ name: EcoliWiki from EcoliHub prefix: EcoliWiki mappings: fairsharing: FAIRsharing.tx95wa go: EcoliWiki miriam: ecoliwiki n2t: ecoliwiki prefixcommons: ECOLIWIKI miriam: deprecated: false description: EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes. homepage: http://ecoliwiki.net/colipedia/ id: '00000442' name: EcoliWiki namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9-]+$ prefix: ecoliwiki sampleId: aaeA uri_format: http://ecoliwiki.net/colipedia/index.php/$1:Gene n2t: description: EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes. example: aaeA homepage: http://ecoliwiki.net/colipedia/ name: EcoliWiki at Texas Agrilife Research namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9-]+$ prefix: ecoliwiki uri_format: http://ecoliwiki.net/colipedia/index.php/$1:Gene prefixcommons: is_identifiers: true is_obo: false prefix: ECOLIWIKI uri_format: http://identifiers.org/ecoliwiki/$1 ecto: biolink: is_identifiers: false is_obo: true prefix: ECTO uri_format: http://purl.obolibrary.org/obo/ECTO_$1 bioportal: name: Environmental conditions, treatments and exposures ontology prefix: ECTO example: '0000001' mappings: biolink: ECTO bioportal: ECTO obofoundry: ecto ols: ecto ontobee: ECTO obofoundry: contact: annethessen@gmail.com contact.github: diatomsRcool contact.label: Anne Thessen contact.orcid: 0000-0002-2908-3327 depends_on: - chebi - envo - exo - go - iao - maxo - nbo - ncbitaxon - ncit - pato - ro - uberon - xco deprecated: false 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 homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology inactive: false license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Environmental conditions, treatments and exposures ontology preferredPrefix: ECTO prefix: ecto repository: https://github.com/EnvironmentOntology/environmental-exposure-ontology ols: 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: http://purl.obolibrary.org/obo/ecto.owl homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology name: Environment Exposure Ontology prefix: ecto version: '2021-08-25' version.iri: http://purl.obolibrary.org/obo/ecto/releases/2021-08-25/ecto.owl ontobee: library: Library name: Environmental conditions, treatments and exposures ontology prefix: ECTO pattern: ^\d{7}$ ecyano.entity: mappings: miriam: ecyano.entity n2t: ecyano.entity prefixcommons: ECYANO.ENTITY miriam: deprecated: false 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 \u2014 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." homepage: http://www.e-cyanobacterium.org/bcs/entity/ id: 00000585 name: E-cyanobacterium entity namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: ecyano.entity sampleId: '23' uri_format: http://e-cyanobacterium.org/bcs/entity/$1/ n2t: description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities. example: '23' homepage: http://www.e-cyanobacterium.org/bcs/entity/ name: e-cyanobacterium entity at Masaryk University Brno namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: ecyano.entity uri_format: http://e-cyanobacterium.org/bcs/entity/$1/ part_of: ecyano prefixcommons: is_identifiers: true is_obo: false prefix: ECYANO.ENTITY uri_format: http://identifiers.org/ecyano.entity/$1 uri_format: https://www.e-cyanobacterium.org/bcs/entity/$1 ecyano.experiment: mappings: miriam: ecyano.experiment miriam: deprecated: false description: E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments. homepage: https://www.e-cyanobacterium.org/experiments-repository/ id: '00000760' name: E-cyanobacterium Experimental Data namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: ecyano.experiment sampleId: '18' uri_format: https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1 part_of: ecyano ecyano.model: mappings: miriam: ecyano.model n2t: ecyano.model prefixcommons: ECYANO.MODEL miriam: deprecated: false description: "E-cyanobacterium.org is a web-based platform for public sharing,\ \ annotation, analysis, and visualisation of dynamical models and wet-lab experiments\ \ related to cyanobacteria. It allows models to be represented at different\ \ levels of abstraction \u2014 as biochemical reaction networks or ordinary\ \ differential equations.It provides concise mappings of mathematical models\ \ to a formalised consortium-agreed biochemical description, with the aim of\ \ connecting the world of biological knowledge with benefits of mathematical\ \ description of dynamic processes. This collection references models." homepage: http://e-cyanobacterium.org/models/ id: 00000586 name: E-cyanobacterium model namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: ecyano.model sampleId: '26' uri_format: http://e-cyanobacterium.org/models/model/$1/ n2t: description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models. example: '26' homepage: http://e-cyanobacterium.org/models/ name: e-cyanobacterium entity at Masaryk University Brno namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: ecyano.model uri_format: http://e-cyanobacterium.org/models/model/$1/ prefixcommons: is_identifiers: true is_obo: false prefix: ECYANO.MODEL uri_format: http://identifiers.org/ecyano.model/$1 uri_format: https://e-cyanobacterium.org/models/model/$1 ecyano.rule: mappings: miriam: ecyano.rule n2t: ecyano.rule prefixcommons: ECYANO.RULE miriam: deprecated: false description: "E-cyanobacterium.org is a web-based platform for public sharing,\ \ annotation, analysis, and visualisation of dynamical models and wet-lab experiments\ \ related to cyanobacteria. It allows models to be represented at different\ \ levels of abstraction \u2014 as biochemical reaction networks or ordinary\ \ differential equations.It provides concise mappings of mathematical models\ \ to a formalised consortium-agreed biochemical description, with the aim of\ \ connecting the world of biological knowledge with benefits of mathematical\ \ description of dynamic processes. This collection references rules." homepage: http://www.e-cyanobacterium.org/bcs/rule/ id: 00000587 name: E-cyanobacterium rule namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: ecyano.rule sampleId: '56' uri_format: http://e-cyanobacterium.org/bcs/rule/$1/ n2t: description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules. example: '56' homepage: http://www.e-cyanobacterium.org/bcs/rule/ name: e-cyanobacterium entity at Masaryk University Brno namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: ecyano.rule uri_format: http://e-cyanobacterium.org/bcs/rule/$1/ part_of: ecyano prefixcommons: is_identifiers: true is_obo: false prefix: ECYANO.RULE uri_format: http://identifiers.org/ecyano.rule/$1 uri_format: https://e-cyanobacterium.org/bcs/rule/$1 edam: bioportal: name: EDAM - Bioscientific data analysis ontology prefix: EDAM fairsharing: abbreviation: EDAM description: "EDAM (originally from \u201CEMBRACE Data and Methods\u201D) is an\ \ ontology of well established, familiar concepts that are prevalent within\ \ bioinformatics, including types of data and data identifiers, data formats,\ \ operations and topics." id: '1205' name: EMBRACE Data and Methods Ontology prefix: FAIRsharing.a6r7zs subjects: - Bioinformatics - Life Science mappings: bioportal: EDAM fairsharing: FAIRsharing.a6r7zs miriam: edam n2t: edam ols: edam ontobee: EDAM prefixcommons: EDAM miriam: deprecated: false description: 'EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).' homepage: http://bioportal.bioontology.org/ontologies/EDAM id: 00000189 name: EDAM Ontology namespaceEmbeddedInLui: false pattern: ^(data|topic|operation|format)\_\d{4}$ prefix: edam sampleId: data_1664 uri_format: http://purl.bioontology.org/ontology/EDAM/$1 n2t: description: 'EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).' example: data_1664 homepage: http://bioportal.bioontology.org/ontologies/EDAM name: EDAM through BioPortal namespaceEmbeddedInLui: false pattern: ^(data|topic|operation|format)\_\d{4}$ prefix: edam uri_format: http://purl.bioontology.org/ontology/EDAM/$1 ols: contact: edam@elixir-dk.org description: EDAM is a simple ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM provides a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use. download: https://raw.githubusercontent.com/edamontology/edamontology/master/releases/EDAM.owl homepage: http://edamontology.org name: Bioinformatics operations, data types, formats, identifiers and topics prefix: edam version: '2019-07-17' ontobee: library: Not Specified/No name: EMBRACE Data and Methods prefix: EDAM prefixcommons: is_identifiers: true is_obo: false prefix: EDAM uri_format: http://identifiers.org/edam/$1 uri_format: https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1 edda: bioportal: name: EDDA Study Designs Taxonomy prefix: EDDA description: Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries. example: health_care_quality_assessment fairsharing: abbreviation: EDDA description: 'Terminology of study designs and publication types (beta version). Developed by the Evidence in Documents, Discovery, and Analysis (EDDA) Group. Tanja Bekhuis (PI); Eugene Tseytlin (Systems Developer); Ashleigh Faith (Taxonomist). Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pennsylvania, US. This work was made possible, in part, by the US National Library of Medicine, National Institutes of Health, grant no. R00LM010943. Based on research described in Bekhuis T, Demner-Fushman D, Crowley RS. Comparative effectiveness research designs: an analysis of terms and coverage in Medical Subject Headings (MeSH) and Emtree. Journal of the Medical Library Association (JMLA). 2013 April;101(2):92-100. PMC3634392. The terminology appearing in JMLA has been enriched with terms from MeSH, NCI Thesaurus (NCIT), and Emtree, the controlled vocabularies for MEDLINE, the National Cancer Institute, and Embase, respectively, as well as from published research literature. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCIT, Emtree, and medical dictionaries. A class for Publication Type is included because investigators consider type and design when screening reports for inclusion in comparative effectiveness research. EDDA Study Designs and Publications by Tanja Bekhuis is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.' id: '1289' name: EDDA Study Designs Taxonomy prefix: FAIRsharing.2ffmsb subjects: [] homepage: https://bioportal.bioontology.org/ontologies/EDDA mappings: bioportal: EDDA fairsharing: FAIRsharing.2ffmsb efo: biolink: is_identifiers: false is_obo: false prefix: EFO uri_format: http://www.ebi.ac.uk/efo/EFO_$1 bioportal: name: Experimental Factor Ontology prefix: EFO cellosaurus: category: Experimental variables resources homepage: https://www.ebi.ac.uk/efo/ name: Experimental Factor Ontology prefix: EFO uri_format: https://www.ebi.ac.uk/efo/$1 contact: email: plwhetzel@gmail.com github: twhetzel name: Trish Whetzel orcid: 0000-0002-3458-4839 download_obo: http://www.ebi.ac.uk/efo/efo.obo example: '0005147' fairsharing: abbreviation: EFO description: The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental variables in multiple resources at the EBI and the Centre for Therapeutic Target Validation. The ontology has been developed to increase the richness of the annotations that are currently made in resources and to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology pulls together classes from reference ontologies such as disease, cell line, cell type and anatomy and adds axiomatisation as necessary to connect areas such as disease to phenotype. id: '1498' name: Experimental Factor Ontology prefix: FAIRsharing.1gr4tz subjects: - Functional Genomics mappings: biolink: EFO bioportal: EFO cellosaurus: EFO fairsharing: FAIRsharing.1gr4tz miriam: efo n2t: efo ols: efo ontobee: EFO prefixcommons: EFO miriam: deprecated: false description: The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team. homepage: https://www.ebi.ac.uk/ols/ontologies/efo id: 00000391 name: Experimental Factor Ontology namespaceEmbeddedInLui: false pattern: ^\d{7}$ 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 sampleId: 0004859 uri_format: https://www.ebi.ac.uk/ols/ontologies/efo/terms?obo_id=EFO:$1 n2t: description: The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team. example: 0004859 homepage: http://bioportal.bioontology.org/ontologies/EFO name: EFO through BioPortal namespaceEmbeddedInLui: false pattern: ^\d{7}$ prefix: efo uri_format: http://purl.bioontology.org/ontology/EFO/efo:EFO_$1 ols: contact: efo-users@lists.sourceforge.net description: The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue. 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 many groups at the EBI and as the core ontology for OpenTargets.org download: http://www.ebi.ac.uk/efo/efo.owl homepage: http://www.ebi.ac.uk/efo name: Experimental Factor Ontology prefix: efo version: 3.42.0 version.iri: http://www.ebi.ac.uk/efo/releases/v3.42.0/efo.owl ontobee: library: Not Specified/No name: Experimental Factor Ontology prefix: EFO preferred_prefix: EFO prefixcommons: is_identifiers: false is_obo: true prefix: EFO uri_format: http://purl.obolibrary.org/obo/EFO_$1 repository: https://github.com/EBISPOT/efo/ uri_format: http://www.ebi.ac.uk/efo/EFO_$1 ega.dataset: fairsharing: abbreviation: EGA description: The European Genome-phenome Archive (EGA) is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. Access to data must be approved by the specified Data Access Committee (DAC). id: '1865' name: The European Genome-phenome Archive prefix: FAIRsharing.mya1ff subjects: - Genomics - Phenomics - Biomedical Science - Biology homepage: https://ega-archive.org/ mappings: fairsharing: FAIRsharing.mya1ff miriam: ega.dataset n2t: ega.dataset prefixcommons: EGA.DATASET miriam: deprecated: false description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'. homepage: https://www.ebi.ac.uk/ega/dataset id: '00000512' name: European Genome-phenome Archive Dataset namespaceEmbeddedInLui: false pattern: ^EGAD\d{11}$ 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 sampleId: EGAD00000000001 uri_format: https://www.ebi.ac.uk/ega/datasets/$1 n2t: description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'. example: EGAD00000000001 homepage: https://www.ebi.ac.uk/ega/dataset name: EGA Dataset at European Bioinformatics Institute namespaceEmbeddedInLui: false pattern: ^EGAD\d{11}$ prefix: ega.dataset uri_format: https://www.ebi.ac.uk/ega/datasets/$1 prefixcommons: is_identifiers: true is_obo: false prefix: EGA.DATASET uri_format: http://identifiers.org/ega.dataset/$1 ega.study: mappings: miriam: ega.study n2t: ega.study prefixcommons: EGA.STUDY miriam: deprecated: false description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets. homepage: https://www.ebi.ac.uk/ega/studies id: '00000511' name: European Genome-phenome Archive Study namespaceEmbeddedInLui: false pattern: ^EGAS\d{11}$ prefix: ega.study providers: - code: omicsdi description: EGA Study through OmicsDI homepage: https://www.omicsdi.org/ name: EGA Study through OmicsDI uri_format: https://www.omicsdi.org/dataset/ega/$1 sampleId: EGAS00000000001 uri_format: https://www.ebi.ac.uk/ega/studies/$1 n2t: description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets. example: EGAS00000000001 homepage: https://www.ebi.ac.uk/ega/studies name: EGA Study at European Bioinformatics Institute namespaceEmbeddedInLui: false pattern: ^EGAS\d{11}$ prefix: ega.study uri_format: https://www.ebi.ac.uk/ega/studies/$1 prefixcommons: is_identifiers: true is_obo: false prefix: EGA.STUDY uri_format: http://identifiers.org/ega.study/$1 eggnog: fairsharing: abbreviation: eggNOG description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).' id: '1577' name: 'Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups' prefix: FAIRsharing.j1wj7d subjects: - Life Science mappings: fairsharing: FAIRsharing.j1wj7d miriam: eggnog n2t: eggnog prefixcommons: EGGNOG uniprot: eggNOG miriam: deprecated: false description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).' homepage: http://eggnog.embl.de/version_3.0/ id: '00000201' name: eggNOG namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: eggnog sampleId: veNOG12876 uri_format: http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1 n2t: description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).' example: veNOG12876 homepage: http://eggnog.embl.de/version_3.0/ name: eggNOG Version 3 at European Molecular Biology Laboratory namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: eggnog uri_format: http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1 prefixcommons: is_identifiers: true is_obo: false prefix: EGGNOG uri_format: http://identifiers.org/eggnog/$1 uniprot: category: Phylogenomic databases identifier: '152' link_is_explicit: 'true' name: 'evolutionary genealogy of genes: Non-supervised Orthologous Groups' prefix: eggNOG uri_format: http://eggnogdb.embl.de/#/app/results?seqid=%u&target_nogs=%s ehda: bioportal: name: Human Developmental Anatomy Ontology, timed version prefix: EHDA example: '1' mappings: bioportal: EHDA obofoundry: ehda prefixcommons: EHDA obofoundry: contact: J.Bard@ed.ac.uk contact.label: Jonathan Bard deprecated: true homepage: http://genex.hgu.mrc.ac.uk/ inactive: true name: Human developmental anatomy, timed version prefix: ehda pattern: ^\d+$ prefixcommons: is_identifiers: false is_obo: true prefix: EHDA uri_format: http://purl.obolibrary.org/obo/EHDA_$1 ehdaa: bioportal: name: Human Developmental Anatomy Ontology, abstract version 1 prefix: EHDAA example: '1' mappings: bioportal: EHDAA obofoundry: ehdaa prefixcommons: EHDAA obofoundry: contact: J.Bard@ed.ac.uk contact.label: Jonathan Bard deprecated: true inactive: true name: Human developmental anatomy, abstract version prefix: ehdaa pattern: ^\d+$ prefixcommons: is_identifiers: false is_obo: true prefix: EHDAA uri_format: http://purl.obolibrary.org/obo/EHDAA_$1 ehdaa2: bioportal: name: Human Developmental Anatomy Ontology, abstract version 2 prefix: EHDAA2 example: '0000000' fairsharing: abbreviation: EHDAA2 description: "The EHDAA2 ontology is a human developmental anatomy covering the\ \ first 49 days [Carnegie stages (CS)1\u201320], primarily structured around\ \ the parts of organ systems and their development. The ontology includes more\ \ than 2000 anatomical entities (AEs) that range from the whole embryo, through\ \ organ systems and organ parts down to simple or leaf tissues (groups of cells\ \ with the same morphological phenotype), as well as features such as cavities.\ \ It represents a complete rebuilding of the EHDA intended to meet current standards.\ \ The intention has been to include as much information about human developmental\ \ anatomy as is practical and as is available in the literature." id: '199' name: Edinburgh human developmental anatomy abstract version 2 prefix: FAIRsharing.7zxrs6 subjects: - Anatomy - Life Science - Biomedical Science mappings: bioportal: EHDAA2 fairsharing: FAIRsharing.7zxrs6 obofoundry: ehdaa2 ols: ehdaa2 ontobee: EHDAA2 prefixcommons: EHDAA2 obofoundry: contact: J.Bard@ed.ac.uk contact.label: Jonathan Bard depends_on: - aeo - caro - cl deprecated: false 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 homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology inactive: true license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Human developmental anatomy, abstract prefix: ehdaa2 publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/22973865 title: A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20). repository: https://github.com/obophenotype/human-developmental-anatomy-ontology ols: description: A structured controlled vocabulary of stage-specific anatomical structures of the developing human. download: http://purl.obolibrary.org/obo/ehdaa2.owl homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology name: Human developmental anatomy, abstract prefix: ehdaa2 version: '2013-07-04' version.iri: http://purl.obolibrary.org/obo/ehdaa2/releases/2013-07-04/ehdaa2.owl ontobee: library: Library name: Human developmental anatomy, abstract prefix: EHDAA2 pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: EHDAA2 uri_format: http://purl.obolibrary.org/obo/EHDAA2_$1 synonyms: - EHDAA2_RETIRED - HDAA2 - RETIRED_EHDAA2 elm: fairsharing: abbreviation: ELM description: This computational biology resource mainly focuses on annotation and detection of eukaryotic linear motifs (ELMs) by providing both a repository of annotated motif data and an exploratory tool for motif prediction. ELMs, or short linear motifs (SLiMs), are compact protein interaction sites composed of short stretches of adjacent amino acids. id: '1578' name: Eukaryotic Linear Motifs prefix: FAIRsharing.rj3kj5 subjects: - Life Science mappings: fairsharing: FAIRsharing.rj3kj5 miriam: elm n2t: elm prefixcommons: ELM uniprot: ELM miriam: deprecated: false description: Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances. homepage: http://elm.eu.org/ id: '00000250' name: ELM namespaceEmbeddedInLui: false pattern: ^[A-Za-z_0-9]+$ prefix: elm sampleId: CLV_MEL_PAP_1 uri_format: http://elm.eu.org/elms/elmPages/$1.html n2t: description: Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances. example: CLV_MEL_PAP_1 homepage: http://elm.eu.org/ name: ELM at EMBL (Germany) namespaceEmbeddedInLui: false pattern: ^[A-Za-z_0-9]+$ prefix: elm uri_format: http://elm.eu.org/elms/elmPages/$1.html name: Eukaryotic Linear Motif Resource prefixcommons: is_identifiers: true is_obo: false prefix: ELM uri_format: http://identifiers.org/elm/$1 uniprot: category: Protein-protein interaction databases identifier: '223' link_is_explicit: 'true' name: The Eukaryotic Linear Motif resource for Functional Sites in Proteins prefix: ELM uri_format: http://elm.eu.org/instances.html?q=$1 emap: bioportal: name: Mouse Gross Anatomy and Development Ontology prefix: EMAP example: '1' mappings: bioportal: EMAP obofoundry: emap prefixcommons: EMAP obofoundry: contact: Terry.Hayamizu@jax.org contact.github: tfhayamizu contact.label: Terry Hayamizu contact.orcid: 0000-0002-0956-8634 deprecated: true description: A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). download.owl: http://purl.obolibrary.org/obo/emap.owl homepage: http://emouseatlas.org inactive: true name: Mouse gross anatomy and development, timed prefix: emap pattern: ^\d+$ prefixcommons: is_identifiers: false is_obo: true prefix: EMAP uri_format: http://purl.obolibrary.org/obo/EMAP_$1 emapa: bioportal: name: Mouse gross anatomy and development, timed prefix: EMAPA example: '26753' fairsharing: abbreviation: EMAPA description: Abstract (i.e. non-stage specific) stage-specific anatomical structures of the mouse. id: '513' name: Mouse gross anatomy and development, timed prefix: FAIRsharing.j0fa1d subjects: [] go: description: A time-independent Mouse Anatomical Dictionary; part of Gene Expression Database homepage: http://emouseatlas.org/ name: Mouse gross anatomy and development, abstract prefix: EMAPA uri_format: http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:$1 mappings: bioportal: EMAPA fairsharing: FAIRsharing.j0fa1d go: EMAPA obofoundry: emapa ols: emapa ontobee: EMAPA prefixcommons: EMAPA obofoundry: contact: Terry.Hayamizu@jax.org contact.github: tfhayamizu contact.label: Terry Hayamizu contact.orcid: 0000-0002-0956-8634 deprecated: false description: An ontology for mouse anatomy covering embryonic development and postnatal stages. download.obo: http://purl.obolibrary.org/obo/emapa.obo download.owl: http://purl.obolibrary.org/obo/emapa.owl homepage: http://www.informatics.jax.org/expression.shtml inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Mouse Developmental Anatomy Ontology preferredPrefix: EMAPA prefix: emapa repository: https://github.com/obophenotype/mouse-anatomy-ontology ols: description: An ontology for mouse anatomy covering embryonic development and postnatal stages. download: http://purl.obolibrary.org/obo/emapa.owl homepage: http://www.informatics.jax.org/expression.shtml name: Mouse Developmental Anatomy Ontology prefix: emapa version: '2021-09-01' version.iri: http://purl.obolibrary.org/obo/emapa/releases/2021-09-01/emapa.owl ontobee: library: Library name: Mouse Developmental Anatomy Ontology prefix: EMAPA pattern: ^\d+$ prefixcommons: is_identifiers: false is_obo: true prefix: EMAPA uri_format: http://purl.obolibrary.org/obo/EMAPA_$1 synonyms: - EMAPA_RETIRED emdb: fairsharing: abbreviation: EMDB description: Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB was founded at EBI in 2002, under the leadership of Kim Henrick. Since 2007 it has been operated jointly by the PDBe, and the Research Collaboratory for Structural Bioinformatics (RCSB PDB) as a part of EMDataBank which is funded by a joint NIH grant to PDBe, the RCSB and the National Center for Macromolecular Imaging (NCMI). id: '2126' name: Electron Microscopy Data Bank prefix: FAIRsharing.651n9j subjects: - Virology - Biology - Epidemiology mappings: fairsharing: FAIRsharing.651n9j miriam: emdb n2t: emdb prefixcommons: EMDB miriam: deprecated: false description: The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community. homepage: https://www.ebi.ac.uk/pdbe/emdb/ id: '00000561' name: Electron Microscopy Data Bank namespaceEmbeddedInLui: false pattern: ^EMD-\d{4}$ prefix: emdb sampleId: EMD-1001 uri_format: https://www.ebi.ac.uk/pdbe/entry/emdb/$1 n2t: description: The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community. example: EMD-1001 homepage: https://www.ebi.ac.uk/pdbe/emdb/ name: EMDB at Protein Data Bank in Europe namespaceEmbeddedInLui: false pattern: ^EMD-\d{4}$ prefix: emdb uri_format: https://www.ebi.ac.uk/pdbe/entry/emdb/$1 prefixcommons: is_identifiers: true is_obo: false prefix: EMDB uri_format: http://identifiers.org/emdb/$1 emolecules: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Catalog of purchasable reagents and building blocks example: '491187' homepage: https://reaxys.emolecules.com name: Reaxys eMolecules pattern: ^\d+$ uri_format: https://reaxys.emolecules.com/cgi-bin/more?vid=$1 empiar: description: EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure example: '10595' fairsharing: abbreviation: EMPIAR description: EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure. The purpose of EMPIAR is to provide easy access to state-of-the-art raw data to facilitate methods development and validation, which will lead to better 3D structures. It complements the Electron Microscopy Data Bank (EMDB), where 3D volumes are stored. id: '2649' name: Electron Microscopy Public Image Archive prefix: FAIRsharing.dff3ef subjects: - Bioinformatics - Biology homepage: https://www.ebi.ac.uk/pdbe/emdb mappings: fairsharing: FAIRsharing.dff3ef name: Electron Microscopy Public Image Archive pattern: ^\d+$ uri_format: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1 ena.embl: fairsharing: abbreviation: ENA description: The European Nucleotide Archive (ENA) is a globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and experimental design. Serving both as the database of record for the output of the world's sequencing activity and as a platform for the management, sharing and publication of sequence data, the ENA provides a portfolio of services for submission, data management, search and retrieval across web and programmatic interfaces. The ENA is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These three organizations exchange data on a daily basis. id: '1850' name: European Nucleotide Archive prefix: FAIRsharing.dj8nt8 subjects: - Functional Genomics - Metagenomics - Genomics - Bioinformatics - Data Management - Biodiversity - Transcriptomics go: description: ENA is made up of a number of distinct databases that includes EMBL-Bank, the newly established Sequence Read Archive (SRA) and the Trace Archive. International nucleotide sequence database collaboration, comprising ENA-EBI nucleotide sequence data library (EMBL-Bank), DNA DataBank of Japan (DDBJ), and NCBI GenBank homepage: http://www.ebi.ac.uk/ena/ name: European Nucleotide Archive prefix: ENA uri_format: http://www.ebi.ac.uk/ena/data/view/$1 mappings: fairsharing: FAIRsharing.dj8nt8 go: ENA miriam: ena.embl n2t: ena.embl prefixcommons: ENA.EMBL miriam: deprecated: false description: The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers. homepage: https://www.ebi.ac.uk/ena/ id: '00000372' name: ENA namespaceEmbeddedInLui: false pattern: ^[A-Z]+[0-9]+(\.\d+)?$ 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 sampleId: BN000065 uri_format: https://www.ebi.ac.uk/ena/browser/view/$1 n2t: description: The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers. example: BN000065 homepage: https://www.ncbi.nlm.nih.gov/Genbank/ name: ENA through GenBank namespaceEmbeddedInLui: false pattern: ^[A-Z]+[0-9]+(\.\d+)?$ prefix: ena.embl uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 prefixcommons: is_identifiers: true is_obo: false prefix: ENA.EMBL uri_format: http://identifiers.org/ena.embl/$1 synonyms: - ena uri_format: https://www.ebi.ac.uk/ena/browser/view/$1 encode: cellosaurus: category: Biological sample resources homepage: https://www.encodeproject.org name: Encyclopedia of DNA Elements prefix: ENCODE uri_format: https://www.encodeproject.org/biosamples/$1 fairsharing: abbreviation: ENCODE description: Encyclopedia of DNA Elements (ENCODE) has created a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. UCSC coordinated data for the ENCODE Consortium from its inception in 2003 (Pilot phase) to the end of the first 5 year phase of whole-genome data production in 2012. All data produced by ENCODE investigators and the results of ENCODE analysis projects from this period are hosted in the UCSC Genome browser and database. id: '1579' name: Encyclopedia of DNA Elements at UCSC prefix: FAIRsharing.v0hbjs subjects: - Life Science homepage: https://www.encodeproject.org mappings: cellosaurus: ENCODE fairsharing: FAIRsharing.v0hbjs miriam: encode n2t: encode prefixcommons: ENCODE miriam: deprecated: false description: The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. homepage: www.encodeproject.org id: '00000662' name: 'ENCODE: Encyclopedia of DNA Elements' namespaceEmbeddedInLui: false pattern: ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$ prefix: encode sampleId: ENCSR163RYW uri_format: https://www.encodeproject.org/$1 n2t: description: The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. example: ENCSR163RYW homepage: www.encodeproject.org name: 'ENCODE: Encyclopedia of DNA Elements' namespaceEmbeddedInLui: false pattern: ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$ prefix: encode uri_format: https://www.encodeproject.org/$1 name: Encyclopedia of DNA Elements prefixcommons: is_identifiers: true is_obo: false prefix: ENCODE uri_format: http://identifiers.org/encode/$1 enm: bioportal: name: eNanoMapper prefix: ENM example: '8000221' fairsharing: abbreviation: ENM description: The eNanoMapper ontology covers the full scope of terminology needed to support research into nanomaterial safety. It builds on multiple pre-existing external ontologies such as the NanoParticle Ontology. id: '493' name: eNanoMapper Ontology prefix: FAIRsharing.2gpf81 subjects: - Health Science mappings: bioportal: ENM fairsharing: FAIRsharing.2gpf81 ols: enm ols: description: 'The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. > This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. ' download: http://enanomapper.github.io/ontologies/enanomapper.owl homepage: http://www.enanomapper.net/ name: eNanoMapper Ontology prefix: enm version: '7.3' pattern: ^\d+$ ensembl: example_extras: - ENSG00000049246.14 - ENSG00000109819.9 - ENSG00000132326.12 - ENSG00000179094.16 - ENST00000264867.7 fairsharing: abbreviation: Ensembl description: Ensembl creates, integrates and distributes reference datasets and analysis tools that enable genomics. Ensembl is a genome browser that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. id: '1867' name: Ensembl prefix: FAIRsharing.fx0mw7 subjects: - Genomics - Biomedical Science - Comparative Genomics go: homepage: http://www.ensembl.org/ name: Ensembl database of automatically annotated genomic data prefix: ENSEMBL synonyms: - Ensembl - ensembl mappings: fairsharing: FAIRsharing.fx0mw7 go: ENSEMBL miriam: ensembl n2t: ensembl ncbi: ENSEMBL prefixcommons: ENSEMBL uniprot: Ensembl wikidata: P594 miriam: deprecated: false 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. homepage: https://www.ensembl.org/ id: '00000003' name: Ensembl namespaceEmbeddedInLui: false 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])?))$ prefix: ensembl providers: - code: CURATOR_REVIEW description: Ensembl US West mirror homepage: http://uswest.ensembl.org/ name: Ensembl US West mirror uri_format: http://uswest.ensembl.org/id/$1 - code: CURATOR_REVIEW description: Ensembl US East mirror homepage: http://useast.ensembl.org/ name: Ensembl US East mirror uri_format: http://useast.ensembl.org/id/$1 - code: CURATOR_REVIEW description: Ensembl Asia mirror homepage: http://asia.ensembl.org/ name: Ensembl Asia mirror uri_format: http://asia.ensembl.org/id/$1 sampleId: ENSG00000139618 uri_format: https://www.ensembl.org/id/$1 n2t: description: Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms. example: ENSG00000139618 homepage: https://www.ensembl.org/ name: Ensembl at Sanger/EMBL-EBI namespaceEmbeddedInLui: false pattern: ^((ENS[FPTG]\\d{11}(\\.\\d+)?)|(FB\\w{2}\\d{7})|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?)|([A-Z_a-z0-9]+(\\.)?(t)?(\\d+)?([a-z])?))$ prefix: ensembl uri_format: https://www.ensembl.org/id/$1 name: Ensembl Gene ncbi: example: HUMAN-Clone-AC005612 homepage: http://useast.ensembl.org/index.html name: Database of automatically annotated genomic data prefix: ENSEMBL pattern: ^((ENS[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$ prefixcommons: is_identifiers: false is_obo: false prefix: ENSEMBL uri_format: http://ensembl.org/id/$1 providers: - code: bgee description: Gene expression in various tissues homepage: https://bgee.org name: Bgee uri_format: https://bgee.org/?page=gene&gene_id=$1 - code: gnomad description: The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community. homepage: https://gnomad.broadinstitute.org name: Genome Aggregation database uri_format: https://gnomad.broadinstitute.org/gene/$1 synonyms: - Ensembl uniprot: category: Genome annotation databases identifier: '23' link_is_explicit: 'true' name: Ensembl eukaryotic genome annotation project prefix: Ensembl uri_format: https://www.ensembl.org/id/$1 wikidata: database: Q1344256 database.homepage: http://www.ensembl.org/ database.label: Ensembl genome database project format.rdf: http://rdf.ebi.ac.uk/resource/ensembl/$1 homepage: https://www.ensembl.org name: Ensembl gene ID pattern: (ENS(|MUS|RNO)G\d{11})|(Y[A-P][LR]\d{3}[CW](-[A-G])?) prefix: P594 uri_format: https://identifiers.org/ensembl/$1 ensembl.bacteria: fairsharing: abbreviation: Ensembl Bacteria description: Ensembl Bacteria is a browser for bacterial and archaeal genomes. These are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Database of Japan). id: '2402' name: Ensembl Bacteria prefix: FAIRsharing.zsgmvd subjects: - Genomics - Comparative Genomics mappings: fairsharing: FAIRsharing.zsgmvd miriam: ensembl.bacteria n2t: ensembl.bacteria prefixcommons: ENSEMBL.BACTERIA uniprot: EnsemblBacteria miriam: deprecated: false description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes. homepage: https://bacteria.ensembl.org/ id: '00000202' name: Ensembl Bacteria namespaceEmbeddedInLui: false pattern: ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$ prefix: ensembl.bacteria sampleId: MU9_3181 uri_format: https://bacteria.ensembl.org/id/$1 n2t: description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes. example: MU9_3181 homepage: https://bacteria.ensembl.org/ name: Ensembl Bacteria at EBI namespaceEmbeddedInLui: false pattern: ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$ prefix: ensembl.bacteria uri_format: https://bacteria.ensembl.org/id/$1 prefixcommons: is_identifiers: true is_obo: false prefix: ENSEMBL.BACTERIA uri_format: http://identifiers.org/ensembl.bacteria/$1 uniprot: category: Genome annotation databases identifier: '147' link_is_explicit: 'true' name: Ensembl bacterial and archaeal genome annotation project prefix: EnsemblBacteria uri_format: http://www.ensemblgenomes.org/id/$1 ensembl.fungi: fairsharing: abbreviation: Ensembl Fungi description: Ensembl Fungi is a browser for fungal genomes. A majority of these are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Database of Japan); in some cases, the annotation has been taken directly from the websites of the data generators. id: '2405' name: Ensembl Fungi prefix: FAIRsharing.bg5xqs subjects: - Genomics - Comparative Genomics go: homepage: http://fungi.ensembl.org/ name: Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi. prefix: EnsemblFungi uri_format: http://www.ensemblgenomes.org/id/$1 mappings: fairsharing: FAIRsharing.bg5xqs go: EnsemblFungi miriam: ensembl.fungi n2t: ensembl.fungi prefixcommons: ENSEMBL.FUNGI uniprot: EnsemblFungi miriam: deprecated: false description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes. homepage: https://fungi.ensembl.org/ id: '00000206' name: Ensembl Fungi namespaceEmbeddedInLui: false pattern: ^[A-Z-a-z0-9]+$ prefix: ensembl.fungi sampleId: CADAFLAT00006211 uri_format: https://fungi.ensembl.org/id/$1 n2t: description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes. example: CADAFLAT00006211 homepage: https://fungi.ensembl.org/ name: Enzembl Fungi at EBI namespaceEmbeddedInLui: false pattern: ^[A-Z-a-z0-9]+$ prefix: ensembl.fungi uri_format: https://fungi.ensembl.org/id/$1 prefixcommons: is_identifiers: true is_obo: false prefix: ENSEMBL.FUNGI uri_format: http://identifiers.org/ensembl.fungi/$1 uniprot: category: Genome annotation databases identifier: '148' link_is_explicit: 'true' name: Ensembl fungal genome annotation project prefix: EnsemblFungi uri_format: http://www.ensemblgenomes.org/id/$1 ensembl.metazoa: fairsharing: abbreviation: Ensembl Metazoa description: Ensembl Metazoa provides access to genomes of metazoans of interest in disease, environmental sciences, agriculture and economic concern. Extensive coverage exists of diptera, nematodes, lepidoptera and hymenoptera. id: '2406' name: Ensembl Metazoa prefix: FAIRsharing.c23cqq subjects: - Genomics - Comparative Genomics go: homepage: http://metazoa.ensembl.org/ name: Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa. prefix: EnsemblMetazoa uri_format: http://www.ensemblgenomes.org/id/$1 mappings: fairsharing: FAIRsharing.c23cqq go: EnsemblMetazoa miriam: ensembl.metazoa n2t: ensembl.metazoa prefixcommons: ENSEMBL.METAZOA uniprot: EnsemblMetazoa miriam: deprecated: false description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes. homepage: https://metazoa.ensembl.org/ id: '00000204' name: Ensembl Metazoa namespaceEmbeddedInLui: false pattern: ^\w+(\.)?\d+$ prefix: ensembl.metazoa sampleId: FBtr0084214 uri_format: https://metazoa.ensembl.org/id/$1 n2t: description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes. example: FBtr0084214 homepage: https://metazoa.ensembl.org/ name: Enzembl Metazoa at EBI namespaceEmbeddedInLui: false pattern: ^\w+(\.)?\d+$ prefix: ensembl.metazoa uri_format: https://metazoa.ensembl.org/id/$1 prefixcommons: is_identifiers: true is_obo: false prefix: ENSEMBL.METAZOA uri_format: http://identifiers.org/ensembl.metazoa/$1 uniprot: category: Genome annotation databases identifier: '149' link_is_explicit: 'true' name: Ensembl metazoan genome annotation project prefix: EnsemblMetazoa uri_format: http://www.ensemblgenomes.org/id/$1 ensembl.plant: mappings: miriam: ensembl.plant n2t: ensembl.plant prefixcommons: ENSEMBL.PLANT miriam: deprecated: false description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes. homepage: https://plants.ensembl.org/ id: '00000205' name: Ensembl Plants namespaceEmbeddedInLui: false pattern: ^\w+(\.\d+)?(\.\d+)?$ prefix: ensembl.plant sampleId: AT1G73965 uri_format: https://plants.ensembl.org/id/$1 n2t: description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes. example: AT1G73965 homepage: https://plants.ensembl.org/ name: Enzembl Plants at EBI namespaceEmbeddedInLui: false pattern: ^\w+(\.\d+)?(\.\d+)?$ prefix: ensembl.plant uri_format: https://plants.ensembl.org/id/$1 prefixcommons: is_identifiers: true is_obo: false prefix: ENSEMBL.PLANT uri_format: http://identifiers.org/ensembl.plant/$1 ensembl.protist: mappings: miriam: ensembl.protist n2t: ensembl.protist prefixcommons: ENSEMBL.PROTIST miriam: deprecated: false description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes. homepage: https://protists.ensembl.org id: '00000203' name: Ensembl Protists namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: ensembl.protist sampleId: PF3D7_1328700 uri_format: https://protists.ensembl.org/id/$1 n2t: description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes. example: PF3D7_1328700 homepage: https://protists.ensembl.org name: Ensembl Protists at EBI namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: ensembl.protist uri_format: https://protists.ensembl.org/id/$1 prefixcommons: is_identifiers: true is_obo: false prefix: ENSEMBL.PROTIST uri_format: http://identifiers.org/ensembl.protist/$1 ensemblglossary: example: 0000198 mappings: ols: ensemblglossary ols: description: The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used. download: https://raw.githubusercontent.com/Ensembl/ensembl-glossary/master/ensembl-glossary.owl homepage: http://ensembl.org/glossary name: Ensembl Glossary prefix: ensemblglossary version: '2021-07-14' version.iri: http://ensembl.org/glossary/ensembl-glossary/releases/2021-07-14/ensembl-glossary.owl pattern: ^\d{7}$ envipath: fairsharing: abbreviation: enviPath description: enviPath is both a database and a prediction system, for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways, and supports the annotation of pathways with experimental and environmental conditions. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products. id: '2242' name: enviPath prefix: FAIRsharing.g0c5qn subjects: - Environmental Science mappings: fairsharing: FAIRsharing.g0c5qn miriam: envipath miriam: deprecated: false 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. homepage: https://envipath.org/ id: '00000727' name: enviPath namespaceEmbeddedInLui: false pattern: ^[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}\/[\w-]+\/[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}$ prefix: envipath sampleId: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea uri_format: https://envipath.org/package/$1 envo: bioportal: name: Environment Ontology prefix: ENVO fairsharing: abbreviation: ENVO description: The Environment Ontology (EnvO) provides a controlled, structured vocabulary that is designed to support the annotation of any organism or biological sample with environment descriptors. EnvO contains terms ranging from astronomical objects, through planetary scale biomes, to nanomaterials. Further, these terms are interlinked with logical axioms describing their composition, colocalisation, and relationships to environmental and biological processes. Using ENVO terms for an environmental description allows a comprehensive description of environment that is key to machine-assisted integration, archiving and federated searching of environmental data. id: '919' name: Environment Ontology prefix: FAIRsharing.azqskx subjects: - Environmental Science - Ecology - Life Science - Nutritional Science - Epidemiology mappings: bioportal: ENVO fairsharing: FAIRsharing.azqskx miriam: envo n2t: envo obofoundry: envo ols: envo ontobee: ENVO prefixcommons: ENVO miriam: deprecated: false description: The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. homepage: https://www.ebi.ac.uk/ols/ontologies/envo id: 00000591 name: Environment Ontology namespaceEmbeddedInLui: true pattern: ^ENVO:\d{7,8}$ prefix: envo sampleId: 09200010 uri_format: https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=ENVO:$1 n2t: description: The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. example: 09200010 homepage: http://purl.bioontology.org/ontology/ENVO/ name: The Environment Ontology through BioPortal namespaceEmbeddedInLui: true pattern: ^ENVO:\d{8}$ prefix: envo uri_format: http://purl.bioontology.org/ontology/ENVO/ENVO:$1 obofoundry: appears_in: - agro - cdno - ecocore - ecto - foodon - ons - pco - rbo - scdo contact: p.buttigieg@gmail.com contact.github: pbuttigieg contact.label: Pier Luigi Buttigieg contact.orcid: 0000-0002-4366-3088 depends_on: - chebi - foodon - go - ncbitaxon - pco - po - ro - uberon deprecated: false description: Ontology of environmental features and habitats download.json: http://purl.obolibrary.org/obo/envo.json download.obo: http://purl.obolibrary.org/obo/envo.obo download.owl: http://purl.obolibrary.org/obo/envo.owl homepage: http://environmentontology.org/ inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Environment Ontology preferredPrefix: ENVO prefix: envo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/24330602 title: 'The environment ontology: contextualising biological and biomedical entities' - id: https://www.ncbi.nlm.nih.gov/pubmed/27664130 title: 'The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation' repository: https://github.com/EnvironmentOntology/envo ols: description: ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities download: http://purl.obolibrary.org/obo/envo.owl homepage: http://environmentontology.org/ name: The Environment Ontology prefix: envo version: '2021-05-14' version.iri: http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl ontobee: library: Library name: Environment Ontology prefix: ENVO pattern: ^\d{7,8}$ prefixcommons: is_identifiers: false is_obo: true prefix: ENVO uri_format: http://purl.obolibrary.org/obo/ENVO_$1 enzo: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Enzo Life Sciences is an antibody vendor. example: ALX-210-175 homepage: https://www.enzolifesciences.com name: Enzo Life Sciences synonyms: - Enzo Life Sciences uri_format: https://www.enzolifesciences.com/$1 eo: banana: EO mappings: miriam: eo n2t: eo obofoundry: eo prefixcommons: EO miriam: deprecated: false description: The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. homepage: http://archive.gramene.org/db/ontology/search_term?id=EO:0007359 id: 00000518 name: Plant Environment Ontology namespaceEmbeddedInLui: true pattern: ^(P)?EO\:\d{7}$ prefix: eo sampleId: '0007404' uri_format: http://archive.gramene.org/db/ontology/search?query=EO:$1 n2t: description: The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. example: '0007404' homepage: http://bioportal.bioontology.org/ontologies/PECO name: Plant Environment Ontology through BioPortal namespaceEmbeddedInLui: true pattern: ^(P)?EO\:\d{7}$ prefix: eo uri_format: http://purl.bioontology.org/ontology/PECO/EO:$1 obofoundry: appears_in: - foodon contact: jaiswalp@science.oregonstate.edu contact.github: jaiswalp contact.label: Pankaj Jaiswal contact.orcid: 0000-0002-1005-8383 deprecated: true description: A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. download.obo: http://purl.obolibrary.org/obo/eo.obo download.owl: http://purl.obolibrary.org/obo/eo.owl homepage: http://planteome.org/ inactive: true license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Plant Environment Ontology prefix: eo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/22847540 title: Ontologies as integrative tools for plant science. repository: https://github.com/Planteome/plant-environment-ontology pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: EO uri_format: http://purl.obolibrary.org/obo/EO_$1 eol: bioportal: name: Environment Ontology for Livestock prefix: EOL contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems. download_owl: https://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=eol.owl example: 0001927 fairsharing: abbreviation: EOL description: The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems. id: '743' name: Environment Ontology for Livestock prefix: FAIRsharing.w7bw2y subjects: - Environmental Science - Animal Husbandry - Agriculture mappings: bioportal: EOL fairsharing: FAIRsharing.w7bw2y ols: eol ols: contact: pylebail@rennes.inra.fr description: "L'ontologie EOL d\xE9crit les conditions d'environnement des \xE9\ levages d'animaux domestiques. Elle d\xE9crit plus particuli\xE8rement les modalit\xE9\ s de l'alimentation, de l'environnement, de la structure des \xE9levages et\ \ des syst\xE8mes d'\xE9levage" download: http://www.atol-ontology.com/public/telechargement/eol.owl homepage: http://www.atol-ontology.com name: Environment Ontology for Livestock prefix: eol version: '2018-09-13' pattern: ^\d{7}$ eolife: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A collaborative project intended to create an encyclopedia documenting all living species known to science example: '1044544' fairsharing: abbreviation: EOL description: The Encyclopedia of Life (EOL) is a collaborative encyclopedia to describe all known living species. It identifies sources of biodiversity knowledge that are legally and practically shareable; integrates them with other sources and adds metadata; provides searching and other services; and collaborates with other projects to support data sharing. id: '2888' name: Encyclopedia of Life prefix: FAIRsharing.3J6NYn subjects: - Taxonomy - Ecology - Biodiversity - Biology homepage: https://eol.org mappings: fairsharing: FAIRsharing.3J6NYn wikidata: P830 name: Encyclopedia of Life pattern: ^\d+$ uri_format: https://eol.org/pages/$1 wikidata: database: Q82486 database.homepage: https://eol.org database.label: Encyclopedia of Life homepage: http://eol.org/api/docs/pages name: Encyclopedia of Life ID pattern: '[1-9]\d{0,7}' prefix: P830 uri_format: https://eol.org/ar/pages/$1 epcc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Collection of European paediatric cardiac coding files homepage: https://www.aepc.org/european-paediatric-cardiac-coding name: European Paediatric Cardiac Codes 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: fairsharing: abbreviation: EPD description: The EPD has been created and is maintained by the Lamond group in the University of Dundee. It combines a polyglot persistent database and web-application that provides open access to integrated proteomics data for >30 000 proteins from published studies on human cells and model organisms. It is designed to provide a user-friendly interface, featuring graphical navigation with interactive visualizations that facilitate powerful data exploration in an intuitive manner. The EPD offers a flexible and scalable ecosystem to integrate proteomics data with genomics information, RNA expression and other related, large-scale datasets. id: '2515' name: The Encyclopedia of Proteome Dynamics prefix: FAIRsharing.sym4ne subjects: - Proteomics - Life Science - Data Visualization mappings: fairsharing: FAIRsharing.sym4ne miriam: epd n2t: epd ncbi: EPD prefixcommons: EPD uniprot: EPD miriam: deprecated: false 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. homepage: http://epd.vital-it.ch/ id: 00000408 name: EPD namespaceEmbeddedInLui: false pattern: ^[A-Z-_0-9]+$ prefix: epd sampleId: TA_H3 uri_format: http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1 n2t: description: The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. example: TA_H3 homepage: http://epd.vital-it.ch/ name: EPD at Swiss Institute of Bioinformatics namespaceEmbeddedInLui: false pattern: ^[A-Z-_0-9]+$ prefix: epd uri_format: http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1 ncbi: example: EP00576 homepage: http://epd.vital-it.ch/ name: Eukaryotic Promoter Database prefix: EPD prefixcommons: is_identifiers: true is_obo: false prefix: EPD uri_format: http://identifiers.org/epd/$1 uniprot: category: Proteomic databases identifier: '205' link_is_explicit: 'true' name: Encyclopedia of Proteome Dynamics prefix: EPD uri_format: https://www.peptracker.com/epd/analytics/?protein_id=$1 epio: bioportal: name: EpilepsyOntology prefix: EPIO example: '0000011' mappings: bioportal: EPIO obofoundry: epio ontobee: EPIO obofoundry: contact: alpha.tom.kodamullil@scai.fraunhofer.de contact.github: akodamullil contact.label: Alpha Tom Kodamullil contact.orcid: 0000-0001-9896-3531 depends_on: - bfo deprecated: false description: A application driven Epilepsy Ontology with official terms from the ILAE. download.owl: http://purl.obolibrary.org/obo/epio.owl homepage: https://github.com/SCAI-BIO/EpilepsyOntology inactive: false license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Epilepsy Ontology preferredPrefix: EPIO prefix: epio repository: https://github.com/SCAI-BIO/EpilepsyOntology ontobee: library: Library name: Epilepsy Ontology prefix: EPIO pattern: ^\d{7}$ epo: bioportal: name: Early Pregnancy Ontology prefix: EPO download_owl: https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/epidemiology-ontology/epo.owl mappings: bioportal: EPO obofoundry: epo ontobee: EPO prefixcommons: EPO obofoundry: deprecated: true description: An ontology designed to support the semantic annotation of epidemiology resources download.owl: http://purl.obolibrary.org/obo/epo.owl homepage: https://code.google.com/p/epidemiology-ontology/ inactive: true name: Epidemiology Ontology prefix: epo ontobee: library: Library name: Epidemiology Ontology prefix: EPO prefixcommons: is_identifiers: false is_obo: true prefix: EPO uri_format: http://purl.obolibrary.org/obo/EPO_$1 epso: bioportal: name: Epilepsy and Seizure Ontology prefix: EPSO example: '0000400' fairsharing: abbreviation: EPSO description: 'The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. ' id: '265' name: Epilepsy and Seizure Ontology prefix: FAIRsharing.ttprgy subjects: - Neurology homepage: http://prism.case.edu/prism/index.php/EpilepsyOntology mappings: bioportal: EPSO fairsharing: FAIRsharing.ttprgy ontobee: EPSO ontobee: library: Library name: Epilepsy Ontology prefix: EPSO pattern: ^\d{7}$ erm: mappings: miriam: erm n2t: erm miriam: deprecated: false 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. homepage: https://nanocommons.github.io/identifiers/ id: '00000763' name: European Registry of Materials namespaceEmbeddedInLui: false pattern: ^ERM[0-9]{8}$ prefix: erm sampleId: ERM00000044 uri_format: https://nanocommons.github.io/identifiers/registry#$1 n2t: description: The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project. example: ERM00000044 homepage: https://nanocommons.github.io/identifiers/ name: European Registry of Materials namespaceEmbeddedInLui: false pattern: ^ERM[0-9]{8}$ prefix: erm uri_format: https://nanocommons.github.io/identifiers/registry#$1 ero: bioportal: name: Eagle-I Research Resource Ontology prefix: ERO example: '0001655' fairsharing: abbreviation: ERO description: "A unique feature of the eagle-i software is that the data collection\ \ and search tools are completely driven by ontologies. These ontologies are\ \ a set of modules that are written in the OWL language and edited and managed\ \ using Prot\xE9g\xE9. Beginning in 2009, the eagle-i Research Resource Ontology\ \ (ERO) was developed alongside the eagle-i applications to model various biomedical\ \ research resources such as instruments, Core Facilities, protocols, reagents,\ \ animal models and biospecimens. It has now been integrated into the VIVO-ISF\ \ Ontology, which leverages and expands upon both the eagle-i and VIVO ontologies\ \ to create a semantic framework that describes not only scientific resources\ \ but research activities and clinical activities." id: '1166' name: eagle-i Research Resource Ontology prefix: FAIRsharing.nwgynk subjects: - Life Science - Biomedical Science mappings: bioportal: ERO fairsharing: FAIRsharing.nwgynk obofoundry: ero ols: ero ontobee: ERO prefixcommons: ERO obofoundry: contact: Marc_Ciriello@hms.harvard.edu contact.label: Marc Ciriello deprecated: false description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. download.owl: http://purl.obolibrary.org/obo/ero.owl homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology inactive: true license: CC BY 2.0 license.url: https://creativecommons.org/licenses/by/2.0/ name: eagle-i resource ontology prefix: ero ols: description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. download: http://purl.obolibrary.org/obo/ero.owl homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology name: eagle-i resource ontology prefix: ero version: '2016-07-27' ontobee: library: Library name: eagle-i resource ontology prefix: ERO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: ERO uri_format: http://purl.obolibrary.org/obo/ERO_$1 erv: mappings: miriam: erv n2t: erv prefixcommons: ERV miriam: deprecated: false description: Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features. homepage: https://herv.img.cas.cz/ id: 00000619 name: Human Endogenous Retrovirus Database namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9\-\_]+$ prefix: erv sampleId: THE1B uri_format: https://herv.img.cas.cz/s/$1 n2t: description: Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features. example: THE1B homepage: https://herv.img.cas.cz/ name: Human Endogenous Retrovirus Database namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9\-\_]+$ prefix: erv uri_format: https://herv.img.cas.cz/s/$1 prefixcommons: is_identifiers: true is_obo: false prefix: ERV uri_format: http://identifiers.org/erv/$1 estdab: cellosaurus: category: Cell line databases/resources homepage: https://www.ebi.ac.uk/ipd/estdab/ name: European Searchable Tumour Line Database prefix: ESTDAB uri_format: https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?$1 comment: Website is dead deprecated: true example: '046' mappings: cellosaurus: ESTDAB pattern: ^\d{3}$ uri_format: https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1 eu89h: mappings: miriam: eu89h n2t: eu89h prefixcommons: EU89H miriam: deprecated: false description: The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union. homepage: http://data.jrc.ec.europa.eu/ id: '00000644' name: JRC Data Catalogue namespaceEmbeddedInLui: false pattern: ^[a-z0-9\-_]+$ prefix: eu89h sampleId: jrc-eurl-ecvam-chemagora uri_format: http://data.europa.eu/89h/$1 n2t: description: The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union. example: jrc-eurl-ecvam-chemagora homepage: http://data.jrc.ec.europa.eu/ name: JRC Data Catalogue namespaceEmbeddedInLui: false pattern: ^[a-z0-9\-_]+$ prefix: eu89h uri_format: http://data.europa.eu/89h/$1 prefixcommons: is_identifiers: true is_obo: false prefix: EU89H uri_format: http://identifiers.org/eu89h/$1 euclinicaltrials: mappings: miriam: euclinicaltrials n2t: euclinicaltrials prefixcommons: EUCLINICALTRIALS miriam: deprecated: false description: "The EU Clinical Trials Register contains information on clinical\ \ trials conducted in the European Union (EU), or the European Economic Area\ \ (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted\ \ outside these areas if they form part of a paediatric investigation plan (PIP),\ \ or are sponsored by a marketing authorisation holder, and involve the use\ \ of a medicine in the paediatric population." homepage: https://www.clinicaltrialsregister.eu/ id: '00000536' name: EU Clinical Trials namespaceEmbeddedInLui: false pattern: ^\d{4}\-\d{6}\-\d{2}$ prefix: euclinicaltrials sampleId: 2008-005144-16 uri_format: https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1 n2t: description: The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004. It also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population. example: 2008-005144-16 homepage: https://www.clinicaltrialsregister.eu/ name: EU Clinical Trials at European Medicines Agency namespaceEmbeddedInLui: false pattern: ^\d{4}\-\d{6}\-\d{2}$ prefix: euclinicaltrials uri_format: https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1 prefixcommons: is_identifiers: true is_obo: false prefix: EUCLINICALTRIALS uri_format: http://identifiers.org/euclinicaltrials/$1 eupath: bioportal: name: VEuPathDB Ontology prefix: EUPATH example: '0010316' fairsharing: abbreviation: VEuPathDB Ontology 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. 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. id: '1484' name: Eukaryotic Pathogen, Host & Vector Genomics Resource Ontology prefix: FAIRsharing.9rhr9j subjects: - Functional Genomics - Biomedical Science - Epidemiology - Population Genetics mappings: bioportal: EUPATH fairsharing: FAIRsharing.9rhr9j obofoundry: eupath ols: eupath ontobee: EUPATH prefixcommons: EUPATH obofoundry: appears_in: - scdo contact: jiezheng@pennmedicine.upenn.edu contact.github: zhengj2007 contact.label: Jie Zheng contact.orcid: 0000-0002-2999-0103 deprecated: false description: An ontology is developed to support Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org). download.owl: http://purl.obolibrary.org/obo/eupath.owl homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology inactive: false license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: VEuPathDB ontology preferredPrefix: EUPATH prefix: eupath repository: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology ols: 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: http://purl.obolibrary.org/obo/eupath.owl homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology name: VEuPathDB Ontology prefix: eupath version: '2022-02-15' version.iri: http://purl.obolibrary.org/obo/eupath/2022-02-15/eupath.owl ontobee: library: Library name: VEuPathDB ontology prefix: EUPATH pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: EUPATH uri_format: http://purl.obolibrary.org/obo/EUPATH_$1 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 proprietary: true ev: appears_in: - cl mappings: obofoundry: ev prefixcommons: EV obofoundry: contact: evoc@sanbi.ac.za contact.label: eVOC mailing list deprecated: true homepage: http://www.evocontology.org/ inactive: true name: eVOC (Expressed Sequence Annotation for Humans) prefix: ev prefixcommons: is_identifiers: false is_obo: true prefix: EV uri_format: http://purl.obolibrary.org/obo/EV_$1 references: - https://twitter.com/Bgeedb/status/1350124337815281664 evm: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: eVOC mouse development stage references: - https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r229 exac.gene: mappings: miriam: exac.gene n2t: exac.gene prefixcommons: EXAC.GENE miriam: deprecated: false description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information. homepage: http://exac.broadinstitute.org/ id: 00000548 name: ExAC Gene namespaceEmbeddedInLui: false pattern: ^ENSG\d{11}$ prefix: exac.gene sampleId: ENSG00000169174 uri_format: http://exac.broadinstitute.org/gene/$1 n2t: description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information. example: ENSG00000169174 homepage: http://exac.broadinstitute.org/ name: ExAC Gene at Exome Aggregation Consortium namespaceEmbeddedInLui: false pattern: ^ENSG\d{11}$ prefix: exac.gene uri_format: http://exac.broadinstitute.org/gene/$1 prefixcommons: is_identifiers: true is_obo: false prefix: EXAC.GENE uri_format: http://identifiers.org/exac.gene/$1 exac.transcript: mappings: miriam: exac.transcript n2t: exac.transcript prefixcommons: EXAC.TRANSCRIPT miriam: deprecated: false description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information. homepage: http://exac.broadinstitute.org/ id: '00000547' name: ExAC Transcript namespaceEmbeddedInLui: false pattern: ^ENST\d{11}$ prefix: exac.transcript sampleId: ENST00000407236 uri_format: http://exac.broadinstitute.org/transcript/$1 n2t: description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information. example: ENST00000407236 homepage: http://exac.broadinstitute.org/ name: ExAC Transcript at Exome Aggregation Consortium namespaceEmbeddedInLui: false pattern: ^ENST\d{11}$ prefix: exac.transcript uri_format: http://exac.broadinstitute.org/transcript/$1 prefixcommons: is_identifiers: true is_obo: false prefix: EXAC.TRANSCRIPT uri_format: http://identifiers.org/exac.transcript/$1 exac.variant: mappings: miriam: exac.variant n2t: exac.variant prefixcommons: EXAC.VARIANT miriam: deprecated: false description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information. homepage: http://exac.broadinstitute.org/ id: '00000541' name: ExAC Variant namespaceEmbeddedInLui: false pattern: ^\d{1,2}\-\d+\-[GATC]\-[GATC]$ prefix: exac.variant sampleId: 22-46615880-T-C uri_format: http://exac.broadinstitute.org/variant/$1 n2t: description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information. example: 22-46615880-T-C homepage: http://exac.broadinstitute.org/ name: ExAC Variant at Exome Aggregation Consortium namespaceEmbeddedInLui: false pattern: ^\d{1,2}\-\d+\-[GATC]\-[GATC]$ prefix: exac.variant uri_format: http://exac.broadinstitute.org/variant/$1 prefixcommons: is_identifiers: true is_obo: false prefix: EXAC.VARIANT uri_format: http://identifiers.org/exac.variant/$1 exo: biolink: is_identifiers: false is_obo: true prefix: ExO uri_format: http://purl.obolibrary.org/obo/ExO_$1 bioportal: name: Exposure Ontology prefix: EXO example: 0000078 fairsharing: abbreviation: ExO description: Exposure Ontology (ExO) is designed to facilitate the centralization and integration of exposure data to inform understanding of environmental health. ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics. id: '512' name: Exposure Ontology prefix: FAIRsharing.6hna78 subjects: - Environmental Science - Epigenetics - Toxicology mappings: biolink: ExO bioportal: EXO fairsharing: FAIRsharing.6hna78 obofoundry: exo ols: exo ontobee: ExO prefixcommons: EXO obofoundry: appears_in: - ecto - scdo contact: annethessen@gmail.com contact.github: diatomsRcool contact.label: Anne Thessen contact.orcid: 0000-0002-2908-3327 deprecated: false description: Vocabularies for describing exposure data to inform understanding of environmental health. download.obo: http://purl.obolibrary.org/obo/exo.obo download.owl: http://purl.obolibrary.org/obo/exo.owl homepage: https://github.com/CTDbase/exposure-ontology inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Exposure ontology preferredPrefix: ExO prefix: exo repository: https://github.com/CTDbase/exposure-ontology ols: description: ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics. download: http://purl.obolibrary.org/obo/exo.owl homepage: https://github.com/CTDbase/exposure-ontology name: Exposure ontology (ExO) prefix: exo version: '2020-03-10' version.iri: http://purl.obolibrary.org/obo/exo/2.1/exo.owl ontobee: library: Library name: Exposure ontology prefix: ExO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: EXO uri_format: http://purl.obolibrary.org/obo/EXO_$1 synonyms: - ExO fabio: biolink: is_identifiers: false is_obo: false prefix: fabio uri_format: http://purl.org/spar/fabio/$1 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references. example: d4e2515 fairsharing: abbreviation: FaBiO description: FaBiO, the FRBR-aligned Bibliographic Ontology, is an ontology for recording and publishing on the Semantic Web descriptions of entities that are published or potentially publishable, and that contain or are referred to by bibliographic references, or entities used to define such bibliographic references. FaBiO entities are primarily textual publications such as books, magazines, newspapers and journals, and items of their content such as poems, conference papers and editorials. However, they also include blogs, web pages, datasets, computer algorithms, experimental protocols, formal specifications and vocabularies, legal records, governmental papers, technical and commercial reports and similar publications, and also anthologies, catalogues and similar collections. id: '3628' name: FRBR-aligned Bibliographic Ontology prefix: FAIRsharing.2f3180 subjects: - Subject Agnostic homepage: https://github.com/sparontologies/fabio mappings: biolink: fabio fairsharing: FAIRsharing.2f3180 name: FaBiO, the FRBR-aligned Bibliographic Ontology repository: https://github.com/sparontologies/fabio uri_format: https://sparontologies.github.io/fabio/current/fabio.html#$1 facebase: fairsharing: abbreviation: FaceBase description: FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects. id: '2254' name: FaceBase prefix: FAIRsharing.mqvqde subjects: - Anatomy - Medicine - Epigenetics - Genetics - Developmental Biology mappings: fairsharing: FAIRsharing.mqvqde miriam: facebase n2t: facebase prefixcommons: FACEBASE miriam: deprecated: false description: FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects. homepage: https://www.facebase.org id: '00000642' name: FaceBase Data Repository namespaceEmbeddedInLui: false pattern: ^FB\d{8}$ prefix: facebase sampleId: FB00000917 uri_format: https://www.facebase.org/data/record/#1/isa:dataset/accession=$1 n2t: description: FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects. example: FB00000917 homepage: https://www.facebase.org name: FaceBase Data Repository namespaceEmbeddedInLui: false pattern: ^FB\d{8}$ prefix: facebase uri_format: https://www.facebase.org/data/record/#1/isa:dataset/accession=$1 prefixcommons: is_identifiers: true is_obo: false prefix: FACEBASE uri_format: http://identifiers.org/facebase/$1 fairsharing: fairsharing: abbreviation: FAIRsharing description: FAIRsharing is a FAIR-supporting resource that provides an informative and educational registry on data standards, databases, repositories and policy, alongside search and visualization tools and services that interoperate with other FAIR-enabling resources. FAIRsharing guides consumers to discover, select and use standards, databases, repositories and policy with confidence, and producers to make their resources more discoverable, more widely adopted and cited. Each record in FAIRsharing is curated in collaboration with the maintainers of the resource themselves, ensuring that the metadata in the FAIRsharing registry is accurate and timely. Every record is manually reviewed at least once a year. Records can be collated into collections, based on a project, society or organisation, or Recommendations, where they are collated around a policy, such as a journal or funder data policy. id: '2521' name: FAIRsharing prefix: FAIRsharing.2abjs5 subjects: - Environmental Science - Humanities - Natural Science - Earth Science - Agriculture - Life Science - Biomedical Science mappings: fairsharing: FAIRsharing.2abjs5 miriam: fairsharing n2t: fairsharing prefixcommons: FAIRSHARING miriam: deprecated: false description: The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies. homepage: https://fairsharing.org/ id: '00000364' name: FAIRsharing namespaceEmbeddedInLui: false pattern: ^bsg-[dscp]?\d{6}$ prefix: fairsharing sampleId: bsg-000052 uri_format: https://fairsharing.org/$1 n2t: description: The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies. example: bsg-000052 homepage: https://fairsharing.org/ name: FAIRSharing at University of Oxford namespaceEmbeddedInLui: false pattern: ^bsg-[dscp]?\d{6}$ prefix: fairsharing uri_format: https://fairsharing.org/$1 prefixcommons: is_identifiers: true is_obo: false prefix: FAIRSHARING uri_format: http://identifiers.org/fairsharing/$1 faldo: bioportal: name: Feature Annotation Location Description Ontology prefix: FALDO description: It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources example: ForwardStrandPosition fairsharing: abbreviation: FALDO description: "The Feature Annotation Location Description Ontology (FALDO), to\ \ describe the positions of annotated features on linear and circular sequences\ \ for data resources represented in RDF and/or OWL. FALDO can be used to describe\ \ nucleotide features in sequence records, protein annotations, and glycan binding\ \ sites, among other features in coordinate systems of the aforementioned \u201C\ omics\u201D areas. Using the same data format to represent sequence positions\ \ that are independent of file formats allows us to integrate sequence data\ \ from multiple sources and data types." id: '478' name: Feature Annotation Location Description Ontology prefix: FAIRsharing.haxp7g subjects: - Genetics homepage: http://biohackathon.org/resource/faldo mappings: bioportal: FALDO fairsharing: FAIRsharing.haxp7g prefixcommons: faldo name: 'Feature Annotation Location Description Ontology ' prefixcommons: is_identifiers: false is_obo: false prefix: faldo uri_format: http://biohackathon.org/resource/faldo#$1 uri_format: http://biohackathon.org/resource/faldo#$1 fao: bioportal: name: Fungal Gross Anatomy Ontology prefix: FAO example: '0000001' fairsharing: abbreviation: FAO description: A structured controlled vocabulary for the anatomy of fungi. id: '168' name: Fungal Gross Anatomy Ontology prefix: FAIRsharing.xs6t67 subjects: - Anatomy - Life Science - Microbiology mappings: bioportal: FAO fairsharing: FAIRsharing.xs6t67 obofoundry: fao ols: fao ontobee: FAO prefixcommons: FAO obofoundry: contact: vw253@cam.ac.uk contact.github: ValWood contact.label: Val Wood contact.orcid: 0000-0001-6330-7526 deprecated: false description: A structured controlled vocabulary for the anatomy of fungi. download.obo: http://purl.obolibrary.org/obo/fao.obo download.owl: http://purl.obolibrary.org/obo/fao.owl homepage: https://github.com/obophenotype/fungal-anatomy-ontology/ inactive: false license: CC0 1.0 license.url: http://creativecommons.org/publicdomain/zero/1.0/ name: Fungal gross anatomy preferredPrefix: FAO prefix: fao repository: https://github.com/obophenotype/fungal-anatomy-ontology ols: description: A structured controlled vocabulary for the anatomy of fungi. download: http://purl.obolibrary.org/obo/fao.owl homepage: https://github.com/obophenotype/fungal-anatomy-ontology/ name: Fungal gross anatomy prefix: fao version: '2020-05-07' version.iri: http://purl.obolibrary.org/obo/fao/releases/2020-05-07/fao.owl ontobee: library: Library name: Fungal gross anatomy prefix: FAO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: FAO uri_format: http://purl.obolibrary.org/obo/FAO_$1 fbbi: bioportal: name: Biological Imaging Methods Ontology prefix: FBbi example: 00000268 fairsharing: abbreviation: FBbi description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. id: '33' name: Biological Imaging methods Ontology prefix: FAIRsharing.ny3z9j subjects: - Life Science - Biomedical Science mappings: bioportal: FBbi fairsharing: FAIRsharing.ny3z9j obofoundry: fbbi ols: fbbi ontobee: FBBI prefixcommons: FBbi obofoundry: contact: wawong@gmail.com contact.github: wawong contact.label: Willy Wong contact.orcid: 0000-0002-8841-5870 deprecated: false description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. download.owl: http://purl.obolibrary.org/obo/fbbi.owl homepage: http://cellimagelibrary.org/ inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Biological Imaging Methods Ontology preferredPrefix: FBbi prefix: fbbi repository: https://github.com/CRBS/Biological_Imaging_Methods_Ontology ols: description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. download: http://purl.obolibrary.org/obo/fbbi.owl homepage: http://cellimagelibrary.org/ name: Biological Imaging Methods Ontology prefix: fbbi version: '2020-11-06' version.iri: http://purl.obolibrary.org/obo/fbbi/releases/2020-11-06/fbbi.owl ontobee: library: Library name: Biological Imaging Methods Ontology prefix: FBBI pattern: ^\d+$ prefixcommons: is_identifiers: false is_obo: true prefix: FBbi uri_format: http://purl.obolibrary.org/obo/FBbi_$1 synonyms: - FBbi fbbt: bioportal: name: Drosophila Gross Anatomy Ontology prefix: FB-BT example: 00007294 fairsharing: abbreviation: FBbt description: An ontology of the anatomy of Drosophila melanogaster. It can be used for annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotype and images. It was originally developed by FlyBase, who continue to maintain it and use it for curation. id: '28' name: Drosophila anatomy ontology prefix: FAIRsharing.y2qkst subjects: - Anatomy - Developmental Biology - Life Science go: homepage: http://flybase.org/ name: Drosophila gross anatomy prefix: FBbt uri_format: http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:$1 mappings: bioportal: FB-BT fairsharing: FAIRsharing.y2qkst go: FBbt obofoundry: fbbt ols: fbbt ontobee: FBBT prefixcommons: FBbt obofoundry: contact: cp390@cam.ac.uk contact.github: Clare72 contact.label: Clare Pilgrim contact.orcid: 0000-0002-1373-1705 deprecated: false description: An ontology representing the gross anatomy of Drosophila melanogaster. download.json: http://purl.obolibrary.org/obo/fbbt.json download.obo: http://purl.obolibrary.org/obo/fbbt.obo download.owl: http://purl.obolibrary.org/obo/fbbt.owl homepage: http://purl.obolibrary.org/obo/fbbt inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Drosophila gross anatomy preferredPrefix: FBbt prefix: fbbt publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/24138933 title: The Drosophila anatomy ontology. [Journal of Biomedical Semantics - id: https://www.ncbi.nlm.nih.gov/pubmed/22402613 title: A strategy for building neuroanatomy ontologies - id: https://www.ncbi.nlm.nih.gov/pubmed/22180411 title: The Virtual Fly Brain Browser and Query Interface - id: https://www.ncbi.nlm.nih.gov/pubmed/16381917 title: 'FlyBase: anatomical data, images and queries' repository: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology ols: description: An ontology of Drosophila melanogaster anatomy. download: http://purl.obolibrary.org/obo/fbbt.owl homepage: http://purl.obolibrary.org/obo/fbbt name: Drosophila Anatomy Ontology (DAO) prefix: fbbt version: '2022-04-13' version.iri: http://purl.obolibrary.org/obo/fbbt/releases/2022-04-13/fbbt.owl ontobee: library: Library name: Drosophila gross anatomy prefix: FBBT part_of: flybase pattern: ^\d{8}$ prefixcommons: is_identifiers: false is_obo: true prefix: FBbt uri_format: http://purl.obolibrary.org/obo/FBbt_$1 synonyms: - FBbt - FBbt_root uri_format: https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:$1 fbcv: bioportal: name: FlyBase Controlled Vocabulary prefix: FB-CV download_obo: https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/fbcv.obo example: 0000586 fairsharing: abbreviation: FBcv description: A structured controlled vocabulary developed and used by FlyBase, including the Drosophila phenotype ontology. It is used in annotation and classification of data related to Drosophila, including phenotypes and expression. id: '147' name: FlyBase Controlled Vocabulary prefix: FAIRsharing.6tgyxf subjects: - Life Science mappings: bioportal: FB-CV fairsharing: FAIRsharing.6tgyxf obofoundry: fbcv ols: fbcv ontobee: FBCV prefixcommons: FBcv obofoundry: appears_in: - ontoavida contact: cp390@cam.ac.uk contact.github: Clare72 contact.label: Clare Pilgrim contact.orcid: 0000-0002-1373-1705 deprecated: false description: A structured controlled vocabulary used for various aspects of annotation by FlyBase. download.json: http://purl.obolibrary.org/obo/fbcv.json download.obo: http://purl.obolibrary.org/obo/fbcv.obo download.owl: http://purl.obolibrary.org/obo/fbcv.owl homepage: http://purl.obolibrary.org/obo/fbcv inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: FlyBase Controlled Vocabulary preferredPrefix: FBcv prefix: fbcv repository: https://github.com/FlyBase/flybase-controlled-vocabulary ols: description: A miscellaneous ontology of terms used for curation in FlyBase, including the DPO. download: http://purl.obolibrary.org/obo/fbcv.owl homepage: http://purl.obolibrary.org/obo/fbcv name: FlyBase Controlled Vocabulary (FBcv) prefix: fbcv version: '2022-04-14' version.iri: http://purl.obolibrary.org/obo/fbcv/releases/2022-04-14/fbcv.owl ontobee: library: Library name: FlyBase Controlled Vocabulary prefix: FBCV part_of: flybase pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: FBcv uri_format: http://purl.obolibrary.org/obo/FBcv_$1 synonyms: - FBcv fbdv: bioportal: name: Drosophila Development Ontology prefix: FB-DV example: '00000000' fairsharing: abbreviation: FBdv description: An ontology of the developmental stages of Drosophila melanogaster. It provides a controlled vocabulary for use in annotation and classification of data related to Drosophila, such as gene expression, phenotypes and images. id: '29' name: Drosophila developmental ontology prefix: FAIRsharing.p52pzj subjects: - Developmental Biology - Life Science mappings: bioportal: FB-DV fairsharing: FAIRsharing.p52pzj obofoundry: fbdv ols: fbdv ontobee: FBdv prefixcommons: FBdv obofoundry: contact: cp390@cam.ac.uk contact.github: Clare72 contact.label: Clare Pilgrim contact.orcid: 0000-0002-1373-1705 deprecated: false description: A structured controlled vocabulary of the development of Drosophila melanogaster. download.json: http://purl.obolibrary.org/obo/fbdv.json download.obo: http://purl.obolibrary.org/obo/fbdv.obo download.owl: http://purl.obolibrary.org/obo/fbdv.owl homepage: http://purl.obolibrary.org/obo/fbdv inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Drosophila development preferredPrefix: FBdv prefix: fbdv repository: https://github.com/FlyBase/drosophila-developmental-ontology ols: description: An ontology of Drosophila melanogaster developmental stages. download: http://purl.obolibrary.org/obo/fbdv.owl homepage: http://purl.obolibrary.org/obo/fbdv name: FlyBase Developmental Ontology (FBdv) prefix: fbdv version: '2022-04-12' version.iri: http://purl.obolibrary.org/obo/fbdv/releases/2022-04-12/fbdv.owl ontobee: library: Library name: Drosophila development prefix: FBdv pattern: ^\d{8}$ prefixcommons: is_identifiers: false is_obo: true prefix: FBdv uri_format: http://purl.obolibrary.org/obo/FBdv_$1 synonyms: - FBdv fbol: comment: Website down, checked on 2021-10-07 deprecated: true mappings: miriam: fbol n2t: fbol ncbi: FBOL prefixcommons: FBOL miriam: deprecated: false description: DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms. homepage: http://www.fungalbarcoding.org/ id: '00000410' name: Fungal Barcode namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: fbol sampleId: '2224' uri_format: http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T n2t: description: DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms. example: '2224' homepage: http://www.fungalbarcoding.org/ name: Fungal Barcode at Fungal Biodiversity Centre namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: fbol uri_format: http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T ncbi: example: '2224' homepage: http://www.fungalbarcoding.org/ name: International Fungal Working Group Fungal Barcoding. prefix: FBOL prefixcommons: is_identifiers: true is_obo: false prefix: FBOL uri_format: http://identifiers.org/fbol/$1 fbql: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true example: '00005254' name: FlyBase Qualifiers pattern: ^\d+$ 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}$ uri_format: https://flybase.org/reports/FBrf$1 fbsp: bioportal: name: Fly Taxonomy prefix: FB-SP example: '00000000' mappings: bioportal: FB-SP obofoundry: fbsp prefixcommons: FBSP obofoundry: contact: cp390@cam.ac.uk contact.github: Clare72 contact.label: Clare Pilgrim contact.orcid: 0000-0002-1373-1705 deprecated: true description: The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. download.owl: http://purl.obolibrary.org/obo/fbsp.owl homepage: http://www.flybase.org/ inactive: true name: Fly taxonomy prefix: fbsp part_of: flybase pattern: ^\d{8}$ prefixcommons: is_identifiers: false is_obo: true prefix: FBSP uri_format: http://purl.obolibrary.org/obo/FBSP_$1 fbtc: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The cell line vocabulary inside FlyBase example: 0000190 homepage: https://flybase.org name: Flybase Cell Line part_of: flybase pattern: ^\d{7}$ uri_format: https://flybase.org/reports/FBtc$1 fcb: mappings: miriam: fcb miriam: deprecated: false 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). ' homepage: https://w3id.org id: 00000891 name: the FAIR Cookbook namespaceEmbeddedInLui: false pattern: ^FCB\d{3} prefix: fcb sampleId: FCB005 uri_format: https://w3id.org/faircookbook/$1 fcsfree: cellosaurus: category: Cell line databases/resources homepage: https://fcs-free.org/ name: Fetal Calf Serum-Free Database prefix: FCS-free uri_format: https://fcs-free.org/fcs-database?$1 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 example: 240-17-488-3-4-12 homepage: https://fcs-free.org mappings: cellosaurus: FCS-free name: Fetal Calf Serum-Free Database uri_format: https://fcs-free.org/fcs-database?$1 fideo: bioportal: name: Food Interactions with Drugs Evidence Ontology prefix: FIDEO example: '00000021' mappings: bioportal: FIDEO obofoundry: fideo ols: fideo ontobee: FIDEO obofoundry: contact: georgeta.bordea@u-bordeaux.fr contact.github: getbordea contact.label: Georgeta Bordea contact.orcid: 0000-0001-9921-8234 deprecated: false description: Food-Drug interactions automatically extracted from scientific literature download.owl: http://purl.obolibrary.org/obo/fideo.owl homepage: https://gitub.u-bordeaux.fr/erias/fideo inactive: false license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Food Interactions with Drugs Evidence Ontology preferredPrefix: FIDEO prefix: fideo repository: https://github.com/getbordea/fideo ols: description: "The Food Interactions with Drugs Evidence Ontology (FIDEO) represents\ \ Food-Drug Interactions and underlying interaction mechanisms described in\ \ scientific publications, drug and adverse effects databases, and drug interactions\ \ compendia. The ontology builds on previous efforts from the FoodOn, DRON,\ \ ChEBI, and DIDEO ontologies as well as the Th\xE9riaque database. This ontology\ \ is maintained at https://gitub.u-bordeaux.fr/erias/fideo, and requests for\ \ changes or additions should be filed at the issue tracker there." download: http://purl.obolibrary.org/obo/fideo.owl homepage: https://gitub.u-bordeaux.fr/erias/fideo name: Food Interactions with Drugs Evidence Ontology prefix: fideo ontobee: library: Library name: Food Interactions with Drugs Evidence Ontology prefix: FIDEO pattern: ^\d{8}$ fishbase.species: description: 'Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years.' example: '6472' homepage: http://fishbase.org name: FishBase pattern: ^\d+$ synonyms: - fishbase wikidata: database: Q837101 prefix: P938 fix: bioportal: name: Physico-Chemical Methods and Properties prefix: FIX example: 0000390 fairsharing: abbreviation: FIX description: 'FIX consists of two ontologies: methods and properties (but not objects, which are subject of the chemical ontology). The methods are applied to study the properties. While this ontology is available via BioPortal and the OBO Foundry, we cannot find a home page or a publication for the resource, and the resource itself is no longer maintained.' id: '1241' name: Physico-chemical methods and properties prefix: FAIRsharing.wwy1ns subjects: - Chemistry homepage: https://www.ebi.ac.uk/chebi/ mappings: bioportal: FIX fairsharing: FAIRsharing.wwy1ns obofoundry: fix ols: fix ontobee: FIX prefixcommons: FIX obofoundry: contact.label: chEBI deprecated: false 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 homepage: http://www.ebi.ac.uk/chebi inactive: true name: Physico-chemical methods and properties prefix: fix ols: description: An ontology of physico-chemical methods and properties. download: http://purl.obolibrary.org/obo/fix.owl homepage: http://www.ebi.ac.uk/chebi name: Physico-chemical methods and properties prefix: fix version: '2020-04-13' version.iri: http://purl.obolibrary.org/obo/fix/releases/2020-04-13/fix.owl ontobee: library: Library name: Physico-chemical methods and properties prefix: FIX part_of: chebi pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: FIX uri_format: http://purl.obolibrary.org/obo/FIX_$1 flopo: bioportal: name: Flora Phenotype Ontology prefix: FLOPO example: '0005250' fairsharing: abbreviation: FLOPO description: 'The Flora Phenotype Ontology is a domain ontology for the description of plant characters. FLOPO contains more than 25000 phenotype and traits classes, the creation of FLOPO is data-driven: For each trait/phenotype class exists a taxon annotation in the underlying Floras.' id: '394' name: Flora Phenotype Ontology prefix: FAIRsharing.ny9vnm subjects: - Botany - Biodiversity - Plant Anatomy mappings: bioportal: FLOPO fairsharing: FAIRsharing.ny9vnm obofoundry: flopo ols: flopo ontobee: FLOPO prefixcommons: FLOPO obofoundry: contact: robert.hoehndorf@kaust.edu.sa contact.github: leechuck contact.label: Robert Hoehndorf contact.orcid: 0000-0001-8149-5890 deprecated: false description: Traits and phenotypes of flowering plants occurring in digitized Floras download.owl: http://purl.obolibrary.org/obo/flopo.owl homepage: https://github.com/flora-phenotype-ontology/flopoontology inactive: false license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Flora Phenotype Ontology preferredPrefix: FLOPO prefix: flopo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27842607 title: 'The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants' repository: https://github.com/flora-phenotype-ontology/flopoontology ols: description: Traits and phenotypes of flowering plants occurring in digitized Floras download: http://purl.obolibrary.org/obo/flopo.owl homepage: https://github.com/flora-phenotype-ontology/flopoontology name: Flora Phenotype Ontology prefix: flopo version: '2019-09-09' ontobee: library: Library name: Flora Phenotype Ontology prefix: FLOPO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: FLOPO uri_format: http://purl.obolibrary.org/obo/FLOPO_$1 flowrepository: fairsharing: abbreviation: FlowRepository description: FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. Data are generally associated with peer reviewed manuscripts. id: '1727' name: FlowRepository prefix: FAIRsharing.veg2d6 subjects: - Life Science - Cell Biology - Biology mappings: fairsharing: FAIRsharing.veg2d6 miriam: flowrepository n2t: flowrepository miriam: deprecated: false description: FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field. homepage: https://flowrepository.org/ id: '00000672' name: FlowRepository namespaceEmbeddedInLui: false pattern: ^FR\-FCM\-\w{4}$ prefix: flowrepository sampleId: FR-FCM-ZYGW uri_format: https://flowrepository.org/id/$1 n2t: description: FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field. example: FR-FCM-ZYGW homepage: https://flowrepository.org/ name: FlowRepository namespaceEmbeddedInLui: false pattern: ^FR\-FCM\-\w{4}$ prefix: flowrepository uri_format: https://flowrepository.org/id/$1 flu: bioportal: name: Influenza Ontology prefix: FLU example: '0000404' mappings: bioportal: FLU obofoundry: flu prefixcommons: FLU obofoundry: contact: burkesquires@gmail.com contact.label: Burke Squires deprecated: true download.owl: http://purl.obolibrary.org/obo/flu.owl homepage: http://purl.obolibrary.org/obo/flu/ inactive: true name: Influenza Ontology prefix: flu pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: FLU uri_format: http://purl.obolibrary.org/obo/FLU_$1 flybase: cellosaurus: category: Organism-specific databases homepage: https://flybase.org name: Drosophila genome database prefix: FlyBase uri_format: https://flybase.org/reports/$1.html fairsharing: abbreviation: FlyBase description: Genetic, genomic and molecular information pertaining to the model organism Drosophila melanogaster and related sequences. This database also contains information relating to human disease models in Drosophila, the use of transgenic constructs containing sequence from other organisms in Drosophila, and information on where to buy Drosophila strains and constructs. id: '1582' name: FlyBase prefix: FAIRsharing.wrvze3 subjects: - Functional Genomics - Anatomy - Molecular biology - Genomics - Bioinformatics - Genetics - Life Science - Molecular Genetics - Comparative Genomics go: homepage: http://flybase.org/ name: FlyBase prefix: FB synonyms: - FlyBase - FLYBASE uri_format: http://flybase.org/reports/$1.html mappings: cellosaurus: FlyBase fairsharing: FAIRsharing.wrvze3 go: FB miriam: fb n2t: fb ncbi: FLYBASE prefixcommons: FlyBase uniprot: FlyBase wikidata: P3852 miriam: deprecated: false description: FlyBase is the database of the Drosophila Genome Projects and of associated literature. homepage: http://flybase.org/ id: '00000030' name: FlyBase namespaceEmbeddedInLui: false pattern: ^FB\w{2}\d{7}$ prefix: fb providers: - code: bioentitylink description: FlyBase through BioEntity Link homepage: https://bioentity.link/ name: FlyBase through BioEntity Link uri_format: https://bioentity.link/#/lexicon/public/$1 - code: agr description: FlyBase through the Alliance of Genome Resources homepage: https://www.alliancegenome.org name: FlyBase through the Alliance of Genome Resources uri_format: https://www.alliancegenome.org/gene/FB:$1 sampleId: FBgn0011293 uri_format: http://flybase.org/reports/$1.html n2t: description: FlyBase is the database of the Drosophila Genome Projects and of associated literature. example: FBgn0011293 homepage: https://www.alliancegenome.org name: FlyBase through the Alliance of Genome Resources namespaceEmbeddedInLui: false pattern: ^FB\w{2}\d{7}$ prefix: fb uri_format: https://www.alliancegenome.org/gene/FB:$1 name: FlyBase Gene ncbi: example: FBgn0000024 homepage: http://www.flybase.org/ name: Database of Genetic and molecular data of Drosophila. prefix: FLYBASE preferred_prefix: FlyBase prefixcommons: is_identifiers: false is_obo: false prefix: FlyBase uri_format: http://flybase.org/reports/$1 synonyms: - FB - FlyBase uniprot: category: Organism-specific databases comment: Replacement for DMAP identifier: '26' link_is_explicit: 'true' name: Drosophila genome database prefix: FlyBase uri_format: http://flybase.org/reports/$1.html uri_format: https://flybase.org/reports/$1 wikidata: database: Q3074571 database.homepage: https://flybase.org/ database.label: FlyBase homepage: http://flybase.org/ name: FlyBase Gene ID pattern: FBgn\d{7} prefix: P3852 uri_format: http://flybase.org/reports/$1 flybrain.ndb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A database of fly neurons and pathways with an associated 3D viewer. example: '10531' homepage: https://flybrain-ndb.virtualflybrain.org name: FlyBrain Neuron Database pattern: ^\d+$ uri_format: https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html fma: bioportal: name: Foundational Model of Anatomy prefix: FMA example: '63189' fairsharing: abbreviation: FMA description: The Foundational Model of Anatomy Ontology (FMA) is an evolving computer-based knowledge source for biomedical informatics; it is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. Its ontological framework can be applied and extended to all other species id: '683' name: Foundational Model of Anatomy prefix: FAIRsharing.x56jsy subjects: - Anatomy - Radiology - Biomedical Science go: homepage: http://sig.biostr.washington.edu/projects/fm/index.html name: Foundational Model of Anatomy prefix: FMA mappings: bioportal: FMA fairsharing: FAIRsharing.x56jsy go: FMA miriam: fma n2t: fma obofoundry: fma ols: fma ontobee: FMA prefixcommons: FMA miriam: deprecated: false description: The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. homepage: https://www.ebi.ac.uk/ols/ontologies/fma/ id: '00000067' name: FMA namespaceEmbeddedInLui: true pattern: ^FMA:\d+$ prefix: fma sampleId: '67112' uri_format: https://www.ebi.ac.uk/ols/ontologies/fma/terms?obo_id=FMA:$1 n2t: description: The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. example: '67112' homepage: http://bioportal.bioontology.org/ontologies/FMA name: Foundational Model of Anatomy through BioPortal namespaceEmbeddedInLui: true pattern: ^FMA:\d+$ prefix: fma uri_format: http://purl.bioontology.org/ontology/FMA_subset/FMA:$1 name: Foundational Model of Anatomy obofoundry: contact: mejino@u.washington.edu contact.label: Onard Mejino deprecated: false description: This is currently a slimmed down version of FMA download.owl: http://purl.obolibrary.org/obo/fma.owl homepage: http://si.washington.edu/projects/fma inactive: true license: CC BY 3.0 license.url: https://creativecommons.org/licenses/by/3.0/ name: Foundational Model of Anatomy Ontology (subset) preferredPrefix: FMA prefix: fma publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/18688289 title: Translating the Foundational Model of Anatomy into OWL - id: https://www.ncbi.nlm.nih.gov/pubmed/18360535 title: 'The foundational model of anatomy in OWL: Experience and perspectives' - id: https://www.ncbi.nlm.nih.gov/pubmed/16779026 title: 'Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study' repository: https://bitbucket.org/uwsig/fma ols: description: This is currently a slimmed down version of FMA download: http://purl.obolibrary.org/obo/fma.owl homepage: http://si.washington.edu/projects/fma name: Foundational Model of Anatomy Ontology (subset) prefix: fma version: '2020-04-13' version.iri: http://purl.obolibrary.org/obo/fma/releases/2020-04-13/fma.owl ontobee: library: Library name: Foundational Model of Anatomy Ontology (subset) prefix: FMA pattern: ^\d+$ prefixcommons: is_identifiers: false is_obo: true prefix: FMA uri_format: http://purl.obolibrary.org/obo/FMA_$1 synonyms: - FMAID - FMA_RETIRED foaf: biolink: is_identifiers: false is_obo: false prefix: foaf uri_format: http://xmlns.com/foaf/0.1/$1 bioportal: name: Friend of a Friend Vocabulary prefix: FOAF description: 'FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people''s heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world.' example: familyName homepage: http://xmlns.com/foaf/spec/ mappings: biolink: foaf bioportal: FOAF prefixcommons: foaf name: Friend of a Friend prefixcommons: is_identifiers: false is_obo: false prefix: foaf uri_format: http://xmlns.com/foaf/0.1/$1 uri_format: http://xmlns.com/foaf/0.1/$1 fobi: bioportal: name: FOBI (Food-Biomarker Ontology) prefix: FOBI example: 030719 homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology mappings: bioportal: FOBI obofoundry: fobi ols: fobi ontobee: FOBI name: Food-Biomarker Ontology obofoundry: contact: polcaes@gmail.com contact.github: pcastellanoescuder contact.label: Pol Castellano Escuder contact.orcid: 0000-0001-6466-877X depends_on: - chebi - foodon deprecated: false description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data download.owl: http://purl.obolibrary.org/obo/fobi.owl homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Food-Biomarker Ontology preferredPrefix: FOBI prefix: fobi publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/32556148 title: 'FOBI: an ontology to represent food intake data and associate it with metabolomic data' - id: https://www.ncbi.nlm.nih.gov/pubmed/34601570 title: 'The fobitools framework: the first steps towards food enrichment analysis' repository: https://github.com/pcastellanoescuder/FoodBiomarkerOntology ols: description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data download: http://purl.obolibrary.org/obo/fobi.owl homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology name: Food-Biomarker Ontology prefix: fobi version.iri: http://purl.obolibrary.org/obo/fobi/fobi.owl ontobee: library: Library name: FOBI prefix: FOBI pattern: ^\d{6}$ foodb.compound: biolink: is_identifiers: false is_obo: false prefix: foodb.compound uri_format: http://foodb.ca/compounds/$1 homepage: https://foodb.ca/ mappings: biolink: foodb.compound miriam: foodb.compound n2t: foodb.compound prefixcommons: FOODB.COMPOUND miriam: deprecated: false description: "FooDB is resource on food and its constituent compounds. It includes\ \ data on the compound\u2019s nomenclature, its description, information on\ \ its structure, chemical class, its physico-chemical data, its food source(s),\ \ its color, its aroma, its taste, its physiological effect, presumptive health\ \ effects (from published studies), and concentrations in various foods. This\ \ collection references compounds." homepage: http://foodb.ca/foods id: '00000530' name: FooDB Compound namespaceEmbeddedInLui: false pattern: ^FDB\d+$ prefix: foodb.compound sampleId: FDB002100 uri_format: http://foodb.ca/compounds/$1 n2t: description: FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds. example: FDB002100 homepage: http://foodb.ca/foods name: FooDB database of food additives at University of Alberta namespaceEmbeddedInLui: false pattern: ^FDB\d+$ prefix: foodb.compound uri_format: http://foodb.ca/compounds/$1 prefixcommons: is_identifiers: true is_obo: false prefix: FOODB.COMPOUND uri_format: http://identifiers.org/foodb.compound/$1 synonyms: - foodb foodon: bioportal: name: The FoodOn Food Ontology prefix: FOODON fairsharing: abbreviation: FOODON description: The need to represent knowledge about food is central to many human activities including agriculture, medicine, food safety inspection, shopping patterns, and sustainable development. FoodOn is built to interoperate with the OBO Library and to represent entities which bear a food role. Initially the ontology will focus on the human-centric categorization and handling of food, but in the future it will also encompass materials in natural ecosystems and food webs. We aim to develop semantics for food safety, food security, the agricultural and animal husbandry practices linked to food production, culinary, nutritional and chemical ingredients and processes. id: '638' name: FoodOn prefix: FAIRsharing.dzxae subjects: - Botany - Environmental Science - Medicine - Agriculture mappings: bioportal: FOODON fairsharing: FAIRsharing.dzxae miriam: foodon n2t: foodon obofoundry: foodon ols: foodon ontobee: FOODON prefixcommons: FOODON miriam: deprecated: false description: FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies. homepage: https://foodon.org id: '00000661' name: FoodOn Food Ontology namespaceEmbeddedInLui: true pattern: ^FOODON:[0-9]{8}$ prefix: foodon sampleId: 03307879 uri_format: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1 n2t: description: FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies. example: 03307879 homepage: https://foodon.org name: FoodOn Food Ontology through OLS namespaceEmbeddedInLui: true pattern: ^FOODON:[0-9]{8}$ prefix: foodon uri_format: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1 name: The Food Ontology obofoundry: appears_in: - agro - envo - fobi - maxo - one - ons contact: damion_dooley@sfu.ca contact.github: ddooley contact.label: Damion Dooley contact.orcid: 0000-0002-8844-9165 depends_on: - bfo - chebi - envo - eo - ncbitaxon - obi - ro - uberon deprecated: false description: "A broadly scoped ontology representing entities which bear a \u201C\ food role\u201D. It encompasses materials in natural ecosystems and agriculture\ \ that are consumed by humans and domesticated animals. This includes any generic\ \ (unbranded) raw or processed food material found in processing plants, markets,\ \ stores or food distribution points. FoodOn also imports nutritional component\ \ and dietary pattern terms from other OBO Foundry ontologies to support interoperability\ \ in diet and nutrition research" download.owl: http://purl.obolibrary.org/obo/foodon.owl homepage: https://foodon.org/ inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Food Ontology preferredPrefix: FOODON prefix: foodon publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31304272 title: 'FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration' repository: https://github.com/FoodOntology/foodon ols: description: FoodOn (http://foodon.org) is a consortium-driven project to build a comprehensive and easily accessible global farm-to-fork ontology about food, that accurately and consistently describes foods commonly known in cultures from around the world. download: http://purl.obolibrary.org/obo/foodon.owl homepage: https://foodon.org/ name: Food Ontology prefix: foodon version: '2022-02-01' version.iri: http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl ontobee: library: Library name: FOODON prefix: FOODON pattern: ^[0-9]{8}$ prefixcommons: is_identifiers: false is_obo: true prefix: FOODON uri_format: http://purl.obolibrary.org/obo/FOODON_$1 fovt: bioportal: name: FuTRES Ontology of Vertebrate Traits prefix: FOVT example: 0000009 mappings: bioportal: FOVT obofoundry: fovt ols: fovt ontobee: FOVT obofoundry: contact: meghan.balk@gmail.com contact.github: megbalk contact.label: Meghan Balk contact.orcid: 0000-0003-2699-3066 depends_on: - bco - bfo - bspo - iao - oba - pato - ro - uberon deprecated: false description: FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA). download.obo: http://purl.obolibrary.org/obo/fovt.obo download.owl: http://purl.obolibrary.org/obo/fovt.owl homepage: https://github.com/futres/fovt inactive: false license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: FuTRES Ontology of Vertebrate Traits preferredPrefix: FOVT prefix: fovt repository: https://github.com/futres/fovt ols: description: None download: http://purl.obolibrary.org/obo/fovt.owl homepage: https://github.com/futres/fovt name: FuTRES Ontology of Vertebrate Traits prefix: fovt version: '2021-11-10' version.iri: http://purl.obolibrary.org/obo/fovt/releases/2021-11-10/fovt.owl ontobee: library: Library name: FuTRES Ontology of Vertebrate Traits prefix: FOVT pattern: ^\d{7}$ fplx: bioportal: name: FamPlex prefix: FPLX example: GPIb_IX_V homepage: https://sorgerlab.github.io/famplex/ mappings: bioportal: FPLX miriam: fplx n2t: fplx prefixcommons: FPLX miriam: deprecated: false description: FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships. homepage: https://sorgerlab.github.io/famplex id: '00000651' name: FamPlex namespaceEmbeddedInLui: false pattern: ^[a-zA-Z0-9][A-Za-z0-9_]+$ prefix: fplx sampleId: RAS uri_format: https://sorgerlab.github.io/famplex/$1 n2t: description: FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships. example: RAS homepage: http://bioportal.bioontology.org/ontologies/FPLX/ name: FPLX through BioPortal namespaceEmbeddedInLui: false pattern: ^[a-zA-Z0-9][A-Za-z0-9_]+$ prefix: fplx uri_format: http://bioportal.bioontology.org/ontologies/FPLX/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FFPLX%23_$1 name: FamPlex prefixcommons: is_identifiers: true is_obo: false prefix: FPLX uri_format: http://identifiers.org/fplx/$1 synonyms: - famplex uri_format: https://sorgerlab.github.io/famplex/$1 wikidata: paper: Q55505864 fsnp: mappings: miriam: fsnp n2t: fsnp prefixcommons: FSNP miriam: deprecated: false description: The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification. homepage: http://compbio.cs.queensu.ca/F-SNP/ id: 00000496 name: F-SNP namespaceEmbeddedInLui: false pattern: ^rs\d+$ prefix: fsnp sampleId: rs17852708 uri_format: http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1 n2t: description: The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification. example: rs17852708 homepage: http://compbio.cs.queensu.ca/F-SNP/ name: F-SNP at Queen's University (Canada) namespaceEmbeddedInLui: false pattern: ^rs\d+$ prefix: fsnp uri_format: http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1 prefixcommons: is_identifiers: true is_obo: false prefix: FSNP uri_format: http://identifiers.org/fsnp/$1 ftt: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific. example: '273' homepage: https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3 name: Feature Type Thesaurus pattern: ^\d+$ 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=$1 funcbase.fly: mappings: miriam: funcbase.fly n2t: funcbase.fly prefixcommons: FUNCBASE.FLY miriam: deprecated: false description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data. homepage: http://func.mshri.on.ca/fly id: '00000461' name: FuncBase Fly namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: funcbase.fly sampleId: '10194' uri_format: http://func.mshri.on.ca/fly/genes/list_functional_scores/$1 n2t: description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data. example: '10194' homepage: http://func.mshri.on.ca/fly name: FuncBase Fly at Harvard Medical School namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: funcbase.fly uri_format: http://func.mshri.on.ca/fly/genes/list_functional_scores/$1 prefixcommons: is_identifiers: true is_obo: false prefix: FUNCBASE.FLY uri_format: http://identifiers.org/funcbase.fly/$1 funcbase.human: mappings: miriam: funcbase.human n2t: funcbase.human prefixcommons: FUNCBASE.HUMAN miriam: deprecated: false description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data. homepage: http://func.mshri.on.ca/human/ id: '00000462' name: FuncBase Human namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: funcbase.human sampleId: '119514' uri_format: http://func.mshri.on.ca/human/genes/list_functional_scores/$1 n2t: description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data. example: '119514' homepage: http://func.mshri.on.ca/human/ name: FuncBase Human at Harvard Medical School namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: funcbase.human uri_format: http://func.mshri.on.ca/human/genes/list_functional_scores/$1 prefixcommons: is_identifiers: true is_obo: false prefix: FUNCBASE.HUMAN uri_format: http://identifiers.org/funcbase.human/$1 funcbase.mouse: mappings: miriam: funcbase.mouse n2t: funcbase.mouse prefixcommons: FUNCBASE.MOUSE miriam: deprecated: false description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse. homepage: http://func.mshri.on.ca/mouse/ id: '00000463' name: FuncBase Mouse namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: funcbase.mouse sampleId: '1351341' uri_format: http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1 n2t: description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse. example: '1351341' homepage: http://func.mshri.on.ca/mouse/ name: FuncBase Mouse at Harvard Medical School namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: funcbase.mouse uri_format: http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1 prefixcommons: is_identifiers: true is_obo: false prefix: FUNCBASE.MOUSE uri_format: http://identifiers.org/funcbase.mouse/$1 funcbase.yeast: mappings: miriam: funcbase.yeast n2t: funcbase.yeast prefixcommons: FUNCBASE.YEAST miriam: deprecated: false description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast. homepage: http://func.mshri.on.ca/yeast id: '00000464' name: FuncBase Yeast namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: funcbase.yeast sampleId: '2701' uri_format: http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1 n2t: description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast. example: '2701' homepage: http://func.mshri.on.ca/yeast name: FuncBase Yeast at Harvard Medical School namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: funcbase.yeast uri_format: http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1 prefixcommons: is_identifiers: true is_obo: false prefix: FUNCBASE.YEAST uri_format: http://identifiers.org/funcbase.yeast/$1 funderregistry: mappings: miriam: funderregistry miriam: deprecated: false description: The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world. homepage: https://www.crossref.org/ id: 00000847 name: FunderRegistry namespaceEmbeddedInLui: false pattern: ^\d{9,9}$ prefix: funderregistry sampleId: '100000001' uri_format: http://data.crossref.org/fundingdata/funder/10.13039/$1 fungidb: fairsharing: abbreviation: FungiDB description: FungiDB is an integrated genomic and functional genomic database for the kingdom Fungi. The database integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining. id: '1585' name: Fungal and Oomycete genomics resource prefix: FAIRsharing.xf30yc subjects: - Genomics mappings: fairsharing: FAIRsharing.xf30yc miriam: fungidb n2t: fungidb prefixcommons: FUNGIDB miriam: deprecated: false description: FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina. homepage: https://fungidb.org/fungidb id: '00000365' name: FungiDB namespaceEmbeddedInLui: false pattern: ^[A-Za-z_0-9]+$ prefix: fungidb sampleId: CNBG_0001 uri_format: https://fungidb.org/fungidb/app/record/gene/$1 n2t: description: FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina. example: CNBG_0001 homepage: https://fungidb.org/fungidb name: FungiDB at University of California namespaceEmbeddedInLui: false pattern: ^[A-Za-z_0-9]+$ prefix: fungidb uri_format: https://fungidb.org/fungidb/app/record/gene/$1 prefixcommons: is_identifiers: true is_obo: false prefix: FUNGIDB uri_format: http://identifiers.org/fungidb/$1 fyeco: biolink: is_identifiers: false is_obo: false prefix: FYECO uri_format: https://www.pombase.org/term/$1 comment: Rather than admitting FYECO to the OBO foundry, we secure the prefix here at bioregistry. The FYECO namespace shows up in a lot of ingests (basically anywhere you ingest PomBase gene-phenotype data). Future work includes mapping FYECO to other OBO ontologies, but this is way ahead in the future. contact: email: vw253@cam.ac.uk github: ValWood name: Val Wood orcid: 0000-0001-6330-7526 contributor: email: vw253@cam.ac.uk github: ValWood name: Val Wood orcid: 0000-0001-6330-7526 description: PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase. example: '0000003' homepage: https://github.com/pombase/fypo mappings: biolink: FYECO name: Fission Yeast Experimental Conditions Ontology pattern: ^\d{7}$ preferred_prefix: FYECO repository: https://github.com/pombase/fypo reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 fyler: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'A hierarchical classification of congenital heart disease ' example: '4447' homepage: https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906 name: Fyler pattern: ^\d+$ references: - https://github.com/obophenotype/human-phenotype-ontology/issues/2568 - https://github.com/obophenotype/human-phenotype-ontology/issues/2511 fypo: biolink: is_identifiers: false is_obo: true prefix: FYPO uri_format: http://purl.obolibrary.org/obo/FYPO_$1 bioportal: name: Fission Yeast Phenotype Ontology prefix: FYPO download_obo: http://purl.obolibrary.org/obo/fypo.obo example: '0001707' fairsharing: abbreviation: FYPO description: FYPO is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the online fission yeast resource (www.pombase.org). Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions. id: '314' name: Fission Yeast Phenotype Ontology prefix: FAIRsharing.4vr0ys subjects: - Genetics - Phylogenetics - Life Science go: homepage: http://www.pombase.org/ name: Fission Yeast Phenotype Ontology prefix: FYPO mappings: biolink: FYPO bioportal: FYPO fairsharing: FAIRsharing.4vr0ys go: FYPO obofoundry: fypo ols: fypo ontobee: FYPO prefixcommons: FYPO name: Fission Yeast Phenotype Ontology obofoundry: contact: vw253@cam.ac.uk contact.github: ValWood contact.label: Val Wood contact.orcid: 0000-0001-6330-7526 deprecated: false description: FYPO is a formal ontology of phenotypes observed in fission yeast. download.obo: http://purl.obolibrary.org/obo/fypo.obo download.owl: http://purl.obolibrary.org/obo/fypo.owl homepage: https://github.com/pombase/fypo inactive: false license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Fission Yeast Phenotype Ontology preferredPrefix: FYPO prefix: fypo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/23658422 title: 'FYPO: The Fission Yeast Phenotype Ontology.' repository: https://github.com/pombase/fypo ols: description: A formal ontology of phenotypes observed in fission yeast. download: http://purl.obolibrary.org/obo/fypo.owl homepage: https://github.com/pombase/fypo name: Fission Yeast Phenotype Ontology (FYPO) prefix: fypo version: '2022-04-28' version.iri: http://purl.obolibrary.org/obo/fypo/releases/2022-04-28/fypo.owl ontobee: library: Library name: Fission Yeast Phenotype Ontology prefix: FYPO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: FYPO uri_format: http://purl.obolibrary.org/obo/FYPO_$1 ga4ghdos: mappings: miriam: ga4ghdos n2t: ga4ghdos prefixcommons: GA4GHDOS miriam: deprecated: false description: Assists in resolving data across cloud resources. homepage: http://github.com/ga4gh/data-object-service-schemas id: '00000671' name: Data Object Service namespaceEmbeddedInLui: false pattern: ^[a-zA-Z0-9\-:#/\.]+$ prefix: ga4ghdos sampleId: dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d uri_format: https://dataguids.org/ga4gh/dos/v1/dataobjects/$1 n2t: description: Assists in resolving data across cloud resources. example: dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d homepage: http://github.com/ga4gh/data-object-service-schemas name: Data Object Service namespaceEmbeddedInLui: false pattern: ^[a-zA-Z0-9\-:#/\.]+$ prefix: ga4ghdos uri_format: https://dataguids.org/ga4gh/dos/v1/dataobjects/$1 prefixcommons: is_identifiers: true is_obo: false prefix: GA4GHDOS uri_format: http://identifiers.org/ga4ghdos/$1 gabi: mappings: miriam: gabi n2t: gabi ncbi: GABI prefixcommons: GABI miriam: deprecated: false description: GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'. homepage: http://www.gabipd.org/ id: '00000164' name: GABI namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: gabi sampleId: '2679240' uri_format: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject n2t: description: GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'. example: '2679240' homepage: http://www.gabipd.org/ name: GABI at Max Planck namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: gabi uri_format: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject ncbi: example: HA05J18 homepage: http://www.gabipd.org/information/about.shtml name: Network of Different Plant Genomic Research Projects prefix: GABI prefixcommons: is_identifiers: true is_obo: false prefix: GABI uri_format: http://identifiers.org/gabi/$1 galen: bioportal: name: Galen Ontology prefix: GALEN comment: I really tried, but could not figure out what GALEN stands for deprecated: true example: MagnitudeValueType homepage: https://www.opengalen.org mappings: bioportal: GALEN name: GALEN gard: description: Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease. example: '6038' homepage: https://rarediseases.info.nih.gov/diseases name: Genetic and Rare Diseases Information Center pattern: ^\d+$ synonyms: - GARD - Genetic and Rare Diseases Information Center wikidata: prefix: P4317 gateway: mappings: miriam: gateway miriam: deprecated: false 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. homepage: https://www.hdruk.ac.uk id: 00000796 name: gateway namespaceEmbeddedInLui: false 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}$ prefix: gateway sampleId: fd8d0743-344a-4758-bb97-f8ad84a37357 uri_format: https://web.www.healthdatagateway.org/dataset/$1 name: Health Data Research Innovation Gateway gaz: bioportal: name: Gazetteer prefix: GAZ download_obo: http://purl.obolibrary.org/obo/gaz.obo example: '00620027' fairsharing: abbreviation: GAZ description: A controlled vocabulary following ontological rules that describes named geographical locations. GAZ represents a first step towards an open source gazetteer, constructed on ontological principles, that describes places and place names and the relations between them. id: '384' name: Gazetteer prefix: FAIRsharing.wkdjpb subjects: - Environmental Science mappings: bioportal: GAZ fairsharing: FAIRsharing.wkdjpb obofoundry: gaz ols: gaz ontobee: GAZ prefixcommons: GAZ obofoundry: appears_in: - scdo contact: lschriml@som.umaryland.edu contact.github: lschriml contact.label: Lynn Schriml contact.orcid: 0000-0001-8910-9851 deprecated: false description: A gazetteer constructed on ontological principles download.obo: http://purl.obolibrary.org/obo/gaz.obo download.owl: http://purl.obolibrary.org/obo/gaz.owl homepage: http://environmentontology.github.io/gaz/ inactive: true license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Gazetteer prefix: gaz repository: https://github.com/EnvironmentOntology/gaz ols: description: A gazetteer constructed on ontological principles download: http://purl.obolibrary.org/obo/gaz.obo homepage: http://environmentontology.github.io/gaz/ name: Gazetteer prefix: gaz version: '2018-06-26' ontobee: library: Library name: Gazetteer prefix: GAZ pattern: ^\d{8}$ prefixcommons: is_identifiers: false is_obo: true prefix: GAZ uri_format: http://purl.obolibrary.org/obo/GAZ_$1 wikidata: prefix: P6778 gbif: description: "Database of living organisms, taxonomic. \n The GBIF\u2014the Global\ \ Biodiversity Information Facility\u2014is 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' fairsharing: abbreviation: GBIF.org description: "GBIF\u2014the Global Biodiversity Information Facility\u2014is an\ \ 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.\n\nStrictly speaking, GBIF is not a data repository. Rather,\ \ GBIF indexes thousands of datasets through a distributed infrastructure involving\ \ more than 100 formal participants that supports hundreds of data-publishing\ \ institutions worldwide. GBIF.org makes the FAIR and open data discoverable\ \ and citable, assigning each download a DOI and storing it for an extended\ \ period of time. More than three peer-reviewed research articles make use of\ \ data from the GBIF network every day, in studies spanning the impacts of climate\ \ change, the spread of pests and diseases, priority areas for conservation\ \ and food security. \n\nTo share data with GBIF, follow this quick guide: http://www.gbif.org/publishing-data/quick-guide.\ \ To deposit or host data, we suggest using one of the trusted data hosting\ \ centres (DHC) listed in FAIRsharing.org that uses GBIF's IPT (Integrated Publishing\ \ Toolkit) software. The DHC provides data publishers with a hosted IPT account\ \ enabling them to manage and publish datasets through GBIF.org." id: '2163' name: GBIF.org prefix: FAIRsharing.zv11j3 subjects: - Metagenomics - Bioinformatics - Taxonomy - Marine Biology - Biodiversity - Natural Science - Natural History homepage: https://www.gbif.org/species mappings: fairsharing: FAIRsharing.zv11j3 name: Global Biodiversity Information Facility pattern: ^\d+$ uri_format: https://www.gbif.org/species/$1 wikidata: prefix: P846 gc: comment: 'see comment here: https://github.com/obophenotype/ncbitaxon/issues/47' contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries. example: '11' homepage: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html name: Genetic Code pattern: ^\d+$ references: - https://github.com/obophenotype/ncbitaxon/issues/47 synonyms: - gc_id uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1 gcst: mappings: miriam: gcst n2t: gcst miriam: deprecated: false description: The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide. homepage: https://www.ebi.ac.uk id: '00000715' name: GWAS Catalog namespaceEmbeddedInLui: false pattern: ^GCST\d{6}\d*$ prefix: gcst sampleId: GCST000035 uri_format: https://www.ebi.ac.uk/gwas/studies/$1 n2t: description: The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide. example: GCST000035 homepage: https://www.ebi.ac.uk/gwas/studies name: GWAS Catalog namespaceEmbeddedInLui: false pattern: ^GCST\d{6}$ prefix: gcst uri_format: https://www.ebi.ac.uk/gwas/studies/$1 gdc: mappings: miriam: gdc n2t: gdc prefixcommons: GDC miriam: deprecated: false description: The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis. homepage: https://gdc.cancer.gov id: '00000604' name: Genomic Data Commons Data Portal namespaceEmbeddedInLui: false pattern: ^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$ prefix: gdc sampleId: ae8c77fe-e6c8-44d5-8265-4a38c637bbef uri_format: https://portal.gdc.cancer.gov/cases/$1 n2t: description: The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis. example: ae8c77fe-e6c8-44d5-8265-4a38c637bbef homepage: https://gdc.cancer.gov name: Genomic Data Commons namespaceEmbeddedInLui: false pattern: ^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$ prefix: gdc uri_format: https://portal.gdc.cancer.gov/cases/$1 prefixcommons: is_identifiers: true is_obo: false prefix: GDC uri_format: http://identifiers.org/gdc/$1 gdsc: cellosaurus: category: Chemistry resources homepage: https://www.cancerrxgene.org name: Genomics of Drug Sensitivity in Cancer Project prefix: GDSC uri_format: https://www.cancerrxgene.org/translation/CellLine/$1 mappings: cellosaurus: GDSC miriam: gdsc n2t: gdsc miriam: deprecated: false description: The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies. homepage: https://www.cancerrxgene.org id: 00000678 name: Genomics of Drug Sensitivity in Cancer namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: gdsc sampleId: '1242' uri_format: https://www.cancerrxgene.org/translation/Drug/$1 n2t: description: The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies. example: '1242' homepage: https://www.cancerrxgene.org name: Genomics of Drug Sensitivity in Cancer namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: gdsc uri_format: https://www.cancerrxgene.org/translation/Drug/$1 gecko: bioportal: name: Genomics Cohorts Knowledge Ontology prefix: GECKO example: '0000044' fairsharing: abbreviation: GECKO description: GECKO is an ontology to represent genomics cohort attributes. The GECKO is maintained by the CINECA project, and standardises attributes commonly used for genomics cohort description as well as individual-level data items. id: '3626' name: Genomics Cohorts Knowledge Ontology prefix: FAIRsharing.3da56b subjects: - Genomics - Statistics - Life Science mappings: bioportal: GECKO fairsharing: FAIRsharing.3da56b obofoundry: gecko ols: gecko ontobee: GECKO obofoundry: contact: rbca.jackson@gmail.com contact.github: beckyjackson contact.label: Rebecca Jackson contact.orcid: 0000-0003-4871-5569 deprecated: false description: An ontology to represent genomics cohort attributes download.owl: http://purl.obolibrary.org/obo/gecko.owl homepage: https://github.com/IHCC-cohorts/GECKO inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Genomics Cohorts Knowledge Ontology preferredPrefix: GECKO prefix: gecko repository: https://github.com/IHCC-cohorts/GECKO ols: description: An ontology to represent genomics cohort attributes. download: http://purl.obolibrary.org/obo/gecko.owl homepage: https://github.com/IHCC-cohorts/GECKO name: Genomics Cohorts Knowledge Ontology prefix: gecko version: '2021-01-18' version.iri: http://purl.obolibrary.org/obo/gecko/releases/2021-01-18/gecko.owl ontobee: library: Library name: Genomics Cohorts Knowledge Ontology prefix: GECKO pattern: ^\d{7}$ gemet: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts. example: '627' homepage: https://www.eionet.europa.eu/gemet/en/themes/ name: General Multilingual Environmental Thesaurus pattern: ^\d+$ uri_format: https://www.eionet.europa.eu/gemet/en/concept/$1 genatlas: fairsharing: abbreviation: GenAtlas description: GenAtlas is a database containing information on human genes, markers and phenotypes. id: '1912' name: GenAtlas prefix: FAIRsharing.pmg2vd subjects: - Life Science mappings: fairsharing: FAIRsharing.pmg2vd miriam: genatlas n2t: genatlas prefixcommons: GENATLAS uniprot: GenAtlas miriam: deprecated: false description: GenAtlas is a database containing information on human genes, markers and phenotypes. homepage: http://genatlas.medecine.univ-paris5.fr/ id: 00000208 name: Genatlas namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: genatlas sampleId: HBB uri_format: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1 n2t: description: GenAtlas is a database containing information on human genes, markers and phenotypes. example: HBB homepage: http://genatlas.medecine.univ-paris5.fr/ name: Genatlas at Paris Descartes University namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: genatlas uri_format: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1 prefixcommons: is_identifiers: true is_obo: false prefix: GENATLAS uri_format: http://identifiers.org/genatlas/$1 uniprot: category: Organism-specific databases identifier: '27' name: 'GenAtlas: human gene database' prefix: GenAtlas uri_format: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1 genbank: cheminf: description: [] name: GenBank Nucleotide Identifier obsolete: false prefix: '000304' description: "GenBank \xAE 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 fairsharing: abbreviation: GenBank description: GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. The complete release notes for the current version of GenBank are available on the NCBI ftp site. A new release is made every two months. GenBank growth statistics for both the traditional GenBank divisions and the WGS division are available from each release. GenBank is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These three organizations exchange data on a daily basis. id: '1547' name: GenBank prefix: FAIRsharing.9kahy4 subjects: - Functional Genomics - Metagenomics - Genomics - Bioinformatics - Data Management - Virology - Transcriptomics - Epidemiology go: description: The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. homepage: http://www.ncbi.nlm.nih.gov/Genbank/ name: GenBank prefix: GenBank synonyms: - GB homepage: https://www.ncbi.nlm.nih.gov/genbank/ mappings: cheminf: '000304' fairsharing: FAIRsharing.9kahy4 go: GenBank prefixcommons: GenBank uniprot: GenBank name: GenBank prefixcommons: is_identifiers: false is_obo: false prefix: GenBank uri_format: http://www.ncbi.nlm.nih.gov/nuccore/$1 uniprot: category: Sequence databases identifier: '28' name: GenBank nucleotide sequence database prefix: GenBank uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 uri_format: https://www.ncbi.nlm.nih.gov/nucleotide/$1 genecards: fairsharing: abbreviation: GeneCards description: GeneCards is a searchable, integrated, database of human genes that provides concise genomic, transcriptomic, genetic, proteomic, functional and disease related information on all known and predicted human genes. id: '2123' name: Human Gene Database prefix: FAIRsharing.g7jbvn subjects: - Genetics - Life Science - Transcriptomics mappings: fairsharing: FAIRsharing.g7jbvn miriam: genecards n2t: genecards prefixcommons: GENECARDS uniprot: GeneCards miriam: deprecated: false description: The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene. homepage: http://www.genecards.org/ id: '00000323' name: GeneCards namespaceEmbeddedInLui: false pattern: ^[A-Za-z-0-9_]+(\@)?$ prefix: genecards sampleId: ABL1 uri_format: https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1 n2t: description: The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene. example: ABL1 homepage: http://www.genecards.org/ name: GeneCards at Weizmann Institute namespaceEmbeddedInLui: false pattern: ^[A-Za-z-0-9_]+(\@)?$ prefix: genecards uri_format: https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1 prefixcommons: is_identifiers: true is_obo: false prefix: GENECARDS uri_format: http://identifiers.org/genecards/$1 uniprot: category: Organism-specific databases identifier: '30' link_is_explicit: 'true' name: 'GeneCards: human genes, protein and diseases' prefix: GeneCards uri_format: https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1 genedb: deprecated: true fairsharing: abbreviation: GeneDB 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. id: '1589' name: GeneDB prefix: FAIRsharing.j7esqq subjects: - Life Science go: homepage: http://www.genedb.org/gene/ name: GeneDB prefix: GeneDB uri_format: http://www.genedb.org/gene/$1 mappings: fairsharing: FAIRsharing.j7esqq go: GeneDB miriam: genedb n2t: genedb ncbi: GeneDB prefixcommons: GENEDB uniprot: GeneDB wikidata: P3382 miriam: deprecated: false description: GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed. homepage: https://www.genedb.org/ id: '00000106' name: GeneDB namespaceEmbeddedInLui: false pattern: ^[\w\d\.-]*$ prefix: genedb sampleId: LinJ.20.0070 uri_format: https://www.genedb.org/gene/$1 n2t: description: GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed. example: LinJ.20.0070 homepage: https://www.genedb.org/ name: GeneDB at Sanger Institute namespaceEmbeddedInLui: false pattern: ^[\w\d\.-]*$ prefix: genedb uri_format: https://www.genedb.org/gene/$1 name: GeneDB ncbi: example: SPCC285.16c homepage: http://www.genedb.org/ name: Curated gene database for Leishmania major and Trypanosoma brucei prefix: GeneDB prefixcommons: is_identifiers: true is_obo: false prefix: GENEDB uri_format: http://identifiers.org/genedb/$1 uniprot: category: Genome annotation databases identifier: '199' link_is_explicit: 'true' name: GeneDB pathogen genome database from Sanger Institute prefix: GeneDB uri_format: https://www.genedb.org/gene/$1 wikidata: database: Q5531047 database.homepage: http://www.genedb.org/ database.label: GeneDB homepage: http://www.genedb.org/ name: GeneDB ID prefix: P3382 uri_format: https://www.genedb.org/gene/$1 genefarm: fairsharing: abbreviation: GeneFarm description: GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products. id: '2116' name: Structural and functional annotation of Arabidopsis thaliana gene and protein families prefix: FAIRsharing.2mayq0 subjects: - Life Science mappings: fairsharing: FAIRsharing.2mayq0 miriam: genefarm n2t: genefarm prefixcommons: GENEFARM miriam: deprecated: false description: GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products. homepage: http://urgi.versailles.inra.fr/Genefarm/ id: '00000211' name: GeneFarm namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: genefarm sampleId: '4892' uri_format: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1 n2t: description: GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products. example: '4892' homepage: http://urgi.versailles.inra.fr/Genefarm/ name: GeneFarm at Unité de Recherche en Génomique Végétale namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: genefarm uri_format: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1 prefixcommons: is_identifiers: true is_obo: false prefix: GENEFARM uri_format: http://identifiers.org/genefarm/$1 genepio: example: 0001885 fairsharing: abbreviation: GenEpiO description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research food-borne pathogens, infectious disease surveillance and outbreak investigations. This includes descriptions of the genomics, laboratory, clinical and epidemiological contextual information required to support data sharing and integration for food-borne infectious disease surveillance and outbreak investigations. id: '279' name: Genomic Epidemiology Ontology prefix: FAIRsharing.y1mmbv subjects: - Genomics - Epidemiology mappings: fairsharing: FAIRsharing.y1mmbv obofoundry: genepio ols: genepio ontobee: GENEPIO prefixcommons: GENEPIO obofoundry: contact: damion_dooley@sfu.ca contact.github: ddooley contact.label: Damion Dooley contact.orcid: 0000-0002-8844-9165 depends_on: - chebi - ncbitaxon - po - ro - uberon deprecated: false description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. download.owl: http://purl.obolibrary.org/obo/genepio.owl homepage: http://genepio.org/ inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Genomic Epidemiology Ontology preferredPrefix: GENEPIO prefix: genepio repository: https://github.com/GenEpiO/genepio ols: description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. download: http://purl.obolibrary.org/obo/genepio.owl homepage: http://genepio.org/ name: Genomic Epidemiology Ontology prefix: genepio version: '2022-02-06' version.iri: http://purl.obolibrary.org/obo/genepio/releases/2022-02-06/genepio.owl ontobee: library: Library name: Genomic Epidemiology Ontology prefix: GENEPIO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: GENEPIO uri_format: http://purl.obolibrary.org/obo/GENEPIO_$1 genetree: mappings: miriam: genetree n2t: genetree prefixcommons: GENETREE uniprot: GeneTree miriam: deprecated: false description: Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl. homepage: http://www.ensembl.org/ id: '00000214' name: GeneTree namespaceEmbeddedInLui: false pattern: ^ENSGT\d+$ prefix: genetree sampleId: ENSGT00550000074763 uri_format: http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1 n2t: description: Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl. example: ENSGT00550000074763 homepage: http://www.ensembl.org/ name: GeneTree at Ensembl namespaceEmbeddedInLui: false pattern: ^ENSGT\d+$ prefix: genetree uri_format: http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1 prefixcommons: is_identifiers: true is_obo: false prefix: GENETREE uri_format: http://identifiers.org/genetree/$1 uniprot: category: Phylogenomic databases identifier: '162' link_is_explicit: 'true' name: Ensembl GeneTree prefix: GeneTree uri_format: http://www.ensemblgenomes.org/id-genetree/$1 genewiki: fairsharing: abbreviation: Gene Wiki description: 'The goal of the Gene Wiki is to apply community intelligence to the annotation of gene and protein function. The Gene Wiki is an informal collection of pages on human genes and proteins, and this effort to develop these pages is tightly coordinated with the Molecular and Cellular Biology Wikiproject. Our specific aims are summarized as follows: To provide a well written and informative Wikipedia article for every notable human gene; To invite participation by interested lay editors, students, professionals, and academics from around the world; To integrate Gene Wiki articles with existing Wikipedia content through the use of internal wiki links increasing the value of both.' id: '1677' name: Gene Wiki prefix: FAIRsharing.t3snf subjects: - Genetics - Life Science mappings: fairsharing: FAIRsharing.t3snf miriam: genewiki n2t: genewiki prefixcommons: GENEWIKI uniprot: GeneWiki miriam: deprecated: false description: The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI. homepage: http://en.wikipedia.org/wiki/Gene_Wiki id: 00000487 name: Gene Wiki namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: genewiki sampleId: '1017' uri_format: http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1 n2t: description: The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI. example: '1017' homepage: http://en.wikipedia.org/wiki/Gene_Wiki name: Gene Wiki through BioGPS namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: genewiki uri_format: http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: GENEWIKI uri_format: http://identifiers.org/genewiki/$1 uniprot: category: Miscellaneous databases identifier: '180' link_is_explicit: 'true' name: The Gene Wiki collection of pages on human genes and proteins prefix: GeneWiki uri_format: https://en.wikipedia.org/wiki/$1 geno: bioportal: name: Genotype Ontology prefix: GENO download_obo: https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/develop/geno-full.obo example: '0000632' fairsharing: abbreviation: GENO description: An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases. id: '688' name: Genotype Ontology prefix: FAIRsharing.kpbna7 subjects: [] mappings: bioportal: GENO fairsharing: FAIRsharing.kpbna7 obofoundry: geno ols: geno ontobee: GENO prefixcommons: GENO obofoundry: contact: mhb120@gmail.com contact.github: mbrush contact.label: Matthew Brush contact.orcid: 0000-0002-1048-5019 deprecated: false description: An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases. download.owl: http://purl.obolibrary.org/obo/geno.owl homepage: https://github.com/monarch-initiative/GENO-ontology/ inactive: false license: CC BY-SA 2.0 license.url: https://creativecommons.org/licenses/by-sa/2.0/ name: Genotype Ontology preferredPrefix: GENO prefix: geno repository: https://github.com/monarch-initiative/GENO-ontology ols: 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: http://purl.obolibrary.org/obo/geno.owl homepage: https://github.com/monarch-initiative/GENO-ontology/ name: GENO ontology prefix: geno version: '2022-03-05' version.iri: http://purl.obolibrary.org/obo/geno/releases/2022-03-05/geno.owl ontobee: library: Library name: Genotype Ontology prefix: GENO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: GENO uri_format: http://purl.obolibrary.org/obo/GENO_$1 genpept: mappings: miriam: genpept n2t: genpept prefixcommons: GENPEPT miriam: deprecated: false description: The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank. homepage: https://www.ncbi.nlm.nih.gov/protein id: '00000345' name: GenPept namespaceEmbeddedInLui: false pattern: ^\w{3}\d{5}(\.\d+)?$ prefix: genpept sampleId: CAA71118.1 uri_format: https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept n2t: description: The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank. example: CAA71118.1 homepage: https://www.ncbi.nlm.nih.gov/protein name: GenPept at NCBI namespaceEmbeddedInLui: false pattern: ^\w{3}\d{5}(\.\d+)?$ prefix: genpept uri_format: https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept prefixcommons: is_identifiers: true is_obo: false prefix: GENPEPT uri_format: http://identifiers.org/genpept/$1 genprop: mappings: miriam: genprop n2t: genprop prefixcommons: GENPROP miriam: deprecated: false description: Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome. homepage: https://www.ebi.ac.uk/interpro/genomeproperties/ id: '00000443' name: Genome Properties namespaceEmbeddedInLui: false pattern: ^GenProp\d+$ prefix: genprop sampleId: GenProp0699 uri_format: https://www.ebi.ac.uk/interpro/genomeproperties/#$1 n2t: description: Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome. example: GenProp0699 homepage: https://www.ebi.ac.uk/interpro/genomeproperties/ name: Genome Properties namespaceEmbeddedInLui: false pattern: ^GenProp\d+$ prefix: genprop uri_format: https://www.ebi.ac.uk/interpro/genomeproperties/#$1 prefixcommons: is_identifiers: true is_obo: false prefix: GENPROP uri_format: http://identifiers.org/genprop/$1 geo: cellosaurus: category: Gene expression databases homepage: https://www.ncbi.nlm.nih.gov/geo/ name: Gene Expression Omnibus prefix: GEO uri_format: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1 fairsharing: abbreviation: GEO description: The Geographical Entity Ontology (GEO) is an ontology of geographical entities (such as sovereign states and their administrative subdivisions) as well as various geographical regions (including but not limited to the specific ones over which the governments have jurisdiction). id: '823' name: Geographical Entity Ontology prefix: FAIRsharing.27rndz subjects: - Human Geography - Physical Geography go: homepage: http://www.ncbi.nlm.nih.gov/geo/ name: NCBI Gene Expression Omnibus prefix: GEO uri_format: http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=$1 mappings: cellosaurus: GEO fairsharing: FAIRsharing.27rndz go: GEO miriam: geo n2t: geo prefixcommons: GEO miriam: deprecated: false description: The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval. homepage: https://www.ncbi.nlm.nih.gov/geo/ id: '00000054' name: GEO namespaceEmbeddedInLui: false pattern: ^G(PL|SM|SE|DS)\d+$ prefix: geo sampleId: GDS1234 uri_format: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1 n2t: description: The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval. example: GDS1234 homepage: https://www.ncbi.nlm.nih.gov/geo/ name: Gene Expression Omnibus at NCBI namespaceEmbeddedInLui: false pattern: ^G(PL|SM|SE|DS)\d+$ prefix: geo uri_format: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1 prefixcommons: formatter: http://purl.obolibrary.org/obo/GEO_$1 is_identifiers: false is_obo: true prefix: GEO geogeo: bioportal: name: Geographical Entity Ontology prefix: GEO example: '000000021' mappings: bioportal: GEO miriam: geogeo obofoundry: geo ols: geo ontobee: GEO prefixcommons: GEO miriam: deprecated: false description: An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in "The US declared war on Germany" vs. the US in "The plane entered US airspace". homepage: https://github.com/ufbmi id: 00000824 name: Geographical Entity Ontology namespaceEmbeddedInLui: false pattern: ^GEO_[0-9]{9}$ prefix: geogeo sampleId: GEO_000000021 uri_format: http://purl.obolibrary.org/obo/$1 obofoundry: contact: hoganwr@gmail.com contact.label: Bill Hogan deprecated: false description: An ontology of geographical entities download.owl: http://purl.obolibrary.org/obo/geo.owl homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki license: CC-BY 4.0 name: Geographical Entity Ontology prefix: geo ols: description: An ontology of geographical entities download: http://purl.obolibrary.org/obo/geo.owl homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki name: Geographical Entity Ontology prefix: geo version: '2016-03-26' ontobee: library: Library name: Geographical Entity Ontology prefix: GEO pattern: ^\d{9}$ preferred_prefix: GEOGEO prefixcommons: is_identifiers: false is_obo: true prefix: GEO 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 geonames: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge. example: ADM1 fairsharing: abbreviation: GeoNames description: GeoNames integrates geographical data such as names of places in various languages, elevation, population and others from various sources. Users may manually edit, correct and add new names using a user friendly wiki interface. id: '2880' name: GeoNames prefix: FAIRsharing.56a0Uj subjects: - Demographics - Geography homepage: https://www.geonames.org mappings: fairsharing: FAIRsharing.56a0Uj name: GeoNames synonyms: - Geomames - Geonamaes uri_format: https://www.geonames.org/recent-changes/featurecode/$1/ gexo: bioportal: name: Gene Expression Ontology prefix: GEXO download_obo: https://www.bio.ntnu.no/ontology/GeXO/gexo.obo download_owl: https://www.bio.ntnu.no/ontology/GeXO/gexo.owl fairsharing: abbreviation: GeXO description: An application ontology for the domain of gene expression. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, and orthology relations using ontological properties from RO and ISO. id: '1230' name: Gene Expression Ontology prefix: FAIRsharing.3e0sn4 subjects: - Life Science mappings: bioportal: GEXO fairsharing: FAIRsharing.3e0sn4 ols: gexo no_own_terms: true ols: contact: vladimir.n.mironov@gmail.com description: Gene Expression Ontology download: http://www.bio.ntnu.no/ontology/GeXO/gexo.rdf homepage: http://www.semantic-systems-biology.org/apo name: Gene Expression Ontology prefix: gexo version: '2019-09-18' ghr: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA). example: saddan homepage: https://medlineplus.gov/genetics/condition name: Genetics Home Reference uri_format: https://medlineplus.gov/genetics/condition/$1 giardiadb: fairsharing: abbreviation: GiardiaDB description: A detailed study of Giardia lamblia's genome will provide insights into an early evolutionary stage of eukaryotic chromosome organization as well as other aspects of the prokaryotic / eukaryotic divergence. id: '1880' name: GiardiaDB prefix: FAIRsharing.e7skwg subjects: - Life Science mappings: fairsharing: FAIRsharing.e7skwg miriam: giardiadb n2t: giardiadb prefixcommons: GIARDIADB miriam: deprecated: false description: GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. homepage: https://giardiadb.org/giardiadb/ id: '00000151' name: GiardiaDB namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: giardiadb sampleId: GL50803_102438 uri_format: https://giardiadb.org/giardiadb/app/record/gene/$1 n2t: description: GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: GL50803_102438 homepage: https://giardiadb.org/giardiadb/ name: GiardiaDB at EuPathDB namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: giardiadb uri_format: https://giardiadb.org/giardiadb/app/record/gene/$1 prefixcommons: is_identifiers: true is_obo: false prefix: GIARDIADB uri_format: http://identifiers.org/giardiadb/$1 github: example: biopragmatics/bioregistry example_extras: - biopragmatics - cthoyt fairsharing: abbreviation: GitHub description: GitHub Inc. is a Git-based software repository that provides version control. It offers all of the distributed version control and source code management (SCM) functionality of Git as well as adding its own features. It provides access control and several collaboration features such as bug tracking, feature requests, task management, and wikis for each project. It provides a number of different access levels, from free through to paid services. id: '2667' name: GitHub prefix: FAIRsharing.c55d5e subjects: - Knowledge and Information Systems - Subject Agnostic - Software Engineering mappings: fairsharing: FAIRsharing.c55d5e miriam: github miriam: deprecated: false description: GitHub is an online host of Git source code repositories. homepage: https://github.com/ id: 00000853 name: github namespaceEmbeddedInLui: false pattern: ^[a-zA-Z0-9-_]+/[a-zA-Z0-9-_]+$ prefix: github sampleId: identifiers-org/registry uri_format: https://github.com/$1 pattern: ^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$ gitlab: fairsharing: abbreviation: GitLab description: GitLab is a Git-based source code repository with wiki and issue tracker functionality. It provides a number of different access levels, from free through to a number of paid services. id: '3277' name: GitLab prefix: FAIRsharing.530e61 subjects: - Knowledge and Information Systems - Subject Agnostic - Software Engineering mappings: fairsharing: FAIRsharing.530e61 miriam: gitlab miriam: deprecated: false 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. homepage: https://gitlab.com/ id: 00000901 name: GitLab namespaceEmbeddedInLui: false pattern: ^[0-9A-Za-z_][0-9A-Za-z-_()\. ]*/[0-9A-Za-z_][0-9A-Za-z-_\. ]*$ prefix: gitlab sampleId: morpheus.lab/morpheus uri_format: https://gitlab.com/$1 pattern: ^.*/.*$ glida.gpcr: mappings: miriam: glida.gpcr n2t: glida.gpcr prefixcommons: GLIDA.GPCR miriam: deprecated: false 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. homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ id: 00000493 name: GLIDA GPCR namespaceEmbeddedInLui: false pattern: ^[A-Z-_0-9]+$ prefix: glida.gpcr sampleId: ACM1_HUMAN uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1 n2t: description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors. example: ACM1_HUMAN homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ name: GLIDA GPCR at Kyoto University namespaceEmbeddedInLui: false pattern: ^[A-Z-_0-9]+$ prefix: glida.gpcr uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: GLIDA.GPCR uri_format: http://identifiers.org/glida.gpcr/$1 glida.ligand: mappings: miriam: glida.ligand n2t: glida.ligand prefixcommons: GLIDA.LIGAND miriam: deprecated: false description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands. homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ id: 00000494 name: GLIDA Ligand namespaceEmbeddedInLui: false pattern: ^L\d+$ prefix: glida.ligand sampleId: L000001 uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1 n2t: description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands. example: L000001 homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ name: GLIDA Ligand at Kyoto University namespaceEmbeddedInLui: false pattern: ^L\d+$ prefix: glida.ligand uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: GLIDA.LIGAND uri_format: http://identifiers.org/glida.ligand/$1 glycoepitope: mappings: miriam: glycoepitope n2t: glycoepitope prefixcommons: GLYCOEPITOPE miriam: deprecated: false description: GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes. homepage: https://www.glycoepitope.jp/epitopes/ id: 00000478 name: GlycoEpitope namespaceEmbeddedInLui: false pattern: ^EP\d{4}$ prefix: glycoepitope sampleId: EP0311 uri_format: https://www.glycoepitope.jp/epitopes/$1 n2t: description: GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes. example: EP0311 homepage: https://www.glycoepitope.jp/epitopes/ name: GlycoEpitope at Ritsumeikan University namespaceEmbeddedInLui: false pattern: ^EP\d{4}$ prefix: glycoepitope uri_format: https://www.glycoepitope.jp/epitopes/$1 prefixcommons: is_identifiers: true is_obo: false prefix: GLYCOEPITOPE uri_format: http://identifiers.org/glycoepitope/$1 glycomedb: comment: this is exactly the same as glytoucan. Idk why there are two different ones fairsharing: abbreviation: GlycomeDB description: GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links. id: '1888' name: GlycomeDB prefix: FAIRsharing.k5k0yh subjects: - Life Science has_canonical: glytoucan mappings: fairsharing: FAIRsharing.k5k0yh miriam: glycomedb n2t: glycomedb prefixcommons: GLYCOMEDB miriam: deprecated: false description: GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links. homepage: https://glytoucan.org/ id: '00000114' name: GlycomeDB namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: glycomedb sampleId: G77500AY uri_format: https://glytoucan.org/Structures/Glycans/$1 n2t: description: GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links. example: G77500AY homepage: https://glytoucan.org/ name: GlycomeDB carbohydrate structure database namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: glycomedb uri_format: https://glytoucan.org/Structures/Glycans/$1 prefixcommons: is_identifiers: true is_obo: false prefix: GLYCOMEDB uri_format: http://identifiers.org/glycomedb/$1 glyconavi: example_extras: - GN_GlyTouCan_G03681DA fairsharing: abbreviation: GlycoNAVI description: GlycoNAVI is a repository of data relevant to carbohydrate research. It contains a free suite of carbohydrate research tools organized by domain, including glycans, proteins, lipids, genes, diseases and samples. id: '1548' name: GlycoNAVI prefix: FAIRsharing.wvp1t7 subjects: - Organic Chemistry - Chemistry - Life Science - Glycomics mappings: fairsharing: FAIRsharing.wvp1t7 miriam: glyconavi miriam: deprecated: false description: GlycoNAVI is a website for carbohydrate research. It consists of the "GlycoNAVI Database" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the "GlycoNAVI tools" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools. homepage: https://www.noguchi.or.jp/ id: 00000830 name: GlycoNAVI namespaceEmbeddedInLui: false pattern: ^GN_[A-Za-z0-9]+$ prefix: glyconavi sampleId: GN_G03681DA uri_format: https://glyconavi.org/hub/?id=$1 pattern: ^GN_[A-Za-z0-9_:]+$ glycopost: fairsharing: abbreviation: GlycoPOST description: GlycoPOST is a mass spectrometry data repository for glycomics. 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. id: '3185' name: GlycoPOST prefix: FAIRsharing.2y1KMt subjects: - Life Science - Glycomics mappings: fairsharing: FAIRsharing.2y1KMt miriam: glycopost miriam: deprecated: false 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. homepage: https://glycopost.glycosmos.org id: '00000721' name: GlycoPOST namespaceEmbeddedInLui: false pattern: ^GPST[0-9]{6}$ prefix: glycopost sampleId: GPST000024 uri_format: https://glycopost.glycosmos.org/entry/$1 glygen: description: GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data. example: G24361QY fairsharing: abbreviation: GlyGen description: GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data. This web portal allows exploring this data and performing unique searches that cannot be executed in any of the integrated databases alone. id: '2874' name: 'GlyGen: Computational and Informatics Resources for Glycoscience' prefix: FAIRsharing.aI1J5W subjects: - Life Science - Glycomics homepage: https://glygen.org/glycan/ mappings: fairsharing: FAIRsharing.aI1J5W uniprot: GlyGen name: Computational and Informatics Resources for Glycoscience uniprot: category: PTM databases identifier: '254' link_is_explicit: 'true' name: 'GlyGen: Computational and Informatics Resources for Glycoscience' prefix: GlyGen uri_format: https://glygen.org/protein/$1#glycosylation uri_format: https://glygen.org/glycan/$1 glytoucan: mappings: miriam: glytoucan n2t: glytoucan prefixcommons: GLYTOUCAN miriam: deprecated: false description: GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data. homepage: https://glytoucan.org id: 00000608 name: GlyTouCan namespaceEmbeddedInLui: false pattern: ^G[0-9]{5}[A-Z]{2}$ prefix: glytoucan sampleId: G00054MO uri_format: https://glytoucan.org/Structures/Glycans/$1 n2t: description: GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data. example: G00054MO homepage: https://glytoucan.org name: The Glycan Repository namespaceEmbeddedInLui: false pattern: ^G[0-9]{5}[A-Z]{2}$ prefix: glytoucan uri_format: https://glytoucan.org/Structures/Glycans/$1 prefixcommons: is_identifiers: true is_obo: false prefix: GLYTOUCAN uri_format: http://identifiers.org/glytoucan/$1 gmd: fairsharing: abbreviation: GMD description: The Golm Metabolome Database (GMD) provides gas chromatography (GC) mass spectrometry (MS) reference spectra, reference metabolite profiles and tools for one of the most widespread routine technologies applied to the large scale screening and discovery of novel metabolic biomarkers. id: '1729' name: Golm Metabolome Database prefix: FAIRsharing.jykmkw subjects: - Life Science - Metabolomics mappings: fairsharing: FAIRsharing.jykmkw miriam: gmd n2t: gmd prefixcommons: GMD miriam: deprecated: false description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena. homepage: http://gmd.mpimp-golm.mpg.de/ id: '00000274' name: Golm Metabolome Database namespaceEmbeddedInLui: false pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ prefix: gmd sampleId: 68513255-fc44-4041-bc4b-4fd2fae7541d uri_format: http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx n2t: description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena. example: 68513255-fc44-4041-bc4b-4fd2fae7541d homepage: http://gmd.mpimp-golm.mpg.de/ name: Golm Metabolome Database at Max Planck Institute of Molecular Plant Physiology namespaceEmbeddedInLui: false pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ prefix: gmd uri_format: http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx prefixcommons: is_identifiers: true is_obo: false prefix: GMD uri_format: http://identifiers.org/gmd/$1 gmd.analyte: mappings: miriam: gmd.analyte n2t: gmd.analyte prefixcommons: GMD.ANALYTE miriam: deprecated: false description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes. homepage: http://gmd.mpimp-golm.mpg.de/ id: '00000426' name: Golm Metabolome Database Analyte namespaceEmbeddedInLui: false pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ prefix: gmd.analyte sampleId: 4f0fa9b6-514f-4ff4-98cc-0009bc08eb80 uri_format: http://gmd.mpimp-golm.mpg.de/Analytes/$1 n2t: description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes. example: 4f0fa9b6-514f-4ff4-98cc-0009bc08eb80 homepage: http://gmd.mpimp-golm.mpg.de/ name: Golm Metabolome Database (Analyte) at Max Planck Institute of Molecular Plant Physiology namespaceEmbeddedInLui: false pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ prefix: gmd.analyte uri_format: http://gmd.mpimp-golm.mpg.de/Analytes/$1 prefixcommons: is_identifiers: true is_obo: false prefix: GMD.ANALYTE uri_format: http://identifiers.org/gmd.analyte/$1 gmd.gcms: mappings: miriam: gmd.gcms n2t: gmd.gcms prefixcommons: GMD.GCMS miriam: deprecated: false description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra. homepage: http://gmd.mpimp-golm.mpg.de/ id: '00000424' name: Golm Metabolome Database GC-MS spectra namespaceEmbeddedInLui: false pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ prefix: gmd.gcms sampleId: 53d583d8-40c6-40e1-9296-23f821cd77a5 uri_format: http://gmd.mpimp-golm.mpg.de/Spectrums/$1 n2t: description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra. example: 53d583d8-40c6-40e1-9296-23f821cd77a5 homepage: http://gmd.mpimp-golm.mpg.de/ name: Golm Metabolome Database (GC-MS Spectra) at Max Planck Institute of Molecular Plant Physiology namespaceEmbeddedInLui: false pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ prefix: gmd.gcms uri_format: http://gmd.mpimp-golm.mpg.de/Spectrums/$1 prefixcommons: is_identifiers: true is_obo: false prefix: GMD.GCMS uri_format: http://identifiers.org/gmd.gcms/$1 gmd.profile: mappings: miriam: gmd.profile n2t: gmd.profile prefixcommons: GMD.PROFILE miriam: deprecated: false description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues. homepage: http://gmd.mpimp-golm.mpg.de/ id: '00000423' name: Golm Metabolome Database Profile namespaceEmbeddedInLui: false pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ prefix: gmd.profile sampleId: 10b38aaf-b977-4950-85b8-f4775f66658d uri_format: http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1 n2t: description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues. example: 10b38aaf-b977-4950-85b8-f4775f66658d homepage: http://gmd.mpimp-golm.mpg.de/ name: Golm Metabolome Database (Profile) at Max Planck Institute of Molecular Plant Physiology namespaceEmbeddedInLui: false pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ prefix: gmd.profile uri_format: http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1 prefixcommons: is_identifiers: true is_obo: false prefix: GMD.PROFILE uri_format: http://identifiers.org/gmd.profile/$1 gmd.ref: mappings: miriam: gmd.ref n2t: gmd.ref prefixcommons: GMD.REF miriam: deprecated: false description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances. homepage: http://gmd.mpimp-golm.mpg.de/ id: '00000425' name: Golm Metabolome Database Reference Substance namespaceEmbeddedInLui: false pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ prefix: gmd.ref sampleId: 8cf84adb-b4db-4807-ac98-0004247c35df uri_format: http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1 n2t: description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances. example: 8cf84adb-b4db-4807-ac98-0004247c35df homepage: http://gmd.mpimp-golm.mpg.de/ name: Golm Metabolome Database (Reference Substance) at Max Planck Institute of Molecular Plant Physiology namespaceEmbeddedInLui: false pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ prefix: gmd.ref uri_format: http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1 prefixcommons: is_identifiers: true is_obo: false prefix: GMD.REF uri_format: http://identifiers.org/gmd.ref/$1 gmelin: description: The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s. example: '1466' homepage: https://link.springer.com/bookseries/562 name: Gmelins Handbuch der anorganischen Chemie pattern: ^[1-9][0-9]{3,6}$ references: - https://en.wikipedia.org/wiki/Gmelin_database wikidata: prefix: P1578 gno: bioportal: name: Glycan Naming Ontology prefix: GNO example: '10004892' mappings: bioportal: GNO obofoundry: gno ols: gno ontobee: GNO name: Glycan Naming and Subsumption Ontology obofoundry: contact: nje5@georgetown.edu contact.github: edwardsnj contact.label: Nathan Edwards contact.orcid: 0000-0001-5168-3196 deprecated: false description: GlyTouCan provides stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations). GNOme organizes these stable accessions for interative browsing, for text-based searching, and for automated reasoning with well-defined characterization levels. 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 homepage: https://gnome.glyomics.org/ inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Glycan Naming and Subsumption Ontology (GNOme) preferredPrefix: GNO prefix: gno repository: https://github.com/glygen-glycan-data/GNOme ols: description: An ontology for glycans based on GlyTouCan, but organized by subsumption. download: http://purl.obolibrary.org/obo/gno.owl homepage: https://gnome.glyomics.org/ name: Glycan Naming Ontology prefix: gno version: 1.10.0 version.iri: http://purl.obolibrary.org/obo/gno/2022-02-23/gno.owl ontobee: library: Library name: Glycan Naming and Subsumption Ontology (GNOme) prefix: GNO pattern: ^\d{8}$ gnpis: fairsharing: abbreviation: GnpIS description: GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, markers, polymorphisms, germplasms, phenotypes and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Institute for Agricultural Research. It is regularly improved and released several times per year. GnpIS is accessible through a web portal and allows to browse different types of data either independently through dedicated interfaces or simultaneously using a quick search ('google like search') or advanced search (Biomart, Galaxy, Intermine) tools. id: '2263' name: Genetic and Genomic Information System prefix: FAIRsharing.dw22y3 subjects: - Life Science mappings: fairsharing: FAIRsharing.dw22y3 miriam: gnpis n2t: gnpis prefixcommons: GNPIS miriam: deprecated: false 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. homepage: https://urgi.versailles.inra.fr/gnpis/ id: '00000627' name: GnpIS namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9]+$ prefix: gnpis sampleId: AY109603 uri_format: https://urgi.versailles.inra.fr/gnpis/#result/term=$1 n2t: description: GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. example: AY109603 homepage: https://urgi.versailles.inra.fr/gnpis/ name: GnpIS namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9]+$ prefix: gnpis uri_format: https://urgi.versailles.inra.fr/gnpis/#result/term=$1 prefixcommons: is_identifiers: true is_obo: false prefix: GNPIS uri_format: http://identifiers.org/gnpis/$1 go: bioportal: name: Gene Ontology prefix: GO example: '0032571' fairsharing: abbreviation: GO description: The Gene Ontology (GO) is a structured vocabulary for use by the research community for the annotation of genes, gene products and sequences. The GO defines concepts/classes used to describe gene function and relationships between these concepts. id: '1417' name: Gene Ontology prefix: FAIRsharing.6xq0ee subjects: - Life Science go: homepage: http://amigo.geneontology.org/ name: Gene Ontology Database prefix: GO mappings: bioportal: GO fairsharing: FAIRsharing.6xq0ee go: GO miriam: go n2t: go ncbi: GO obofoundry: go ols: go ontobee: GO prefixcommons: GO uniprot: GO miriam: deprecated: false description: The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. homepage: http://amigo.geneontology.org/ id: '00000022' name: Gene Ontology namespaceEmbeddedInLui: true pattern: ^GO:\d{7}$ prefix: go providers: - code: quickgo description: QuickGO (Gene Ontology browser) homepage: https://www.ebi.ac.uk/QuickGO/ name: QuickGO (Gene Ontology browser) uri_format: https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:$1 - code: CURATOR_REVIEW description: GO Browser homepage: http://www.informatics.jax.org/searches/GO_form.shtml name: GO Browser uri_format: http://www.informatics.jax.org/searches/GO.cgi?id=GO:$1 - code: CURATOR_REVIEW description: GO through PANTHER homepage: http://www.pantherdb.org/ name: GO through PANTHER uri_format: http://www.pantherdb.org/panther/category.do?categoryAcc=GO:$1 sampleId: 0006915 uri_format: http://amigo.geneontology.org/amigo/term/GO:$1 n2t: description: The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. example: 0006915 homepage: http://amigo.geneontology.org/ name: AmiGO 2 namespaceEmbeddedInLui: true pattern: ^GO:\d{7}$ prefix: go uri_format: http://amigo.geneontology.org/amigo/term/GO:$1 ncbi: example: '123' homepage: http://amigo.geneontology.org/ name: Gene Ontology Database identifier prefix: GO obofoundry: appears_in: - agro - chiro - cl - ecocore - ecto - envo - maxo - pcl - pco - planp - uberon - xpo - zp contact: suzia@stanford.edu contact.github: suzialeksander contact.label: Suzi Aleksander contact.orcid: 0000-0001-6787-2901 depends_on: - cl - ncbitaxon - ro - uberon deprecated: false description: An ontology for describing the function of genes and gene products download.json: http://purl.obolibrary.org/obo/go.json download.obo: http://purl.obolibrary.org/obo/go.obo download.owl: http://purl.obolibrary.org/obo/go.owl homepage: http://geneontology.org/ inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Gene Ontology preferredPrefix: GO prefix: go publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/10802651 title: 'Gene ontology: tool for the unification of biology. The Gene Ontology Consortium' - id: https://www.ncbi.nlm.nih.gov/pubmed/33290552 title: 'The Gene Ontology resource: enriching a GOld mine' repository: https://github.com/geneontology/go-ontology twitter: news4go ols: description: The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms. download: http://purl.obolibrary.org/obo/go.owl homepage: http://geneontology.org/ name: Gene Ontology prefix: go version: '2022-03-10' version.iri: http://purl.obolibrary.org/obo/go/releases/2022-03-10/go.owl ontobee: library: Foundry name: Gene Ontology prefix: GO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: GO uri_format: http://purl.obolibrary.org/obo/GO_$1 synonyms: - gobp - gobpid - gocc - goccid - gomf - gomfid uniprot: category: Ontologies identifier: '37' link_is_explicit: 'true' name: Gene Ontology prefix: GO uri_format: https://www.ebi.ac.uk/QuickGO/term/$1 wikidata: prefix: P686 go.model: description: "GO-Causal Activity Models (GO-CAMs) use a defined \u201Cgrammar\u201D\ \ for linking multiple GO annotations into larger models of biological function\ \ (such as \u201Cpathways\u201D) in a semantically structured manner. GO-CAMs\ \ are created by expert biocurators from the GO Consortium, using the Noctua Curation\ \ Platform." example: 5fce9b7300001250 go: homepage: http://www.geneontology.org/gocam name: Gene Ontology Causal Activity Model Database prefix: gomodel uri_format: http://www.geneontology.org/gocam/$1 mappings: go: gomodel name: Gene Ontology Causal Assembly Model uri_format: noctua.geneontology.org/editor/graph/gomodel:$1 go.ref: banana: GO_REF go: homepage: http://current.geneontology.org/metadata/gorefs/index.html name: Gene Ontology Database references prefix: GO_REF mappings: go: GO_REF miriam: go_ref n2t: go.ref prefixcommons: GO_REF miriam: deprecated: false description: The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of "GO content" meetings at which substantial changes in the ontologies are discussed and made. homepage: http://www.geneontology.org/cgi-bin/references.cgi id: '00000450' name: Gene Ontology Reference namespaceEmbeddedInLui: true pattern: ^GO_REF:\d{7}$ prefix: go_ref sampleId: '0000041' uri_format: https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-$1.md n2t: description: The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of "GO content" meetings at which substantial changes in the ontologies are discussed and made. example: GO_REF:0000041 homepage: http://www.geneontology.org/cgi-bin/references.cgi name: Gene Ontology Reference at The Gene Ontology Consortium namespaceEmbeddedInLui: false pattern: ^GO_REF:\d{7}$ prefix: go.ref uri_format: http://www.geneontology.org/cgi-bin/references.cgi#$1 pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: false prefix: GO_REF uri_format: http://www.geneontology.org/cgi-bin/references.cgi#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: http://geneontology.org/ name: Gene Ontology Registry uri_format: https://bioregistry.io/metaregistry/go/$1 goa: fairsharing: abbreviation: GOA description: The GO Annotation Database (GOA) provides Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. GOA files contain a mixture of manual annotation supplied by members of the Gene Onotology Consortium and computationally assigned GO terms describing gene products. Annotation type is clearly indicated by associated evidence codes and there are links to the source data. id: '1852' name: Gene Ontology Annotation Database prefix: FAIRsharing.7zffgc subjects: - Life Science - Biology mappings: fairsharing: FAIRsharing.7zffgc miriam: goa n2t: goa ncbi: GOA prefixcommons: GOA miriam: deprecated: false description: The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. homepage: https://www.ebi.ac.uk/GOA/ id: 00000196 name: GOA namespaceEmbeddedInLui: false pattern: ^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$ prefix: goa sampleId: P12345 uri_format: https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1 n2t: description: The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. example: P12345 homepage: https://www.ebi.ac.uk/GOA/ name: GOA through QuickGO namespaceEmbeddedInLui: false pattern: ^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$ prefix: goa uri_format: https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1 name: Gene Ontology Annotation Database ncbi: example: P01100 homepage: http://www.ebi.ac.uk/GOA/ name: Gene Ontology Annotation Database Identifier prefix: GOA prefixcommons: is_identifiers: true is_obo: false prefix: GOA uri_format: http://identifiers.org/goa/$1 provides: uniprot goche: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Represent chemical entities having particular CHEBI roles download_owl: https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl example: '25512' homepage: https://github.com/geneontology/go-ontology name: GO Chemicals pattern: ^\d+$ preferred_prefix: GOCHE references: - https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638472847049400 - https://github.com/geneontology/go-ontology/issues/19535 repository: https://github.com/geneontology/go-ontology synonyms: - go.chebi - go.chemical - go.chemicals goeco: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported. example: IPI homepage: http://geneontology.org/docs/guide-go-evidence-codes/ name: GO Evidence Code gold: fairsharing: abbreviation: GOLD description: 'The Genomes Online Database provides access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.' id: '1661' name: Genomes OnLine Database prefix: FAIRsharing.5q1p14 subjects: - Metagenomics - Genomics - Phylogenetics - Metabolomics mappings: fairsharing: FAIRsharing.5q1p14 miriam: gold miriam: deprecated: false 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.' homepage: https://gold.jgi.doe.gov/ id: '00000733' name: Genomes OnLine Database (GOLD) namespaceEmbeddedInLui: false pattern: ^[A-Z][a-z][0-9]+$ prefix: gold sampleId: Gs0000008 uri_format: https://gold.jgi.doe.gov/resolver?id=$1 name: Genomes Online Database gold.genome: mappings: miriam: gold.genome n2t: gold.genome prefixcommons: GOLD.GENOME miriam: deprecated: false description: "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has\ \ been superseeded by \u2018gold\u2019 prefix at https://registry.identifiers.org/registry/gold,\ \ and this namespace is kept here for support to already existing citations,\ \ new ones would need to use the pointed \u2018gold\u2019 namespace.\n\nThe\ \ GOLD (Genomes OnLine Database)is a resource for centralised monitoring of\ \ genome and metagenome projects worldwide. It stores information on complete\ \ and ongoing projects, along with their associated metadata. This collection\ \ references the sequencing status of individual genomes." homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi id: '00000401' name: GOLD genome namespaceEmbeddedInLui: false pattern: ^(Gi|Gc)\d+$ prefix: gold.genome sampleId: Gi07796 uri_format: http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1 n2t: description: The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes. example: Gi07796 homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi name: GOLD genome at Department of Energy Joint Genome Institute namespaceEmbeddedInLui: false pattern: ^[Gi|Gc]\d+$ prefix: gold.genome uri_format: http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1 prefixcommons: is_identifiers: true is_obo: false prefix: GOLD.GENOME uri_format: http://identifiers.org/gold.genome/$1 gold.meta: mappings: miriam: gold.meta n2t: gold.meta prefixcommons: GOLD.META miriam: deprecated: false description: "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has\ \ been superseeded by \u2018gold\u2019 prefix at https://registry.identifiers.org/registry/gold,\ \ and this namespace is kept here for support to already existing citations,\ \ new ones would need to use the pointed \u2018gold\u2019 namespace. \n\nThe\ \ GOLD (Genomes OnLine Database)is a resource for centralized monitoring of\ \ genome and metagenome projects worldwide. It stores information on complete\ \ and ongoing projects, along with their associated metadata. This collection\ \ references metadata associated with samples." homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi id: '00000402' name: GOLD metadata namespaceEmbeddedInLui: false pattern: ^Gm\d+$ prefix: gold.meta sampleId: Gm00047 uri_format: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1 n2t: description: The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples. example: Gm00047 homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi name: GOLD metadata at Department of Energy Joint Genome Institute namespaceEmbeddedInLui: false pattern: ^Gm\d+$ prefix: gold.meta uri_format: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1 prefixcommons: is_identifiers: true is_obo: false prefix: GOLD.META uri_format: http://identifiers.org/gold.meta/$1 google.patent: cellosaurus: category: Reference resources homepage: https://patents.google.com name: Google Patents prefix: Patent uri_format: https://patents.google.com/patent/$1 mappings: cellosaurus: Patent miriam: google.patent n2t: google.patent prefixcommons: GOOGLE.PATENT miriam: deprecated: false description: Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date. homepage: https://www.google.com/patents/ id: '00000537' name: Google Patents namespaceEmbeddedInLui: false pattern: ^[A-Z]{2}\d+([A-Z])?$ prefix: google.patent sampleId: US4145692 uri_format: https://www.google.com/patents/$1 n2t: description: Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date. example: US4145692 homepage: https://www.google.com/patents/ name: Google Patents at Google namespaceEmbeddedInLui: false pattern: ^[A-Z]{2}\d+([A-Z])?$ prefix: google.patent uri_format: https://www.google.com/patents/$1 prefixcommons: is_identifiers: true is_obo: false prefix: GOOGLE.PATENT uri_format: http://identifiers.org/google.patent/$1 synonyms: - patent google.scholar: biolink: is_identifiers: false is_obo: false prefix: GSID uri_format: https://scholar.google.com/citations?user=$1 description: 'Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.' example: PjrpzUIAAAAJ homepage: https://scholar.google.com/ mappings: biolink: GSID name: Google Scholar Researcher gorel: biolink: is_identifiers: false is_obo: true prefix: GOREL uri_format: http://purl.obolibrary.org/obo/GOREL_$1 description: Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO. download_owl: ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl example: '0002005' go: description: Additional relations pending addition into RO name: GO Extensions to OBO Relation Ontology Ontology prefix: GOREL homepage: http://geneontology.org/docs/ontology-relations/ mappings: biolink: GOREL go: GOREL name: GO Relations pattern: ^\d{7}$ gpcrdb: fairsharing: abbreviation: GPCRdb description: The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). The GPCRDB contains data on sequences, ligand binding constants and mutations. In addition, many different types of computationally derived data are stored such as multiple sequence alignments and homology models. id: '1832' name: Information system for G protein-coupled receptors prefix: FAIRsharing.e4n3an subjects: - Life Science mappings: fairsharing: FAIRsharing.e4n3an miriam: gpcrdb n2t: gpcrdb prefixcommons: GPCRDB uniprot: GPCRDB miriam: deprecated: false 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. homepage: http://www.gpcrdb.org/ id: '00000212' name: GPCRDB namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: gpcrdb sampleId: RL3R1_HUMAN uri_format: http://www.gpcrdb.org/protein/$1/ n2t: description: The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models. example: RL3R1_HUMAN homepage: http://www.gpcrdb.org/ name: GPCRDB at Radboud University namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: gpcrdb uri_format: http://www.gpcrdb.org/protein/$1/ name: G protein-coupled receptor database prefixcommons: is_identifiers: true is_obo: false prefix: GPCRDB uri_format: http://identifiers.org/gpcrdb/$1 uniprot: category: Protein family/group databases identifier: '38' name: Information system for G protein-coupled receptors (GPCRs) prefix: GPCRDB uri_format: https://gpcrdb.org/protein/$1/ uri_format: https://gpcrdb.org/protein/$1 gpmdb: fairsharing: abbreviation: gpmDB description: 'The Global Proteome Machine Database (gpmDB holds the minimum amount of information necessary for common bioinformatics-related tasks (such as sequence assignment validation) rather than being a complete record of a proteomics experiment. It was also created to aid in the process of validating peptide MS/MS spectra as well as protein coverage patterns. Most of the data is held in a set of XML files: the database serves as an index to those files, allowing for rapid lookups and reduced database storage requirements.' id: '1949' name: The Global Proteome Machine Database prefix: FAIRsharing.fhcmwq subjects: - Bioinformatics - Proteomics mappings: fairsharing: FAIRsharing.fhcmwq miriam: gpmdb n2t: gpmdb prefixcommons: GPMDB miriam: deprecated: false description: The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. homepage: http://gpmdb.thegpm.org/ id: 00000649 name: GPMDB namespaceEmbeddedInLui: false pattern: ^GPM\d+$ 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 sampleId: GPM32310002988 uri_format: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1 n2t: description: The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. example: GPM32310002988 homepage: http://gpmdb.thegpm.org/ name: GPMDB namespaceEmbeddedInLui: false pattern: ^GPM\d+$ prefix: gpmdb uri_format: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1 name: Global Proteome Machine Database prefixcommons: is_identifiers: true is_obo: false prefix: GPMDB uri_format: http://identifiers.org/gpmdb/$1 gramene.gene: go: homepage: http://www.gramene.org/ name: Gramene prefix: GR_GENE synonyms: - GR_gene uri_format: http://www.gramene.org/db/genes/search_gene?acc=$1 mappings: go: GR_GENE miriam: gramene.gene n2t: gramene.gene prefixcommons: GRAMENE.GENE miriam: deprecated: false description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene. homepage: http://www.gramene.org/ id: 00000182 name: Gramene genes namespaceEmbeddedInLui: false pattern: ^GR\:\d+$ prefix: gramene.gene sampleId: GR:0080039 uri_format: http://www.gramene.org/db/genes/search_gene?acc=$1 n2t: description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene. example: GR:0080039 homepage: http://www.gramene.org/ name: Gramene Genes at Cold Spring Harbor namespaceEmbeddedInLui: false pattern: ^GR\:\d+$ prefix: gramene.gene uri_format: http://www.gramene.org/db/genes/search_gene?acc=$1 name: Gramene Gene prefixcommons: is_identifiers: true is_obo: false prefix: GRAMENE.GENE uri_format: http://identifiers.org/gramene.gene/$1 synonyms: - GR_GENE gramene.growthstage: banana: gramene.growthstage:GRO\ mappings: miriam: gramene.growthstage n2t: gramene.growthstage prefixcommons: GRAMENE.GROWTHSTAGE miriam: deprecated: false description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene. homepage: http://www.gramene.org/ id: 00000508 name: Gramene Growth Stage Ontology namespaceEmbeddedInLui: true pattern: ^GRO\:\d+$ prefix: gramene.growthstage sampleId: '0007133' uri_format: http://www.gramene.org/db/ontology/search?id=GRO:$1 n2t: description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene. example: '0007133' homepage: http://www.gramene.org/ name: Gramene Growth Stage Ontology at Cold Spring Harbor namespaceEmbeddedInLui: true pattern: ^GRO\:\d+$ prefix: gramene.growthstage uri_format: http://www.gramene.org/db/ontology/search?id=GRO:$1 name: Gramene Growth Stage Ontology pattern: ^\d{7}$ prefixcommons: is_identifiers: true is_obo: false prefix: GRAMENE.GROWTHSTAGE uri_format: http://identifiers.org/gramene.growthstage/$1 uri_format: http://www.gramene.org/db/ontology/search?id=GRO:$1 gramene.protein: go: homepage: http://www.gramene.org/ name: Gramene prefix: GR_PROTEIN synonyms: - GR_protein uri_format: http://www.gramene.org/db/protein/protein_search?acc=$1 mappings: go: GR_PROTEIN miriam: gramene.protein n2t: gramene.protein prefixcommons: GRAMENE.PROTEIN miriam: deprecated: false description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene. homepage: http://www.gramene.org/ id: 00000181 name: Gramene protein namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: gramene.protein sampleId: '78073' uri_format: http://www.gramene.org/db/protein/protein_search?protein_id=$1 n2t: description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene. example: '78073' homepage: http://www.gramene.org/ name: Gramene Protein at Cold Spring Harbor namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: gramene.protein uri_format: http://www.gramene.org/db/protein/protein_search?protein_id=$1 name: Gramene protein prefixcommons: is_identifiers: true is_obo: false prefix: GRAMENE.PROTEIN uri_format: http://identifiers.org/gramene.protein/$1 synonyms: - GR_PROTEIN gramene.qtl: go: homepage: http://www.gramene.org/ name: Gramene prefix: GR_QTL uri_format: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1 mappings: go: GR_QTL miriam: gramene.qtl n2t: gramene.qtl prefixcommons: GRAMENE.QTL miriam: deprecated: false description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene. homepage: http://www.gramene.org/ id: 00000184 name: Gramene QTL namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: gramene.qtl sampleId: CQG5 uri_format: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1 n2t: description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene. example: CQG5 homepage: http://www.gramene.org/ name: Gramene Quantitative Trait Loci at Cold Spring Harbor namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: gramene.qtl uri_format: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1 name: Gramene QTL prefixcommons: is_identifiers: true is_obo: false prefix: GRAMENE.QTL uri_format: http://identifiers.org/gramene.qtl/$1 synonyms: - GR_QTL gramene.taxonomy: mappings: miriam: gramene.taxonomy n2t: gramene.taxonomy prefixcommons: GRAMENE.TAXONOMY miriam: deprecated: false description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene. homepage: http://www.gramene.org/ id: 00000183 name: Gramene Taxonomy namespaceEmbeddedInLui: false pattern: ^GR\_tax\:\d+$ prefix: gramene.taxonomy sampleId: GR_tax:013681 uri_format: http://www.gramene.org/db/ontology/search?id=$1 n2t: description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene. example: GR_tax:013681 homepage: http://www.gramene.org/ name: Gramene Taxonomy at Cold Spring Harbor namespaceEmbeddedInLui: false pattern: ^GR\_tax\:\d+$ prefix: gramene.taxonomy uri_format: http://www.gramene.org/db/ontology/search?id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: GRAMENE.TAXONOMY uri_format: http://identifiers.org/gramene.taxonomy/$1 grassbase: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species. example: imp10873 homepage: https://www.kew.org/data/grasses-syn/index.htm name: GrassBase pattern: ^(imp|gen)\d{5}$ uri_format: https://www.kew.org/data/grasses-db/www/$1 greengenes: fairsharing: abbreviation: Greengenes description: A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. id: '1947' name: Greengenes prefix: FAIRsharing.bpxgb6 subjects: - Genetics - Life Science mappings: fairsharing: FAIRsharing.bpxgb6 miriam: greengenes n2t: greengenes ncbi: Greengenes prefixcommons: GREENGENES miriam: deprecated: false description: A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. homepage: http://greengenes.lbl.gov/ id: '00000165' name: GreenGenes namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: greengenes sampleId: '100000' uri_format: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1 n2t: description: A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. example: '100000' homepage: http://greengenes.lbl.gov/ name: GreenGenes at Lawrence Berkeley namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: greengenes uri_format: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1 ncbi: example: '269185' homepage: http://greengenes.lbl.gov/ name: 16S rRNA gene database prefix: Greengenes prefixcommons: is_identifiers: true is_obo: false prefix: GREENGENES uri_format: http://identifiers.org/greengenes/$1 grid: fairsharing: abbreviation: GRID description: Global Research Identifier Database (GRID) stores information on research-related organisations worldwide. GRID record contains a unique GRID ID, relevant metadata, and relationships between associated institutions. id: '3040' name: Global Research Identifier Database prefix: FAIRsharing.0pUMYW subjects: - Data Management mappings: fairsharing: FAIRsharing.0pUMYW miriam: grid n2t: grid prefixcommons: GRID miriam: deprecated: false description: International coverage of the world's leading research organisations, indexing 92% of funding allocated globally. homepage: https://www.grid.ac/ id: 00000593 name: GRID namespaceEmbeddedInLui: false pattern: ^grid\.[0-9]+\.[a-f0-9]{1,2}$ prefix: grid sampleId: grid.225360.0 uri_format: https://www.grid.ac/institutes/$1 n2t: description: International coverage of the world's leading research organisations, indexing 92% of funding allocated globally. example: grid.225360.0 homepage: https://www.grid.ac/ name: GRID at Digital Science & Research Ltd. namespaceEmbeddedInLui: false pattern: ^grid\.[0-9]+\.[a-f0-9]{1,2}$ prefix: grid uri_format: https://www.grid.ac/institutes/$1 name: Global Research Identifier Database prefixcommons: is_identifiers: true is_obo: false prefix: GRID uri_format: http://identifiers.org/grid/$1 grin.taxonomy: go: homepage: https://www.ars-grin.gov/ name: Germplasm Resources Information Network prefix: GRIN synonyms: - grin uri_format: https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=$1 mappings: go: GRIN miriam: grin.taxonomy n2t: grin.taxonomy ncbi: GRIN prefixcommons: GRIN.TAXONOMY miriam: deprecated: false description: GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact. homepage: http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en id: '00000166' name: GRIN Plant Taxonomy namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: grin.taxonomy sampleId: '19333' uri_format: http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1 n2t: description: GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact. example: '19333' homepage: http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en name: GRIN at Maryland namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: grin.taxonomy uri_format: http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1 ncbi: example: '1005973' homepage: http://www.ars-grin.gov/ name: Germplasm Resources Information Network prefix: GRIN prefixcommons: is_identifiers: true is_obo: false prefix: GRIN.TAXONOMY uri_format: http://identifiers.org/grin.taxonomy/$1 gro: bioportal: name: Gene Regulation Ontology prefix: GRO deprecated: true mappings: bioportal: GRO grsdb: mappings: miriam: grsdb n2t: grsdb prefixcommons: GRSDB miriam: deprecated: false description: GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank. homepage: http://bioinformatics.ramapo.edu/GRSDB2/ id: 00000495 name: GRSDB namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: grsdb sampleId: '10142' uri_format: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1 n2t: description: GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank. example: '10142' homepage: http://bioinformatics.ramapo.edu/GRSDB2/ name: GRSDB v2 at Ramapo College of New Jersey namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: grsdb uri_format: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1 name: G-Rich Sequences Database prefixcommons: is_identifiers: true is_obo: false prefix: GRSDB uri_format: http://identifiers.org/grsdb/$1 gsfa: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The "Codex General Standard for Food Additives" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database. example: '174' homepage: http://www.fao.org/gsfaonline name: General Standard for Food Additives Online Database pattern: ^\d+$ synonyms: - FAO/WHO_standards uri_format: http://www.fao.org/gsfaonline/additives/details.html?id=$1 gsso: bioportal: name: Gender, Sex, and Sexual Orientation Ontology prefix: GSSO mappings: bioportal: GSSO miriam: gsso obofoundry: gsso ols: gsso ontobee: GSSO miriam: deprecated: false description: The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology. homepage: https://bioportal.bioontology.org/ id: '00000712' name: Gender, Sex, and Sexual Orientation (GSSO) Ontology namespaceEmbeddedInLui: true pattern: ^GSSO:\d{6}$ prefix: gsso sampleId: 002368 uri_format: http://purl.obolibrary.org/obo/GSSO_$1 name: Gender, Sex, and Sexual Orientation Ontology obofoundry: appears_in: - ontoavida - scdo contact: kronkcj@mail.uc.edu contact.github: Superraptor contact.label: Clair Kronk contact.orcid: 0000-0001-8397-8810 deprecated: false description: The Gender, Sex, and Sexual Orientation (GSSO) ontology has terms for annotating interdisciplinary information concerning gender, sex, and sexual orientation for primary usage in the biomedical and adjacent sciences. download.json: http://purl.obolibrary.org/obo/gsso.json download.obo: http://purl.obolibrary.org/obo/gsso.obo download.owl: http://purl.obolibrary.org/obo/gsso.owl homepage: https://gsso.research.cchmc.org/ inactive: false license: Apache 2.0 License license.url: http://www.apache.org/licenses/LICENSE-2.0 name: Gender, Sex, and Sexual Orientation (GSSO) ontology preferredPrefix: GSSO prefix: gsso repository: https://github.com/Superraptor/GSSO ols: description: GSSO is the Gender, Sex, and Sex Orientation ontology, including terms related to gender identity and expression, sexual and romantic identity and orientation, and sexual and reproductive behavior. download: http://purl.obolibrary.org/obo/gsso.owl homepage: https://gsso.research.cchmc.org/ name: GSSO - the Gender, Sex, and Sexual Orientation ontology prefix: gsso version: 2.0.5 version.iri: http://purl.obolibrary.org/obo/gsso/releases/2.0.5/gsso.owl ontobee: library: Library name: Gender, Sex, and Sexual Orientation (GSSO) ontology prefix: GSSO pattern: ^\d{6}$ gtex: biolink: is_identifiers: false is_obo: false prefix: GTEx uri_format: https://www.gtexportal.org/home/gene/$1 mappings: biolink: GTEx miriam: gtex n2t: gtex prefixcommons: GTEX miriam: deprecated: false description: The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. homepage: https://www.gtexportal.org id: '00000663' name: GTEx namespaceEmbeddedInLui: false pattern: ^\w.+$ prefix: gtex sampleId: BRIP1 uri_format: https://www.gtexportal.org/home/gene/$1 n2t: description: 'The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. ' example: BRIP1 homepage: https://www.gtexportal.org name: The GTEx Project namespaceEmbeddedInLui: false pattern: ^\w.+$ prefix: gtex uri_format: https://www.gtexportal.org/home/gene/$1 name: Genotype-Tissue Expression prefixcommons: is_identifiers: true is_obo: false prefix: GTEX uri_format: http://identifiers.org/gtex/$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\xAE) 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 synonyms: - medgen.gtr uri_format: https://www.ncbi.nlm.nih.gov/gtr/conditions/$1 gudmap: fairsharing: abbreviation: GUDMAP description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) provides data and tools to facilitate research on the GenitoUrinary (GU) tract for the scientific and medical community. In addition to current GUDMAP data, this resource incorporates data generated by previous phases of GUDMAP and by the (Re)Building a Kidney (RBK) consortium. id: '3324' name: GenitoUrinary Development Molecular Anatomy Project prefix: FAIRsharing.910c39 subjects: - Molecular biology - Genomics - Developmental Biology - Cell Biology mappings: fairsharing: FAIRsharing.910c39 miriam: gudmap n2t: gudmap prefixcommons: GUDMAP miriam: deprecated: false description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract. homepage: http://www.gudmap.org/ id: '00000643' name: GUDMAP namespaceEmbeddedInLui: false pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$ prefix: gudmap sampleId: Q-2958 uri_format: https://gudmap.org/id/$1 n2t: description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract. example: Q-2958 homepage: http://www.gudmap.org/ name: GUDMAP namespaceEmbeddedInLui: false pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$ prefix: gudmap uri_format: https://gudmap.org/id/$1 name: Genitourinary Development Molecular Anatomy Project prefixcommons: is_identifiers: true is_obo: false prefix: GUDMAP uri_format: http://identifiers.org/gudmap/$1 gwascentral.marker: homepage: https://www.gwascentral.org/markers mappings: miriam: gwascentral.marker n2t: gwascentral.marker prefixcommons: GWASCENTRAL.MARKER miriam: deprecated: false description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker. homepage: https://www.gwascentral.org/markers/ id: '00000542' name: GWAS Central Marker namespaceEmbeddedInLui: false pattern: ^HGVM\d+$ prefix: gwascentral.marker sampleId: HGVM15354 uri_format: https://www.gwascentral.org/marker/$1 n2t: description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker. example: HGVM15354 homepage: https://www.gwascentral.org/markers/ name: GWAS Central Marker at University of Leicester namespaceEmbeddedInLui: false pattern: ^HGVM\d+$ prefix: gwascentral.marker uri_format: https://www.gwascentral.org/marker/$1 prefixcommons: is_identifiers: true is_obo: false prefix: GWASCENTRAL.MARKER uri_format: http://identifiers.org/gwascentral.marker/$1 gwascentral.phenotype: homepage: https://www.gwascentral.org/phenotypes mappings: miriam: gwascentral.phenotype n2t: gwascentral.phenotype prefixcommons: GWASCENTRAL.PHENOTYPE miriam: deprecated: false description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype. homepage: https://www.gwascentral.org/phenotypes id: '00000543' name: GWAS Central Phenotype namespaceEmbeddedInLui: false pattern: ^HGVPM\d+$ prefix: gwascentral.phenotype sampleId: HGVPM623 uri_format: https://www.gwascentral.org/phenotype/$1 n2t: description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype. example: HGVPM623 homepage: https://www.gwascentral.org/phenotypes name: GWAS Central Phenotype at University of Leicester namespaceEmbeddedInLui: false pattern: ^HGVP\d+$ prefix: gwascentral.phenotype uri_format: https://www.gwascentral.org/phenotype/$1 pattern: ^HGVPM\d+$ prefixcommons: is_identifiers: true is_obo: false prefix: GWASCENTRAL.PHENOTYPE uri_format: http://identifiers.org/gwascentral.phenotype/$1 gwascentral.study: homepage: https://www.gwascentral.org/studies mappings: miriam: gwascentral.study n2t: gwascentral.study prefixcommons: GWASCENTRAL.STUDY miriam: deprecated: false description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study. homepage: https://www.gwascentral.org/studies id: '00000540' name: GWAS Central Study namespaceEmbeddedInLui: false pattern: ^HGVST\d+$ prefix: gwascentral.study sampleId: HGVST1828 uri_format: https://www.gwascentral.org/study/$1 n2t: description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study. example: HGVST1828 homepage: https://www.gwascentral.org/studies name: GWAS Central Study at University of Leicester namespaceEmbeddedInLui: false pattern: ^HGVST\d+$ prefix: gwascentral.study uri_format: https://www.gwascentral.org/study/$1 prefixcommons: is_identifiers: true is_obo: false prefix: GWASCENTRAL.STUDY uri_format: http://identifiers.org/gwascentral.study/$1 gxa.expt: mappings: miriam: gxa.expt n2t: gxa.expt prefixcommons: GXA.EXPT miriam: deprecated: false description: The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments. homepage: https://www.ebi.ac.uk/gxa/ id: 00000379 name: GXA Expt namespaceEmbeddedInLui: false pattern: ^[AEP]-\w{4}-\d+$ 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 sampleId: E-MTAB-2037 uri_format: https://www.ebi.ac.uk/gxa/experiments/$1 n2t: description: The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments. example: E-MTAB-2037 homepage: https://www.ebi.ac.uk/gxa/ name: GXA Expt at EBI namespaceEmbeddedInLui: false pattern: ^[AEP]-\w{4}-\d+$ prefix: gxa.expt uri_format: https://www.ebi.ac.uk/gxa/experiments/$1 prefixcommons: is_identifiers: true is_obo: false prefix: GXA.EXPT uri_format: http://identifiers.org/gxa.expt/$1 gxa.gene: mappings: miriam: gxa.gene n2t: gxa.gene prefixcommons: GXA.GENE miriam: deprecated: false description: The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes. homepage: https://www.ebi.ac.uk/gxa/ id: 00000378 name: GXA Gene namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: gxa.gene sampleId: AT4G01080 uri_format: https://www.ebi.ac.uk/gxa/genes/$1 n2t: description: The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes. example: AT4G01080 homepage: https://www.ebi.ac.uk/gxa/ name: GXA Gene at EBI namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: gxa.gene uri_format: https://www.ebi.ac.uk/gxa/genes/$1 prefixcommons: is_identifiers: true is_obo: false prefix: GXA.GENE uri_format: http://identifiers.org/gxa.gene/$1 habronattus: mappings: obofoundry: habronattus prefixcommons: HABRONATTUS obofoundry: contact: peteremidford@yahoo.com contact.label: Peter Midford contact.orcid: 0000-0001-6512-3296 deprecated: true homepage: http://www.mesquiteproject.org/ontology/Habronattus/index.html inactive: true name: Habronattus courtship prefix: habronattus prefixcommons: is_identifiers: false is_obo: true prefix: HABRONATTUS uri_format: http://purl.obolibrary.org/obo/HABRONATTUS_$1 hamap: fairsharing: abbreviation: HAMAP description: 'HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.' id: '2059' name: HAMAP database of microbial protein families prefix: FAIRsharing.63m4ss subjects: - Life Science go: homepage: http://hamap.expasy.org/ name: High-quality Automated and Manual Annotation of microbial Proteomes prefix: HAMAP uri_format: http://hamap.expasy.org/unirule/$1 mappings: fairsharing: FAIRsharing.63m4ss go: HAMAP miriam: hamap n2t: hamap prefixcommons: HAMAP uniprot: HAMAP miriam: deprecated: false description: HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries. homepage: https://hamap.expasy.org/ id: 00000292 name: HAMAP namespaceEmbeddedInLui: false pattern: ^MF_\d+$ prefix: hamap sampleId: MF_01400 uri_format: https://hamap.expasy.org/unirule/$1 n2t: description: HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries. example: MF_01400 homepage: https://hamap.expasy.org/ name: HAPMAP at Swiss Institute of Bioinformatics namespaceEmbeddedInLui: false pattern: ^MF_\d+$ prefix: hamap uri_format: https://hamap.expasy.org/unirule/$1 prefixcommons: is_identifiers: true is_obo: false prefix: HAMAP uri_format: http://identifiers.org/hamap/$1 uniprot: category: Family and domain databases identifier: '41' link_is_explicit: 'true' name: HAMAP database of protein families prefix: HAMAP uri_format: https://hamap.expasy.org/signature/$1 hancestro: biolink: is_identifiers: false is_obo: false prefix: HANCESTRO uri_format: http://www.ebi.ac.uk/ancestro/ancestro_$1 bioportal: name: Human Ancestry Ontology prefix: HANCESTRO example: 0290 fairsharing: abbreviation: HANCESTRO description: The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies. id: '681' name: Human Ancestry Ontology prefix: FAIRsharing.rja8qp subjects: - Demographics - Human Genetics - Population Genetics mappings: biolink: HANCESTRO bioportal: HANCESTRO fairsharing: FAIRsharing.rja8qp obofoundry: hancestro ols: hancestro ontobee: HANCESTRO obofoundry: contact: danielle.welter@uni.lu contact.github: daniwelter contact.label: Danielle Welter contact.orcid: 0000-0003-1058-2668 deprecated: false description: The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies. download.owl: http://purl.obolibrary.org/obo/hancestro.owl homepage: https://github.com/EBISPOT/ancestro inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Human Ancestry Ontology preferredPrefix: HANCESTRO prefix: hancestro publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/29448949 title: A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog repository: https://github.com/EBISPOT/ancestro ols: description: Human ancestry ontology for the NHGRI GWAS Catalog download: http://purl.obolibrary.org/obo/hancestro.owl homepage: https://github.com/EBISPOT/ancestro name: Human Ancestry Ontology prefix: hancestro version: '2.5' version.iri: http://purl.obolibrary.org/obo/hancestro/releases/2020-12-18/hancestro.owl ontobee: library: Library name: Human Ancestry Ontology prefix: HANCESTRO pattern: ^\d{4}$ hao: bioportal: name: Hymenoptera Anatomy Ontology prefix: HAO example: 0000187 fairsharing: abbreviation: HAO description: The Hymenoptera Anatomy Ontology is a structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) id: '219' name: Hymenoptera Anatomy Ontology prefix: FAIRsharing.kj3m5n subjects: - Anatomy - Life Science mappings: bioportal: HAO fairsharing: FAIRsharing.kj3m5n obofoundry: hao ols: hao ontobee: HAO prefixcommons: HAO obofoundry: contact: diapriid@gmail.com contact.github: mjy contact.label: Matt Yoder contact.orcid: 0000-0002-5640-5491 deprecated: false 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 homepage: http://hymao.org inactive: false license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Hymenoptera Anatomy Ontology preferredPrefix: HAO prefix: hao publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/21209921 title: A gross anatomy ontology for hymenoptera repository: https://github.com/hymao/hao ols: description: A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) download: http://purl.obolibrary.org/obo/hao.owl homepage: http://hymao.org name: Hymenoptera Anatomy Ontology prefix: hao version: '2021-03-05' version.iri: http://purl.obolibrary.org/obo/hao/2021-03-05/hao.owl ontobee: library: Library name: Hymenoptera Anatomy Ontology prefix: HAO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: HAO uri_format: http://purl.obolibrary.org/obo/HAO_$1 hba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A controlled vocabulary to support the study of transcription in the human brain download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-hba.obo example: '4005' example_extras: - '265504410' homepage: https://human.brain-map.org name: Human Brain Atlas pattern: ^\d+$ preferred_prefix: HBA hcao: homepage: https://www.humancellatlas.org mappings: ols: hcao no_own_terms: true ols: description: Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas. download: https://raw.githubusercontent.com/ebi-ait/ontology/master/hcao.owl name: Human Cell Atlas Ontology prefix: hcao version: '2022-04-19' version.iri: http://ontology.data.humancellatlas.org/ontologies/hcao/releases/2022-04-19/hcao.owl hcpcs: biolink: is_identifiers: false is_obo: false prefix: HCPCS uri_format: http://purl.bioontology.org/ontology/HCPCS/$1 bioportal: name: Healthcare Common Procedure Coding System prefix: HCPCS description: HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers. example: G8944 fairsharing: abbreviation: HCPCS description: Each year, in the United States, health care insurers process over 5 billion claims for payment. For Medicare and other health insurance programs to ensure that these claims are processed in an orderly and consistent manner, standardized coding systems are essential. The HCPCS is divided into two principal subsystems, referred to as level I and level II of the HCPCS. Level I of the HCPCS is comprised of CPT (Current Procedural Terminology), a numeric coding system maintained by the American Medical Association (AMA). Level II of the HCPCS is a standardized coding system that is used primarily to identify products, supplies, and services not included in the CPT codes, such as ambulance services and durable medical equipment, prosthetics, orthotics, and supplies (DMEPOS) when used outside a physician's office. id: '1006' name: Healthcare Common Procedure Coding System prefix: FAIRsharing.x81wz8 subjects: - Business Administration - Biomedical Science homepage: https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo mappings: biolink: HCPCS bioportal: HCPCS fairsharing: FAIRsharing.x81wz8 name: Healthcare Common Procedure Coding System hcvdb: homepage: http://euhcvdb.ibcp.fr mappings: miriam: hcvdb n2t: hcvdb prefixcommons: HCVDB miriam: deprecated: false description: the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses. homepage: http://euhcvdb.ibcp.fr/euHCVdb/ id: '00000207' name: HCVDB namespaceEmbeddedInLui: false pattern: ^M\d{5}$ prefix: hcvdb sampleId: M58335 uri_format: https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1 n2t: description: the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses. example: M58335 homepage: http://euhcvdb.ibcp.fr/euHCVdb/ name: HCVDB at CNRS namespaceEmbeddedInLui: false pattern: ^M\d{5}$ prefix: hcvdb uri_format: https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1 name: Hepatitis C Virus Database prefixcommons: is_identifiers: true is_obo: false prefix: HCVDB uri_format: http://identifiers.org/hcvdb/$1 hdr: mappings: miriam: hdr n2t: hdr prefixcommons: HDR miriam: deprecated: false description: The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders. homepage: http://research.nhgri.nih.gov/apps/homeodomain/web/ id: 00000497 name: Homeodomain Research namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: hdr sampleId: '63' uri_format: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1 n2t: description: The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders. example: '63' homepage: http://research.nhgri.nih.gov/apps/homeodomain/web/ name: Homeodomain Research at National Human Genome Research Institute (NIH) namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: hdr uri_format: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: HDR uri_format: http://identifiers.org/hdr/$1 hgmd: mappings: miriam: hgmd n2t: hgmd prefixcommons: HGMD miriam: deprecated: false description: The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases. homepage: http://www.hgmd.cf.ac.uk/ac/index.php id: 00000392 name: HGMD namespaceEmbeddedInLui: false pattern: ^[A-Z_0-9]+$ prefix: hgmd sampleId: CALM1 uri_format: http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1 n2t: description: The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases. example: CALM1 homepage: http://www.hgmd.cf.ac.uk/ac/index.php name: HGMD at Cardiff University namespaceEmbeddedInLui: false pattern: ^[A-Z_0-9]+$ prefix: hgmd uri_format: http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1 name: Human Gene Mutation Database prefixcommons: is_identifiers: false is_obo: false prefix: HGMD uri_format: http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1 hgnc: bioportal: name: HUGO Gene Nomenclature prefix: HGNC cellosaurus: category: Organism-specific databases homepage: https://www.genenames.org name: Human Gene Nomenclature Committee Database prefix: HGNC uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$1 example: '16793' fairsharing: abbreviation: HGNC description: The HGNC approves both a short-form abbreviation known as a gene symbol, and also a longer and more descriptive name. Each symbol is unique and the committee ensures that each gene is only given one approved gene symbol. This allows for clear and unambiguous reference to genes in scientific communications, and facilitates electronic data retrieval from databases and publications. id: '741' name: HGNC Gene Symbols, Gene Names and IDs prefix: FAIRsharing.amcv1e subjects: - Life Science go: homepage: http://www.genenames.org/ name: HUGO Gene Nomenclature Committee prefix: HGNC uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$1 homepage: http://www.genenames.org mappings: bioportal: HGNC cellosaurus: HGNC fairsharing: FAIRsharing.amcv1e go: HGNC miriam: hgnc n2t: hgnc ncbi: HGNC prefixcommons: HGNC uniprot: HGNC miriam: deprecated: false description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database. homepage: https://www.genenames.org id: 00000080 name: HGNC namespaceEmbeddedInLui: false pattern: ^((HGNC|hgnc):)?\d{1,5}$ prefix: hgnc sampleId: '2674' uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1 n2t: description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database. example: '2674' homepage: https://www.genenames.org name: HUGO Genome Nomenclature Committee namespaceEmbeddedInLui: false pattern: ^((HGNC|hgnc):)?\d{1,5}$ prefix: hgnc uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1 name: HUGO Gene Nomenclature Committee ncbi: example: HGNC:2041 homepage: http://www.genenames.org/cgi-bin/search name: Human Gene Nomenclature Database prefix: HGNC prefixcommons: is_identifiers: false is_obo: false prefix: HGNC uri_format: http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$1 providers: - code: indra description: A large scale database of biomedical statements. homepage: https://db.indra.bio name: INDRA Database uri_format: https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@HGNC uniprot: category: Organism-specific databases comment: Replacement for Genew identifier: '42' link_is_explicit: 'true' name: Human Gene Nomenclature Database prefix: HGNC uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1 wikidata: prefix: P354 hgnc.genefamily: example: '2029' has_canonical: hgnc.genegroup homepage: http://www.genenames.org mappings: miriam: hgnc.family n2t: hgnc.genefamily prefixcommons: HGNC.GENEFAMILY miriam: deprecated: true description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides symbols for both structural and functional gene families. This collection refers to records using the HGNC family symbol. id: '00000520' name: HGNC Family namespaceEmbeddedInLui: false pattern: ^[A-Z0-9-]+(#[A-Z0-9-]+)?$ prefix: hgnc.family sampleId: PADI n2t: 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/ name: HGNC gene family at HUGO Genome Nomenclature Committee namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: hgnc.genefamily uri_format: https://www.genenames.org/cgi-bin/genefamilies/set/$1 prefixcommons: is_identifiers: true is_obo: false prefix: HGNC.GENEFAMILY uri_format: http://identifiers.org/hgnc.genefamily/$1 synonyms: - GFAM - HGNC_GROUP - hgnc.family hgnc.genegroup: mappings: miriam: hgnc.genegroup miriam: deprecated: false description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families. homepage: https://www.genenames.org id: 00000709 name: HGNC Gene Group namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: hgnc.genegroup sampleId: '141' uri_format: https://www.genenames.org/cgi-bin/genefamilies/set/$1 hgnc.symbol: mappings: miriam: hgnc.symbol n2t: hgnc.symbol prefixcommons: HGNC.SYMBOL miriam: deprecated: false description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol. homepage: https://www.genenames.org/ id: '00000362' name: HGNC Symbol namespaceEmbeddedInLui: false pattern: ^[A-Za-z-0-9_]+(\@)?$ prefix: hgnc.symbol sampleId: DAPK1 uri_format: https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1 n2t: description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol. example: DAPK1 homepage: https://www.genenames.org/ name: HGNC Symbol at HUGO Genome Nomenclature Committee namespaceEmbeddedInLui: false pattern: ^[A-Za-z-0-9_]+(\@)?$ prefix: hgnc.symbol uri_format: https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1 prefixcommons: is_identifiers: true is_obo: false prefix: HGNC.SYMBOL uri_format: http://identifiers.org/hgnc.symbol/$1 providers: - code: depmap description: DepMap summary of the given gene homepage: https://depmap.org name: DepMap Gene Summary uri_format: https://depmap.org/portal/gene/$1 - code: pathwaycommons description: Interactions between a given gene and other molecular entities homepage: https://www.pathwaycommons.org/ name: Pathway Commons Gene Interations uri_format: https://apps.pathwaycommons.org/interactions?source=$1 - code: oncomx description: Mutation profiles for a gene homepage: https://oncomx.org name: OncoMX uri_format: https://oncomx.org/searchview/?gene=$1 hinv.locus: mappings: miriam: hinv.locus n2t: hinv.locus prefixcommons: HINV.LOCUS miriam: deprecated: false description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view. homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp id: '00000167' name: H-InvDb Locus namespaceEmbeddedInLui: false pattern: ^HIX\d{7}(\.\d+)?$ prefix: hinv.locus sampleId: HIX0004394 uri_format: http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1 n2t: description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view. example: HIX0004394 homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp name: H-Invitational Locus View at BIRC namespaceEmbeddedInLui: false pattern: ^HIX\d{7}(\.\d+)?$ prefix: hinv.locus uri_format: http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: HINV.LOCUS uri_format: http://identifiers.org/hinv.locus/$1 hinv.protein: mappings: miriam: hinv.protein n2t: hinv.protein prefixcommons: HINV.PROTEIN miriam: deprecated: false description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view. homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp id: 00000169 name: H-InvDb Protein namespaceEmbeddedInLui: false pattern: ^HIP\d{9}(\.\d+)?$ prefix: hinv.protein sampleId: HIP000030660 uri_format: http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1 n2t: description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view. example: HIP000030660 homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp name: H-Invitational Protein View at BIRC namespaceEmbeddedInLui: false pattern: ^HIP\d{9}(\.\d+)?$ prefix: hinv.protein uri_format: http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: HINV.PROTEIN uri_format: http://identifiers.org/hinv.protein/$1 hinv.transcript: mappings: miriam: hinv.transcript n2t: hinv.transcript prefixcommons: HINV.TRANSCRIPT miriam: deprecated: false description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view. homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp id: 00000168 name: H-InvDb Transcript namespaceEmbeddedInLui: false pattern: ^HIT\d{9}(\.\d+)?$ prefix: hinv.transcript sampleId: HIT000195363 uri_format: http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1 n2t: description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view. example: HIT000195363 homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp name: H-Invitational Transcript View at BIRC namespaceEmbeddedInLui: false pattern: ^HIT\d{9}(\.\d+)?$ prefix: hinv.transcript uri_format: http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: HINV.TRANSCRIPT uri_format: http://identifiers.org/hinv.transcript/$1 hipsci: cellosaurus: category: Cell line databases/resources homepage: http://www.hipsci.org name: Human Induced Pluripotent Stem Cells Initiative prefix: HipSci uri_format: http://www.hipsci.org/lines/#/lines/$1 example: HPSI0114i-bezi_1 mappings: cellosaurus: HipSci hivreagentprogram: cellosaurus: category: Cell line collections homepage: https://www.hivreagentprogram.org/Home.aspx name: NIH HIV Reagent Program prefix: HIVReagentProgram uri_format: https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx example: ARP-1513 mappings: cellosaurus: HIVReagentProgram hmdb: cheminf: description: Database identifier used by Human Metabolome Database. name: HMDB obsolete: false prefix: 000408 fairsharing: abbreviation: HMDB description: The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data. id: '2084' name: The Human Metabolome Database prefix: FAIRsharing.sye5js subjects: - Molecular biology - Biochemistry - Life Science - Metabolomics mappings: cheminf: 000408 fairsharing: FAIRsharing.sye5js miriam: hmdb n2t: hmdb prefixcommons: HMDB wikidata: P2057 miriam: deprecated: false description: The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data. homepage: http://www.hmdb.ca/ id: '00000051' name: HMDB namespaceEmbeddedInLui: false pattern: ^HMDB\d+$ prefix: hmdb sampleId: HMDB00001 uri_format: http://www.hmdb.ca/metabolites/$1 n2t: description: The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data. example: HMDB00001 homepage: http://www.hmdb.ca/ name: The Human Metabolome Database namespaceEmbeddedInLui: false pattern: ^HMDB\d+$ prefix: hmdb uri_format: http://www.hmdb.ca/metabolites/$1 name: Human Metabolome Database prefixcommons: is_identifiers: false is_obo: false prefix: HMDB uri_format: http://www.hmdb.ca/metabolites/$1 synonyms: - HMDB wikidata: database: Q5937262 database.homepage: https://hmdb.ca database.label: Human Metabolome Database name: Human Metabolome Database ID pattern: HMDB\d+ prefix: P2057 uri_format: https://www.hmdb.ca/metabolites/$1 hms.lincs.compound: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols. example: 10001-101 homepage: https://lincs.hms.harvard.edu/db/sm/ name: HMS LINCS Compound synonyms: - HMS-LINCS - hmsl_id uri_format: https://lincs.hms.harvard.edu/db/sm/$1 hog: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc. download_obo: ftp://ftp.bgee.org/general/ontologies/HOG.obo example: '0000255' homepage: https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships name: Homologous Organ Groups pattern: ^\d{7}$ hogenom: fairsharing: abbreviation: HOGENOM description: HOGENOM is a phylogenomic database providing families of homologous genes and associated phylogenetic trees (and sequence alignments) for a wide set sequenced organisms. id: '2033' name: HOGENOM prefix: FAIRsharing.qe8tz8 subjects: - Phylogeny - Phylogenetics - Life Science mappings: fairsharing: FAIRsharing.qe8tz8 miriam: hogenom n2t: hogenom prefixcommons: HOGENOM uniprot: HOGENOM miriam: deprecated: false 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. homepage: http://pbil.univ-lyon1.fr/databases/hogenom/ id: '00000213' name: HOGENOM namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: hogenom sampleId: HBG284870 uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1 n2t: description: HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier. example: HBG284870 homepage: http://pbil.univ-lyon1.fr/databases/hogenom/ name: HOGENOM at CNRS namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: hogenom uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1 name: Database of Complete Genome Homologous Genes Families prefixcommons: is_identifiers: true is_obo: false prefix: HOGENOM uri_format: http://identifiers.org/hogenom/$1 uniprot: category: Phylogenomic databases identifier: '44' link_is_explicit: 'true' name: The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms prefix: HOGENOM uri_format: http://hogenom.univ-lyon1.fr/query_sequence?seq=$1 hom: bioportal: name: Ontology of Homology and Related Concepts in Biology prefix: HOM example: 0000049 fairsharing: abbreviation: HOM description: This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. id: '48' name: HOMology prefix: FAIRsharing.efv7gw subjects: - Anatomy - Life Science mappings: bioportal: HOM fairsharing: FAIRsharing.efv7gw obofoundry: hom ols: hom ontobee: HOM prefixcommons: HOM obofoundry: contact: bgee@sib.swiss contact.github: fbastian contact.label: Frederic Bastian contact.orcid: 0000-0002-9415-5104 deprecated: false description: This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. download.owl: http://purl.obolibrary.org/obo/hom.owl homepage: https://github.com/BgeeDB/homology-ontology inactive: false license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Homology Ontology preferredPrefix: HOM prefix: hom repository: https://github.com/BgeeDB/homology-ontology ols: description: This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. download: http://purl.obolibrary.org/obo/hom.owl homepage: https://github.com/BgeeDB/homology-ontology name: Homology Ontology prefix: hom version: '2015-01-07' version.iri: http://purl.obolibrary.org/obo/hom/releases/2015-01-07/hom.owl ontobee: library: Library name: Homology Ontology prefix: HOM pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: HOM uri_format: http://purl.obolibrary.org/obo/HOM_$1 homd.seq: mappings: miriam: homd.seq n2t: homd.seq prefixcommons: HOMD.SEQ miriam: deprecated: false description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information. homepage: http://www.homd.org/index.php id: '00000170' name: HOMD Sequence Metainformation namespaceEmbeddedInLui: false pattern: ^SEQF\d+$ prefix: homd.seq sampleId: SEQF1003 uri_format: http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1 n2t: description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information. example: SEQF1003 homepage: http://www.homd.org/index.php name: HOMD sequence metainformation at The Forsyth Institute namespaceEmbeddedInLui: false pattern: ^SEQF\d+$ prefix: homd.seq uri_format: http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1 prefixcommons: is_identifiers: true is_obo: false prefix: HOMD.SEQ uri_format: http://identifiers.org/homd.seq/$1 homd.taxon: mappings: miriam: homd.taxon n2t: homd.taxon prefixcommons: HOMD.TAXON miriam: deprecated: false description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information. homepage: http://www.homd.org/index.php id: '00000171' name: HOMD Taxonomy namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: homd.taxon sampleId: '811' uri_format: http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$1&view=dynamic n2t: description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information. example: '811' homepage: http://www.homd.org/index.php name: HOMD taxon information at The Forsyth Institute namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: homd.taxon uri_format: http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$1&view=dynamic prefixcommons: is_identifiers: true is_obo: false prefix: HOMD.TAXON uri_format: http://identifiers.org/homd.taxon/$1 uri_format: www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1 homologene: fairsharing: abbreviation: HomoloGene description: HomoloGene is an automated system for the detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. HomoloGene takes protein sequences from differing species and compares them to one another (using blastp) and matches are placed into groups, using a tree built from sequence similarity to guide the process, where closer related organisms are matched up first, and then further organisms are added as the tree is traversed toward the root. The protein alignments are mapped back to their corresponding DNA sequences, where distance metrics can be calculated (e.g. molecular distance, Ka/Ks ratio). Sequences are matched using synteny when applicable. Remaining sequences are matched up by using an algorithm for maximizing the score globally, rather than locally, in a bipartite matching. Cutoffs on bits per position and Ks values are set to prevent unlikely "orthologs" from being grouped together. These cutoffs are calculated based on the respective score distribution for the given groups of organisms. Paralogs are identified by finding sequences that are closer within species than other species. id: '1977' name: NCBI HomoloGene Database prefix: FAIRsharing.mzc066 subjects: - Life Science mappings: fairsharing: FAIRsharing.mzc066 miriam: homologene n2t: homologene prefixcommons: HOMOLOGENE wikidata: P593 miriam: deprecated: false description: HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. homepage: https://www.ncbi.nlm.nih.gov/homologene/ id: '00000275' name: HomoloGene namespaceEmbeddedInLui: false pattern: ^\d+$ 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 sampleId: '1000' uri_format: https://www.ncbi.nlm.nih.gov/homologene/$1 n2t: description: HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. example: '1000' homepage: https://www.ncbi.nlm.nih.gov/homologene/ name: Homologene at NCBI namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: homologene uri_format: https://www.ncbi.nlm.nih.gov/homologene/$1 name: HomoloGene prefixcommons: is_identifiers: false is_obo: false prefix: HOMOLOGENE uri_format: http://www.ncbi.nlm.nih.gov/homologene/$1 wikidata: database: Q468215 database.homepage: http://www.ncbi.nlm.nih.gov/homologene database.label: HomoloGene homepage: http://www.ncbi.nlm.nih.gov/homologene name: HomoloGene ID pattern: '[1-9]\d{0,5}' prefix: P593 uri_format: https://www.ncbi.nlm.nih.gov/homologene?term=$1 horizon_discovery: cellosaurus: category: Cell line collections homepage: https://horizondiscovery.com/ name: Horizon Discovery cell line collection prefix: Horizon_Discovery uri_format: https://horizondiscovery.com/en/search?searchterm=$1 example: HD+118-001 mappings: cellosaurus: Horizon_Discovery hovergen: fairsharing: abbreviation: HOVERGEN description: HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees. id: '2034' name: Homologous Vertebrate Genes Database prefix: FAIRsharing.dg1f0e subjects: - Life Science homepage: https://pbil.univ-lyon1.fr/databases/hovergen.php mappings: fairsharing: FAIRsharing.dg1f0e miriam: hovergen n2t: hovergen prefixcommons: HOVERGEN miriam: deprecated: false description: HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees. homepage: http://pbil.univ-lyon1.fr/databases/hovergen.php id: '00000074' name: HOVERGEN namespaceEmbeddedInLui: false pattern: ^HBG\d+$ prefix: hovergen sampleId: HBG004341 uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN n2t: description: HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees. example: HBG004341 homepage: http://pbil.univ-lyon1.fr/databases/hovergen.php name: Hovergen namespaceEmbeddedInLui: false pattern: ^HBG\d+$ prefix: hovergen uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN name: Homologous Vertebrate Genes Database prefixcommons: is_identifiers: true is_obo: false prefix: HOVERGEN uri_format: http://identifiers.org/hovergen/$1 hp: bioportal: name: Human Phenotype Ontology prefix: HP download_obo: http://purl.obolibrary.org/obo/hp.obo example: '0011140' fairsharing: abbreviation: HP description: The Human Phenotype Ontology has been developed to provide a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. The goal is to provide resource for the computational analysis of the human phenome, with a focus on monogenic diseases listed in the Online Mendelian Inheritance in Man (OMIM) and Orphanet databases, for which annotations are also provided. id: '757' name: Human Phenotype Ontology prefix: FAIRsharing.kbtt7f subjects: - Genetics - Phenomics - Biomedical Science - Preclinical Studies mappings: bioportal: HP fairsharing: FAIRsharing.kbtt7f miriam: hp n2t: hp obofoundry: hp ols: hp ontobee: HP prefixcommons: HPO wikidata: P3841 miriam: deprecated: false description: The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. homepage: http://human-phenotype-ontology.github.io/ id: '00000571' name: Human Phenotype Ontology namespaceEmbeddedInLui: true pattern: ^HP:\d{7}$ prefix: hp sampleId: 0000118 uri_format: https://hpo.jax.org/app/browse/term/HP:$1 n2t: description: The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. example: 0000118 homepage: http://human-phenotype-ontology.github.io/ name: Human Phenotype Ontology at Institute for Medical Genetics and Human Genetics namespaceEmbeddedInLui: true pattern: ^HP:\d{7}$ prefix: hp uri_format: http://compbio.charite.de/hpoweb/showterm?id=HP:$1 obofoundry: appears_in: - chiro - scdo contact: dr.sebastian.koehler@gmail.com contact.github: drseb contact.label: Sebastian Koehler contact.orcid: 0000-0002-5316-1399 deprecated: false description: A structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. download.obo: http://purl.obolibrary.org/obo/hp.obo download.owl: http://purl.obolibrary.org/obo/hp.owl homepage: http://www.human-phenotype-ontology.org/ inactive: false license: hpo license.url: https://hpo.jax.org/app/license name: Human Phenotype Ontology preferredPrefix: HP prefix: hp publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/18950739 title: 'The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.' - id: https://www.ncbi.nlm.nih.gov/pubmed/26119816 title: 'The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.' - id: https://www.ncbi.nlm.nih.gov/pubmed/24217912 title: 'The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.' - id: https://www.ncbi.nlm.nih.gov/pubmed/30476213 title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. repository: https://github.com/obophenotype/human-phenotype-ontology twitter: hp_ontology ols: description: The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities and clinical features encountered in human disease. download: http://purl.obolibrary.org/obo/hp.owl homepage: http://www.human-phenotype-ontology.org/ name: Human Phenotype Ontology prefix: hp version: '2022-04-14' version.iri: http://purl.obolibrary.org/obo/hp/releases/2022-04-14/hp.owl ontobee: library: Library name: Human Phenotype Ontology prefix: HP pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: false prefix: HPO uri_format: http://human-phenotype-ontology.org/$1 synonyms: - hpo wikidata: database: Q17027854 database.homepage: http://www.human-phenotype-ontology.org/ database.label: Human Phenotype Ontology homepage: http://human-phenotype-ontology.github.io/about.html name: Human Phenotype Ontology ID pattern: HP:[0-9]{7} prefix: P3841 uri_format: https://hpo.jax.org/app/browse/term/$1 hpa: fairsharing: abbreviation: HPA description: 'The Human Protein Atlas (HPA) portal is a publicly available database with millions of high-resolution images showing the spatial distribution of proteins in a number of different wild-type tissues, cancer types and human cell lines. The goal of the HPA is to map all the human proteins in cells, tissues and organs using an integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. The HPA is composed of six parts: the Tissue Atlas, the Single Cell Type Atlas, the Pathology Atlas, the Blood Atlas, the Brain Atlas, and the Cell Atlas.' id: '1945' name: Human Protein Atlas prefix: FAIRsharing.j0t0pe subjects: - Proteomics - Transcriptomics - Biomedical Science - Systems Biology go: homepage: http://www.proteinatlas.org/ name: Human Protein Atlas tissue profile information prefix: HPA uri_format: http://www.proteinatlas.org/tissue_profile.php?antibody_id=$1 mappings: fairsharing: FAIRsharing.j0t0pe go: HPA miriam: hpa n2t: hpa prefixcommons: HPA uniprot: HPA miriam: deprecated: false description: The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers. homepage: http://www.proteinatlas.org/ id: '00000336' name: HPA namespaceEmbeddedInLui: false pattern: ^ENSG\d{11}$ prefix: hpa sampleId: ENSG00000026508 uri_format: http://www.proteinatlas.org/$1 n2t: description: The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers. example: ENSG00000026508 homepage: http://www.proteinatlas.org/ name: Human Protein Atlas at AlbaNova University namespaceEmbeddedInLui: false pattern: ^ENSG\d{11}$ prefix: hpa uri_format: http://www.proteinatlas.org/$1 prefixcommons: is_identifiers: true is_obo: false prefix: HPA uri_format: http://identifiers.org/hpa/$1 uniprot: category: Organism-specific databases identifier: '46' link_is_explicit: 'true' name: Human Protein Atlas prefix: HPA uri_format: https://www.proteinatlas.org/$1 hpath: example: '2000191' mappings: ols: hpath ols: description: An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species. download: https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo homepage: https://github.com/Novartis/hpath name: Histopathology Ontology prefix: hpath version: '2019-07-05' pattern: ^\d+$ repository: https://github.com/Novartis/hpath synonyms: - MC hpm.peptide: mappings: miriam: hpm.peptide n2t: hpm.peptide prefixcommons: HPM.PEPTIDE miriam: deprecated: false 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. homepage: http://www.humanproteomemap.org/index.php id: '00000527' name: Human Proteome Map Peptide namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: hpm.peptide sampleId: '9606117' uri_format: http://www.humanproteomemap.org/spectrum.php?pep_id=$1 n2t: description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra. example: '9606117' homepage: http://www.humanproteomemap.org/index.php name: Human Proteome Map Peptide at Institute of Bioinformatics (Bangalore) namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: hpm.peptide uri_format: http://www.humanproteomemap.org/spectrum.php?pep_id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: HPM.PEPTIDE uri_format: http://identifiers.org/hpm.peptide/$1 hpm.protein: mappings: miriam: hpm.protein n2t: hpm.protein prefixcommons: HPM.PROTEIN miriam: deprecated: false description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins. homepage: http://www.humanproteomemap.org/index.php id: '00000526' name: Human Proteome Map Protein namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: hpm.protein sampleId: '1968' uri_format: http://www.humanproteomemap.org/protein.php?hpm_id=$1 n2t: description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins. example: '1968' homepage: http://www.humanproteomemap.org/index.php name: Human Proteome Map Protein at Institute of Bioinformatics (Bangalore) namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: hpm.protein uri_format: http://www.humanproteomemap.org/protein.php?hpm_id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: HPM.PROTEIN uri_format: http://identifiers.org/hpm.protein/$1 hprd: fairsharing: abbreviation: HPRD description: The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. id: '1930' name: Human Protein Reference Database prefix: FAIRsharing.y2qws7 subjects: [] mappings: fairsharing: FAIRsharing.y2qws7 miriam: hprd n2t: hprd prefixcommons: HPRD miriam: deprecated: false description: The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. homepage: http://www.hprd.org/ id: '00000377' name: HPRD namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: hprd sampleId: '00001' uri_format: http://www.hprd.org/protein/$1 n2t: description: The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. example: '00001' homepage: http://www.hprd.org/ name: Human Protein Reference Database namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: hprd uri_format: http://www.hprd.org/protein/$1 name: Human Protein Reference Database prefixcommons: is_identifiers: false is_obo: false prefix: HPRD uri_format: http://www.hprd.org/protein/$1 hpscreg: cellosaurus: category: Cell line databases/resources homepage: https://hpscreg.eu name: Human Pluripotent Stem Cell Registry prefix: hPSCreg uri_format: https://hpscreg.eu/cell-line/$1 fairsharing: abbreviation: hPSCreg description: The human pluripotent stem cell registry (hPSCreg) is a public registry and data portal for human embryonic and induced pluripotent stem cell lines (hESC and hiPSC). The Registry provides comprehensive and standardized biological and legal information as well as tools to search and compare information from multiple hPSC sources and hence addresses a translational research need. To facilitate unambiguous identification over different resources, hPSCreg automatically creates a unique standardized name for each cell line registered. In addition to biological information, hPSCreg stores extensive data about ethical standards regarding cell sourcing and conditions for application and privacy protection. hPSCreg is the first global registry that holds both, manually validated scientific and ethical information on hPSC lines, and provides access by means of a user-friendly, mobile-ready web application. id: '2664' name: Human Pluripotent Stem Cell Registry prefix: FAIRsharing.7C0aVE subjects: - Life Science - Biomedical Science mappings: cellosaurus: hPSCreg fairsharing: FAIRsharing.7C0aVE miriam: hpscreg n2t: hpscreg miriam: deprecated: false description: hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines). homepage: https://hpscreg.eu/ id: '00000674' name: Human Pluripotent Stem Cell Registry namespaceEmbeddedInLui: false pattern: ^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$ prefix: hpscreg sampleId: BCRTi001-A uri_format: https://hpscreg.eu/cell-line/$1 n2t: description: hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines). example: BCRTi001-A homepage: https://hpscreg.eu/ name: Human Pluripotent Stem Cell Registry namespaceEmbeddedInLui: false pattern: ^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$ prefix: hpscreg uri_format: https://hpscreg.eu/cell-line/$1 hsapdv: biolink: is_identifiers: false is_obo: true prefix: HsapDv uri_format: http://purl.obolibrary.org/obo/HsapDv_$1 bioportal: name: Human Developmental Stages Ontology prefix: HSAPDV example: 0000194 fairsharing: abbreviation: HSAPDV description: Life cycle stages for Human. HsapDv was developed by the Bgee group with assistance from the core Uberon developers and the Human developmental anatomy ontology (EHDAA2) developers. Currently it includes both embryonic (Carnegie) stages and adult stages. id: '804' name: Human Developmental Stages Ontology prefix: FAIRsharing.c6vhm3 subjects: [] mappings: biolink: HsapDv bioportal: HSAPDV fairsharing: FAIRsharing.c6vhm3 obofoundry: hsapdv ols: hsapdv ontobee: HSAPDV prefixcommons: HSAPDV obofoundry: appears_in: - scdo contact: frederic.bastian@unil.ch contact.github: fbastian contact.label: "Fr\xE9d\xE9ric Bastian" contact.orcid: 0000-0002-9415-5104 deprecated: false description: Life cycle stages for Human download.obo: http://purl.obolibrary.org/obo/hsapdv.obo download.owl: http://purl.obolibrary.org/obo/hsapdv.owl homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Human Developmental Stages preferredPrefix: HsapDv prefix: hsapdv repository: https://github.com/obophenotype/developmental-stage-ontologies ols: description: Life cycle stages for Human download: http://purl.obolibrary.org/obo/hsapdv.owl homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv name: Human Developmental Stages prefix: hsapdv version: '2020-03-10' version.iri: http://purl.obolibrary.org/obo/hsapdv/releases/2020-03-10/hsapdv.owl ontobee: library: Library name: Human Developmental Stages prefix: HSAPDV pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: HSAPDV uri_format: http://purl.obolibrary.org/obo/HSAPDV_$1 synonyms: - HsapDv hsdb: description: The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. example: '5621' homepage: https://pubchem.ncbi.nlm.nih.gov/source/hsdb name: Hazardous Substances Data Bank pattern: ^\d+$ uri_format: https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1 wikidata: prefix: P2062 hso: bioportal: name: Health Surveillance Ontology prefix: HSO example: '0000062' mappings: bioportal: HSO obofoundry: hso ols: hso ontobee: HSO obofoundry: contact: fernanda.dorea@sva.se contact.github: nandadorea contact.label: Fernanda Dorea contact.orcid: 0000-0001-8638-8525 depends_on: - bfo - ncbitaxon - obi - ro - uberon deprecated: false description: The health Surveillance Ontology (HSO) focuses on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance. download.owl: http://purl.obolibrary.org/obo/hso.owl homepage: https://w3id.org/hso inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Health Surveillance Ontology preferredPrefix: HSO prefix: hso repository: https://github.com/SVA-SE/HSO ols: description: The health Surveillance Ontology (HSO) focuses on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance. download: http://purl.obolibrary.org/obo/hso.owl homepage: https://w3id.org/hso name: Health Surveillance Ontology prefix: hso version: '2021-12-13' version.iri: http://purl.obolibrary.org/obo/hso/2021-12-13/hso.owl ontobee: library: Library name: Health Surveillance Ontology prefix: HSO pattern: ^\d{7}$ hssp: mappings: miriam: hssp n2t: hssp ncbi: HSSP prefixcommons: HSSP miriam: deprecated: false 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. homepage: http://swift.cmbi.kun.nl/swift/hssp/ id: '00000215' name: HSSP namespaceEmbeddedInLui: false pattern: ^\w{4}$ 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 sampleId: 102l uri_format: ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2 n2t: description: HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein. example: 102l homepage: ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/ name: HSSP at CMBI namespaceEmbeddedInLui: false pattern: ^\w{4}$ prefix: hssp uri_format: ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$1.hssp.bz2 ncbi: example: 12GS name: Database of homology-derived secondary structure of proteins prefix: HSSP prefixcommons: is_identifiers: true is_obo: false prefix: HSSP uri_format: http://identifiers.org/hssp/$1 htn: bioportal: name: Hypertension Ontology prefix: HTN example: '00000014' mappings: bioportal: HTN obofoundry: htn ols: htn ontobee: HTN obofoundry: contact: aellenhicks@gmail.com contact.github: aellenhicks contact.label: Amanda Hicks contact.orcid: 0000-0002-1795-5570 deprecated: false description: An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines download.owl: http://purl.obolibrary.org/obo/htn.owl homepage: https://github.com/aellenhicks/htn_owl inactive: false license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Hypertension Ontology preferredPrefix: HTN prefix: htn repository: https://github.com/aellenhicks/htn_owl ols: description: An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines download: http://purl.obolibrary.org/obo/htn.owl homepage: https://github.com/aellenhicks/htn_owl name: Hypertension Ontology For Clinical Data prefix: htn version: '2019-06-10' ontobee: library: Library name: Hypertension Ontology prefix: HTN pattern: ^\d{8}$ huge: fairsharing: abbreviation: HUGE description: HUGE is a database for human large proteins newly identified in the Kazusa cDNA project, the aim of which is to predict the primary structure of proteins from the sequences of human large cDNAs (>4 kb). id: '1941' name: Human Unidentified Gene-Encoded large proteins database prefix: FAIRsharing.zx2ztd subjects: - Computational Biology - Life Science mappings: fairsharing: FAIRsharing.zx2ztd miriam: huge n2t: huge prefixcommons: HUGE uniprot: HUGE miriam: deprecated: false 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. homepage: http://www.kazusa.or.jp/huge/ id: '00000263' name: HUGE namespaceEmbeddedInLui: false pattern: ^KIAA\d{4}$ prefix: huge sampleId: KIAA0001 uri_format: http://www.kazusa.or.jp/huge/gfpage/$1/ n2t: description: The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. example: KIAA0001 homepage: http://www.kazusa.or.jp/huge/ name: HUGE at Kazusa DNA Research Institute namespaceEmbeddedInLui: false pattern: ^KIAA\d{4}$ prefix: huge uri_format: http://www.kazusa.or.jp/huge/gfpage/$1/ name: Human Unidentified Gene-Encoded prefixcommons: is_identifiers: true is_obo: false prefix: HUGE uri_format: http://identifiers.org/huge/$1 uniprot: category: Organism-specific databases identifier: '49' name: Human Unidentified Gene-Encoded large proteins database prefix: HUGE uri_format: http://www.kazusa.or.jp/huge/gfpage/$1 uri_format: https://www.kazusa.or.jp/huge/gfpage/$1 iao: bioportal: name: Information Artifact Ontology prefix: IAO fairsharing: abbreviation: IAO description: The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. id: '58' name: Information Artifact Ontology prefix: FAIRsharing.gq1xtx subjects: - Knowledge and Information Systems - Data Management - Subject Agnostic - Biomedical Science go: description: Ontology of information entities, including ontology metadata relations. name: Information Artifact Ontology prefix: IAO mappings: bioportal: IAO fairsharing: FAIRsharing.gq1xtx go: IAO miriam: iao n2t: iao obofoundry: iao ols: iao ontobee: IAO prefixcommons: IAO miriam: deprecated: false description: An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch. homepage: http://www.ontobee.org/ontology/IAO id: '00000603' name: Information Artifact Ontology namespaceEmbeddedInLui: false pattern: ^\d{7}$ prefix: iao sampleId: '0000030' uri_format: http://purl.obolibrary.org/obo/IAO_$1 n2t: description: An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch. example: '0000030' homepage: http://www.ontobee.org/ontology/IAO name: IAO through Ontobee namespaceEmbeddedInLui: false pattern: ^\d{7}$ prefix: iao uri_format: http://purl.obolibrary.org/obo/IAO_$1 obofoundry: appears_in: - agro - clyh - duo - ecocore - ecto - fovt - labo - maxo - pco - psdo - xpo contact: jiezheng@pennmedicine.upenn.edu contact.github: zhengj2007 contact.label: Jie Zheng contact.orcid: 0000-0002-2999-0103 deprecated: false description: An ontology of information entities. download.owl: http://purl.obolibrary.org/obo/iao.owl homepage: https://github.com/information-artifact-ontology/IAO/ inactive: false license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Information Artifact Ontology preferredPrefix: IAO prefix: iao repository: https://github.com/information-artifact-ontology/IAO ols: description: The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. download: http://purl.obolibrary.org/obo/iao.owl homepage: https://github.com/information-artifact-ontology/IAO/ name: Information Artifact Ontology (IAO) prefix: iao version: '2020-12-09' version.iri: http://purl.obolibrary.org/obo/iao/2020-12-09/iao.owl ontobee: library: Library name: Information Artifact Ontology prefix: IAO prefixcommons: is_identifiers: false is_obo: true prefix: IAO uri_format: http://purl.obolibrary.org/obo/IAO_$1 icd10: biolink: is_identifiers: false is_obo: false prefix: ICD10 uri_format: https://icd.codes/icd9cm/$1 bioportal: name: International Classification of Diseases, Version 10 prefix: ICD10 fairsharing: abbreviation: ICD-10 description: The ICD is the international standard diagnostic classification for all general epidemiological, many health management purposes and clinical use. ICD-10 is the 10th revision of the International Statistical Classification of Diseases and Related Health Problems (ICD), a medical classification list by the World Health Organization (WHO). It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases. id: '1315' name: International Classification of Diseases Version 10 prefix: FAIRsharing.nj16g subjects: - Health Science - Global Health - Biomedical Science - Epidemiology homepage: https://icd.who.int/browse10 mappings: biolink: ICD10 bioportal: ICD10 fairsharing: FAIRsharing.nj16g miriam: icd n2t: icd prefixcommons: ICD miriam: deprecated: false description: The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes. homepage: http://www.who.int/classifications/icd/en/ id: 00000009 name: ICD namespaceEmbeddedInLui: false pattern: ^[A-Z]\d+(\.[-\d+])?$ prefix: icd sampleId: C34 uri_format: http://apps.who.int/classifications/icd10/browse/2010/en#/$1 n2t: description: The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes. example: C34 homepage: http://www.who.int/classifications/icd/en/ name: International Statistical Classification of Diseases and Related Health Problems namespaceEmbeddedInLui: false pattern: ^[A-Z]\d+(\.[-\d+])?$ prefix: icd uri_format: http://apps.who.int/classifications/icd10/browse/2010/en#/$1 name: International Classification of Diseases, 10th Revision prefixcommons: is_identifiers: true is_obo: false prefix: ICD uri_format: http://identifiers.org/icd/$1 references: - https://icdcodelookup.com/icd-10/codes/A01.1 synonyms: - ICD - ICD-10 - ICD10 wikidata: prefix: P494 icd10cm: bioportal: name: International Classification of Diseases, Version 10 - Clinical Modification prefix: ICD10CM description: ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States. example: F4521 fairsharing: abbreviation: ICD-10-CM description: The International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) is a morbidity classification for classifying diagnoses and reason for visits in all American health care settings. The ICD-10-CM is based on the ICD-10, the statistical classification of disease published by the World Health Organization (WHO) which replaces ICD-9. ICD-10-CM replaced ICD-9-CM Volumes 1 and 2 from October 2015 onwards. id: '1523' name: International Classification of Diseases, Tenth Revision, Clinical Modification prefix: FAIRsharing.hpvbxb subjects: - Medicine - Health Science - Biomedical Science homepage: https://www.icd10data.com/ICD10CM mappings: bioportal: ICD10CM fairsharing: FAIRsharing.hpvbxb name: International Classification of Diseases, 10th Revision, Clinical Modification synonyms: - ICD10CM uri_format: https://icd.codes/icd10cm/$1 wikidata: prefix: P4229 icd10pcs: bioportal: name: International Classification of Diseases, Version 10 - Procedure Coding System prefix: ICD10PCS description: 'ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis. ICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records.' example: 01N50ZZ fairsharing: abbreviation: ICD-10-PCS description: The ICD-10 Procedure Coding System (ICD-10-PCS) is an international system of medical classification used for procedural coding. The ICD-10-PCS is a procedure classification published by the United States for classifying procedures performed in hospital inpatient health care settings. The ICD-10-PCS replaces the procedural coding portion (Volume 3) of ICD-9-CM. id: '1522' name: International Classification of Diseases Version 10 - Procedure Coding System prefix: FAIRsharing.85k1jm subjects: - Health Science - Biomedical Science - Epidemiology homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10PCS mappings: bioportal: ICD10PCS fairsharing: FAIRsharing.85k1jm name: International Classification of Diseases, 10th Revision, Procedure Coding System uri_format: https://www.findacode.com/code.php?set=ICD10PCS&c=$1 wikidata: prefix: P1690 icd11: description: Diagnostic tool for epidemiology, health management and clinical purposes, maintained by the World Health Organization (WHO). It provides a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease. example: RA01.0 fairsharing: abbreviation: ICD 11 description: The International Classification of Diseases (ICD) was created to allow the recording, reporting and grouping of conditions and factors that influence health. It contains categories for diseases, health related conditions, and external causes of illness or death. The purpose of the ICD is to allow the systematic recording, analysis, interpretation and comparison of mortality and morbidity data collected in different countries or areas and at different times. The ICD is used to translate diagnoses of diseases and other health problems into an alphanumeric code, which allows storage, retrieval, and analysis of the data. The ICD has become the international standard diagnostic classification for all general epidemiological and many health management purposes. ICD-11 was released in 2018 to allow Member States to prepare for implementation, including translating ICD into their national languages. Member States will start reporting using ICD-11 on 1 January 2022. id: '1188' name: International Classification of Diseases Version 11 prefix: FAIRsharing.97805c subjects: - Health Science - Global Health - Biomedical Science - Epidemiology homepage: https://icd.who.int/ mappings: fairsharing: FAIRsharing.97805c name: International Classification of Diseases, 11th Revision synonyms: - ICD-11 uri_format: https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1 wikidata: prefix: P7807 icd9: biolink: is_identifiers: false is_obo: false prefix: ICD9 uri_format: http://translator.ncats.nih.gov/ICD9_$1 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 name: International Classification of Diseases, 9th Revision synonyms: - ICD9 - ICD9_2005 - MTHICD9_2006 uri_format: http://www.icd9data.com/getICD9Code.ashx?icd9=$1 wikidata: prefix: P493 icd9cm: bioportal: name: International Classification of Diseases, Version 9 - Clinical Modification prefix: ICD9CM description: ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States. example: '784' fairsharing: abbreviation: ICD-9-CM description: The ICD is the international standard diagnostic classification for all general epidemiological, many health management purposes and clinical use. The International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) is an adaption created by the U.S. National Center for Health Statistics (NCHS) and used in assigning diagnostic and procedure codes associated with inpatient, outpatient, and physician office utilization in the United States. The ICD-9-CM is based on the ICD-9 but provides for additional morbidity detail. id: '1208' name: International Classification of Diseases, Ninth Revision, Clinical Modification prefix: FAIRsharing.10zsxb subjects: - Medicine - Health Science - Biomedical Science - Epidemiology - Preclinical Studies homepage: https://www.cdc.gov/nchs/icd/icd9cm.htm mappings: bioportal: ICD9CM fairsharing: FAIRsharing.10zsxb name: International Classification of Diseases, 9th Revision, Clinical Modification pattern: ^([\dA-Z]\d{2}(\.\d{1,3}|))|(\d{2}(\.\d{1,2}|))$ synonyms: - IC9CM - ICD9CM - ICD9CM_2005 - ICD9CM_2005 - ICD9CM_2006 - ICDCM_2005 uri_format: http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1 wikidata: prefix: P1692 icdc: fairsharing: abbreviation: ICDC description: The Integrated Climate Data Center (ICDC) allows easy access to climate relevant data from in-situ measurements and satellite remote sensing. These data are important to determine the status and the changes in the climate system. Some relevant re-analysis data are included, which are modeled on the basis of observational data. id: '3094' name: Integrated Climate Data Center prefix: FAIRsharing.d95034 subjects: - Social Science - Meteorology - Earth Science - Atmospheric Science - Remote Sensing - Oceanography mappings: fairsharing: FAIRsharing.d95034 miriam: icdc miriam: deprecated: false description: The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer. homepage: https://caninecommons.cancer.gov/#/ id: 00000812 name: Integrated Canine Data Commons namespaceEmbeddedInLui: false pattern: ^\d{6}$ prefix: icdc sampleId: 000009 uri_format: https://caninecommons.cancer.gov/#/study/$1 icdo: description: The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases example: 9861/3 homepage: https://www.who.int/classifications/icd/adaptations/oncology/en/ name: International Classification of Diseases for Oncology pattern: ^[8-9]\d{3}(/[0-3])?$ 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=$1 wikidata: prefix: P563 iceberg.element: mappings: miriam: iceberg.element n2t: iceberg.element prefixcommons: ICEBERG.ELEMENT miriam: deprecated: false description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements. homepage: http://db-mml.sjtu.edu.cn/ICEberg/ id: 00000469 name: ICEberg element namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: iceberg.element sampleId: '100' uri_format: http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1 n2t: description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements. example: '100' homepage: http://db-mml.sjtu.edu.cn/ICEberg/ name: ICEberg element at Shanghai Jiaotong University namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: iceberg.element uri_format: http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: ICEBERG.ELEMENT uri_format: http://identifiers.org/iceberg.element/$1 iceberg.family: mappings: miriam: iceberg.family n2t: iceberg.family prefixcommons: ICEBERG.FAMILY miriam: deprecated: false description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families. homepage: http://db-mml.sjtu.edu.cn/ICEberg/ id: '00000470' name: ICEberg family namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: iceberg.family sampleId: '1' uri_format: http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$1 n2t: description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families. example: '1' homepage: http://db-mml.sjtu.edu.cn/ICEberg/ name: ICEberg family at Shanghai Jiaotong University namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: iceberg.family uri_format: http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: ICEBERG.FAMILY uri_format: http://identifiers.org/iceberg.family/$1 iceo: bioportal: name: Integrative and Conjugative Element Ontology prefix: ICEO example: '0000712_1' example_extras: - '0000712' mappings: bioportal: ICEO obofoundry: iceo ols: iceo ontobee: ICEO obofoundry: contact: liumeng94@sjtu.edu.cn contact.github: Lemon-Liu contact.label: Meng LIU contact.orcid: 0000-0003-3781-6962 deprecated: false description: ICEO is an integrated biological ontology for the description of bacterial integrative and conjugative elements (ICEs). download.owl: http://purl.obolibrary.org/obo/iceo.owl homepage: https://github.com/ontoice/ICEO inactive: false license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Integrative and Conjugative Element Ontology preferredPrefix: ICEO prefix: iceo repository: https://github.com/ontoice/ICEO ols: description: A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning. download: http://purl.obolibrary.org/obo/iceo.owl homepage: https://github.com/ontoice/ICEO name: 'ICEO: Ontology of Integrative and Conjugative Elements' prefix: iceo version: '2.1' ontobee: library: Library name: Integrative and Conjugative Element Ontology prefix: ICEO pattern: ^\d{7}(_\d)?$ icepo: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. ' download_obo: https://download.nextprot.org/pub/current_release/controlled_vocabularies/icepo.obo example: '0000002' homepage: https://download.nextprot.org/pub/current_release/controlled_vocabularies/ name: Ion Channel Electrophysiology Ontology pattern: ^\d{7}$ references: - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4823818/ twitter: neXtProt_news iclc: cellosaurus: category: Cell line collections homepage: http://www.iclc.it name: Interlab Cell Line Collection prefix: ICLC uri_format: http://www.iclc.it/details/det_list.php?line_id=$1 example: ATL98012 mappings: cellosaurus: ICLC ico: bioportal: name: Informed Consent Ontology prefix: ICO example: '0000066' fairsharing: abbreviation: ICO description: Informed Consent Ontology (ICO) represents the documentations and processes involved in informed consent. ICO aims to support informed consent data integration and reasoning in the clinical research space. The core terms of ICO covers informed consent forms, the component inside the informed consent form, and various informed consent processes. id: '651' name: Informed Consent Ontology prefix: FAIRsharing.b9znd5 subjects: - Medicine - Health Science - Biomedical Science mappings: bioportal: ICO fairsharing: FAIRsharing.b9znd5 obofoundry: ico ols: ico ontobee: ICO prefixcommons: ICO obofoundry: appears_in: - scdo contact: yongqunh@med.umich.edu contact.github: yongqunh contact.label: Yongqun Oliver He contact.orcid: 0000-0001-9189-9661 deprecated: false description: An ontology of clinical informed consents download.owl: http://purl.obolibrary.org/obo/ico.owl homepage: https://github.com/ICO-ontology/ICO inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Informed Consent Ontology preferredPrefix: ICO prefix: ico repository: https://github.com/ICO-ontology/ICO ols: description: The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field. download: http://purl.obolibrary.org/obo/ico.owl homepage: https://github.com/ICO-ontology/ICO name: Informed Consent Ontology (ICO) prefix: ico version: 1.0.187 version.iri: http://purl.obolibrary.org/obo/2020-08-27/ico.owl ontobee: library: Library name: Informed Consent Ontology prefix: ICO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: ICO uri_format: http://purl.obolibrary.org/obo/ICO_$1 ideal: fairsharing: abbreviation: IDEAL description: IDEAL (Intrinsically Disordered proteins with Extensive Annotations and Literature) is a collection of experimentally-verified intrinsically disordered proteins (IDPs) that cannot adopt stable globular structures under physiological conditions. IDEAL contains manually curated annotations on IDPs in locations, structures, and functional sites such as protein binding regions and post-translational modification sites together with references and structural domain assignments. id: '1597' name: Intrinsically Disordered proteins with Extensive Annotations and Literature prefix: FAIRsharing.h3y42f subjects: - Biology homepage: https://www.ideal-db.org mappings: fairsharing: FAIRsharing.h3y42f miriam: ideal n2t: ideal prefixcommons: IDEAL uniprot: IDEAL miriam: deprecated: false description: IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. homepage: http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/ id: 00000398 name: IDEAL namespaceEmbeddedInLui: false pattern: ^IID\d+$ prefix: ideal sampleId: IID00001 uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1 n2t: description: IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. example: IID00001 homepage: http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/ name: IDEAL at Maebashi Institute of Technology namespaceEmbeddedInLui: false pattern: ^IID\d+$ prefix: ideal uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/idealItem.php?id=$1 name: Intrinsically Disordered proteins with Extensive Annotations and Literature prefixcommons: is_identifiers: true is_obo: false prefix: IDEAL uri_format: http://identifiers.org/ideal/$1 uniprot: category: Family and domain databases identifier: '251' link_is_explicit: 'true' name: Intrinsically Disordered proteins with Extensive Annotations and Literature prefix: IDEAL uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1 ido: bioportal: name: Infectious Disease Ontology prefix: IDO fairsharing: abbreviation: IDO description: The IDO ontologies are designed as a set of interoperable ontologies that will together provide coverage of the infectious disease domain. At the core of the set is a general Infectious Disease Ontology (IDO-Core) of entities relevant to both biomedical and clinical aspects of most infectious diseases. Sub-domain specific extensions of IDO-Core complete the set providing ontology coverage of entities relevant to specific pathogens or diseases. id: '1275' name: Infectious Disease Ontology Core prefix: FAIRsharing.aae3v6 subjects: - Molecular Infection Biology - Biomedical Science - Preclinical Studies mappings: bioportal: IDO fairsharing: FAIRsharing.aae3v6 miriam: ido n2t: ido obofoundry: ido ols: ido ontobee: IDO prefixcommons: IDO miriam: deprecated: false description: Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases. homepage: https://www.ebi.ac.uk/ols/ontologies/ido id: '00000677' name: Infectious Disease Ontology namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: ido sampleId: '0000504' uri_format: https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1 n2t: description: Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases. example: '0000504' homepage: https://www.ebi.ac.uk/ols/ontologies/ido name: IDO through OLS namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: ido uri_format: https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1 obofoundry: appears_in: - scdo contact: Lindsay.Cowell@utsouthwestern.edu contact.github: lgcowell contact.label: Lindsay Cowell contact.orcid: 0000-0003-1617-8244 deprecated: false description: A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology that hosts terms of general relevance across the domain, while extension ontologies host terms to specific to a particular part of the domain. download.owl: http://purl.obolibrary.org/obo/ido.owl homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology inactive: false license: CC BY 3.0 license.url: https://creativecommons.org/licenses/by/3.0/ name: Infectious Disease Ontology preferredPrefix: IDO prefix: ido repository: https://github.com/infectious-disease-ontology/infectious-disease-ontology ols: description: A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology that hosts terms of general relevance across the domain, while extension ontologies host terms to specific to a particular part of the domain. download: http://purl.obolibrary.org/obo/ido.owl homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology name: Infectious Disease Ontology prefix: ido version: '2017-11-03' version.iri: http://purl.obolibrary.org/obo/ido/2017-11-03/ido.owl ontobee: library: Library name: Infectious Disease Ontology prefix: IDO prefixcommons: is_identifiers: false is_obo: true prefix: IDO uri_format: http://purl.obolibrary.org/obo/IDO_$1 idocovid19: bioportal: name: The COVID-19 Infectious Disease Ontology prefix: IDO-COVID-19 contact: email: johnbeverley2021@u.northwestern.edu github: johnbeve name: John Beverly orcid: 0000-0002-1118-1738 example: 0001191 mappings: bioportal: IDO-COVID-19 ols: idocovid19 ols: contact: johnbeverley2021@u.northwestern.edu description: The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease. download: https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19 homepage: https://github.com/infectious-disease-ontology-extensions/ido-covid-19 name: The COVID-19 Infectious Disease Ontology prefix: idocovid19 version: '2020-07-21' version.iri: http://purl.obolibrary.org/obo/2020-21-07/ido-covid-19.owl pattern: ^\d{7}$ repository: https://github.com/infectious-disease-ontology-extensions/ido-covid-19 idoden: bioportal: name: Dengue Fever Ontology prefix: IDODEN description: An ontology for dengue fever. example: '0003463' fairsharing: abbreviation: IDODEN description: An ontology for dengue fever. id: '756' name: Dengue Fever Ontology prefix: FAIRsharing.askzq4 subjects: [] homepage: https://bioportal.bioontology.org/ontologies/IDODEN mappings: bioportal: IDODEN fairsharing: FAIRsharing.askzq4 name: Dengue Fever Ontology pattern: ^\d{7}$ references: - https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003479 idomal: bioportal: name: Malaria Ontology prefix: IDOMAL download_obo: http://purl.obolibrary.org/obo/idomal.obo example: '0002350' fairsharing: abbreviation: IDOMAL description: An application ontology for malaria extending the infectious disease ontology (IDO). With about half a billion cases, of which nearly one million fatal ones, malaria constitutes one of the major infectious diseases worldwide. A recently revived effort to eliminate the disease also focuses on IT resources for its efficient control, which prominently includes the control of the mosquito vectors that transmit the Plasmodium pathogens. As part of this effort, IDOMAL has been developed and it is continually being updated. id: '549' name: Infection Disease Ontology Malaria prefix: FAIRsharing.2q8c28 subjects: - Molecular Infection Biology - Life Science - Biomedical Science mappings: bioportal: IDOMAL fairsharing: FAIRsharing.2q8c28 obofoundry: idomal ols: idomal ontobee: IDOMAL prefixcommons: IDOMAL obofoundry: appears_in: - scdo contact: topalis@imbb.forth.gr contact.label: Pantelis Topalis deprecated: false 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 homepage: https://www.vectorbase.org/ontology-browser inactive: true license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Malaria Ontology prefix: idomal repository: https://github.com/VEuPathDB-ontology/IDOMAL ols: description: An application ontology to cover all aspects of malaria as well as the intervention attempts to control it. download: http://purl.obolibrary.org/obo/idomal.owl homepage: https://www.vectorbase.org/ontology-browser name: Malaria Ontology prefix: idomal version: '2015-03-16' version.iri: http://purl.obolibrary.org/obo/idomal/2015-03-16/idomal.owl ontobee: library: Library name: Malaria Ontology prefix: IDOMAL pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: IDOMAL uri_format: http://purl.obolibrary.org/obo/IDOMAL_$1 idoo: mappings: miriam: idoo n2t: idoo miriam: deprecated: false description: Identifiers.org Ontology homepage: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology id: 00000683 name: Identifiers.org Ontology namespaceEmbeddedInLui: false pattern: ^[0-9a-zA-Z]+$ prefix: idoo sampleId: DataCollection uri_format: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1 n2t: description: Identifiers.org Ontology example: DataCollection homepage: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology name: Identifiers.org Ontology namespaceEmbeddedInLui: false pattern: ^[0-9a-zA-Z]+$ prefix: idoo uri_format: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1 idot: homepage: http://biomodels.net/vocab/idot.rdf mappings: miriam: idot n2t: idot prefixcommons: IDOT miriam: deprecated: false description: Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets. homepage: https://identifiers.org/ id: 00000519 name: Identifiers.org Terms namespaceEmbeddedInLui: false pattern: ^[A-Za-z]+$ prefix: idot sampleId: identifierPattern uri_format: https://biomodels.net/vocab/idot.rdf#$1 n2t: description: Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets. example: identifierPattern homepage: https://identifiers.org/ name: IdoT via biomodels.net namespaceEmbeddedInLui: false pattern: ^[A-Za-z]+$ prefix: idot uri_format: https://biomodels.net/vocab/idot.rdf#$1 prefixcommons: is_identifiers: true is_obo: false prefix: IDOT uri_format: http://identifiers.org/idot/$1 uri_format: https://biomodels.net/vocab/idot.rdf#$1 idpo: contact: email: f.quaglia@ibiom.cnr.it github: federicaquaglia name: Federica Quaglia orcid: 0000-0002-0341-4888 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR. example: '00056' homepage: https://www.disprot.org/ontology name: Intrinsically Disordered Proteins Ontology pattern: ^\d{5}$ uri_format: https://www.disprot.org/idpo/IDPO:$1 idr: fairsharing: abbreviation: IDR description: "IDR is a prototype platform for publishing, mining and integrating\ \ bioimaging data at scale, following the Euro-BioImaging/ELIXIR imaging strategy\ \ using the OMERO and Bio-Formats open source software built by the Open Microscopy\ \ Environment. Deployed on an OpenStack cloud running on the EMBL-EBI\u2019\ s Embassy resource, it includes image data linked to independent studies from\ \ genetic, RNAi, chemical, localisation and geographic high content screens,\ \ super-resolution microscopy, and digital pathology." id: '2303' name: Image Data Resource prefix: FAIRsharing.6wf1zw subjects: - Botany - Life Science - Biomedical Science mappings: fairsharing: FAIRsharing.6wf1zw miriam: idr miriam: deprecated: false description: "Image Data Resource (IDR) is an online, public data repository that\ \ seeks to store, integrate and serve image datasets from published scientific\ \ studies. We have collected and are continuing to receive existing and newly\ \ created \u201Creference image\" datasets that are valuable resources for a\ \ broad community of users, either because they will be frequently accessed\ \ and cited or because they can serve as a basis for re-analysis and the development\ \ of new computational tools." homepage: https://idr.openmicroscopy.org id: '00000743' name: Image Data Resource namespaceEmbeddedInLui: false pattern: ^[0-9]{4}$ prefix: idr sampleId: '0001' uri_format: https://idr.openmicroscopy.org/search/?query=Name:idr$1 iedb: fairsharing: abbreviation: IEDB description: The IEDB provides the scientific community with a central repository of freely accessible epitope data and epitope prediction and analysis resources. The IEDB is a publicly accessible, comprehensive immune epitope database containing peptidic linear and conformational epitopes and non peptidic epitopes such as lipids, metals, drugs, carbohydrates, etc, with published or submitted antibody, T cell, MHC binding or MHC ligand elution experimental assays. Epitope data related to infectious diseases, allergy, autoimmunity and transplant tested in humans, non human primates, and any other species can be found in the IEDB. id: '2346' name: Immune Epitope Database prefix: FAIRsharing.c886cd subjects: - Bioinformatics - Immunology - Life Science mappings: fairsharing: FAIRsharing.c886cd miriam: iedb miriam: deprecated: false description: The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes. homepage: https://www.lji.org/ id: 00000865 name: Immune Epitope Database (IEDB) namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: iedb sampleId: '1038233' uri_format: https://www.iedb.org/reference/$1 name: Immune Epitope Database iev: example: '0000000' mappings: obofoundry: iev prefixcommons: IEV obofoundry: deprecated: true homepage: http://www.inoh.org inactive: true name: Event (INOH pathway ontology) prefix: iev pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: IEV uri_format: http://purl.obolibrary.org/obo/IEV_$1 igrhcellid: cellosaurus: category: Cell line databases/resources homepage: http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi name: Integrated Genomic Resources of human Cell Lines for Identification prefix: IGRhCellID uri_format: http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1 example: ACHN mappings: cellosaurus: IGRhCellID igsn: fairsharing: abbreviation: IGSN description: IGSN is a globally unique and persistent identifier for material samples. The IGSN registration service will facilitate the discovery, access, and sharing of samples, ensure preservation and access of sample data, aid identification of samples in the literature, and advance the exchange of digital sample data among interoperable data systems. id: '51' name: International GeoSample Number prefix: FAIRsharing.Yvc76F subjects: - Geochemistry - Hydrogeology - Environmental Science - Geology - Earth Science mappings: fairsharing: FAIRsharing.Yvc76F miriam: igsn n2t: igsn miriam: deprecated: false description: IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents. homepage: http://www.geosamples.org/ id: 00000806 name: International Geo Sample Number namespaceEmbeddedInLui: false pattern: ^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$ prefix: igsn sampleId: AU124 uri_format: http://igsn.org/$1 n2t: example: SSH000SUA homepage: http://www.geosamples.org/ name: International Geo Sample Number namespaceEmbeddedInLui: false prefix: igsn uri_format: hdl.handle.net/10273/$1 igsr: cellosaurus: category: Biological sample resources homepage: https://www.internationalgenome.org/ name: International Genome Sample Resource prefix: IGSR uri_format: https://www.internationalgenome.org/data-portal/sample/$1 example: NA06985 fairsharing: abbreviation: IGSR description: 'The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project.' id: '2737' name: The International Genome Sample Resource prefix: FAIRsharing.4Vs9VM subjects: - Genomics - Comparative Genomics mappings: cellosaurus: IGSR fairsharing: FAIRsharing.4Vs9VM ihw: cellosaurus: category: Cell line databases/resources homepage: https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html name: International Histocompatibility Workshop cell lines prefix: IHW description: The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics. example: IHW09326 homepage: https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html mappings: cellosaurus: IHW name: International Histocompatibility Workshop cell lines pattern: ^IHW\d+$ imanis: cellosaurus: category: Cell line collections homepage: https://www.imanislife.com/collections/cell-lines/ name: Imanis Life Sciences cell line products prefix: Imanis uri_format: https://www.imanislife.com/?s=$1 example: CL070 mappings: cellosaurus: Imanis imdrf: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence. homepage: http://www.imdrf.org/ name: International Medical Device Regulators Forum no_own_terms: true references: - https://www.fda.gov/medical-devices/mandatory-reporting-requirements-manufacturers-importers-and-device-user-facilities/mdr-adverse-event-codes imex: mappings: miriam: imex n2t: imex prefixcommons: IMEX miriam: deprecated: false description: The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources. homepage: https://www.imexconsortium.org/ id: '00000122' name: IMEx namespaceEmbeddedInLui: false pattern: ^IM-\d+(-?)(\d+?)$ 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 sampleId: IM-19210-3 uri_format: https://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1 n2t: description: The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources. example: IM-19210-3 homepage: https://www.imexconsortium.org/ name: IMEx Consortium running at EBI namespaceEmbeddedInLui: false pattern: ^IM-\d+(-?)(\d+?)$ prefix: imex uri_format: https://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1 name: International Molecular Exchange prefixcommons: is_identifiers: true is_obo: false prefix: IMEX uri_format: http://identifiers.org/imex/$1 img.gene: mappings: miriam: img.gene n2t: img.gene prefixcommons: IMG.GENE miriam: deprecated: false description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information. homepage: http://img.jgi.doe.gov/ id: '00000176' name: Integrated Microbial Genomes Gene namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: img.gene sampleId: '638309541' uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1 n2t: description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information. example: '638309541' homepage: http://img.jgi.doe.gov/ name: Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: img.gene uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1 prefixcommons: is_identifiers: true is_obo: false prefix: IMG.GENE uri_format: http://identifiers.org/img.gene/$1 img.taxon: mappings: miriam: img.taxon n2t: img.taxon prefixcommons: IMG.TAXON miriam: deprecated: false description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information. homepage: http://img.jgi.doe.gov/ id: '00000175' name: Integrated Microbial Genomes Taxon namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: img.taxon sampleId: '648028003' uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1 n2t: description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information. example: '648028003' homepage: http://img.jgi.doe.gov/ name: Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: img.taxon uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1 prefixcommons: is_identifiers: true is_obo: false prefix: IMG.TAXON uri_format: http://identifiers.org/img.taxon/$1 imgt.hla: cellosaurus: category: Cell line databases/resources homepage: https://www.ebi.ac.uk/ipd/imgt/hla/ name: IPD-IMGT/HLA database prefix: IPD-IMGT/HLA uri_format: https://www.ebi.ac.uk/cgi-bin/imgt/hla/fetch_cell.cgi?$1 fairsharing: abbreviation: IPD-IMGT/HLA description: The IPD-IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (MHC) and includes the official sequences named by the WHO Nomenclature Committee For Factors of the HLA System. The IMGT/HLA Database was established to provide a locus-specific database (LSDB) for the allelic sequences of the genes in the HLA system, also known as the human MHC. The IMGT/HLA Database was first released in 1998 and subsequently incorporated as a module of IPD in 2012. id: '1714' name: IPD-IMGT/HLA - Human Leukocyte Antigen Sequence Database prefix: FAIRsharing.e28v7g subjects: - Immunogenetics - Immunology - Biomedical Science go: homepage: http://www.ebi.ac.uk/imgt/hla name: IMGT/HLA human major histocompatibility complex sequence database prefix: IMGT_HLA mappings: cellosaurus: IPD-IMGT/HLA fairsharing: FAIRsharing.e28v7g go: IMGT_HLA miriam: imgt.hla n2t: imgt.hla ncbi: IMGT/HLA prefixcommons: IMGT.HLA miriam: deprecated: false description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature. homepage: https://www.ebi.ac.uk/imgt/hla/allele.html id: '00000331' name: IMGT HLA namespaceEmbeddedInLui: false pattern: ^[A-Z0-9*:]+$ prefix: imgt.hla sampleId: A*01:01:01:01 uri_format: https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1 n2t: description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature. example: A*01:01:01:01 homepage: https://www.ebi.ac.uk/imgt/hla/allele.html name: IMGT HLA at EBI namespaceEmbeddedInLui: false pattern: ^[A-Z0-9*:]+$ prefix: imgt.hla uri_format: https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1 ncbi: example: HLA00031 homepage: http://www.ebi.ac.uk/imgt/hla/ name: Immunogenetics database, human MHC prefix: IMGT/HLA prefixcommons: is_identifiers: true is_obo: false prefix: IMGT.HLA uri_format: http://identifiers.org/imgt.hla/$1 synonyms: - IPD-IMGT/HLA imgt.ligm: go: description: Database of immunoglobulins and T cell receptors from human and other vertebrates, with translation for fully annotated sequences. homepage: http://www.imgt.org/ name: ImMunoGeneTics database covering immunoglobulins and T-cell receptors prefix: IMGT_LIGM mappings: go: IMGT_LIGM miriam: imgt.ligm n2t: imgt.ligm ncbi: IMGT/LIGM prefixcommons: IMGT.LIGM miriam: deprecated: false description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates. homepage: http://www.imgt.org/ id: 00000287 name: IMGT LIGM namespaceEmbeddedInLui: false pattern: ^M\d+$ prefix: imgt.ligm providers: - code: CURATOR_REVIEW description: IMGT LIGM through DKFZ (SRS) homepage: http://genius.embnet.dkfz-heidelberg.de/ name: IMGT LIGM through DKFZ (SRS) uri_format: http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-id+4ktAl1fNMTA+-e+[IMGT:'$1'] sampleId: M94112 uri_format: http://www.imgt.org/ligmdb/view?id=$1 n2t: description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates. example: M94112 homepage: http://www.imgt.org/ name: IMGT LIGM at CNRS namespaceEmbeddedInLui: false pattern: ^M\d+$ prefix: imgt.ligm uri_format: http://www.imgt.org/ligmdb/view?id=$1 ncbi: example: U03895 homepage: http://www.imgt.org/IMGTinformation/LIGM.html name: Immunogenetics database, immunoglobulins and T-cell receptors prefix: IMGT/LIGM prefixcommons: is_identifiers: true is_obo: false prefix: IMGT.LIGM uri_format: http://identifiers.org/imgt.ligm/$1 imr: example: '0000001' mappings: obofoundry: imr prefixcommons: IMR obofoundry: contact: curator@inoh.org contact.label: INOH curators deprecated: true homepage: http://www.inoh.org inactive: true name: Molecule role (INOH Protein name/family name ontology) prefix: imr pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: IMR uri_format: http://purl.obolibrary.org/obo/IMR_$1 inchi: fairsharing: abbreviation: InChI description: Originally developed by the International Union of Pure and Applied Chemistry (IUPAC), the IUPAC International Chemical Identifier (InChI) is a machine-readable string generated from a chemical structure. InChIs are unique to the compound they describe and can encode absolute stereochemistry making chemicals and chemistry machine-readable and discoverable. A simple analogy is that InChI is the bar-code for chemistry and chemical structures. A hashed fixed-length version of the InChI, the InChIKey, is also widely used. The InChI format and algorithm are non-proprietary and the software is open source, with ongoing development done by the community. A number of IUPAC working groups are working on extensions and new applications of the standard. id: '1477' name: IUPAC International Chemical Identifier prefix: FAIRsharing.ddk9t9 subjects: - Knowledge and Information Systems - Cheminformatics - Chemistry mappings: fairsharing: FAIRsharing.ddk9t9 miriam: inchi n2t: inchi prefixcommons: INCHI miriam: deprecated: false 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. homepage: http://www.chemspider.com/ id: 00000383 name: InChI namespaceEmbeddedInLui: false pattern: ^InChI\=1S?\/[A-Za-z0-9\.]+(\+[0-9]+)?(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,\/\?\;\.]+)*$ 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 sampleId: InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 uri_format: http://www.chemspider.com/$1 n2t: 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://webbook.nist.gov/chemistry name: InChI through NIST namespaceEmbeddedInLui: false pattern: ^InChI\=1S?\/[A-Za-z0-9\.]+(\+[0-9]+)?(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,\/\?\;\.]+)*$ prefix: inchi uri_format: http://webbook.nist.gov/cgi/cbook.cgi?$1 prefixcommons: is_identifiers: true is_obo: false prefix: INCHI uri_format: http://identifiers.org/inchi/$1 wikidata: prefix: P234 inchikey: mappings: miriam: inchikey n2t: inchikey prefixcommons: INCHIKEY scholia: inchikey miriam: deprecated: false 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. homepage: http://www.chemspider.com/ id: 00000387 name: InChIKey namespaceEmbeddedInLui: false pattern: ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? 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 sampleId: RYYVLZVUVIJVGH-UHFFFAOYSA-N uri_format: http://www.chemspider.com/inchikey=$1 n2t: 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://cactus.nci.nih.gov/chemical/structure name: InChiKey resolver at NCI namespaceEmbeddedInLui: false pattern: ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? prefix: inchikey uri_format: http://cactus.nci.nih.gov/chemical/structure/$1/names prefixcommons: is_identifiers: true is_obo: false prefix: INCHIKEY uri_format: http://identifiers.org/inchikey/$1 wikidata: prefix: P235 inhand: comment: This nomenclature is available via email. Truly a disgrace. contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The standard reference for nomenclature and diagnostic criteria in toxicologic pathology. fairsharing: abbreviation: INHAND description: Standard reference for nomenclature and diagnostic criteria in toxicologic pathology. id: '392' name: International Harmonization of Nomenclature and Diagnostic criteria prefix: FAIRsharing.9gqfpm subjects: - Biomedical Science homepage: https://www.goreni.org/gr3_nomenclature.php mappings: fairsharing: FAIRsharing.9gqfpm name: The International Harmonization of Nomenclature and Diagnostic criteria proprietary: true inn: comment: can not find a place to resolve to description: Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO. example: fluticasone homepage: https://www.who.int/teams/health-product-and-policy-standards/inn name: International Nonproprietary Names synonyms: - INN_ID uri_format: https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1 wikidata: prefix: P2275 ino: biolink: is_identifiers: false is_obo: true prefix: INO uri_format: http://purl.obolibrary.org/obo/INO_$1 bioportal: name: Interaction Network Ontology prefix: INO example: '0000003' fairsharing: abbreviation: INO description: The Interaction Network Ontology (INO) aims to standardize interaction network annotation, integrate various interaction network data, and support computer-assisted reasoning. It models general interactions (e.g., molecular interactions) and interaction networks (e.g., Bayesian network). INO is aligned with the Basic Formal Ontology (BFO) and imports terms from 10 other existing ontologies, and includes over 500 terms. In terms of interaction-related terms, INO imports and aligns PSI-MI and GO interaction terms and includes over 100 newly generated ontology terms. id: '891' name: Interaction Network Ontology prefix: FAIRsharing.mm72as subjects: - Life Science mappings: biolink: INO bioportal: INO fairsharing: FAIRsharing.mm72as obofoundry: ino ols: ino ontobee: INO obofoundry: contact: yongqunh@med.umich.edu contact.github: yongqunh contact.label: Yongqun Oliver He contact.orcid: 0000-0001-9189-9661 deprecated: false description: An ontology of interactions and interaction networks download.owl: http://purl.obolibrary.org/obo/ino.owl homepage: https://github.com/INO-ontology/ino inactive: false license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Interaction Network Ontology preferredPrefix: INO prefix: ino repository: https://github.com/INO-ontology/ino ols: 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: http://purl.obolibrary.org/obo/ino.owl homepage: https://github.com/INO-ontology/ino name: 'INO: Interaction Network Ontology' prefix: ino version: 1.0.112 ontobee: library: Library name: Interaction Network Ontology prefix: INO pattern: ^\d{7}$ insdc: mappings: miriam: insdc n2t: insdc prefixcommons: INSDC miriam: deprecated: false description: The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. homepage: https://www.ncbi.nlm.nih.gov/Genbank/ id: 00000029 name: Nucleotide Sequence Database namespaceEmbeddedInLui: false pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ prefix: insdc providers: - code: CURATOR_REVIEW description: INSDC through DDBJ homepage: http://www.ddbj.nig.ac.jp/ name: INSDC through DDBJ uri_format: http://getentry.ddbj.nig.ac.jp/getentry?database=ddbj&accession_number=$1 - code: ebi description: INSDC through European Nucleotide Archive (ENA) homepage: https://www.ebi.ac.uk/ena/ name: INSDC through European Nucleotide Archive (ENA) uri_format: https://www.ebi.ac.uk/ena/data/view/$1 - code: ncbi description: INSDC through Nucleotide database at NCBI homepage: https://www.ncbi.nlm.nih.gov/nuccore/ name: INSDC through Nucleotide database at NCBI uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 sampleId: X58356 uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 n2t: description: The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. example: X58356 homepage: https://www.ncbi.nlm.nih.gov/nuccore/ name: INSDC through Nucleotide database at NCBI namespaceEmbeddedInLui: false pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ prefix: insdc uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 prefixcommons: is_identifiers: true is_obo: false prefix: INSDC uri_format: http://identifiers.org/insdc/$1 insdc.cds: has_canonical: ncbiprotein mappings: miriam: insdc.cds n2t: insdc.cds prefixcommons: INSDC.CDS miriam: deprecated: false description: The coding sequence or protein identifiers as maintained in INSDC. homepage: http://getentry.ddbj.nig.ac.jp id: '00000606' name: INSDC CDS namespaceEmbeddedInLui: false pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ 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 sampleId: AAA35559 uri_format: http://getentry.ddbj.nig.ac.jp/getentry/dad/$1 n2t: description: The coding sequence or protein identifiers as maintained in INSDC. example: AAA35559 homepage: https://www.ncbi.nlm.nih.gov/protein/ name: INSDC CDS through NCBI namespaceEmbeddedInLui: false pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ prefix: insdc.cds uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 prefixcommons: is_identifiers: true is_obo: false prefix: INSDC.CDS uri_format: http://identifiers.org/insdc.cds/$1 insdc.gca: mappings: miriam: insdc.gca n2t: insdc.gca prefixcommons: INSDC.GCA miriam: deprecated: false description: The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage. homepage: https://www.ebi.ac.uk/ena/browse/genome-assembly-database id: '00000607' name: Genome assembly database namespaceEmbeddedInLui: false pattern: ^GC[AF]_[0-9]{9}\.[0-9]+$ prefix: insdc.gca providers: - code: ncbi description: Genome assembly database NCBI homepage: https://www.ncbi.nlm.nih.gov/assembly/ name: Genome assembly database NCBI uri_format: https://www.ncbi.nlm.nih.gov/assembly/$1 sampleId: GCA_000155495.1 uri_format: https://www.ebi.ac.uk/ena/data/view/$1 n2t: description: The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage. example: GCA_000155495.1 homepage: https://www.ncbi.nlm.nih.gov/assembly/ name: Genome assembly database NCBI namespaceEmbeddedInLui: false pattern: ^GCA_[0-9]{9}\.[0-9]$ prefix: insdc.gca uri_format: https://www.ncbi.nlm.nih.gov/assembly/$1 prefixcommons: is_identifiers: true is_obo: false prefix: INSDC.GCA uri_format: http://identifiers.org/insdc.gca/$1 insdc.run: comment: 'https://www.insdc.org/ is the authoritative source for INSDC. However, confusingly, they don''t mention runs in this table. I think we should ask them to include. ENA is a partner and they have documentation here: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html Runs | (E\|D\|S)RR[0-9]{6,} | ERR123456 -- | -- | --' contributor: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: An experimental run, served thrugh the ENA example: ERR436051 has_canonical: ena.embl homepage: https://www.insdc.org/ name: International Nucleotide Sequence Database Collaboration (INSDC) Run pattern: ^(E|D|S)RR[0-9]{6,}$ 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/$1 insdc.sra: fairsharing: abbreviation: SRA description: 'The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.' id: '1978' name: Sequence Read Archive prefix: FAIRsharing.g7t2hv subjects: - Virology - Life Science - Epidemiology mappings: fairsharing: FAIRsharing.g7t2hv miriam: insdc.sra n2t: insdc.sra prefixcommons: INSDC.SRA miriam: deprecated: false description: 'The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.' homepage: https://www.ncbi.nlm.nih.gov/sra id: '00000243' name: Sequence Read Archive namespaceEmbeddedInLui: false pattern: ^[SED]R[APRSXZ]\d+$ prefix: insdc.sra providers: - code: ebi description: European Nucleotide Archive (ENA) homepage: https://www.ebi.ac.uk/ena name: European Nucleotide Archive (ENA) uri_format: https://www.ebi.ac.uk/ena/data/view/$1 - code: ddbj description: DDBJ Sequence Read Archive (DRA) homepage: http://trace.ddbj.nig.ac.jp/dra/ name: DDBJ Sequence Read Archive (DRA) uri_format: http://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc=$1 sampleId: SRX000007 uri_format: https://www.ncbi.nlm.nih.gov/sra/$1 n2t: description: 'The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.' example: SRX000007 homepage: https://www.ncbi.nlm.nih.gov/sra name: Sequence Read Archive at NCBI namespaceEmbeddedInLui: false pattern: ^[SED]R[APRSXZ]\d+$ prefix: insdc.sra uri_format: https://www.ncbi.nlm.nih.gov/sra/$1 prefixcommons: is_identifiers: true is_obo: false prefix: INSDC.SRA uri_format: http://identifiers.org/insdc.sra/$1 intact: fairsharing: abbreviation: IntAct description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available. id: '1599' name: IntAct molecular interaction database prefix: FAIRsharing.d05nwx subjects: - Biology go: homepage: https://www.ebi.ac.uk/intact/ name: IntAct protein interaction database prefix: IntAct mappings: fairsharing: FAIRsharing.d05nwx go: IntAct miriam: intact n2t: intact prefixcommons: INTACT uniprot: IntAct miriam: deprecated: false description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. homepage: https://www.ebi.ac.uk/intact/ id: '00000010' name: IntAct namespaceEmbeddedInLui: false pattern: ^EBI\-[0-9]+$ prefix: intact sampleId: EBI-2307691 uri_format: https://www.ebi.ac.uk/intact/interaction/$1 n2t: description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. example: EBI-2307691 homepage: https://www.ebi.ac.uk/intact/ name: IntAct at EBI namespaceEmbeddedInLui: false pattern: ^EBI\-[0-9]+$ prefix: intact uri_format: https://www.ebi.ac.uk/intact/interaction/$1 prefixcommons: is_identifiers: true is_obo: false prefix: INTACT uri_format: http://identifiers.org/intact/$1 uniprot: category: Protein-protein interaction databases identifier: '51' link_is_explicit: 'true' name: Protein interaction database and analysis system prefix: IntAct uri_format: https://www.ebi.ac.uk/intact/interactors/id:$1* intact.molecule: mappings: miriam: intact.molecule n2t: intact.molecule prefixcommons: INTACT.MOLECULE miriam: deprecated: false description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules. homepage: https://www.ebi.ac.uk/intact/ id: '00000427' name: IntAct Molecule namespaceEmbeddedInLui: false pattern: ^EBI\-[0-9]+$ prefix: intact.molecule sampleId: EBI-366083 uri_format: https://www.ebi.ac.uk/intact/molecule/$1 n2t: description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules. example: EBI-366083 homepage: https://www.ebi.ac.uk/intact/ name: IntAct Molecule at EBI namespaceEmbeddedInLui: false pattern: ^EBI\-[0-9]+$ prefix: intact.molecule uri_format: https://www.ebi.ac.uk/intact/molecule/$1 prefixcommons: is_identifiers: true is_obo: false prefix: INTACT.MOLECULE uri_format: http://identifiers.org/intact.molecule/$1 interlex: fairsharing: abbreviation: InterLex description: The InterLex terminology is a lexicon of biomedical terms built on the foundation of NeuroLex and contains all of the existing NeuroLex terms. The initial entries in NeuroLex were built from the NIFSTD ontologies and BIRNLex (Biomedical Informatics Research Network Project Lexicon). Final content review from NeuroLex is still ongoing. id: '1118' name: InterLex prefix: FAIRsharing.67sssf subjects: - Anatomy - Neurobiology - Biomedical Science mappings: fairsharing: FAIRsharing.67sssf miriam: ilx miriam: deprecated: false description: 'InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. ' homepage: https://www.fdilab.org id: 00000814 name: InterLex namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: ilx sampleId: 0101963 uri_format: https://scicrunch.org/scicrunch/interlex/view/ilx_$1 name: InterLex references: - https://github.com/AllenInstitute/nomenclature synonyms: - ILX interpro: biolink: is_identifiers: false is_obo: false prefix: interpro uri_format: https://www.ebi.ac.uk/interpro/entry/$1 example: IPR016380 fairsharing: abbreviation: InterPro description: InterPro is a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as signatures, provided by several different databases (referred to as member databases) that make up the InterPro consortium. id: '1854' name: Integrated resource of protein families, domains and functional sites prefix: FAIRsharing.pda11d subjects: - Bioinformatics - Biology go: homepage: http://www.ebi.ac.uk/interpro/ name: InterPro database of protein domains and motifs prefix: InterPro synonyms: - INTERPRO - IPR uri_format: http://www.ebi.ac.uk/interpro/entry/$1 mappings: biolink: interpro fairsharing: FAIRsharing.pda11d go: InterPro miriam: interpro n2t: interpro ncbi: InterPro obofoundry: ipr prefixcommons: IPR uniprot: InterPro miriam: deprecated: false description: InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. homepage: https://www.ebi.ac.uk/interpro/ id: '00000011' name: InterPro namespaceEmbeddedInLui: false pattern: ^IPR\d{6}$ 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 sampleId: IPR000100 uri_format: https://www.ebi.ac.uk/interpro/entry/$1 n2t: description: InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. example: IPR000100 homepage: https://www.ebi.ac.uk/interpro/ name: InterPro namespaceEmbeddedInLui: false pattern: ^IPR\d{6}$ prefix: interpro uri_format: https://www.ebi.ac.uk/interpro/entry/$1 name: InterPro ncbi: example: IPR002928 homepage: http://www.ebi.ac.uk/interpro/ name: InterPro protein sequence database prefix: InterPro obofoundry: contact: interhelp@ebi.ac.uk contact.label: InterPro Help deprecated: true homepage: http://www.ebi.ac.uk/interpro/index.html inactive: true name: Protein Domains prefix: ipr preferred_prefix: interpro prefixcommons: is_identifiers: false is_obo: true prefix: IPR uri_format: http://purl.obolibrary.org/obo/IPR_$1 synonyms: - IP - IPR - InterPro uniprot: category: Family and domain databases identifier: '52' link_is_explicit: 'true' name: Integrated resource of protein families, domains and functional sites prefix: InterPro uri_format: https://www.ebi.ac.uk/interpro/entry/$1 wikidata: prefix: P2926 ird.segment: mappings: miriam: ird.segment n2t: ird.segment prefixcommons: IRD.SEGMENT miriam: deprecated: false description: Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s). homepage: http://www.fludb.org/ id: '00000172' name: IRD Segment Sequence namespaceEmbeddedInLui: false pattern: ^\w+(\_)?\d+(\.\d+)?$ prefix: ird.segment sampleId: CY077097 uri_format: http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1 n2t: description: Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s). example: CY077097 homepage: http://www.fludb.org/ name: IRD at BioHealthBase namespaceEmbeddedInLui: false pattern: ^\w+(\_)?\d+(\.\d+)?$ prefix: ird.segment uri_format: http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1 prefixcommons: is_identifiers: true is_obo: false prefix: IRD.SEGMENT uri_format: http://identifiers.org/ird.segment/$1 irefweb: fairsharing: abbreviation: iRefWeb description: 'iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID.' id: '2071' name: Interaction Reference Index Web Interface prefix: FAIRsharing.t31wcb subjects: - Life Science mappings: fairsharing: FAIRsharing.t31wcb miriam: irefweb n2t: irefweb prefixcommons: IREFWEB miriam: deprecated: false description: 'iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.' homepage: http://wodaklab.org/iRefWeb/ id: '00000123' name: iRefWeb namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: irefweb sampleId: '617102' uri_format: http://wodaklab.org/iRefWeb/interaction/show/$1 n2t: description: 'iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.' example: '617102' homepage: http://wodaklab.org/iRefWeb/ name: iRefWeb Protein Interaction Reference Index namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: irefweb uri_format: http://wodaklab.org/iRefWeb/interaction/show/$1 prefixcommons: is_identifiers: true is_obo: false prefix: IREFWEB uri_format: http://identifiers.org/ire