3dmet: mappings: 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 url: https://data.4dnucleome.org/biosources/$1 example: 4DNSR73BT2A2 homepage: https://data.4dnucleome.org/biosources mappings: cellosaurus: 4DN miriam: 4dn miriam: deprecated: false description: The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases. homepage: https://data.4dnucleome.org/ id: 00000833 name: 4D Nucleome namespaceEmbeddedInLui: false pattern: ^4DN[A-Z]{2}[A-Z0-9]{7}$ 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 4dn.replicate: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Database portal containing replicate experiments of different assays and samples example: 4DNESWX1J3QU homepage: https://data.4dnucleome.org/experiment-set-replicates/ name: 4D Nucleome Data Portal Experiment Replicate uri_format: https://data.4dnucleome.org/experiment-set-replicates/$1 aao: description: A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon. mappings: 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 url: https://web.expasy.org/abcd/$1 description: The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies example: AD834 homepage: https://web.expasy.org/abcd/ mappings: cellosaurus: ABCD 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_$1 abs: mappings: miriam: abs n2t: abs prefixcommons: ABS miriam: deprecated: false description: The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. homepage: http://genome.crg.es/datasets/abs2005/ id: '00000277' name: ABS namespaceEmbeddedInLui: false pattern: ^A\d+$ 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 ac: contributor: email: cthoyt@gmail.com 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/$1 addgene: mappings: miriam: addgene n2t: addgene miriam: deprecated: false description: Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world. homepage: http://addgene.org/ id: '00000675' name: Addgene Plasmid Repository namespaceEmbeddedInLui: false pattern: ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[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/$1 adw: bioportal: name: Animal Natural History and Life History Ontology prefix: ADW mappings: bioportal: ADW miriam: adw n2t: adw obofoundry: adw prefixcommons: ADW miriam: deprecated: false description: Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology. homepage: https://animaldiversity.org/ id: 00000492 name: Animal Diversity Web namespaceEmbeddedInLui: false pattern: ^[A-Z_a-z]+$ 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/$1 aeo: bioportal: name: Anatomical Entity Ontology prefix: AEO download_obo: https://raw.githubusercontent.com/obophenotype/human-developmental-anatomy-ontology/master/src/ontology/aeo.obo example: '0001017' mappings: bioportal: AEO obofoundry: aeo ols: aeo ontobee: AEO prefixcommons: AEO obofoundry: contact: J.Bard@ed.ac.uk contact.label: Jonathan Bard deprecated: false description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology download.owl: http://purl.obolibrary.org/obo/aeo.owl homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/ inactive: false license: CC-BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Anatomical Entity Ontology preferredPrefix: AEO prefix: aeo repository: https://github.com/obophenotype/human-developmental-anatomy-ontology ols: description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology download: http://purl.obolibrary.org/obo/aeo.owl homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/ name: Anatomical Entity Ontology prefix: aeo version: '2014-12-05' version.iri: http://purl.obolibrary.org/obo/aeo/releases/2014-12-05/aeo.owl ontobee: library: Library name: Anatomical Entity Ontology prefix: AEO url: http://www.ontobee.org/ontology/AEO pattern: ^\d{7}$ 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' mappings: bioportal: AERO obofoundry: aero prefixcommons: AERO obofoundry: contact: mcourtot@gmail.com contact.label: Melanie Courtot 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 license.url: http://creativecommons.org/licenses/by/3.0/ name: Adverse Event Reporting Ontology prefix: aero 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/$1 afo: bioportal: name: Allotrope Merged Ontology Suite prefix: AFO homepage: https://www.allotrope.org/ mappings: bioportal: AFO ols: afo no_own_terms: true ols: description: Allotrope Merged Ontology Suite download: http://afo-ols.semanticsfirst.com/ontologies/afo license: creative-commons-attribution-license name: Allotrope Merged Ontology Suite prefix: afo version: '2019-05-10' version.iri: http://purl.allotrope.org/voc/afo/merged-OLS/REC/2019/05/10 aftol.taxonomy: mappings: miriam: aftol.taxonomy n2t: aftol.taxonomy prefixcommons: AFTOL.TAXONOMY miriam: deprecated: false description: The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species. homepage: http://aftol.org/data.php id: '00000411' name: AFTOL namespaceEmbeddedInLui: false pattern: ^\d+$ 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/$1 agricola: go: homepage: http://agricola.nal.usda.gov/ name: AGRICultural OnLine Access prefix: AGRICOLA_ID mappings: go: AGRICOLA_ID miriam: agricola n2t: agricola prefixcommons: AGRICOLA miriam: deprecated: false description: AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century. homepage: http://agricola.nal.usda.gov/ id: 00000589 name: AGRICOLA namespaceEmbeddedInLui: false pattern: ^\d+$ 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 agro: bioportal: name: AGRonomy Ontology prefix: AGRO example: '00020007' mappings: bioportal: AGRO obofoundry: agro ols: agro ontobee: AGRO prefixcommons: AGRO obofoundry: contact: m.a.laporte@cgiar.org contact.github: marieALaporte contact.label: "Marie-Ang\xE9lique Laporte" 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 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 license: http://creativecommons.org/licenses/by/4.0/ 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 url: http://www.ontobee.org/ontology/AGRO prefixcommons: is_identifiers: false is_obo: true prefix: AGRO uri_format: http://purl.obolibrary.org/obo/AGRO_$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: contact: entiminae@gmail.com contact.label: "Jennifer C. Gir\xF3n" 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 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 license: https://creativecommons.org/licenses/by/4.0/ name: Ontology for the Anatomy of the Insect SkeletoMuscular system prefix: aism version: '2021-09-08' version.iri: http://purl.obolibrary.org/obo/aism/releases/2021-09-08/aism.owl ontobee: library: Library name: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) prefix: AISM url: http://www.ontobee.org/ontology/AISM allergome: mappings: 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 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/$1 amoebadb: mappings: miriam: amoebadb n2t: amoebadb prefixcommons: AMOEBADB miriam: deprecated: false description: AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. homepage: http://amoebadb.org/amoeba/ id: 00000148 name: AmoebaDB namespaceEmbeddedInLui: false pattern: ^EDI_\d+$ 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/$1 amphx: bioportal: name: The Amphioxus Development and Anatomy Ontology prefix: AMPHX example: '1000160' mappings: bioportal: AMPHX obofoundry: amphx ols: amphx ontobee: AMPHX obofoundry: contact: hescriva@obs-banyuls.fr contact.label: Hector Escriva deprecated: false description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). download.obo: http://purl.obolibrary.org/obo/amphx.obo download.owl: http://purl.obolibrary.org/obo/amphx.owl homepage: https://github.com/EBISPOT/amphx_ontology inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: The Amphioxus Development and Anatomy Ontology preferredPrefix: AMPHX prefix: amphx repository: https://github.com/EBISPOT/amphx_ontology ols: description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). download: https://raw.githubusercontent.com/EBISPOT/amphx_ontology/master/amphx.owl homepage: https://github.com/EBISPOT/amphx_ontology license: https://creativecommons.org/licenses/by/3.0/ name: Amphioxus Development and Anatomy Ontology (AMPHX) prefix: amphx version: '2020-12-18' version.iri: http://purl.obolibrary.org/obo/amphx/releases/2020-12-18/amphx.owl ontobee: library: Library name: The Amphioxus Development and Anatomy Ontology prefix: AMPHX url: http://www.ontobee.org/ontology/AMPHX antibodyregistry: mappings: miriam: antibodyregistry n2t: antibodyregistry prefixcommons: ANTIBODYREGISTRY miriam: deprecated: false description: The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information. homepage: http://antibodyregistry.org/ id: '00000516' name: Antibody Registry namespaceEmbeddedInLui: false pattern: ^\d{6}$ 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/$1 antweb: mappings: miriam: antweb n2t: antweb ncbi: AntWeb prefixcommons: ANTWEB miriam: deprecated: false description: AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures. homepage: http://www.antweb.org/ id: '00000146' name: AntWeb namespaceEmbeddedInLui: false pattern: ^casent\d+(\-D\d+)?$ 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/$1 apd: mappings: miriam: apd n2t: apd prefixcommons: APD miriam: deprecated: false description: The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides. homepage: http://aps.unmc.edu/AP/ id: 00000278 name: APD namespaceEmbeddedInLui: false pattern: ^\d{5}$ 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/$1 provides: uniprot apo: bioportal: name: Ascomycete Phenotype Ontology prefix: APO example: 0000184 mappings: bioportal: APO obofoundry: ypo ols: apo ontobee: APO prefixcommons: YPO obofoundry: contact: cherry@genome.stanford.edu contact.label: Mike Cherry deprecated: true homepage: http://www.yeastgenome.org/ inactive: true name: Yeast phenotypes prefix: ypo ols: description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi. download: http://purl.obolibrary.org/obo/apo.owl homepage: http://www.yeastgenome.org/ license: http://creativecommons.org/licenses/by/4.0/ name: Ascomycete Phenotype Ontology (APO) prefix: apo version: '2021-10-07' version.iri: http://purl.obolibrary.org/obo/apo/releases/2021-10-07/apo.owl ontobee: library: Library name: Ascomycete phenotype ontology prefix: APO url: http://www.ontobee.org/ontology/APO pattern: ^\d{7}$ preferred_prefix: APO prefixcommons: is_identifiers: false is_obo: true prefix: YPO uri_format: http://purl.obolibrary.org/obo/YPO_$1 synonyms: - YPO uri_format: https://www.yeastgenome.org/observable/APO:$1 apollosv: bioportal: name: Apollo Structured Vocabulary prefix: APOLLO-SV example: '00000443' mappings: bioportal: APOLLO-SV obofoundry: apollo_sv ols: apollo_sv ontobee: APOLLO_SV obofoundry: contact: MBrochhausen@uams.edu contact.label: Mathias Brochhausen deprecated: false description: Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models download.owl: http://purl.obolibrary.org/obo/apollo_sv.owl homepage: https://github.com/ApolloDev/apollo-sv inactive: false license: CC-BY 3.0 license.url: https://creativecommons.org/licenses/by/3.0/ name: Apollo Structured Vocabulary preferredPrefix: APOLLO_SV prefix: apollo_sv repository: https://github.com/ApolloDev/apollo-sv ols: description: Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models download: http://purl.obolibrary.org/obo/apollo_sv.owl homepage: https://github.com/ApolloDev/apollo-sv license: https://creativecommons.org/licenses/by/4.0/ name: Apollo Structured Vocabulary (Apollo-SV) prefix: apollo_sv version: 4.1.1 version.iri: http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl ontobee: library: Library name: Apollo Structured Vocabulary prefix: APOLLO_SV url: http://www.ontobee.org/ontology/APOLLO_SV arachnoserver: mappings: miriam: arachnoserver n2t: arachnoserver prefixcommons: ARACHNOSERVER uniprot: ArachnoServer miriam: deprecated: false description: ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information. homepage: http://www.arachnoserver.org/ id: 00000193 name: ArachnoServer namespaceEmbeddedInLui: false pattern: ^AS\d{6}$ 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:$1 aro: bioportal: name: Antibiotic Resistance Ontology prefix: ARO example: '1000001' mappings: bioportal: ARO obofoundry: aro ols: aro ontobee: ARO prefixcommons: ARO obofoundry: contact: card@mcmaster.ca contact.github: raphenya contact.label: CARD deprecated: false description: Antibiotic resistance genes and mutations download.owl: http://purl.obolibrary.org/obo/aro.owl homepage: https://github.com/arpcard/aro inactive: false license: CC-BY license.url: https://creativecommons.org/licenses/by/4.0/ name: Antibiotic Resistance Ontology preferredPrefix: ARO prefix: aro repository: https://github.com/arpcard/aro ols: description: Antibiotic resistance genes and mutations download: http://purl.obolibrary.org/obo/aro.owl homepage: https://github.com/arpcard/aro name: Antibiotic Resistance Ontology prefix: aro version: '2019-10-24' ontobee: library: Library name: Antibiotic Resistance Ontology prefix: ARO url: http://www.ontobee.org/ontology/ARO pattern: ^\d{7}$ 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 url: https://www.ebi.ac.uk/arrayexpress/experiments/$1 mappings: cellosaurus: ArrayExpress miriam: arrayexpress n2t: arrayexpress prefixcommons: ARRAYEXPRESS miriam: deprecated: false description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations. homepage: https://www.ebi.ac.uk/arrayexpress/ id: '00000036' name: ArrayExpress namespaceEmbeddedInLui: false pattern: ^[AEP]-\w{4}-\d+$ 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/$1 arraymap: mappings: miriam: arraymap n2t: arraymap prefixcommons: ARRAYMAP miriam: deprecated: false description: arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome. homepage: https://www.arraymap.org id: '00000621' name: ArrayMap namespaceEmbeddedInLui: false pattern: ^[\w\-:,]{3,64}$ 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: 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=$1 mappings: go: ASAP miriam: asap n2t: asap ncbi: ASAP prefixcommons: ASAP miriam: deprecated: false description: ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. homepage: http://asap.ahabs.wisc.edu/asap/home.php id: 00000283 name: ASAP namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9-]+$ 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/$1 ascl: mappings: miriam: ascl n2t: ascl prefixcommons: ASCL miriam: deprecated: false description: The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001). homepage: http://ascl.net/ id: '00000641' name: Astrophysics Source Code Library namespaceEmbeddedInLui: false pattern: ^[0-9\.]+$ 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/$1 asrp: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes. example: ASRP1423 homepage: https://asrp.danforthcenter.org/ name: Arabidopsis Small RNA Project assembly: mappings: miriam: assembly miriam: deprecated: false description: A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. homepage: https://www.ncbi.nlm.nih.gov/ id: 00000884 name: Assembly namespaceEmbeddedInLui: false pattern: ^[a-zA-Z0-9_\.]+$ prefix: assembly sampleId: GCF_000005845.2 uri_format: https://www.ncbi.nlm.nih.gov/assembly/$1 atc: bioportal: name: Anatomical Therapeutic Chemical Classification prefix: ATC mappings: bioportal: ATC miriam: atc n2t: atc prefixcommons: ATC miriam: deprecated: false description: The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels. homepage: http://www.whocc.no/atc_ddd_index/ id: 00000088 name: Anatomical Therapeutic Chemical namespaceEmbeddedInLui: false pattern: ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$ 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 url: https://www.atcc.org/Products/All/$1.aspx homepage: https://www.lgcstandards-atcc.org mappings: cellosaurus: ATCC miriam: atcc n2t: atcc ncbi: ATCC prefixcommons: ATCC miriam: deprecated: false description: The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences. homepage: http://www.atcc.org/ id: 00000284 name: ATCC namespaceEmbeddedInLui: false pattern: ^\d+$ 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 mappings: bioportal: ATO 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 prefixcommons: is_identifiers: false is_obo: true prefix: ATO uri_format: http://purl.obolibrary.org/obo/ATO_$1 atol: bioportal: name: Animal Trait Ontology for Livestock prefix: ATOL example: '0002233' mappings: bioportal: ATOL ols: atol ols: contact: pylebail@rennes.inra.fr description: 'ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production.' download: http://www.atol-ontology.com/public/telechargement/atol.owl homepage: http://www.atol-ontology.com name: Animal Trait Ontology for Livestock prefix: atol version: '2018-09-13' autdb: mappings: miriam: autdb n2t: autdb prefixcommons: AUTDB miriam: deprecated: false description: AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder. homepage: http://autism.mindspec.org/autdb/ id: '00000415' name: AutDB namespaceEmbeddedInLui: false pattern: ^[A-Z]+[A-Z-0-9]{2,}$ 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/$1 bacdive: mappings: miriam: bacdive n2t: bacdive miriam: deprecated: false description: "BacDive\u2014the Bacterial Diversity Metadatabase merges detailed\ \ strain-linked information on the different aspects of bacterial and archaeal\ \ biodiversity." homepage: https://bacdive.dsmz.de/ id: '00000676' name: Bacterial Diversity Metadatabase namespaceEmbeddedInLui: false pattern: ^[0-9]+$ 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 name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria. example: BAC045 homepage: http://bactibase.hammamilab.org name: 'Bactibase: a database dedicated to bacteriocins' uri_format: http://bactibase.hammamilab.org/$1 bams: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: 'BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions.' homepage: https://bams1.org name: Brain Architecture Knowledge Management System Neuroanatomical Ontology references: - https://www.frontiersin.org/articles/10.3389/neuro.11.002.2008/full bao: bioportal: name: BioAssay Ontology prefix: BAO mappings: bioportal: BAO miriam: bao n2t: bao ols: bao prefixcommons: BAO miriam: deprecated: false description: The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. homepage: http://bioportal.bioontology.org/ontologies/BAO/ id: 00000597 name: BioAssay Ontology namespaceEmbeddedInLui: false pattern: ^\d{7}$ 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 license: https://creativecommons.org/licenses/by-sa/4.0/ name: BioAssay Ontology prefix: bao version: 2.7.2 version.iri: http://www.bioassayontology.org/bao/bao_complete.owl prefixcommons: is_identifiers: true is_obo: false prefix: BAO uri_format: http://identifiers.org/bao/$1 synonyms: - BAO bcgo: bioportal: name: Breast Cancer Grading Ontology prefix: BCGO cellosaurus: category: Ontologies homepage: https://github.com/obi-bcgo/bcgo name: Beta Cell Genomics Ontology prefix: BCGO url: http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/$1 mappings: bioportal: BCGO cellosaurus: BCGO obofoundry: bcgo ontobee: BCGO prefixcommons: BCGO obofoundry: contact: jiezheng@pennmedicine.upenn.edu contact.github: zhengj2007 contact.label: Jie Zheng 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 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 url: http://www.ontobee.org/ontology/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 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: '2020-12-15' version.iri: http://humanbehaviourchange.org/ontology/bcio.owl/2021-01-28 bco: bioportal: name: Biological Collections Ontology prefix: BCO example: 0000081 mappings: bioportal: BCO obofoundry: bco ols: bco ontobee: BCO prefixcommons: BCO obofoundry: contact: rlwalls2008@gmail.com contact.github: ramonawalls contact.label: Ramona Walls 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/tucotuco/bco inactive: false license: CC-0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Biological Collections Ontology preferredPrefix: BCO prefix: bco repository: https://github.com/tucotuco/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/tucotuco/bco license: http://creativecommons.org/publicdomain/zero/1.0/ name: Biological Collections Ontology prefix: bco version: '2020-03-27' version.iri: http://purl.obolibrary.org/obo/bco/releases/2020-03-27/bco.owl ontobee: library: Library name: Biological Collections Ontology prefix: BCO url: http://www.ontobee.org/ontology/BCO prefixcommons: is_identifiers: false is_obo: true prefix: BCO uri_format: http://purl.obolibrary.org/obo/BCO_$1 bdgp.est: has_canonical: dbest mappings: miriam: bdgp.est n2t: bdgp.est ncbi: BDGP_EST prefixcommons: BDGP.EST miriam: deprecated: false description: The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI). homepage: https://www.ncbi.nlm.nih.gov/dbEST/index.html id: 00000285 name: BDGP EST namespaceEmbeddedInLui: false pattern: ^\w+(\.)?(\d+)?$ 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/$1 beetlebase: mappings: miriam: beetlebase n2t: beetlebase ncbi: BEETLEBASE prefixcommons: BEETLEBASE miriam: deprecated: false description: BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications. homepage: http://beetlebase.org/ id: '00000157' name: BeetleBase namespaceEmbeddedInLui: false pattern: ^TC\d+$ 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/$1 begdb: mappings: miriam: begdb n2t: begdb prefixcommons: BEGDB miriam: deprecated: false description: The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods. homepage: http://www.begdb.com id: '00000622' name: Benchmark Energy & Geometry Database namespaceEmbeddedInLui: false pattern: ^[0-9]+$ 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/$1 bel: comment: INDRA uses bel as a catch-all for scomp/sfam contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents. example: 9-1-1 Complex homepage: https://biological-expression-language.github.io/ name: Biological Expression Language bfo: bioportal: name: Basic Formal Ontology prefix: BFO example: '0000001' go: description: An upper ontology used by Open Bio Ontologies (OBO) Foundry. BFO contains upper-level classes as well as core relations such as part_of (BFO_0000050) name: Basic Formal Ontology prefix: BFO mappings: bioportal: BFO go: BFO obofoundry: bfo ols: bfo ontobee: BFO prefixcommons: BFO obofoundry: contact: phismith@buffalo.edu contact.github: phismith contact.label: Barry Smith deprecated: false description: The upper level ontology upon which OBO Foundry ontologies are built. download.obo: http://purl.obolibrary.org/obo/bfo.obo download.owl: http://purl.obolibrary.org/obo/bfo.owl homepage: http://ifomis.org/bfo/ inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/4.0/ name: Basic Formal Ontology preferredPrefix: BFO prefix: bfo repository: https://github.com/BFO-ontology/BFO ols: description: The upper level ontology upon which OBO Foundry ontologies are built. download: http://purl.obolibrary.org/obo/bfo.owl homepage: https://github.com/BFO-ontology/BFO name: Basic Formal Ontology prefix: bfo version: '2019-08-26' version.iri: http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl ontobee: library: Foundry name: Basic Formal Ontology prefix: BFO url: http://www.ontobee.org/ontology/BFO pattern: ^\d{7}$ 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 mappings: 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_$1 bindingdb: mappings: miriam: bindingdb n2t: bindingdb prefixcommons: BINDINGDB uniprot: BindingDB miriam: deprecated: false description: BindingDB is the first public database of protein-small molecule affinity data. homepage: https://www.bindingdb.org id: '00000264' name: BindingDB namespaceEmbeddedInLui: false pattern: ^\w\d+$ 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=$1 biogrid: mappings: miriam: biogrid n2t: biogrid prefixcommons: BIOGRID uniprot: BioGRID miriam: deprecated: false description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. homepage: http://thebiogrid.org/ id: 00000058 name: BioGRID namespaceEmbeddedInLui: false pattern: ^\d+$ 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 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/$1 biogrid.interaction: contact: biogridadmin@gmail.com contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. example: '2649230' homepage: https://thebiogrid.org/ name: BioGRID Interactions part_of: biogrid pattern: ^\d+$ uri_format: https://thebiogrid.org/interaction/$1 biolegend: description: BioLegend is a life sciences supply vendor. example: '3403' homepage: https://www.biolegend.com name: BioLegend 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/$1 homepage: https://biolink.github.io/biolink-model/ mappings: biolink: biolink miriam: biolink miriam: deprecated: false description: A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations. homepage: https://biolink.github.io/biolink-model id: 00000782 name: BioLink Model namespaceEmbeddedInLui: false pattern: ^\S+$ 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/$1 synonyms: - BIOMD biomodels.kisao: bioportal: name: Kinetic Simulation Algorithm Ontology prefix: KISAO mappings: bioportal: KISAO miriam: biomodels.kisao n2t: biomodels.kisao obofoundry: kisao ols: kisao ontobee: KISAO prefixcommons: KISAO miriam: deprecated: false description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment. homepage: http://bioportal.bioontology.org/ontologies/KISAO id: 00000108 name: KiSAO namespaceEmbeddedInLui: false pattern: ^KISAO_\d+$ 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: sed-ml-editors@googlegroups.com contact.label: SED-ML Editors deprecated: false description: A classification of algorithms for simulating biology and their outputs download.owl: http://purl.obolibrary.org/obo/kisao.owl homepage: http://co.mbine.org/standards/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 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 url: http://www.ontobee.org/ontology/KISAO preferred_prefix: biomodels.kisao prefixcommons: is_identifiers: false is_obo: true prefix: KISAO uri_format: http://purl.obolibrary.org/obo/KISAO_$1 synonyms: - kisao biomodels.teddy: bioportal: name: Terminology for the Description of Dynamics prefix: TEDDY example: '0000066' mappings: bioportal: TEDDY miriam: biomodels.teddy n2t: biomodels.teddy ols: teddy prefixcommons: BIOMODELS.TEDDY miriam: deprecated: false description: The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. homepage: http://teddyontology.sourceforge.net/ id: '00000107' name: TEDDY namespaceEmbeddedInLui: false pattern: ^TEDDY_\d{7}$ 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/$1 bioportal: mappings: miriam: bioportal n2t: bioportal prefixcommons: BIOPORTAL miriam: deprecated: false description: "BioPortal is an open repository of biomedical ontologies that provides\ \ access via Web services and Web browsers to ontologies developed in OWL, RDF,\ \ OBO format and Prot\xE9g\xE9 frames. BioPortal functionality includes the\ \ ability to browse, search and visualize ontologies." homepage: http://bioportal.bioontology.org/ id: 00000187 name: BioPortal namespaceEmbeddedInLui: false pattern: ^\d+$ 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/$1 bioproject: mappings: miriam: bioproject n2t: bioproject prefixcommons: BIOPROJECT miriam: deprecated: false description: "BioProject provides an organizational framework to access metadata\ \ about research projects and the data from the projects that are deposited\ \ into different databases. It provides information about a project\u2019s scope,\ \ material, objectives, funding source and general relevance categories." homepage: http://trace.ddbj.nig.ac.jp/bioproject/ id: 00000349 name: BioProject namespaceEmbeddedInLui: false pattern: ^PRJ[DEN][A-Z]\d+$ 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: cthoyt@gmail.com contributor: email: cthoyt@gmail.com 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/$1 bioregistry.collection: contact: cthoyt@gmail.com contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Manually curated collections of resources stored in the bioregistry example: '0000001' homepage: https://bioregistry.io/collection name: Bioregistry Collections pattern: ^\d{7}$ uri_format: https://bioregistry.io/collection/$1 bioregistry.schema: contact: cthoyt@gmail.com contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Schema for the export of the Bioregistry as RDF example: '0000001' homepage: https://bioregistry.io/schema name: Bioregistry Schema pattern: ^\d{7}$ uri_format: https://bioregistry.io/schema/#$1 biorxiv: description: The bioRxiv is a preprint server for biology example: 2021.07.23.453588 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 biosample: cellosaurus: category: Biological sample resources homepage: https://www.ncbi.nlm.nih.gov/biosample name: BioSample database prefix: BioSample url: https://www.ncbi.nlm.nih.gov/biosample/?term=$1 mappings: cellosaurus: BioSample miriam: biosample n2t: biosample prefixcommons: BIOSAMPLE miriam: deprecated: false description: The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation. homepage: https://www.ebi.ac.uk/biosamples/ id: '00000350' name: BioSample namespaceEmbeddedInLui: false pattern: ^SAM[NED](\w)?\d+$ 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/$1 biosimulations: mappings: miriam: biosimulations miriam: deprecated: false description: BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools. homepage: https://icahn.mssm.edu/ id: 00000880 name: biosimulations namespaceEmbeddedInLui: false pattern: ^[a-zA-Z0-9_-]{3,}$ prefix: biosimulations sampleId: Yeast-cell-cycle-Irons-J-Theor-Biol-2009 uri_format: https://biosimulations.org/projects/$1 biosimulators: mappings: 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/$1 biostudies: mappings: fairsharing: biodbcore-000989 miriam: biostudies n2t: biostudies miriam: deprecated: false description: The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication. homepage: https://www.ebi.ac.uk/biostudies/ id: 00000694 name: BioStudies database namespaceEmbeddedInLui: false pattern: ^S-[A-Z]{4}[A-Z\d\-]+$ 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/$1 biosystems: mappings: miriam: biosystems n2t: biosystems prefixcommons: BIOSYSTEMS miriam: deprecated: false description: The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. homepage: https://www.ncbi.nlm.nih.gov/biosystems/ id: 00000097 name: BioSystems namespaceEmbeddedInLui: false pattern: ^\d+$ 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/$1 biotools: description: BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research. mappings: miriam: biotools n2t: biotools prefixcommons: BIOTOOLS miriam: deprecated: false description: Tool and data services registry. homepage: https://bio.tools/ id: '00000616' name: BioTools namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9\_]*$ 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 prefixcommons: is_identifiers: true is_obo: false prefix: BIOTOOLS uri_format: http://identifiers.org/biotools/$1 biozil: 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/$1 birnlex: bioportal: name: Biomedical Informatics Research Network Project Lexicon prefix: BIRNLEX comment: Part of the NeuroLex namespace now description: The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. example: birnlex_2023 homepage: https://bioportal.bioontology.org/ontologies/BIRNLEX mappings: bioportal: BIRNLEX name: Biomedical Informatics Research Network Lexicon bitterdb.cpd: mappings: miriam: bitterdb.cpd n2t: bitterdb.cpd prefixcommons: BITTERDB.CPD miriam: deprecated: false description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds. homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php id: 00000348 name: BitterDB Compound namespaceEmbeddedInLui: false pattern: ^\d+$ 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/$1 bmrb: mappings: fairsharing: FAIRsharing.p06nme miriam: bmrb uniprot: BMRB miriam: deprecated: false description: BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy. homepage: http://www.bmrb.wisc.edu/ id: '00000716' name: Biological Magnetic Resonance Data Bank namespaceEmbeddedInLui: false pattern: ^(bmr|bmse|bmst)?[0-9]{1,6}$ 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 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 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 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 uri_format: https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm brenda: 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=$1 mappings: go: BRENDA miriam: brenda n2t: brenda prefixcommons: BRENDA uniprot: BRENDA miriam: deprecated: false description: BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. homepage: https://www.brenda-enzymes.org/ id: '00000071' name: BRENDA namespaceEmbeddedInLui: false pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ 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/$1 bs: comment: An alernative vocabulary that has been aligned and integrated in Sequence Ontology (SO). contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library. download_obo: https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/subsets/biosapiens.obo example: '00042' homepage: https://github.com/The-Sequence-Ontology/SO-Ontologies name: Biosapiens Protein Feature Ontology pattern: ^\d+$ bspo: bioportal: name: Spatial Ontology prefix: BSPO download_obo: https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo example: 0000029 mappings: bioportal: BSPO obofoundry: bspo ols: bspo ontobee: BSPO prefixcommons: BSPO obofoundry: contact: cjmungall@lbl.gov contact.github: cmungall contact.label: Chris Mungall 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 license.url: http://creativecommons.org/licenses/by/3.0/ name: Biological Spatial Ontology preferredPrefix: BSPO prefix: bspo 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 license: https://creativecommons.org/licenses/by/3.0/ 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 url: http://www.ontobee.org/ontology/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: Ontologies homepage: https://bioportal.bioontology.org/ontologies/BTO name: BRENDA Tissue Ontology prefix: BTO url: https://bioportal.bioontology.org/ontologies/BTO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_$1 example: 0000590 go: description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. name: BRENDA tissue / enzyme ontology prefix: BTO mappings: bioportal: BTO cellosaurus: BTO go: BTO miriam: bto n2t: bto obofoundry: bto ols: bto ontobee: BTO prefixcommons: BTO wikidata: P5501 miriam: deprecated: false description: The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. homepage: https://www.ebi.ac.uk/ols/ontologies/bto id: '00000111' name: Brenda Tissue Ontology namespaceEmbeddedInLui: true pattern: ^BTO:\d{7}$ 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:$1 obofoundry: contact: a.chang@tu-bs.de contact.label: Antje Chang deprecated: false description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. download.json: http://purl.obolibrary.org/obo/bto.json download.obo: http://purl.obolibrary.org/obo/bto.obo download.owl: http://purl.obolibrary.org/obo/bto.owl homepage: http://www.brenda-enzymes.org inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: BRENDA tissue / enzyme source preferredPrefix: BTO prefix: bto repository: https://github.com/BRENDA-Enzymes/BTO ols: description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. download: http://purl.obolibrary.org/obo/bto.owl homepage: http://www.brenda-enzymes.org license: https://creativecommons.org/licenses/by/4.0/ name: The BRENDA Tissue Ontology (BTO) prefix: bto version: '2021-10-26' version.iri: http://purl.obolibrary.org/obo/bto/releases/2021-10-26/bto.owl ontobee: library: Library name: BRENDA tissue / enzyme source prefix: BTO url: http://www.ontobee.org/ontology/BTO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: BTO uri_format: http://purl.obolibrary.org/obo/BTO_$1 synonyms: - BTO wikidata: database: Q4836352 database.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/$1 bykdb: mappings: miriam: bykdb n2t: bykdb prefixcommons: BYKDB miriam: deprecated: false description: The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information. homepage: https://bykdb.ibcp.fr/BYKdb/ id: '00000253' name: BYKdb namespaceEmbeddedInLui: false pattern: ^[A-Z0-9]+$ 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/$1 cabri: mappings: miriam: cabri n2t: cabri ncbi: CABRI prefixcommons: CABRI miriam: deprecated: false description: CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it. homepage: http://www.cabri.org/ id: '00000261' name: CABRI namespaceEmbeddedInLui: false pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$ 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=$1] caloha: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins. download_obo: ftp://ftp.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo example: '0001' homepage: https://github.com/calipho-sib/controlled-vocabulary name: CALIPHO Group Ontology of Human Anatomy pattern: ^\d+$ references: - https://twitter.com/neXtProt_news/status/1350105997633867781 cameo: mappings: 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 download_owl: https://github.com/obophenotype/caro/raw/master/src/ontology/caro.owl example: '0000000' 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 go: CARO obofoundry: caro ols: caro ontobee: CARO prefixcommons: CARO obofoundry: contact: haendel@ohsu.edu contact.github: mellybelly contact.label: Melissa Haendel 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: An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species download: http://purl.obolibrary.org/obo/caro.owl homepage: https://github.com/obophenotype/caro/ name: Common Anatomy Reference Ontology prefix: caro version: '2019-05-24' version.iri: http://purl.obolibrary.org/obo/caro/2.0/beta/caro.owl ontobee: library: Library name: Common Anatomy Reference Ontology prefix: CARO url: http://www.ontobee.org/ontology/CARO prefixcommons: is_identifiers: false is_obo: true prefix: CARO uri_format: http://purl.obolibrary.org/obo/CARO_$1 cas: go: description: CAS REGISTRY is the most authoritative collection of disclosed chemical substance information, containing more than 54 million organic and inorganic substances and 62 million sequences. CAS REGISTRY covers substances identified from the scientific literature from 1957 to the present, with additional substances going back to the early 1900s. homepage: http://www.cas.org/expertise/cascontent/registry/index.html name: CAS Chemical Registry prefix: CAS mappings: go: CAS miriam: cas n2t: cas prefixcommons: CAS scholia: cas miriam: deprecated: false description: CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information. homepage: https://commonchemistry.cas.org/ id: '00000237' name: CAS namespaceEmbeddedInLui: false pattern: ^\d{1,7}\-\d{2}\-\d$ 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/$1 synonyms: - CASID - CAS_RN - SECONDARY_CAS_RN - cas_id wikidata: prefix: P231 cath: mappings: miriam: cath n2t: cath prefixcommons: CATH miriam: deprecated: false description: CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence. homepage: http://www.cathdb.info id: '00000612' name: CATH Protein Structural Domain Superfamily namespaceEmbeddedInLui: false pattern: ^[1-6]\.[0-9]+\.[0-9]+\.[0-9]+$ 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: 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/$1.html mappings: go: CAZY miriam: cazy n2t: cazy prefixcommons: CAZY uniprot: CAZy miriam: deprecated: false description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features. homepage: http://www.cazy.org/ id: 00000195 name: CAZy namespaceEmbeddedInLui: false pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$ 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 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 uri_format: https://europepmc.org/article/CBA/$1 cbioportal: mappings: miriam: cbioportal n2t: cbioportal miriam: deprecated: false description: The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. homepage: http://www.cbioportal.org id: 00000679 name: The cBioPortal for Cancer Genomics namespaceEmbeddedInLui: false pattern: ^[a-z0-9\_]+$ 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:$1&sid=IDORG ccds: mappings: miriam: ccds n2t: ccds prefixcommons: CCDS uniprot: CCDS miriam: deprecated: false description: The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations. homepage: http://www.ncbi.nlm.nih.gov/CCDS/ id: '00000375' name: Consensus CDS namespaceEmbeddedInLui: false pattern: ^CCDS\d+\.\d+$ 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 url: 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 (CCLE) Cells synonyms: - ccle.cell uri_format: https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1 cco: banana: CCO bioportal: name: Cell Cycle Ontology prefix: CCO mappings: bioportal: CCO miriam: cco n2t: cco ols: cco prefixcommons: CCO miriam: deprecated: false description: The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process. homepage: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CCO id: '00000234' name: Cell Cycle Ontology namespaceEmbeddedInLui: true pattern: ^CCO\:\w+$ 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 cdao: bioportal: name: Comparative Data Analysis Ontology prefix: CDAO example: '0000072' mappings: bioportal: CDAO obofoundry: cdao ols: cdao ontobee: CDAO prefixcommons: CDAO obofoundry: contact: balhoff@renci.org contact.label: Jim Balhoff 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 Universal license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Comparative Data Analysis Ontology preferredPrefix: CDAO prefix: cdao 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 url: http://www.ontobee.org/ontology/CDAO prefixcommons: is_identifiers: false is_obo: true prefix: CDAO uri_format: http://purl.obolibrary.org/obo/CDAO_$1 cdd: 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=$1 mappings: go: CDD miriam: cdd n2t: cdd ncbi: CDD prefixcommons: CDD uniprot: CDD miriam: deprecated: false description: The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd id: 00000119 name: Conserved Domain Database namespaceEmbeddedInLui: false pattern: ^(cd)?\d{5}$ 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=$1 cdno: example: '0000013' mappings: obofoundry: cdno ols: cdno ontobee: CDNO obofoundry: contact: l.andres.hernandez.18@student.scu.edu.au contact.github: LilyAndres contact.label: Liliana Andres Hernandez deprecated: false description: CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. download.obo: http://purl.obolibrary.org/obo/cdno.obo download.owl: http://purl.obolibrary.org/obo/cdno.owl homepage: https://github.com/Southern-Cross-Plant-Science/cdno inactive: false license: CC-BY license.url: https://creativecommons.org/licenses/by/3.0/ name: Compositional Dietary Nutrition Ontology preferredPrefix: CDNO prefix: cdno repository: https://github.com/Southern-Cross-Plant-Science/cdno ols: description: None download: http://purl.obolibrary.org/obo/cdno.owl homepage: https://github.com/Southern-Cross-Plant-Science/cdno license: unspecified name: Compositional Dietary Nutrition Ontology prefix: cdno version: '2021-10-20' version.iri: http://purl.obolibrary.org/obo/cdno/releases/2021-10-20/cdno.owl ontobee: library: Library name: Compositional Dietary Nutrition Ontology prefix: CDNO url: http://www.ontobee.org/ontology/CDNO cdpd: mappings: miriam: cdpd n2t: cdpd prefixcommons: CDPD miriam: deprecated: false description: The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN). homepage: http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp id: '00000272' name: Canadian Drug Product Database namespaceEmbeddedInLui: false pattern: ^\d+$ 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 cellbank.australia: cellosaurus: category: Cell line collections homepage: http://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/ name: CellBank Australia prefix: CBA url: 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/$1.html cellimage: mappings: fairsharing: FAIRsharing.8t18te miriam: cellimage n2t: cellimage prefixcommons: CELLIMAGE miriam: deprecated: false description: "The Cell: An Image Library\u2122 is a freely accessible, public\ \ repository of reviewed and annotated images, videos, and animations of cells\ \ from a variety of organisms, showcasing cell architecture, intracellular functionalities,\ \ and both normal and abnormal processes." homepage: http://cellimagelibrary.org/ id: '00000257' name: Cell Image Library namespaceEmbeddedInLui: false pattern: ^\d+$ 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/$1 cellosaurus: download_obo: https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo example: CVCL_0440 mappings: miriam: cellosaurus n2t: cellosaurus prefixcommons: CELLOSAURUS wikidata: P3289 miriam: deprecated: false description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.' homepage: https://web.expasy.org/cellosaurus/ id: 00000598 name: Cellosaurus namespaceEmbeddedInLui: false pattern: ^CVCL_[A-Z0-9]{4}$ 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/$1 pattern: ^CVCL_[A-Z0-9]{4}$ 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/$1 cellrepo: mappings: miriam: cellrepo miriam: deprecated: false description: The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines homepage: https://cellrepo.ico2s.org/ id: 00000829 name: Cell Version Control Repository namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: cellrepo sampleId: '82' uri_format: https://cellrepo.ico2s.org/repositories/$1 ceph: bioportal: name: Cephalopod Ontology prefix: CEPH download_obo: https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo example: 0000109 mappings: bioportal: CEPH obofoundry: ceph ols: ceph ontobee: CEPH prefixcommons: CEPH obofoundry: contact: cjmungall@lbl.gov contact.github: cmungall contact.label: Chris Mungall deprecated: false description: An anatomical and developmental ontology for cephalopods download.obo: http://purl.obolibrary.org/obo/ceph.obo download.owl: http://purl.obolibrary.org/obo/ceph.owl homepage: https://github.com/obophenotype/cephalopod-ontology inactive: true license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: Cephalopod Ontology prefix: ceph repository: https://github.com/obophenotype/cephalopod-ontology ols: description: An anatomical and developmental ontology for cephalopods download: http://purl.obolibrary.org/obo/ceph.owl homepage: https://github.com/obophenotype/cephalopod-ontology name: Cephalopod Ontology prefix: ceph version: '2016-01-12' version.iri: http://purl.obolibrary.org/obo/ceph/releases/2016-01-12/ceph.owl ontobee: library: Library name: Cephalopod Ontology prefix: CEPH url: http://www.ontobee.org/ontology/CEPH pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: CEPH uri_format: http://purl.obolibrary.org/obo/CEPH_$1 cgd: 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=$1 mappings: go: CGD miriam: cgd n2t: cgd ncbi: CGD prefixcommons: CGD uniprot: CGD miriam: deprecated: false description: The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products. homepage: http://www.candidagenome.org/ id: '00000145' name: Candida Genome Database namespaceEmbeddedInLui: false pattern: ^CAL\d{7}$ 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 cgnc: contributor: email: cthoyt@gmail.com 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 synonyms: - BirdBase - CGNC uri_format: http://birdgenenames.org/cgnc/GeneReport?id=$1 cgsc: go: homepage: http://cgsc.biology.yale.edu/ name: CGSC prefix: CGSC mappings: go: CGSC miriam: cgsc n2t: cgsc prefixcommons: CGSC miriam: deprecated: false description: The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. homepage: http://cgsc.biology.yale.edu/index.php id: 00000295 name: CGSC Strain namespaceEmbeddedInLui: false pattern: ^\d+$ 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 url: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=$1 example: '24867' 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:$1 mappings: bioportal: CHEBI cellosaurus: ChEBI go: CHEBI miriam: chebi n2t: chebi obofoundry: chebi ols: chebi ontobee: CHEBI prefixcommons: CHEBI wikidata: P683 miriam: deprecated: false description: Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. homepage: https://www.ebi.ac.uk/chebi/ id: '00000002' name: ChEBI namespaceEmbeddedInLui: true pattern: ^CHEBI:\d+$ 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:$1 name: Chemical Entities of Biological Interest obofoundry: contact: amalik@ebi.ac.uk contact.github: amalik01 contact.label: Adnan Malik deprecated: false description: A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds. download.obo: http://purl.obolibrary.org/obo/chebi.obo download.owl: http://purl.obolibrary.org/obo/chebi.owl homepage: http://www.ebi.ac.uk/chebi inactive: false license: CC-BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Chemical Entities of Biological Interest preferredPrefix: CHEBI prefix: chebi repository: https://github.com/ebi-chebi/ChEBI ols: description: A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds. download: http://purl.obolibrary.org/obo/chebi.owl homepage: http://www.ebi.ac.uk/chebi name: Chemical Entities of Biological Interest prefix: chebi version: '205' version.iri: http://purl.obolibrary.org/obo/chebi/205/chebi.owl ontobee: library: Foundry name: Chemical Entities of Biological Interest prefix: CHEBI url: http://www.ontobee.org/ontology/CHEBI pattern: ^\d+$ 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:$1 chembl: homepage: https://www.ebi.ac.uk/chembl mappings: miriam: chembl uniprot: ChEMBL miriam: deprecated: false description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. homepage: https://www.ebi.ac.uk/chembl id: 00000799 name: ChEMBL namespaceEmbeddedInLui: false pattern: ^CHEMBL\d+$ 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/$1 chembl.compound: example: CHEMBL465070 mappings: miriam: chembl.compound n2t: chembl.compound prefixcommons: CHEMBL.COMPOUND wikidata: P592 miriam: deprecated: false description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. homepage: https://www.ebi.ac.uk/chembldb/ id: 00000084 name: ChEMBL compound namespaceEmbeddedInLui: false pattern: ^CHEMBL\d+$ 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/$1 part_of: chembl pattern: ^CHEMBL\d+$ 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/$1/ chembl.target: mappings: miriam: chembl.target n2t: chembl.target prefixcommons: CHEMBL.TARGET miriam: deprecated: false description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. homepage: https://www.ebi.ac.uk/chembldb/ id: 00000085 name: ChEMBL target namespaceEmbeddedInLui: false pattern: ^CHEMBL\d+$ 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/$1 chemdb: mappings: miriam: chemdb n2t: chemdb prefixcommons: CHEMDB miriam: deprecated: false description: ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. homepage: http://cdb.ics.uci.edu/ id: 00000279 name: ChemDB namespaceEmbeddedInLui: false pattern: ^\d+$ 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/$1 chemidplus: mappings: miriam: chemidplus n2t: chemidplus prefixcommons: CHEMIDPLUS miriam: deprecated: false description: ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. homepage: https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp id: 00000096 name: ChemIDplus namespaceEmbeddedInLui: false pattern: ^\d+\-\d+\-\d+$ 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' mappings: bioportal: CHEMINF obofoundry: cheminf ols: cheminf ontobee: CHEMINF prefixcommons: CHEMINF name: Chemical Information Ontology obofoundry: contact: egon.willighagen@gmail.com contact.label: Egon Willighagen 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 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 url: http://www.ontobee.org/ontology/CHEMINF prefixcommons: is_identifiers: false is_obo: true prefix: CHEMINF uri_format: http://purl.obolibrary.org/obo/CHEMINF_$1 chemspider: mappings: miriam: chemspider n2t: chemspider prefixcommons: CHEMSPIDER wikidata: P661 miriam: deprecated: false description: ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources. homepage: http://www.chemspider.com/ id: 00000138 name: ChemSpider namespaceEmbeddedInLui: false pattern: ^\d+$ 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 prefixcommons: is_identifiers: true is_obo: false prefix: CHEMSPIDER uri_format: http://identifiers.org/chemspider/$1 synonyms: - 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 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: CC-0 license.url: http://creativecommons.org/publicdomain/zero/1.0/ name: CHEBI Integrated Role Ontology preferredPrefix: CHIRO prefix: chiro 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 url: http://www.ontobee.org/ontology/CHIRO chmo: bioportal: name: Chemical Methods Ontology prefix: CHMO example: 0002902 mappings: bioportal: CHMO obofoundry: chmo ols: chmo ontobee: CHMO prefixcommons: CHMO obofoundry: contact: batchelorc@rsc.org contact.github: batchelorc contact.label: Colin Batchelor 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 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 license: http://creativecommons.org/licenses/by/4.0/ name: Chemical Methods Ontology prefix: chmo version: '2019-11-14' version.iri: http://purl.obolibrary.org/obo/chmo/releases/2014-11-20/chmo.owl ontobee: library: Library name: Chemical Methods Ontology prefix: CHMO url: http://www.ontobee.org/ontology/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' mappings: bioportal: CIDO obofoundry: cido ols: cido ontobee: CIDO obofoundry: contact: yongqunh@med.umich.edu contact.label: Yongqun Oliver He 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 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 license: http://creativecommons.org/licenses/by/4.0/ name: 'CIDO: Ontology of Coronavirus Infectious Disease' prefix: cido version: 1.0.259 ontobee: library: Library name: Coronavirus Infectious Disease Ontology prefix: CIDO url: http://www.ontobee.org/ontology/CIDO cio: bioportal: name: Confidence Information Ontology prefix: CIO example: '0000040' mappings: bioportal: CIO obofoundry: cio ols: cio ontobee: CIO prefixcommons: CIO obofoundry: contact: bgee@sib.swiss contact.github: fbastian contact.label: Frederic Bastian 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 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 url: http://www.ontobee.org/ontology/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 name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes. example: C6155 homepage: https://www.ebi.ac.uk/citexplore/ 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/$1 cl: bioportal: name: Cell Ontology prefix: CL download_obo: https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-full.obo example: '0000062' go: homepage: http://cellontology.org name: Cell Type Ontology prefix: CL mappings: bioportal: CL go: CL miriam: cl n2t: cl obofoundry: cl ols: cl ontobee: CL prefixcommons: CL miriam: deprecated: false description: The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi. homepage: https://www.ebi.ac.uk/ols/ontologies/cl id: '00000110' name: Cell Type Ontology namespaceEmbeddedInLui: true pattern: ^CL:\d{7}$ 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:$1 obofoundry: contact: addiehl@buffalo.edu contact.github: addiehl contact.label: Alexander Diehl deprecated: false description: The Cell Ontology is a structured controlled vocabulary for cell types in animals. download.obo: http://purl.obolibrary.org/obo/cl.obo download.owl: http://purl.obolibrary.org/obo/cl.owl homepage: https://obophenotype.github.io/cell-ontology/ inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/4.0/ name: Cell Ontology preferredPrefix: CL prefix: cl repository: https://github.com/obophenotype/cell-ontology ols: description: An ontology of cell types. download: http://purl.obolibrary.org/obo/cl.owl homepage: https://obophenotype.github.io/cell-ontology/ license: http://creativecommons.org/licenses/by/4.0/ name: Cell Ontology prefix: cl version: '2021-09-09' version.iri: http://purl.obolibrary.org/obo/cl/releases/2021-09-09/cl.owl ontobee: library: Library name: Cell Ontology prefix: CL url: http://www.ontobee.org/ontology/CL pattern: ^\d{7}$ 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 format: http://purl.obolibrary.org/obo/$1 homepage: http://www.ontobee.org/ontology/CL name: Cell Ontology ID pattern: CL_[0-9]{7} prefix: P7963 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" 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: CC-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 license: https://creativecommons.org/licenses/by/4.0/ 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 url: http://www.ontobee.org/ontology/CLAO 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 url: 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 url: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1 mappings: biolink: CLINVAR cellosaurus: ClinVar miriam: clinvar n2t: clinvar prefixcommons: ClinVar wikidata: P1929 miriam: deprecated: false description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier. homepage: http://www.ncbi.nlm.nih.gov/clinvar/ id: 00000596 name: ClinVar Variant namespaceEmbeddedInLui: false pattern: ^\d+$ 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 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: Ontologies homepage: http://www.clo-ontology.org name: Cell Line Ontology prefix: CLO url: https://www.ebi.ac.uk/ols/ontologies/clo/terms?iri=http://purl.obolibrary.org/obo/$1 example: 0000091 mappings: bioportal: CLO cellosaurus: CLO obofoundry: clo ols: clo ontobee: CLO prefixcommons: CLO obofoundry: contact: siiraa@umich.edu contact.label: Sirarat Sarntivijai 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 license.url: http://creativecommons.org/licenses/by/3.0/ name: Cell Line Ontology preferredPrefix: CLO prefix: clo 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: 2.1.162 ontobee: library: Library name: Cell Line Ontology prefix: CLO url: http://www.ontobee.org/ontology/CLO prefixcommons: is_identifiers: false is_obo: true prefix: CLO uri_format: http://purl.obolibrary.org/obo/CLO_$1 synonyms: - CLO wikidata: prefix: P2158 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 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 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 url: http://www.ontobee.org/ontology/CLYH cmf: deprecated: true description: This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain mappings: obofoundry: cmf prefixcommons: CMF obofoundry: contact: engelsta@ohsu.edu contact.label: Mark Engelstad deprecated: true homepage: https://code.google.com/p/craniomaxillofacial-ontology/ inactive: true name: CranioMaxilloFacial ontology prefix: cmf prefixcommons: is_identifiers: false is_obo: true prefix: CMF uri_format: http://purl.obolibrary.org/obo/CMF_$1 cmo: bioportal: name: Clinical Measurement Ontology prefix: CMO example: '0001350' mappings: bioportal: CMO obofoundry: cmo ols: cmo ontobee: CMO prefixcommons: CMO obofoundry: contact: shimoyama@mcw.edu contact.label: Mary Shimoyama deprecated: false description: Morphological and physiological measurement records generated from clinical and model organism research and health programs. download.obo: http://purl.obolibrary.org/obo/cmo.obo download.owl: http://purl.obolibrary.org/obo/cmo.owl homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html inactive: false license: CC-0 license.url: http://creativecommons.org/publicdomain/zero/1.0/ name: Clinical measurement ontology preferredPrefix: CMO prefix: cmo repository: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology ols: description: Morphological and physiological measurement records generated from clinical and model organism research and health programs. download: http://purl.obolibrary.org/obo/cmo.owl homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html name: Clinical measurement ontology prefix: cmo version: '2019-02-19' version.iri: http://purl.obolibrary.org/obo/cmo/releases/2019-02-19/cmo.owl ontobee: library: Library name: Clinical measurement ontology prefix: CMO url: http://www.ontobee.org/ontology/CMO pattern: ^\d{7}$ 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' mappings: bioportal: CMPO 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 co_320: example: 0000618 mappings: 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: http://127.0.0.1:5900/ontology/CO_320/Rice/owl homepage: http://127.0.0.1:5900/ontology/CO_320/Rice name: Rice ontology prefix: co_320 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_320:$1 co_321: example: 0000449 mappings: ols: co_321 ols: contact: helpdesk@cropontology-curationtool.org description: July 2018 download: http://127.0.0.1:5900/ontology/CO_321/Wheat/owl homepage: http://127.0.0.1:5900/ontology/CO_321/Wheat name: Wheat ontology prefix: co_321 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_321:$1 co_322: example: '0000773' mappings: ols: co_322 ols: contact: helpdesk@cropontology-curationtool.org description: Maize Trait Dictionary in template 5 - CIMMYT- September 2016 download: http://127.0.0.1:5900/ontology/CO_322/Maize/owl homepage: http://127.0.0.1:5900/ontology/CO_322/Maize name: Maize ontology prefix: co_322 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_322:$1 co_323: example: '0000252' mappings: ols: co_323 ols: contact: helpdesk@cropontology-curationtool.org description: ICARDA - TDv5 - Sept 2018 download: http://127.0.0.1:5900/ontology/CO_323/Barley/owl homepage: http://127.0.0.1:5900/ontology/CO_323/Barley name: Barley ontology prefix: co_323 version: '2019-11-20' uri_format: https://www.cropontology.org/rdf/CO_323:$1 co_324: example: '0000111' mappings: ols: co_324 ols: contact: helpdesk@cropontology-curationtool.org description: Sorghum TDv5 - Oct 2019 download: http://127.0.0.1:5900/ontology/CO_324/Sorghum/owl homepage: http://127.0.0.1:5900/ontology/CO_324/Sorghum name: Sorghum ontology prefix: co_324 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_324:$1 co_325: example: 0000519 mappings: ols: co_325 ols: contact: helpdesk@cropontology-curationtool.org description: Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019 download: http://127.0.0.1:5900/ontology/CO_325/Banana/owl homepage: http://127.0.0.1:5900/ontology/CO_325/Banana name: Banana ontology prefix: co_325 version: '2019-10-09' 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: http://127.0.0.1:5900/ontology/CO_326/Coconut/owl homepage: http://127.0.0.1:5900/ontology/CO_326/Coconut name: Coconut ontology prefix: co_326 co_327: example: 0000095 mappings: 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 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_327:$1 co_330: example: '0000106' mappings: ols: co_330 ols: contact: helpdesk@cropontology-curationtool.org description: CIP - potato ontology - december 2018 download: http://127.0.0.1:5900/ontology/CO_330/Potato/owl homepage: http://127.0.0.1:5900/ontology/CO_330/Potato name: Potato ontology prefix: co_330 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_330:$1 co_331: example: 0000088 mappings: 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 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_331:$1 co_333: example: '3000045' mappings: 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 version: '2019-01-23' uri_format: https://www.cropontology.org/rdf/CO_333:$1 co_334: example: '0000070' mappings: ols: co_334 ols: contact: helpdesk@cropontology-curationtool.org description: Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016 download: http://127.0.0.1:5900/ontology/CO_334/Cassava/owl homepage: http://127.0.0.1:5900/ontology/CO_334/Cassava name: Cassava ontology prefix: co_334 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_334:$1 co_335: example: 0000189 mappings: 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 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_335:$1 co_336: example: 0000339 mappings: ols: co_336 ols: contact: helpdesk@cropontology-curationtool.org description: Soybean Trait Dictionary in template v5 - IITA - July 2015 download: http://127.0.0.1:5900/ontology/CO_336/Soybean/owl homepage: http://127.0.0.1:5900/ontology/CO_336/Soybean name: Soybean ontology prefix: co_336 uri_format: https://www.cropontology.org/rdf/CO_336:$1 co_337: example: '0000054' mappings: ols: co_337 ols: contact: helpdesk@cropontology-curationtool.org description: Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015 download: http://127.0.0.1:5900/ontology/CO_337/Groundnut/owl homepage: http://127.0.0.1:5900/ontology/CO_337/Groundnut name: Groundnut ontology prefix: co_337 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_337:$1 co_338: example: 0000138 mappings: ols: co_338 ols: contact: helpdesk@cropontology-curationtool.org description: Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015 download: http://127.0.0.1:5900/ontology/CO_338/Chickpea/owl homepage: http://127.0.0.1:5900/ontology/CO_338/Chickpea name: Chickpea ontology prefix: co_338 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_338:$1 co_339: example: '0000032' mappings: ols: co_339 ols: contact: helpdesk@cropontology-curationtool.org description: Lentil Trait Dictionary in template v5 - ICARDA - July 2015 download: http://127.0.0.1:5900/ontology/CO_339/Lentil/owl homepage: http://127.0.0.1:5900/ontology/CO_339/Lentil name: Lentil ontology prefix: co_339 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_339:$1 co_340: example: 0000639 mappings: ols: co_340 ols: contact: helpdesk@cropontology-curationtool.org description: Cowpea Trait Dictionary in template v5 - IITA - August 2015 download: http://127.0.0.1:5900/ontology/CO_340/Cowpea/owl homepage: http://127.0.0.1:5900/ontology/CO_340/Cowpea name: Cowpea ontology prefix: co_340 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_340:$1 co_341: example: '0000140' mappings: ols: co_341 ols: contact: helpdesk@cropontology-curationtool.org description: Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015 download: http://127.0.0.1:5900/ontology/CO_341/Pigeonpea/owl homepage: http://127.0.0.1:5900/ontology/CO_341/Pigeonpea name: Pigeonpea ontology prefix: co_341 version: '2019-11-18' uri_format: https://www.cropontology.org/rdf/CO_341:$1 co_343: example: '0100010' mappings: ols: co_343 ols: contact: helpdesk@cropontology-curationtool.org description: version 2019 - pvs download: http://127.0.0.1:5900/ontology/CO_343/Yam/owl homepage: http://127.0.0.1:5900/ontology/CO_343/Yam name: Yam ontology prefix: co_343 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_343:$1 co_345: example: '0000127' mappings: ols: co_345 ols: contact: helpdesk@cropontology-curationtool.org description: Brachiaria (forages) ontology TD v5 - Version Oct 2016 download: http://127.0.0.1:5900/ontology/CO_345/Brachiaria/owl homepage: http://127.0.0.1:5900/ontology/CO_345/Brachiaria name: Brachiaria ontology prefix: co_345 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_345:$1 co_346: example: 0000199 mappings: ols: co_346 ols: contact: helpdesk@cropontology-curationtool.org description: oct 2016 download: http://127.0.0.1:5900/ontology/CO_346/Mungbean/owl homepage: http://127.0.0.1:5900/ontology/CO_346/Mungbean name: Mungbean ontology prefix: co_346 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_346:$1 co_347: example: 0000108 mappings: 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 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_347:$1 co_348: example: '1100107' mappings: 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: http://127.0.0.1:5900/ontology/CO_348/Brassica/owl homepage: http://127.0.0.1:5900/ontology/CO_348/Brassica name: Brassica ontology prefix: co_348 version: '2019-11-29' uri_format: https://www.cropontology.org/rdf/CO_348:$1 co_350: example: '0000215' mappings: 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: http://127.0.0.1:5900/ontology/CO_350/Oat/owl homepage: http://127.0.0.1:5900/ontology/CO_350/Oat name: Oat ontology prefix: co_350 version: '2019-10-09' uri_format: https://www.cropontology.org/rdf/CO_350:$1 co_356: example: '4000027' mappings: ols: co_356 ols: contact: helpdesk@cropontology-curationtool.org description: Grape Ontology including OIV and bioversity descriptors. INRA July 2017 download: http://127.0.0.1:5900/ontology/CO_356/Vitis/owl homepage: http://127.0.0.1:5900/ontology/CO_356/Vitis name: Vitis ontology prefix: co_356 version: '2019-11-29' uri_format: https://www.cropontology.org/rdf/CO_356:$1 co_357: example: '1000290' mappings: 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 version: '2019-11-18' 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: http://127.0.0.1:5900/ontology/CO_358/Cotton/owl homepage: http://127.0.0.1:5900/ontology/CO_358/Cotton name: Cotton ontology prefix: co_358 version: '2020-01-03' 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: http://127.0.0.1:5900/ontology/CO_359/Sunflower/owl homepage: http://127.0.0.1:5900/ontology/CO_359/Sunflower name: Sunflower ontology prefix: co_359 uri_format: https://www.cropontology.org/rdf/CO_359:$1 co_360: example: '0000071' mappings: 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 version: '2019-06-26' 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: http://127.0.0.1:5900/ontology/CO_365/Fababean/owl homepage: http://127.0.0.1:5900/ontology/CO_365/Fababean name: Fababean ontology prefix: co_365 version: '2019-10-15' 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 version: '2019-12-23' 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 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 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 license: https://creativecommons.org/publicdomain/zero/1.0/ name: Core Ontology for Biology and Biomedicine prefix: cob version: '2021-09-13' version.iri: http://purl.obolibrary.org/obo/cob/releases/2021-09-13/cob-native.owl ontobee: library: Library name: Core Ontology for Biology and Biomedicine prefix: COB url: http://www.ontobee.org/ontology/COB coconut: comment: '@mSorok is the dev of the resource, hope I got it right!' contributor: email: null 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 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: cogs@ncbi.nlm.nih.gov 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 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=$1 homepage: https://www.ncbi.nlm.nih.gov/research/cog/ mappings: biolink: COG go: COG_Cluster name: Cluster of orthologous genes pattern: ^COG\d+$ synonyms: - COG_Cluster uri_format: https://www.ncbi.nlm.nih.gov/research/cog/cog/$1 cog.category: contact: cogs@ncbi.nlm.nih.gov contributor: email: cthoyt@gmail.com 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: cogs@ncbi.nlm.nih.gov 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/$1 cohd: comment: not really sure where the source is. this also links to a system called athena. I was not able to figure out what COHD stands for. contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012 homepage: https://github.com/MIT-LCP/mimic-omop name: MIMIC III Database no_own_terms: true combine.specifications: mappings: miriam: combine.specifications n2t: combine.specifications prefixcommons: COMBINE.SPECIFICATIONS miriam: deprecated: false description: The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network. homepage: https://co.mbine.org/standards/ id: 00000258 name: COMBINE specifications namespaceEmbeddedInLui: false pattern: ^\w+(\-|\.|\w)*$ 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 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 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/$1 compulyeast: mappings: miriam: compulyeast n2t: compulyeast prefixcommons: COMPULYEAST miriam: deprecated: false description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record. homepage: http://compluyeast2dpage.dacya.ucm.es/ id: 00000198 name: Compulyeast namespaceEmbeddedInLui: false pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ 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/$1 conoserver: mappings: miriam: conoserver n2t: conoserver prefixcommons: CONOSERVER uniprot: ConoServer miriam: deprecated: false description: ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails. homepage: http://www.conoserver.org/ id: '00000254' name: Conoserver namespaceEmbeddedInLui: false pattern: ^\d+$ 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=$1 conso: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases. example: CONSO00010 homepage: https://pharmacome.github.io/conso/ name: Curation of Neurodegeneration Supporting Ontology pattern: ^CONSO\d{5}$ 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 url: 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=$1 corrdb: mappings: miriam: corrdb miriam: deprecated: false description: A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies. homepage: https://www.animalgenome.org id: 00000831 name: CorrDB namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: corrdb sampleId: '37232' uri_format: https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1 corum: 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=$1 mappings: go: CORUM miriam: corum n2t: corum prefixcommons: CORUM uniprot: CORUM miriam: deprecated: false description: The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded. homepage: https://mips.helmholtz-muenchen.de/genre/proj/corum/ id: '00000440' name: CORUM namespaceEmbeddedInLui: false pattern: ^\d+$ 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 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 url: https://cancer.sanger.ac.uk/cosmic/sample/overview?id=$1 mappings: cellosaurus: Cosmic miriam: cosmic n2t: cosmic prefixcommons: COSMIC miriam: deprecated: false description: COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes. homepage: http://cancer.sanger.ac.uk/cosmic/ id: '00000601' name: COSMIC Gene namespaceEmbeddedInLui: false pattern: ^[A-Z0-9]+$ 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: contributor: email: cthoyt@gmail.com 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/ name: COSMIC Cell Lines 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/$1 covoc: example: '0010034' mappings: ols: covoc ols: description: The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more. download: https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl homepage: https://github.com/EBISPOT/covoc license: http://creativecommons.org/licenses/by/4.0/ name: CoVoc Coronavirus Vocabulary prefix: covoc version: '2020-08-28' version.iri: http://purl.obolibrary.org/obo/covoc/releases/2020-08-28/covoc.owl cp: appears_in: - cl comment: Part of cell ontology but deprecated, see https://github.com/obophenotype/cell-ontology/issues/572 contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: Cellular Phenotypes cpc: mappings: miriam: cpc n2t: cpc prefixcommons: CPC miriam: deprecated: false description: The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013. homepage: https://worldwide.espacenet.com/classification id: 00000539 name: Cooperative Patent Classification namespaceEmbeddedInLui: false pattern: ^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H, Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$ 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/$1 cpga: bioportal: name: Cereal Plant Gross Anatomy Ontology prefix: GRO-CPGA deprecated: true mappings: bioportal: GRO-CPGA obofoundry: gro prefixcommons: gro.cpga obofoundry: contact: po-discuss@plantontology.org contact.label: Plant Ontology Administrators deprecated: true homepage: http://www.gramene.org/plant_ontology/ inactive: true name: Cereal Plant Gross Anatomy prefix: gro crisprdb: mappings: miriam: crisprdb n2t: crisprdb prefixcommons: CRISPRDB miriam: deprecated: false description: Repeated CRISPR ("clustered regularly interspaced short palindromic repeats") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data. homepage: http://crispr.i2bc.paris-saclay.fr/ id: '00000626' name: CRISPRdb namespaceEmbeddedInLui: false pattern: ^[0-9]+$ 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/$1 cro: bioportal: name: Contributor Role Ontology prefix: CRO download_obo: https://raw.githubusercontent.com/data2health/contributor-role-ontology/master/cro.obo example: 0000038 mappings: bioportal: CRO obofoundry: cro ols: cro ontobee: CRO prefixcommons: CRO obofoundry: contact: whimar@ohsu.edu contact.github: marijane contact.label: Marijane White deprecated: false description: A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. download.owl: http://purl.obolibrary.org/obo/cro.owl homepage: https://github.com/data2health/contributor-role-ontology inactive: false license: CC-BY license.url: https://creativecommons.org/licenses/by/2.0/ name: Contributor Role Ontology preferredPrefix: CRO prefix: cro repository: https://github.com/data2health/contributor-role-ontology ols: description: A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. download: http://purl.obolibrary.org/obo/cro.owl homepage: https://github.com/data2health/contributor-role-ontology name: Contributor Role Ontology prefix: cro version: '2019-12-11' version.iri: http://purl.obolibrary.org/obo/cro/releases/2019-12-11/cro.owl ontobee: library: Library name: Contributor Role Ontology prefix: CRO url: http://www.ontobee.org/ontology/CRO pattern: ^\d{7}$ 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 license: https://creativecommons.org/licenses/by/3.0/ 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 cryptodb: mappings: 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/$1 csa: mappings: miriam: csa n2t: csa prefixcommons: CSA miriam: deprecated: false description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme. homepage: https://www.ebi.ac.uk/thornton-srv/databases/CSA/ id: '00000144' name: CSA namespaceEmbeddedInLui: false pattern: ^[0-9][A-Za-z0-9]{3}$ 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/$1 csd: mappings: miriam: csd miriam: deprecated: false description: The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode. homepage: https://www.ccdc.cam.ac.uk/ id: 00000820 name: Cambridge Structural Database namespaceEmbeddedInLui: false pattern: ^[A-Z]{6}(\d{2})?$ prefix: csd sampleId: PELNAW uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG csp: bioportal: name: Computer Retrieval of Information on Scientific Projects Thesaurus prefix: CRISP deprecated: true example: 2004-2820 homepage: https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm mappings: bioportal: CRISP name: Computer Retrieval of Information on Science Projects (CRISP) Thesaurus synonyms: - CRISP Thesaurus - CRISP Thesaurus, 2006 - CSP2005 cst: bioportal: name: Cancer Staging Terms prefix: CST mappings: bioportal: CST miriam: cst n2t: cst prefixcommons: CST miriam: deprecated: false description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways. homepage: http://www.cellsignal.com/pathways/index.html id: 00000429 name: Cell Signaling Technology Pathways namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9_-]+$ 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/$1 ctd.chemical: mappings: miriam: ctd.chemical n2t: ctd.chemical prefixcommons: CTD.CHEMICAL miriam: deprecated: false description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. homepage: http://ctdbase.org/ id: 00000098 name: CTD Chemical namespaceEmbeddedInLui: false pattern: ^[CD]\d+$ 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/$1 provides: mesh ctd.disease: mappings: miriam: ctd.disease n2t: ctd.disease prefixcommons: CTD.DISEASE miriam: deprecated: false description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. homepage: http://ctdbase.org/ id: 00000099 name: CTD Disease namespaceEmbeddedInLui: false pattern: ^D\d+$ 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/$1 provides: mesh ctd.gene: mappings: miriam: ctd.gene n2t: ctd.gene prefixcommons: CTD.GENE miriam: deprecated: false description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. homepage: http://ctdbase.org/ id: '00000100' name: CTD Gene namespaceEmbeddedInLui: false pattern: ^\d+$ 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/$1 provides: ncbigene cteno: bioportal: name: Ctenophore Ontology prefix: CTENO download_obo: https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo example: '0000047' mappings: bioportal: CTENO obofoundry: cteno ols: cteno ontobee: CTENO prefixcommons: CTENO obofoundry: contact: cjmungall@lbl.gov contact.github: cmungall contact.label: Chris Mungall deprecated: false description: An anatomical and developmental ontology for ctenophores (Comb Jellies) download.owl: http://purl.obolibrary.org/obo/cteno.owl homepage: https://github.com/obophenotype/ctenophore-ontology inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: Ctenophore Ontology preferredPrefix: CTENO prefix: cteno repository: https://github.com/obophenotype/ctenophore-ontology ols: description: An anatomical and developmental ontology for ctenophores (Comb Jellies) download: http://purl.obolibrary.org/obo/cteno.owl homepage: https://github.com/obophenotype/ctenophore-ontology name: Ctenophore Ontology prefix: cteno version: '2016-10-19' version.iri: http://purl.obolibrary.org/obo/cteno/releases/2016-10-19/cteno.owl ontobee: library: Library name: Ctenophore Ontology prefix: CTENO url: http://www.ontobee.org/ontology/CTENO pattern: ^\d{7}$ 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' mappings: bioportal: CTO obofoundry: cto ols: cto ontobee: CTO obofoundry: contact: alpha.tom.kodamullil@scai.fraunhofer.de contact.github: akodamullil contact.label: Dr. Alpha Tom Kodamullil 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 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 license: http://creativecommons.org/licenses/by/4.0 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 url: http://www.ontobee.org/ontology/CTO 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' mappings: bioportal: CVDO obofoundry: cvdo ols: cvdo ontobee: CVDO prefixcommons: CVDO obofoundry: contact: paul.fabry@usherbrooke.ca contact.label: Paul Fabry 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 url: http://www.ontobee.org/ontology/CVDO 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/$1 darc: mappings: miriam: darc n2t: darc prefixcommons: DARC miriam: deprecated: false description: DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors. homepage: http://darcsite.genzentrum.lmu.de/darc/index.php id: '00000366' name: DARC namespaceEmbeddedInLui: false pattern: ^\d+$ 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/$1 dashr: mappings: miriam: dashr n2t: dashr prefixcommons: DASHR miriam: deprecated: false description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records. homepage: http://lisanwanglab.org/DASHR/ id: '00000564' name: DASHR namespaceEmbeddedInLui: false pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ 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/$1 dbest: mappings: miriam: dbest n2t: dbest ncbi: dbEST prefixcommons: DBEST miriam: deprecated: false description: The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. homepage: https://www.ncbi.nlm.nih.gov/nucest id: 00000159 name: dbEST namespaceEmbeddedInLui: false pattern: ^([A-Z]+)?\d+(\.\d+)?$ 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/$1 dbgap: mappings: miriam: dbgap n2t: dbgap prefixcommons: DBGAP miriam: deprecated: false description: The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. homepage: https://www.ncbi.nlm.nih.gov/projects/gap id: '00000602' name: dbGaP namespaceEmbeddedInLui: false pattern: ^phs[0-9]{6}(.v\d+.p\d+)?$ 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/$1 dbmhc: appears_in: - cellosaurus cellosaurus: category: Cell line databases/resources homepage: https://www.ncbi.nlm.nih.gov/gv/mhc/ name: dbMHC database prefix: dbMHC deprecated: true example: '48439' mappings: cellosaurus: dbMHC name: Database of human Major Histocompatibility Complex dbprobe: mappings: miriam: dbprobe n2t: dbprobe ncbi: dbProbe prefixcommons: DBPROBE miriam: deprecated: false description: The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities. homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe id: '00000160' name: dbProbe namespaceEmbeddedInLui: false pattern: ^\d+$ 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 url: https://www.ncbi.nlm.nih.gov/snp/$1 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=$1 mappings: cellosaurus: dbSNP go: dbSNP miriam: dbsnp n2t: dbsnp ncbi: dbSNP prefixcommons: dbSNP uniprot: dbSNP miriam: deprecated: false description: The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. homepage: https://www.ncbi.nlm.nih.gov/snp/ id: '00000161' name: dbSNP namespaceEmbeddedInLui: false pattern: ^rs\d+$ 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: appears_in: - efo bioportal: name: Dublin Core prefix: DC deprecated: true download_obo: https://github.com/obophenotype/human-disease-ontology/raw/master/src/experimental/missing-omc.obo example: 0000598 mappings: bioportal: DC prefixcommons: dc name: Disease Class prefixcommons: is_identifiers: false is_obo: false prefix: dc uri_format: http://purl.org/dc/elements/1.1/$1 dc_cl: mappings: obofoundry: dc_cl prefixcommons: DC_CL obofoundry: contact: Lindsay.Cowell@utsouthwestern.edu contact.label: Lindsay Cowell deprecated: true homepage: http://www.dukeontologygroup.org/Projects.html inactive: true name: Dendritic cell prefix: dc_cl 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 homepage: https://www.w3.org/ns/dcat mappings: biolink: dcat bioportal: DCAT 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 homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ mappings: biolink: dct bioportal: DCTERMS 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: https://dublincore.org/specifications/dublin-core/dcmi-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/$1 ddanat: bioportal: name: Dictyostelium Discoideum Anatomy Ontology prefix: DDANAT example: '0000006' go: homepage: http://dictybase.org/Dicty_Info/dicty_anatomy_ontology.html name: Dictyostelium discoideum anatomy prefix: DDANAT mappings: bioportal: DDANAT go: DDANAT obofoundry: ddanat ols: ddanat ontobee: DDANAT prefixcommons: DDANAT obofoundry: contact: pfey@northwestern.edu contact.github: pfey03 contact.label: Petra Fey deprecated: false description: A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum download.obo: http://purl.obolibrary.org/obo/ddanat.obo download.owl: http://purl.obolibrary.org/obo/ddanat.owl homepage: http://dictybase.org/ inactive: false license: CC0 1.0 Universal license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Dictyostelium discoideum anatomy preferredPrefix: DDANAT prefix: ddanat repository: https://github.com/dictyBase/migration-data ols: description: A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum download: http://purl.obolibrary.org/obo/ddanat.owl homepage: http://dictybase.org/ name: Dictyostelium discoideum anatomy prefix: ddanat version: '2020-04-13' version.iri: http://purl.obolibrary.org/obo/ddanat/releases/2020-04-13/ddanat.owl ontobee: library: Library name: Dictyostelium discoideum anatomy prefix: DDANAT url: http://www.ontobee.org/ontology/DDANAT pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: DDANAT uri_format: http://purl.obolibrary.org/obo/DDANAT_$1 ddpheno: bioportal: name: Dictyostelium Discoideum Phenotype Ontology prefix: DDPHENO download_obo: https://raw.githubusercontent.com/obophenotype/dicty-phenotype-ontology/master/ddpheno.obo example: '0001417' mappings: bioportal: DDPHENO obofoundry: ddpheno ols: ddpheno ontobee: DDPHENO prefixcommons: DDPHENO obofoundry: contact: pfey@northwestern.edu contact.github: pfey03 contact.label: Petra Fey deprecated: false description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. download.obo: http://purl.obolibrary.org/obo/ddpheno.obo download.owl: http://purl.obolibrary.org/obo/ddpheno.owl homepage: http://dictybase.org/ inactive: false license: CC-0 license.url: http://creativecommons.org/publicdomain/zero/1.0/ name: Dictyostelium discoideum phenotype ontology preferredPrefix: DDPHENO prefix: ddpheno repository: https://github.com/obophenotype/dicty-phenotype-ontology ols: description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. download: http://purl.obolibrary.org/obo/ddpheno.owl homepage: http://dictybase.org/ name: Dicty Phenotype Ontology (DDPHENO) prefix: ddpheno version: '2020-06-19' version.iri: http://purl.obolibrary.org/obo/ddpheno/releases/2020-06-19/ddpheno.owl ontobee: library: Library name: Dictyostelium discoideum phenotype ontology prefix: DDPHENO url: http://www.ontobee.org/ontology/DDPHENO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: DDPHENO uri_format: http://purl.obolibrary.org/obo/DDPHENO_$1 degradome: mappings: miriam: degradome n2t: degradome prefixcommons: DEGRADOME miriam: deprecated: false description: The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced. homepage: http://degradome.uniovi.es/ id: '00000454' name: Degradome Database namespaceEmbeddedInLui: false pattern: ^[AMCST][0-9x][0-9]$ 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 url: 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/$1 depod: mappings: miriam: depod n2t: depod prefixcommons: DEPOD uniprot: DEPOD miriam: deprecated: false description: The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources. homepage: http://www.depod.bioss.uni-freiburg.de id: 00000428 name: DEPOD namespaceEmbeddedInLui: false pattern: ^[A-Z0-9]+$ 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=$1 dermo: bioportal: name: Human Dermatological Disease Ontology prefix: DERMO description: DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders example: '0000000' homepage: https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x mappings: bioportal: DERMO name: Human Dermatological Disease Ontology dev.ga4ghdos: mappings: miriam: dev.ga4ghdos n2t: dev.ga4ghdos prefixcommons: DEV.GA4GHDOS miriam: deprecated: false description: Assists in resolving data across cloud resources. homepage: http://github.com/ga4gh/data-object-service-schemas id: '00000656' name: Development Data Object Service namespaceEmbeddedInLui: false pattern: ^[a-zA-Z0-9\-:#\.]+$ 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 dicom: bioportal: name: DICOM Controlled Terminology prefix: DCM example: '109082' mappings: bioportal: DCM 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: 2021d_20210910 dictybase: description: A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics go: homepage: http://dictybase.org name: dictyBase prefix: dictyBase synonyms: - DDB - DictyBase uri_format: http://dictybase.org/gene/$1 mappings: 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 mappings: bioportal: DIDEO obofoundry: dideo ols: dideo ontobee: DIDEO prefixcommons: DIDEO obofoundry: contact: mbrochhausen@gmail.com contact.github: mbrochhausen contact.label: Mathias Brochhausen 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 license: http://creativecommons.org/licenses/by/4.0/ 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 url: http://www.ontobee.org/ontology/DIDEO 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 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 license.url: https://creativecommons.org/licenses/by/3.0/ name: The Drug-Drug Interactions Ontology prefix: dinto repository: https://github.com/labda/DINTO prefixcommons: is_identifiers: false is_obo: true prefix: DINTO uri_format: http://purl.obolibrary.org/obo/DINTO_$1 dip: mappings: miriam: dip n2t: dip prefixcommons: DIP uniprot: DIP miriam: deprecated: false description: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions homepage: https://dip.doe-mbi.ucla.edu/ id: '00000044' name: Database of Interacting Proteins namespaceEmbeddedInLui: false pattern: ^DIP(\:)?\-\d{1,}[ENXS]$ 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=$1 diseasesdb: description: 'The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities.' example: '1784' homepage: http://www.diseasesdatabase.com/ name: Diseases Database wikidata: database: Q213103 prefix: P557 disprot: mappings: miriam: disprot n2t: disprot prefixcommons: DISPROT uniprot: DisProt miriam: deprecated: false description: DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature. homepage: https://disprot.org/ id: 00000199 name: DisProt namespaceEmbeddedInLui: false pattern: ^DP\d{5}$ 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 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 url: https://dx.doi.org/$1 go: homepage: http://dx.doi.org/ name: Digital Object Identifier prefix: DOI uri_format: http://dx.doi.org/$1 mappings: biolink: doi cellosaurus: DOI go: DOI miriam: doi n2t: doi prefixcommons: DOI scholia: doi miriam: deprecated: false description: The Digital Object Identifier System is for identifying content objects in the digital environment. homepage: https://www.doi.org/ id: 00000019 name: DOI namespaceEmbeddedInLui: false pattern: ^(doi\:)?\d{2}\.\d{4}.*$ 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/$1 doid: bioportal: name: Human Disease Ontology prefix: DOID download_obo: https://github.com/DiseaseOntology/HumanDiseaseOntology/raw/main/src/ontology/doid.obo example: 0110974 mappings: bioportal: DOID miriam: doid n2t: doid obofoundry: doid ols: doid ontobee: DOID prefixcommons: DOID wikidata: P699 miriam: deprecated: false description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. homepage: https://www.ebi.ac.uk/ols/ontologies/doid id: '00000233' name: Human Disease Ontology namespaceEmbeddedInLui: true pattern: ^DOID:\d+$ 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:$1 obofoundry: contact: lynn.schriml@gmail.com contact.github: lschriml contact.label: Lynn Schriml deprecated: false description: An ontology for describing the classification of human diseases organized by etiology. download.obo: http://purl.obolibrary.org/obo/doid.obo download.owl: http://purl.obolibrary.org/obo/doid.owl homepage: http://www.disease-ontology.org inactive: false license: CC0 1.0 Universal license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Human Disease Ontology preferredPrefix: DOID prefix: doid repository: https://github.com/DiseaseOntology/HumanDiseaseOntology ols: description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. download: http://purl.obolibrary.org/obo/doid.owl homepage: http://www.disease-ontology.org license: https://creativecommons.org/publicdomain/zero/1.0/ name: Human Disease Ontology prefix: doid version: '2021-10-12' version.iri: http://purl.obolibrary.org/obo/doid/releases/2021-10-12/doid.owl ontobee: library: Foundry name: Human Disease Ontology prefix: DOID url: http://www.ontobee.org/ontology/DOID pattern: ^\d+$ 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/$1 dpo: bioportal: name: Drosophila Phenotype Ontology prefix: DPO comment: DPO is a subset of terms from FBcv mappings: bioportal: DPO obofoundry: dpo ols: dpo ontobee: DPO no_own_terms: true obofoundry: contact: cp390@cam.ac.uk contact.label: Clare Pilgrim deprecated: false description: An ontology of commonly encountered and/or high level Drosophila phenotypes. download.json: http://purl.obolibrary.org/obo/dpo.json download.obo: http://purl.obolibrary.org/obo/dpo.obo download.owl: http://purl.obolibrary.org/obo/dpo.owl homepage: http://purl.obolibrary.org/obo/fbcv inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: Drosophila Phenotype Ontology preferredPrefix: FBcv prefix: dpo repository: https://github.com/FlyBase/drosophila-phenotype-ontology ols: description: An ontology for the description of Drosophila melanogaster phenotypes. download: http://purl.obolibrary.org/obo/dpo.owl homepage: http://purl.obolibrary.org/obo/fbcv license: https://creativecommons.org/licenses/by/3.0/ name: Drosophila Phenotype Ontology (DPO) prefix: dpo version: '2021-10-15' version.iri: http://purl.obolibrary.org/obo/dpo/releases/2021-10-15/dpo.owl ontobee: library: Library name: Drosophila Phenotype Ontology prefix: DPO url: http://www.ontobee.org/ontology/DPO part_of: fbcv preferred_prefix: DPO dpv: mappings: miriam: dpv n2t: dpv prefixcommons: DPV miriam: deprecated: false description: Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. homepage: http://www.dpvweb.net/ id: 00000280 name: DPV namespaceEmbeddedInLui: false pattern: ^\d+$ 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' mappings: bioportal: DRON obofoundry: dron ols: dron ontobee: DRON prefixcommons: DRON obofoundry: contact: hoganwr@gmail.com contact.label: William Hogan 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 license.url: http://creativecommons.org/licenses/by/3.0/ name: The Drug Ontology preferredPrefix: DRON prefix: dron 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 license: https://creativecommons.org/licenses/by/3.0/ name: The Drug Ontology prefix: dron version: '2021-10-20' version.iri: http://purl.obolibrary.org/obo/dron/releases/2021-10-20/dron.owl ontobee: library: Library name: The Drug Ontology prefix: DRON url: http://www.ontobee.org/ontology/DRON 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 url: https://go.drugbank.com/drugs/$1 example: DB14938 homepage: http://www.drugbank.ca mappings: cellosaurus: DrugBank miriam: drugbank n2t: drugbank prefixcommons: DrugBank uniprot: DrugBank miriam: deprecated: false description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information. homepage: http://www.drugbank.ca/ id: '00000102' name: DrugBank namespaceEmbeddedInLui: false pattern: ^DB\d{5}$ 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 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/$1 wikidata: prefix: P715 drugbank.salt: description: DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets. example: DBSALT001211 homepage: http://www.drugbank.ca mappings: prefixcommons: DRUGBANK.TARGET name: DrugBank Salts part_of: drugbank pattern: ^DBSALT\d{6}$ 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://translator.ncats.nih.gov/DrugCentral_$1 description: DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action. example: '307' homepage: http://drugcentral.org mappings: biolink: DrugCentral uniprot: DrugCentral name: Drug Central 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: contributor: email: cthoyt@gmail.com 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 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' homepage: https://github.com/DrugTargetOntology/DTO mappings: bioportal: DTO name: Drug Target Ontology duo: bioportal: name: The Data Use Ontology prefix: DUO example: '0000046' mappings: bioportal: DUO obofoundry: duo ols: duo ontobee: DUO prefixcommons: DUO obofoundry: contact: mcourtot@gmail.com contact.github: mcourtot contact.label: Melanie Courtot 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 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 license: http://creativecommons.org/licenses/by/4.0/ 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 url: http://www.ontobee.org/ontology/DUO prefixcommons: is_identifiers: false is_obo: true prefix: DUO uri_format: http://purl.obolibrary.org/obo/DUO_$1 eaglei: contributor: email: cthoyt@gmail.com 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 name: eagle-i uri_format: http://hawaii.eagle-i.net/i/$1 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 url: 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 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 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 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 url: http://www.ontobee.org/ontology/ECAO eccode: go: homepage: http://enzyme.expasy.org/ name: Enzyme Commission prefix: EC uri_format: https://enzyme.expasy.org/EC/$1 mappings: go: EC miriam: ec-code n2t: ec-code prefixcommons: EC miriam: deprecated: false description: The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions. homepage: https://www.ebi.ac.uk/intenz/ id: '00000004' name: Enzyme Nomenclature namespaceEmbeddedInLui: false pattern: ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$ 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=$1 name: Enzyme Nomenclature pattern: ^\d{1,2}(\.\d{0,3}){0,3}$ 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=$1 wikidata: prefix: P591 ecg: bioportal: name: Electrocardiography Ontology prefix: ECG description: The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms. example: 000000159 homepage: https://bioportal.bioontology.org/ontologies/ECG mappings: bioportal: ECG name: Electrocardiogram Ontology pattern: ^\d+$ 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: http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1 ecmdb: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: "The ECMDB is an expertly curated database containing extensive metabolomic\ \ data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655).\ \ This database includes significant quantities of \u201Coriginal\u201D data compiled\ \ by members of the Wishart laboratory as well as additional material derived\ \ from hundreds of textbooks, scientific journals, metabolic reconstructions and\ \ other electronic databases. Each metabolite is linked to more than 100 data\ \ fields describing the compound, its ontology, physical properties, reactions,\ \ pathways, references, external links and associated proteins or enzymes." example: ECMDB00005 homepage: https://ecmdb.ca name: E. coli Metabolite Database pattern: ^ECMDB\d+$ synonyms: - ECMDB uri_format: http://ecmdb.ca/compounds/$1 wikidata: database: Q17052437 eco: bioportal: name: Evidence and Conclusion Ontology prefix: ECO example: 0007807 go: homepage: http://www.evidenceontology.org/ name: Evidence Code Ontology prefix: ECO uri_format: http://www.evidenceontology.org/browse/#ECO_$1 mappings: bioportal: ECO go: ECO miriam: eco n2t: eco obofoundry: eco ols: eco ontobee: ECO prefixcommons: ECO miriam: deprecated: false description: Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity. homepage: https://www.ebi.ac.uk/ols/ontologies/eco id: '00000055' name: Evidence Code Ontology namespaceEmbeddedInLui: true pattern: ECO:\d{7}$ 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:$1 obofoundry: contact: mgiglio@som.umaryland.edu contact.github: mgiglio99 contact.label: Michelle Giglio deprecated: false description: An ontology for experimental and other evidence statements. download.obo: http://purl.obolibrary.org/obo/eco.obo download.owl: http://purl.obolibrary.org/obo/eco.owl homepage: https://github.com/evidenceontology/evidenceontology/ inactive: false license: CC0 1.0 Universal license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Evidence ontology preferredPrefix: ECO prefix: eco repository: https://github.com/evidenceontology/evidenceontology ols: description: The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the biological research domain that arise from laboratory experiments, computational methods, literature curation, or other means. download: http://purl.obolibrary.org/obo/eco.owl homepage: https://github.com/evidenceontology/evidenceontology/ license: https://creativecommons.org/publicdomain/zero/1.0/ name: Evidence & Conclusion Ontology (ECO) prefix: eco version: '2021-10-20' version.iri: http://purl.obolibrary.org/obo/eco/releases/2021-10-20/eco.owl ontobee: library: Library name: Evidence ontology prefix: ECO url: http://www.ontobee.org/ontology/ECO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: ECO uri_format: http://purl.obolibrary.org/obo/ECO_$1 ecocore: bioportal: name: An ontology of core ecological entities prefix: ECOCORE example: '00000001' mappings: bioportal: ECOCORE obofoundry: ecocore ols: ecocore ontobee: ECOCORE prefixcommons: ECOCORE obofoundry: contact: p.buttigieg@gmail.com contact.github: pbuttigieg contact.label: Pier Luigi Buttigieg deprecated: false description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. download.obo: http://purl.obolibrary.org/obo/ecocore.obo download.owl: http://purl.obolibrary.org/obo/ecocore.owl homepage: https://github.com/EcologicalSemantics/ecocore inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: An ontology of core ecological entities preferredPrefix: ECOCORE prefix: ecocore repository: https://github.com/EcologicalSemantics/ecocore ols: description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. download: http://purl.obolibrary.org/obo/ecocore.owl homepage: https://github.com/EcologicalSemantics/ecocore name: An ontology of core ecological entities prefix: ecocore version: '2021-02-17' version.iri: http://purl.obolibrary.org/obo/ecocore/releases/2021-02-17/ecocore.owl ontobee: library: Library name: An ontology of core ecological entities prefix: ECOCORE url: http://www.ontobee.org/ontology/ECOCORE pattern: ^\d+$ 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 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: 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=$1 ecogene: mappings: miriam: ecogene n2t: ecogene ncbi: EcoGene prefixcommons: EcoGene miriam: deprecated: false description: The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. homepage: http://ecogene.org/ id: '00000163' name: EcoGene namespaceEmbeddedInLui: false pattern: ^EG\d+$ 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/$1 ecoliwiki: go: description: EcoliHub\'s subsystem for community annotation of E. coli K-12 homepage: http://ecoliwiki.net/ name: EcoliWiki from EcoliHub prefix: EcoliWiki mappings: go: EcoliWiki miriam: ecoliwiki n2t: ecoliwiki prefixcommons: ECOLIWIKI miriam: deprecated: false description: EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes. homepage: http://ecoliwiki.net/colipedia/ id: '00000442' name: EcoliWiki namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9-]+$ 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 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 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 license: https://creativecommons.org/publicdomain/zero/1.0/ 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 url: http://www.ontobee.org/ontology/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/$1 edam: bioportal: name: EDAM - Bioscientific data analysis ontology prefix: EDAM mappings: bioportal: EDAM miriam: edam n2t: edam ols: edam ontobee: EDAM prefixcommons: EDAM miriam: deprecated: false description: 'EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).' homepage: http://bioportal.bioontology.org/ontologies/EDAM id: 00000189 name: EDAM Ontology namespaceEmbeddedInLui: false pattern: ^(data|topic|operation|format)\_\d{4}$ 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 url: http://www.ontobee.org/ontology/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 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: Ontologies homepage: https://www.ebi.ac.uk/efo/ name: Experimental Factor Ontology prefix: EFO url: https://www.ebi.ac.uk/efo/$1 download_obo: http://www.ebi.ac.uk/efo/efo.obo example: '0005147' mappings: biolink: EFO bioportal: EFO cellosaurus: EFO miriam: efo n2t: efo ols: efo ontobee: EFO prefixcommons: EFO miriam: deprecated: false description: The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team. homepage: https://www.ebi.ac.uk/ols/ontologies/efo id: 00000391 name: Experimental Factor Ontology namespaceEmbeddedInLui: false pattern: ^\d{7}$ 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 license: www.apache.org/licenses/LICENSE-2.0 name: Experimental Factor Ontology prefix: efo version: 3.35.0 version.iri: http://www.ebi.ac.uk/efo/releases/v3.35.0/efo.owl ontobee: library: Not Specified/No name: Experimental Factor Ontology prefix: EFO url: http://www.ontobee.org/ontology/EFO preferred_prefix: EFO prefixcommons: is_identifiers: false is_obo: true prefix: EFO uri_format: http://purl.obolibrary.org/obo/EFO_$1 uri_format: http://www.ebi.ac.uk/efo/EFO_$1 ega.dataset: homepage: https://ega-archive.org/ mappings: fairsharing: FAIRsharing.mya1ff miriam: ega.dataset n2t: ega.dataset prefixcommons: EGA.DATASET miriam: deprecated: false description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'. homepage: https://www.ebi.ac.uk/ega/dataset id: '00000512' name: European Genome-phenome Archive Dataset namespaceEmbeddedInLui: false pattern: ^EGAD\d{11}$ 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/$1 eggnog: mappings: miriam: eggnog n2t: eggnog prefixcommons: EGGNOG uniprot: eggNOG miriam: deprecated: false description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).' homepage: http://eggnog.embl.de/version_3.0/ id: '00000201' name: eggNOG namespaceEmbeddedInLui: false pattern: ^\w+$ 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 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 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 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 prefixcommons: is_identifiers: false is_obo: true prefix: EHDAA uri_format: http://purl.obolibrary.org/obo/EHDAA_$1 ehdaa2: bioportal: name: Human Developmental Anatomy Ontology, abstract version 2 prefix: EHDAA2 example: '0000000' mappings: bioportal: EHDAA2 obofoundry: ehdaa2 ols: ehdaa2 ontobee: EHDAA2 prefixcommons: EHDAA2 obofoundry: contact: J.Bard@ed.ac.uk contact.label: Jonathan Bard deprecated: false description: A structured controlled vocabulary of stage-specific anatomical structures of the developing human. download.obo: http://purl.obolibrary.org/obo/ehdaa2.obo download.owl: http://purl.obolibrary.org/obo/ehdaa2.owl homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology inactive: true license: CC-BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Human developmental anatomy, abstract prefix: ehdaa2 repository: https://github.com/obophenotype/human-developmental-anatomy-ontology ols: description: A structured controlled vocabulary of stage-specific anatomical structures of the developing human. download: http://purl.obolibrary.org/obo/ehdaa2.owl homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology name: Human developmental anatomy, abstract prefix: ehdaa2 version: '2013-07-04' version.iri: http://purl.obolibrary.org/obo/ehdaa2/releases/2013-07-04/ehdaa2.owl ontobee: library: Library name: Human developmental anatomy, abstract prefix: EHDAA2 url: http://www.ontobee.org/ontology/EHDAA2 pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: EHDAA2 uri_format: http://purl.obolibrary.org/obo/EHDAA2_$1 synonyms: - EHDAA2_RETIRED - HDAA2 - RETIRED_EHDAA2 elm: mappings: miriam: elm n2t: elm prefixcommons: ELM uniprot: ELM miriam: deprecated: false description: Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances. homepage: http://elm.eu.org/ id: '00000250' name: ELM namespaceEmbeddedInLui: false pattern: ^[A-Za-z_0-9]+$ 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 mappings: bioportal: EMAP obofoundry: emap prefixcommons: EMAP obofoundry: contact: Terry.Hayamizu@jax.org contact.github: tfhayamizu contact.label: Terry Hayamizu 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 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' 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:$1 mappings: bioportal: EMAPA go: EMAPA obofoundry: emapa ols: emapa ontobee: EMAPA prefixcommons: EMAPA obofoundry: contact: Terry.Hayamizu@jax.org contact.github: tfhayamizu contact.label: Terry Hayamizu deprecated: false description: An ontology for mouse anatomy covering embryonic development and postnatal stages. download.obo: http://purl.obolibrary.org/obo/emapa.obo download.owl: http://purl.obolibrary.org/obo/emapa.owl homepage: http://www.informatics.jax.org/expression.shtml inactive: false license: CC-BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Mouse Developmental Anatomy Ontology preferredPrefix: EMAPA prefix: emapa repository: https://github.com/obophenotype/mouse-anatomy-ontology ols: description: An ontology for mouse anatomy covering embryonic development and postnatal stages. download: http://purl.obolibrary.org/obo/emapa.owl homepage: http://www.informatics.jax.org/expression.shtml name: Mouse Developmental Anatomy Ontology prefix: emapa version: '2021-09-01' version.iri: http://purl.obolibrary.org/obo/emapa/releases/2021-09-01/emapa.owl ontobee: library: Library name: Mouse Developmental Anatomy Ontology prefix: EMAPA url: http://www.ontobee.org/ontology/EMAPA pattern: ^\d+$ prefixcommons: is_identifiers: false is_obo: true prefix: EMAPA uri_format: http://purl.obolibrary.org/obo/EMAPA_$1 synonyms: - EMAPA_RETIRED emdb: mappings: fairsharing: FAIRsharing.651n9j miriam: emdb n2t: emdb prefixcommons: EMDB miriam: deprecated: false description: The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community. homepage: https://www.ebi.ac.uk/pdbe/emdb/ id: '00000561' name: Electron Microscopy Data Bank namespaceEmbeddedInLui: false pattern: ^EMD-\d{4}$ 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/$1 emolecules: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Catalog of purchasable reagents and building blocks example: '491187' homepage: https://reaxys.emolecules.com name: Reaxys eMolecules pattern: ^\d+$ 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' homepage: https://www.ebi.ac.uk/pdbe/emdb mappings: fairsharing: biodbcore-001140 name: Electron Microscopy Public Image Archive uri_format: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1 ena.embl: 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/$1 mappings: go: ENA miriam: ena.embl n2t: ena.embl prefixcommons: ENA.EMBL miriam: deprecated: false description: The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers. homepage: https://www.ebi.ac.uk/ena/ id: '00000372' name: ENA namespaceEmbeddedInLui: false pattern: ^[A-Z]+[0-9]+(\.\d+)?$ 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 url: https://www.encodeproject.org/biosamples/$1 homepage: https://www.encodeproject.org mappings: cellosaurus: ENCODE miriam: encode n2t: encode prefixcommons: ENCODE miriam: deprecated: false description: The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. homepage: www.encodeproject.org id: '00000662' name: 'ENCODE: Encyclopedia of DNA Elements' namespaceEmbeddedInLui: false pattern: ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$ 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 prefixcommons: is_identifiers: true is_obo: false prefix: ENCODE uri_format: http://identifiers.org/encode/$1 enm: bioportal: name: eNanoMapper prefix: ENM example: '8000221' mappings: bioportal: ENM ols: enm ols: description: 'The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. > This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. ' download: http://enanomapper.github.io/ontologies/enanomapper.owl homepage: http://www.enanomapper.net/ license: CC-BY 3.0 https://creativecommons.org/licenses/by/3.0/ name: eNanoMapper Ontology prefix: enm version: '7.2' ensembl: go: homepage: http://www.ensembl.org/ name: Ensembl database of automatically annotated genomic data prefix: ENSEMBL synonyms: - Ensembl - ensembl mappings: go: ENSEMBL miriam: ensembl n2t: ensembl ncbi: ENSEMBL prefixcommons: ENSEMBL uniprot: Ensembl wikidata: P594 miriam: deprecated: false description: Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms. homepage: https://www.ensembl.org/ id: '00000003' name: Ensembl namespaceEmbeddedInLui: false pattern: ^((ENS[FPTG]\\d{11}(\\.\\d+)?)|(FB\\w{2}\\d{7})|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?)|([A-Z_a-z0-9]+(\\.)?(t)?(\\d+)?([a-z])?))$ 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 ncbi: example: HUMAN-Clone-AC005612 homepage: http://useast.ensembl.org/index.html name: Database of automatically annotated genomic data prefix: ENSEMBL 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/$1 ensembl.bacteria: mappings: miriam: ensembl.bacteria n2t: ensembl.bacteria prefixcommons: ENSEMBL.BACTERIA uniprot: EnsemblBacteria miriam: deprecated: false description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes. homepage: https://bacteria.ensembl.org/ id: '00000202' name: Ensembl Bacteria namespaceEmbeddedInLui: false pattern: ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$ 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: 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/$1 mappings: go: EnsemblFungi miriam: ensembl.fungi n2t: ensembl.fungi prefixcommons: ENSEMBL.FUNGI uniprot: EnsemblFungi miriam: deprecated: false description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes. homepage: https://fungi.ensembl.org/ id: '00000206' name: Ensembl Fungi namespaceEmbeddedInLui: false pattern: ^[A-Z-a-z0-9]+$ 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: 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/$1 mappings: go: EnsemblMetazoa miriam: ensembl.metazoa n2t: ensembl.metazoa prefixcommons: ENSEMBL.METAZOA uniprot: EnsemblMetazoa miriam: deprecated: false description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes. homepage: https://metazoa.ensembl.org/ id: '00000204' name: Ensembl Metazoa namespaceEmbeddedInLui: false pattern: ^\w+(\.)?\d+$ 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/$1 ensemblglossary: example: 0000198 mappings: ols: ensemblglossary ols: description: The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used. download: https://raw.githubusercontent.com/Ensembl/ensembl-glossary/master/ensembl-glossary.owl homepage: http://ensembl.org/glossary name: Ensembl Glossary prefix: ensemblglossary version: '2021-07-14' version.iri: http://ensembl.org/glossary/ensembl-glossary/releases/2021-07-14/ensembl-glossary.owl envipath: mappings: miriam: envipath miriam: deprecated: false description: enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products. homepage: https://envipath.org/ id: '00000727' name: enviPath namespaceEmbeddedInLui: false pattern: ^[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}\/[\w-]+\/[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}$ prefix: envipath sampleId: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea uri_format: https://envipath.org/package/$1 envo: bioportal: name: Environment Ontology prefix: ENVO mappings: bioportal: ENVO miriam: envo n2t: envo obofoundry: envo ols: envo ontobee: ENVO prefixcommons: ENVO miriam: deprecated: false description: The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. homepage: https://www.ebi.ac.uk/ols/ontologies/envo id: 00000591 name: Environment Ontology namespaceEmbeddedInLui: true pattern: ^ENVO:\d{7,8}$ 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:$1 obofoundry: contact: p.buttigieg@gmail.com contact.github: pbuttigieg contact.label: Pier Luigi Buttigieg deprecated: false description: Ontology of environmental features and habitats download.json: http://purl.obolibrary.org/obo/envo.json download.obo: http://purl.obolibrary.org/obo/envo.obo download.owl: http://purl.obolibrary.org/obo/envo.owl homepage: http://environmentontology.org/ inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: Environment Ontology preferredPrefix: ENVO prefix: envo repository: https://github.com/EnvironmentOntology/envo ols: description: ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities download: http://purl.obolibrary.org/obo/envo.owl homepage: http://environmentontology.org/ license: https://creativecommons.org/publicdomain/zero/1.0/ name: The Environment Ontology prefix: envo version: '2021-05-14' version.iri: http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl ontobee: library: Library name: Environment Ontology prefix: ENVO url: http://www.ontobee.org/ontology/ENVO pattern: ^\d{7,8}$ prefixcommons: is_identifiers: false is_obo: true prefix: ENVO uri_format: http://purl.obolibrary.org/obo/ENVO_$1 enzo: 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/$1 eol: bioportal: name: Environment Ontology for Livestock prefix: EOL example: 0001927 mappings: bioportal: EOL ols: eol ols: contact: pylebail@rennes.inra.fr description: "L'ontologie EOL d\xE9crit les conditions d'environnement des \xE9\ levages d'animaux domestiques. Elle d\xE9crit plus particuli\xE8rement les modalit\xE9\ s de l'alimentation, de l'environnement, de la structure des \xE9levages et\ \ des syst\xE8mes d'\xE9levage" download: http://www.atol-ontology.com/public/telechargement/eol.owl homepage: http://www.atol-ontology.com name: Environment Ontology for Livestock prefix: eol version: '2018-09-13' epcc: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Collection of European paediatric cardiac coding files homepage: https://www.aepc.org/european-paediatric-cardiac-coding name: European Paediatric Cardiac Codes proprietary: true references: - https://www.cambridge.org/core/journals/cardiology-in-the-young/article/abs/european-paediatric-cardiac-codes-the-long-list-with-icd9-icd10-crossmapping-and-crossmap-to-epcc-short-list/FCA4DFCCB661298294A3D113FC79D5BE epd: mappings: miriam: epd n2t: epd ncbi: EPD prefixcommons: EPD uniprot: EPD miriam: deprecated: false description: The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. homepage: http://epd.vital-it.ch/ id: 00000408 name: EPD namespaceEmbeddedInLui: false pattern: ^[A-Z-_0-9]+$ 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 epo: bioportal: name: Early Pregnancy Ontology prefix: EPO 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 url: http://www.ontobee.org/ontology/EPO prefixcommons: is_identifiers: false is_obo: true prefix: EPO uri_format: http://purl.obolibrary.org/obo/EPO_$1 erm: mappings: miriam: erm n2t: erm miriam: deprecated: false description: The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project. homepage: https://nanocommons.github.io/identifiers/ id: '00000763' name: European Registry of Materials namespaceEmbeddedInLui: false pattern: ^ERM[0-9]{8}$ 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' mappings: bioportal: ERO 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 url: http://www.ontobee.org/ontology/ERO 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/$1 eu89h: mappings: miriam: eu89h n2t: eu89h prefixcommons: EU89H miriam: deprecated: false description: The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union. homepage: http://data.jrc.ec.europa.eu/ id: '00000644' name: JRC Data Catalogue namespaceEmbeddedInLui: false pattern: ^[a-z0-9\-_]+$ 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' mappings: bioportal: EUPATH obofoundry: eupath ols: eupath ontobee: EUPATH prefixcommons: EUPATH obofoundry: contact: stoeckrt@pennmedicine.upenn.edu contact.github: cstoeckert contact.label: Chris Stoeckert 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 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 license: http://creativecommons.org/licenses/by/4.0/ name: VEuPathDB Ontology prefix: eupath version: '2021-09-09' version.iri: http://purl.obolibrary.org/obo/eupath/2021-09-09/eupath.owl ontobee: library: Library name: VEuPathDB ontology prefix: EUPATH url: http://www.ontobee.org/ontology/EUPATH prefixcommons: is_identifiers: false is_obo: true prefix: EUPATH uri_format: http://purl.obolibrary.org/obo/EUPATH_$1 eurofir: contributor: email: cthoyt@gmail.com 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_$1 references: - https://twitter.com/Bgeedb/status/1350124337815281664 evm: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: eVOC mouse development stage references: - https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r229 exac.gene: mappings: miriam: exac.gene n2t: exac.gene prefixcommons: EXAC.GENE miriam: deprecated: false description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information. homepage: http://exac.broadinstitute.org/ id: 00000548 name: ExAC Gene namespaceEmbeddedInLui: false pattern: ^ENSG\d{11}$ 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_$1 bioportal: name: Exposure Ontology prefix: EXO example: 0000078 mappings: biolink: ExO bioportal: EXO obofoundry: exo ols: exo ontobee: ExO prefixcommons: EXO obofoundry: contact: cjmattin@ncsu.edu contact.label: Carolyn Mattingly deprecated: false description: Vocabularies for describing exposure data to inform understanding of environmental health. download.obo: http://purl.obolibrary.org/obo/exo.obo download.owl: http://purl.obolibrary.org/obo/exo.owl homepage: http://ctdbase.org/help/exposureHelp.jsp inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Exposure ontology preferredPrefix: ExO prefix: exo repository: https://github.com/CTDbase/exposure-ontology ols: description: ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics. download: http://purl.obolibrary.org/obo/exo.owl homepage: http://ctdbase.org/help/exposureHelp.jsp license: https://creativecommons.org/licenses/by/4.0/ name: Exposure ontology (ExO) prefix: exo version: '2020-03-10' version.iri: http://purl.obolibrary.org/obo/exo/2.1/exo.owl ontobee: library: Library name: Exposure ontology prefix: ExO url: http://www.ontobee.org/ontology/ExO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: EXO uri_format: http://purl.obolibrary.org/obo/EXO_$1 synonyms: - ExO facebase: mappings: miriam: facebase n2t: facebase prefixcommons: FACEBASE miriam: deprecated: false description: FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects. homepage: https://www.facebase.org id: '00000642' name: FaceBase Data Repository namespaceEmbeddedInLui: false pattern: ^FB\d{8}$ 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/$1 fairsharing: mappings: miriam: fairsharing n2t: fairsharing prefixcommons: FAIRSHARING miriam: deprecated: false description: The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies. homepage: https://fairsharing.org/ id: '00000364' name: FAIRsharing namespaceEmbeddedInLui: false pattern: ^bsg-[dscp]?\d{6}$ 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 homepage: http://biohackathon.org/resource/faldo mappings: bioportal: FALDO 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#$1 fao: bioportal: name: Fungal Gross Anatomy Ontology prefix: FAO example: '0000001' mappings: bioportal: FAO obofoundry: fao ols: fao ontobee: FAO prefixcommons: FAO obofoundry: contact: mah79@cam.ac.uk contact.github: mah11 contact.label: Midori Harris deprecated: false description: A structured controlled vocabulary for the anatomy of fungi. download.obo: http://purl.obolibrary.org/obo/fao.obo download.owl: http://purl.obolibrary.org/obo/fao.owl homepage: https://github.com/obophenotype/fungal-anatomy-ontology/ inactive: false license: CC-0 license.url: http://creativecommons.org/publicdomain/zero/1.0/ name: Fungal gross anatomy preferredPrefix: FAO prefix: fao repository: https://github.com/obophenotype/fungal-anatomy-ontology ols: description: A structured controlled vocabulary for the anatomy of fungi. download: http://purl.obolibrary.org/obo/fao.owl homepage: https://github.com/obophenotype/fungal-anatomy-ontology/ name: Fungal gross anatomy prefix: fao version: '2020-05-07' version.iri: http://purl.obolibrary.org/obo/fao/releases/2020-05-07/fao.owl ontobee: library: Library name: Fungal gross anatomy prefix: FAO url: http://www.ontobee.org/ontology/FAO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: FAO uri_format: http://purl.obolibrary.org/obo/FAO_$1 fbbi: bioportal: name: Biological Imaging Methods Ontology prefix: FBbi example: 00000268 mappings: bioportal: FBbi obofoundry: fbbi ols: fbbi ontobee: FBBI prefixcommons: FBbi obofoundry: contact: dorloff@ncmir.ucsd.edu contact.label: David Orloff deprecated: false description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. download.owl: http://purl.obolibrary.org/obo/fbbi.owl homepage: http://cellimagelibrary.org/ inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Biological Imaging Methods Ontology preferredPrefix: FBbi prefix: fbbi repository: https://github.com/CRBS/Biological_Imaging_Methods_Ontology ols: description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. download: http://purl.obolibrary.org/obo/fbbi.owl homepage: http://cellimagelibrary.org/ name: Biological Imaging Methods Ontology prefix: fbbi version: '2020-11-06' version.iri: http://purl.obolibrary.org/obo/fbbi/releases/2020-11-06/fbbi.owl ontobee: library: Library name: Biological Imaging Methods Ontology prefix: FBBI url: http://www.ontobee.org/ontology/FBBI pattern: ^\d+$ 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 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 go: FBbt obofoundry: fbbt ols: fbbt ontobee: FBBT prefixcommons: FBbt obofoundry: contact: cp390@cam.ac.uk contact.label: Clare Pilgrim 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 license.url: http://creativecommons.org/licenses/by/3.0/ name: Drosophila gross anatomy preferredPrefix: FBbt prefix: fbbt ols: description: An ontology of Drosophila melanogaster anatomy. download: http://purl.obolibrary.org/obo/fbbt.owl homepage: http://purl.obolibrary.org/obo/fbbt license: https://creativecommons.org/licenses/by/3.0/ name: Drosophila Anatomy Ontology (DAO) prefix: fbbt version: '2021-10-14' version.iri: http://purl.obolibrary.org/obo/fbbt/releases/2021-10-14/fbbt.owl ontobee: library: Library name: Drosophila gross anatomy prefix: FBBT url: http://www.ontobee.org/ontology/FBBT part_of: flybase 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:$1 fbcv: bioportal: name: FlyBase Controlled Vocabulary prefix: FB-CV download_obo: https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/fbcv.obo example: 0000586 mappings: bioportal: FB-CV obofoundry: fbcv ols: fbcv ontobee: FBCV prefixcommons: FBcv obofoundry: contact: cp390@cam.ac.uk contact.label: Clare Pilgrim deprecated: false description: A structured controlled vocabulary used for various aspects of annotation by FlyBase. download.json: http://purl.obolibrary.org/obo/fbcv.json download.obo: http://purl.obolibrary.org/obo/fbcv.obo download.owl: http://purl.obolibrary.org/obo/fbcv.owl homepage: http://purl.obolibrary.org/obo/fbcv inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: FlyBase Controlled Vocabulary preferredPrefix: FBcv prefix: fbcv repository: https://github.com/FlyBase/flybase-controlled-vocabulary ols: description: A miscellaneous ontology of terms used for curation in FlyBase, including the DPO. download: http://purl.obolibrary.org/obo/fbcv.owl homepage: http://purl.obolibrary.org/obo/fbcv license: https://creativecommons.org/licenses/by/3.0/ name: FlyBase Controlled Vocabulary (FBcv) prefix: fbcv version: '2021-10-18' version.iri: http://purl.obolibrary.org/obo/fbcv/releases/2021-10-18/fbcv.owl ontobee: library: Library name: FlyBase Controlled Vocabulary prefix: FBCV url: http://www.ontobee.org/ontology/FBCV part_of: flybase pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: FBcv uri_format: http://purl.obolibrary.org/obo/FBcv_$1 synonyms: - FBcv fbdv: bioportal: name: Drosophila Development Ontology prefix: FB-DV example: '00000000' mappings: bioportal: FB-DV obofoundry: fbdv ols: fbdv ontobee: FBdv prefixcommons: FBdv obofoundry: contact: cp390@cam.ac.uk contact.label: Clare Pilgrim deprecated: false description: A structured controlled vocabulary of the development of Drosophila melanogaster. download.json: http://purl.obolibrary.org/obo/fbdv.json download.obo: http://purl.obolibrary.org/obo/fbdv.obo download.owl: http://purl.obolibrary.org/obo/fbdv.owl homepage: http://purl.obolibrary.org/obo/fbdv inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: Drosophila development preferredPrefix: FBdv prefix: fbdv ols: description: An ontology of Drosophila melanogaster developmental stages. download: http://purl.obolibrary.org/obo/fbdv.owl homepage: http://purl.obolibrary.org/obo/fbdv license: https://creativecommons.org/licenses/by/3.0/ name: FlyBase Developmental Ontology (FBdv) prefix: fbdv version: '2021-10-13' version.iri: http://purl.obolibrary.org/obo/fbdv/releases/2021-10-13/fbdv.owl ontobee: library: Library name: Drosophila development prefix: FBdv url: http://www.ontobee.org/ontology/FBdv pattern: ^\d{8}$ 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 fbrf: contributor: email: cthoyt@gmail.com 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 uri_format: https://flybase.org/reports/FBrf$1 fbsp: bioportal: name: Fly Taxonomy prefix: FB-SP mappings: bioportal: FB-SP obofoundry: fbsp prefixcommons: FBSP obofoundry: contact: mmc46@gen.cam.ac.uk contact.label: Marta Costa 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 prefixcommons: is_identifiers: false is_obo: true prefix: FBSP uri_format: http://purl.obolibrary.org/obo/FBSP_$1 fbtc: contributor: email: cthoyt@gmail.com 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 uri_format: https://flybase.org/reports/FBtc$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 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 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 url: http://www.ontobee.org/ontology/FIDEO 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 synonyms: - fishbase wikidata: database: Q837101 prefix: P938 fix: bioportal: name: Physico-Chemical Methods and Properties prefix: FIX example: 0000390 homepage: https://www.ebi.ac.uk/chebi/ mappings: bioportal: FIX 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 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 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 url: http://www.ontobee.org/ontology/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' mappings: bioportal: FLOPO obofoundry: flopo ols: flopo ontobee: FLOPO prefixcommons: FLOPO obofoundry: contact: robert.hoehndorf@kaust.edu.sa contact.github: leechuck contact.label: Robert Hoehndorf 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: CC-0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Flora Phenotype Ontology preferredPrefix: FLOPO prefix: flopo 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 url: http://www.ontobee.org/ontology/FLOPO prefixcommons: is_identifiers: false is_obo: true prefix: FLOPO uri_format: http://purl.obolibrary.org/obo/FLOPO_$1 flowrepository: mappings: miriam: flowrepository n2t: flowrepository miriam: deprecated: false description: FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field. homepage: https://flowrepository.org/ id: '00000672' name: FlowRepository namespaceEmbeddedInLui: false pattern: ^FR\-FCM\-\w{4}$ 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 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 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 url: https://flybase.org/reports/$1.html go: homepage: http://flybase.org/ name: FlyBase prefix: FB synonyms: - FlyBase - FLYBASE uri_format: http://flybase.org/reports/$1.html mappings: cellosaurus: FlyBase go: FB miriam: fb n2t: fb ncbi: FLYBASE prefixcommons: FlyBase uniprot: FlyBase wikidata: P3852 miriam: deprecated: false description: FlyBase is the database of the Drosophila Genome Projects and of associated literature. homepage: http://flybase.org/ id: '00000030' name: FlyBase namespaceEmbeddedInLui: false pattern: ^FB\w{2}\d{7}$ 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 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: http://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/$1 fma: bioportal: name: Foundational Model of Anatomy prefix: FMA example: '63189' go: homepage: http://sig.biostr.washington.edu/projects/fm/index.html name: Foundational Model of Anatomy prefix: FMA mappings: bioportal: FMA go: FMA miriam: fma n2t: fma obofoundry: fma ols: fma ontobee: FMA prefixcommons: FMA miriam: deprecated: false description: The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. homepage: https://www.ebi.ac.uk/ols/ontologies/fma/ id: '00000067' name: FMA namespaceEmbeddedInLui: true pattern: ^FMA:\d+$ 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:$1 name: Foundational Model of Anatomy obofoundry: contact: mejino@u.washington.edu contact.label: Onard Mejino deprecated: false description: This is currently a slimmed down version of FMA download.owl: http://purl.obolibrary.org/obo/fma.owl homepage: http://si.washington.edu/projects/fma inactive: false license: CC-BY 3.0 license.url: https://creativecommons.org/licenses/by/3.0/ name: Foundational Model of Anatomy Ontology (subset) preferredPrefix: FMA prefix: fma ols: description: This is currently a slimmed down version of FMA download: http://purl.obolibrary.org/obo/fma.owl homepage: http://si.washington.edu/projects/fma name: Foundational Model of Anatomy Ontology (subset) prefix: fma version: '2020-04-13' version.iri: http://purl.obolibrary.org/obo/fma/releases/2020-04-13/fma.owl ontobee: library: Library name: Foundational Model of Anatomy Ontology (subset) prefix: FMA url: http://www.ontobee.org/ontology/FMA pattern: ^\d+$ 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 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 license.url: http://creativecommons.org/licenses/by/3.0/ name: FOBI preferredPrefix: FOBI prefix: fobi 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 license: http://creativecommons.org/licenses/by/4.0/ name: FOBI prefix: fobi version.iri: http://purl.obolibrary.org/obo/fobi/fobi.owl ontobee: library: Library name: FOBI prefix: FOBI url: http://www.ontobee.org/ontology/FOBI 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/$1 synonyms: - foodb foodon: bioportal: name: The FoodOn Food Ontology prefix: FOODON mappings: bioportal: FOODON miriam: foodon n2t: foodon obofoundry: foodon ols: foodon ontobee: FOODON prefixcommons: FOODON miriam: deprecated: false description: FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies. homepage: https://foodon.org id: '00000661' name: FoodOn Food Ontology namespaceEmbeddedInLui: true pattern: ^FOODON:[0-9]{8}$ 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:$1 name: The Food Ontology obofoundry: contact: damion_dooley@sfu.ca contact.github: Public-Health-Bioinformatics contact.label: Damion Dooley deprecated: false description: "A broadly scoped ontology representing entities which bear a \u201C\ food role\u201D. It encompasses materials in natural ecosystems and food webs\ \ as well as human-centric categorization and handling of food." download.owl: http://purl.obolibrary.org/obo/foodon.owl homepage: https://foodon.org/ inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: FOODON preferredPrefix: FOODON prefix: foodon repository: https://github.com/FoodOntology/foodon ols: description: FoodOn (http://foodon.org) is a consortium-driven project to build a comprehensive and easily accessible global farm-to-fork ontology about food, that accurately and consistently describes foods commonly known in cultures from around the world. download: http://purl.obolibrary.org/obo/foodon.owl homepage: https://foodon.org/ license: https://creativecommons.org/licenses/by/3.0/ name: Food Ontology prefix: foodon version: '2021-09-15' version.iri: http://purl.obolibrary.org/obo/foodon/releases/2021-09-15/foodon.owl ontobee: library: Library name: FOODON prefix: FOODON url: http://www.ontobee.org/ontology/FOODON pattern: ^[0-9]{8}$ prefixcommons: is_identifiers: false is_obo: true prefix: FOODON uri_format: http://purl.obolibrary.org/obo/FOODON_$1 fovt: bioportal: name: FuTRES Ontology of Vertebrate Traits prefix: FOVT example: 0000009 mappings: bioportal: FOVT obofoundry: fovt ols: fovt ontobee: FOVT obofoundry: contact: rlwalls2008@gmail.com contact.github: https://github.com/futres/fovt contact.label: FuTRES Ontology of Vertebrate Traits deprecated: false description: FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA). download.obo: http://purl.obolibrary.org/obo/fovt.obo download.owl: http://purl.obolibrary.org/obo/fovt.owl homepage: https://github.com/futres/fovt inactive: false license: CC0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: FuTRES Ontology of Vertebrate Traits preferredPrefix: FOVT prefix: fovt repository: https://github.com/futres/fovt ols: description: None download: http://purl.obolibrary.org/obo/fovt.owl homepage: https://github.com/futres/fovt license: http://creativecommons.org/publicdomain/zero/1.0/ name: FuTRES Ontology of Vertebrate Traits prefix: fovt version: '2021-11-10' version.iri: http://purl.obolibrary.org/obo/fovt/releases/2021-11-10/fovt.owl ontobee: library: Library name: FuTRES Ontology of Vertebrate Traits prefix: FOVT url: http://www.ontobee.org/ontology/FOVT fplx: bioportal: name: FamPlex prefix: FPLX example: GPIb_IX_V homepage: https://sorgerlab.github.io/famplex/ mappings: bioportal: FPLX miriam: fplx n2t: fplx prefixcommons: FPLX miriam: deprecated: false description: FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships. homepage: https://sorgerlab.github.io/famplex id: '00000651' name: FamPlex namespaceEmbeddedInLui: false pattern: ^[a-zA-Z0-9][A-Za-z0-9_]+$ 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/$1 funcbase.fly: mappings: miriam: funcbase.fly n2t: funcbase.fly prefixcommons: FUNCBASE.FLY miriam: deprecated: false description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data. homepage: http://func.mshri.on.ca/fly id: '00000461' name: FuncBase Fly namespaceEmbeddedInLui: false pattern: ^\d+$ 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/$1 fungidb: mappings: miriam: fungidb n2t: fungidb prefixcommons: FUNGIDB miriam: deprecated: false description: FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina. homepage: https://fungidb.org/fungidb id: '00000365' name: FungiDB namespaceEmbeddedInLui: false pattern: ^[A-Za-z_0-9]+$ 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/$1 fyler: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'A hierarchical classification of congenital heart disease ' example: '4447' homepage: https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906 name: Fyler pattern: ^\d+$ 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_$1 bioportal: name: Fission Yeast Phenotype Ontology prefix: FYPO download_obo: http://purl.obolibrary.org/obo/fypo.obo example: '0001707' go: homepage: http://www.pombase.org/ name: Fission Yeast Phenotype Ontology prefix: FYPO mappings: biolink: FYPO bioportal: FYPO go: FYPO obofoundry: fypo ols: fypo ontobee: FYPO prefixcommons: FYPO name: Fission Yeast Phenotype Ontology obofoundry: contact: mah79@cam.ac.uk contact.github: mah11 contact.label: Midori Harris deprecated: false description: FYPO is a formal ontology of phenotypes observed in fission yeast. download.obo: http://purl.obolibrary.org/obo/fypo.obo download.owl: http://purl.obolibrary.org/obo/fypo.owl homepage: https://github.com/pombase/fypo inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/4.0/ name: Fission Yeast Phenotype Ontology preferredPrefix: FYPO prefix: fypo repository: https://github.com/pombase/fypo ols: description: A formal ontology of phenotypes observed in fission yeast. download: http://purl.obolibrary.org/obo/fypo.owl homepage: https://github.com/pombase/fypo license: https://creativecommons.org/licenses/by/4.0/ name: Fission Yeast Phenotype Ontology (FYPO) prefix: fypo version: '2021-11-08' version.iri: http://purl.obolibrary.org/obo/fypo/releases/2021-11-08/fypo.owl ontobee: library: Library name: Fission Yeast Phenotype Ontology prefix: FYPO url: http://www.ontobee.org/ontology/FYPO pattern: ^\d{7}$ 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/$1 galen: bioportal: name: Galen Ontology prefix: GALEN deprecated: true example: MagnitudeValueType homepage: https://www.opengalen.org mappings: bioportal: GALEN name: Galen Ontology gard: description: Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease. example: '6038' homepage: https://rarediseases.info.nih.gov/diseases name: Genetic and Rare Diseases Information Center synonyms: - GARD - Genetic and Rare Diseases Information Center wikidata: prefix: P4317 gateway: mappings: miriam: gateway miriam: deprecated: false description: The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access. homepage: https://www.hdruk.ac.uk id: 00000796 name: gateway namespaceEmbeddedInLui: false pattern: ^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$ prefix: gateway sampleId: fd8d0743-344a-4758-bb97-f8ad84a37357 uri_format: https://web.www.healthdatagateway.org/dataset/$1 name: Health Data Research Innovation Gateway gaz: bioportal: name: Gazetteer prefix: GAZ download_obo: http://purl.obolibrary.org/obo/gaz.obo example: '00620027' mappings: bioportal: GAZ obofoundry: gaz ols: gaz ontobee: GAZ prefixcommons: GAZ obofoundry: contact: lschriml@som.umaryland.edu contact.github: lschriml contact.label: Lynn Schriml deprecated: false description: A gazetteer constructed on ontological principles download.obo: http://purl.obolibrary.org/obo/gaz.obo download.owl: http://purl.obolibrary.org/obo/gaz.owl homepage: http://environmentontology.github.io/gaz/ inactive: true license: CC0 1.0 Universal license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Gazetteer prefix: gaz repository: https://github.com/EnvironmentOntology/gaz ols: description: A gazetteer constructed on ontological principles download: http://purl.obolibrary.org/obo/gaz.obo homepage: http://environmentontology.github.io/gaz/ name: Gazetteer prefix: gaz version: '2018-06-26' ontobee: library: Library name: Gazetteer prefix: GAZ url: http://www.ontobee.org/ontology/GAZ pattern: ^\d{8}$ 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' homepage: https://www.gbif.org/species name: Global Biodiversity Information Facility uri_format: https://www.gbif.org/species/$1 wikidata: prefix: P846 gc: comment: 'see comment here: https://github.com/obophenotype/ncbitaxon/issues/47' contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries. example: '11' homepage: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html name: Genetic Code pattern: ^\d+$ 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 url: 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/$1 gecko: bioportal: name: Genomics Cohorts Knowledge Ontology prefix: GECKO example: '0000044' mappings: bioportal: GECKO obofoundry: gecko ols: gecko ontobee: GECKO obofoundry: contact: rbca.jackson@gmail.com contact.github: beckyjackson contact.label: Rebecca Jackson deprecated: false description: An ontology to represent genomics cohort attributes download.owl: http://purl.obolibrary.org/obo/gecko.owl homepage: https://github.com/IHCC-cohorts/GECKO inactive: false license: CC-BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Genomics Cohorts Knowledge Ontology preferredPrefix: GECKO prefix: gecko repository: https://github.com/IHCC-cohorts/GECKO ols: description: An ontology to represent genomics cohort attributes. download: http://purl.obolibrary.org/obo/gecko.owl homepage: https://github.com/IHCC-cohorts/GECKO license: https://creativecommons.org/licenses/by/4.0/ name: Genomics Cohorts Knowledge Ontology prefix: gecko version: '2021-01-18' version.iri: http://purl.obolibrary.org/obo/gecko/releases/2021-01-18/gecko.owl ontobee: library: Library name: Genomics Cohorts Knowledge Ontology prefix: GECKO url: http://www.ontobee.org/ontology/GECKO genatlas: mappings: miriam: genatlas n2t: genatlas prefixcommons: GENATLAS uniprot: GenAtlas miriam: deprecated: false description: GenAtlas is a database containing information on human genes, markers and phenotypes. homepage: http://genatlas.medecine.univ-paris5.fr/ id: 00000208 name: Genatlas namespaceEmbeddedInLui: false pattern: ^\w+$ 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: 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 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: 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/$1 genecards: mappings: miriam: genecards n2t: genecards prefixcommons: GENECARDS uniprot: GeneCards miriam: deprecated: false description: The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene. homepage: http://www.genecards.org/ id: '00000323' name: GeneCards namespaceEmbeddedInLui: false pattern: ^[A-Za-z-0-9_]+(\@)?$ 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: go: homepage: http://www.genedb.org/gene/ name: GeneDB prefix: GeneDB uri_format: http://www.genedb.org/gene/$1 mappings: go: GeneDB miriam: genedb n2t: genedb ncbi: GeneDB prefixcommons: GENEDB uniprot: GeneDB wikidata: P3382 miriam: deprecated: false description: GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed. homepage: https://www.genedb.org/ id: '00000106' name: GeneDB namespaceEmbeddedInLui: false pattern: ^[\w\d\.-]*$ 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 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/$1 genefarm: mappings: miriam: genefarm n2t: genefarm prefixcommons: GENEFARM miriam: deprecated: false description: GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products. homepage: http://urgi.versailles.inra.fr/Genefarm/ id: '00000211' name: GeneFarm namespaceEmbeddedInLui: false pattern: ^\d+$ 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 mappings: obofoundry: genepio ols: genepio ontobee: GENEPIO prefixcommons: GENEPIO obofoundry: contact: damion_dooley@sfu.ca contact.label: Damion Dooley 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 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/ license: http://creativecommons.org/licenses/by/3.0/ name: Genomic Epidemiology Ontology prefix: genepio version: '2021-05-24' version.iri: http://purl.obolibrary.org/obo/genepio/releases/2021-05-24/genepio.owl ontobee: library: Library name: Genomic Epidemiology Ontology prefix: GENEPIO url: http://www.ontobee.org/ontology/GENEPIO 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/$1 genewiki: mappings: miriam: genewiki n2t: genewiki prefixcommons: GENEWIKI uniprot: GeneWiki miriam: deprecated: false description: The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI. homepage: http://en.wikipedia.org/wiki/Gene_Wiki id: 00000487 name: Gene Wiki namespaceEmbeddedInLui: false pattern: ^\d+$ 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' mappings: bioportal: GENO obofoundry: geno ols: geno ontobee: GENO prefixcommons: GENO obofoundry: contact: mhb120@gmail.com contact.github: mbrush contact.label: Matthew Brush 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 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: '2020-03-08' version.iri: http://purl.obolibrary.org/obo/geno/releases/2020-03-08/geno.owl ontobee: library: Library name: Genotype Ontology prefix: GENO url: http://www.ontobee.org/ontology/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 url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1 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=$1 mappings: cellosaurus: GEO fairsharing: FAIRsharing.5hc8vt go: GEO miriam: geo n2t: geo ontobee: GEO prefixcommons: GEO miriam: deprecated: false description: The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval. homepage: https://www.ncbi.nlm.nih.gov/geo/ id: '00000054' name: GEO namespaceEmbeddedInLui: false pattern: ^G(PL|SM|SE|DS)\d+$ 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 ontobee: library: Library name: Geographical Entity Ontology prefix: GEO url: http://www.ontobee.org/ontology/GEO prefixcommons: formatter: http://purl.obolibrary.org/obo/GEO_$1 is_identifiers: false is_obo: true prefix: GEO geogeo: bioportal: name: Geographical Entity Ontology prefix: GEO example: '000000021' mappings: bioportal: GEO miriam: geogeo obofoundry: geo ols: geo prefixcommons: GEO miriam: deprecated: false description: An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in "The US declared war on Germany" vs. the US in "The plane entered US airspace". homepage: https://github.com/ufbmi id: 00000824 name: Geographical Entity Ontology namespaceEmbeddedInLui: false pattern: ^GEO_[0-9]{9}$ prefix: geogeo sampleId: GEO_000000021 uri_format: http://purl.obolibrary.org/obo/$1 obofoundry: contact: hoganwr@gmail.com contact.label: Bill Hogan deprecated: false description: An ontology of geographical entities download.owl: http://purl.obolibrary.org/obo/geo.owl homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki license: CC-BY 4.0 name: Geographical Entity Ontology prefix: geo ols: description: An ontology of geographical entities download: http://purl.obolibrary.org/obo/geo.owl homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki license: https://creativecommons.org/licenses/by/4.0/ name: Geographical Entity Ontology prefix: geo version: '2016-03-26' pattern: ^\d{9}$ preferred_prefix: GEOGEO prefixcommons: is_identifiers: false is_obo: true prefix: GEO uri_format: http://purl.obolibrary.org/obo/GEO_$1 uri_format: http://purl.obolibrary.org/obo/GEO_$1 gexo: bioportal: name: Gene Expression Ontology prefix: GEXO mappings: bioportal: GEXO 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 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/$1 giardiadb: mappings: miriam: giardiadb n2t: giardiadb prefixcommons: GIARDIADB miriam: deprecated: false description: GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. homepage: https://giardiadb.org/giardiadb/ id: '00000151' name: GiardiaDB namespaceEmbeddedInLui: false pattern: ^\w+$ 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/$1 github: mappings: miriam: github miriam: deprecated: false description: GitHub is an online host of Git source code repositories. homepage: https://github.com/ id: 00000853 name: github namespaceEmbeddedInLui: false pattern: ^[a-zA-Z0-9-_]+/[a-zA-Z0-9-_]+$ prefix: github sampleId: identifiers-org/registry uri_format: https://github.com/$1 glida.gpcr: mappings: miriam: glida.gpcr n2t: glida.gpcr prefixcommons: GLIDA.GPCR miriam: deprecated: false description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors. homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ id: 00000493 name: GLIDA GPCR namespaceEmbeddedInLui: false pattern: ^[A-Z-_0-9]+$ 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/$1 glycomedb: comment: this is exactly the same as glytoucan. Idk why there are two different ones has_canonical: glytoucan mappings: miriam: glycomedb n2t: glycomedb prefixcommons: GLYCOMEDB miriam: deprecated: false description: GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links. homepage: https://glytoucan.org/ id: '00000114' name: GlycomeDB namespaceEmbeddedInLui: false pattern: ^\w+$ 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/$1 glyconavi: mappings: miriam: glyconavi miriam: deprecated: false description: GlycoNAVI is a website for carbohydrate research. It consists of the "GlycoNAVI Database" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the "GlycoNAVI tools" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools. homepage: https://www.noguchi.or.jp/ id: 00000830 name: GlycoNAVI namespaceEmbeddedInLui: false pattern: ^GN_[A-Za-z0-9]+$ prefix: glyconavi sampleId: GN_G03681DA uri_format: https://glyconavi.org/hub/?id=$1 glycopost: mappings: miriam: glycopost miriam: deprecated: false description: GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their "raw/processed" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines. homepage: https://glycopost.glycosmos.org id: '00000721' name: GlycoPOST namespaceEmbeddedInLui: false pattern: ^GPST[0-9]{6}$ 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 homepage: https://glygen.org/glycan/ mappings: uniprot: GlyGen name: 'GlyGen: 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/$1 gmd: mappings: miriam: gmd n2t: gmd prefixcommons: GMD miriam: deprecated: false description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena. homepage: http://gmd.mpimp-golm.mpg.de/ id: '00000274' name: Golm Metabolome Database namespaceEmbeddedInLui: false pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ 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 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/ license: http://creativecommons.org/licenses/by/4.0/ name: Glycan Naming Ontology prefix: gno version: 1.9.0 version.iri: http://purl.obolibrary.org/obo/gno/2021-08-13/gno.owl ontobee: library: Library name: Glycan Naming and Subsumption Ontology (GNOme) prefix: GNO url: http://www.ontobee.org/ontology/GNO pattern: ^\d{8}$ gnpis: mappings: 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/$1 go: bioportal: name: Gene Ontology prefix: GO example: '0032571' go: homepage: http://amigo.geneontology.org/ name: Gene Ontology Database prefix: GO mappings: bioportal: GO go: GO miriam: go n2t: go ncbi: GO obofoundry: go ols: go ontobee: GO prefixcommons: GO uniprot: GO miriam: deprecated: false description: The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. homepage: http://amigo.geneontology.org/ id: '00000022' name: Gene Ontology namespaceEmbeddedInLui: true pattern: ^GO:\d{7}$ 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:$1 ncbi: example: '123' homepage: http://amigo.geneontology.org/ name: Gene Ontology Database identifier prefix: GO obofoundry: contact: suzia@stanford.edu contact.label: Suzi Aleksander deprecated: false description: An ontology for describing the function of genes and gene products download.json: http://purl.obolibrary.org/obo/go.json download.obo: http://purl.obolibrary.org/obo/go.obo download.owl: http://purl.obolibrary.org/obo/go.owl homepage: http://geneontology.org/ inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Gene Ontology preferredPrefix: GO prefix: go repository: https://github.com/geneontology/go-ontology ols: description: The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms. download: http://purl.obolibrary.org/obo/go.owl homepage: http://geneontology.org/ license: http://creativecommons.org/licenses/by/4.0/ name: Gene Ontology prefix: go version: '2021-10-26' version.iri: http://purl.obolibrary.org/obo/go/releases/2021-10-26/go.owl ontobee: library: Foundry name: Gene Ontology prefix: GO url: http://www.ontobee.org/ontology/GO pattern: ^\d{7}$ 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:$1 goa: mappings: miriam: goa n2t: goa ncbi: GOA prefixcommons: GOA miriam: deprecated: false description: The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. homepage: https://www.ebi.ac.uk/GOA/ id: 00000196 name: GOA namespaceEmbeddedInLui: false pattern: ^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$ 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 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/$1 goeco: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported. example: IPI homepage: http://geneontology.org/docs/guide-go-evidence-codes/ name: GO Evidence Code gold: mappings: miriam: gold miriam: deprecated: false description: 'The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.' homepage: https://gold.jgi.doe.gov/ id: '00000733' name: Genomes OnLine Database (GOLD) namespaceEmbeddedInLui: false pattern: ^[A-Z][a-z][0-9]+$ 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 url: 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 ID gorel: biolink: is_identifiers: false is_obo: true prefix: GOREL uri_format: http://purl.obolibrary.org/obo/GOREL_$1 description: Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO. download_owl: ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl example: '0002005' go: description: Additional relations pending addition into RO name: GO Extensions to OBO Relation Ontology Ontology prefix: GOREL homepage: http://geneontology.org/docs/ontology-relations/ mappings: biolink: GOREL go: GOREL name: GO Relations gpcrdb: mappings: miriam: gpcrdb n2t: gpcrdb prefixcommons: GPCRDB uniprot: GPCRDB miriam: deprecated: false description: The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models. homepage: http://www.gpcrdb.org/ id: '00000212' name: GPCRDB namespaceEmbeddedInLui: false pattern: ^\w+$ 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/$1 gpmdb: mappings: miriam: gpmdb n2t: gpmdb prefixcommons: GPMDB miriam: deprecated: false description: The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. homepage: http://gpmdb.thegpm.org/ id: 00000649 name: GPMDB namespaceEmbeddedInLui: false pattern: ^GPM\d+$ 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/$1 grassbase: contributor: email: null name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species. example: imp10873 homepage: https://www.kew.org/data/grasses-syn/index.htm name: GrassBase pattern: ^(imp|gen)\d{5}$ uri_format: https://www.kew.org/data/grasses-db/www/$1 greengenes: mappings: miriam: greengenes n2t: greengenes ncbi: Greengenes prefixcommons: GREENGENES miriam: deprecated: false description: A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. homepage: http://greengenes.lbl.gov/ id: '00000165' name: GreenGenes namespaceEmbeddedInLui: false pattern: ^\d+$ 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/$1 grid: mappings: miriam: grid n2t: grid prefixcommons: GRID miriam: deprecated: false description: International coverage of the world's leading research organisations, indexing 92% of funding allocated globally. homepage: https://www.grid.ac/ id: 00000593 name: GRID namespaceEmbeddedInLui: false pattern: ^grid\.[0-9]+\.[a-f0-9]{1,2}$ 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 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 (GSFA) Online Database 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_$1 name: Gender, Sex, and Sexual Orientation Ontology obofoundry: contact: kronkcj@mail.uc.edu contact.github: Superraptor contact.label: Clair Kronk deprecated: false description: The Gender, Sex, and Sexual Orientation (GSSO) ontology has terms for annotating interdisciplinary information concerning gender, sex, and sexual orientation for primary usage in the biomedical and adjacent sciences. download.json: http://purl.obolibrary.org/obo/gsso.json download.obo: http://purl.obolibrary.org/obo/gsso.obo download.owl: http://purl.obolibrary.org/obo/gsso.owl homepage: https://gsso.research.cchmc.org/ inactive: false license: Apache 2.0 License license.url: http://www.apache.org/licenses/LICENSE-2.0 name: Gender, Sex, and Sexual Orientation (GSSO) ontology preferredPrefix: GSSO prefix: gsso repository: https://github.com/Superraptor/GSSO ols: description: GSSO is the Gender, Sex, and Sex Orientation ontology, including terms related to gender identity and expression, sexual and romantic identity and orientation, and sexual and reproductive behavior. download: http://purl.obolibrary.org/obo/gsso.owl homepage: https://gsso.research.cchmc.org/ license: LICENSE-2.0 name: GSSO - the Gender, Sex, and Sexual Orientation ontology prefix: gsso version: 2.0.5 version.iri: http://purl.obolibrary.org/obo/gsso/releases/2.0.5/gsso.owl ontobee: library: Library name: Gender, Sex, and Sexual Orientation (GSSO) ontology prefix: GSSO url: http://www.ontobee.org/ontology/GSSO pattern: ^\d{6}$ 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/$1 gtr: appears_in: - mondo comment: Identifiers appearing in MONDO don't match any of the resources apparent endpoints contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: "The Genetic Testing Registry (GTR\xAE) provides a central location\ \ for voluntary submission of genetic test information by providers. The scope\ \ includes the test's purpose, methodology, validity, evidence of the test's usefulness,\ \ and laboratory contacts and credentials. The overarching goal of the GTR is\ \ to advance the public health and research into the genetic basis of health and\ \ disease" example: AN0097748 homepage: https://www.ncbi.nlm.nih.gov/gtr/ name: Genetic Testing Registry gudmap: mappings: miriam: gudmap n2t: gudmap prefixcommons: GUDMAP miriam: deprecated: false description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract. homepage: http://www.gudmap.org/ id: '00000643' name: GUDMAP namespaceEmbeddedInLui: false pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$ 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 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: 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/$1 mappings: go: HAMAP miriam: hamap n2t: hamap prefixcommons: HAMAP uniprot: HAMAP miriam: deprecated: false description: HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries. homepage: https://hamap.expasy.org/ id: 00000292 name: HAMAP namespaceEmbeddedInLui: false pattern: ^MF_\d+$ 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 mappings: biolink: HANCESTRO bioportal: HANCESTRO obofoundry: hancestro ols: hancestro ontobee: HANCESTRO obofoundry: contact: danielle.welter@uni.lu contact.label: Danielle Welter 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 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 license: http://creativecommons.org/licenses/by/4.0/ 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 url: http://www.ontobee.org/ontology/HANCESTRO hao: bioportal: name: Hymenoptera Anatomy Ontology prefix: HAO example: 0000187 mappings: bioportal: HAO obofoundry: hao ols: hao ontobee: HAO prefixcommons: HAO obofoundry: contact: diapriid@gmail.com contact.label: Matt Yoder 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: CC-0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Hymenoptera Anatomy Ontology preferredPrefix: HAO prefix: hao 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 url: http://www.ontobee.org/ontology/HAO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: HAO uri_format: http://purl.obolibrary.org/obo/HAO_$1 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: '2021-10-19' version.iri: http://ontology.data.humancellatlas.org/ontologies/hcao/releases/2021-10-19/hcao.owl hcpcs: biolink: is_identifiers: false is_obo: false prefix: HCPCS uri_format: http://purl.bioontology.org/ontology/HCPCS/$1 bioportal: name: Healthcare Common Procedure Coding System prefix: HCPCS description: HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers. example: G8944 homepage: https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo mappings: biolink: HCPCS bioportal: HCPCS name: Healthcare Common Procedure Coding System hcvdb: homepage: http://euhcvdb.ibcp.fr mappings: miriam: hcvdb n2t: hcvdb prefixcommons: HCVDB miriam: deprecated: false description: the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses. homepage: http://euhcvdb.ibcp.fr/euHCVdb/ id: '00000207' name: HCVDB namespaceEmbeddedInLui: false pattern: ^M\d{5}$ 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 url: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$1 example: '16793' 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:$1 homepage: http://www.genenames.org mappings: bioportal: HGNC cellosaurus: HGNC go: HGNC miriam: hgnc n2t: hgnc ncbi: HGNC prefixcommons: HGNC uniprot: HGNC miriam: deprecated: false description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database. homepage: https://www.genenames.org id: 00000080 name: HGNC namespaceEmbeddedInLui: false pattern: ^((HGNC|hgnc):)?\d{1,5}$ 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 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/$1 hmdb: mappings: miriam: hmdb n2t: hmdb prefixcommons: HMDB wikidata: P2057 miriam: deprecated: false description: The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data. homepage: http://www.hmdb.ca/ id: '00000051' name: HMDB namespaceEmbeddedInLui: false pattern: ^HMDB\d+$ 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 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/$1 hog: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc. download_obo: ftp://ftp.bgee.org/general/ontologies/HOG.obo example: '0000255' homepage: https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships name: Homologous Organ Groups hogenom: mappings: miriam: hogenom n2t: hogenom prefixcommons: HOGENOM uniprot: HOGENOM miriam: deprecated: false description: HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier. homepage: http://pbil.univ-lyon1.fr/databases/hogenom/ id: '00000213' name: HOGENOM namespaceEmbeddedInLui: false pattern: ^\w+$ 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 mappings: bioportal: HOM obofoundry: hom ols: hom ontobee: HOM prefixcommons: HOM obofoundry: contact: bgee@sib.swiss contact.github: fbastian contact.label: Frederic Bastian 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 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 url: http://www.ontobee.org/ontology/HOM 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=$1 homologene: mappings: miriam: homologene n2t: homologene prefixcommons: HOMOLOGENE wikidata: P593 miriam: deprecated: false description: HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. homepage: https://www.ncbi.nlm.nih.gov/homologene/ id: '00000275' name: HomoloGene namespaceEmbeddedInLui: false pattern: ^\d+$ 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 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=$1 hovergen: homepage: https://pbil.univ-lyon1.fr/databases/hovergen.php mappings: miriam: hovergen n2t: hovergen prefixcommons: HOVERGEN miriam: deprecated: false description: HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees. homepage: http://pbil.univ-lyon1.fr/databases/hovergen.php id: '00000074' name: HOVERGEN namespaceEmbeddedInLui: false pattern: ^HBG\d+$ 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/$1 hp: bioportal: name: Human Phenotype Ontology prefix: HP download_obo: http://purl.obolibrary.org/obo/hp.obo example: '0011140' mappings: bioportal: HP miriam: hp n2t: hp obofoundry: hp ols: hp ontobee: HP prefixcommons: HP wikidata: P3841 miriam: deprecated: false description: The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. homepage: http://human-phenotype-ontology.github.io/ id: '00000571' name: Human Phenotype Ontology namespaceEmbeddedInLui: true pattern: ^HP:\d{7}$ 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:$1 obofoundry: contact: dr.sebastian.koehler@gmail.com contact.github: drseb contact.label: Sebastian Koehler deprecated: false description: A structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. download.obo: http://purl.obolibrary.org/obo/hp.obo download.owl: http://purl.obolibrary.org/obo/hp.owl homepage: http://www.human-phenotype-ontology.org/ inactive: false license: hpo license.url: https://hpo.jax.org/app/license name: Human Phenotype Ontology preferredPrefix: HP prefix: hp repository: https://github.com/obophenotype/human-phenotype-ontology ols: description: The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities and clinical features encountered in human disease. download: http://purl.obolibrary.org/obo/hp.owl homepage: http://www.human-phenotype-ontology.org/ license: license name: Human Phenotype Ontology prefix: hp version: '2021-10-10' version.iri: http://purl.obolibrary.org/obo/hp/releases/2021-10-10/hp.owl ontobee: library: Library name: Human Phenotype Ontology prefix: HP url: http://www.ontobee.org/ontology/HP pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: HP uri_format: http://purl.obolibrary.org/obo/HP_$1 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: 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=$1 mappings: go: HPA miriam: hpa n2t: hpa prefixcommons: HPA uniprot: HPA miriam: deprecated: false description: The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers. homepage: http://www.proteinatlas.org/ id: '00000336' name: HPA namespaceEmbeddedInLui: false pattern: ^ENSG\d{11}$ 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/$1 hpath: example: '2000191' mappings: ols: hpath ols: description: An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species. download: https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo homepage: https://github.com/Novartis/hpath name: Histopathology Ontology prefix: hpath version: '2019-07-05' hpm.peptide: mappings: miriam: hpm.peptide n2t: hpm.peptide prefixcommons: HPM.PEPTIDE miriam: deprecated: false description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra. homepage: http://www.humanproteomemap.org/index.php id: '00000527' name: Human Proteome Map Peptide namespaceEmbeddedInLui: false pattern: ^\d+$ 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/$1 hprd: mappings: miriam: hprd n2t: hprd prefixcommons: HPRD miriam: deprecated: false description: The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. homepage: http://www.hprd.org/ id: '00000377' name: HPRD namespaceEmbeddedInLui: false pattern: ^\d+$ 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 url: https://hpscreg.eu/cell-line/$1 mappings: cellosaurus: hPSCreg miriam: hpscreg n2t: hpscreg miriam: deprecated: false description: hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines). homepage: https://hpscreg.eu/ id: '00000674' name: Human Pluripotent Stem Cell Registry namespaceEmbeddedInLui: false pattern: ^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$ 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_$1 bioportal: name: Human Developmental Stages Ontology prefix: HSAPDV example: 0000194 mappings: biolink: HsapDv bioportal: HSAPDV obofoundry: hsapdv ols: hsapdv ontobee: HSAPDV prefixcommons: HSAPDV obofoundry: contact: bgee@sib.swiss contact.label: bgee deprecated: false description: Life cycle stages for Human download.obo: http://purl.obolibrary.org/obo/hsapdv.obo download.owl: http://purl.obolibrary.org/obo/hsapdv.owl homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: Human Developmental Stages preferredPrefix: HsapDv prefix: hsapdv repository: https://github.com/obophenotype/developmental-stage-ontologies ols: description: Life cycle stages for Human download: http://purl.obolibrary.org/obo/hsapdv.owl homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv name: Human Developmental Stages prefix: hsapdv version: '2020-03-10' version.iri: http://purl.obolibrary.org/obo/hsapdv/releases/2020-03-10/hsapdv.owl ontobee: library: Library name: Human Developmental Stages prefix: HSAPDV url: http://www.ontobee.org/ontology/HSAPDV pattern: ^\d{7}$ 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 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 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 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 license: http://creativecommons.org/licenses/by/3.0/ name: Health Surveillance Ontology prefix: hso version: '2020-11-28' version.iri: http://purl.obolibrary.org/obo/hso/2020-11-28/hso.owl ontobee: library: Library name: Health Surveillance Ontology prefix: HSO url: http://www.ontobee.org/ontology/HSO 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/$1 htn: bioportal: name: Hypertension Ontology prefix: HTN example: '00000014' mappings: bioportal: HTN obofoundry: htn ols: htn ontobee: HTN obofoundry: contact: aellenhicks@gmail.com contact.label: Amanda Hicks deprecated: false description: An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines download.owl: http://purl.obolibrary.org/obo/htn.owl homepage: https://github.com/aellenhicks/htn_owl inactive: false license: CC-BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Hypertension Ontology preferredPrefix: HTN prefix: htn repository: https://github.com/aellenhicks/htn_owl ols: description: An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines download: http://purl.obolibrary.org/obo/htn.owl homepage: https://github.com/aellenhicks/htn_owl name: Hypertension Ontology For Clinical Data prefix: htn version: '2019-06-10' ontobee: library: Library name: Hypertension Ontology prefix: HTN url: http://www.ontobee.org/ontology/HTN huge: mappings: miriam: huge n2t: huge prefixcommons: HUGE uniprot: HUGE miriam: deprecated: false description: The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. homepage: http://www.kazusa.or.jp/huge/ id: '00000263' name: HUGE namespaceEmbeddedInLui: false pattern: ^KIAA\d{4}$ 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/$1 iao: bioportal: name: Information Artifact Ontology prefix: IAO go: description: Ontology of information entities, including ontology metadata relations. name: Information Artifact Ontology prefix: IAO mappings: bioportal: IAO go: IAO miriam: iao n2t: iao obofoundry: iao ols: iao ontobee: IAO prefixcommons: IAO miriam: deprecated: false description: An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch. homepage: http://www.ontobee.org/ontology/IAO id: '00000603' name: Information Artifact Ontology namespaceEmbeddedInLui: false pattern: ^\d{7}$ 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: contact: jiezheng@pennmedicine.upenn.edu contact.github: zhengj2007 contact.label: Jie Zheng 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 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/ license: http://creativecommons.org/licenses/by/4.0/ 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 url: http://www.ontobee.org/ontology/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: http://translator.ncats.nih.gov/ICD10_$1 bioportal: name: International Classification of Diseases, Version 10 prefix: ICD10 homepage: https://icd.who.int/browse10 mappings: biolink: ICD10 bioportal: ICD10 miriam: icd n2t: icd prefixcommons: ICD miriam: deprecated: false description: The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes. homepage: http://www.who.int/classifications/icd/en/ id: 00000009 name: ICD namespaceEmbeddedInLui: false pattern: ^[A-Z]\d+(\.[-\d+])?$ 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 prefixcommons: is_identifiers: true is_obo: false prefix: ICD uri_format: http://identifiers.org/icd/$1 synonyms: - ICD - ICD-10 - ICD10 - ICD10CM wikidata: prefix: P4229 icd11: description: Diagnostic tool for epidemiology, health management and clinical purposes, maintained by the World Health Organization (WHO). It provides a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease. example: RA01.0 homepage: https://icd.who.int/ name: International Classification of Diseases 11th Revision synonyms: - ICD-11 wikidata: prefix: P7807 icd9: biolink: is_identifiers: false is_obo: false prefix: ICD9 uri_format: http://translator.ncats.nih.gov/ICD9_$1 bioportal: name: International Classification of Diseases, Version 9 - Clinical Modification prefix: ICD9CM description: ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States. example: '277.9' homepage: https://www.cdc.gov/nchs/icd/icd9cm.htm mappings: biolink: ICD9 bioportal: ICD9CM name: International Classification of Diseases 9th Revision synonyms: - IC9CM - ICD9 - ICD9CM - ICD9CM_2005 - ICD9CM_2005 - ICD9CM_2006 - ICD9_2005 - ICDCM_2005 - MTHICD9_2006 wikidata: prefix: P493 icdc: mappings: miriam: icdc miriam: deprecated: false description: The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer. homepage: https://caninecommons.cancer.gov/#/ id: 00000812 name: Integrated Canine Data Commons namespaceEmbeddedInLui: false pattern: ^ICDC[0-9][0-9][0-9][0-9][0-9][0-9]$ prefix: icdc sampleId: ICDC000101 uri_format: https://caninecommons.cancer.gov/#/study/$1 icdo: bioportal: name: International Classification of Diseases Ontology prefix: ICDO description: An ontologied version of ICD example: M9861/3 homepage: https://www.who.int/classifications/icd/adaptations/oncology/en/ mappings: bioportal: ICDO ontobee: ICDO name: The International Classification of Diseases for Oncology ontobee: library: Not Specified/No name: International Classification of Disease Ontology prefix: ICDO url: http://www.ontobee.org/ontology/ICDO synonyms: - ICD-O - ICDO wikidata: prefix: P563 iceberg.element: mappings: miriam: iceberg.element n2t: iceberg.element prefixcommons: ICEBERG.ELEMENT miriam: deprecated: false description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements. homepage: http://db-mml.sjtu.edu.cn/ICEberg/ id: 00000469 name: ICEberg element namespaceEmbeddedInLui: false pattern: ^\d+$ 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' mappings: bioportal: ICEO obofoundry: iceo ols: iceo ontobee: ICEO obofoundry: contact: liumeng94@sjtu.edu.cn contact.label: Meng LIU 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 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 license: http://creativecommons.org/licenses/by/4.0/ name: 'ICEO: Ontology of Integrative and Conjugative Elements' prefix: iceo version: '2.1' ontobee: library: Library name: Integrative and Conjugative Element Ontology prefix: ICEO url: http://www.ontobee.org/ontology/ICEO ico: bioportal: name: Informed Consent Ontology prefix: ICO example: ICODEV_0000066 mappings: bioportal: ICO obofoundry: ico ols: ico ontobee: ICO prefixcommons: ICO obofoundry: contact: yongqunh@med.umich.edu contact.github: yongqunh contact.label: Yongqun Oliver He 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 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 license: http://creativecommons.org/licenses/by/3.0/ 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 url: http://www.ontobee.org/ontology/ICO prefixcommons: is_identifiers: false is_obo: true prefix: ICO uri_format: http://purl.obolibrary.org/obo/ICO_$1 ideal: homepage: https://www.ideal-db.org mappings: miriam: ideal n2t: ideal prefixcommons: IDEAL uniprot: IDEAL miriam: deprecated: false description: IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. homepage: http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/ id: 00000398 name: IDEAL namespaceEmbeddedInLui: false pattern: ^IID\d+$ 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=$1 identifiers.namespace: mappings: miriam: identifiers.namespace miriam: deprecated: false description: Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain. homepage: https://www.ebi.ac.uk id: 00000859 name: Identifiers.org namespace namespaceEmbeddedInLui: false pattern: ^[a-z_\.]+$ prefix: identifiers.namespace sampleId: pubmed uri_format: https://registry.identifiers.org/registry/$1 ido: bioportal: name: Infectious Disease Ontology prefix: IDO mappings: bioportal: IDO miriam: ido n2t: ido obofoundry: ido ols: ido ontobee: IDO prefixcommons: IDO miriam: deprecated: false description: Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases. homepage: https://www.ebi.ac.uk/ols/ontologies/ido id: '00000677' name: Infectious Disease Ontology namespaceEmbeddedInLui: false pattern: ^[0-9]+$ 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: contact: Lindsay.Cowell@utsouthwestern.edu contact.github: lgcowell contact.label: Lindsay Cowell 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 url: http://www.ontobee.org/ontology/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 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 license: http://creativecommons.org/licenses/by/3.0/ 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 idoden: bioportal: name: Dengue Fever Ontology prefix: IDODEN description: An ontology for dengue fever. example: '0003463' homepage: https://bioportal.bioontology.org/ontologies/IDODEN mappings: bioportal: IDODEN name: Dengue Fever Ontology 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' mappings: bioportal: IDOMAL obofoundry: idomal ols: idomal ontobee: IDOMAL prefixcommons: IDOMAL obofoundry: 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 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Malaria Ontology prefix: 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 url: http://www.ontobee.org/ontology/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#$1 idr: mappings: fairsharing: FAIRsharing.6wf1zw miriam: idr miriam: deprecated: false description: "Image Data Resource (IDR) is an online, public data repository that\ \ seeks to store, integrate and serve image datasets from published scientific\ \ studies. We have collected and are continuing to receive existing and newly\ \ created \u201Creference image\" datasets that are valuable resources for a\ \ broad community of users, either because they will be frequently accessed\ \ and cited or because they can serve as a basis for re-analysis and the development\ \ of new computational tools." homepage: https://idr.openmicroscopy.org id: '00000743' name: Image Data Resource namespaceEmbeddedInLui: false pattern: ^[0-9]{4}$ prefix: idr sampleId: '0001' uri_format: https://idr.openmicroscopy.org/search/?query=Name:idr$1 iedb: mappings: miriam: iedb miriam: deprecated: false description: The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes. homepage: https://www.lji.org/ id: 00000865 name: Immune Epitope Database (IEDB) namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: iedb sampleId: '1038233' uri_format: https://www.iedb.org/reference/$1 name: Immune Epitope Database iev: mappings: obofoundry: iev prefixcommons: IEV obofoundry: deprecated: true homepage: http://www.inoh.org inactive: true name: Event (INOH pathway ontology) prefix: iev prefixcommons: is_identifiers: false is_obo: true prefix: IEV uri_format: http://purl.obolibrary.org/obo/IEV_$1 igsn: mappings: miriam: igsn n2t: igsn miriam: deprecated: false description: IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents. homepage: http://www.geosamples.org/ id: 00000806 name: International Geo Sample Number namespaceEmbeddedInLui: false pattern: ^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$ 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/$1 ihw: cellosaurus: category: Cell line databases/resources homepage: https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html name: International Histocompatibility Workshop cell lines prefix: IHW description: The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics. example: IHW09326 homepage: https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html mappings: cellosaurus: IHW name: International Histocompatibility Workshop cell lines pattern: ^IHW\d+$ imdrf: contributor: email: cthoyt@gmail.com 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 url: https://www.ebi.ac.uk/cgi-bin/imgt/hla/fetch_cell.cgi?$1 go: homepage: http://www.ebi.ac.uk/imgt/hla name: IMGT/HLA human major histocompatibility complex sequence database prefix: IMGT_HLA mappings: cellosaurus: IPD-IMGT/HLA go: IMGT_HLA miriam: imgt.hla n2t: imgt.hla ncbi: IMGT/HLA prefixcommons: IMGT.HLA miriam: deprecated: false description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature. homepage: https://www.ebi.ac.uk/imgt/hla/allele.html id: '00000331' name: IMGT HLA namespaceEmbeddedInLui: false pattern: ^[A-Z0-9*:]+$ 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: 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 prefixcommons: is_identifiers: false is_obo: true prefix: IMR uri_format: http://purl.obolibrary.org/obo/IMR_$1 inchi: mappings: 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 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_$1 bioportal: name: Interaction Network Ontology prefix: INO example: '0000003' mappings: biolink: INO bioportal: INO obofoundry: ino ols: ino ontobee: INO obofoundry: contact: yongqunh@med.umich.edu contact.label: Yongqun Oliver He deprecated: false description: An ontology of interactions and interaction networks download.owl: http://purl.obolibrary.org/obo/ino.owl homepage: https://github.com/INO-ontology/ino inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: Interaction Network Ontology preferredPrefix: INO prefix: ino repository: https://github.com/INO-ontology/ino ols: description: he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles. download: http://purl.obolibrary.org/obo/ino.owl homepage: https://github.com/INO-ontology/ino name: 'INO: Interaction Network Ontology' prefix: ino version: 1.0.112 ontobee: library: Library name: Interaction Network Ontology prefix: INO url: http://www.ontobee.org/ontology/INO insdc: mappings: miriam: insdc n2t: insdc prefixcommons: INSDC miriam: deprecated: false description: The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. homepage: https://www.ncbi.nlm.nih.gov/Genbank/ id: 00000029 name: Nucleotide Sequence Database namespaceEmbeddedInLui: false pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ 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/$1 insdc.run: comment: 'https://www.insdc.org/ is the authoritative source for INSDC. However, confusingly, they don''t mention runs in this table. I think we should ask them to include. ENA is a partner and they have documentation here: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html Runs | (E\|D\|S)RR[0-9]{6,} | ERR123456 -- | -- | --' contributor: email: cjmungall@lbl.gov name: Chris Mungall orcid: 0000-0002-6601-2165 description: An experimental run, served thrugh the ENA example: ERR436051 has_canonical: ena.embl homepage: https://www.insdc.org/ name: International Nucleotide Sequence Database Collaboration (INSDC) Run pattern: ^(E|D|S)RR[0-9]{6,}$ reviewer: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://www.ebi.ac.uk/ena/browser/view/$1 insdc.sra: mappings: fairsharing: FAIRsharing.g7t2hv miriam: insdc.sra n2t: insdc.sra prefixcommons: INSDC.SRA miriam: deprecated: false description: 'The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.' homepage: https://www.ncbi.nlm.nih.gov/sra id: '00000243' name: Sequence Read Archive namespaceEmbeddedInLui: false pattern: ^[SED]R[APRSXZ]\d+$ 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/$1 intact: go: homepage: https://www.ebi.ac.uk/intact/ name: IntAct protein interaction database prefix: IntAct mappings: go: IntAct miriam: intact n2t: intact prefixcommons: INTACT uniprot: IntAct miriam: deprecated: false description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. homepage: https://www.ebi.ac.uk/intact/ id: '00000010' name: IntAct namespaceEmbeddedInLui: false pattern: ^EBI\-[0-9]+$ 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/$1 interlex: mappings: miriam: ilx miriam: deprecated: false description: 'InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. ' homepage: https://www.fdilab.org id: 00000814 name: InterLex namespaceEmbeddedInLui: false pattern: ^[0-9]+$ 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 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/$1 mappings: biolink: interpro go: InterPro miriam: interpro n2t: interpro ncbi: InterPro obofoundry: ipr prefixcommons: IPR uniprot: InterPro miriam: deprecated: false description: InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. homepage: https://www.ebi.ac.uk/interpro/ id: '00000011' name: InterPro namespaceEmbeddedInLui: false pattern: ^IPR\d{6}$ 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/$1 irefweb: mappings: miriam: irefweb n2t: irefweb prefixcommons: IREFWEB miriam: deprecated: false description: 'iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.' homepage: http://wodaklab.org/iRefWeb/ id: '00000123' name: iRefWeb namespaceEmbeddedInLui: false pattern: ^\d+$ 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/irefweb/$1 iro: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true example: 0000008 name: Insect Resistance Ontology uri_format: https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1 isbn: biolink: is_identifiers: false is_obo: false prefix: isbn uri_format: https://www.isbn-international.org/identifier/$1 go: homepage: https://www.worldcat.org name: International Standard Book Number prefix: ISBN uri_format: https://www.worldcat.org/search?q=bn%3A$1 mappings: biolink: isbn go: ISBN miriam: isbn n2t: isbn prefixcommons: ISBN-13 miriam: deprecated: false description: The International Standard Book Number (ISBN) is for identifying printed books. homepage: http://isbndb.com/ id: '00000064' name: ISBN namespaceEmbeddedInLui: false pattern: ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ prefix: isbn providers: - code: CURATOR_REVIEW description: ISBN database at WorldCat homepage: http://www.worldcat.org/ name: ISBN database at WorldCat uri_format: http://www.worldcat.org/isbn/$1 sampleId: '9781584885658' uri_format: http://isbndb.com/search-all.html?kw=$1 n2t: description: The International Standard Book Number (ISBN) is for identifying printed books. example: '9781584885658' homepage: http://isbndb.com/ name: ISBNDB - ISBN Database namespaceEmbeddedInLui: false pattern: ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ prefix: isbn uri_format: http://isbndb.com/search-all.html?kw=$1 prefixcommons: is_identifiers: false is_obo: false prefix: ISBN-13 uri_format: https://monarchinitiative.org/ISBN13_$1 synonyms: - ISBN-10 - ISBN-13 isfinder: mappings: miriam: isfinder n2t: isfinder ncbi: ISFinder prefixcommons: ISFINDER miriam: deprecated: false description: ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available. homepage: http://www-is.biotoul.fr/i id: '00000173' name: ISFinder namespaceEmbeddedInLui: false pattern: ^IS\w+(\-\d)?$ prefix: isfinder sampleId: ISA1083-2 uri_format: https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1 n2t: description: ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available. example: ISA1083-2 homepage: http://www-is.biotoul.fr/i name: IS Finder at CNRS namespaceEmbeddedInLui: false pattern: ^IS\w+(\-\d)?$ prefix: isfinder uri_format: https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1 ncbi: example: ISA1083-2 homepage: http://www-is.biotoul.fr/ name: Insertion sequence elements database prefix: ISFinder prefixcommons: is_identifiers: true is_obo: false prefix: ISFINDER uri_format: http://identifiers.org/isfinder/$1 isni: biolink: is_identifiers: false is_obo: false prefix: isni uri_format: https://isni.org/isni/$1 mappings: biolink: isni miriam: isni n2t: isni miriam: deprecated: false description: "ISNI is the ISO certified global standard number for identifying\ \ the millions of contributors to creative works and those active in their distribution,\ \ including researchers, inventors, writers, artists, visual creators, performers,\ \ producers, publishers, aggregators, and more. It is part of a family of international\ \ standard identifiers that includes identifiers of works, recordings, products\ \ and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC,\ \ and ISWC.\r\n\r\nThe mission of the ISNI International Authority (ISNI-IA)\ \ is to assign to the public name(s) of a researcher, inventor, writer, artist,\ \ performer, publisher, etc. a persistent unique identifying number in order\ \ to resolve the problem of name ambiguity in search and discovery; and diffuse\ \ each assigned ISNI across all repertoires in the global supply chain so that\ \ every published work can be unambiguously attributed to its creator wherever\ \ that work is described." homepage: http://www.isni.org id: 00000684 name: International Standard Name Identifier namespaceEmbeddedInLui: false pattern: ^[0-9]{15}[0-9X]{1}$ prefix: isni sampleId: 000000012281955X uri_format: http://www.isni.org/isni/$1 n2t: description: ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC. The mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described. example: 000000012281955X homepage: http://www.isni.org name: International Standard Name Identifier namespaceEmbeddedInLui: false pattern: ^[0-9]{15}[0-9X]{1}$ prefix: isni uri_format: http://www.isni.org/isni/$1 issn: biolink: is_identifiers: false is_obo: false prefix: issn uri_format: https://portal.issn.org/resource/ISSN/$1 go: homepage: http://www.issn.org/ name: International Standard Serial Number prefix: ISSN mappings: biolink: issn go: ISSN miriam: issn n2t: issn prefixcommons: ISSN miriam: deprecated: false description: The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books. homepage: https://portal.issn.org id: '00000301' name: ISSN namespaceEmbeddedInLui: false pattern: ^\d{4}-\d{3}[\dX]$ prefix: issn providers: - code: CURATOR_REVIEW description: ISSN at Library of Congress homepage: http://catalog.loc.gov/webvoy.htm name: ISSN at Library of Congress uri_format: https://catalog.loc.gov/vwebv/search?searchCode=STNO&searchArg=$1&searchType=1&recCount=25 sampleId: 0745-4570 uri_format: https://portal.issn.org/resource/ISSN/$1 n2t: description: The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books. example: 1776-3045 homepage: https://portal.issn.org name: ISSN Portal namespaceEmbeddedInLui: false pattern: ^\d{4}-\d{3}[\dX]$ prefix: issn uri_format: https://portal.issn.org/resource/ISSN/$1 prefixcommons: is_identifiers: true is_obo: false prefix: ISSN uri_format: http://identifiers.org/issn/$1 itis: description: Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world. example: '589462' homepage: https://www.itis.gov/ name: Integrated Taxonomic Information System pattern: ^\d+$ uri_format: https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1 wikidata: prefix: P815 ito: bioportal: name: Intelligence Task Ontology prefix: ITO mappings: bioportal: ITO miriam: ito miriam: deprecated: false description: The Intelligence Task Ontology (ITO) provides a comprehensive map of machine intelligence tasks, as well as broader human intelligence or hybrid human/machine intelligence tasks. homepage: https://bioportal.bioontology.org/ id: 00000802 name: Intelligence Task Ontology namespaceEmbeddedInLui: false pattern: ^.+$ prefix: ito sampleId: ITO_01625 uri_format: https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https%3A%2F%2Fai-strategies.org%2Fontology%2F$1 iuphar.family: mappings: miriam: iuphar.family n2t: iuphar.family prefixcommons: IUPHAR.FAMILY miriam: deprecated: false description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits. homepage: http://www.guidetopharmacology.org/ id: '00000317' name: IUPHAR family namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: iuphar.family sampleId: '78' uri_format: http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1 n2t: description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits. example: '78' homepage: http://www.guidetopharmacology.org/ name: The IUPHAR/BPS Guide to PHARMACOLOGY namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: iuphar.family uri_format: http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1 prefixcommons: is_identifiers: true is_obo: false prefix: IUPHAR.FAMILY uri_format: http://identifiers.org/iuphar.family/$1 synonyms: - IUPHARfam iuphar.ligand: biolink: is_identifiers: false is_obo: false prefix: GTOPDB uri_format: https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1 mappings: biolink: GTOPDB miriam: iuphar.ligand n2t: iuphar.ligand prefixcommons: IUPHAR.LIGAND wikidata: P595 miriam: deprecated: false description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands. homepage: http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all id: '00000457' name: IUPHAR ligand namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: iuphar.ligand sampleId: '1755' uri_format: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1 n2t: description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands. example: '1755' homepage: http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all name: IUPHAR ligand at University of Edinburgh namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: iuphar.ligand uri_format: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1 prefixcommons: is_identifiers: true is_obo: false prefix: IUPHAR.LIGAND uri_format: http://identifiers.org/iuphar.ligand/$1 synonyms: - IUPHAR_LIGAND - IUPHAR_LIGAND_ID wikidata: database: Q17091219 database.homepage: http://www.guidetopharmacology.org database.label: IUPHAR/BPS Guide to PHARMACOLOGY homepage: https://www.guidetopharmacology.org/ name: Guide to Pharmacology Ligand ID pattern: \d{1,4} prefix: P595 uri_format: https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1 iuphar.receptor: go: homepage: http://www.iuphar.org/ name: International Union of Pharmacology prefix: IUPHAR_RECEPTOR uri_format: https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1 mappings: go: IUPHAR_RECEPTOR miriam: iuphar.receptor n2t: iuphar.receptor prefixcommons: IUPHAR.RECEPTOR wikidata: P5458 miriam: deprecated: false description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits. homepage: http://www.guidetopharmacology.org/targets.jsp id: 00000281 name: IUPHAR receptor namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: iuphar.receptor sampleId: '101' uri_format: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1 n2t: description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits. example: '101' homepage: http://www.guidetopharmacology.org/targets.jsp name: IUPHAR Receptor at University of Edinburgh namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: iuphar.receptor uri_format: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1 prefixcommons: is_identifiers: true is_obo: false prefix: IUPHAR.RECEPTOR uri_format: http://identifiers.org/iuphar.receptor/$1 synonyms: - IUPHAR_GPCR - IUPHARobj wikidata: database: Q17091219 database.homepage: http://www.guidetopharmacology.org database.label: IUPHAR/BPS Guide to PHARMACOLOGY homepage: http://www.guidetopharmacology.org/GRAC/ name: Guide to Pharmacology Target ID pattern: '[1-9]\d{0,3}' prefix: P5458 uri_format: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1 jax: description: Information about the C57BL/6J. Includes genetic background and disease data. example: '004435' homepage: https://www.jax.org/strain mappings: prefixcommons: JAX name: Jackson Laboratories Strain prefixcommons: is_identifiers: false is_obo: false prefix: JAX uri_format: http://jaxmice.jax.org/strain/$1 uri_format: https://www.jax.org/strain/$1 jaxmice: mappings: miriam: jaxmice n2t: jaxmice prefixcommons: JAXMICE miriam: deprecated: false description: JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory. homepage: http://jaxmice.jax.org/ id: '00000337' name: JAX Mice namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: jaxmice sampleId: '005012' uri_format: http://jaxmice.jax.org/strain/$1.html n2t: description: JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory. example: '005012' homepage: http://jaxmice.jax.org/ name: JAX Mice at Jackson Laboratory namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: jaxmice uri_format: http://jaxmice.jax.org/strain/$1.html prefixcommons: is_identifiers: true is_obo: false prefix: JAXMICE uri_format: http://identifiers.org/jaxmice/$1 jcggdb: mappings: miriam: jcggdb n2t: jcggdb prefixcommons: JCGGDB miriam: deprecated: false description: JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc. homepage: http://jcggdb.jp/index_en.html id: 00000479 name: JCGGDB namespaceEmbeddedInLui: false pattern: ^JCGG-STR\d{6}$ prefix: jcggdb sampleId: JCGG-STR008690 uri_format: http://jcggdb.jp/idb/jcggdb/$1 n2t: description: JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc. example: JCGG-STR008690 homepage: http://jcggdb.jp/index_en.html name: JCGGDB at Advanced Science Institute (Japan) namespaceEmbeddedInLui: false pattern: ^JCGG-STR\d{6}$ prefix: jcggdb uri_format: http://jcggdb.jp/idb/jcggdb/$1 name: Japan Consortium for Glycobiology and Glycotechnology Database prefixcommons: is_identifiers: true is_obo: false prefix: JCGGDB uri_format: http://identifiers.org/jcggdb/$1 jcm: mappings: miriam: jcm n2t: jcm ncbi: JCM prefixcommons: JCM miriam: deprecated: false description: The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2. homepage: http://www.jcm.riken.go.jp/ id: '00000174' name: Japan Collection of Microorganisms namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: jcm sampleId: '17254' uri_format: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1 n2t: description: The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2. example: '17254' homepage: http://www.jcm.riken.go.jp/ name: JCM at RIKEN BioResource Center namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: jcm uri_format: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1 ncbi: example: '1339' homepage: http://www.jcm.riken.go.jp/ name: Japan Collection of Microorganisms prefix: JCM prefixcommons: is_identifiers: true is_obo: false prefix: JCM uri_format: http://identifiers.org/jcm/$1 jcsd: mappings: miriam: jcsd n2t: jcsd prefixcommons: JCSD miriam: deprecated: false description: The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST). homepage: http://jglobal.jst.go.jp/en/ id: '00000241' name: Japan Chemical Substance Dictionary namespaceEmbeddedInLui: false pattern: ^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$ prefix: jcsd sampleId: J55.713G uri_format: http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1 n2t: description: The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST). example: J55.713G homepage: http://jglobal.jst.go.jp/en/ name: Japan Chemical Substance Dictionary namespaceEmbeddedInLui: false pattern: ^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$ prefix: jcsd uri_format: http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1 prefixcommons: is_identifiers: true is_obo: false prefix: JCSD uri_format: http://identifiers.org/jcsd/$1 jstor: go: homepage: https://www.jstor.org/ name: Digital archive of scholarly articles prefix: JSTOR uri_format: https://www.jstor.org/stable/$1 mappings: go: JSTOR miriam: jstor n2t: jstor prefixcommons: JSTOR miriam: deprecated: false description: JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration. homepage: http://www.jstor.org/ id: '00000444' name: JSTOR namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: jstor sampleId: '3075966' uri_format: http://www.jstor.org/stable/$1 n2t: description: JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration. example: '3075966' homepage: http://www.jstor.org/ name: JSTOR Online namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: jstor uri_format: http://www.jstor.org/stable/$1 prefixcommons: is_identifiers: true is_obo: false prefix: JSTOR uri_format: http://identifiers.org/jstor/$1 jws: example: achcar11 mappings: miriam: jws n2t: jws prefixcommons: JWS miriam: deprecated: false description: JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser. homepage: http://jjj.biochem.sun.ac.za/models/ id: '00000130' name: JWS Online namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: jws providers: - code: CURATOR_REVIEW description: JWS Online Model Repository at Manchester homepage: http://jjj.mib.ac.uk/index.html name: JWS Online Model Repository at Manchester uri_format: http://jjj.mib.ac.uk/models/$1 - code: CURATOR_REVIEW description: JWS Online Model Repository at Amsterdam homepage: http://jjj.bio.vu.nl/models/ name: JWS Online Model Repository at Amsterdam uri_format: http://jjj.bio.vu.nl/models/$1/ sampleId: curien uri_format: http://jjj.biochem.sun.ac.za/models/$1/ n2t: description: JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser. example: curien homepage: http://jjj.mib.ac.uk/index.html name: JWS Online Model Repository at Manchester namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: jws uri_format: http://jjj.mib.ac.uk/models/$1 prefixcommons: is_identifiers: true is_obo: false prefix: JWS uri_format: http://identifiers.org/jws/$1 uri_format: https://jjj.bio.vu.nl/models/$1 kaggle: mappings: miriam: kaggle n2t: kaggle miriam: deprecated: false description: Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions. homepage: https://kaggle.com id: 00000682 name: Kaggle namespaceEmbeddedInLui: false pattern: ^[0-9a-zA-Z\-]+\/[0-9a-zA-Z\-]+$ prefix: kaggle sampleId: nasa/kepler-exoplanet-search-results uri_format: https://www.kaggle.com/$1 n2t: description: Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions. example: nasa/kepler-exoplanet-search-results homepage: https://kaggle.com name: Kaggle namespaceEmbeddedInLui: false pattern: ^[0-9a-zA-Z\-]+\/[0-9a-zA-Z\-]+$ prefix: kaggle uri_format: https://www.kaggle.com/$1 kegg: comment: KEGG prefix has been split into several others deprecated: true go: homepage: http://www.genome.ad.jp/kegg/ name: Kyoto Encyclopedia of Genes and Genomes prefix: KEGG mappings: go: KEGG miriam: kegg n2t: kegg prefixcommons: KEGG uniprot: KEGG miriam: deprecated: false description: Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies. homepage: http://www.kegg.jp/ id: 00000578 name: Kyoto Encyclopedia of Genes and Genomes namespaceEmbeddedInLui: false pattern: ^([CHDEGTMKR]\d+)|(\w+:[\w\d\.-]*)|([a-z]{3,5})|(\w{2,4}\d{5})$ prefix: kegg sampleId: hsa00190 uri_format: http://www.kegg.jp/entry/$1 n2t: description: Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies. example: hsa00190 homepage: http://www.kegg.jp/ name: KEGG at Kyoto University Bioinformatics Center namespaceEmbeddedInLui: false pattern: ^([CHDEGTMKR]\d+)|(\w+:[\w\d\.-]*)|([a-z]{3,5})|(\w{2,4}\d{5})$ prefix: kegg uri_format: http://www.kegg.jp/entry/$1 prefixcommons: is_identifiers: true is_obo: false prefix: KEGG uri_format: http://identifiers.org/kegg/$1 synonyms: - KEGG uniprot: category: Genome annotation databases identifier: '53' link_is_explicit: 'true' name: 'KEGG: Kyoto Encyclopedia of Genes and Genomes' prefix: KEGG uri_format: https://www.genome.jp/dbget-bin/www_bget?$1 kegg.compound: mappings: miriam: kegg.compound n2t: kegg.compound prefixcommons: KEGG.COMPOUND miriam: deprecated: false description: KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life. homepage: https://www.genome.jp/kegg/ligand.html id: '00000013' name: KEGG Compound namespaceEmbeddedInLui: false pattern: ^C\d+$ prefix: kegg.compound sampleId: C12345 uri_format: https://www.kegg.jp/entry/$1 n2t: description: KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life. example: C12345 homepage: https://www.genome.jp/kegg/ligand.html name: KEGG LIGAND Database namespaceEmbeddedInLui: false pattern: ^C\d+$ prefix: kegg.compound uri_format: https://www.kegg.jp/entry/$1 part_of: kegg prefixcommons: is_identifiers: true is_obo: false prefix: KEGG.COMPOUND uri_format: http://identifiers.org/kegg.compound/$1 synonyms: - KEGG COMPOUND - KEGG.COMPOUND wikidata: prefix: P665 kegg.disease: mappings: miriam: kegg.disease n2t: kegg.disease prefixcommons: KEGG.DISEASE miriam: deprecated: false description: The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system. homepage: http://www.genome.jp/kegg/disease/ id: '00000475' name: KEGG Disease namespaceEmbeddedInLui: false pattern: ^H\d+$ prefix: kegg.disease sampleId: H00076 uri_format: http://www.kegg.jp/entry/$1 n2t: description: The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system. example: H00076 homepage: http://www.genome.jp/kegg/disease/ name: KEGG Disease at Kyoto University Bioinformatics Center namespaceEmbeddedInLui: false pattern: ^H\d+$ prefix: kegg.disease uri_format: http://www.kegg.jp/entry/$1 part_of: kegg prefixcommons: is_identifiers: true is_obo: false prefix: KEGG.DISEASE uri_format: http://identifiers.org/kegg.disease/$1 kegg.drug: mappings: miriam: kegg.drug n2t: kegg.drug prefixcommons: KEGG.DRUG miriam: deprecated: false description: KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules. homepage: https://www.genome.jp/kegg/drug/ id: '00000025' name: KEGG Drug namespaceEmbeddedInLui: false pattern: ^D\d+$ prefix: kegg.drug sampleId: D00123 uri_format: https://www.kegg.jp/entry/$1 n2t: description: KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules. example: D00123 homepage: https://www.genome.jp/kegg/drug/ name: KEGG DRUG Database namespaceEmbeddedInLui: false pattern: ^D\d+$ prefix: kegg.drug uri_format: https://www.kegg.jp/entry/$1 part_of: kegg prefixcommons: is_identifiers: true is_obo: false prefix: KEGG.DRUG uri_format: http://identifiers.org/kegg.drug/$1 synonyms: - KEGG DRUG - KEGG.DRUG wikidata: prefix: P665 kegg.environ: mappings: miriam: kegg.environ n2t: kegg.environ prefixcommons: KEGG.ENVIRON miriam: deprecated: false description: KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable. homepage: http://www.genome.jp/kegg/drug/environ.html id: 00000389 name: KEGG Environ namespaceEmbeddedInLui: false pattern: ^(ev\:)?E\d+$ prefix: kegg.environ sampleId: ev:E00032 uri_format: http://www.kegg.jp/entry/$1 n2t: description: KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable. example: ev:E00032 homepage: http://www.genome.jp/kegg/drug/environ.html name: KEGG ENVIRON Database namespaceEmbeddedInLui: false pattern: ^(ev\:)?E\d+$ prefix: kegg.environ uri_format: http://www.kegg.jp/entry/$1 part_of: kegg prefixcommons: is_identifiers: true is_obo: false prefix: KEGG.ENVIRON uri_format: http://identifiers.org/kegg.environ/$1 kegg.enzyme: biolink: is_identifiers: false is_obo: false prefix: KEGG.ENZYME uri_format: http://www.kegg.jp/entry/$1 description: KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links. go: homepage: http://www.genome.jp/dbget-bin/www_bfind?enzyme name: KEGG Enzyme Database prefix: KEGG_ENZYME uri_format: http://www.genome.jp/dbget-bin/www_bget?ec:$1 mappings: biolink: KEGG.ENZYME go: KEGG_ENZYME name: KEGG Enzyme part_of: kegg provides: eccode kegg.genes: biolink: is_identifiers: false is_obo: false prefix: KEGG.GENE uri_format: http://www.kegg.jp/entry/$1 example: bsu:BSU01340 mappings: biolink: KEGG.GENE miriam: kegg.genes n2t: kegg.genes prefixcommons: KEGG.GENES miriam: deprecated: false description: KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources. homepage: http://www.genome.jp/kegg/genes.html id: '00000070' name: KEGG Genes namespaceEmbeddedInLui: false pattern: ^\w+:[\w\d\.-]*$ prefix: kegg.genes sampleId: syn:ssr3451 uri_format: http://www.kegg.jp/entry/$1 n2t: description: KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources. example: syn:ssr3451 homepage: http://www.genome.jp/kegg/genes.html name: KEGG GENES Database namespaceEmbeddedInLui: false pattern: ^\w+:[\w\d\.-]*$ prefix: kegg.genes uri_format: http://www.kegg.jp/entry/$1 part_of: kegg prefixcommons: is_identifiers: true is_obo: false prefix: KEGG.GENES uri_format: http://identifiers.org/kegg.genes/$1 wikidata: prefix: P665 kegg.genome: example: T06648 mappings: miriam: kegg.genome n2t: kegg.genome prefixcommons: KEGG.GENOME miriam: deprecated: false description: KEGG Genome is a collection of organisms whose genomes have been completely sequenced. homepage: http://www.genome.jp/kegg/catalog/org_list.html id: 00000238 name: KEGG Genome namespaceEmbeddedInLui: false pattern: ^(T0\d+|\w{3,5})$ prefix: kegg.genome sampleId: eco uri_format: http://www.kegg.jp/entry/$1 n2t: description: KEGG Genome is a collection of organisms whose genomes have been completely sequenced. example: eco homepage: http://www.genome.jp/kegg/catalog/org_list.html name: KEGG Genome Database namespaceEmbeddedInLui: false pattern: ^(T0\d+|\w{3,5})$ prefix: kegg.genome uri_format: http://www.kegg.jp/entry/$1 part_of: kegg prefixcommons: is_identifiers: true is_obo: false prefix: KEGG.GENOME uri_format: http://identifiers.org/kegg.genome/$1 synonyms: - kegg_genome - kegg_genomes wikidata: prefix: P665 kegg.glycan: mappings: miriam: kegg.glycan n2t: kegg.glycan prefixcommons: KEGG.GLYCAN miriam: deprecated: false description: KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways. homepage: https://www.genome.jp/kegg/glycan/ id: '00000026' name: KEGG Glycan namespaceEmbeddedInLui: false pattern: ^G\d+$ prefix: kegg.glycan sampleId: G00123 uri_format: https://www.kegg.jp/entry/$1 n2t: description: KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways. example: G00123 homepage: https://www.genome.jp/kegg/glycan/ name: KEGG GLYCAN Database namespaceEmbeddedInLui: false pattern: ^G\d+$ prefix: kegg.glycan uri_format: https://www.kegg.jp/entry/$1 part_of: kegg prefixcommons: is_identifiers: true is_obo: false prefix: KEGG.GLYCAN uri_format: http://identifiers.org/kegg.glycan/$1 kegg.ligand: comment: This database has been discontinued by KEGG. It now lives inside the compound database deprecated: true go: homepage: http://www.genome.ad.jp/kegg/docs/upd_ligand.html name: KEGG LIGAND Database prefix: KEGG_LIGAND uri_format: http://www.genome.jp/dbget-bin/www_bget?cpd:$1 mappings: go: KEGG_LIGAND name: KEGG LIGAND part_of: kegg kegg.metagenome: mappings: miriam: kegg.metagenome n2t: kegg.metagenome prefixcommons: KEGG.METAGENOME miriam: deprecated: false description: The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species. homepage: http://www.genome.jp/kegg/catalog/org_list3.html id: 00000239 name: KEGG Metagenome namespaceEmbeddedInLui: false pattern: ^T3\d+$ prefix: kegg.metagenome sampleId: T30002 uri_format: http://www.kegg.jp/entry/$1 n2t: description: The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species. example: T30002 homepage: http://www.genome.jp/kegg/catalog/org_list3.html name: KEGG Metagenome Database namespaceEmbeddedInLui: false pattern: ^T3\d+$ prefix: kegg.metagenome uri_format: http://www.kegg.jp/entry/$1 part_of: kegg prefixcommons: is_identifiers: true is_obo: false prefix: KEGG.METAGENOME uri_format: http://identifiers.org/kegg.metagenome/$1 kegg.module: mappings: miriam: kegg.module n2t: kegg.module prefixcommons: KEGG.MODULE miriam: deprecated: false description: KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules. homepage: http://www.kegg.jp/kegg/module.html id: '00000474' name: KEGG Module namespaceEmbeddedInLui: false pattern: ^([a-z]{3,5}_)?M\d{5}$ prefix: kegg.module sampleId: M00002 uri_format: http://www.kegg.jp/entry/$1 n2t: description: KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules. example: M00002 homepage: http://www.kegg.jp/kegg/module.html name: KEGG Module at Kyoto University Bioinformatics Center namespaceEmbeddedInLui: false pattern: ^([a-z]{3,5}_)?M\d{5}$ prefix: kegg.module uri_format: http://www.kegg.jp/entry/$1 part_of: kegg prefixcommons: is_identifiers: true is_obo: false prefix: KEGG.MODULE uri_format: http://identifiers.org/kegg.module/$1 kegg.orthology: mappings: miriam: kegg.orthology n2t: kegg.orthology prefixcommons: KEGG.ORTHOLOGY miriam: deprecated: false description: KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms. homepage: http://www.genome.jp/kegg/ko.html id: '00000116' name: KEGG Orthology namespaceEmbeddedInLui: false pattern: ^K\d+$ prefix: kegg.orthology sampleId: K00001 uri_format: http://www.kegg.jp/entry/$1 n2t: description: KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms. example: K00001 homepage: http://www.genome.jp/kegg/ko.html name: KEGG Orthology Database namespaceEmbeddedInLui: false pattern: ^K\d+$ prefix: kegg.orthology uri_format: http://www.kegg.jp/entry/$1 part_of: kegg prefixcommons: is_identifiers: true is_obo: false prefix: KEGG.ORTHOLOGY uri_format: http://identifiers.org/kegg.orthology/$1 kegg.pathway: biolink: is_identifiers: false is_obo: false prefix: KEGG.PATHWAY uri_format: https://www.kegg.jp/entry/$1 example: rsk00410 go: homepage: http://www.genome.jp/kegg/pathway.html name: KEGG Pathways Database prefix: KEGG_PATHWAY uri_format: http://www.genome.jp/dbget-bin/www_bget?path:$1 mappings: biolink: KEGG.PATHWAY go: KEGG_PATHWAY miriam: kegg.pathway n2t: kegg.pathway prefixcommons: KEGG-path miriam: deprecated: false description: KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks. homepage: https://www.genome.jp/kegg/pathway.html id: '00000012' name: KEGG Pathway namespaceEmbeddedInLui: false pattern: ^\w{2,4}\d{5}$ prefix: kegg.pathway sampleId: hsa00620 uri_format: https://www.kegg.jp/entry/$1 n2t: description: KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks. example: hsa00620 homepage: https://www.genome.jp/kegg/pathway.html name: KEGG PATHWAY Database namespaceEmbeddedInLui: false pattern: ^\w{2,4}\d{5}$ prefix: kegg.pathway uri_format: https://www.kegg.jp/entry/$1 part_of: kegg prefixcommons: is_identifiers: false is_obo: false prefix: KEGG-path uri_format: http://www.kegg.jp/dbget-bin/www_bget?path:$1 synonyms: - KEGG-path - KEGG_PATHWAY wikidata: prefix: P665 kegg.reaction: go: homepage: http://www.genome.jp/kegg/reaction/ name: KEGG Reaction Database prefix: KEGG_REACTION uri_format: http://www.genome.jp/dbget-bin/www_bget?rn:$1 mappings: go: KEGG_REACTION miriam: kegg.reaction n2t: kegg.reaction prefixcommons: KEGG.REACTION wikidata: P665 miriam: deprecated: false description: KEGG reaction contains our knowledge on the universe of reactions that are relevant to life. homepage: https://www.genome.jp/kegg/reaction/ id: '00000014' name: KEGG Reaction namespaceEmbeddedInLui: false pattern: ^R\d+$ prefix: kegg.reaction sampleId: R00100 uri_format: https://www.kegg.jp/entry/$1 n2t: description: KEGG reaction contains our knowledge on the universe of reactions that are relevant to life. example: R00100 homepage: https://www.genome.jp/kegg/reaction/ name: KEGG Reaction Database namespaceEmbeddedInLui: false pattern: ^R\d+$ prefix: kegg.reaction uri_format: https://www.kegg.jp/entry/$1 part_of: kegg prefixcommons: is_identifiers: true is_obo: false prefix: KEGG.REACTION uri_format: http://identifiers.org/kegg.reaction/$1 synonyms: - KEGG_REACTION wikidata: database: Q909442 database.homepage: http://www.genome.jp/kegg/ database.label: Kyoto Encyclopedia of Genes and Genomes format.rdf: https://www.kegg.jp/entry/$1 homepage: https://www.kegg.jp/ name: KEGG ID pattern: '[A-Z]\d+' prefix: P665 uri_format: https://www.kegg.jp/entry/$1 knapsack: mappings: miriam: knapsack n2t: knapsack prefixcommons: KNAPSACK wikidata: P2064 miriam: deprecated: false description: 'KNApSAcK provides information on metabolites and the taxonomic class with which they are associated.' homepage: http://www.knapsackfamily.com/KNApSAcK/ id: '00000271' name: KNApSAcK namespaceEmbeddedInLui: false pattern: ^C\d{8} prefix: knapsack sampleId: C00000001 uri_format: http://www.knapsackfamily.com/knapsack_core/information.php?word=$1 n2t: description: Knapsack provides information on metabolites and the taxonomic class with which they are associated. example: C00000001 homepage: http://kanaya.aist-nara.ac.jp/KNApSAcK/ name: KnapSack at Nara Institute namespaceEmbeddedInLui: false pattern: ^C\d{8} prefix: knapsack uri_format: http://kanaya.naist.jp/knapsack_jsp/information.jsp?word=$1 prefixcommons: is_identifiers: true is_obo: false prefix: KNAPSACK uri_format: http://identifiers.org/knapsack/$1 wikidata: database: Q20900436 database.homepage: http://kanaya.naist.jp/KNApSAcK/ database.label: KNApSAcK name: KNApSAcK ID pattern: C\d{8} prefix: P2064 uri_format: http://www.knapsackfamily.com/knapsack_core/information.php?sname=C_ID&word=$1 kupo: appears_in: - cl comment: Website is down, now it redirects to something else that is not related contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true example: 0001009 homepage: http://www.kupkb.org/ name: Kidney and Urinary Pathway Ontology references: - https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-2-S2-S7 labo: bioportal: name: clinical LABoratory Ontology prefix: LABO example: '0000124' mappings: bioportal: LABO obofoundry: labo ols: labo ontobee: LABO obofoundry: contact: paul.fabry@usherbrooke.ca contact.label: Paul Fabry deprecated: false description: LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents. download.owl: http://purl.obolibrary.org/obo/labo.owl homepage: https://github.com/OpenLHS/LABO inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: clinical LABoratory Ontology preferredPrefix: LABO prefix: labo repository: https://github.com/OpenLHS/LABO ols: description: LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents. download: http://purl.obolibrary.org/obo/labo.owl homepage: https://github.com/OpenLHS/LABO name: clinical LABoratory Ontology prefix: labo version: '2021-06-08' version.iri: http://purl.obolibrary.org/obo/labo/2021-06-08/labo.owl ontobee: library: Library name: clinical LABoratory Ontology prefix: LABO url: http://www.ontobee.org/ontology/LABO lbo: bioportal: name: Livestock Breed Ontology prefix: LBO example: 0000487 mappings: bioportal: LBO ols: lbo ols: contact: jreecy@iastate.edu description: A vocabulary for cattle, chicken, horse, pig, and sheep breeds. download: http://data.bioontology.org/ontologies/LBO/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb homepage: http://bioportal.bioontology.org/ontologies/LBO name: Livestock Breed Ontology prefix: lbo version: '2019-03-26' lei: mappings: miriam: lei n2t: lei miriam: deprecated: false description: Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland. homepage: https://www.gleif.org/ id: 00000686 name: Global LEI Index namespaceEmbeddedInLui: false pattern: ^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$ prefix: lei sampleId: HWUPKR0MPOU8FGXBT394 uri_format: https://www.gleif.org/lei/$1 n2t: description: Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland. example: HWUPKR0MPOU8FGXBT394 homepage: https://www.gleif.org/ name: Global LEI Index namespaceEmbeddedInLui: false pattern: ^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$ prefix: lei uri_format: https://www.gleif.org/lei/$1 lgai.cede: mappings: miriam: lgai.cede miriam: deprecated: false description: LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR). homepage: https://www.lgresearch.ai id: 00000867 name: LG Chemical Entity Detection Dataset (LGCEDe) namespaceEmbeddedInLui: false pattern: ^LGCEDe-S-\d{9}$ prefix: lgai.cede sampleId: LGCEDe-S-000002244 uri_format: https://s3.us-east-2.amazonaws.com/lg.cede/$1 lgic: comment: Website is gone deprecated: true mappings: miriam: lgic n2t: lgic prefixcommons: LGIC miriam: deprecated: false description: The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available. homepage: https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php id: 00000087 name: Ligand-Gated Ion Channel database namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: lgic sampleId: 5HT3Arano uri_format: https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php n2t: description: The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available. example: 5HT3Arano homepage: https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php name: Ligand-Gated Ion Channel database at EBI namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: lgic uri_format: https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php prefixcommons: is_identifiers: true is_obo: false prefix: LGIC uri_format: http://identifiers.org/lgic/$1 licebase: mappings: miriam: licebase n2t: licebase prefixcommons: LICEBASE miriam: deprecated: false description: Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects. homepage: https://licebase.org id: 00000628 name: LiceBase namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9\-\/]+$ prefix: licebase sampleId: EMLSAT00000003403 uri_format: https://licebase.org/?q=$1 n2t: description: Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects. example: EMLSAT00000003403 homepage: https://licebase.org name: LiceBase namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9\-\/]+$ prefix: licebase uri_format: https://licebase.org/?q=$1 prefixcommons: is_identifiers: true is_obo: false prefix: LICEBASE uri_format: http://identifiers.org/licebase/$1 ligandbook: mappings: miriam: ligandbook n2t: ligandbook miriam: deprecated: false description: Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community. homepage: https://ligandbook.org/ id: 00000681 name: LigandBook namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: ligandbook sampleId: '785' uri_format: https://ligandbook.org/package/$1 n2t: description: Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community. example: '785' homepage: https://ligandbook.org/ name: LigandBook namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: ligandbook uri_format: https://ligandbook.org/package/$1 ligandbox: mappings: miriam: ligandbox n2t: ligandbox prefixcommons: LIGANDBOX miriam: deprecated: false description: LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. homepage: http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en id: '00000477' name: LigandBox namespaceEmbeddedInLui: false pattern: ^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$ prefix: ligandbox sampleId: D00001 uri_format: http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1 n2t: description: LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. example: D00001 homepage: http://ligandbox.protein.osaka-u.ac.jp/ligandbox//cgi-bin/index.cgi?LANG=en name: LigandBox at namespaceEmbeddedInLui: false pattern: ^D\d{5} prefix: ligandbox uri_format: http://ligandbox.protein.osaka-u.ac.jp/ligandbox/cgi-bin/liginf.cgi?id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: LIGANDBOX uri_format: http://identifiers.org/ligandbox/$1 ligandexpo: mappings: miriam: ligandexpo n2t: ligandexpo prefixcommons: LIGANDEXPO miriam: deprecated: false description: Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. homepage: http://ligand-depot.rutgers.edu/index.html id: '00000062' name: Ligand Expo namespaceEmbeddedInLui: false pattern: ^(\w){3}$ prefix: ligandexpo providers: - code: CURATOR_REVIEW description: Ligand Expo at Rutgers homepage: http://ligand-expo.rcsb.org/ name: Ligand Expo at Rutgers uri_format: http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid sampleId: ABC uri_format: http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid n2t: description: Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. example: ABC homepage: http://ligand-expo.rcsb.org/ name: Ligand Expo at Rutgers namespaceEmbeddedInLui: false pattern: ^(\w){3}$ prefix: ligandexpo uri_format: http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid prefixcommons: is_identifiers: true is_obo: false prefix: LIGANDEXPO uri_format: http://identifiers.org/ligandexpo/$1 lincs.cell: mappings: miriam: lincs.cell n2t: lincs.cell prefixcommons: LINCS.CELL miriam: deprecated: false description: 'The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.' homepage: http://lincsportal.ccs.miami.edu/cells/ id: '00000544' name: LINCS Cell namespaceEmbeddedInLui: false pattern: (^LCL-\d+$)|(^LDC-\d+$)|(^ES-\d+$)|(^LSC-\d+$)|(^LPC-\d+$) prefix: lincs.cell sampleId: LCL-2085 uri_format: http://lincsportal.ccs.miami.edu/cells/#/view/$1 n2t: description: 'The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.' example: LCL-2085 homepage: http://lincsportal.ccs.miami.edu/cells/ name: LINCS Portal namespaceEmbeddedInLui: false pattern: (^LCL-\d+$)|(^LDC-\d+$)|(^ES-\d+$)|(^LSC-\d+$)|(^LPC-\d+$) prefix: lincs.cell uri_format: http://lincsportal.ccs.miami.edu/cells/#/view/$1 pattern: ^(LCL|LDC|ES|LSC|LPC)-\d+$ prefixcommons: is_identifiers: true is_obo: false prefix: LINCS.CELL uri_format: http://identifiers.org/lincs.cell/$1 lincs.data: mappings: miriam: lincs.data n2t: lincs.data prefixcommons: LINCS.DATA miriam: deprecated: false description: The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level). homepage: http://lincsportal.ccs.miami.edu/datasets/ id: 00000588 name: LINCS Data namespaceEmbeddedInLui: false pattern: ^[EL]D[SG]-\d+$ prefix: lincs.data providers: - code: omicsdi description: Lincs through OmicsDI homepage: https://www.omicsdi.org/ name: Lincs through OmicsDI uri_format: https://www.omicsdi.org/dataset/lincs/$1 sampleId: LDS-1110 uri_format: http://lincsportal.ccs.miami.edu/datasets/#/view/$1 n2t: description: The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level). example: LDS-1110 homepage: http://lincsportal.ccs.miami.edu/datasets/ name: LINCS Data at University of Miami namespaceEmbeddedInLui: false pattern: ^[EL]D[SG]-\d+$ prefix: lincs.data uri_format: http://lincsportal.ccs.miami.edu/datasets/#/view/$1 prefixcommons: is_identifiers: true is_obo: false prefix: LINCS.DATA uri_format: http://identifiers.org/lincs.data/$1 lincs.protein: mappings: miriam: lincs.protein n2t: lincs.protein prefixcommons: LINCS.PROTEIN miriam: deprecated: false description: The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins. homepage: http://lincs.hms.harvard.edu/db/proteins/ id: '00000545' name: LINCS Protein namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: lincs.protein sampleId: '200282' uri_format: http://lincs.hms.harvard.edu/db/proteins/$1/ n2t: description: The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins. example: '200282' homepage: http://lincs.hms.harvard.edu/db/proteins/ name: LINCS Protein at Harvard Medical School namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: lincs.protein uri_format: http://lincs.hms.harvard.edu/db/proteins/$1/ prefixcommons: is_identifiers: true is_obo: false prefix: LINCS.PROTEIN uri_format: http://identifiers.org/lincs.protein/$1 uri_format: https://lincs.hms.harvard.edu/db/proteins/$1 lincs.smallmolecule: mappings: miriam: lincs.smallmolecule n2t: lincs.smallmolecule prefixcommons: LINCS.SMALLMOLECULE miriam: deprecated: false description: The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC). homepage: http://lincsportal.ccs.miami.edu/SmallMolecules/ id: '00000546' name: LINCS Small Molecule namespaceEmbeddedInLui: false pattern: ^LSM-\d+$ prefix: lincs.smallmolecule sampleId: LSM-6306 uri_format: http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1 n2t: description: The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC). example: LSM-6306 homepage: http://lincsportal.ccs.miami.edu/SmallMolecules/ name: LINCS Portal namespaceEmbeddedInLui: false pattern: ^LSM-\d+$ prefix: lincs.smallmolecule uri_format: http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1 prefixcommons: is_identifiers: true is_obo: false prefix: LINCS.SMALLMOLECULE uri_format: http://identifiers.org/lincs.smallmolecule/$1 synonyms: - lincs linguist: mappings: miriam: linguist miriam: deprecated: false description: Registry of programming languages for the Linguist program for detecting and highlighting programming languages. homepage: https://github.com/ id: 00000849 name: Linguist namespaceEmbeddedInLui: false pattern: ^[a-zA-Z0-9 +#'*]+$ prefix: linguist sampleId: Python uri_format: https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1 lipidbank: mappings: miriam: lipidbank n2t: lipidbank prefixcommons: LIPIDBANK miriam: deprecated: false description: LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. homepage: http://lipidbank.jp/index.html id: '00000115' name: LipidBank namespaceEmbeddedInLui: false pattern: ^\w+\d+$ prefix: lipidbank sampleId: BBA0001 uri_format: http://lipidbank.jp/cgi-bin/detail.cgi?id=$1 n2t: description: LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. example: BBA0001 homepage: http://lipidbank.jp/index.html name: LipidBank the Lipid database namespaceEmbeddedInLui: false pattern: ^\w+\d+$ prefix: lipidbank uri_format: http://lipidbank.jp/cgi-bin/detail.cgi?id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: LIPIDBANK uri_format: http://identifiers.org/lipidbank/$1 lipidmaps: mappings: miriam: lipidmaps n2t: lipidmaps prefixcommons: LIPIDMAPS scholia: lipidmaps miriam: deprecated: false description: The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy. homepage: http://www.lipidmaps.org id: '00000052' name: LIPID MAPS namespaceEmbeddedInLui: false pattern: ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$ prefix: lipidmaps providers: - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/lipidmaps/$1 sampleId: LMPR0102010012 uri_format: http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1 n2t: description: The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy. example: LMPR0102010012 homepage: http://www.lipidmaps.org name: Department of Bioengineering and the San Diego Supercomputer Center namespaceEmbeddedInLui: false pattern: ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$ prefix: lipidmaps uri_format: http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1 prefixcommons: is_identifiers: true is_obo: false prefix: LIPIDMAPS uri_format: http://identifiers.org/lipidmaps/$1 synonyms: - LIPID MAPS - LIPID_MAPS_class - LIPID_MAPS_instance wikidata: prefix: P2063 lipro: bioportal: name: Lipid Ontology prefix: LIPRO mappings: bioportal: LIPRO obofoundry: lipro prefixcommons: LIPRO obofoundry: contact: bakerc@unb.ca contact.label: Christipher Baker deprecated: true description: An ontology representation of the LIPIDMAPS nomenclature classification. inactive: true name: Lipid Ontology prefix: lipro prefixcommons: is_identifiers: false is_obo: true prefix: LIPRO uri_format: http://purl.obolibrary.org/obo/LIPRO_$1 lncipedia: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A comprehensive compendium of human long non-coding RNAs example: SNHG3 homepage: https://lncipedia.org name: LNCipedia loggerhead: mappings: obofoundry: loggerhead prefixcommons: LOGGERHEAD obofoundry: contact: peteremidford@yahoo.com contact.label: Peter Midford deprecated: true homepage: http://www.mesquiteproject.org/ontology/Loggerhead/index.html inactive: true name: Loggerhead nesting prefix: loggerhead prefixcommons: is_identifiers: false is_obo: true prefix: LOGGERHEAD uri_format: http://purl.obolibrary.org/obo/LOGGERHEAD_$1 loinc: biolink: is_identifiers: false is_obo: false prefix: LOINC uri_format: http://loinc.org/rdf/$1 bioportal: name: Logical Observation Identifier Names and Codes prefix: LOINC description: The international standard for identifying health measurements, observations, and documents. example: LL379-9 homepage: https://loinc.org/ mappings: biolink: LOINC bioportal: LOINC name: Logical Observation Identifiers Names and Codes uri_format: https://loinc.org/$1 lotus: comment: IDs are actually leading to the structural part of LOTUS only, which might change in the future. Will adapt the regexp in case. contact: adriano.rutz@ik.me contributor: email: null name: Adriano Rutz orcid: 0000-0003-0443-9902 description: "LOTUS, actually, represents the most exhaustive resource of documented\ \ structure-organism pairs. Within the frame of current computational approaches\ \ in Natural Produts\u2019s research and related fields, these documented structure-organism\ \ pairs should allow a more complete understanding of organisms and their chemistry." example: LTS0004651 homepage: https://lotus.naturalproducts.net name: LOTUS Initiative for Open Natural Products Research pattern: ^LTS\d{7}$ reviewer: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://lotus.naturalproducts.net/compound/lotus_id/$1 wikidata: database: Q104225190 lrg: mappings: miriam: lrg n2t: lrg prefixcommons: LRG miriam: deprecated: false description: A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI. homepage: http://www.lrg-sequence.org/ id: '00000376' name: Locus Reference Genomic namespaceEmbeddedInLui: false pattern: ^LRG_\d+$ prefix: lrg providers: - code: CURATOR_REVIEW description: Locus Reference Genomic through Ensembl homepage: http://www.ensembl.org/ name: Locus Reference Genomic through Ensembl uri_format: http://www.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1 - code: CURATOR_REVIEW description: Locus Reference Genomic through Ensembl mirror (asia) homepage: http://asia.ensembl.org/ name: Locus Reference Genomic through Ensembl mirror (asia) uri_format: http://asia.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1 - code: CURATOR_REVIEW description: Locus Reference Genomic through Ensembl mirror (US west) homepage: http://uswest.ensembl.org/ name: Locus Reference Genomic through Ensembl mirror (US west) uri_format: http://uswest.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1 - code: CURATOR_REVIEW description: Locus Reference Genomic through Ensembl mirror (US east) homepage: http://useast.ensembl.org/ name: Locus Reference Genomic through Ensembl mirror (US east) uri_format: http://useast.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1 sampleId: LRG_1 uri_format: ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml n2t: description: Locus Reference Genomic (LRG) provides identifiers to stable genomic DNA sequences for regions of the human genome, providing a recognized reference-sequence standard for reporting sequence variants. LRG is maintained by the NCBI and the European Bioinformatics Institute (EBI). example: LRG_1 homepage: http://uswest.ensembl.org/ name: Locus Reference Genomic through Ensembl mirror (US west) namespaceEmbeddedInLui: false pattern: ^LRG_\d+$ prefix: lrg uri_format: http://uswest.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1 prefixcommons: is_identifiers: true is_obo: false prefix: LRG uri_format: http://identifiers.org/lrg/$1 lspci: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions) example: '1' homepage: https://labsyspharm.github.io/lspci/ name: Laboratory of Systems Pharmacology Compound ID pattern: ^\d+$ uri_format: https://labsyspharm.github.io/lspci/$1 ma: bioportal: name: Mouse Adult Gross Anatomy Ontology prefix: MA go: description: Adult Mouse Anatomical Dictionary; part of Gene Expression Database homepage: http://www.informatics.jax.org/ name: Adult Mouse Anatomical Dictionary prefix: MA uri_format: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1 mappings: bioportal: MA go: MA miriam: ma n2t: ma obofoundry: ma ols: ma ontobee: MA prefixcommons: MA miriam: deprecated: false description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus) homepage: http://www.informatics.jax.org/ id: '00000445' name: Mouse Adult Gross Anatomy namespaceEmbeddedInLui: true pattern: ^MA:\d+$ prefix: ma sampleId: '0002502' uri_format: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1 n2t: description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus) example: '0002502' homepage: http://www.informatics.jax.org/ name: Mouse Adult Gross Anatomy at The Jackson Laboratory namespaceEmbeddedInLui: true pattern: ^MA:\d+$ prefix: ma uri_format: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1 obofoundry: contact: Terry.Hayamizu@jax.org contact.github: tfhayamizu contact.label: Terry Hayamizu deprecated: false description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus). download.obo: http://purl.obolibrary.org/obo/ma.obo download.owl: http://purl.obolibrary.org/obo/ma.owl homepage: https://github.com/obophenotype/mouse-anatomy-ontology inactive: false license: CC-BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Mouse adult gross anatomy preferredPrefix: MA prefix: ma repository: https://github.com/obophenotype/mouse-anatomy-ontology ols: description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus). download: http://purl.obolibrary.org/obo/ma.owl homepage: https://github.com/obophenotype/mouse-anatomy-ontology name: Mouse adult gross anatomy prefix: ma version: '2017-02-07' version.iri: http://purl.obolibrary.org/obo/ma/releases/2017-02-07/ma.owl ontobee: library: Library name: Mouse adult gross anatomy prefix: MA url: http://www.ontobee.org/ontology/MA pattern: ^\d+$ prefixcommons: is_identifiers: false is_obo: true prefix: MA uri_format: http://purl.obolibrary.org/obo/MA_$1 macie: mappings: miriam: macie n2t: macie prefixcommons: MACIE miriam: deprecated: false description: MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved. homepage: https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html id: '00000077' name: MACiE namespaceEmbeddedInLui: false pattern: ^M\d{4}$ prefix: macie sampleId: M0001 uri_format: https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1 n2t: description: MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved. example: M0001 homepage: https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html name: MACiE database of mechanisms, annotation and classification in enzymes namespaceEmbeddedInLui: false pattern: ^M\d{4}$ prefix: macie uri_format: https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1 name: Mechanism, Annotation and Classification in Enzymes prefixcommons: is_identifiers: true is_obo: false prefix: MACIE uri_format: http://identifiers.org/macie/$1 maizegdb.locus: go: homepage: https://www.maizegdb.org/ name: MaizeGDB prefix: MaizeGDB_Locus uri_format: https://www.maizegdb.org/gene_center/gene/$1 mappings: go: MaizeGDB_Locus miriam: maizegdb.locus n2t: maizegdb.locus prefixcommons: MAIZEGDB.LOCUS miriam: deprecated: false description: MaizeGDB is the maize research community's central repository for genetics and genomics information. homepage: http://www.maizegdb.org/ id: '00000177' name: MaizeGDB Locus namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: maizegdb.locus sampleId: '25011' uri_format: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1 n2t: description: MaizeGDB is the maize research community's central repository for genetics and genomics information. example: '25011' homepage: http://www.maizegdb.org/ name: MaizeGDB at Missouri namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: maizegdb.locus uri_format: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1 name: MaizeGDB Locus prefixcommons: is_identifiers: true is_obo: false prefix: MAIZEGDB.LOCUS uri_format: http://identifiers.org/maizegdb.locus/$1 mamo: bioportal: name: Mathematical Modelling Ontology prefix: MAMO example: '0000026' mappings: bioportal: MAMO miriam: mamo n2t: mamo obofoundry: mamo ols: mamo ontobee: MAMO prefixcommons: MAMO miriam: deprecated: false description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. homepage: http://bioportal.bioontology.org/ontologies/MAMO id: '00000517' name: Mathematical Modelling Ontology namespaceEmbeddedInLui: false pattern: ^MAMO_\d{7}$ prefix: mamo sampleId: MAMO_0000026 uri_format: http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/$1 n2t: description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. example: MAMO_0000026 homepage: http://bioportal.bioontology.org/ontologies/MAMO name: MAMO through BioPortal namespaceEmbeddedInLui: false pattern: ^MAMO_\d{7}$ prefix: mamo uri_format: http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/$1 obofoundry: contact: n.lenovere@gmail.com contact.label: Nicolas Le Novere deprecated: false description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. download.owl: http://purl.obolibrary.org/obo/mamo.owl homepage: http://sourceforge.net/p/mamo-ontology/wiki/Home/ inactive: false license: Artistic License 2.0 license.url: http://opensource.org/licenses/Artistic-2.0 name: Mathematical modeling ontology preferredPrefix: MAMO prefix: mamo ols: description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. download: http://purl.obolibrary.org/obo/mamo.owl homepage: http://sourceforge.net/p/mamo-ontology/wiki/Home/ name: Mathematical Modelling Ontology prefix: mamo version: '2020-08-24' ontobee: library: Library name: Mathematical modeling ontology prefix: MAMO url: http://www.ontobee.org/ontology/MAMO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: MAMO uri_format: http://purl.obolibrary.org/obo/MAMO_$1 uri_format: http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1 mao: mappings: obofoundry: mao prefixcommons: MAO obofoundry: contact: julie@igbmc.u-strasbg.fr contact.label: Julie Thompson deprecated: true homepage: http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html inactive: true name: Multiple alignment prefix: mao prefixcommons: is_identifiers: false is_obo: true prefix: MAO uri_format: http://purl.obolibrary.org/obo/MAO_$1 massbank: mappings: miriam: massbank n2t: massbank prefixcommons: MASSBANK miriam: deprecated: false description: MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da). homepage: http://www.massbank.jp id: '00000273' name: MassBank namespaceEmbeddedInLui: false pattern: ^[A-Z]{2}[A-Z0-9][0-9]{5}$ prefix: massbank providers: - code: CURATOR_REVIEW description: MassBank in Europe homepage: https://massbank.eu/ name: MassBank in Europe uri_format: https://massbank.eu/MassBank/RecordDisplay?id=$1 sampleId: PB000166 uri_format: http://www.massbank.jp/RecordDisplay?id=$1 n2t: description: MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da). example: PB000166 homepage: http://www.massbank.jp name: MassBank in Japan namespaceEmbeddedInLui: false pattern: ^[A-Z]{2}[A-Z0-9][0-9]{5}$ prefix: massbank uri_format: http://www.massbank.jp/jsp/FwdRecord.jsp?id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MASSBANK uri_format: http://identifiers.org/massbank/$1 wikidata: database: Q24088019 prefix: P6689 massive: mappings: fairsharing: FAIRsharing.LYsiMd miriam: massive n2t: massive prefixcommons: MASSIVE uniprot: MassIVE miriam: deprecated: false description: MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. homepage: https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp id: '00000650' name: MassIVE namespaceEmbeddedInLui: false pattern: ^MSV\d+$ prefix: massive providers: - code: omicsdi description: MassIVE through OmicsDI homepage: https://www.omicsdi.org/ name: MassIVE through OmicsDI uri_format: https://www.omicsdi.org/dataset/massive/$1 sampleId: MSV000082131 uri_format: https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1 n2t: description: MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. example: MSV000082131 homepage: https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp name: MassIVE namespaceEmbeddedInLui: false pattern: ^MSV\d+$ prefix: massive uri_format: https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MASSIVE uri_format: http://identifiers.org/massive/$1 uniprot: category: Proteomic databases identifier: '241' link_is_explicit: 'true' name: MassIVE - Mass Spectrometry Interactive Virtual Environment prefix: MassIVE uri_format: https://massive.ucsd.edu/ProteoSAFe/protein_explorer.jsp?libraries=2&protein_name=$1 mat: bioportal: name: Minimal Anatomical Terminology prefix: MAT mappings: bioportal: MAT obofoundry: mat prefixcommons: MAT name: Minimal Anatomical Terminology obofoundry: contact: j.bard@ed.ac.uk contact.label: Jonathan Bard deprecated: true inactive: true name: Minimal anatomical terminology prefix: mat prefixcommons: is_identifiers: false is_obo: true prefix: MAT uri_format: http://purl.obolibrary.org/obo/MAT_$1 matrixdb: appears_in: - complexportal contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides example: MULT_4_VAR1_bovine homepage: http://matrixdb.univ-lyon1.fr/ name: MatrixDB uri_format: http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1 matrixdb.association: mappings: miriam: matrixdb.association n2t: matrixdb.association prefixcommons: MATRIXDB.ASSOCIATION miriam: deprecated: false description: MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations. homepage: http://matrixdb.univ-lyon1.fr/ id: 00000068 name: MatrixDB namespaceEmbeddedInLui: false pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$ prefix: matrixdb.association sampleId: P00747__P07355 uri_format: http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association n2t: description: MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations. example: P00747__P07355 homepage: http://matrixdb.univ-lyon1.fr/ name: MatrixDB Association namespaceEmbeddedInLui: false pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$ prefix: matrixdb.association uri_format: http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association name: MatrixDB Association prefixcommons: is_identifiers: true is_obo: false prefix: MATRIXDB.ASSOCIATION uri_format: http://identifiers.org/matrixdb.association/$1 maxo: biolink: is_identifiers: false is_obo: true prefix: MAXO uri_format: http://purl.obolibrary.org/obo/MAXO_$1 bioportal: name: Medical Action Ontology prefix: MAXO example: 0000008 mappings: biolink: MAXO bioportal: MAXO obofoundry: maxo ols: maxo ontobee: MAXO obofoundry: contact: Leigh.Carmody@jax.org contact.github: LCCarmody contact.label: Leigh Carmody deprecated: false description: Medical Action Ontology is an ontology... download.json: http://purl.obolibrary.org/obo/maxo.json download.obo: http://purl.obolibrary.org/obo/maxo.obo download.owl: http://purl.obolibrary.org/obo/maxo.owl homepage: https://github.com/monarch-initiative/MAxO inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: Medical Action Ontology preferredPrefix: MAXO prefix: maxo repository: https://github.com/monarch-initiative/MAxO ols: description: An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations. download: http://purl.obolibrary.org/obo/maxo.owl homepage: https://github.com/monarch-initiative/MAxO license: https://creativecommons.org/licenses/by/4.0/ name: Medical Action Ontology prefix: maxo version: '2021-08-19' version.iri: http://purl.obolibrary.org/obo/maxo/releases/2021-08-19/maxo.owl ontobee: library: Library name: Medical Action Ontology prefix: MAXO url: http://www.ontobee.org/ontology/MAXO mcc: bioportal: name: Cell Line Ontology [by Mahadevan] prefix: MCCL deprecated: true mappings: bioportal: MCCL name: Cell Line Ontology [derivative] mco: bioportal: name: Microbial Conditions Ontology prefix: MCO example: 0000858 mappings: bioportal: MCO obofoundry: mco ols: mco ontobee: MCO obofoundry: contact: citlalli.mejiaalmonte@gmail.com contact.label: "Citlalli Mej\xEDa-Almonte" deprecated: false description: Microbial Conditions Ontology is an ontology... download.obo: http://purl.obolibrary.org/obo/mco.obo download.owl: http://purl.obolibrary.org/obo/mco.owl homepage: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: Microbial Conditions Ontology preferredPrefix: MCO prefix: mco repository: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology ols: description: Microbial Conditions Ontology is an ontology... download: http://purl.obolibrary.org/obo/mco.owl homepage: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology name: Microbial Conditions Ontology prefix: mco version: '2019-05-15' version.iri: http://purl.obolibrary.org/obo/mco/releases/2019-05-15/mco.owl ontobee: library: Library name: Microbial Conditions Ontology prefix: MCO url: http://www.ontobee.org/ontology/MCO pattern: ^\d+$ mdm: bioportal: name: Mapping of Drug Names and MeSH 2021 prefix: MDM mappings: bioportal: MDM miriam: mdm n2t: mdm prefixcommons: MDM miriam: deprecated: false description: The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems. homepage: https://medical-data-models.org/ id: '00000574' name: MDM namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: mdm sampleId: '4776' uri_format: https://medical-data-models.org/forms/$1 n2t: description: The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems. example: '4776' homepage: https://medical-data-models.org/ name: MDM at University of Muenster namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: mdm uri_format: https://medical-data-models.org/forms/$1 name: Medical Data Models prefixcommons: is_identifiers: true is_obo: false prefix: MDM uri_format: http://identifiers.org/mdm/$1 meddra: bioportal: name: Medical Dictionary for Regulatory Activities Terminology (MedDRA) prefix: MEDDRA mappings: bioportal: MEDDRA miriam: meddra n2t: meddra prefixcommons: MEDDRA miriam: deprecated: false description: The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT). homepage: http://bioportal.bioontology.org/ontologies/MEDDRA id: '00000563' name: MedDRA namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: meddra sampleId: '10015919' uri_format: http://purl.bioontology.org/ontology/MEDDRA/$1 n2t: description: The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT). example: '10015919' homepage: http://bioportal.bioontology.org/ontologies/MEDDRA name: MedDRA through BioPortal namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: meddra uri_format: http://purl.bioontology.org/ontology/MEDDRA/$1 name: Medical Dictionary for Regulatory Activities Terminology prefixcommons: is_identifiers: false is_obo: false prefix: MEDDRA uri_format: http://purl.bioontology.org/ontology/MEDDRA/$1 synonyms: - MEDRA - MeDRA - MedDRA - Medical Dictionary for Regulatory Activities wikidata: prefix: P3201 medgen: biolink: is_identifiers: false is_obo: false prefix: medgen uri_format: https://www.ncbi.nlm.nih.gov/medgen/$1 mappings: biolink: medgen miriam: medgen n2t: medgen ncbi: MedGen prefixcommons: MedGen miriam: deprecated: false description: MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder. homepage: https://www.ncbi.nlm.nih.gov/medgen/ id: 00000594 name: MedGen namespaceEmbeddedInLui: false pattern: ^[CN]*\d{4,7}$ prefix: medgen sampleId: '760050' uri_format: https://www.ncbi.nlm.nih.gov/medgen/$1 n2t: description: MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder. example: '760050' homepage: https://www.ncbi.nlm.nih.gov/medgen/ name: MedGen at NCBI namespaceEmbeddedInLui: false pattern: ^[CN]*\d{4,7}$ prefix: medgen uri_format: https://www.ncbi.nlm.nih.gov/medgen/$1 ncbi: example: C0010674 homepage: https://www.ncbi.nlm.nih.gov/medgen name: Human Medical Genetics prefix: MedGen prefixcommons: is_identifiers: false is_obo: false prefix: MedGen uri_format: http://www.ncbi.nlm.nih.gov/medgen/$1 medlineplus: bioportal: name: MedlinePlus Health Topics prefix: MEDLINEPLUS mappings: bioportal: MEDLINEPLUS miriam: medlineplus n2t: medlineplus prefixcommons: MEDLINEPLUS miriam: deprecated: false description: MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language. homepage: http://www.nlm.nih.gov/medlineplus/ id: '00000476' name: MedlinePlus namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: medlineplus sampleId: 002804 uri_format: http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm n2t: description: MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language. example: 002804 homepage: http://www.nlm.nih.gov/medlineplus/ name: MedlinePlus at NCBI namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: medlineplus uri_format: http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm prefixcommons: is_identifiers: true is_obo: false prefix: MEDLINEPLUS uri_format: http://identifiers.org/medlineplus/$1 merops: go: homepage: https://www.ebi.ac.uk/merops/ name: MEROPS peptidase database prefix: MEROPS uri_format: https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1 mappings: go: MEROPS miriam: merops n2t: merops prefixcommons: MEROPS uniprot: MEROPS miriam: deprecated: false description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. homepage: http://merops.sanger.ac.uk/index.htm id: 00000059 name: MEROPS namespaceEmbeddedInLui: false pattern: ^[SCTAGMNU]\d{2}\.([AB]\d{2}|\d{3})$ prefix: merops sampleId: S01.001 uri_format: http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=$1 n2t: description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. example: S01.001 homepage: http://merops.sanger.ac.uk/index.htm name: MEROPS database at Sanger Institute namespaceEmbeddedInLui: false pattern: ^[SCTAGMNU]\d{2}\.([AB]\d{2}|\d{3})$ prefix: merops uri_format: http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MEROPS uri_format: http://identifiers.org/merops/$1 uniprot: category: Protein family/group databases identifier: '59' link_is_explicit: 'true' name: MEROPS protease database prefix: MEROPS uri_format: https://www.ebi.ac.uk/merops/cgi-bin/pepsum?mid=$1 merops.family: mappings: miriam: merops.family n2t: merops.family prefixcommons: MEROPS.FAMILY miriam: deprecated: false description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families. homepage: http://merops.sanger.ac.uk/index.htm id: '00000302' name: MEROPS Family namespaceEmbeddedInLui: false pattern: ^[SCTAGMNU]\d+$ prefix: merops.family sampleId: S1 uri_format: http://merops.sanger.ac.uk/cgi-bin/famsum?family=$1 n2t: description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families. example: S1 homepage: http://merops.sanger.ac.uk/index.htm name: Merops Family at Sanger Institute namespaceEmbeddedInLui: false pattern: ^[SCTAGMNU]\d+$ prefix: merops.family uri_format: http://merops.sanger.ac.uk/cgi-bin/famsum?family=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MEROPS.FAMILY uri_format: http://identifiers.org/merops.family/$1 merops.inhibitor: mappings: miriam: merops.inhibitor n2t: merops.inhibitor prefixcommons: MEROPS.INHIBITOR miriam: deprecated: false description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors. homepage: http://merops.sanger.ac.uk/index.htm id: 00000491 name: MEROPS Inhibitor namespaceEmbeddedInLui: false pattern: ^I\d{2}\.\d{3}$ prefix: merops.inhibitor sampleId: I31.952 uri_format: http://merops.sanger.ac.uk/cgi-bin/pepsum?id=$1 n2t: description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors. example: I31.952 homepage: http://merops.sanger.ac.uk/index.htm name: MEROPS Inhibitor at Sanger Institute namespaceEmbeddedInLui: false pattern: ^I\d{2}\.\d{3}$ prefix: merops.inhibitor uri_format: http://merops.sanger.ac.uk/cgi-bin/pepsum?id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MEROPS.INHIBITOR uri_format: http://identifiers.org/merops.inhibitor/$1 mesh: biolink: is_identifiers: false is_obo: false prefix: MESH uri_format: http://id.nlm.nih.gov/mesh/$1 bioportal: name: Medical Subject Headings prefix: MESH cellosaurus: category: Ontologies homepage: https://www.ncbi.nlm.nih.gov/mesh name: Medical Subject Headings prefix: MeSH url: https://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?field=uid&term=$1 example: C063233 go: homepage: https://meshb.nlm.nih.gov name: Medical Subject Headings prefix: MeSH synonyms: - MESH - MSH uri_format: http://id.nlm.nih.gov/mesh/$1 mappings: biolink: MESH bioportal: MESH cellosaurus: MeSH go: MeSH miriam: mesh n2t: mesh prefixcommons: MESH scholia: mesh miriam: deprecated: false description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc. homepage: http://id.nlm.nih.gov/mesh/ id: '00000560' name: MeSH namespaceEmbeddedInLui: false pattern: ^(C|D)\d{6,9}$ prefix: mesh sampleId: C000100 uri_format: http://id.nlm.nih.gov/mesh/$1 n2t: description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc. example: C000100 homepage: http://id.nlm.nih.gov/mesh/ name: MeSH Linked Data at National Library of Medicine namespaceEmbeddedInLui: false pattern: ^(C|D)\d{6}$ prefix: mesh uri_format: http://id.nlm.nih.gov/mesh/$1 name: Medical Subject Headings prefixcommons: is_identifiers: false is_obo: true prefix: MESH uri_format: http://purl.obolibrary.org/obo/MESH_$1 synonyms: - MESH - MESHA - MESHC - MESHCS - MESHD - MESHPP - MESH_DESCRIPTOR_UI - MESH_SUPPLEMENTAL_RECORD_UI - MSH uri_format: https://meshb.nlm.nih.gov/record/ui?ui=$1 wikidata: database: Q199897 database.label: Medical Subject Headings format: http://id.nlm.nih.gov/mesh/$1 homepage: https://www.wikidata.org/wiki/Q6589563 name: MeSH descriptor ID pattern: ^[CD]\w{6}(\w{3}|)$ prefix: P486 mesh.2012: mappings: miriam: mesh.2012 n2t: mesh.2012 prefixcommons: MESH.2012 miriam: deprecated: false description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012. homepage: http://www.nlm.nih.gov/mesh/ id: '00000270' name: MeSH 2012 namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9]+$ prefix: mesh.2012 sampleId: '17186' uri_format: http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded n2t: description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012. example: '17186' homepage: http://www.nlm.nih.gov/mesh/ name: MeSH at National Library of Medicine namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9]+$ prefix: mesh.2012 uri_format: http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded prefixcommons: is_identifiers: true is_obo: false prefix: MESH.2012 uri_format: http://identifiers.org/mesh.2012/$1 mesh.2013: mappings: miriam: mesh.2013 n2t: mesh.2013 prefixcommons: MESH.2013 miriam: deprecated: false description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013. homepage: http://www.nlm.nih.gov/mesh/ id: '00000473' name: MeSH 2013 namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9]+$ prefix: mesh.2013 sampleId: '17165' uri_format: http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded n2t: description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013. example: '17165' homepage: http://www.nlm.nih.gov/mesh/ name: MeSH 2013 at National Library of Medicine namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9]+$ prefix: mesh.2013 uri_format: http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded prefixcommons: is_identifiers: true is_obo: false prefix: MESH.2013 uri_format: http://identifiers.org/mesh.2013/$1 metabolights: cellosaurus: category: Metabolomic databases homepage: https://www.ebi.ac.uk/metabolights/ name: MetaboLights database for metabolomics experiments and derived information prefix: MetaboLights url: https://www.ebi.ac.uk/metabolights/$1 mappings: cellosaurus: MetaboLights miriam: metabolights n2t: metabolights prefixcommons: METABOLIGHTS wikidata: P3890 miriam: deprecated: false description: MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies. homepage: https://www.ebi.ac.uk/metabolights/ id: 00000380 name: MetaboLights namespaceEmbeddedInLui: false pattern: ^MTBLS\d+$ prefix: metabolights providers: - code: omicsdi description: MataboLights through OmicsDI homepage: https://www.omicsdi.org/ name: MataboLights through OmicsDI uri_format: https://www.omicsdi.org/dataset/metabolights_dataset/$1 sampleId: MTBLS1 uri_format: https://www.ebi.ac.uk/metabolights/$1 n2t: description: MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies. example: MTBLS1 homepage: https://www.ebi.ac.uk/metabolights/ name: MetaboLights at EBI namespaceEmbeddedInLui: false pattern: ^MTBLS\d+$ prefix: metabolights uri_format: https://www.ebi.ac.uk/metabolights/$1 prefixcommons: is_identifiers: true is_obo: false prefix: METABOLIGHTS uri_format: http://identifiers.org/metabolights/$1 wikidata: database: Q24174701 database.homepage: http://www.ebi.ac.uk/metabolights database.label: MetaboLights name: MetaboLights Compound ID pattern: MTBLC\d+ prefix: P3890 uri_format: http://www.ebi.ac.uk/metabolights/$1 metacyc.compound: biolink: is_identifiers: false is_obo: false prefix: MetaCyc uri_format: http://translator.ncats.nih.gov/MetaCyc_$1 go: homepage: http://metacyc.org/ name: Metabolic Encyclopedia of metabolic and other pathways prefix: MetaCyc synonyms: - METACYC uri_format: http://biocyc.org/META/NEW-IMAGE?type=NIL&object=$1 mappings: biolink: MetaCyc go: MetaCyc miriam: metacyc.compound n2t: metacyc.compound prefixcommons: METACYC.COMPOUND miriam: deprecated: false description: MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. homepage: https://metacyc.org id: 00000609 name: MetaCyc Compound namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9+_.%-:]+$ prefix: metacyc.compound sampleId: CPD-10330 uri_format: https://metacyc.org/compound?orgid=META&id=$1 n2t: description: MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. example: CPD-10330 homepage: https://metacyc.org name: MetaCyc Metabolic Pathway Database namespaceEmbeddedInLui: false pattern: ^CPD-\d{5}$ prefix: metacyc.compound uri_format: https://metacyc.org/compound?orgid=META&id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: METACYC.COMPOUND uri_format: http://identifiers.org/metacyc.compound/$1 synonyms: - MetaCyc metacyc.reaction: mappings: miriam: metacyc.reaction n2t: metacyc.reaction prefixcommons: METACYC.REACTION miriam: deprecated: false description: MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. homepage: https://metacyc.org id: '00000610' name: MetaCyc Reaction namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9+_.%-:]+$ prefix: metacyc.reaction sampleId: RXN-14904 uri_format: https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1 n2t: description: MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. example: RXN-14904 homepage: https://metacyc.org name: MetaCyc Metabolic Pathway Database - Reaction namespaceEmbeddedInLui: false pattern: ^RXN-\d{5}$ prefix: metacyc.reaction uri_format: https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1 prefixcommons: is_identifiers: true is_obo: false prefix: METACYC.REACTION uri_format: http://identifiers.org/metacyc.reaction/$1 metanetx.chemical: mappings: miriam: metanetx.chemical n2t: metanetx.chemical prefixcommons: METANETX.CHEMICAL miriam: deprecated: false description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components. homepage: https://www.metanetx.org/ id: '00000567' name: MetaNetX chemical namespaceEmbeddedInLui: false pattern: ^(MNXM\d+|BIOMASS|WATER)$ prefix: metanetx.chemical sampleId: MNXM1723 uri_format: https://www.metanetx.org/chem_info/$1 n2t: description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components. example: MNXM1723 homepage: http://www.metanetx.org/ name: MetaNetX chemical at SIB Swiss Institute of Bioinformatics namespaceEmbeddedInLui: false pattern: ^(MNXM\d+|BIOMASS)$ prefix: metanetx.chemical uri_format: https://www.metanetx.org/chem_info/$1 prefixcommons: is_identifiers: true is_obo: false prefix: METANETX.CHEMICAL uri_format: http://identifiers.org/metanetx.chemical/$1 metanetx.compartment: mappings: miriam: metanetx.compartment n2t: metanetx.compartment prefixcommons: METANETX.COMPARTMENT miriam: deprecated: false description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments. homepage: https://www.metanetx.org/ id: 00000569 name: MetaNetX compartment namespaceEmbeddedInLui: false pattern: ^(MNX[CD]\d+|BOUNDARY|IN|OUT)$ prefix: metanetx.compartment sampleId: MNXC15 uri_format: https://www.metanetx.org/comp_info/$1 n2t: description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments. example: MNXC15 homepage: http://www.metanetx.org/ name: MetaNetX compartment at SIB Swiss Institute of Bioinformatics namespaceEmbeddedInLui: false pattern: ^(MNX[CD]\d+|BOUNDARY)$ prefix: metanetx.compartment uri_format: http://www.metanetx.org/comp_info/$1 prefixcommons: is_identifiers: true is_obo: false prefix: METANETX.COMPARTMENT uri_format: http://identifiers.org/metanetx.compartment/$1 metanetx.reaction: biolink: is_identifiers: false is_obo: false prefix: METANETX.REACTION uri_format: https://www.metanetx.org/equa_info/$1 mappings: biolink: METANETX.REACTION miriam: metanetx.reaction n2t: metanetx.reaction prefixcommons: METANETX.REACTION miriam: deprecated: false description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions. homepage: https://www.metanetx.org/ id: 00000568 name: MetaNetX reaction namespaceEmbeddedInLui: false pattern: ^(MNXR\d+|EMPTY)$ prefix: metanetx.reaction sampleId: MNXR101574 uri_format: https://www.metanetx.org/equa_info/$1 n2t: description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions. example: MNXR101574 homepage: http://www.metanetx.org/ name: MetaNetX reaction at SIB Swiss Institute of Bioinformatics namespaceEmbeddedInLui: false pattern: ^MNXR\d+$ prefix: metanetx.reaction uri_format: http://www.metanetx.org/equa_info/$1 prefixcommons: is_identifiers: true is_obo: false prefix: METANETX.REACTION uri_format: http://identifiers.org/metanetx.reaction/$1 metlin: mappings: miriam: metlin n2t: metlin prefixcommons: METLIN miriam: deprecated: false description: The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry. homepage: http://masspec.scripps.edu/ id: '00000322' name: METLIN namespaceEmbeddedInLui: false pattern: ^\d{4}$ prefix: metlin sampleId: '1455' uri_format: http://metlin.scripps.edu/metabo_info.php?molid=$1 n2t: description: The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry. example: '1455' homepage: http://masspec.scripps.edu/ name: METLIN at Scripps Center, Molecular Biology and Center for Mass Spectrometry, La Jolla namespaceEmbeddedInLui: false pattern: ^\d{4}$ prefix: metlin uri_format: http://metlin.scripps.edu/metabo_info.php?molid=$1 name: Metabolite and Tandem Mass Spectrometry Database prefixcommons: is_identifiers: true is_obo: false prefix: METLIN uri_format: http://identifiers.org/metlin/$1 mex: mappings: miriam: mex n2t: mex prefixcommons: MEX miriam: deprecated: false description: A public place to process, interpret and share GC/MS metabolomics datasets. homepage: https://www.metabolome-express.org/ id: 00000648 name: Metabolome Express namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: mex providers: - code: omicsdi description: Metabolome Express through OmicsDI homepage: https://www.omicsdi.org/ name: Metabolome Express through OmicsDI uri_format: https://www.omicsdi.org/dataset/metabolome_express/MEX$1 sampleId: '36' uri_format: https://www.metabolome-express.org/datasetview.php?datasetid=$1 n2t: description: A public place to process, interpret and share GC/MS metabolomics datasets. example: '36' homepage: https://www.metabolome-express.org/ name: Metabolome Express namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: mex uri_format: https://www.metabolome-express.org/datasetview.php?datasetid=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MEX uri_format: http://identifiers.org/mex/$1 mf: bioportal: name: Mental Functioning Ontology prefix: MF example: 0000091 mappings: bioportal: MF obofoundry: mf ols: mf ontobee: MF prefixcommons: MF obofoundry: contact: janna.hastings@gmail.com contact.github: jannahastings contact.label: Janna Hastings deprecated: false description: The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning. download.owl: http://purl.obolibrary.org/obo/mf.owl homepage: https://github.com/jannahastings/mental-functioning-ontology inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: Mental Functioning Ontology preferredPrefix: MF prefix: mf repository: https://github.com/jannahastings/mental-functioning-ontology ols: description: The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning. download: http://purl.obolibrary.org/obo/mf.owl homepage: https://github.com/jannahastings/mental-functioning-ontology license: https://creativecommons.org/licenses/by/3.0/ name: Mental Functioning Ontology prefix: mf version: '2021-09-21' version.iri: http://purl.obolibrary.org/obo/MF/2021-09-21/MF.owl ontobee: library: Library name: Mental Functioning Ontology prefix: MF url: http://www.ontobee.org/ontology/MF prefixcommons: is_identifiers: false is_obo: true prefix: MF uri_format: http://purl.obolibrary.org/obo/MF_$1 mfmo: bioportal: name: Mammalian Feeding Muscle Ontology prefix: MFMO example: 0000208 mappings: bioportal: MFMO obofoundry: mfmo ols: mfmo ontobee: MFMO prefixcommons: MFMO obofoundry: contact: druzinsk@uic.edu contact.github: RDruzinsky contact.label: Robert Druzinsky deprecated: false description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors. download.owl: http://purl.obolibrary.org/obo/mfmo.owl homepage: https://github.com/rdruzinsky/feedontology inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: Mammalian Feeding Muscle Ontology preferredPrefix: MFMO prefix: mfmo repository: https://github.com/RDruzinsky/feedontology ols: description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors. download: http://purl.obolibrary.org/obo/mfmo.owl homepage: https://github.com/rdruzinsky/feedontology name: Mammalian Feeding Muscle Ontology prefix: mfmo version: '2013-11-16' version.iri: http://purl.obolibrary.org/obo/mfmo/2013-11-16/mfmo.owl ontobee: library: Library name: Mammalian Feeding Muscle Ontology prefix: MFMO url: http://www.ontobee.org/ontology/MFMO prefixcommons: is_identifiers: false is_obo: true prefix: MFMO uri_format: http://purl.obolibrary.org/obo/MFMO_$1 mfo: bioportal: name: Medaka Fish Anatomy and Development Ontology prefix: MFO mappings: bioportal: MFO obofoundry: mfo prefixcommons: MFO obofoundry: contact: Thorsten.Henrich@embl-heidelberg.de contact.label: Thorsten Henrich deprecated: true description: A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes. download.owl: http://purl.obolibrary.org/obo/mfo.owl inactive: true name: Medaka fish anatomy and development prefix: mfo prefixcommons: is_identifiers: false is_obo: true prefix: MFO uri_format: http://purl.obolibrary.org/obo/MFO_$1 mfoem: bioportal: name: Emotion Ontology prefix: MFOEM example: '000204' mappings: bioportal: MFOEM obofoundry: mfoem ols: mfoem ontobee: MFOEM prefixcommons: MFOEM obofoundry: contact: janna.hastings@gmail.com contact.github: jannahastings contact.label: Janna Hastings deprecated: false description: An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings. download.owl: http://purl.obolibrary.org/obo/mfoem.owl homepage: https://github.com/jannahastings/emotion-ontology inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: Emotion Ontology preferredPrefix: MFOEM prefix: mfoem repository: https://github.com/jannahastings/emotion-ontology ols: description: An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings. download: http://purl.obolibrary.org/obo/mfoem.owl homepage: https://github.com/jannahastings/emotion-ontology license: https://creativecommons.org/licenses/by/3.0/ name: Emotion Ontology prefix: mfoem version: '2021-09-21' version.iri: http://purl.obolibrary.org/obo/MFOEM/2021-09-21/MFOEM.owl ontobee: library: Library name: Emotion Ontology prefix: MFOEM url: http://www.ontobee.org/ontology/MFOEM prefixcommons: is_identifiers: false is_obo: true prefix: MFOEM uri_format: http://purl.obolibrary.org/obo/MFOEM_$1 mfomd: bioportal: name: MFO Mental Disease Ontology prefix: MFOMD example: '0000046' mappings: bioportal: MFOMD obofoundry: mfomd ols: mfomd ontobee: MFOMD prefixcommons: MFOMD obofoundry: contact: janna.hastings@gmail.com contact.label: Janna Hastings deprecated: false description: An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable download.owl: http://purl.obolibrary.org/obo/mfomd.owl homepage: https://github.com/jannahastings/mental-functioning-ontology inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: Mental Disease Ontology preferredPrefix: MFOMD prefix: mfomd repository: https://github.com/jannahastings/mental-functioning-ontology ols: description: The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF). download: http://purl.obolibrary.org/obo/mfomd.owl homepage: https://github.com/jannahastings/mental-functioning-ontology name: Mental Disease Ontology prefix: mfomd version: '2020-04-26' version.iri: http://purl.obolibrary.org/obo/MFOMD/2020-04-26/MFOMD.owl ontobee: library: Library name: Mental Disease Ontology prefix: MFOMD url: http://www.ontobee.org/ontology/MFOMD prefixcommons: is_identifiers: false is_obo: true prefix: MFOMD uri_format: http://purl.obolibrary.org/obo/MFOMD_$1 mge: banana: mge mappings: miriam: mge n2t: mge miriam: deprecated: false description: ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. homepage: http://aclame.ulb.ac.be/ id: '00000063' name: Aclame namespaceEmbeddedInLui: true pattern: ^mge:\d+$ prefix: mge sampleId: '2' uri_format: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1 n2t: description: ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. example: '2' homepage: http://aclame.ulb.ac.be/ name: Aclame database of mobile genetic elements namespaceEmbeddedInLui: true pattern: ^mge:\d+$ prefix: mge uri_format: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1 pattern: ^\d+$ mgi: banana: MGI cellosaurus: category: Organism-specific databases homepage: http://www.informatics.jax.org name: Mouse Genome Database (MGD) from Mouse Genome Informatics prefix: MGI url: http://www.informatics.jax.org/marker/$1 example: '6017782' go: homepage: http://www.informatics.jax.org/ name: Mouse Genome Informatics prefix: MGI mappings: cellosaurus: MGI go: MGI miriam: mgi n2t: mgi ncbi: MGI prefixcommons: MGI uniprot: MGI miriam: deprecated: false description: The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data. homepage: http://www.informatics.jax.org/ id: '00000037' name: Mouse Genome Database namespaceEmbeddedInLui: true pattern: ^MGI:\d+$ prefix: mgi providers: - code: bioentitylink description: MGD through BioEntity Link homepage: https://bioentity.link/ name: MGD through BioEntity Link uri_format: https://bioentity.link/#/lexicon/public/MGI:$1 - code: agr description: MGI through the Alliance of Genome Resources homepage: https://www.alliancegenome.org name: MGI through the Alliance of Genome Resources uri_format: https://www.alliancegenome.org/gene/MGI:$1 sampleId: '2442292' uri_format: http://www.informatics.jax.org/accession/MGI:$1 n2t: description: The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data. example: '2442292' homepage: http://www.informatics.jax.org/ name: Mouse Genome Informatics Database namespaceEmbeddedInLui: true pattern: ^MGI:\d+$ prefix: mgi uri_format: http://www.informatics.jax.org/accession/MGI:$1 ncbi: example: MGI:1894891 homepage: http://www.informatics.jax.org/ name: Mouse Genome Informatics prefix: MGI pattern: ^\d+$ preferred_prefix: MGI prefixcommons: is_identifiers: false is_obo: false prefix: MGI uri_format: http://www.informatics.jax.org/accession/MGI:$1 synonyms: - MGD - MGI uniprot: category: Organism-specific databases comment: Replacement for MGD identifier: '60' link_is_explicit: 'true' name: Mouse genome database (MGD) from Mouse Genome Informatics (MGI) prefix: MGI uri_format: http://www.informatics.jax.org/marker/$1 wikidata: database: Q1951035 prefix: P671 mgnify.analysis: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Analyses of microbiome data within MGnify example: MGYA00002270 homepage: https://www.ebi.ac.uk/metagenomics/ name: MGnify Analysis pattern: ^MGYA\d+$ uri_format: https://www.ebi.ac.uk/metagenomics/analyses/$1 mgnify.proj: mappings: miriam: mgnify.proj n2t: mgnify.proj miriam: deprecated: false description: MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis. homepage: https://www.ebi.ac.uk/metagenomics id: '00000535' name: MGnify Project namespaceEmbeddedInLui: false pattern: ^[A-Z]+[0-9]+$ prefix: mgnify.proj sampleId: ERP004492 uri_format: https://www.ebi.ac.uk/metagenomics/projects/$1 n2t: description: MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis. example: ERP004492 homepage: https://www.ebi.ac.uk/metagenomics name: MGnify Project namespaceEmbeddedInLui: false pattern: ^[A-Z]+[0-9]+$ prefix: mgnify.proj uri_format: https://www.ebi.ac.uk/metagenomics/projects/$1 mgnify.samp: mappings: miriam: mgnify.samp n2t: mgnify.samp miriam: deprecated: false description: The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples. homepage: https://www.ebi.ac.uk/metagenomics id: '00000510' name: MGnify Sample namespaceEmbeddedInLui: false pattern: ^[A-Z]+[0-9]+$ prefix: mgnify.samp sampleId: SRS086444 uri_format: https://www.ebi.ac.uk/metagenomics/samples/$1 n2t: description: The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples. example: SRS086444 homepage: https://www.ebi.ac.uk/metagenomics name: MGnify Sample namespaceEmbeddedInLui: false pattern: ^[A-Z]+[0-9]+$ prefix: mgnify.samp uri_format: https://www.ebi.ac.uk/metagenomics/samples/$1 mi: biolink: is_identifiers: false is_obo: true prefix: MI uri_format: http://purl.obolibrary.org/obo/MI_$1 bioportal: name: Molecular Interactions prefix: MI example: 0058 go: homepage: http://www.psidev.info/ name: Proteomic Standard Initiative for Molecular Interaction prefix: PSI-MI synonyms: - MI mappings: biolink: MI bioportal: MI go: PSI-MI miriam: mi n2t: psimi obofoundry: mi ols: mi ontobee: MI prefixcommons: MI miriam: deprecated: false description: The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative. homepage: https://www.ebi.ac.uk/ols/ontologies/mi id: 00000109 name: Molecular Interactions Ontology namespaceEmbeddedInLui: true pattern: ^MI:\d{4}$ prefix: mi sampleId: 0308 uri_format: https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1 n2t: description: The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative. example: 0308 homepage: https://www.ebi.ac.uk/ols/ontologies/mi name: Molecular Interactions Ontology through OLS namespaceEmbeddedInLui: true pattern: ^MI:\d{4}$ prefix: psimi uri_format: https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1 obofoundry: contact: pporras@ebi.ac.uk contact.label: "Pablo Porras Mill\xE1n" deprecated: false description: A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. download.obo: http://purl.obolibrary.org/obo/mi.obo download.owl: http://purl.obolibrary.org/obo/mi.owl homepage: https://github.com/HUPO-PSI/psi-mi-CV inactive: false license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Molecular Interactions Controlled Vocabulary preferredPrefix: MI prefix: mi repository: https://github.com/HUPO-PSI/psi-mi-CV ols: description: A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. download: https://raw.githubusercontent.com/HUPO-PSI/psi-mi-CV/master/psi-mi.obo homepage: https://github.com/HUPO-PSI/psi-mi-CV name: Molecular Interactions Controlled Vocabulary prefix: mi version: '2020-04-13' version.iri: http://purl.obolibrary.org/obo/mi/releases/2020-04-13/mi.owl ontobee: library: Library name: Molecular Interactions Controlled Vocabulary prefix: MI url: http://www.ontobee.org/ontology/MI pattern: ^\d{4}$ prefixcommons: is_identifiers: false is_obo: true prefix: MI uri_format: http://purl.obolibrary.org/obo/MI_$1 synonyms: - PSI-MI miaa: comment: same as MAT contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true name: Minimal Information About Anatomy ontology references: - https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/rols/inst/doc/rols.pdf miapa: bioportal: name: MIAPA Ontology prefix: MIAPA example: '0000010' mappings: bioportal: MIAPA obofoundry: miapa ols: miapa ontobee: MIAPA prefixcommons: MIAPA obofoundry: contact: hilmar.lapp@duke.edu contact.github: hlapp contact.label: Hilmar Lapp deprecated: false description: An application ontology to formalize annotation of phylogenetic data. download.owl: http://purl.obolibrary.org/obo/miapa.owl homepage: http://www.evoio.org/wiki/MIAPA inactive: false license: CC-0 license.url: http://creativecommons.org/publicdomain/zero/1.0/ name: MIAPA Ontology preferredPrefix: MIAPA prefix: miapa repository: https://github.com/evoinfo/miapa ols: description: 'The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies. This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project''s main page at http://evoio.org/wiki/MIAPA.' download: http://purl.obolibrary.org/obo/miapa.owl homepage: http://www.evoio.org/wiki/MIAPA name: Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology prefix: miapa version: '2017-05-09' version.iri: http://purl.obolibrary.org/obo/miapa/2013-02-01/miapa.owl ontobee: library: Library name: MIAPA Ontology prefix: MIAPA url: http://www.ontobee.org/ontology/MIAPA prefixcommons: is_identifiers: false is_obo: true prefix: MIAPA uri_format: http://purl.obolibrary.org/obo/MIAPA_$1 micro: example: 0002999 mappings: obofoundry: micro ols: micro prefixcommons: MICRO obofoundry: contact: carrine.blank@umontana.edu contact.label: Carrine Blank deprecated: false description: An ontology of prokaryotic phenotypic and metabolic characters download.owl: http://purl.obolibrary.org/obo/micro.owl homepage: https://github.com/carrineblank/MicrO inactive: false license: CC-BY 2.0 license.url: https://creativecommons.org/licenses/by/2.0/ name: Ontology of Prokaryotic Phenotypic and Metabolic Characters preferredPrefix: MICRO prefix: micro repository: https://github.com/carrineblank/MicrO ols: description: An ontology of prokaryotic phenotypic and metabolic characters download: http://purl.obolibrary.org/obo/micro.owl homepage: https://github.com/carrineblank/MicrO name: Ontology of Prokaryotic Phenotypic and Metabolic Characters prefix: micro version: 1.5.1 prefixcommons: is_identifiers: false is_obo: true prefix: MICRO uri_format: http://purl.obolibrary.org/obo/MICRO_$1 microscope: mappings: miriam: microscope n2t: microscope prefixcommons: MICROSCOPE miriam: deprecated: false description: MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. homepage: http://www.genoscope.cns.fr/agc/microscope id: '00000631' name: MicroScope namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: microscope sampleId: '5601141' uri_format: http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1 n2t: description: MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. example: '5601141' homepage: http://www.genoscope.cns.fr/agc/microscope name: MicroScope namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: microscope uri_format: http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MICROSCOPE uri_format: http://identifiers.org/microscope/$1 microsporidia: mappings: miriam: microsporidia n2t: microsporidia prefixcommons: MICROSPORIDIA miriam: deprecated: false description: MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. homepage: http://microsporidiadb.org/micro/ id: '00000152' name: MicrosporidiaDB namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: microsporidia sampleId: ECU03_0820i uri_format: http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 n2t: description: MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. example: ECU03_0820i homepage: http://microsporidiadb.org/micro/ name: MicrosporidiaDB at EuPathDB namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: microsporidia uri_format: http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MICROSPORIDIA uri_format: http://identifiers.org/microsporidia/$1 mim: bioportal: name: Molecular Interaction Map prefix: MIM go: homepage: https://omim.org/ name: Mendelian Inheritance in Man prefix: OMIM synonyms: - MIM uri_format: https://omim.org/entry/$1 mappings: bioportal: MIM go: OMIM miriam: mim n2t: mim ncbi: MIM prefixcommons: OMIM uniprot: MIM wikidata: P492 miriam: deprecated: false description: Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. homepage: https://omim.org/ id: '00000016' name: OMIM namespaceEmbeddedInLui: false pattern: ^[*#+%^]?\d{6}$ prefix: mim providers: - code: CURATOR_REVIEW description: OMIM mirror at John Hopkins homepage: http://mirror.omim.org/ name: OMIM mirror at John Hopkins uri_format: http://mirror.omim.org/entry/$1 sampleId: '603903' uri_format: https://omim.org/entry/$1 n2t: description: Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. example: '603903' homepage: https://omim.org/ name: OMIM at John Hopkins namespaceEmbeddedInLui: false pattern: ^[*#+%^]?\d{6}$ prefix: mim uri_format: https://omim.org/entry/$1 ncbi: example: '123456' homepage: https://www.ncbi.nlm.nih.gov/omim name: Mendelian Inheritance in Man numbers prefix: MIM pattern: ^\d+$ prefixcommons: is_identifiers: false is_obo: true prefix: OMIM uri_format: http://purl.obolibrary.org/obo/OMIM_$1 synonyms: - OMIM uniprot: category: Organism-specific databases identifier: '62' link_is_explicit: 'true' name: Online Mendelian Inheritance in Man (OMIM) prefix: MIM uri_format: https://www.omim.org/entry/$1 wikidata: database: Q241953 database.homepage: https://www.omim.org database.label: Online Mendelian Inheritance in Man name: OMIM ID pattern: \d{6} prefix: P492 uri_format: https://omim.org/entry/$1 mim.ps: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome. example: PS214100 homepage: https://www.omim.org/phenotypicSeriesTitles/all name: OMIM Phenotypic Series synonyms: - OMIMPS - PS uri_format: https://omim.org/phenotypicSeries/$1 mimodb: mappings: miriam: mimodb n2t: mimodb prefixcommons: MIMODB miriam: deprecated: false description: MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank. homepage: http://immunet.cn/bdb/ id: '00000251' name: MimoDB namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: mimodb sampleId: '1' uri_format: http://immunet.cn/bdb/index.php/mimoset/$1 n2t: description: MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank. example: '1' homepage: http://immunet.cn/bdb/ name: BDB at University of Electronic Science and Technology of China namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: mimodb uri_format: http://immunet.cn/bdb/index.php/mimoset/$1 prefixcommons: is_identifiers: true is_obo: false prefix: MIMODB uri_format: http://identifiers.org/mimodb/$1 minid: mappings: miriam: minid n2t: minid prefixcommons: MINID miriam: deprecated: false description: Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. homepage: https://fair-research.org id: '00000645' name: Minimal Viable Identifier namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9]+$ prefix: minid sampleId: b97957 uri_format: https://hdl.handle.net/hdl:20.500.12582/$1 n2t: description: Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. example: b97957 homepage: http://minid.bd2k.org name: Minimal Identifiers for Transient Data namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9]+$ prefix: minid uri_format: http://n2t.net/ark:/57799/$1 prefixcommons: is_identifiers: true is_obo: false prefix: MINID uri_format: http://identifiers.org/minid/$1 minid.test: mappings: miriam: minid.test miriam: deprecated: false description: 'Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. ' homepage: https://fair-research.org id: '00000707' name: MINID Test namespaceEmbeddedInLui: false pattern: '[A-Za-z0-9]+$' prefix: minid.test sampleId: 3SBPLMKKVEVR uri_format: https://hdl.handle.net/hdl:20.500.12633/$1 mint: mappings: miriam: mint n2t: mint prefixcommons: MINT uniprot: MINT miriam: deprecated: false description: The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals. homepage: http://mint.bio.uniroma2.it/mint/ id: '00000042' name: MINT namespaceEmbeddedInLui: false pattern: ^MINT\-\d{1,7}$ prefix: mint providers: - code: ebi description: MINT subset through IntAct homepage: https://www.ebi.ac.uk/intact/ name: MINT subset through IntAct uri_format: https://www.ebi.ac.uk/intact/query/interaction_id:$1 sampleId: MINT-10000 uri_format: http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$1 n2t: description: The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals. example: MINT-7905142 homepage: https://www.ebi.ac.uk/intact/ name: MINT subset through IntAct namespaceEmbeddedInLui: false pattern: ^MINT\-\d{1,7}$ prefix: mint uri_format: https://www.ebi.ac.uk/intact/query/interaction_id:$1 name: Molecular Interaction Database prefixcommons: is_identifiers: true is_obo: false prefix: MINT uri_format: http://identifiers.org/mint/$1 uniprot: category: Protein-protein interaction databases identifier: '158' link_is_explicit: 'true' name: Molecular INTeraction database prefix: MINT uri_format: https://mint.bio.uniroma2.it/cgi-bin/protein.py?id=$1 mipmod: mappings: miriam: mipmod n2t: mipmod prefixcommons: MIPMOD miriam: deprecated: false description: MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures. homepage: http://bioinfo.iitk.ac.in/MIPModDB id: '00000256' name: MIPModDB namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: mipmod sampleId: HOSAPI0399 uri_format: http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1 n2t: description: MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures. example: HOSAPI0399 homepage: http://bioinfo.iitk.ac.in/MIPModDB name: MIPModDB at Indian Institute of Technology Kanpur namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: mipmod uri_format: http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MIPMOD uri_format: http://identifiers.org/mipmod/$1 mir: banana: MIR mappings: miriam: mir n2t: mir prefixcommons: MIR miriam: deprecated: false description: "The Identifiers.org registry contains registered namespace and provider\ \ prefixes with associated access URIs for a large number of high quality data\ \ collections. These prefixes are used in web resolution of compact identifiers\ \ of the form \u201CPREFIX:ACCESSION\u201D or \"PROVIDER/PREFIX:ACCESSION\u201D\ \ commonly used to specify bioinformatics and other data resources." homepage: https://registry.identifiers.org/registry id: 00000599 name: Identifiers.org Registry namespaceEmbeddedInLui: true pattern: ^MIR:\d{8}$ prefix: mir sampleId: '00100037' uri_format: https://registry.identifiers.org/registry?query="MIR:$1" n2t: description: The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or "PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources. example: '00100037' homepage: https://identifiers.org/registry name: Identifiers.org Registry through EBI namespaceEmbeddedInLui: true pattern: ^MIR:\d{8}$ prefix: mir uri_format: https://identifiers.org/registry?query="MIR:$1" pattern: ^\d{8}$ prefixcommons: is_identifiers: true is_obo: false prefix: MIR uri_format: http://identifiers.org/mir/$1 mirbase: biolink: is_identifiers: true is_obo: false prefix: mirbase uri_format: http://identifiers.org/mirbase$1 example: MI0026471 homepage: http://www.mirbase.org/ mappings: biolink: mirbase miriam: mirbase n2t: mirbase ncbi: miRBase prefixcommons: MIRBASE wikidata: P2870 miriam: deprecated: false description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). homepage: http://www.mirbase.org/ id: 00000078 name: miRBase Sequence namespaceEmbeddedInLui: false pattern: MI\d{7} prefix: mirbase sampleId: MI0000001 uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1 n2t: description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). example: MI0000001 homepage: http://www.mirbase.org/ name: miRBase Sequence Database namespaceEmbeddedInLui: false pattern: MI\d{7} prefix: mirbase uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1 ncbi: example: MI0000681 homepage: http://www.mirbase.org/ name: miRNA Database prefix: miRBase prefixcommons: is_identifiers: true is_obo: false prefix: MIRBASE uri_format: http://identifiers.org/mirbase/$1 uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1 wikidata: database: Q6826947 database.homepage: http://www.mirbase.org/ database.label: miRBase homepage: http://www.mirbase.org/ name: miRBase pre-miRNA ID pattern: MI\d{7} prefix: P2870 uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1 mirbase.family: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download. example: MIPF0000002 homepage: http://www.mirbase.org/ name: miRBase Families synonyms: - MIRBASE_FAMILY uri_format: http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1 wikidata: database: Q6826947 mirbase.mature: example: MIMAT0046872 homepage: http://www.mirbase.org/ mappings: miriam: mirbase.mature n2t: mirbase.mature prefixcommons: MIRBASE.MATURE wikidata: P2871 miriam: deprecated: false description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence. homepage: http://www.mirbase.org/ id: '00000235' name: miRBase mature sequence namespaceEmbeddedInLui: false pattern: MIMAT\d{7} prefix: mirbase.mature sampleId: MIMAT0000001 uri_format: http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1 n2t: description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence. example: MIMAT0000001 homepage: http://www.mirbase.org/ name: miRBase namespaceEmbeddedInLui: false pattern: MIMAT\d{7} prefix: mirbase.mature uri_format: http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MIRBASE.MATURE uri_format: http://identifiers.org/mirbase.mature/$1 synonyms: - MIRBASEM uri_format: http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1 wikidata: database: Q6826947 database.homepage: http://www.mirbase.org/ database.label: miRBase homepage: http://www.mirbase.org/ name: miRBase mature miRNA ID pattern: MIMAT\d{7} prefix: P2871 uri_format: http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1 mirex: mappings: miriam: mirex n2t: mirex prefixcommons: MIREX miriam: deprecated: false description: "mirEX is a comprehensive platform for comparative analysis of primary\ \ microRNA expression data, storing RT\u2013qPCR-based gene expression profile\ \ over seven development stages of Arabidopsis. It also provides RNA structural\ \ models, publicly available deep sequencing results and experimental procedure\ \ details. This collection provides profile information for a single microRNA\ \ over all development stages." homepage: http://comgen.pl/mirex/?page=home id: 00000329 name: mirEX namespaceEmbeddedInLui: false pattern: ^\d+(\w+)?$ prefix: mirex sampleId: 165a uri_format: http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes n2t: description: mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages. example: 165a homepage: http://comgen.pl/mirex/?page=home name: mirEX at Adam Mickiewicz University namespaceEmbeddedInLui: false pattern: ^\d+(\w+)?$ prefix: mirex uri_format: http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes prefixcommons: is_identifiers: true is_obo: false prefix: MIREX uri_format: http://identifiers.org/mirex/$1 miriam.collection: mappings: miriam: miriam.collection n2t: miriam.collection prefixcommons: MIRIAM.COLLECTION miriam: deprecated: true description: MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections. id: 00000008 name: MIRIAM Registry collection namespaceEmbeddedInLui: false pattern: ^MIR:000\d{5}$ prefix: miriam.collection sampleId: MIR:00000008 n2t: description: MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections. example: MIR:00000008 homepage: https://www.ebi.ac.uk/miriam/ name: MIRIAM Resources (data collection) namespaceEmbeddedInLui: false pattern: ^MIR:000\d{5}$ prefix: miriam.collection uri_format: https://www.ebi.ac.uk/miriam/main/$1 prefixcommons: is_identifiers: true is_obo: false prefix: MIRIAM.COLLECTION uri_format: http://identifiers.org/miriam.collection/$1 miriam.resource: comment: yo dawg i heard you like registries... mappings: miriam: miriam.resource n2t: miriam.resource prefixcommons: MIRIAM.RESOURCE miriam: deprecated: false description: MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases. homepage: https://www.ebi.ac.uk/miriam/ id: 00000188 name: MIRIAM Registry resource namespaceEmbeddedInLui: false pattern: ^MIR:001\d{5}$ prefix: miriam.resource sampleId: MIR:00100005 uri_format: https://www.ebi.ac.uk/miriam/main/resources/$1 n2t: description: MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases. example: MIR:00100005 homepage: https://www.ebi.ac.uk/miriam/ name: MIRIAM Registry (resources) namespaceEmbeddedInLui: false pattern: ^MIR:001\d{5}$ prefix: miriam.resource uri_format: https://www.ebi.ac.uk/miriam/main/resources/$1 prefixcommons: is_identifiers: true is_obo: false prefix: MIRIAM.RESOURCE uri_format: http://identifiers.org/miriam.resource/$1 mirnao: bioportal: name: MicroRNA Ontology prefix: MIRNAO mappings: bioportal: MIRNAO obofoundry: mirnao ontobee: miRNAO prefixcommons: MIRNAO obofoundry: contact: topalis@imbb.forth.gr contact.label: Pantelis Topalis deprecated: true description: An application ontology for use with miRNA databases. download.owl: http://purl.obolibrary.org/obo/mirnao.owl homepage: http://code.google.com/p/mirna-ontology/ inactive: true license: CC0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: microRNA Ontology prefix: mirnao ontobee: library: Library name: microRNA Ontology prefix: miRNAO url: http://www.ontobee.org/ontology/miRNAO prefixcommons: is_identifiers: false is_obo: true prefix: MIRNAO uri_format: http://purl.obolibrary.org/obo/MIRNAO_$1 mirnest: mappings: miriam: mirnest n2t: mirnest prefixcommons: MIRNEST miriam: deprecated: false description: miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species. homepage: http://rhesus.amu.edu.pl/mirnest/copy/ id: '00000246' name: miRNEST namespaceEmbeddedInLui: false pattern: ^MNEST\d+$ prefix: mirnest sampleId: MNEST029358 uri_format: http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1 n2t: description: miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species. example: MNEST029358 homepage: http://rhesus.amu.edu.pl/mirnest/copy/ name: miRNEST at Adam Mickiewicz University namespaceEmbeddedInLui: false pattern: ^MNEST\d+$ prefix: mirnest uri_format: http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MIRNEST uri_format: http://identifiers.org/mirnest/$1 miro: bioportal: name: Mosquito Insecticide Resistance prefix: MIRO download_obo: http://purl.obolibrary.org/obo/miro.obo example: '40000617' mappings: bioportal: MIRO obofoundry: miro ols: miro ontobee: MIRO prefixcommons: MIRO obofoundry: contact: louis@imbb.forth.gr contact.label: C. Louis deprecated: false description: Application ontology for entities related to insecticide resistance in mosquitos download.obo: http://purl.obolibrary.org/obo/miro.obo download.owl: http://purl.obolibrary.org/obo/miro.owl inactive: true name: Mosquito insecticide resistance prefix: miro ols: description: Application ontology for entities related to insecticide resistance in mosquitos download: http://purl.obolibrary.org/obo/miro.owl homepage: http://anobase.vectorbase.org name: Mosquito insecticide resistance prefix: miro version: '2014-05-14' version.iri: http://purl.obolibrary.org/obo/miro/releases/2014-05-14/miro.owl ontobee: library: Library name: Mosquito insecticide resistance prefix: MIRO url: http://www.ontobee.org/ontology/MIRO pattern: ^\d{8}$ prefixcommons: is_identifiers: false is_obo: true prefix: MIRO uri_format: http://purl.obolibrary.org/obo/MIRO_$1 mirtarbase: mappings: miriam: mirtarbase n2t: mirtarbase prefixcommons: MIRTARBASE miriam: deprecated: false description: miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. homepage: http://mirtarbase.mbc.nctu.edu.tw/ id: '00000562' name: miRTarBase namespaceEmbeddedInLui: false pattern: ^MIRT\d{6}$ prefix: mirtarbase sampleId: MIRT000002 uri_format: http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1 n2t: description: miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. example: MIRT000002 homepage: http://mirtarbase.mbc.nctu.edu.tw/ name: miRTarBase at National Chiao Tung University namespaceEmbeddedInLui: false pattern: ^MIRT\d{6}$ prefix: mirtarbase uri_format: http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MIRTARBASE uri_format: http://identifiers.org/mirtarbase/$1 mirte: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs example: miR-1 homepage: http://www.russelllab.org/miRNAs/ name: miRNA Target Prediction at EMBL mlc: mappings: miriam: mlc miriam: deprecated: false description: MLCommons Association artifacts, including benchmark results, datasets, and saved models. homepage: https://mlcommons.org/en/ id: 00000828 name: MLCommons Association namespaceEmbeddedInLui: false pattern: ^[0-9a-zA-Z\.\-\_]+$ prefix: mlc sampleId: 0.7-123 uri_format: https://www.mlcommons.org/mlc-id/$1 mmdb: mappings: miriam: mmdb n2t: mmdb prefixcommons: MMDB miriam: deprecated: false description: The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites. homepage: http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure id: '00000121' name: Molecular Modeling Database namespaceEmbeddedInLui: false pattern: ^\d{1,5}$ prefix: mmdb sampleId: '50885' uri_format: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1 n2t: description: The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites. example: '50885' homepage: http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure name: MMDB at NCBI namespaceEmbeddedInLui: false pattern: ^\d{1,5}$ prefix: mmdb uri_format: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MMDB uri_format: http://identifiers.org/mmdb/$1 mmmp.biomaps: mappings: miriam: mmmp:biomaps n2t: biomaps prefixcommons: MMMP:BIOMAPS miriam: deprecated: false description: A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma. homepage: http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp id: '00000075' name: Melanoma Molecular Map Project Biomaps namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: mmmp:biomaps sampleId: '37' uri_format: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1 n2t: description: A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma. example: '37' homepage: http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp name: main webpage namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: biomaps uri_format: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MMMP:BIOMAPS uri_format: http://identifiers.org/mmmp:biomaps/$1 synonyms: - mmmp:biomaps mmo: bioportal: name: Measurement Method Ontology prefix: MMO example: '0000574' mappings: bioportal: MMO obofoundry: mmo ols: mmo ontobee: MMO prefixcommons: MMO obofoundry: contact: jrsmith@mcw.edu contact.label: Jennifer Smith deprecated: false description: 'A representation of the variety of methods used to make clinical and phenotype measurements. ' download.obo: http://purl.obolibrary.org/obo/mmo.obo download.owl: http://purl.obolibrary.org/obo/mmo.owl homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 inactive: false license: CC-0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Measurement method ontology preferredPrefix: MMO prefix: mmo repository: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology ols: description: 'A representation of the variety of methods used to make clinical and phenotype measurements. ' download: http://purl.obolibrary.org/obo/mmo.owl homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 name: Measurement method ontology prefix: mmo version: '2019-03-27' version.iri: http://purl.obolibrary.org/obo/mmo/2.39/mmo.owl ontobee: library: Library name: Measurement method ontology prefix: MMO url: http://www.ontobee.org/ontology/MMO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: MMO uri_format: http://purl.obolibrary.org/obo/MMO_$1 mmp.cat: mappings: miriam: mmp.cat n2t: mmp.cat prefixcommons: MMP.CAT miriam: deprecated: false description: MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples. homepage: https://mmp.sfb.uit.no/databases/marcat/ id: '00000615' name: MarCat namespaceEmbeddedInLui: false pattern: ^MMP\d+.\d+$ prefix: mmp.cat sampleId: MMP743597.11 uri_format: https://mmp.sfb.uit.no/databases/marcat/#/records/$1 n2t: description: MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples. example: MMP743597.11 homepage: https://mmp.sfb.uit.no/databases/marcat/ name: MarCat through SfB namespaceEmbeddedInLui: false pattern: ^MMP\d+.\d+$ prefix: mmp.cat uri_format: https://mmp.sfb.uit.no/databases/marcat/#/records/$1 prefixcommons: is_identifiers: true is_obo: false prefix: MMP.CAT uri_format: http://identifiers.org/mmp.cat/$1 mmp.db: mappings: miriam: mmp.db n2t: mmp.db prefixcommons: MMP.DB miriam: deprecated: false description: MarDB includes all sequenced marine microbial genomes regardless of level of completeness. homepage: https://mmp.sfb.uit.no/databases/mardb/ id: '00000614' name: MarDB namespaceEmbeddedInLui: false pattern: ^MMP\d+.\d+$ prefix: mmp.db sampleId: MMP02954345.1 uri_format: https://mmp.sfb.uit.no/databases/mardb/#/records/$1 n2t: description: MarDB includes all sequenced marine microbial genomes regardless of level of completeness. example: MMP02954345.1 homepage: https://mmp.sfb.uit.no/databases/mardb/ name: MarDB through SfB namespaceEmbeddedInLui: false pattern: ^MMP\d+.\d+$ prefix: mmp.db uri_format: https://mmp.sfb.uit.no/databases/mardb/#/records/$1 prefixcommons: is_identifiers: true is_obo: false prefix: MMP.DB uri_format: http://identifiers.org/mmp.db/$1 mmp.fun: mappings: miriam: mmp.fun miriam: deprecated: false description: MarFun is manually curated database for marine fungi which is a part of the MAR databases. homepage: https://mmp.sfb.uit.no/databases/marfun id: 00000729 name: MarFun namespaceEmbeddedInLui: false pattern: ^MMP\d+.\d+$ prefix: mmp.fun sampleId: MMP3888430 uri_format: https://mmp.sfb.uit.no/databases/marfun/#/records/$1 mmp.ref: mappings: miriam: mmp.ref n2t: mmp.ref prefixcommons: MMP.REF miriam: deprecated: false description: MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes. homepage: https://mmp.sfb.uit.no/databases/marref/ id: '00000613' name: MarRef namespaceEmbeddedInLui: false pattern: ^MMP\d+.\d+$ prefix: mmp.ref sampleId: MMP3312982.2 uri_format: https://mmp.sfb.uit.no/databases/marref/#/records/$1 n2t: description: MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes. example: MMP3312982.2 homepage: https://mmp.sfb.uit.no/databases/marref/ name: MarRef through SfB namespaceEmbeddedInLui: false pattern: ^MMP\d+.\d+$ prefix: mmp.ref uri_format: https://mmp.sfb.uit.no/databases/marref/#/records/$1 prefixcommons: is_identifiers: true is_obo: false prefix: MMP.REF uri_format: http://identifiers.org/mmp.ref/$1 mmrrc: cellosaurus: category: Cell line collections homepage: https://www.mmrrc.org/ name: Mutant Mouse Resource & Research Centers prefix: MMRRC url: https://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1 homepage: https://www.mmrrc.org mappings: cellosaurus: MMRRC miriam: mmrrc n2t: mmrrc prefixcommons: MMRRC miriam: deprecated: false description: The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections. homepage: http://www.mmrrc.org/ id: '00000324' name: MMRRC namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: mmrrc sampleId: '70' uri_format: http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1 n2t: description: The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections. example: '70' homepage: http://www.mmrrc.org/ name: MMRRC at University of North Carolina namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: mmrrc uri_format: http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1 name: Mutant Mouse Resource and Research Centers prefixcommons: is_identifiers: false is_obo: false prefix: MMRRC uri_format: https://www.mmrrc.org/catalog/sds.php?mmrrc_id=$1 mmsl: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included. example: '3355' homepage: https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html name: Multum MediSource Lexicon synonyms: - MMSL_CODE mmusdv: bioportal: name: Mouse Developmental Stages prefix: MMUSDV example: '0000066' mappings: bioportal: MMUSDV obofoundry: mmusdv ols: mmusdv ontobee: MMUSDV prefixcommons: MMUSDV obofoundry: contact: bgee@sib.swiss contact.label: bgee deprecated: false description: Life cycle stages for Mus Musculus download.obo: http://purl.obolibrary.org/obo/mmusdv.obo download.owl: http://purl.obolibrary.org/obo/mmusdv.owl homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: Mouse Developmental Stages preferredPrefix: MmusDv prefix: mmusdv repository: https://github.com/obophenotype/developmental-stage-ontologies ols: description: Life cycle stages for Mus Musculus download: http://purl.obolibrary.org/obo/mmusdv.owl homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv name: Mouse Developmental Stages prefix: mmusdv version: '2020-03-10' version.iri: http://purl.obolibrary.org/obo/mmusdv/releases/2020-03-10/mmusdv.owl ontobee: library: Library name: Mouse Developmental Stages prefix: MMUSDV url: http://www.ontobee.org/ontology/MMUSDV pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: MMUSDV uri_format: http://purl.obolibrary.org/obo/MMUSDV_$1 synonyms: - MmusDv mo: bioportal: name: Microarray and Gene Expression Data Ontology prefix: MO mappings: bioportal: MO miriam: mo n2t: mo obofoundry: mo prefixcommons: MO miriam: deprecated: false description: The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. homepage: http://bioportal.bioontology.org/ id: '00000303' name: MGED Ontology namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: mo providers: - code: ebi description: MGED Ontology at SourceForge homepage: https://mged.sourceforge.net/ontologies/MGEDontology.php name: MGED Ontology at SourceForge uri_format: https://mged.sourceforge.net/ontologies/MGEDontology.php#$1 sampleId: ArrayGroup uri_format: http://purl.bioontology.org/ontology/MO/$1 n2t: description: The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. example: ArrayGroup homepage: http://bioportal.bioontology.org/ name: MGED Ontology at BioPortal namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: mo uri_format: http://purl.bioontology.org/ontology/MO/$1 obofoundry: contact: stoeckrt@pcbi.upenn.edu contact.label: Chris Stoeckert deprecated: true description: A standardized description of a microarray experiment in support of MAGE v.1. download.owl: http://purl.obolibrary.org/obo/mo.owl homepage: http://mged.sourceforge.net/ontologies/MGEDontology.php inactive: true name: Microarray experimental conditions prefix: mo prefixcommons: is_identifiers: false is_obo: true prefix: MO uri_format: http://purl.obolibrary.org/obo/MO_$1 mobidb: homepage: http://mobidb.bio.unipd.it mappings: miriam: mobidb n2t: mobidb prefixcommons: MOBIDB uniprot: MobiDB miriam: deprecated: false description: MobiDB is a database of protein disorder and mobility annotations. homepage: https://mobidb.org/ id: '00000637' name: MobiDB namespaceEmbeddedInLui: false pattern: ^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$ prefix: mobidb sampleId: P10636 uri_format: https://mobidb.org/$1 n2t: description: MobiDB is a database of protein disorder and mobility annotations. example: P10636 homepage: http://mobidb.bio.unipd.it name: MobiDB namespaceEmbeddedInLui: false pattern: ^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$ prefix: mobidb uri_format: http://mobidb.bio.unipd.it/$1 prefixcommons: is_identifiers: true is_obo: false prefix: MOBIDB uri_format: http://identifiers.org/mobidb/$1 uniprot: category: Family and domain databases identifier: '183' name: 'MobiDB: a database of protein disorder and mobility annotations' prefix: MobiDB uri_format: https://mobidb.bio.unipd.it/entries/$1 mod: bioportal: name: Protein Modification Ontology prefix: PSIMOD example: '01467' go: homepage: http://www.psidev.info/groups/protein-modifications name: Proteomics Standards Initiative protein modification ontology prefix: PSI-MOD synonyms: - MOD mappings: bioportal: PSIMOD go: PSI-MOD miriam: mod n2t: mod obofoundry: mod ols: mod ontobee: MOD prefixcommons: MOD miriam: deprecated: false description: The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications. homepage: https://www.ebi.ac.uk/ols/ontologies/mod id: '00000056' name: Protein Modification Ontology namespaceEmbeddedInLui: true pattern: ^MOD:\d{5} prefix: mod sampleId: '00001' uri_format: https://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=MOD:$1 n2t: description: The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications. example: '00001' homepage: http://bioportal.bioontology.org/ontologies/PSIMOD name: Protein modifications ontology through BioPortal namespaceEmbeddedInLui: true pattern: ^MOD:\d{5} prefix: mod uri_format: http://bioportal.bioontology.org/ontologies/1041?p=terms&conceptid=MOD:$1 obofoundry: contact: pierre-alain.binz@chuv.ch contact.label: Pierre-Alain Binz deprecated: false description: PSI-MOD is an ontology consisting of terms that describe protein chemical modifications download.obo: http://purl.obolibrary.org/obo/mod.obo download.owl: http://purl.obolibrary.org/obo/mod.owl homepage: http://www.psidev.info/MOD inactive: false license: CC-BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Protein modification preferredPrefix: MOD prefix: mod repository: https://github.com/HUPO-PSI/psi-mod-CV ols: description: PSI-MOD is an ontology consisting of terms that describe protein chemical modifications download: http://purl.obolibrary.org/obo/mod.owl homepage: http://www.psidev.info/MOD name: Protein modification prefix: mod version: '2020-04-14' version.iri: http://purl.obolibrary.org/obo/mod/releases/2020-04-14/mod.owl ontobee: library: Library name: Protein modification prefix: MOD url: http://www.ontobee.org/ontology/MOD pattern: ^\d{5}$ prefixcommons: is_identifiers: false is_obo: true prefix: MOD uri_format: http://purl.obolibrary.org/obo/MOD_$1 modeldb: mappings: miriam: modeldb n2t: modeldb prefixcommons: MODELDB miriam: deprecated: false description: ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment. homepage: http://senselab.med.yale.edu/ModelDB/ id: '00000131' name: ModelDB namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: modeldb sampleId: '45539' uri_format: http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1 n2t: description: ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment. example: '45539' homepage: http://senselab.med.yale.edu/ModelDB/ name: ModelDB at SenseLab namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: modeldb uri_format: http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MODELDB uri_format: http://identifiers.org/modeldb/$1 molbase: mappings: miriam: molbase n2t: molbase prefixcommons: MOLBASE miriam: deprecated: false description: Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier. homepage: http://www.molbase.com/ id: 00000458 name: Molbase namespaceEmbeddedInLui: false pattern: ^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$ prefix: molbase sampleId: 128796-39-4 uri_format: http://www.molbase.com/en/index.php?app=search&search_keyword=$1 n2t: description: Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier. example: 128796-39-4 homepage: http://www.molbase.com/ name: Molbase at Chinese Academy of Sciences namespaceEmbeddedInLui: false pattern: ^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$ prefix: molbase uri_format: http://www.molbase.com/en/index.php?app=search&search_keyword=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MOLBASE uri_format: http://identifiers.org/molbase/$1 molbase.sheffield: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 deprecated: true description: An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students. example: '1868' homepage: https://winter.group.shef.ac.uk/molbase/ name: MolBase pattern: ^\d+$ molmedb: mappings: miriam: molmedb miriam: deprecated: false description: 'MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations. ' homepage: http://www.upol.cz/en/ id: 00000768 name: MolMeDB namespaceEmbeddedInLui: false pattern: ^[m,M]{2}[0-9]{5}[0-9]*$ prefix: molmedb sampleId: MM00040 uri_format: https://molmedb.upol.cz/mol/$1 mondo: bioportal: name: Mondo Disease Ontology prefix: MONDO download_obo: http://purl.obolibrary.org/obo/mondo.obo example: '0000001' mappings: bioportal: MONDO obofoundry: mondo ols: mondo ontobee: MONDO prefixcommons: MONDO name: Monarch Disease Ontology obofoundry: contact: nicole@tislab.org contact.github: nicolevasilevsky contact.label: Nicole Vasilevsky deprecated: false description: A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. download.json: http://purl.obolibrary.org/obo/mondo.json download.obo: http://purl.obolibrary.org/obo/mondo.obo download.owl: http://purl.obolibrary.org/obo/mondo.owl homepage: https://monarch-initiative.github.io/mondo inactive: false license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Mondo Disease Ontology preferredPrefix: MONDO prefix: mondo repository: https://github.com/monarch-initiative/mondo ols: description: A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. download: http://purl.obolibrary.org/obo/mondo.owl homepage: http://obofoundry.org/ontology/mondo.html license: http://creativecommons.org/licenses/by/4.0/ name: Mondo Disease Ontology prefix: mondo version: '2021-11-01' version.iri: http://purl.obolibrary.org/obo/mondo/releases/2021-11-01/mondo.owl ontobee: library: Library name: Mondo Disease Ontology prefix: MONDO url: http://www.ontobee.org/ontology/MONDO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: MONDO uri_format: http://purl.obolibrary.org/obo/MONDO_$1 wikidata: prefix: P5270 mop: bioportal: name: Molecular Process Ontology prefix: MOP download_obo: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.obo example: 0000079 mappings: bioportal: MOP obofoundry: mop ols: mop ontobee: MOP prefixcommons: MOP name: Molecular Process Ontology obofoundry: contact: batchelorc@rsc.org contact.label: Colin Batchelor deprecated: false description: Processes at the molecular level download.owl: http://purl.obolibrary.org/obo/mop.owl homepage: https://github.com/rsc-ontologies/rxno inactive: false license: CC-BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Molecular Process Ontology preferredPrefix: MOP prefix: mop repository: https://github.com/rsc-ontologies/rxno ols: contact: chemistry-ontologies@googlegroups.com description: MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation. download: http://purl.obolibrary.org/obo/mop.owl homepage: https://github.com/rsc-ontologies/rxno license: http://creativecommons.org/licenses/by/4.0/ name: MOP prefix: mop version: '2014-09-03' version.iri: http://purl.obolibrary.org/obo/mop/releases/2014-09-03/mop.owl ontobee: library: Library name: Molecular Process Ontology prefix: MOP url: http://www.ontobee.org/ontology/MOP pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: MOP uri_format: http://purl.obolibrary.org/obo/MOP_$1 morpheus: mappings: miriam: morpheus miriam: deprecated: false description: 'The Morpheus model repository is an open-access data resource to store, search and retrieve unpublished and published computational models of spatio-temporal and multicellular biological systems, encoded in the MorpheusML language and readily executable with the Morpheus software. ' homepage: https://morpheus.gitlab.io/ id: '00000725' name: Morpheus model repository namespaceEmbeddedInLui: false pattern: ^M[0-9]{4,}$ prefix: morpheus sampleId: M0001 uri_format: https://morpheus.gitlab.io/models/$1 mp: bioportal: name: Mammalian Phenotype Ontology prefix: MP mappings: bioportal: MP miriam: mp n2t: mp obofoundry: mp ols: mp ontobee: MP prefixcommons: MP miriam: deprecated: false description: The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways. homepage: http://www.informatics.jax.org/ id: 00000580 name: Mammalian Phenotype Ontology namespaceEmbeddedInLui: true pattern: ^MP:\d{7}$ prefix: mp sampleId: '0005452' uri_format: http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1 n2t: description: The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways. example: '0005452' homepage: https://bioportal.bioontology.org/ontologies/MP name: Mammalian Phenotype Ontology through BioPortal namespaceEmbeddedInLui: true pattern: ^MP:\d{7}$ prefix: mp uri_format: https://bioportal.bioontology.org/ontologies/MP/MP:$1 obofoundry: contact: pheno@jax.org contact.label: JAX phenotype list deprecated: false description: Standard terms for annotating mammalian phenotypic data. download.json: http://purl.obolibrary.org/obo/mp.json download.obo: http://purl.obolibrary.org/obo/mp.obo download.owl: http://purl.obolibrary.org/obo/mp.owl homepage: http://www.informatics.jax.org/searches/MP_form.shtml inactive: false license: CC-BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Mammalian Phenotype Ontology preferredPrefix: MP prefix: mp repository: https://github.com/obophenotype/mammalian-phenotype-ontology ols: description: The Mammalian Phenotype Ontology is being developed by Cynthia L. Smith, Susan M. Bello, Anna, Anagnostopoulos, Carroll W. Goldsmith and Janan T. Eppig, as part of the Mouse Genome Database (MGD) Project, Mouse Genome Informatics (MGI), The Jackson Laboratory, Bar Harbor, ME. This file contains pre-coordinated phenotype terms, definitions and synonyms that can be used to describe mammalian phenotypes. The ontology is represented as a directed acyclic graph (DAG). It organizes phenotype terms into major biological system headers such as nervous system and respiratory system. This ontology is currently under development. Weekly updates are available at the Mouse Genome Informatics (MGI) ftp site (ftp://ftp.informatics.jax.org/pub/reports/index.html#pheno) as well as the OBO Foundry site (http://obofoundry.org/). Questions, comments and suggestions are welcome, and should be directed to pheno@jax.org, Susan.Bello@jax.org or to GitHub tracker (https://github.com/mgijax/mammalian-phenotype-ontology/issues) MGD is funded by NIH/NHGRI grant HG000330. download: http://purl.obolibrary.org/obo/mp.owl homepage: http://www.informatics.jax.org/searches/MP_form.shtml license: https://creativecommons.org/licenses/by/4.0/ name: The Mammalian Phenotype Ontology prefix: mp version: '2019-11-11' version.iri: http://purl.obolibrary.org/obo/mp/releases/2021-11-04 ontobee: library: Library name: Mammalian Phenotype Ontology prefix: MP url: http://www.ontobee.org/ontology/MP pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: MP uri_format: http://purl.obolibrary.org/obo/MP_$1 mpath: bioportal: name: Mouse Pathology Ontology prefix: MPATH download_obo: https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo example: '728' mappings: bioportal: MPATH obofoundry: mpath ols: mpath ontobee: MPATH prefixcommons: MPATH obofoundry: contact: pns12@hermes.cam.ac.uk contact.label: Paul Schofield deprecated: false description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes download.owl: http://purl.obolibrary.org/obo/mpath.owl homepage: http://www.pathbase.net inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: Mouse pathology ontology preferredPrefix: MPATH prefix: mpath repository: https://github.com/PaulNSchofield/mpath ols: description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes download: http://purl.obolibrary.org/obo/mpath.owl homepage: http://www.pathbase.net name: Mouse pathology ontology prefix: mpath version: '2020-05-19' version.iri: http://purl.obolibrary.org/obo/mpath/2020-05-19/mpath.owl ontobee: library: Not Specified/No name: Mouse pathology prefix: MPATH url: http://www.ontobee.org/ontology/MPATH pattern: ^\d+$ prefixcommons: is_identifiers: false is_obo: true prefix: MPATH uri_format: http://purl.obolibrary.org/obo/MPATH_$1 synonyms: - MPATH mpid: mappings: miriam: mpid n2t: mpid prefixcommons: MPID miriam: deprecated: false description: The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts. homepage: http://www.jcvi.org/mpidb/about.php id: '00000124' name: Microbial Protein Interaction Database namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: mpid providers: - code: ebi description: Microbial Protein Interaction Database subset through IntAct homepage: https://www.ebi.ac.uk/intact/ name: Microbial Protein Interaction Database subset through IntAct uri_format: https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$1 sampleId: '172' uri_format: http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1 n2t: description: The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts. example: '172' homepage: http://www.jcvi.org/mpidb/about.php name: Microbial Protein Interaction Database namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: mpid uri_format: http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MPID uri_format: http://identifiers.org/mpid/$1 mpio: bioportal: name: Minimum PDDI Information Ontology prefix: MPIO example: '0000004' mappings: bioportal: MPIO obofoundry: mpio ols: mpio ontobee: MPIO prefixcommons: MPIO obofoundry: contact: mbrochhausen@uams.edu contact.github: mbrochhausen contact.label: Mathias Brochhausen deprecated: false description: An ontology of minimum information regarding potential drug-drug interaction information. download.owl: http://purl.obolibrary.org/obo/mpio.owl homepage: https://github.com/MPIO-Developers/MPIO inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/4.0/ name: Minimum PDDI Information Ontology preferredPrefix: MPIO prefix: mpio repository: https://github.com/MPIO-Developers/MPIO ols: description: An ontology of minimum information regarding potential drug-drug interaction information. download: http://purl.obolibrary.org/obo/mpio.owl homepage: https://github.com/MPIO-Developers/MPIO name: Minimum PDDI Information Ontology prefix: mpio version: '2019-01-30' version.iri: http://purl.obolibrary.org/obo/mpio/release/2019-01-30/mpio.owl ontobee: library: Library name: Minimum PDDI Information Ontology prefix: MPIO url: http://www.ontobee.org/ontology/MPIO prefixcommons: is_identifiers: false is_obo: true prefix: MPIO uri_format: http://purl.obolibrary.org/obo/MPIO_$1 mro: bioportal: name: Defen prefix: MRO example: '0000634' mappings: bioportal: MRO obofoundry: mro ols: mro ontobee: MRO prefixcommons: MRO obofoundry: contact: bpeters@lji.org contact.github: bpeters42 contact.label: Bjoern Peters deprecated: false description: An ontology for Major Histocompatibility Complex (MHC) restriction in experiments download.owl: http://purl.obolibrary.org/obo/mro.owl homepage: https://github.com/IEDB/MRO inactive: false license: CC-BY license.url: https://creativecommons.org/licenses/by/3.0/ name: MHC Restriction Ontology preferredPrefix: MRO prefix: mro repository: https://github.com/IEDB/MRO ols: description: The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions. download: http://purl.obolibrary.org/obo/mro.owl homepage: https://github.com/IEDB/MRO license: http://creativecommons.org/licenses/by/3.0/ name: MHC Restriction Ontology prefix: mro version: '2021-11-04' version.iri: http://purl.obolibrary.org/obo/mro/2021-11-04/mro.owl ontobee: library: Library name: MHC Restriction Ontology prefix: MRO url: http://www.ontobee.org/ontology/MRO prefixcommons: is_identifiers: false is_obo: true prefix: MRO uri_format: http://purl.obolibrary.org/obo/MRO_$1 ms: bioportal: name: Mass Spectrometry Ontology prefix: MS example: '1000560' mappings: bioportal: MS miriam: ms n2t: ms obofoundry: ms ols: ms ontobee: MS prefixcommons: MS miriam: deprecated: false description: The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. homepage: https://www.ebi.ac.uk/ols/ontologies/ms id: 00000590 name: Mass Spectrometry Controlled Vocabulary namespaceEmbeddedInLui: true pattern: ^MS:\d{7}$ prefix: ms sampleId: '1000001' uri_format: https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:$1 n2t: description: The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. example: '1000001' homepage: https://bioportal.bioontology.org/ontologies/MS name: Mass Spectrometry Controlled Vocabulary through BioPortal namespaceEmbeddedInLui: true pattern: ^MS:\d{7}$ prefix: ms uri_format: http://purl.bioontology.org/ontology/MS/MS:$1 obofoundry: contact: gerhard.mayer@rub.de contact.label: Gerhard Mayer deprecated: false description: A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry. download.obo: http://purl.obolibrary.org/obo/ms.obo download.owl: http://purl.obolibrary.org/obo/ms.owl homepage: http://www.psidev.info/groups/controlled-vocabularies inactive: false license: CC-BY license.url: https://creativecommons.org/licenses/by/3.0/ name: Mass spectrometry ontology preferredPrefix: MS prefix: ms repository: https://github.com/HUPO-PSI/psi-ms-CV ols: contact: psidev-ms-vocab@lists.sourceforge.net description: A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry. download: http://purl.obolibrary.org/obo/ms.owl homepage: http://www.psidev.info/groups/controlled-vocabularies name: Mass spectrometry ontology prefix: ms version: '2019-11-21' version.iri: http://purl.obolibrary.org/obo/ms/4.1.62/ms.owl ontobee: library: Library name: Mass spectrometry ontology prefix: MS url: http://www.ontobee.org/ontology/MS pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: MS uri_format: http://purl.obolibrary.org/obo/MS_$1 msigdb: biolink: is_identifiers: false is_obo: false prefix: MSigDB uri_format: https://www.gsea-msigdb.org/gsea/msigdb/$1 description: The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can example: NADELLA_PRKAR1A_TARGETS_DN homepage: https://www.gsea-msigdb.org mappings: biolink: MSigDB name: Molecular Signatures Database synonyms: - msig wikidata: paper: Q34509167 msio: example: '0000111' mappings: ols: msio name: Metabolomics Standards Initiative Ontology ols: description: an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies. download: https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl homepage: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO name: Metabolomics Standards Initiative Ontology (MSIO) prefix: msio version: 1.0.1 multicellds: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata. example: MCDS_S_0000000001 homepage: http://multicellds.org/MultiCellDB.php name: MultiCellDS uri_format: http://multicellds.org/MultiCellDB/$1 multicellds.cell_line: mappings: miriam: multicellds.cell_line n2t: multicellds.cell_line prefixcommons: MULTICELLDS.CELL_LINE miriam: deprecated: false description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata. homepage: http://multicellds.org/MultiCellDB.php id: 00000584 name: MultiCellDS Digital Cell Line namespaceEmbeddedInLui: false pattern: ^MCDS_L_[a-zA-Z0-9]{1,10}$ prefix: multicellds.cell_line sampleId: MCDS_L_0000000001 uri_format: http://multicellds.org/MultiCellDB/$1 n2t: description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata. example: MCDS_L_0000000001 homepage: http://multicellds.org/MultiCellDB.php name: MultiCellDS Digital Cell Line at Keck School of Medicine namespaceEmbeddedInLui: false pattern: ^MCDS_L_[a-zA-Z0-9]{1,10}$ prefix: multicellds.cell_line uri_format: http://multicellds.org/MultiCellDB/$1 part_of: multicellds prefixcommons: is_identifiers: true is_obo: false prefix: MULTICELLDS.CELL_LINE uri_format: http://identifiers.org/multicellds.cell_line/$1 multicellds.collection: mappings: miriam: multicellds.collection n2t: multicellds.collection prefixcommons: MULTICELLDS.COLLECTION miriam: deprecated: false description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections). homepage: http://multicellds.org/MultiCellDB.php id: 00000582 name: MultiCellDS collection namespaceEmbeddedInLui: false pattern: ^MCDS_C_[a-zA-Z0-9]{1,10}$ prefix: multicellds.collection sampleId: MCDS_C_0000000001 uri_format: http://multicellds.org/MultiCellDB/$1 n2t: description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections). example: MCDS_C_0000000001 homepage: http://multicellds.org/MultiCellDB.php name: MultiCellDScollection at Keck School of Medicine namespaceEmbeddedInLui: false pattern: ^MCDS_C_[a-zA-Z0-9]{1,10}$ prefix: multicellds.collection uri_format: http://multicellds.org/MultiCellDB/$1 part_of: multicellds prefixcommons: is_identifiers: true is_obo: false prefix: MULTICELLDS.COLLECTION uri_format: http://identifiers.org/multicellds.collection/$1 multicellds.snapshot: mappings: miriam: multicellds.snapshot n2t: multicellds.snapshot prefixcommons: MULTICELLDS.SNAPSHOT miriam: deprecated: false description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data. homepage: http://multicellds.org/MultiCellDB.php id: 00000583 name: MultiCellDS Digital snapshot namespaceEmbeddedInLui: false pattern: ^MCDS_S_[a-zA-Z0-9]{1,10}$ prefix: multicellds.snapshot sampleId: MCDS_S_0000000001 uri_format: http://multicellds.org/MultiCellDB/$1 n2t: description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data. example: MCDS_S_0000000001 homepage: http://multicellds.org/MultiCellDB.php name: MultiCellDS snapshot at Keck School of Medicine namespaceEmbeddedInLui: false pattern: ^MCDS_S_[a-zA-Z0-9]{1,10}$ prefix: multicellds.snapshot uri_format: http://multicellds.org/MultiCellDB/$1 part_of: multicellds prefixcommons: is_identifiers: true is_obo: false prefix: MULTICELLDS.SNAPSHOT uri_format: http://identifiers.org/multicellds.snapshot/$1 mw.project: mappings: miriam: mw.project n2t: mw.project prefixcommons: MW.PROJECT miriam: deprecated: false description: Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC). homepage: http://www.metabolomicsworkbench.org/ id: '00000647' name: Metabolomics Workbench Project namespaceEmbeddedInLui: false pattern: ^PR[0-9]{6}$ prefix: mw.project sampleId: PR000001 uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1 n2t: description: Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC). example: PR000001 homepage: http://www.metabolomicsworkbench.org/ name: Metabolomics Workbench Project namespaceEmbeddedInLui: false pattern: ^PR[0-9]{6}$ prefix: mw.project uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MW.PROJECT uri_format: http://identifiers.org/mw.project/$1 mw.study: mappings: miriam: mw.study n2t: mw.study prefixcommons: MW.STUDY miriam: deprecated: false description: Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC). homepage: http://www.metabolomicsworkbench.org/ id: '00000646' name: Metabolomics Workbench Study namespaceEmbeddedInLui: false pattern: ^ST[0-9]{6}$ prefix: mw.study providers: - code: omicsdi description: Metabolomics Workbench Study through OmicsDI homepage: https://www.omicsdi.org/ name: Metabolomics Workbench Study through OmicsDI uri_format: https://www.omicsdi.org/dataset/metabolomics_workbench/$1 sampleId: ST000900 uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1 n2t: description: Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC). example: ST000900 homepage: http://www.metabolomicsworkbench.org/ name: Metabolomics Workbench Study namespaceEmbeddedInLui: false pattern: ^ST[0-9]{6}$ prefix: mw.study uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MW.STUDY uri_format: http://identifiers.org/mw.study/$1 myco.lepra: mappings: miriam: myco.lepra n2t: myco.lepra prefixcommons: MYCO.LEPRA miriam: deprecated: false description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information. homepage: http://mycobrowser.epfl.ch/leprosy.html id: '00000217' name: MycoBrowser leprae namespaceEmbeddedInLui: false pattern: ^ML\w+$ prefix: myco.lepra sampleId: ML0224 uri_format: http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1 n2t: description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information. example: ML0224 homepage: http://mycobrowser.epfl.ch/leprosy.html name: MycoBrowser leprae at Global Health Institute namespaceEmbeddedInLui: false pattern: ^ML\w+$ prefix: myco.lepra uri_format: http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MYCO.LEPRA uri_format: http://identifiers.org/myco.lepra/$1 myco.marinum: mappings: miriam: myco.marinum n2t: myco.marinum prefixcommons: MYCO.MARINUM miriam: deprecated: false description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information. homepage: http://mycobrowser.epfl.ch/marinolist.html id: 00000218 name: MycoBrowser marinum namespaceEmbeddedInLui: false pattern: ^MMAR\_\d+$ prefix: myco.marinum sampleId: MMAR_2462 uri_format: http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1 n2t: description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information. example: MMAR_2462 homepage: http://mycobrowser.epfl.ch/marinolist.html name: MycoBrowser marinum at Global Health Institute namespaceEmbeddedInLui: false pattern: ^MMAR\_\d+$ prefix: myco.marinum uri_format: http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MYCO.MARINUM uri_format: http://identifiers.org/myco.marinum/$1 myco.smeg: mappings: miriam: myco.smeg n2t: myco.smeg prefixcommons: MYCO.SMEG miriam: deprecated: false description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information. homepage: http://mycobrowser.epfl.ch/smegmalist.html id: 00000219 name: MycoBrowser smegmatis namespaceEmbeddedInLui: false pattern: ^MSMEG\w+$ prefix: myco.smeg sampleId: MSMEG_3769 uri_format: http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1 n2t: description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information. example: MSMEG_3769 homepage: http://mycobrowser.epfl.ch/smegmalist.html name: MycoBrowser smegmatis at Global Health Institute namespaceEmbeddedInLui: false pattern: ^MSMEG\w+$ prefix: myco.smeg uri_format: http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MYCO.SMEG uri_format: http://identifiers.org/myco.smeg/$1 myco.tuber: mappings: miriam: myco.tuber n2t: myco.tuber prefixcommons: MYCO.TUBER miriam: deprecated: false description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information. homepage: http://tuberculist.epfl.ch/ id: '00000216' name: MycoBrowser tuberculosis namespaceEmbeddedInLui: false pattern: ^Rv\d{4}(A|B|c)?$ prefix: myco.tuber sampleId: Rv1908c uri_format: http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1 n2t: description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information. example: Rv1908c homepage: http://tuberculist.epfl.ch/ name: MycoBrowser tuberculosis at Global Health Institute namespaceEmbeddedInLui: false pattern: ^Rv\d{4}(A|B|c)?$ prefix: myco.tuber uri_format: http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1 prefixcommons: is_identifiers: true is_obo: false prefix: MYCO.TUBER uri_format: http://identifiers.org/myco.tuber/$1 mycobank: mappings: miriam: mycobank n2t: mycobank ncbi: MycoBank prefixcommons: MYCOBANK miriam: deprecated: false description: MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations. homepage: http://www.mycobank.org/ id: 00000178 name: MycoBank namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: mycobank sampleId: '349124' uri_format: http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1 n2t: description: MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations. example: '349124' homepage: http://www.mycobank.org/ name: MycoBank at Fungal Biodiversity Centre namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: mycobank uri_format: http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1 ncbi: example: '8284' homepage: http://www.mycobank.org name: Fungal Nomenclature and Species Bank prefix: MycoBank prefixcommons: is_identifiers: true is_obo: false prefix: MYCOBANK uri_format: http://identifiers.org/mycobank/$1 mzspec: banana: mzspec mappings: miriam: mzspec n2t: mzspec prefixcommons: MZSPEC miriam: deprecated: false description: The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it. homepage: http://proteomecentral.proteomexchange.org/ id: '00000625' name: Universal Spectrum Identifier namespaceEmbeddedInLui: true pattern: ^mzspec:.+$ prefix: mzspec providers: - code: CURATOR_REVIEW description: Universal Spectrum Identifier through Peptide Atlas homepage: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum name: Universal Spectrum Identifier through Peptide Atlas uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum?usi=mzspec:$1 sampleId: PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2 uri_format: http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1 n2t: description: The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it. example: PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2 homepage: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum name: Universal Spectrum Identifier through Peptide Atlas namespaceEmbeddedInLui: true pattern: ^mzspec:.+$ prefix: mzspec uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum?usi=mzspec:$1 pattern: ^.+$ prefixcommons: is_identifiers: true is_obo: false prefix: MZSPEC uri_format: http://identifiers.org/mzspec/$1 namerxn: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO). example: 4.2.78 homepage: https://www.nextmovesoftware.com/namerxn.html name: NameRXN proprietary: true references: - https://www.nextmovesoftware.com/products/HazELNutPoster.pdf - https://twitter.com/cthoyt/status/1443929184745758723 - https://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.6b00153 - https://www.nature.com/articles/s42256-020-00284-w napdi: mappings: miriam: napdi n2t: napdi prefixcommons: NAPDI miriam: deprecated: false description: The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs). homepage: https://repo.napdi.org/ id: '00000620' name: Natural Product-Drug Interaction Research Data Repository namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: napdi sampleId: '28' uri_format: https://repo.napdi.org/study/$1 n2t: description: The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs). example: '28' homepage: https://repo.napdi.org/ name: Natural Product-Drug Interaction Research Data Repository namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: napdi uri_format: https://repo.napdi.org/study/$1 prefixcommons: is_identifiers: true is_obo: false prefix: NAPDI uri_format: http://identifiers.org/napdi/$1 napp: mappings: miriam: napp n2t: napp prefixcommons: NAPP miriam: deprecated: false description: NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters. homepage: http://napp.u-psud.fr/ id: '00000247' name: NAPP namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: napp sampleId: '351' uri_format: http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1 n2t: description: NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters. example: '351' homepage: http://napp.u-psud.fr/ name: NAPP at CNRS namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: napp uri_format: http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1 name: Nucleic Acids Phylogenetic Profiling prefixcommons: is_identifiers: true is_obo: false prefix: NAPP uri_format: http://identifiers.org/napp/$1 narcis: homepage: http://www.narcis.nl mappings: miriam: narcis n2t: narcis prefixcommons: NARCIS miriam: deprecated: false description: NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases. homepage: http://www.narcis.nl/?Language=en id: '00000240' name: NARCIS namespaceEmbeddedInLui: false pattern: ^oai\:cwi\.nl\:\d+$ prefix: narcis sampleId: oai:cwi.nl:4725 uri_format: http://www.narcis.nl/publication/RecordID/$1 n2t: description: NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases. example: oai:cwi.nl:4725 homepage: http://www.narcis.nl/?Language=en name: NARCIS at The Hague namespaceEmbeddedInLui: false pattern: ^oai\:cwi\.nl\:\d+$ prefix: narcis uri_format: http://www.narcis.nl/publication/RecordID/$1 name: National Academic Research and Collaborations Information System prefixcommons: is_identifiers: true is_obo: false prefix: NARCIS uri_format: http://identifiers.org/narcis/$1 nasc: mappings: miriam: nasc n2t: nasc prefixcommons: NASC miriam: deprecated: false description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. homepage: http://arabidopsis.info/ id: '00000304' name: NASC code namespaceEmbeddedInLui: false pattern: ^(\w+)?\d+$ prefix: nasc sampleId: N1899 uri_format: http://arabidopsis.info/StockInfo?NASC_id=$1 n2t: description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. example: N1899 homepage: http://arabidopsis.info/ name: NASC at University of Nottingham namespaceEmbeddedInLui: false pattern: ^(\w+)?\d+$ prefix: nasc uri_format: http://arabidopsis.info/StockInfo?NASC_id=$1 prefixcommons: is_identifiers: true is_obo: false prefix: NASC uri_format: http://identifiers.org/nasc/$1 nbn: mappings: miriam: nbn n2t: nbn prefixcommons: NBN miriam: deprecated: false description: The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier. homepage: http://nbn-resolving.org/resolve_urn.htm id: 00000381 name: National Bibliography Number namespaceEmbeddedInLui: false pattern: ^urn\:nbn\:[A-Za-z_0-9]+\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$ prefix: nbn sampleId: urn:nbn:fi:tkk-004781 uri_format: http://nbn-resolving.org/resolver?identifier=$1&verb=redirect n2t: description: The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier. example: urn:nbn:fi:tkk-004781 homepage: http://nbn-resolving.org/resolve_urn.htm name: NBN through URN Resolver at German National Library namespaceEmbeddedInLui: false pattern: ^urn\:nbn\:[A-Za-z_0-9]+\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$ prefix: nbn uri_format: http://nbn-resolving.org/resolver?identifier=urn:nbn:$1&verb=redirect prefixcommons: is_identifiers: true is_obo: false prefix: NBN uri_format: http://identifiers.org/nbn/$1 nbo: bioportal: name: Neuro Behavior Ontology prefix: NBO download_obo: https://github.com/obo-behavior/behavior-ontology/raw/master/nbo.obo example: '0000564' mappings: bioportal: NBO obofoundry: nbo ols: nbo ontobee: NBO prefixcommons: NBO obofoundry: contact: g.gkoutos@bham.ac.uk contact.github: gkoutos contact.label: George Gkoutos deprecated: false description: An ontology of human and animal behaviours and behavioural phenotypes download.owl: http://purl.obolibrary.org/obo/nbo.owl homepage: https://github.com/obo-behavior/behavior-ontology/ inactive: false license: CC-BY license.url: http://creativecommons.org/licenses/by/3.0/ name: Neuro Behavior Ontology preferredPrefix: NBO prefix: nbo repository: https://github.com/obo-behavior/behavior-ontology ols: description: An ontology of human and animal behaviours and behavioural phenotypes download: http://purl.obolibrary.org/obo/nbo.owl homepage: https://github.com/obo-behavior/behavior-ontology/ name: Neuro Behavior Ontology prefix: nbo version: '2021-02-15' version.iri: http://purl.obolibrary.org/obo/nbo/releases/2021-02-15/nbo.owl ontobee: library: Library name: Neuro Behavior Ontology prefix: NBO url: http://www.ontobee.org/ontology/NBO pattern: ^\d{7}$ prefixcommons: is_identifiers: false is_obo: true prefix: NBO uri_format: http://purl.obolibrary.org/obo/NBO_$1 nbrc: mappings: miriam: nbrc n2t: nbrc ncbi: NBRC prefixcommons: NBRC miriam: deprecated: false description: NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information. homepage: http://www.nbrc.nite.go.jp/e/index.html id: 00000179 name: NITE Biological Research Center Catalogue namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: nbrc sampleId: '00001234' uri_format: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1 n2t: description: NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information. example: '00001234' homepage: http://www.nbrc.nite.go.jp/e/index.html name: NBRC Catalogue at National Institute of Technology Evaluation namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: nbrc uri_format: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1 ncbi: example: '3189' homepage: http://www.nbrc.nite.go.jp/e/catalog-e.html name: NITE Biological Resource Center prefix: NBRC prefixcommons: is_identifiers: true is_obo: false prefix: NBRC uri_format: http://identifiers.org/nbrc/$1 ncats.drug: contributor: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The National Center for Advancing Translational Sciences (NCATS) has developed Inxight: Drugs as a comprehensive portal for drug development information. NCATS Inxight: Drugs contains information on ingredients in medicinal products, including:' example: '44259' homepage: https://drugs.ncats.io/ name: NCATS Drugs uri_format: https://drugs.ncats.io/drug/$1 ncbigene: biolink: is_identifiers: true is_obo: false prefix: NCBIGene uri_format: http://identifiers.org/ncbigene/$1 go: homepage: http://www.ncbi.nlm.nih.gov/ name: NCBI Gene prefix: NCBIGene synonyms: - GeneID - LocusID - NCBI_Gene uri_format: https://www.ncbi.nlm.nih.gov/gene/$1 mappings: biolink: NCBIGene go: NCBIGene miriam: ncbigene n2t: ncbigene ncbi: GeneID prefixcommons: NCBIGene scholia: ncbi-gene wikidata: P351 miriam: deprecated: false description: Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis. homepage: https://www.ncbi.nlm.nih.gov/gene id: 00000069 name: NCBI Gene namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: ncbigene providers: - code: CURATOR_REVIEW description: Bio2RDF homepage: http://ncbigene.bio2rdf.org/fct name: Bio2RDF uri_format: http://ncbigene.bio2rdf.org/describe/?url=http://bio2rdf.org/ncbigene:$1 sampleId: '100010' uri_format: https://www.ncbi.nlm.nih.gov/gene/$1 n2t: description: Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis. example: '100010' homepage: https://www.ncbi.nlm.nih.gov/gene name: Entrez Gene (NCBI) namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: ncbigene uri_format: https://www.ncbi.nlm.nih.gov/gene/$1 ncbi: example: '3054987' homepage: https://www.ncbi.nlm.nih.gov/gene name: Entrez Gene Database (replaces NCBI Locus Link) prefix: GeneID preferred_prefix: NCBIGene prefixcommons: is_identifiers: false is_obo: false prefix: NCBIGene uri_format: http://www.ncbi.nlm.nih.gov/gene/$1 providers: - code: marrvel description: Helps browse potential orthologs in model organisms for a given gene homepage: http://marrvel.org name: Model organism Aggregated Resources for Rare Variant ExpLoration uri_format: http://marrvel.org/model/gene/$1 synonyms: - EGID - NCBIGene - entrez - entrez gene/locuslink wikidata: database: Q1345229 database.homepage: http://www.ncbi.nlm.nih.gov/gquery/ database.label: Entrez format.rdf: http://purl.uniprot.org/geneid/$1 name: Entrez Gene ID pattern: '[1-9]\d{0,8}' prefix: P351 uri_format: https://www.ncbi.nlm.nih.gov/gene/$1 ncbiprotein: go: homepage: https://www.ncbi.nlm.nih.gov/protein name: NCBI Protein prefix: NCBI_NP mappings: go: NCBI_NP miriam: ncbiprotein n2t: ncbiprotein prefixcommons: NCBIProtein miriam: deprecated: false description: The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. homepage: https://www.ncbi.nlm.nih.gov/protein id: '00000344' name: NCBI Protein namespaceEmbeddedInLui: false pattern: ^(\w+\d+(\.\d+)?)|(NP_\d+)$ prefix: ncbiprotein sampleId: CAA71118.1 uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 n2t: description: The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. example: CAA71118.1 homepage: https://www.ncbi.nlm.nih.gov/protein name: NCBI Protein at NCBI namespaceEmbeddedInLui: false pattern: ^(\w+\d+(\.\d+)?)|(NP_\d+)$ prefix: ncbiprotein uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 preferred_prefix: NCBIProtein prefixcommons: is_identifiers: false is_obo: false prefix: NCBIProtein uri_format: http://www.ncbi.nlm.nih.gov/protein/$1 ncbitaxon: bioportal: name: National Center for Biotechnology Information (NCBI) Organismal Classification prefix: NCBITAXON cellosaurus: category: Taxonomy homepage: https://www.ncbi.nlm.nih.gov/taxonomy name: NCBI taxonomy database prefix: NCBI_TaxID url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1&lvl=3 download_obo: http://purl.obolibrary.org/obo/ncbitaxon.obo example: '2170610' go: homepage: http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ name: NCBI Taxonomy prefix: taxon synonyms: - NCBITaxon - ncbi_taxid uri_format: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=$1 mappings: bioportal: NCBITAXON cellosaurus: NCBI_TaxID go: taxon miriam: taxonomy n2t: taxonomy ncbi: taxon obofoundry: ncbitaxon ols: ncbitaxon ontobee: NCBITaxon prefixcommons: NCBITaxon scholia: ncbi-taxon wikidata: P685 miriam: deprecated: false description: The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined. homepage: https://www.ncbi.nlm.nih.gov/Taxonomy/ id: '00000006' name: Taxonomy namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: taxonomy providers: - code: CURATOR_REVIEW description: Taxonomy through UniProt PURL homepage: https://www.uniprot.org/taxonomy/ name: Taxonomy through UniProt PURL uri_format: https://purl.uniprot.org/taxonomy/$1 - code: ebi description: European Nucleotide Archive (ENA) homepage: https://www.ebi.ac.uk/ena/ name: European Nucleotide Archive (ENA) uri_format: https://www.ebi.ac.uk/ena/data/view/Taxon:$1 - code: CURATOR_REVIEW description: Bio2RDF homepage: https://bio2rdf.org/ name: Bio2RDF uri_format: https://bio2rdf.org/taxonomy:$1 sampleId: '9606' uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1 n2t: description: The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined. example: '9606' homepage: https://www.ncbi.nlm.nih.gov/Taxonomy/ name: NCBI Taxonomy namespaceEmbeddedInLui: false pattern: ^\d+$ prefi