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Allotrope Merged Ontology Suite

The AFO is an ontology suite that provides a standard vocabulary and semantic model for the representation of laboratory analytical processes. The AFO suite is aligned at the upper layer to the Basic Formal Ontology (BFO). The core domains modeled include: Equipment, Material, Process, and Results.

This version of Allotrope Foundation Ontology (AFO) has been prepared specifically for publication on the NCBO platform.

license: http://purl.allotrope.org/voc/creative-commons-attribution-license
rights: http://purl.allotrope.org/voc/copyright

Please get the latest version of AFO from http://purl.allotrope.org

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Allotrope Merged Ontology Suite

The AFO is an ontology suite that provides a standard vocabulary and semantic model for the representation of laboratory analytical processes. The AFO suite is aligned at the upper layer to the Basic Formal Ontology (BFO). The core domains modeled include: Equipment, Material, Process, and Results.

This version of Allotrope Foundation Ontology (AFO) has been prepared specifically for publication on the NCBO platform.

license: http://purl.allotrope.org/voc/creative-commons-attribution-license
rights: http://purl.allotrope.org/voc/copyright

Please get the latest version of AFO from http://purl.allotrope.org

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AGRO is being built using traits identified by agronomists, the ICASA variables, and other existing ontologies such as ENVO, UO, and PATO, IAO, and CHEBI. Further, AGRO will power an Agronomy Management System and fieldbook modeled on a CGIAR Breeding Management System to capture agronomic data.", "homepage": "https://github.com/AgriculturalSemantics/agro", "name": "AGRonomy Ontology", "prefix": "AGRO"}, "agroportal": {"contact": {"email": "c.aubert@cgiar.org", "name": "Céline Aubert"}, "description": "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities", "example_uri": "http://purl.obolibrary.org/obo/AGRO_00000002", "homepage": "https://bigdata.cgiar.org/resources/agronomy-ontology/", "license": "CC BY 4.0", "name": "Agronomy Ontology", "prefix": "AGRO", "publication": "http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf", "repository": "https://github.com/AgriculturalSemantics/agro", "version": "1.0"}, "ols": {"description": "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities", "download": "http://purl.obolibrary.org/obo/agro.owl", "homepage": "https://github.com/AgriculturalSemantics/agro", "name": "Agronomy Ontology", "prefix": "agro", "version": "2021-11-05", "version.iri": "http://purl.obolibrary.org/obo/agro/releases/2021-11-05/agro.owl"}, "aberowl": {"description": "Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments", "download_owl": "http://aber-owl.net/media/ontologies/AGRO/6/agro.owl", "homepage": "https://github.com/AgriculturalSemantics/agro", "name": "Agronomy Ontology", "prefix": "AGRO"}, "ontobee": {"library": "Library", "name": "Agronomy Ontology", "prefix": "AGRO"}, "fairsharing": {"abbreviation": "AgrO", "description": "AgrO, the Agronomy Ontology, describes agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments. AgrO is being built by CGIAR using traits identified by agronomists, the ICASA variables, and other existing ontologies such as ENVO, UO, and PATO. It will complement existing crop, livestock, and fish ontologies to enable harmonized approaches to data collection, facilitating easier data sharing and reuse. A key use case for AgrO is the Agronomy Field Information Management System (AgroFIMS). 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Your library can use AGROVOC to index its documents or datasets, or you can use it from inside your content management system (e.g., Drupal) to organize your documents or web site. You can also use AGROVOC as an hub to access many other vocabularies available on the web. To date, AGROVOC is used by researchers, librarians and information managers for indexing, retrieving and organizing data in agricultural information systems and Web pages. Currently, AGROVOC is an SKOS-XL concept scheme and a Linked Open Data (LOD*) set aligned with over 20 other multilingual knowledge organization systems related to agriculture. 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The long-term goal is the construction of a library of images that will serve as primary data for research.", "id": "1723", "name": "Cell Image Library", "prefix": "FAIRsharing.8t18te", "subjects": ["Life Science", "Cell Biology"]}, "biocontext": {"is_identifiers": true, "is_obo": false, "prefix": "CELLIMAGE", "uri_format": "http://identifiers.org/cellimage/$1"}}, "cellopub": {"name": "Cellosaurus Publication", "description": "Cellosaurus identifeirs for publications, like Pubmed", "pattern": "^CLPUB\\d+$", "uri_format": "https://web.expasy.org/cellosaurus/cellopub/$1", "homepage": "https://web.expasy.org/cellosaurus/", "example": "CLPUB00496", "mappings": {"cellosaurus": "CelloPub"}, "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}, "cellosaurus": {"category": "Reference resources", "homepage": "https://www.cellosaurus.org/", "name": "Cellosaurus Publication", "prefix": "CelloPub", "uri_format": "https://www.cellosaurus.org/cellopub/$1"}}, "cellosaurus": {"name": "Cellosaurus", "pattern": "^[A-Z0-9]{4}$", "uri_format": "https://www.cellosaurus.org/CVCL_$1", "providers": [{"code": "legacy", "name": "Legacy Endpoint", "description": "The legacy URI for the Cellosaurus website, updated on August 30, 2022 [ref](https://twitter.com/Cellosaurus/status/1564658792691810305).", "homepage": "https://web.expasy.org/cellosaurus", "uri_format": "https://web.expasy.org/cellosaurus/CVCL_$1"}], "homepage": "https://cellosaurus.org", "contact": {"name": "Amos Bairoch", "orcid": "0000-0003-2826-6444", "email": "Amos.Bairoch@sib.swiss", "github": "AmosBairoch"}, "example": "0440", "download_obo": "https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo", "banana": "CVCL", "banana_peel": "_", "mappings": {"biocontext": "CELLOSAURUS", "cellosaurus": "Cellosaurus", "fairsharing": "FAIRsharing.hkk309", "miriam": "cellosaurus", "n2t": "cellosaurus", "re3data": "r3d100013293", "wikidata": "P3289"}, "synonyms": ["CVCL"], "twitter": "cellosaurus", "miriam": {"deprecated": false, "description": "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.", "homepage": "https://web.expasy.org/cellosaurus/", "id": "00000598", "name": "Cellosaurus", "namespaceEmbeddedInLui": false, "pattern": "^CVCL_[A-Z0-9]{4}$", "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"}, "wikidata": {"database": "Q24691710", "database.homepage": "https://www.cellosaurus.org/", "database.label": "Cellosaurus", "description": "Cellosaurus cell line identifier", "name": "Cellosaurus ID", "pattern": "CVCL_[A-Z\\d][A-Z\\d][A-Z\\d][A-Z\\d]", "prefix": "P3289", "uri_format": "https://www.cellosaurus.org/$1"}, "cellosaurus": {"category": "Cell line databases/resources", "homepage": "https://www.cellosaurus.org/", "name": "Cellosaurus - a knowledge resource on cell lines", "prefix": "Cellosaurus", "uri_format": "https://www.cellosaurus.org/$1"}, "fairsharing": {"abbreviation": "Cellosaurus", "description": "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.", "id": "2348", "name": "Cellosaurus", "prefix": "FAIRsharing.hkk309", "subjects": ["Life Science"]}, "biocontext": {"is_identifiers": true, "is_obo": false, "prefix": "CELLOSAURUS", "uri_format": "http://identifiers.org/cellosaurus/$1"}, "re3data": {"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, 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), Plant cell lines. Cellosaurus was initiated to be used as a cell line controlled vocabulary in the context of the neXtProt knowledgebase, but it quickly become apparent that there was a need for a cell line knowledge resource that would serve the needs of individual researchers, cell line distributors and bioinformatic resources. This leads to an increase of the scope and depth of the content of the Cellosaurus. The Cellosaurus is a participant of the Resource Identification Initiative and contributes actively to the work of the International Cell Line Authentication Committee (ICLAC).", "homepage": "https://web.expasy.org/cellosaurus/", "name": "Cellosaurus", "prefix": "r3d100013293", "synonyms": ["The Cellosaurus On ExPASy"], "xrefs": {"fairsharing": "FAIRsharing.hkk309", "scr": "013869"}}}, "cellosaurus.resource": {"name": "Cellosaurus Registry", "description": "The set of prefixes used in the Cellosaurus resource", "uri_format": "https://bioregistry.io/metaregistry/cellosaurus/$1", "homepage": "https://web.expasy.org/cellosaurus/", "example": "4DN", "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}}, "cellrepo": {"mappings": {"miriam": "cellrepo"}, "miriam": {"deprecated": false, "description": "The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines", "homepage": "https://cellrepo.ico2s.org/", "id": "00000829", "name": "Cell Version Control Repository", "namespaceEmbeddedInLui": false, "pattern": "^[0-9]+$", "prefix": "cellrepo", "sampleId": "82", "uri_format": "https://cellrepo.ico2s.org/repositories/$1"}}, "ceph": {"pattern": "^\\d{7}$", "example": "0000109", "download_obo": "https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo", "mappings": {"aberowl": "CEPH", "biocontext": "CEPH", "bioportal": "CEPH", "fairsharing": "FAIRsharing.p58bm4", "obofoundry": "ceph", "ols": "ceph", "ontobee": "CEPH"}, "obofoundry": {"contact": "cjmungall@lbl.gov", "contact.github": "cmungall", "contact.label": "Chris Mungall", "contact.orcid": "0000-0002-6601-2165", "deprecated": true, "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", "license": "CC BY 3.0", "license.url": "http://creativecommons.org/licenses/by/3.0/", "name": "Cephalopod Ontology", "prefix": "ceph", "repository": "https://github.com/obophenotype/cephalopod-ontology"}, "bioportal": {"contact": {"email": "cjmungall@lbl.gov", "name": "Chris Mungall"}, "description": "An anatomical and developmental ontology for cephalopods", "homepage": "https://github.com/obophenotype/cephalopod-ontology", "name": "Cephalopod Ontology", "prefix": "CEPH"}, "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"}, "aberowl": {"description": "An anatomical and developmental ontology for cephalopods", "download_owl": "http://aber-owl.net/media/ontologies/CEPH/2/ceph.owl", "homepage": "https://github.com/obophenotype/cephalopod-ontology", "name": "Cephalopod Ontology", "prefix": "CEPH"}, "ontobee": {"library": "Library", "name": "Cephalopod Ontology", "prefix": "CEPH"}, "fairsharing": {"abbreviation": "CEPH", "description": "An anatomical and developmental ontology for cephalopods", "id": "668", "name": "Cephalopod Ontology", "prefix": "FAIRsharing.p58bm4", "publications": [], "subjects": []}, "biocontext": {"is_identifiers": false, "is_obo": true, "prefix": "CEPH", "uri_format": "http://purl.obolibrary.org/obo/CEPH_$1"}}, "cgd": {"mappings": {"biocontext": "CGD", "fairsharing": "FAIRsharing.j7j53", "go": "CGD", "miriam": "cgd", "n2t": "cgd", "ncbi": "CGD", "prefixcommons": "cgd", "uniprot": "CGD"}, "publications": [{"pubmed": "15608216", "doi": "10.1093/nar/gki003", "pmc": "PMC539957", "title": "The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information.", "year": 2005}], "miriam": {"deprecated": false, "description": "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.", "homepage": "http://www.candidagenome.org/", "id": "00000145", "name": "Candida Genome Database", "namespaceEmbeddedInLui": false, "pattern": "^CAL\\d{7}$", "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=$1"}, "prefixcommons": {"description": "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.", "example": "CAL0003079", "homepage": "http://www.candidagenome.org/", "keywords": ["eukaryotic", "genome", "nucleotide"], "name": "Candida Genome Database", "pattern": "^CAL\\d{7}$", "prefix": "cgd", "pubmed_ids": ["15608216"], "uri_format": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"}, "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"}, "ncbi": {"example": "CAL0005934", "homepage": "http://www.candidagenome.org/", "name": "Candida Genome Database", "prefix": "CGD"}, "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"}, "fairsharing": {"abbreviation": "CGD", "description": "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.", "id": "1816", "name": "Candida Genome Database", "prefix": "FAIRsharing.j7j53", "subjects": ["Life Science"]}, "biocontext": {"is_identifiers": true, "is_obo": false, "prefix": "CGD", "uri_format": "http://identifiers.org/cgd/$1"}}, "cghdb": {"example": "300165/p13898_2106T", "mappings": {"cellosaurus": "CGH-DB"}, "cellosaurus": {"category": "Cell line databases/resources", "homepage": "http://www.cghtmd.jp/CGHDatabase/index_e.jsp", "name": "CGH Data Base", "prefix": "CGH-DB", "uri_format": "http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en"}}, "cgnc": {"name": "Chicken Gene Nomenclature Consortium", "description": "Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)", "pattern": "^\\d+$", "uri_format": "http://birdgenenames.org/cgnc/GeneReport?id=$1", "homepage": "http://birdgenenames.org/cgnc/", "example": "10087", "mappings": {"prefixcommons": "cgnc", "re3data": "r3d100012429"}, "synonyms": ["BirdBase", "CGNC"], "publications": [{"pubmed": "19607656", "doi": "10.1186/1471-2164-10-s2-s5", "pmc": "PMC2966335", "title": "The Chicken Gene Nomenclature Committee report.", "year": 2009}], "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}, "prefixcommons": {"description": "The Chicken Gene Nomenclature Consortium (CGNC) provides standardized gene nomenclature for chicken genes.", "example": "2218", "homepage": "http://www.agnc.msstate.edu/", "keywords": ["gene"], "name": "Chicken Gene Nomenclature Consortium", "pattern": "^\\d+$", "prefix": "cgnc", "pubmed_ids": ["19607656"], "uri_format": "http://www.agnc.msstate.edu/GeneReport.aspx?a=$1"}, "re3data": {"description": "The sequencing of several bird genomes and the anticipated sequencing of many more provided the impetus to develop a model organism database devoted to the taxonomic class: Aves. Birds provide model organisms important to the study of neurobiology, immunology, genetics, development, oncology, virology, cardiovascular biology, evolution and a variety of other life sciences. Many bird species are also important to agriculture, providing an enormous worldwide food source worldwide. Genomic approaches are proving invaluable to studying traits that affect meat yield, disease resistance, behavior, and bone development along with many other factors affecting productivity. In this context, BirdBase will serve both biomedical and agricultural researchers.", "homepage": "http://birdbase.arizona.edu/birdbase/", "name": "Birdbase", "prefix": "r3d100012429", "synonyms": ["A database of avian genes & genomes"]}}, "cgsc": {"name": "Coli Genetic Stock Center", "mappings": {"biocontext": "CGSC", "fairsharing": "FAIRsharing.1tbrdz", "go": "CGSC", "miriam": "cgsc", "n2t": "cgsc", "prefixcommons": "cgsc"}, "miriam": {"deprecated": false, "description": "The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature.", "homepage": "http://cgsc.biology.yale.edu/index.php", "id": "00000295", "name": "CGSC Strain", "namespaceEmbeddedInLui": false, "pattern": "^\\d+$", "prefix": "cgsc", "sampleId": "74", "uri_format": "http://cgsc.biology.yale.edu/Site.php?ID=$1"}, "n2t": {"description": "The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature.", "example": "74", "homepage": "http://cgsc.biology.yale.edu/index.php", "name": "CGSC at Yale university", "namespaceEmbeddedInLui": false, "pattern": "^\\d+$", "prefix": "cgsc", "uri_format": "http://cgsc.biology.yale.edu/Site.php?ID=$1"}, "prefixcommons": {"description": "The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature.", "example": "96846", "homepage": "http://cgsc.biology.yale.edu/", "keywords": ["gene"], "name": "The Coli Genetic Stock Center", "pattern": "^\\d+$", "prefix": "cgsc", "uri_format": "http://cgsc.biology.yale.edu/Site.php?ID=$1"}, "go": {"homepage": "http://cgsc.biology.yale.edu/", "name": "CGSC", "prefix": "CGSC"}, "fairsharing": {"abbreviation": "CGSC", "description": "The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature.", "id": "1818", "name": "Coli Genetic Stock Center", "prefix": "FAIRsharing.1tbrdz", "subjects": ["Life Science"]}, "biocontext": {"is_identifiers": true, "is_obo": false, "prefix": "CGSC", "uri_format": "http://identifiers.org/cgsc/$1"}}, "charprot": {"mappings": {"biocontext": "CHARPROT", "miriam": "charprot", "n2t": "charprot"}, "miriam": {"deprecated": false, "description": "CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession.", "homepage": "http://www.jcvi.org/charprotdb", "id": "00000341", "name": "CharProt", "namespaceEmbeddedInLui": false, "pattern": "^CH_\\d+$", "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. 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"biocontext": "CHEBI", "bioportal": "CHEBI", "cellosaurus": "ChEBI", "cheminf": "000407", "edam": "1174", "fairsharing": "FAIRsharing.62qk8w", "go": "CHEBI", "miriam": "chebi", "n2t": "chebi", "obofoundry": "chebi", "ols": "chebi", "ontobee": "CHEBI", "prefixcommons": "chebi", "re3data": "r3d100012626", "wikidata": "P683"}, "synonyms": ["CHEBI", "CHEBIID", "ChEBI"], "publications": [{"pubmed": "17932057", "doi": "10.1093/nar/gkm791", "pmc": "PMC2238832", "title": "ChEBI: a database and ontology for chemical entities of biological interest.", "year": 2007}, {"pubmed": "19496059", "doi": "10.1002/0471250953.bi1409s26", "pmc": null, "title": "ChEBI: an open bioinformatics and cheminformatics resource.", "year": 2009}, {"pubmed": "19854951", "doi": "10.1093/nar/gkp886", "pmc": "PMC2808869", "title": "Chemical Entities of Biological Interest: an update.", "year": 2009}, {"pubmed": "23180789", "doi": "10.1093/nar/gks1146", "pmc": "PMC3531142", "title": "The ChEBI reference database and 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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/$1"}}, "civic.did": {"mappings": {"miriam": "civic.did"}, "miriam": {"deprecated": false, "description": "Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement.", "homepage": "https://civicdb.org/", "id": "00000957", "name": "CIViC Disease", "namespaceEmbeddedInLui": false, "pattern": "^[0-9]+$", "prefix": "civic.did", "sampleId": "46", "uri_format": "https://civicdb.org/links/diseases/$1"}}, "civic.eid": {"mappings": {"miriam": "civic.eid"}, "miriam": {"deprecated": false, "description": "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract).", "homepage": "https://civicdb.org/", "id": "00000839", "name": "CIViC Evidence", "namespaceEmbeddedInLui": false, "pattern": "^[0-9]+$", "prefix": "civic.eid", "sampleId": "1199", "uri_format": "https://civicdb.org/links/evidence/$1"}}, "civic.gid": {"mappings": {"miriam": "civic.gid"}, "miriam": {"deprecated": false, "description": "A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus on emphasizing the clinical relevance from a molecular perspective rather than describing the biological function of the gene unless necessary to contextualize its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes, specific treatments for the gene’s associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis", "homepage": "https://civicdb.org/", "id": "00000907", "name": "CIViC Gene", "namespaceEmbeddedInLui": false, "pattern": "^[0-9]+$", "prefix": "civic.gid", "sampleId": "272", "uri_format": "https://civicdb.org/links/gene/$1"}}, "civic.sid": {"mappings": {"miriam": "civic.sid"}, "miriam": {"deprecated": false, "description": "In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source.", "homepage": "https://civicdb.org/", "id": "00000953", "name": "CIViC Source", "namespaceEmbeddedInLui": false, "pattern": "^[0-9]+$", "prefix": "civic.sid", "sampleId": "62", "uri_format": "https://civicdb.org/links/sources/$1"}}, "civic.tid": {"mappings": {"miriam": "civic.tid"}, "miriam": {"deprecated": false, "description": "Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant.", "homepage": "https://civicdb.org/", "id": "00000955", "name": "CIViC Therapy", "namespaceEmbeddedInLui": false, "pattern": "^[0-9]+$", "prefix": "civic.tid", "sampleId": "14", "uri_format": "https://civicdb.org/links/drugs/$1"}}, "civic.vid": {"mappings": {"miriam": "civic.vid"}, "miriam": {"deprecated": false, "description": "CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making.", "homepage": "https://civicdb.org/", "id": "00000909", "name": "CIViC Variant", "namespaceEmbeddedInLui": false, "pattern": "^[0-9]+$", "prefix": "civic.vid", "sampleId": "12", "uri_format": "https://civicdb.org/links/variant/$1"}}, "cl": {"pattern": "^\\d{7}$", "example": "0000062", "download_obo": "https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-full.obo", "mappings": {"aberowl": "CL", "agroportal": "CL", "biocontext": "CL", "bioportal": "CL", "cellosaurus": "CL", "fairsharing": "FAIRsharing.j9y503", "go": "CL", "miriam": "cl", "n2t": "cl", "obofoundry": "cl", "ols": "cl", "ontobee": "CL", "prefixcommons": "cl", "wikidata": "P7963"}, "publications": [{"pubmed": "21208450", "doi": "10.1186/1471-2105-12-6", "pmc": "PMC3024222", "title": "Logical development of the cell ontology.", "year": 2011}, {"pubmed": "27377652", "doi": "10.1186/s13326-016-0088-7", "pmc": "PMC4932724", "title": "The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.", "year": 2016}], "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:$1"}, "prefixcommons": {"bioportal": "1006", "description": "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.", "example": "CL:0000232", "homepage": "http://lists.sourceforge.net/lists/listinfo/obo-cell-type", "keywords": ["obo", "cell"], "name": "Cell Ontology", "pattern": "^CL:\\d+$", "prefix": "cl"}, "wikidata": {"database": "Q55118285", "database.label": "Cell Ontology", "homepage": "http://www.ontobee.org/ontology/CL", "name": "Cell Ontology ID", "pattern": "CL_[0-9]{7}", "prefix": "P7963", "uri_format": "http://purl.obolibrary.org/obo/$1"}, "go": {"homepage": "http://cellontology.org", "name": "Cell Type Ontology", "prefix": "CL"}, "obofoundry": {"appears_in": ["clo", "ecao", "go", "mco", "pcl", "xpo", "uberon", "ehdaa2"], "contact": "addiehl@buffalo.edu", "contact.github": "addiehl", "contact.label": "Alexander Diehl", "contact.orcid": "0000-0001-9990-8331", "depends_on": ["chebi", "go", "ncbitaxon", "pato", "pr", "ro", "uberon"], "deprecated": false, "description": "The Cell Ontology is a structured controlled vocabulary for cell types in animals.", "download.obo": "http://purl.obolibrary.org/obo/cl.obo", "download.owl": "http://purl.obolibrary.org/obo/cl.owl", "homepage": "https://obophenotype.github.io/cell-ontology/", "license": "CC BY 4.0", "license.url": "http://creativecommons.org/licenses/by/4.0/", "name": "Cell Ontology", "preferredPrefix": "CL", "prefix": "cl", "publications": [{"id": "https://www.ncbi.nlm.nih.gov/pubmed/27377652", "title": "The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability."}], "repository": "https://github.com/obophenotype/cell-ontology"}, "bioportal": {"homepage": "http://cellontology.org", "name": "Cell Ontology", "prefix": "CL", "version": "2022-08-16"}, "agroportal": {"contact": {"email": "addiehl@buffalo.edu", "name": "Alex Diehl"}, "description": "An ontology of cell types.", "example_uri": "http://purl.obolibrary.org/obo/PR_000001889", "homepage": "https://github.com/obophenotype/cell-ontology", "license": "CC BY 4.0", "name": "Cell Ontology", "prefix": "CL", "publication": "http://dx.doi.org/doi:10.1093/database/bav010, http://dx.doi.org/doi:10.1186/s13059-014-0560-6", "repository": "https://github.com/obophenotype/cell-ontology", "version": "2022-09-15"}, "ols": {"description": "An ontology of cell types.", "download": "http://purl.obolibrary.org/obo/cl.owl", "name": "Cell Ontology", "prefix": "cl", "version": "2022-08-16", "version.iri": "http://purl.obolibrary.org/obo/cl/releases/2022-08-16/cl.owl"}, "aberowl": {"description": "The Cell Ontology is a structured controlled vocabulary for cell types in animals.", "download_owl": "http://aber-owl.net/media/ontologies/CL/88/cl.owl", "homepage": "https://obophenotype.github.io/cell-ontology/", "name": "Cell Ontology", "prefix": "CL"}, "cellosaurus": {"category": "Anatomy/cell type resources", "homepage": "https://obophenotype.github.io/cell-ontology/", "name": "Cell Ontology", "prefix": "CL", "uri_format": "https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http://purl.obolibrary.org/obo/$1"}, "ontobee": {"library": "Library", "name": "Cell Ontology", "prefix": "CL"}, "fairsharing": {"abbreviation": "CL", "description": "The Cell Ontology (CL) is a candidate OBO Foundry ontology for the representation of cell types. First described in 2005, the CL integrates cell types from the prokaryotic, fungal, and eukaryotic organisms. As a core component of the OBO Foundry, the CL merges information contained in species-specific anatomical ontologies as well as referencing other OBO Foundry ontologies such as the Protein Ontology (PR) for uniquely expressed biomarkers and the Gene Ontology (GO) for the biological processes a cell type participates in. The CL is under continuous revision to expand representation of cell types and to better integrate with other biomedical ontologies.", "id": "1004", "name": "Cell Ontology", "prefix": "FAIRsharing.j9y503", "publications": [{"doi": "10.1186/1471-2105-12-6", "pubmed_id": 21208450, "title": "Logical development of the cell ontology."}, {"doi": "10.1186/s13326-016-0088-7", "pubmed_id": 27377652, "title": "The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability."}], "subjects": ["Anatomy", "Life Science", "Cell Biology"]}, "biocontext": {"is_identifiers": false, "is_obo": true, "prefix": "CL", "uri_format": "http://purl.obolibrary.org/obo/CL_$1"}}, "clao": {"pattern": "^\\d{7}$", "example": "0000088", "mappings": {"aberowl": "CLAO", "bioportal": "CLAO", "obofoundry": "clao", "ols": "clao", "ontobee": "CLAO"}, "obofoundry": {"contact": "lagonzalezmo@unal.edu.co", "contact.github": "luis-gonzalez-m", "contact.label": "Luis González-Montaña", "contact.orcid": "0000-0002-9136-9932", "depends_on": ["ro"], "deprecated": false, "description": "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).", "download.obo": "http://purl.obolibrary.org/obo/clao.obo", "download.owl": "http://purl.obolibrary.org/obo/clao.owl", "homepage": "https://github.com/luis-gonzalez-m/Collembola", "license": "CC0 1.0", "license.url": "http://creativecommons.org/publicdomain/zero/1.0/", "name": "Collembola Anatomy Ontology", "preferredPrefix": "CLAO", "prefix": "clao", "repository": "https://github.com/luis-gonzalez-m/Collembola"}, "bioportal": {"contact": {"email": "lagonzalezmo@unal.edu.co", "name": "Luis A. González-Montaña"}, "description": "Collembola Anatomy Ontology (CLAO) includes anatomical terms to refer to sclerites, anatomical systems, cell components, and chaetotaxy. CLAO is directed towards building semantic annotations or the production of morphological data employing a standardized language. CLAO is intended as a complementary tool to morhological descriptions during taxonomic work, before obtaining phylogenetic characters.", "homepage": "http://github/luis-gonzalez-m", "name": "Collembola Anatomy Ontology", "prefix": "CLAO", "version": "2020-16-05"}, "ols": {"description": "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).", "download": "http://purl.obolibrary.org/obo/clao.owl", "homepage": "https://github.com/luis-gonzalez-m/Collembola", "name": "Collembola Anatomy Ontology", "prefix": "clao", "version": "2021-09-27", "version.iri": "http://purl.obolibrary.org/obo/clao/releases/2021-09-27/clao.owl"}, "aberowl": {"description": "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).", "download_owl": "http://aber-owl.net/media/ontologies/CLAO/2/clao.owl", "homepage": "https://github.com/luis-gonzalez-m/Collembola", "name": "Collembola Anatomy Ontology", "prefix": "CLAO"}, "ontobee": {"library": "Library", "name": "Collembola Anatomy Ontology", "prefix": "CLAO"}}, "classyfire": {"pattern": "^\\d{7}$", "uri_format": "http://classyfire.wishartlab.com/tax_nodes/C$1", "example": "0004828", "download_obo": "http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip", "banana": "C", "mappings": {"miriam": "classyfire"}, "synonyms": ["CHEMONTID"], "comment": "There's a mismatch between the MIRIAM URI format string, which has a C prefix in front of class identifiers and the ontology which does not use them.", "miriam": {"deprecated": false, "description": "ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API.", "homepage": "http://classyfire.wishartlab.com/", "id": "00000770", "name": "ClassyFire", "namespaceEmbeddedInLui": false, "pattern": "^C[0-9]{7}$", "prefix": "classyfire", "sampleId": "C0004828", "uri_format": "http://classyfire.wishartlab.com/tax_nodes/$1"}}, "cldb": {"name": "Cell Line Database", "mappings": {"biocontext": "CLDB", "cellosaurus": "CLDB", "miriam": "cldb", "n2t": "cldb"}, "miriam": {"deprecated": false, "description": "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories.", "homepage": "http://bioinformatics.hsanmartino.it/hypercldb/indexes.html", "id": "00000390", "name": "CLDB", "namespaceEmbeddedInLui": false, "pattern": "^(cl|tum)\\d+$", "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"}, "cellosaurus": {"category": "Cell line databases/resources", "homepage": "http://bioinformatics.hsanmartino.it/cldb/", "name": "Cell Line Data Base", "prefix": "CLDB", "uri_format": "http://bioinformatics.hsanmartino.it/cldb/$1.html"}, "biocontext": {"is_identifiers": true, "is_obo": false, "prefix": "CLDB", "uri_format": "http://identifiers.org/cldb/$1"}}, "clingene": {"name": "ClinGen Allele Registry", "description": "The allele registry provides and maintains identifiers for genetic variants", "uri_format": "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1", "homepage": "https://reg.clinicalgenome.org", "example": "CA981206459", "mappings": {"biolink": "CAID"}, "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}, "biolink": {"is_identifiers": false, "is_obo": false, "prefix": "CAID", "uri_format": "http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1"}}, "clinicaltrials": {"providers": [{"code": "smartpatients", "name": "Smart Patients", "description": "Smart Patients is an online community for patients and their families. 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It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier.", "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", "id": "00000596", "name": "ClinVar Variant", "namespaceEmbeddedInLui": false, "pattern": "^\\d+$", "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. 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The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works in collaboration with interested organizations to meet the needs of the medical genetics community as efficiently and effectively as possible", "homepage": "https://www.ncbi.nlm.nih.gov/clinvar/", "name": "ClinVar", "prefix": "r3d100013331", "xrefs": {"fairsharing": "FAIRsharing.wx5r6f", "nlx": "151671", "scr": "006169"}}}, "clinvar.record": {"uri_format": "http://www.ncbi.nlm.nih.gov/clinvar/$1", "part_of": "clinvar", "mappings": {"biocontext": "CLINVAR.RECORD", "miriam": "clinvar.record", "n2t": "clinvar.record"}, "miriam": {"deprecated": false, "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession.", "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", "id": "00000534", "name": "ClinVar Record", "namespaceEmbeddedInLui": false, "pattern": "^RCV\\d+(\\.\\d+)?$", "prefix": "clinvar.record", "sampleId": "RCV000033555.3", "uri_format": "http://www.ncbi.nlm.nih.gov/clinvar/$1/"}, "n2t": {"description": "ClinVar archives reports of relationships among medically important variants and phenotypes. 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Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession.", "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", "id": "00000595", "name": "ClinVar Submission", "namespaceEmbeddedInLui": false, "pattern": "^SCV\\d+(\\.\\d+)?$", "prefix": "clinvar.submission", "sampleId": "SCV000151292", "uri_format": "http://www.ncbi.nlm.nih.gov/clinvar?term=$1"}, "n2t": {"description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. 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This collection references submitters (submitter ids) that submit the submissions (SCVs).", "homepage": "https://www.ncbi.nlm.nih.gov/clinvar/", "id": "00000769", "name": "ClinVar Submitter", "namespaceEmbeddedInLui": false, "pattern": "^\\d+$", "prefix": "clinvar.submitter", "sampleId": "26957", "uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1"}}, "clo": {"pattern": "^\\d{7}$", "example": "0000091", "mappings": {"aberowl": "CLO", "biocontext": "CLO", "bioportal": "CLO", "cellosaurus": "CLO", "fairsharing": "FAIRsharing.4dvtcz", "obofoundry": "clo", "ols": "clo", "ontobee": "CLO", "prefixcommons": "clo", "wikidata": "P2158"}, "synonyms": ["CLO"], "publications": [{"pubmed": "15693950", "doi": "10.1186/gb-2005-6-2-r21", "pmc": "PMC551541", "title": "An ontology for cell types.", "year": 2005}, {"pubmed": "25852852", "doi": "10.1186/2041-1480-5-37", "pmc": "PMC4387853", "title": "CLO: The cell line ontology.", "year": 2014}], "prefixcommons": {"bioportal": "1314", "description": "The Cell Line Ontology (CLO) is a community-based ontology in domain of biological cell lines with a focus on permanent cell lines from culture collections. 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The OWL-based CLO is machine-readable and can be used in various applications.", "example": "CL:0000232", "homepage": "http://sourceforge.net/projects/clo-ontology/", "keywords": ["ontology"], "name": "Cell Line Ontology", "pattern": "^CL:\\d{7}$", "prefix": "clo", "pubmed_ids": ["15693950"], "synonyms": ["obo.clo"]}, "wikidata": {"prefix": "P2158"}, "obofoundry": {"appears_in": ["mco"], "contact": "siiraa@umich.edu", "contact.github": "siiraa", "contact.label": "Sirarat Sarntivijai", "contact.orcid": "0000-0002-2548-641X", "depends_on": ["cl", "doid", "ncbitaxon", "uberon"], "deprecated": false, "description": "An ontology to standardize and integrate cell line information and to support computer-assisted reasoning.", "download.owl": "http://purl.obolibrary.org/obo/clo.owl", "homepage": "http://www.clo-ontology.org", "license": "CC BY 3.0", "license.url": "http://creativecommons.org/licenses/by/3.0/", "name": "Cell Line Ontology", "preferredPrefix": "CLO", "prefix": "clo", "publications": [{"id": "https://www.ncbi.nlm.nih.gov/pubmed/25852852", "title": "CLO: The Cell Line Ontology"}], "repository": "https://github.com/CLO-Ontology/CLO"}, "bioportal": {"contact": {"email": "yongqunh@med.umich.edu", "name": "Oliver He"}, "description": "The Cell Line Ontology (CLO) is a community-based ontology in domain of biological cell lines with a focus on permanent cell lines from culture collections. 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The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.", "download": "http://purl.obolibrary.org/obo/clo.owl", "homepage": "http://www.clo-ontology.org", "name": "CLO: Cell Line Ontology", "prefix": "clo", "version": "2.1.178"}, "aberowl": {"description": "An ontology to standardize and integrate cell line information and to support computer-assisted reasoning.", "download_owl": "http://aber-owl.net/media/ontologies/CLO/6/clo.owl", "homepage": "http://www.clo-ontology.org", "name": "Cell Line Ontology", "prefix": "CLO"}, "cellosaurus": {"category": "Cell line databases/resources", "homepage": "http://www.clo-ontology.org", "name": "Cell Line Ontology", "prefix": "CLO", "uri_format": "https://www.ebi.ac.uk/ols/ontologies/clo/terms?iri=http://purl.obolibrary.org/obo/$1"}, "ontobee": {"library": "Library", "name": "Cell Line Ontology", "prefix": "CLO"}, "fairsharing": {"abbreviation": "CLO", "description": "The Cell Line Ontology (CLO) is a community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. Thousands of cell lines have been artificially developed and used for different applications. Integration of data from multiple sources is a challenge, confounded by lack of consistent naming conventions, contamination of cell lines, and provision of the same cell lines by multiple commercial sources but with different biological attributes. CLO is a community-based effort to represent all cell lines in a standard ontology approach.", "id": "1012", "name": "Cell Line Ontology", "prefix": "FAIRsharing.4dvtcz", "publications": [{"doi": "10.1186/2041-1480-5-37", "pubmed_id": 25852852, "title": "CLO: The cell line ontology."}], "subjects": ["Life Science", "Cell Biology"]}, "biocontext": {"is_identifiers": false, "is_obo": true, "prefix": "CLO", "uri_format": "http://purl.obolibrary.org/obo/CLO_$1"}}, "cls": {"example": "300108/p3934_A-172", "mappings": {"cellosaurus": "CLS"}, "cellosaurus": {"category": "Cell line collections", "homepage": "https://cls.shop/", "name": "Cell Lines Service", "prefix": "CLS", "uri_format": "https://cls.shop/$1"}}, "clyh": {"pattern": "^\\d+$", "example": "1000100", "mappings": {"aberowl": "CLYH", "bioportal": "CLYH", "obofoundry": "clyh", "ols": "clyh", "ontobee": "CLYH"}, "obofoundry": {"contact": "lucas.leclere@obs-vlfr.fr", "contact.github": "L-Leclere", "contact.label": "Lucas Leclere", "contact.orcid": "0000-0002-7440-0467", "depends_on": ["iao", "ro", "uberon"], "deprecated": false, "description": "The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle.", "download.obo": "http://purl.obolibrary.org/obo/clyh.obo", "download.owl": "http://purl.obolibrary.org/obo/clyh.owl", "homepage": "https://github.com/EBISPOT/clyh_ontology", "license": "CC BY 3.0", "license.url": "http://creativecommons.org/licenses/by/3.0/", "name": "Clytia hemisphaerica Development and Anatomy Ontology", "preferredPrefix": "CLYH", "prefix": "clyh", "repository": "https://github.com/EBISPOT/clyh_ontology"}, "bioportal": {"contact": {"email": "lucas.leclere@obs-vlfr.fr", "name": "Lucas Leclere"}, "description": "The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle.", "homepage": "https://github.com/EBISPOT/clyh_ontology", "name": "Clytia hemisphaerica Development and Anatomy Ontology", "prefix": "CLYH"}, "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", "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"}, "aberowl": {"description": "The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle.", "download_owl": "http://aber-owl.net/media/ontologies/CLYH/3/clyh.owl", "homepage": "https://github.com/EBISPOT/clyh_ontology", "name": "Clytia hemisphaerica Development and Anatomy Ontology", "prefix": "CLYH"}, "ontobee": {"library": "Library", "name": "Clytia hemisphaerica Development and Anatomy Ontology", "prefix": "CLYH"}}, "cmecs": {"name": "Costal and Marine Ecological Classification Standard", "description": "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. 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"CranioMaxilloFacial ontology", "prefix": "cmf"}, "aberowl": {"name": "CranioMaxilloFacial ontology", "prefix": "CMF"}, "ontobee": {"library": "Library", "name": "CranioMaxilloFacial ontology", "prefix": "CMF"}, "biocontext": {"is_identifiers": false, "is_obo": true, "prefix": "CMF", "uri_format": "http://purl.obolibrary.org/obo/CMF_$1"}}, "cmo": {"pattern": "^\\d{7}$", "example": "0001350", "mappings": {"aberowl": "CMO", "biocontext": "CMO", "bioportal": "CMO", "fairsharing": "FAIRsharing.dq78pn", "obofoundry": "cmo", "ols": "cmo", "ontobee": "CMO"}, "publications": [{"pubmed": "22654893", "doi": "10.3389/fgene.2012.00087", "pmc": "PMC3361058", "title": "Three ontologies to define phenotype measurement data.", "year": 2012}, {"pubmed": "24103152", "doi": "10.1186/2041-1480-4-26", "pmc": "PMC3882879", "title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.", "year": 2013}], "twitter": "ratgenome", "obofoundry": {"appears_in": ["scdo"], "contact": "jrsmith@mcw.edu", "contact.github": "jrsjrs", "contact.label": "Jennifer Smith", "contact.orcid": "0000-0002-6443-9376", "deprecated": false, "description": "Morphological and physiological measurement records generated from clinical and model organism research and health programs.", "download.obo": "http://purl.obolibrary.org/obo/cmo.obo", "download.owl": "http://purl.obolibrary.org/obo/cmo.owl", "homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html", "license": "CC0 1.0", "license.url": "http://creativecommons.org/publicdomain/zero/1.0/", "name": "Clinical measurement ontology", "preferredPrefix": "CMO", "prefix": "cmo", "publications": [{"id": "https://www.ncbi.nlm.nih.gov/pubmed/22654893", "title": "Three ontologies to define phenotype measurement data."}, {"id": "https://www.ncbi.nlm.nih.gov/pubmed/24103152", "title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements 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"http://purl.obolibrary.org/obo/cmo/releases/2019-02-19/cmo.owl"}, "aberowl": {"description": "Morphological and physiological measurement records generated from clinical and model organism research and health programs.", "download_owl": "http://aber-owl.net/media/ontologies/CMO/91/cmo.owl", "homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html", "name": "Clinical measurement ontology", "prefix": "CMO"}, "ontobee": {"library": "Library", "name": "Clinical measurement ontology", "prefix": "CMO"}, "fairsharing": {"abbreviation": "CMO", "description": "The Clinical Measurement Ontology is designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs.", "id": "885", "name": "Clinical Measurement Ontology", "prefix": "FAIRsharing.dq78pn", "publications": [{"doi": "10.3389/fgene.2012.00087", "pubmed_id": 22654893, "title": "Three ontologies to define phenotype measurement data."}, {"doi": 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Based on SES, Rice Descriptor and IRIS DB.", "id": "832", "name": "Rice Ontology", "prefix": "FAIRsharing.2jkxp5", "publications": [], "subjects": ["Botany", "Agriculture", "Life Science"]}}, "co_321": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_321:$1", "example": "0000449", "mappings": {"agroportal": "CO_321", "cropoct": "CO_321", "fairsharing": "FAIRsharing.czzmpg", "ols": "co_321"}, "publications": [{"pubmed": "22476066", "doi": "10.1093/aobpla/plq008", "pmc": "PMC3000699", "title": "Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature.", "year": 2010}], "agroportal": {"contact": {"email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk"}, "description": "Wheat Trait Dictionary in template v5.", "example_uri": "http://www.cropontology.org/rdf/CO_321:0000238", "homepage": "http://www.cropontology.org/", "license": "CC BY 4.0", "name": "Wheat Ontology", "prefix": "CO_321", "publication": "https://doi.org/10.1093/aobpla/plq008", "version": "Feb 2016"}, "cropoct": {"description": "July 2018", "download_owl": "https://cropontology.org/ontology/CO_321/Wheat/owl", "homepage": "https://cropontology.org/term/CO_321:ROOT", "name": "Wheat ontology", "prefix": "CO_321"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "July 2018", "download": "https://cropontology.org/ontology/CO_321/Wheat/owl", "homepage": "https://cropontology.org/ontology/CO_321/Wheat", "name": "Wheat ontology", "prefix": "co_321", "version": "2019-10-09"}, "fairsharing": {"abbreviation": "CO_321", "description": "This ontology defines traits of the International Wheat Information System (IWIS) database and wheat descriptor. The Wheat Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.", "id": "728", "name": "Wheat Ontology", "prefix": "FAIRsharing.czzmpg", "publications": [{"doi": "10.1093/aobpla/plq008", "pubmed_id": 22476066, "title": "Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature."}], "subjects": ["Agriculture", "Life Science"]}}, "co_322": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_322:$1", "example": "0000773", "mappings": {"agroportal": "CO_322", "cropoct": "CO_322", "fairsharing": "FAIRsharing.eeyne8", "ols": "co_322"}, "agroportal": {"contact": {"email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk"}, "description": "Maize Trait Dictionary in template 5.", "example_uri": "http://www.cropontology.org/rdf/CO_322:0000850", "homepage": "http://www.cropontology.org/", "license": "CC BY 4.0", "name": "Maize Ontology", "prefix": "CO_322", "version": "September 2016"}, "cropoct": {"description": "Maize Trait Dictionary in template 5 - CIMMYT- September 2016", "download_owl": "https://cropontology.org/ontology/CO_322/Maize/owl", "homepage": "https://cropontology.org/term/CO_322:ROOT", "name": "Maize ontology", "prefix": "CO_322"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "Maize Trait Dictionary in template 5 - CIMMYT- September 2016", "download": "https://cropontology.org/ontology/CO_322/Maize/owl", "homepage": "https://cropontology.org/ontology/CO_322/Maize", "name": "Maize ontology", "prefix": "co_322", "version": "2019-10-09"}, "fairsharing": {"abbreviation": "CO_322", "description": "The Maize Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.", "id": "925", "name": "Maize Ontology", "prefix": "FAIRsharing.eeyne8", "publications": [], "subjects": ["Botany", "Agriculture", "Life Science"]}}, "co_323": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_323:$1", "example": "0000252", "mappings": {"agroportal": "CO_323", "cropoct": "CO_323", "fairsharing": "FAIRsharing.f69084", "ols": "co_323"}, "agroportal": {"contact": {"email": "r.verma@cgiar.org", "name": "Ramesh Verna"}, "description": "Reference Plant Ontologies are being developed in the context of the Plantome project and are being integrated with the Crop Ontology, which provides harmonized breeder's trait names, measurement methods, scales, and standard variables for many crops. The barley Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", "example_uri": "http://www.cropontology.org/rdf/CO_323:0000005/4", "homepage": "http://www.cropontology.org/", "license": "CC BY 4.0", "name": "Barley ontology", "prefix": "CO_323", "version": "1.2"}, "cropoct": {"description": "ICARDA - TDv5 - Sept 2018", "download_owl": "https://cropontology.org/ontology/CO_323/Barley/owl", "homepage": "https://cropontology.org/term/CO_323:ROOT", "name": "Barley ontology", "prefix": "CO_323"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "ICARDA - TDv5 - Sept 2018", "download": "https://cropontology.org/ontology/CO_323/Barley/owl", "homepage": "https://cropontology.org/ontology/CO_323/Barley", "name": "Barley ontology", "prefix": "co_323", "version": "2019-11-20"}, "fairsharing": {"abbreviation": "CO_323", "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Barley Ontology is one of these reference plant ontologies integrated within the Crop Ontology. Its focus is on traits and variable used in field trials for breeding.", "id": "872", "name": "Barley Ontology", "prefix": "FAIRsharing.f69084", "publications": [], "subjects": ["Botany", "Agriculture"]}}, "co_324": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_324:$1", "example": "0000111", "mappings": {"agroportal": "CO_324", "cropoct": "CO_324", "fairsharing": "FAIRsharing.dxx0c", "ols": "co_324"}, "agroportal": {"contact": {"email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk"}, "description": "Sorghum TDv5 Ontology", "example_uri": "http://www.cropontology.org/rdf/CO_324:0000660", "homepage": "http://www.cropontology.org/", "license": "CC BY 4.0", "name": "Sorghum Ontology", "prefix": "CO_324", "version": "1.0"}, "cropoct": {"description": "Sorghum TDv5 - Oct 2019", "download_owl": "https://cropontology.org/ontology/CO_324/Sorghum/owl", "homepage": "https://cropontology.org/term/CO_324:ROOT", "name": "Sorghum ontology", "prefix": "CO_324"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "Sorghum TDv5 - Oct 2019", "download": "https://cropontology.org/ontology/CO_324/Sorghum/owl", "homepage": "https://cropontology.org/ontology/CO_324/Sorghum", "name": "Sorghum ontology", "prefix": "co_324", "version": "2019-10-09"}, "fairsharing": {"abbreviation": "CO_324", "description": "The Sorghum Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.", "id": "1077", "name": "Sorghum Ontology", "prefix": "FAIRsharing.dxx0c", "publications": [], "subjects": ["Botany", "Agriculture"]}}, "co_325": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_325:$1", "example": "0000519", "mappings": {"agroportal": "CO_325", "cropoct": "CO_325", "fairsharing": "FAIRsharing.gdszhh", "ols": "co_325"}, "agroportal": {"contact": {"email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk"}, "description": "Banana Trait Dictionary in template 5 - characterization and breeding variables, drought experiment variables.", "example_uri": "http://www.cropontology.org/rdf/CO_325:0000267", "homepage": "http://www.cropontology.org/", "license": "CC BY 4.0", "name": "Banana Ontology", "prefix": "CO_325", "version": "April 2019"}, "cropoct": {"description": "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019", "download_owl": "https://cropontology.org/ontology/CO_325/Banana/owl", "homepage": "https://cropontology.org/term/CO_325:ROOT", "name": "Banana ontology", "prefix": "CO_325"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019", "download": "https://cropontology.org/ontology/CO_325/Banana/owl", "homepage": "https://cropontology.org/ontology/CO_325/Banana", "name": "Banana ontology", "prefix": "co_325", "version": "2019-10-09"}, "fairsharing": {"abbreviation": "CO_325", "description": "The Banana Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.", "id": "642", "name": "Banana Ontology", "prefix": "FAIRsharing.gdszhh", "publications": [], "subjects": ["Agriculture", "Life Science"]}}, "co_326": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_326:$1", "example": "0000254", "mappings": {"cropoct": "CO_326", "ols": "co_326"}, "cropoct": {"download_owl": "https://cropontology.org/ontology/CO_326/Coconut/owl", "homepage": "https://cropontology.org/term/CO_326:ROOT", "name": "Coconut ontology", "prefix": "CO_326"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "Draft version", "download": "https://cropontology.org/ontology/CO_326/Coconut/owl", "homepage": "https://cropontology.org/ontology/CO_326/Coconut", "name": "Coconut ontology", "prefix": "co_326"}}, "co_327": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_327:$1", "example": "0000095", "mappings": {"agroportal": "CO_327", "cropoct": "CO_327", "fairsharing": "FAIRsharing.4e3qh9", "ols": "co_327"}, "agroportal": {"contact": {"email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk"}, "description": "Pearl millet Trait Dictionary in template 5.", "example_uri": "http://www.cropontology.org/rdf/CO_327:0000185", "homepage": "http://www.cropontology.org/", "license": "CC BY 4.0", "name": "Pearl Millet Ontology", "prefix": "CO_327", "version": "April 2016"}, "cropoct": {"description": "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016", "download_owl": "https://cropontology.org/ontology/CO_327/Pearl millet/owl", "homepage": "https://cropontology.org/term/CO_327:ROOT", "name": "Pearl millet ontology", "prefix": "CO_327"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016", "download": "http://www.cropontology.org/ontology/CO_327/Pearl%20millet/owl", "homepage": "http://www.cropontology.org/ontology/CO_327/Pearl%20millet", "name": "Pearl millet ontology", "prefix": "co_327"}, "fairsharing": {"abbreviation": "CO_327", "description": "The goal of the CGIAR Pearl Millet Ontology is to help improve food security for subsistence smallholder farmers in East and West Africa with productive and nutritious pearl millet food and fodder production technologies.", "id": "495", "name": "Pearl Millet Ontology", "prefix": "FAIRsharing.4e3qh9", "publications": [], "subjects": ["Botany", "Agriculture"]}}, "co_330": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_330:$1", "example": "0000106", "mappings": {"agroportal": "CO_330", "cropoct": "CO_330", "fairsharing": "FAIRsharing.4fa657", "ols": "co_330"}, "agroportal": {"contact": {"email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk"}, "description": "Potato Ontology", "example_uri": "http://www.cropontology.org/rdf/CO_330:0000056/2", "homepage": "http://www.cropontology.org/", "license": "CC BY 4.0", "name": "Potato Ontology", "prefix": "CO_330", "version": "december 2017"}, "cropoct": {"description": "CIP - potato ontology - december 2018", "download_owl": "https://cropontology.org/ontology/CO_330/Potato/owl", "homepage": "https://cropontology.org/term/CO_330:ROOT", "name": "Potato ontology", "prefix": "CO_330"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "CIP - potato ontology - december 2018", "download": "https://cropontology.org/ontology/CO_330/Potato/owl", "homepage": "https://cropontology.org/ontology/CO_330/Potato", "name": "Potato ontology", "prefix": "co_330", "version": "2019-10-09"}, "fairsharing": {"abbreviation": "CO_330", "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Potato Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", "id": "1307", "name": "Potato Ontology", "prefix": "FAIRsharing.4fa657", "publications": [], "subjects": ["Botany", "Agriculture", "Life Science"]}}, "co_331": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_331:$1", "example": "0000088", "mappings": {"agroportal": "CO_331", "cropoct": "CO_331", "fairsharing": "FAIRsharing.4g5qcw", "ols": "co_331"}, "agroportal": {"contact": {"email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk"}, "description": "Sweet Potato Trait Dictionary in template v5", "example_uri": "http://www.cropontology.org/rdf/CO_331:0000601/1", "homepage": "http://www.cropontology.org/", "license": "CC BY 4.0", "name": "Sweet Potato Ontology", "prefix": "CO_331", "version": "June 2016"}, "cropoct": {"description": "Sweetpotato Trait Dictionary in template v5 - CIP - November 2019", "download_owl": "https://cropontology.org/ontology/CO_331/Sweet Potato/owl", "homepage": "https://cropontology.org/term/CO_331:ROOT", "name": "Sweet Potato ontology", "prefix": "CO_331"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019", "download": "http://www.cropontology.org/ontology/CO_331/Sweet%20Potato/owl", "homepage": "http://www.cropontology.org/ontology/CO_331/Sweet%20Potato", "name": "Sweet Potato ontology", "prefix": "co_331"}, "fairsharing": {"abbreviation": "CO_331", "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Sweet Potato Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", "id": "496", "name": "Sweet Potato Ontology", "prefix": "FAIRsharing.4g5qcw", "publications": [], "subjects": ["Botany", "Agriculture", "Life Science"]}}, "co_333": {"pattern": "^\\d+$", "uri_format": "https://www.cropontology.org/rdf/CO_333:$1", "example": "3000045", "mappings": {"agroportal": "CO_333", "cropoct": "CO_333", "fairsharing": "FAIRsharing.af5655", "ols": "co_333"}, "agroportal": {"contact": {"email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk"}, "description": "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRA, Geves, ITB, Unversité d'Angers) and breeding companies (Florimond Desprez).", "example_uri": "http://www.cropontology.org/rdf/CO_333:0001137", "homepage": "http://www.cropontology.org/", "license": "CC BY 4.0", "name": "Beet Ontology", "prefix": "CO_333", "version": "November 2017"}, "cropoct": {"description": "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017.", "download_owl": "https://cropontology.org/ontology/CO_333/Beet Ontology/owl", "homepage": "https://cropontology.org/term/CO_333:ROOT", "name": "Beet Ontology ontology", "prefix": "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"}, "fairsharing": {"abbreviation": "CO_333", "description": "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution and breeding company within the project. Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Beet Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", "id": "1079", "name": "Beet Ontology", "prefix": "FAIRsharing.af5655", "publications": [], "subjects": ["Botany", "Plant Breeding", "Agriculture", "Life Science"]}}, "co_334": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_334:$1", "example": "0000070", "mappings": {"agroportal": "CO_334", "cropoct": "CO_334", "fairsharing": "FAIRsharing.v06c4q", "ols": "co_334"}, "agroportal": {"contact": {"email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk"}, "description": "Cassava Trait Dictionary in template 5", "example_uri": "http://www.cropontology.org/rdf/CO_334:0100676", "homepage": "http://www.cropontology.org/", "license": "CC BY 4.0", "name": "Cassava Ontology", "prefix": "CO_334", "publication": "http://www.cropontology.org/", "version": "February 2016"}, "cropoct": {"description": "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016", "download_owl": "https://cropontology.org/ontology/CO_334/Cassava/owl", "homepage": "https://cropontology.org/term/CO_334:ROOT", "name": "Cassava ontology", "prefix": "CO_334"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016", "download": "https://cropontology.org/ontology/CO_334/Cassava/owl", "homepage": "https://cropontology.org/ontology/CO_334/Cassava", "name": "Cassava ontology", "prefix": "co_334", "version": "2019-10-09"}, "fairsharing": {"abbreviation": "CO_334", "description": "Crop-specific trait ontologies enhance the interoperability and effectiveness of data exchange between the data sources which adopt it, by providing standard concepts that are use to describe phenotypes stored in those sources. As one of them, the Cassava Ontology is actively used and shared in different databases such as the BMS (Breeding Management system) of the IBP or the CassavaBase. Cassava, a major staple crop, is the main source of calories for 500 million people across the globe. A perennial woody shrub native to Latin America, cassava is primarily grown as an annual crop in the humid tropics. A cash crop as well as a subsistence crop, cassava's large edible starchy roots are a source of low-cost carbohydrates for millions. Cassava end products range from fresh roots cooked, boiled, baked or fried at the household level, to highly processed starch as a food additive.", "id": "1099", "name": "IBP Cassava Trait Ontology", "prefix": "FAIRsharing.v06c4q", "publications": [], "subjects": ["Botany", "Agriculture", "Nutritional Science"]}}, "co_335": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_335:$1", "example": "0000189", "mappings": {"agroportal": "CO_335", "cropoct": "CO_335", "fairsharing": "FAIRsharing.a14123", "ols": "co_335"}, "agroportal": {"contact": {"email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk"}, "description": "Common bean trait dictionary", "example_uri": "http://www.cropontology.org/rdf/CO_335:0000475/4", "homepage": "http://www.cropontology.org/", "license": "CC BY 4.0", "name": "Common Bean Ontology", "prefix": "CO_335", "version": "August 2014"}, "cropoct": {"description": "CIAT Common bean trait dictionary - version Oct 2021", "download_owl": "https://cropontology.org/ontology/CO_335/Common Bean/owl", "homepage": "https://cropontology.org/term/CO_335:ROOT", "name": "Common Bean ontology", "prefix": "CO_335"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "CIAT Common bean trait dictionary - version August 2014", "download": "http://www.cropontology.org/ontology/CO_335/Common%20Bean/owl", "homepage": "http://www.cropontology.org/ontology/CO_335/Common%20Bean", "name": "Common Bean ontology", "prefix": "co_335"}, "fairsharing": {"abbreviation": "CO_335", "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Common Bean Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", "id": "1096", "name": "Common Bean Ontology", "prefix": "FAIRsharing.a14123", "publications": [], "subjects": ["Botany", "Agriculture"]}}, "co_336": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_336:$1", "example": "0000339", "mappings": {"agroportal": "CO_336", "cropoct": "CO_336", "fairsharing": "FAIRsharing.j75srj", "ols": "co_336"}, "agroportal": {"contact": {"email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk"}, "description": "Soybean Trait Dictionary in template v5", "example_uri": "http://www.cropontology.org/rdf/CO_336:0000230/2", "homepage": "http://www.cropontology.org/", "license": "CC BY 4.0", "name": "Soybean Ontology", "prefix": "CO_336", "version": "July 2015"}, "cropoct": {"description": "Soybean Trait Dictionary in template v5 - IITA - July 2015", "download_owl": "https://cropontology.org/ontology/CO_336/Soybean/owl", "homepage": "https://cropontology.org/term/CO_336:ROOT", "name": "Soybean ontology", "prefix": "CO_336"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "Soybean Trait Dictionary in template v5 - IITA - July 2015", "download": "https://cropontology.org/ontology/CO_336/Soybean/owl", "homepage": "https://cropontology.org/ontology/CO_336/Soybean", "name": "Soybean ontology", "prefix": "co_336"}, "fairsharing": {"abbreviation": "CO_336", "description": "The Soybean Ontology is part of the Crop Ontology (CO) project. 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The Brassica Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", "id": "1019", "name": "Brassica Ontology", "prefix": "FAIRsharing.af7a2d", "publications": [], "subjects": ["Botany", "Agriculture", "Life Science"]}}, "co_350": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_350:$1", "example": "0000215", "mappings": {"agroportal": "CO_350", "cropoct": "CO_350", "fairsharing": "FAIRsharing.35e1c3", "ols": "co_350"}, "agroportal": {"contact": {"email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk"}, "description": "Oat trait dictionary commissioned by Oat Global (http://oatglobal.org/) to hold the traits used in the T3/Oat database (http://triticeaetoolbox.org/oat/).", "example_uri": "http://www.cropontology.org/rdf/CO_350:0000091", "homepage": "http://www.cropontology.org/", "license": "CC BY 4.0", "name": "Oat Ontology", "prefix": "CO_350", "version": "1.0"}, "cropoct": {"description": "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo", "download_owl": "https://cropontology.org/ontology/CO_350/Oat/owl", "homepage": "https://cropontology.org/term/CO_350:ROOT", "name": "Oat ontology", "prefix": "CO_350"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo", "download": "https://cropontology.org/ontology/CO_350/Oat/owl", "homepage": "https://cropontology.org/ontology/CO_350/Oat", "name": "Oat ontology", "prefix": "co_350", "version": "2019-10-09"}, "fairsharing": {"abbreviation": "CO_350", "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. 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INRA July 2017", "example_uri": "http://www.cropontology.org/rdf/CO_356:1000182", "homepage": "http://www.cropontology.org/", "license": "CC BY 4.0", "name": "Vitis Ontology", "prefix": "CO_356", "version": "2019-11-29"}, "cropoct": {"description": "Grape Ontology including OIV and bioversity descriptors. INRA July 2017", "download_owl": "https://cropontology.org/ontology/CO_356/Vitis/owl", "homepage": "https://cropontology.org/term/CO_356:ROOT", "name": "Vitis ontology", "prefix": "CO_356"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "Grape Ontology including OIV and bioversity descriptors. INRA July 2017", "download": "https://cropontology.org/ontology/CO_356/Vitis/owl", "homepage": "https://cropontology.org/ontology/CO_356/Vitis", "name": "Vitis ontology", "prefix": "co_356", "version": "2019-11-29"}, "fairsharing": {"abbreviation": "CO_356", "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Vitis Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", "id": "1092", "name": "Vitis Ontology", "prefix": "FAIRsharing.c7f4d7", "publications": [], "subjects": ["Botany", "Agriculture", "Life Science"]}}, "co_357": {"pattern": "^\\d+$", "uri_format": "https://www.cropontology.org/rdf/CO_357:$1", "example": "1000290", "mappings": {"agroportal": "CO_357", "cropoct": "CO_357", "fairsharing": "FAIRsharing.2b04ae", "ols": "co_357"}, "agroportal": {"contact": {"email": "celia.michotey@inrae.fr", "name": "Célia Michotey"}, "description": "This ontology list all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels).", "example_uri": "http://www.cropontology.org/rdf/CO_357:0000088", "license": "CC BY 4.0", "name": "Woody Plant Ontology", "prefix": "CO_357", "version": "August 2017"}, "cropoct": {"description": "This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE.", "download_owl": "https://cropontology.org/ontology/CO_357/Woody Plant Ontology/owl", "homepage": "https://cropontology.org/term/CO_357:ROOT", "name": "Woody Plant Ontology ontology", "prefix": "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"}, "fairsharing": {"abbreviation": "CO_357", "description": "The Woody Plant Ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Woody Plant Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", "id": "1103", "name": "Woody Plant Ontology", "prefix": "FAIRsharing.2b04ae", "publications": [], "subjects": ["Botany", "Life Science"]}}, "co_358": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_358:$1", "example": "0000139", "mappings": {"agroportal": "CO_358", "cropoct": "CO_358", "ols": "co_358"}, "agroportal": {"contact": {"email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk"}, "description": "Cotton ontology from CottonGen database - June 2019", "example_uri": "http://www.cropontology.org/rdf/CO_358:0000215", "homepage": "http://www.cropontology.org/", "license": "CC BY 4.0", "name": "Cotton Ontology", "prefix": "CO_358", "version": "2020-01-03"}, "cropoct": {"description": "Cotton ontology from CottonGen database - June 2019", "download_owl": "https://cropontology.org/ontology/CO_358/Cotton/owl", "homepage": "https://cropontology.org/term/CO_358:ROOT", "name": "Cotton ontology", "prefix": "CO_358"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "Cotton ontology from CottonGen database - June 2019", "download": "https://cropontology.org/ontology/CO_358/Cotton/owl", "homepage": "https://cropontology.org/ontology/CO_358/Cotton", "name": "Cotton ontology", "prefix": "co_358", "version": "2020-01-03"}}, "co_359": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_359:$1", "example": "0000947", "mappings": {"agroportal": "CO_359", "cropoct": "CO_359", "ols": "co_359"}, "agroportal": {"contact": {"email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk"}, "description": "Created in December 2019.", "example_uri": "https://cropontology.org/rdf/CO_359:0000568", "homepage": "https://www.cropontology.org/", "license": "CC BY 4.0", "name": "Sunflower", "prefix": "CO_359", "version": "2019-12-16"}, "cropoct": {"description": "December 2019", "download_owl": "https://cropontology.org/ontology/CO_359/Sunflower/owl", "homepage": "https://cropontology.org/term/CO_359:ROOT", "name": "Sunflower ontology", "prefix": "CO_359"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "December 2019", "download": "https://cropontology.org/ontology/CO_359/Sunflower/owl", "homepage": "https://cropontology.org/ontology/CO_359/Sunflower", "name": "Sunflower ontology", "prefix": "co_359"}}, "co_360": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_360:$1", "example": "0000071", "mappings": {"agroportal": "CO_360", "cropoct": "CO_360", "fairsharing": "FAIRsharing.1c1738", "ols": "co_360"}, "agroportal": {"contact": {"email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk"}, "description": "Sugar Kelp trait ontology", "example_uri": "http://www.cropontology.org/rdf/CO_360:0000085", "homepage": "http://www.cropontology.org/", "license": "CC BY 4.0", "name": "Sugar Kelp Ontology", "prefix": "CO_360", "version": "June 2019"}, "cropoct": {"description": "Sugar Kelp trait ontology", "download_owl": "https://cropontology.org/ontology/CO_360/Sugar Kelp trait/owl", "homepage": "https://cropontology.org/term/CO_360:ROOT", "name": "Sugar Kelp trait ontology", "prefix": "CO_360"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "Sugar Kelp trait ontology", "download": "http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait/owl", "homepage": "http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait", "name": "Sugar Kelp trait ontology", "prefix": "co_360"}, "fairsharing": {"abbreviation": "CO_360", "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Sugar Kelp Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", "id": "1093", "name": "Sugar Kelp Trait Ontology", "prefix": "FAIRsharing.1c1738", "publications": [], "subjects": ["Botany", "Life Science"]}}, "co_365": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_365:$1", "example": "0000205", "mappings": {"agroportal": "CO_365", "cropoct": "CO_365", "ols": "co_365"}, "agroportal": {"contact": {"email": "ICARDA-ethiopia@cgiar.org", "name": "ICARDA Ethiopia"}, "description": "developed by ICARDA - Dec 2018", "example_uri": "http://www.cropontology.org/rdf/CO_365:0000146", "homepage": "http://www.cropontology.org", "license": "CC BY 4.0", "name": "Fababean Ontology", "prefix": "CO_365", "version": "2019-10-15"}, "cropoct": {"description": "developed by ICARDA - Dec 2018", "download_owl": "https://cropontology.org/ontology/CO_365/Fababean/owl", "homepage": "https://cropontology.org/term/CO_365:ROOT", "name": "Fababean ontology", "prefix": "CO_365"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "developed by ICARDA - Dec 2018", "download": "https://cropontology.org/ontology/CO_365/Fababean/owl", "homepage": "https://cropontology.org/ontology/CO_365/Fababean", "name": "Fababean ontology", "prefix": "co_365", "version": "2019-10-15"}}, "co_366": {"pattern": "^\\d{7}$", "uri_format": "https://www.cropontology.org/rdf/CO_366:$1", "example": "0000072", "mappings": {"agroportal": "CO_366", "cropoct": "CO_366", "ols": "co_366"}, "agroportal": {"contact": {"email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk"}, "description": "version Dec 2019", "example_uri": "http://www.cropontology.org/rdf/CO_366:0000253/9", "homepage": "http://www.cropontology.org", "license": "CC BY 4.0", "name": "Bambara Groundnut Ontology", "prefix": "CO_366", "publication": "https://doi.org/10.1093/database/baab028", "version": "2019-12-23"}, "cropoct": {"description": "version Dec 2019", "download_owl": "https://cropontology.org/ontology/CO_366/Bambara groundnut/owl", "homepage": "https://cropontology.org/term/CO_366:ROOT", "name": "Bambara groundnut ontology", "prefix": "CO_366"}, "ols": {"contact": "helpdesk@cropontology-curationtool.org", "description": "version Dec 2019", "download": "http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut/owl", "homepage": "http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut", "name": "Bambara groundnut ontology", "prefix": "co_366"}}, "co_367": {"pattern": "^\\d{7}$", "example": "0000004", "mappings": {"cropoct": "CO_367"}, "cropoct": {"description": "Curator name: Clara S. Stanschewski; Curator Affiliation: King Abdullah University of Science and Technology; Contributing Scientists or Crop expert group: The Salt Lab and the Quinoa Phenotyping Consortium Creation Date: 23.05.2021", "download_owl": "https://cropontology.org/ontology/CO_367/Quinoa Ontology/owl", "homepage": "https://cropontology.org/term/CO_367:ROOT", "name": "Quinoa Ontology ontology", "prefix": "CO_367"}}, "co_370": {"pattern": "^\\d{7}$", "example": "0000890", "mappings": {"cropoct": "CO_370"}, "cropoct": {"description": "Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales.", "download_owl": "https://cropontology.org/ontology/CO_370/Apple/owl", "homepage": "https://cropontology.org/term/CO_370:ROOT", "name": "Apple ontology", "prefix": "CO_370"}}, "cob": {"pattern": "^\\d{7}$", "example": "0000080", "mappings": {"aberowl": "COB", "bioportal": "COB", "obofoundry": "cob", "ols": "cob", "ontobee": "COB"}, "obofoundry": {"contact": "bpeters@lji.org", "contact.github": "bpeters42", "contact.label": "Bjoern Peters", "contact.orcid": "0000-0002-8457-6693", "deprecated": false, "description": "COB brings together key terms from a wide range of OBO projects to improve interoperability.", "download.owl": "http://purl.obolibrary.org/obo/cob.owl", "homepage": "https://obofoundry.org/COB/", "license": "CC0 1.0", "license.url": "https://creativecommons.org/publicdomain/zero/1.0/", "name": "Core Ontology for Biology and Biomedicine", "preferredPrefix": "COB", "prefix": "cob", "repository": "https://github.com/OBOFoundry/COB"}, "bioportal": {"contact": {"email": "bpeters@lji.org", "name": "Bjoern Peters"}, "description": "The Core Ontology for Biology and Biomedicine (COB) brings together key terms from a wide range of OBO projects into a single, small ontology. The goal is to improve interoperabilty and reuse across the OBO community through better coordination of key terms.", "homepage": "https://github.com/OBOFoundry/COB", "name": "Core Ontology for Biology and Biomedicine", "prefix": "COB", "version": "2022-05-02"}, "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://obofoundry.org/COB/", "name": "Core Ontology for Biology and Biomedicine", "prefix": "cob", "version": "2022-05-02", "version.iri": "http://purl.obolibrary.org/obo/cob/releases/2022-05-02/cob.owl"}, "aberowl": {"description": "COB brings together key terms from a wide range of OBO projects to improve interoperability.", "download_owl": "http://aber-owl.net/media/ontologies/COB/7/cob.owl", "homepage": "https://github.com/OBOFoundry/COB", "name": "Core Ontology for Biology and Biomedicine", "prefix": "COB"}, "ontobee": {"library": "Library", "name": "Core Ontology for Biology and Biomedicine", "prefix": "COB"}}, "coconut": {"name": "COlleCtion of Open Natural ProdUcTs", "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.", "pattern": "^CNP\\d{7}$", "uri_format": "https://coconut.naturalproducts.net/compound/coconut_id/$1", "homepage": "https://coconut.naturalproducts.net", "example": "CNP0171505", "comment": "@mSorok is the dev of the resource, hope I got it right!", "contributor": {"name": "Adriano Rutz", "orcid": "0000-0003-0443-9902", "email": "adriano.rutz@ik.me", "github": "adafede"}, "reviewer": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}, "github_request_issue": 221}, "codelink": {"name": "GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray", "description": "GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release).", "pattern": "^GE\\d+$", "homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt", "example": "GE86325", "references": ["https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-8060/A-GEOD-8060.adf.txt", "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt"], "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}}, "cog": {"name": "Cluster of orthologous genes", "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.", "pattern": "^COG\\d+$", "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1", "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/", "contact": {"name": "Michael Y Galperin", "orcid": "0000-0002-2265-5572", "email": "cogs@ncbi.nlm.nih.gov", "github": null}, "example": "COG0001", "mappings": {"biolink": "COG", "fairsharing": "FAIRsharing.djsbw2", "go": "COG_Cluster", "prefixcommons": "cog"}, "synonyms": ["COG_Cluster"], "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}, "prefixcommons": {"description": "Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.", "example": "145262", "homepage": "http://www.ncbi.nlm.nih.gov/COG", "keywords": ["protein", "genome"], "name": "Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes", "pattern": "^\\d+$", "prefix": "cog", "uri_format": "http://www.ncbi.nlm.nih.gov/COG/grace/cogenome.cgi?g=$1"}, "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"}, "biolink": {"is_identifiers": false, "is_obo": false, "prefix": "COG", "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog-project/$1"}, "fairsharing": {"abbreviation": "COG", "description": "Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.", "id": "1968", "name": "Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes", "prefix": "FAIRsharing.djsbw2", "subjects": ["Life Science"]}}, "cog.category": {"name": "COG Categories", "description": "Higher-level classifications of COG Pathways", "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1", "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/", "contact": {"name": "Michael Y Galperin", "orcid": "0000-0002-2265-5572", "email": "cogs@ncbi.nlm.nih.gov", "github": null}, "example": "K", "part_of": "cog", "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}}, "cog.pathway": {"name": "COG Pathways", "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.", "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1", "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/pathways", "contact": {"name": "Michael Y Galperin", "orcid": "0000-0002-2265-5572", "email": "cogs@ncbi.nlm.nih.gov", "github": null}, "example": "NAD%20biosynthesis", "part_of": "cog", "mappings": {"go": "COG_Pathway"}, "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}, "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=$1"}}, "cohd": {"name": "MIMIC III Database", "description": "MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012", "homepage": "https://github.com/MIT-LCP/mimic-omop", "repository": "https://github.com/MIT-LCP/mimic-omop", "no_own_terms": true, "comment": "not really sure where the source is. this also links to a system called athena. I was not able to figure out what COHD stands for.", "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}}, "col.taiwan": {"name": "Catalogue of Life in Taiwan", "description": "Identifier (name code) for a taxon in the catalogue of life in taiwan", "pattern": "^[1-9]\\d{5}$", "uri_format": "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1", "homepage": "http://taibnet.sinica.edu.tw/home.php", "example": "431472", "mappings": {"wikidata": "P3088"}, "contributor": {"name": "Meghan Balk", "orcid": "0000-0003-2699-3066", "email": "meghan.balk@gmail.com", "github": "megbalk"}, "reviewer": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}, "github_request_issue": 466, "wikidata": {"database": "Q26218155", "database.homepage": "https://taibnet.sinica.edu.tw/home.php", "database.label": "Catalogue of Life in Taiwan", "description": "identifier (name code) for a taxon in the Catalogue of Life in Taiwan", "homepage": "http://taibnet.sinica.edu.tw/home.php", "name": "Catalogue of Life in Taiwan ID", "pattern": "([1-9]\\d{5})", "prefix": "P3088", "uri_format": "http://taibnet.sinica.edu.tw/chi/taibnet_species_detail.php?name_code=$1"}}, "colao": {"name": "Coleoptera Anatomy Ontology", "pattern": "^\\d{7}$", "example": "0000000", "mappings": {"aberowl": "COLAO", "bioportal": "COLAO", "obofoundry": "colao", "ols": "colao", "ontobee": "COLAO"}, "obofoundry": {"contact": "entiminae@gmail.com", "contact.github": "JCGiron", "contact.label": "Jennifer C. 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At NCBI side, thhe work of QL and EB was supported by the Intramural Research Program of the National Library of Medicine, National Institutes of Health.", "name": "Clinical Trials Ontology", "prefix": "CTO", "version": "Version Release: 1.0.0"}, "ols": {"description": "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials.", "download": "http://purl.obolibrary.org/obo/cto.owl", "homepage": "https://github.com/BFO-ontology/BFO", "name": "CTO: Core Ontology of Clinical Trials", "prefix": "cto", "version": "1.0.0"}, "aberowl": {"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. 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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. 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The latest build id is 130, and the dbSNP web query for built 130 was available on Apr 30, 2009.dbSNP is a database that can be used freely by the public.More information may be fouond at: http://www.ncbi.nlm.nih.gov/projects/SNP/", "homepage": "https://lhncbc.nlm.nih.gov/", "name": "The Short Genetic Variations database", "organization": "National Center for Biotechnology Information,National Center for Biotechnology Information", "preferred_prefix": "dbSNP", "prefix": "2.16.840.1.113883.6.284", "status": "Complete"}}, "dbvar.study": {"name": "Database of Genomic Structural Variation - Study", "description": "Studies in dbVar.", "uri_format": "https://www.ncbi.nlm.nih.gov/dbvar/studies/$1", "homepage": "https://www.ncbi.nlm.nih.gov/dbvar", "example": "nstd102", "synonyms": ["dbvar.studies"], "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}}, "dbvar.variant": {"name": "Database of Genomic Structural Variation - Variant", "description": "Variants in dbVar.", "uri_format": "https://www.ncbi.nlm.nih.gov/dbvar/variants/$1", "homepage": "https://www.ncbi.nlm.nih.gov/dbvar", "example": "nsv3875336", "synonyms": ["dbvar.variants"], "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}}, "dc": {"name": "Dublin Core", "description": "Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.", "uri_format": "http://purl.org/dc/elements/1.1/$1", "homepage": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/", "example": "contributor", "mappings": {"aberowl": "DC", "biocontext": "dc", "bioportal": "DC", "fairsharing": "FAIRsharing.3nx7t"}, "synonyms": ["dc11"], "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}, "bioportal": {"contact": {"email": "kdurante@stanford.edu", "name": "Kim Durante"}, "description": "The Dublin Core Schema is a small set of vocabulary terms that can be used to describe several kinds of resources. 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It defines the structural makeup of Dictyostelium and its composing parts including the different cell types, throughout its life cycle. It has two main goals: (1) promote the consistent annotation of Dictyostelium-specific events, such as phenotypes and gene expression information; and (2) encourage researchers to use the same terms with the same intended meaning.", "id": "928", "name": "Dictyostelium Anatomy Ontology", "prefix": "FAIRsharing.z656ab", "publications": [{"doi": "10.1186/1471-2164-9-130", "pubmed_id": 18366659, "title": "An anatomy ontology to represent biological knowledge in Dictyostelium discoideum."}], "subjects": ["Anatomy", "Life Science"]}, "biocontext": {"is_identifiers": false, "is_obo": true, "prefix": "DDANAT", "uri_format": "http://purl.obolibrary.org/obo/DDANAT_$1"}}, "ddinter.drug": {"name": "Curated Drug-Drug Interactions Database - Drug", "description": "Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety.", "pattern": "^DDInter\\d+$", "uri_format": "http://ddinter.scbdd.com/ddinter/drug-detail/$1", "homepage": "http://ddinter.scbdd.com", "contact": {"name": "Dongsheng Cao", "orcid": "0000-0003-3604-3785", "email": "oriental-cds@163.com", "github": null}, "example": "DDInter20", "license": "CC-BY-NC-SA-4.0", "contributor": {"name": "Sierra Moxon", "orcid": "0000-0002-8719-7760", "email": null, "github": "sierra-moxon"}, "reviewer": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}, "github_request_issue": 492}, "ddinter.interaction": {"name": "Curated Drug-Drug Interactions Database - 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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", "license": "CC0 1.0", "license.url": "https://creativecommons.org/publicdomain/zero/1.0/", "name": "Environmental conditions, treatments and exposures ontology", "preferredPrefix": "ECTO", "prefix": "ecto", "repository": "https://github.com/EnvironmentOntology/environmental-exposure-ontology"}, "bioportal": {"homepage": "https://github.com/EnvironmentOntology/environmental-exposure-ontology", "name": "Environmental conditions, treatments and exposures ontology", "prefix": "ECTO", "version": "2022-08-12"}, "ols": {"description": "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology).", "download": "http://purl.obolibrary.org/obo/ecto.owl", "homepage": "https://github.com/EnvironmentOntology/environmental-exposure-ontology", "name": "Environment Exposure Ontology", "prefix": "ecto", "version": "2022-08-12", "version.iri": "http://purl.obolibrary.org/obo/ecto/releases/2022-08-12/ecto.owl"}, "aberowl": {"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. 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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.", "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/$1/"}, "n2t": {"description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. 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This collection references models.", "example": "26", "homepage": "http://e-cyanobacterium.org/models/", "name": "e-cyanobacterium entity at Masaryk University Brno", "namespaceEmbeddedInLui": false, "pattern": "^\\d+$", "prefix": "ecyano.model", "uri_format": "http://e-cyanobacterium.org/models/model/$1/"}, "biocontext": {"is_identifiers": true, "is_obo": false, "prefix": "ECYANO.MODEL", "uri_format": "http://identifiers.org/ecyano.model/$1"}}, "ecyano.rule": {"uri_format": "https://e-cyanobacterium.org/bcs/rule/$1", "part_of": "ecyano", "mappings": {"biocontext": "ECYANO.RULE", "miriam": "ecyano.rule", "n2t": "ecyano.rule"}, "miriam": {"deprecated": false, "description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules.", "homepage": "http://www.e-cyanobacterium.org/bcs/rule/", "id": "00000587", "name": "E-cyanobacterium rule", "namespaceEmbeddedInLui": false, "pattern": "^\\d+$", "prefix": "ecyano.rule", "sampleId": "56", "uri_format": "http://e-cyanobacterium.org/bcs/rule/$1/"}, "n2t": {"description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. 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This collection references rules.", "example": "56", "homepage": "http://www.e-cyanobacterium.org/bcs/rule/", "name": "e-cyanobacterium entity at Masaryk University Brno", "namespaceEmbeddedInLui": false, "pattern": "^\\d+$", "prefix": "ecyano.rule", "uri_format": "http://e-cyanobacterium.org/bcs/rule/$1/"}, "biocontext": {"is_identifiers": true, "is_obo": false, "prefix": "ECYANO.RULE", "uri_format": "http://identifiers.org/ecyano.rule/$1"}}, "edam": {"uri_format": "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1", "repository": "https://github.com/edamontology/edamontology", "contact": {"name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981", "email": "matus.kalas@uib.no", "github": "matuskalas"}, "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "mappings": {"aberowl": "EDAM", "agroportal": "EDAM", "biocontext": "EDAM", "bioportal": "EDAM", "fairsharing": "FAIRsharing.a6r7zs", "miriam": "edam", "n2t": "edam", "ols": "edam", "ontobee": "EDAM", "prefixcommons": "edam"}, "publications": [{"pubmed": "23479348", "doi": "10.1093/bioinformatics/btt113", "pmc": "PMC3654706", "title": "EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.", "year": 2013}], "twitter": "edamontology", "miriam": {"deprecated": false, "description": "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).", "homepage": "http://bioportal.bioontology.org/ontologies/EDAM", "id": "00000189", "name": "EDAM Ontology", "namespaceEmbeddedInLui": false, "pattern": "^(data|topic|operation|format)\\_\\d{4}$", "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/$1"}, "prefixcommons": {"bioportal": "1498", "description": "EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. The applications of EDAM are within organising tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web.", "example": "EDAM_data:1664", "homepage": "https://sourceforge.net/projects/edamontology/", "keywords": ["obo", "ontology"], "name": "Bioinformatics operations, types of data, data formats and topics", "pattern": "^EDAM_(data|topic)\\:\\d{4}$", "prefix": "edam", "synonyms": ["edam"], "uri_format": "http://www.ebi.ac.uk/ontology-lookup/?termId=$1"}, "bioportal": {"contact": {"email": "matus.kalas@uib.no", "name": "Matúš Kalaš"}, "description": "EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within bioscientific data analysis and data management. EDAM includes topics, operations, types of data and data identifiers, and data formats, relevant in data analysis and management in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use. EDAM is particularly suitable for semantic annotations and categorisation of diverse resources related to data analysis and management: e.g. tools, workflows, learning materials, or standards. EDAM is also useful in data management itself, for recording provenance metadata of processed bioscientific data.", "homepage": "http://edamontology.org", "name": "EDAM - Bioscientific data analysis ontology", "prefix": "EDAM", "publication": "https://doi.org/10.7490/f1000research.1118900.1", "version": "unstable(1.26_dev)"}, "agroportal": {"contact": {"email": "jison@bioinformatics.dtu.dk", "name": "Jon Ison"}, "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.", "example_uri": "http://edamontology.org/topic_3519", "homepage": "http://edamontology.org/page", "license": "CC BY 4.0", "name": "EDAM bioinformatics operations, data types, formats, identifiers and topics", "prefix": "EDAM", "publication": "http://dx.doi.org/10.1093/bioinformatics/btt113", "repository": "https://github.com/edamontology/edamontology", "version": "1.25"}, "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"}, "aberowl": {"description": "EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within bioinformatics and computational biology, including types of data and data identifiers, data formats, operations and topics. EDAM is a simply-structured ontology - essentially a set of concepts with preferred terms and synonyms, definitions, and some additional information - organised into a simple and intuitive hierarchy for convenient use by information curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries.", "download_owl": "http://aber-owl.net/media/ontologies/EDAM/36/edam.owl", "homepage": "http://edamontology.org", "name": "EDAM bioinformatics operations, types of data, data formats, identifiers, and topics", "prefix": "EDAM", "version": "1.19"}, "ontobee": {"library": "Not Specified/No", "name": "EMBRACE Data and Methods", "prefix": "EDAM"}, "fairsharing": {"abbreviation": "EDAM", "description": "EDAM (originally from “EMBRACE Data and Methods”) is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics.", "id": "1205", "name": "EMBRACE Data and Methods Ontology", "prefix": "FAIRsharing.a6r7zs", "publications": [{"doi": "10.1093/bioinformatics/btt113", "pubmed_id": 23479348, "title": "EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats."}], "subjects": ["Bioinformatics", "Life Science"]}, "biocontext": {"is_identifiers": true, "is_obo": false, "prefix": "EDAM", "uri_format": "http://identifiers.org/edam/$1"}}, "edam.data": {"name": "EDAM Data", "description": "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.", "pattern": "^\\d+$", "uri_format": "http://edamontology.org/data_$1", "homepage": "http://edamontology.org", "repository": "https://github.com/edamontology/edamontology", "contact": {"name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981", "email": "matus.kalas@uib.no", "github": "matuskalas"}, "example": "1664", "part_of": "edam", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "mappings": {"biolink": "EDAM-DATA"}, "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}, "twitter": "edamontology", "biolink": {"is_identifiers": false, "is_obo": false, "prefix": "EDAM-DATA", "uri_format": "http://edamontology.org/data_$1"}}, "edam.format": {"name": "EDAM Format", "description": "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data.", "pattern": "^\\d+$", "uri_format": "http://edamontology.org/format_$1", "homepage": "http://edamontology.org", "repository": "https://github.com/edamontology/edamontology", "contact": {"name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981", "email": "matus.kalas@uib.no", "github": "matuskalas"}, "example": "1915", "part_of": "edam", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "mappings": {"biolink": "EDAM-FORMAT"}, "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}, "twitter": "edamontology", "biolink": {"is_identifiers": false, "is_obo": false, "prefix": "EDAM-FORMAT", "uri_format": "http://edamontology.org/format_$1"}}, "edam.operation": {"name": "EDAM Operation", "description": "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.", "pattern": "^\\d+$", "uri_format": "http://edamontology.org/operation_$1", "homepage": "http://edamontology.org", "repository": "https://github.com/edamontology/edamontology", "contact": {"name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981", "email": "matus.kalas@uib.no", "github": "matuskalas"}, "example": "0004", "part_of": "edam", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "mappings": {"biolink": "EDAM-OPERATION"}, "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}, "twitter": "edamontology", "biolink": {"is_identifiers": false, "is_obo": false, "prefix": "EDAM-OPERATION", "uri_format": "http://edamontology.org/operation_$1"}}, "edam.topic": {"name": "EDAM Topic", "description": "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.", "pattern": "^\\d+$", "uri_format": "http://edamontology.org/topic_$1", "homepage": "http://edamontology.org", "repository": "https://github.com/edamontology/edamontology", "contact": {"name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981", "email": "matus.kalas@uib.no", "github": "matuskalas"}, "example": "0003", "part_of": "edam", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "mappings": {"biolink": "EDAM-TOPIC"}, "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}, "twitter": "edamontology", "biolink": {"is_identifiers": false, "is_obo": false, "prefix": "EDAM-TOPIC", "uri_format": "http://edamontology.org/topic_$1"}}, "edda": {"description": "Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries.", "uri_format": "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1", "homepage": "https://bioportal.bioontology.org/ontologies/EDDA", "example": "health_care_quality_assessment", "mappings": {"aberowl": "EDDA", "bioportal": "EDDA", "fairsharing": "FAIRsharing.2ffmsb"}, "bioportal": {"contact": {"email": "tanja.bekhuis@tcbinfosci.com", "name": "Tanja Bekhuis"}, "description": "The EDDA Study Designs Taxonomy (v2.0) was developed by the Evidence in Documents, Discovery, and Analytics (EDDA) Group: Tanja Bekhuis (Principal Scientist); Eugene Tseytlin (Systems Developer); Ashleigh Faith (Taxonomist); Faina Linkov (Epidemiologist). The EDDA Group is a division of TCB Research & Indexing LLC. This work was made possible, in part, by the US National Library of Medicine, National Institutes of Health, grant no. R00LM010943. Foundational research is described in Bekhuis T, Demner Fushman D, Crowley RS. Comparative effectiveness research designs: an analysis of terms and coverage in Medical Subject Headings (MeSH) and Emtree. Journal of the Medical Library Association (JMLA). 2013 April;101(2):92-100. PMC3634392. Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries. A PDF of this taxonomy is available in ResearchGate DOI: 10.13140/RG.2.1.3769.2406/1. The EDDA Study Designs Taxonomy by Tanja Bekhuis and Eugene Tseytlin is licensed under a Creative Commons Attribution–NonCommercial–ShareAlike 4.0 International License (CC BY-NC-SA 4.0). For information about this license, see https://creativecommons.org/licenses/by-nc-sa/4.0/.", "name": "EDDA Study Designs Taxonomy", "prefix": "EDDA", "version": "2.0"}, "aberowl": {"description": "The EDDA Study Designs Taxonomy (v2.0) was developed by the Evidence in Documents, Discovery, and Analytics (EDDA) Group: Tanja Bekhuis (Principal Scientist); Eugene Tseytlin (Systems Developer); Ashleigh Faith (Taxonomist); Faina Linkov (Epidemiologist). The EDDA Group is a division of TCB Research & Indexing LLC. This work was made possible, in part, by the US National Library of Medicine, National Institutes of Health, grant no. R00LM010943. Foundational research is described in Bekhuis T, Demner Fushman D, Crowley RS. Comparative effectiveness research designs: an analysis of terms and coverage in Medical Subject Headings (MeSH) and Emtree. Journal of the Medical Library Association (JMLA). 2013 April;101(2):92-100. PMC3634392. Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries. A PDF of this taxonomy is available in ResearchGate DOI: 10.13140/RG.2.1.3769.2406/1. The EDDA Study Designs Taxonomy by Tanja Bekhuis and Eugene Tseytlin is licensed under a Creative Commons Attribution–NonCommercial–ShareAlike 4.0 International License (CC BY-NC-SA 4.0). For information about this license, see https://creativecommons.org/licenses/by-nc-sa/4.0/.", "download_owl": "http://aber-owl.net/media/ontologies/EDDA/11/edda.owl", "name": "EDDA Study Designs Taxonomy", "prefix": "EDDA", "version": "2.0"}, "fairsharing": {"abbreviation": "EDDA", "description": "Terminology of study designs and publication types (beta version). Developed by the Evidence in Documents, Discovery, and Analysis (EDDA) Group. Tanja Bekhuis (PI); Eugene Tseytlin (Systems Developer); Ashleigh Faith (Taxonomist). Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pennsylvania, US. This work was made possible, in part, by the US National Library of Medicine, National Institutes of Health, grant no. R00LM010943. Based on research described in Bekhuis T, Demner-Fushman D, Crowley RS. Comparative effectiveness research designs: an analysis of terms and coverage in Medical Subject Headings (MeSH) and Emtree. Journal of the Medical Library Association (JMLA). 2013 April;101(2):92-100. PMC3634392. The terminology appearing in JMLA has been enriched with terms from MeSH, NCI Thesaurus (NCIT), and Emtree, the controlled vocabularies for MEDLINE, the National Cancer Institute, and Embase, respectively, as well as from published research literature. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCIT, Emtree, and medical dictionaries. A class for Publication Type is included because investigators consider type and design when screening reports for inclusion in comparative effectiveness research. EDDA Study Designs and Publications by Tanja Bekhuis is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.", "id": "1289", "name": "EDDA Study Designs Taxonomy", "prefix": "FAIRsharing.2ffmsb", "publications": [], "subjects": []}}, "efo": {"uri_format": "http://www.ebi.ac.uk/efo/EFO_$1", "repository": "https://github.com/EBISPOT/efo/", "contact": {"name": "Trish Whetzel", "orcid": "0000-0002-3458-4839", "email": "plwhetzel@gmail.com", "github": "twhetzel"}, "example": "0005147", "download_obo": "http://www.ebi.ac.uk/efo/efo.obo", "mappings": {"aberowl": "EFO", "agroportal": "EFO", "biocontext": "EFO", "biolink": "EFO", "bioportal": "EFO", "cellosaurus": "EFO", "fairsharing": "FAIRsharing.1gr4tz", "miriam": "efo", "n2t": "efo", "ols": "efo", "ontobee": "EFO"}, "publications": [{"pubmed": "20200009", "doi": "10.1093/bioinformatics/btq099", "pmc": "PMC2853691", "title": "Modeling sample variables with an Experimental Factor Ontology.", "year": 2010}], "preferred_prefix": "EFO", "miriam": {"deprecated": false, "description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.", "homepage": "https://www.ebi.ac.uk/ols/ontologies/efo", "id": "00000391", "name": "Experimental Factor Ontology", "namespaceEmbeddedInLui": false, "pattern": "^\\d{7}$", "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"}, "bioportal": {"contact": {"email": "efo-users@ebi.ac.uk", "name": "EFO User List"}, "description": "The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental variables in multiple resources at the EBI and Open Targets. The ontology has been developed to increase the richness of the annotations that are currently made in resources and to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology pulls together classes from reference ontologies such as disease, cell line, cell type and anatomy and adds axiomatisation as necessary to connect areas such as disease to phenotype. Contact EFO users list for information: efo-users@ebi.ac.uk.", "homepage": "http://www.ebi.ac.uk/efo", "name": "Experimental Factor Ontology", "prefix": "EFO", "version": "3.46.0"}, "agroportal": {"contact": {"email": "efo-users@lists.sourceforge.net", "name": "EFO User List"}, "description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for projects such as the GWAS catalog. It combines parts of several biological ontologies, such as UBERON anatomy, ChEBI chemical compounds, and Cell Ontology. EFO is developed by the EMBL-EBI Samples, Phenotypes and Ontologies Team (SPOT). We also add terms for external users when requested.", "example_uri": "http://www.orpha.net/ORDO/Orphanet_1390", "homepage": "http://www.ebi.ac.uk/efo/", "license": "Apache 2.0 License", "name": "Experimental Factor Ontology", "prefix": "EFO", "publication": "https://doi.org/10.1093/bioinformatics/btq099", "repository": "https://github.com/EBISPOT/efo", "version": "3.46.0"}, "ols": {"contact": "efo-users@lists.sourceforge.net", "description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for OpenTargets.org", "download": "http://www.ebi.ac.uk/efo/efo.owl", "homepage": "http://www.ebi.ac.uk/efo", "name": "Experimental Factor Ontology", "prefix": "efo", "version": "3.45.0", "version.iri": "http://www.ebi.ac.uk/efo/releases/v3.45.0/efo.owl"}, "aberowl": {"description": "The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental variables in multiple resources at the EBI and Open Targets. The ontology has been developed to increase the richness of the annotations that are currently made in resources and to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology pulls together classes from reference ontologies such as disease, cell line, cell type and anatomy and adds axiomatisation as necessary to connect areas such as disease to phenotype. 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The ontology pulls together classes from reference ontologies such as disease, cell line, cell type and anatomy and adds axiomatisation as necessary to connect areas such as disease to phenotype.", "id": "1498", "name": "Experimental Factor Ontology", "prefix": "FAIRsharing.1gr4tz", "publications": [{"doi": "10.1093/bioinformatics/btq099", "pubmed_id": 20200009, "title": "Modeling sample variables with an Experimental Factor Ontology."}], "subjects": ["Functional Genomics"]}, "biocontext": {"is_identifiers": false, "is_obo": true, "prefix": "EFO", "uri_format": "http://purl.obolibrary.org/obo/EFO_$1"}}, "ega.dataset": {"homepage": "https://ega-archive.org/", "mappings": {"biocontext": "EGA.DATASET", "fairsharing": "FAIRsharing.mya1ff", "miriam": "ega.dataset", "n2t": "ega.dataset"}, "miriam": {"deprecated": false, "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.", "homepage": "https://www.ebi.ac.uk/ega/dataset", "id": "00000512", "name": "European Genome-phenome Archive Dataset", "namespaceEmbeddedInLui": false, "pattern": "^EGAD\\d{11}$", "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/$1"}, "n2t": {"description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. 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This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.", "homepage": "https://www.ebi.ac.uk/ega/studies", "id": "00000511", "name": "European Genome-phenome Archive Study", "namespaceEmbeddedInLui": false, "pattern": "^EGAS\\d{11}$", "prefix": "ega.study", "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"}, "biocontext": {"is_identifiers": true, "is_obo": false, "prefix": "EGA.STUDY", "uri_format": "http://identifiers.org/ega.study/$1"}}, "eggnog": {"mappings": {"biocontext": "EGGNOG", "fairsharing": "FAIRsharing.j1wj7d", "miriam": "eggnog", "n2t": "eggnog", "prefixcommons": "eggnog", "uniprot": "eggNOG"}, "publications": [{"pubmed": "19900971", "doi": "10.1093/nar/gkp951", "pmc": "PMC2808932", "title": "eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.", "year": 2009}], "miriam": {"deprecated": false, "description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).", "homepage": "http://eggnog.embl.de/version_3.0/", "id": "00000201", "name": "eggNOG", "namespaceEmbeddedInLui": false, "pattern": "^\\w+$", "prefix": "eggnog", "sampleId": "veNOG12876", "uri_format": "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1"}, "n2t": {"description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. 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The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).", "example": "NOG80852", "homepage": "http://eggnog.embl.de", "keywords": ["gene"], "name": "Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups", "pattern": "^\\w+$", "prefix": "eggnog", "pubmed_ids": ["19900971"], "uri_format": "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$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"}, "fairsharing": {"abbreviation": "eggNOG", "description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).", "id": "1577", "name": "Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups", "prefix": "FAIRsharing.j1wj7d", "subjects": ["Life Science"]}, "biocontext": {"is_identifiers": true, "is_obo": false, "prefix": "EGGNOG", "uri_format": "http://identifiers.org/eggnog/$1"}}, "ehda": {"pattern": "^\\d+$", "example": "1", "mappings": {"aberowl": "EHDA", "biocontext": "EHDA", "bioportal": "EHDA", "obofoundry": "ehda", "prefixcommons": "ehda"}, "prefixcommons": {"bioportal": "1022", "description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. 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The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once.", "homepage": "http://obofoundry.org/ontology/ehda.html", "name": "Human Developmental Anatomy Ontology, timed version", "prefix": "EHDA", "version": "unknown"}, "aberowl": {"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once.", "download_obo": "http://aber-owl.net/media/ontologies/EHDA/6/ehda.obo", "homepage": "http://genex.hgu.mrc.ac.uk/", "name": "Human Developmental Anatomy Ontology, timed version", "prefix": "EHDA", "version": "unknown"}, "biocontext": {"is_identifiers": false, "is_obo": true, "prefix": "EHDA", "uri_format": "http://purl.obolibrary.org/obo/EHDA_$1"}}, "ehdaa": {"pattern": "^\\d+$", "example": "1", "mappings": {"aberowl": "EHDAA", "biocontext": "EHDAA", "bioportal": "EHDAA", "obofoundry": "ehdaa", "prefixcommons": "ehdaa"}, "prefixcommons": {"bioportal": "1021", "description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. 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The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release.", "homepage": "http://obofoundry.org/ontology/ehdaa.html", "name": "Human Developmental Anatomy Ontology, abstract version 1", "prefix": "EHDAA", "version": "unknown"}, "aberowl": {"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). 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Entities and definitions are collected from the latest International League against Epilepsy (ILAE) classification, as well as from domain-specific ontologies such as Epilepsy Ontology (EPILONT), Epilepsy Syndrome Seizure Ontology (ESSO), Epilepsy Semiology(EPISEM) and Epilepsy and Seizure Ontology (EPSO) and scientific literature. This ontology is intended to be used for data management and for text mining purposes. The current release of the ontology is publicly available and is a community based effort to assemble various facets of the complex disease Epilepsy.", "name": "EpilepsyOntology", "prefix": "EPIO", "version": "2021-05-28"}, "aberowl": {"description": "A application driven Epilepsy Ontology with official terms from the ILAE.", "download_owl": "http://aber-owl.net/media/ontologies/EPIO/2/epio.owl", "name": "Epilepsy Ontology", "prefix": "EPIO"}, "ontobee": {"library": "Library", "name": "Epilepsy Ontology", "prefix": "EPIO"}}, "epo": {"download_owl": "https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/epidemiology-ontology/epo.owl", "mappings": {"aberowl": "EPO", "biocontext": "EPO", "bioportal": "EPO", "obofoundry": "epo", "ontobee": "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/", "name": "Epidemiology Ontology", "prefix": "epo"}, "bioportal": {"contact": {"email": "ferdinand.dhombres@inserm.fr", "name": "Ferdinand Dhombres"}, "description": "The early pregnancy ontology contains the concepts to describe ectopic pregnancy ultrasound images, organized into several subsumption hierarchies for types of ectopic pregnancies and the signs, anatomical structures and technical elements of imaging associated with ectopic pregnancy. Version 1.1 was used for ultrasound image annotations (Dhombres et al. Developing a knowledge base to support the annotation of ultrasound images of ectopic pregnancy. J Biomed Semantics, 2017)", "name": "Early Pregnancy Ontology", "prefix": "EPO", "version": "1.1"}, "aberowl": {"description": "The early pregnancy ontology contains the concepts to describe ectopic pregnancy ultrasound images, organized into several subsumption hierarchies for types of ectopic pregnancies and the signs, anatomical structures and technical elements of imaging associated with ectopic pregnancy. Version 1.1 was used for ultrasound image annotations (Dhombres et al. Developing a knowledge base to support the annotation of ultrasound images of ectopic pregnancy. J Biomed Semantics, 2017)", "download_owl": "http://aber-owl.net/media/ontologies/EPO/1/epo.owl", "name": "Early Pregnancy Ontology", "prefix": "EPO", "version": "1.1"}, "ontobee": {"library": "Library", "name": "Epidemiology Ontology", "prefix": "EPO"}, "biocontext": {"is_identifiers": false, "is_obo": true, "prefix": "EPO", "uri_format": "http://purl.obolibrary.org/obo/EPO_$1"}}, "epso": {"pattern": "^\\d{7}$", "uri_format": "http://www.case.edu/EpilepsyOntology.owl#$1", "homepage": "http://prism.case.edu/prism/index.php/EpilepsyOntology", "example": "0000400", "mappings": {"aberowl": "EPSO", "bioportal": "EPSO", "fairsharing": "FAIRsharing.ttprgy", "ontobee": "EPSO"}, "bioportal": {"contact": {"email": "satyasahoo@ieee.org", "name": "Satya Sahoo"}, "description": "The Epilepsy Ontology (BioPortal ID: EpSO) is an application ontology developed to support epilepsy research, patient care, and health system management. The updated version of the Epilepsy Ontology adds neuropathology terms, including immunohistochemistry, microscopy, anatomical description, and referential mappings to the ILAE 2017 classification of seizure types. This work is co-funded by the International League Against Epilepsy (ILAE), which also retains intellectual ownership of the ontology, together with the Case Western Reserve University and collaborating institutions. Contact: satya.sahoo@case.edu", "homepage": "https://bmhinformatics.case.edu/", "name": "Epilepsy and Seizure Ontology", "prefix": "EPSO", "publication": "https://bmhinformatics.case.edu/", "version": "2.1"}, "aberowl": {"description": "A application driven Epilepsy Ontology sith official terms from the ILAE.", "download_owl": "http://aber-owl.net/media/ontologies/EPSO/3/epso.owl", "name": "Epilepsy Ontology", "prefix": "EPSO"}, "ontobee": {"library": "Library", "name": "Epilepsy Ontology", "prefix": "EPSO"}, "fairsharing": {"abbreviation": "EPSO", "description": "The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. ", "id": "265", "name": "Epilepsy and Seizure Ontology", "prefix": "FAIRsharing.ttprgy", "publications": [{"doi": "10.1136/amiajnl-2013-001696", "pubmed_id": null, "title": "Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care"}], "subjects": ["Neurology"]}}, "erm": {"contact": {"name": "Egon Willighagen", "orcid": "0000-0001-7542-0286", "email": "egon.willighagen@gmail.com", "github": "egonw"}, "download_rdf": "https://nanocommons.github.io/identifiers/registry", "mappings": {"cheminf": "000569", "miriam": "erm", "n2t": "erm"}, "publications": [{"pubmed": null, "doi": "10.1186/s13321-022-00614-7", "pmc": null, "title": "European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials", "year": null}], "twitter": "nanocommons", "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#$1"}, "cheminf": {"description": "Identifier used by the European Registry of Materials (https://nanocommons.github.io/identifiers/).", "name": "European Registry of Materials", "obsolete": false, "prefix": "000569"}}, "ero": {"pattern": "^\\d{7}$", "example": "0001655", "mappings": {"aberowl": "ERO", "biocontext": "ERO", "bioportal": "ERO", "fairsharing": "FAIRsharing.nwgynk", "obofoundry": "ero", "ols": "ero", "ontobee": "ERO"}, "publications": [{"pubmed": "22434835", "doi": "10.1093/database/bar067", "pmc": "PMC3308157", "title": "Research resources: curating the new eagle-i discovery system.", "year": 2012}, {"pubmed": "29599662", "doi": "10.1109/jcdl.2017.7991571", "pmc": "PMC5868434", "title": "Automating data citation: the eagle-i experience.", "year": 2017}], "obofoundry": {"contact": "Marc_Ciriello@hms.harvard.edu", "contact.label": "Marc Ciriello", "deprecated": true, "description": "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.", "download.owl": "http://purl.obolibrary.org/obo/ero.owl", "homepage": "https://open.med.harvard.edu/wiki/display/eaglei/Ontology", "license": "CC BY 2.0", "license.url": "https://creativecommons.org/licenses/by/2.0/", "name": "eagle-i resource ontology", "prefix": "ero"}, "bioportal": {"contact": {"email": "carlotorniai@gmail.com", "name": "Carlo Torniai"}, "description": "This ontology models research resources such instruments. protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/).", "homepage": "http://code.google.com/p/eagle-i/", "name": "Eagle-I Research Resource Ontology", "prefix": "ERO", "publication": "http://code.google.com/p/eagle-i/wiki/Publications", "version": "2013-08-02"}, "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"}, "aberowl": {"description": "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.", "download_owl": "http://aber-owl.net/media/ontologies/ERO/15/ero.owl", "homepage": "https://open.med.harvard.edu/wiki/display/eaglei/Ontology", "name": "eagle-i resource ontology", "prefix": "ERO"}, "ontobee": {"library": "Library", "name": "eagle-i resource ontology", "prefix": "ERO"}, "fairsharing": {"abbreviation": "ERO", "description": "A unique feature of the eagle-i software is that the data collection and search tools are completely driven by ontologies. These ontologies are a set of modules that are written in the OWL language and edited and managed using Protégé. Beginning in 2009, the eagle-i Research Resource Ontology (ERO) was developed alongside the eagle-i applications to model various biomedical research resources such as instruments, Core Facilities, protocols, reagents, animal models and biospecimens. It has now been integrated into the VIVO-ISF Ontology, which leverages and expands upon both the eagle-i and VIVO ontologies to create a semantic framework that describes not only scientific resources but research activities and clinical activities.", "id": "1166", "name": "eagle-i Research Resource Ontology", "prefix": "FAIRsharing.nwgynk", "publications": [{"doi": "10.1109/JCDL.2017.7991571", "pubmed_id": 29599662, "title": "Automating data citation: the eagle-i experience."}, {"doi": "10.1093/database/bar067", "pubmed_id": 22434835, "title": "Research resources: curating the new eagle-i discovery system."}], "subjects": ["Life Science", "Biomedical Science"]}, "biocontext": {"is_identifiers": false, "is_obo": true, "prefix": "ERO", "uri_format": "http://purl.obolibrary.org/obo/ERO_$1"}}, "erv": {"mappings": {"biocontext": "ERV", "miriam": "erv", "n2t": "erv"}, "miriam": {"deprecated": false, "description": "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. 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This collection references variant information.", "example": "22-46615880-T-C", "homepage": "http://exac.broadinstitute.org/", "name": "ExAC Variant at Exome Aggregation Consortium", "namespaceEmbeddedInLui": false, "pattern": "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$", "prefix": "exac.variant", "uri_format": "http://exac.broadinstitute.org/variant/$1"}, "biocontext": {"is_identifiers": true, "is_obo": false, "prefix": "EXAC.VARIANT", "uri_format": "http://identifiers.org/exac.variant/$1"}}, "exo": {"pattern": "^\\d{7}$", "example": "0000078", "mappings": {"aberowl": "EXO", "biocontext": "EXO", "biolink": "ExO", "bioportal": "EXO", "fairsharing": "FAIRsharing.6hna78", "obofoundry": "exo", "ols": "exo", "ontobee": "ExO"}, "synonyms": ["ExO"], "publications": [{"pubmed": "22324457", "doi": "10.1021/es2033857", "pmc": "PMC3314380", "title": "Providing the missing link: the exposure science ontology ExO.", "year": 2012}], "obofoundry": {"appears_in": ["ecto", "scdo"], "contact": "annethessen@gmail.com", "contact.github": "diatomsRcool", "contact.label": "Anne Thessen", "contact.orcid": "0000-0002-2908-3327", "deprecated": false, "description": "Vocabularies for describing exposure data to inform understanding of environmental health.", "download.obo": "http://purl.obolibrary.org/obo/exo.obo", "download.owl": "http://purl.obolibrary.org/obo/exo.owl", "homepage": "https://github.com/CTDbase/exposure-ontology", "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"}, "bioportal": {"contact": {"email": "cjmattin@ncsu.edu", "name": "Carolyn Mattingly"}, "description": "Significant progress has been made over the last several years in collecting and improving access to genomic, toxicology, and health data to promote understanding about environmental influences on human health. The resulting information resources, however, lack extensive and reliable exposure data, which are required to translate molecular insights, elucidate environmental contributions to diseases, and assess human health risks at the individual and population levels. We report our development of an Exposure Ontology, ExO, designed to address this information gap by facilitating centralization and integration of exposure data to inform understanding of environmental health. Like other widely used ontologies, ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics", "name": "Exposure Ontology", "prefix": "EXO"}, "ols": {"description": "ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics.", "download": "http://purl.obolibrary.org/obo/exo.owl", "homepage": "https://github.com/CTDbase/exposure-ontology", "name": "Exposure ontology (ExO)", "prefix": "exo", "version": "2022-06-29", "version.iri": "http://purl.obolibrary.org/obo/exo/releases/2022-06-29/exo.owl"}, "aberowl": {"description": "Vocabularies for describing exposure data to inform understanding of environmental health.", "download_owl": "http://aber-owl.net/media/ontologies/EXO/15/exo.owl", "homepage": "https://github.com/CTDbase/exposure-ontology", "name": "Exposure ontology", "prefix": "EXO"}, "biolink": {"is_identifiers": false, "is_obo": true, "prefix": "ExO", "uri_format": "http://purl.obolibrary.org/obo/ExO_$1"}, "ontobee": {"library": "Library", "name": "Exposure ontology", "prefix": "ExO"}, "fairsharing": {"abbreviation": "ExO", "description": "Exposure Ontology (ExO) is designed to facilitate the centralization and integration of exposure data to inform understanding of environmental health. ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics.", "id": "512", "name": "Exposure Ontology", "prefix": "FAIRsharing.6hna78", "publications": [{"doi": "10.1021/es2033857", "pubmed_id": 22324457, "title": "Providing the missing link: the exposure science ontology ExO."}], "subjects": ["Environmental Science", "Epigenetics", "Toxicology"]}, "biocontext": {"is_identifiers": false, "is_obo": true, "prefix": "EXO", "uri_format": "http://purl.obolibrary.org/obo/EXO_$1"}}, "fabio": {"name": "FaBiO, the FRBR-aligned Bibliographic Ontology", "description": "The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references.", "uri_format": "https://sparontologies.github.io/fabio/current/fabio.html#$1", "providers": [{"code": "rdf", "name": "FABIO PURL", "description": "A persistent URL for FaBiO", "homepage": "https://github.com/sparontologies/fabio", "uri_format": "http://purl.org/spar/fabio/$1"}], "homepage": "https://github.com/sparontologies/fabio", "repository": "https://github.com/sparontologies/fabio", "example": "d4e2515", "mappings": {"aberowl": "FaBiO", "biolink": "fabio", "fairsharing": "FAIRsharing.2f3180"}, "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}, "aberowl": {"description": "This file is imported by the vivo-core-public-1.5.owl file. It contains terms relating to documents from the http://purl.org/spar/fabio/ namespace that are included in the VIVO ontology. FaBiO is a FRBR-aligned Bibliographic Ontology that is part of the Semantic Publishing and Referencing (SPAR) suite of ontologies.", "download_owl": "http://aber-owl.net/media/ontologies/FaBiO/1/fabio.owl", "homepage": "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology", "name": "FaBiO (bibliographic)", "prefix": "FaBiO", "version": "1.5"}, "biolink": {"is_identifiers": false, "is_obo": false, "prefix": "fabio", "uri_format": "http://purl.org/spar/fabio/$1"}, "fairsharing": {"abbreviation": "FaBiO", "description": "FaBiO, the FRBR-aligned Bibliographic Ontology, is an ontology for recording and publishing on the Semantic Web descriptions of entities that are published or potentially publishable, and that contain or are referred to by bibliographic references, or entities used to define such bibliographic references. FaBiO entities are primarily textual publications such as books, magazines, newspapers and journals, and items of their content such as poems, conference papers and editorials. However, they also include blogs, web pages, datasets, computer algorithms, experimental protocols, formal specifications and vocabularies, legal records, governmental papers, technical and commercial reports and similar publications, and also anthologies, catalogues and similar collections.", "id": "3628", "name": "FRBR-aligned Bibliographic Ontology", "prefix": "FAIRsharing.2f3180", "publications": [{"doi": "10.1016/j.websem.2012.08.001", "pubmed_id": null, "title": "FaBiO and CiTO: Ontologies for describing bibliographic resources and citations"}], "subjects": ["Subject Agnostic"]}}, "facebase": {"mappings": {"biocontext": "FACEBASE", "fairsharing": "FAIRsharing.mqvqde", "miriam": "facebase", "n2t": "facebase", "re3data": "r3d100013263"}, "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"}, "fairsharing": {"abbreviation": "FaceBase", "description": "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.", "id": "2254", "name": "FaceBase", "prefix": "FAIRsharing.mqvqde", "subjects": ["Anatomy", "Medicine", "Epigenetics", "Genetics", "Developmental Biology"]}, "biocontext": {"is_identifiers": true, "is_obo": false, "prefix": "FACEBASE", "uri_format": "http://identifiers.org/facebase/$1"}, "re3data": {"description": "FaceBase is a collaborative NIDCR-funded project that houses comprehensive data in support of advancing research into craniofacial development and malformation. It serves as a community resource by curating large datasets of a variety of types from the craniofacial research community and sharing them via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this project is to facilitate cooperation and collaboration between the central coordinating center (ie, the Hub) and the craniofacial research community.", "homepage": "https://www.facebase.org", "name": "FaceBase", "prefix": "r3d100013263", "xrefs": {"fairsharing": "FAIRsharing.mqvqde", "nlx": "151372", "scr": "005998"}}}, "fairsharing": {"mappings": {"biocontext": "FAIRSHARING", "fairsharing": "FAIRsharing.2abjs5", "miriam": "fairsharing", "n2t": "fairsharing", "re3data": "r3d100010142"}, "miriam": {"deprecated": false, "description": "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies.", "homepage": "https://fairsharing.org/", "id": "00000364", "name": "FAIRsharing", "namespaceEmbeddedInLui": false, "pattern": "^bsg-[dscp]?\\d{6}$", "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"}, "fairsharing": {"abbreviation": "FAIRsharing", "description": "FAIRsharing is a FAIR-supporting resource that provides an informative and educational registry on data standards, databases, repositories and policy, alongside search and visualization tools and services that interoperate with other FAIR-enabling resources. FAIRsharing guides consumers to discover, select and use standards, databases, repositories and policy with confidence, and producers to make their resources more discoverable, more widely adopted and cited. Each record in FAIRsharing is curated in collaboration with the maintainers of the resource themselves, ensuring that the metadata in the FAIRsharing registry is accurate and timely. Every record is manually reviewed at least once a year. Records can be collated into collections, based on a project, society or organisation, or Recommendations, where they are collated around a policy, such as a journal or funder data policy.", "id": "2521", "name": "FAIRsharing", "prefix": "FAIRsharing.2abjs5", "subjects": ["Environmental Science", "Humanities", "Natural Science", "Earth Science", "Agriculture", "Life Science", "Biomedical Science"]}, "biocontext": {"is_identifiers": true, "is_obo": false, "prefix": "FAIRSHARING", "uri_format": "http://identifiers.org/fairsharing/$1"}, "re3data": {"description": "FAIRsharing is a web-based, searchable portal of three interlinked registries, containing both in-house and crowdsourced manually curated descriptions of standards, databases and data policies, combined with an integrated view across all three types of resource. By registering your resource on FAIRsharing, you not only gain credit for your work, but you increase its visibility outside of your direct domain, so reducing the potential for unnecessary reinvention and proliferation of standards and databases.", "homepage": "https://fairsharing.org/", "name": "FAIRsharing", "prefix": "r3d100010142", "synonyms": ["formerly: biosharing"], "xrefs": {"fairsharing": "FAIRsharing.2abjs5", "miriam": "00100463", "nlx": "143602", "omics": "17902", "scr": "004177"}}}, "faldo": {"name": "Feature Annotation Location Description Ontology ", "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", "uri_format": "http://biohackathon.org/resource/faldo#$1", "homepage": "http://biohackathon.org/resource/faldo", "example": "ForwardStrandPosition", "mappings": {"aberowl": "FALDO", "agroportal": "FALDO", "biocontext": "faldo", "bioportal": "FALDO", "fairsharing": "FAIRsharing.haxp7g"}, "publications": [{"pubmed": "27296299", "doi": "10.1186/s13326-016-0067-z", "pmc": "PMC4907002", "title": "FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.", "year": 2016}], "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}, "bioportal": {"contact": {"email": "faldo@googlegroups.com", "name": "FALDO group"}, "description": "FALDO is the Feature Annotation Location Description Ontology. 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. The aim of this ontology is to describe the position of a sequence region or a feature. It does not aim to describe features or regions itself, but instead depends on resources such as the Sequence Ontology or the UniProt core ontolgy.", "homepage": "http://biohackathon.org/resource/faldo", "name": "Feature Annotation Location Description Ontology", "prefix": "FALDO", "publication": "https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0067-z", "version": "Created at the Biohackathon 2012 and 2013"}, "agroportal": {"contact": {"email": "jerven.bolleman@isb-sib.ch", "name": "Jerven Bolleman"}, "description": "FALDO is the Feature Annotation Location Description Ontology. 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. The aim of this ontology is to describe the position of a sequence region or a feature. It does not aim to describe features or regions itself, but instead depends on resources such as the Sequence Ontology or the UniProt core ontolgy.", "example_uri": "http://biohackathon.org/resource/faldo#CollectionOfRegions", "homepage": "https://github.com/JervenBolleman/FALDO", "license": "CC0 1.0", "name": "Feature Annotation Location Description Ontology", "prefix": "FALDO", "publication": "doi.org/10.1186/s13326-016-0067-z", "version": "Created at the Biohackathon 2012 and 2013"}, "aberowl": {"description": "FALDO is the Feature Annotation Location Description Ontology. 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. The aim of this ontology is to describe the position of a sequence region or a feature. It does not aim to describe features or regions itself, but instead depends on resources such as the Sequence Ontology or the UniProt core ontolgy.", "download_owl": "http://aber-owl.net/media/ontologies/FALDO/1/faldo.owl", "homepage": "http://biohackathon.org/resource/faldo", "name": "Feature Annotation Location Description Ontology ", "prefix": "FALDO", "version": "Created at the Biohackathon 2012 and 2013"}, "fairsharing": {"abbreviation": "FALDO", "description": "The Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences for data resources represented in RDF and/or OWL. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned “omics” areas. Using the same data format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types.", "id": "478", "name": "Feature Annotation Location Description Ontology", "prefix": "FAIRsharing.haxp7g", "publications": [{"doi": "10.1186/s13326-016-0067-z", "pubmed_id": 27296299, "title": "FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation."}], "subjects": ["Genetics"]}, "biocontext": {"is_identifiers": false, "is_obo": false, "prefix": "faldo", "uri_format": "http://biohackathon.org/resource/faldo#$1"}}, "fao": {"pattern": "^\\d{7}$", "example": "0000001", "mappings": {"aberowl": "FAO", "biocontext": "FAO", "bioportal": "FAO", "fairsharing": "FAIRsharing.xs6t67", "obofoundry": "fao", "ols": "fao", "ontobee": "FAO", "prefixcommons": "fao"}, "prefixcommons": {"bioportal": "1019", "description": "The project aims to develop a controlled vocabulary to describe the 'anatomy' of fungi and other microbes, called the fungal anatomy ontology (FAO).", "example": "FAO_0000001", "homepage": "http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/", "keywords": ["obo", "anatomy", "fungi"], "name": "Fungal Anatomy Ontology", "pattern": "^FAO_\\d+$", "prefix": "fao"}, "obofoundry": {"contact": "vw253@cam.ac.uk", "contact.github": "ValWood", "contact.label": "Val Wood", "contact.orcid": "0000-0001-6330-7526", "deprecated": false, "description": "A structured controlled vocabulary for the anatomy of fungi.", "download.obo": "http://purl.obolibrary.org/obo/fao.obo", "download.owl": "http://purl.obolibrary.org/obo/fao.owl", "homepage": "https://github.com/obophenotype/fungal-anatomy-ontology/", "license": "CC0 1.0", "license.url": "http://creativecommons.org/publicdomain/zero/1.0/", "name": "Fungal gross anatomy", "preferredPrefix": "FAO", "prefix": "fao", "repository": "https://github.com/obophenotype/fungal-anatomy-ontology"}, "bioportal": {"contact": {"email": "dinglis@stanford.edu", "name": "Diane Inglis"}, "description": "A structured controlled vocabulary for the anatomy of fungi.", "homepage": "https://github.com/obophenotype/fungal-anatomy-ontology", "name": "Fungal Gross Anatomy Ontology", "prefix": "FAO"}, "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"}, "aberowl": {"description": "A structured controlled vocabulary for the anatomy of fungi.", "download_owl": "http://aber-owl.net/media/ontologies/FAO/28/fao.owl", "homepage": "https://github.com/obophenotype/fungal-anatomy-ontology/", "name": "Fungal gross anatomy", "prefix": "FAO"}, "ontobee": {"library": "Library", "name": "Fungal gross anatomy", "prefix": "FAO"}, "fairsharing": {"abbreviation": "FAO", "description": "A structured controlled vocabulary for the anatomy of fungi.", "id": "168", "name": "Fungal Gross Anatomy Ontology", "prefix": "FAIRsharing.xs6t67", "publications": [], "subjects": ["Anatomy", "Life Science", "Microbiology"]}, "biocontext": {"is_identifiers": false, "is_obo": true, "prefix": "FAO", "uri_format": "http://purl.obolibrary.org/obo/FAO_$1"}}, "fbbi": {"pattern": "^\\d+$", "example": "00000268", "mappings": {"aberowl": "FBbi", "biocontext": "FBbi", "bioportal": "FBbi", "fairsharing": "FAIRsharing.ny3z9j", "obofoundry": "fbbi", "ols": "fbbi", "ontobee": "FBBI", "prefixcommons": "fbbi"}, "synonyms": ["FBbi"], "prefixcommons": {"bioportal": "1023", "description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.", "example": "FBbi_00000222", "homepage": "http://cellimagelibrary.org/", "keywords": ["obo", "experiment", "imaging"], "name": "Biological imaging methods", "pattern": "^FBbi_\\d+$", "prefix": "fbbi", "synonyms": ["fbbi.root"]}, "obofoundry": {"contact": "wawong@gmail.com", "contact.github": "wawong", "contact.label": "Willy Wong", "contact.orcid": "0000-0002-8841-5870", "deprecated": false, "description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.", "download.owl": "http://purl.obolibrary.org/obo/fbbi.owl", "homepage": "http://cellimagelibrary.org/", "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"}, "bioportal": {"contact": {"email": "chris@bio.umass.edu", "name": "Chris Woodcock"}, "description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.", "homepage": "http://cellimagelibrary.org/", "name": "Biological Imaging Methods Ontology", "prefix": "FBbi"}, "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"}, "aberowl": {"description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.", "download_obo": "http://aber-owl.net/media/ontologies/FBbi/14/fbbi.obo", "homepage": "http://cellimagelibrary.org/", "name": "Biological Imaging Methods Ontology", "prefix": "FBbi", "version": "unknown"}, "ontobee": {"library": "Library", "name": "Biological Imaging Methods Ontology", "prefix": "FBBI"}, "fairsharing": {"abbreviation": "FBbi", "description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.", "id": "33", "name": "Biological Imaging methods Ontology", "prefix": "FAIRsharing.ny3z9j", "publications": [], "subjects": ["Life Science", "Biomedical Science"]}, "biocontext": {"is_identifiers": false, "is_obo": true, "prefix": "FBbi", "uri_format": "http://purl.obolibrary.org/obo/FBbi_$1"}}, "fbbt": {"pattern": "^\\d{8}$", "uri_format": "https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:$1", "example": "00007294", "part_of": "flybase", "mappings": {"aberowl": "FBBT", "biocontext": "FBbt", "bioportal": "FB-BT", "fairsharing": "FAIRsharing.y2qkst", "go": "FBbt", "obofoundry": "fbbt", "ols": "fbbt", "ontobee": "FBBT", "prefixcommons": "fbbt"}, "synonyms": ["FBbt", "FBbt_root"], "publications": [{"pubmed": "16381917", "doi": "10.1093/nar/gkj068", "pmc": "PMC1347431", "title": "FlyBase: anatomical data, images and queries.", 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