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ontologies.jsonld
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ontologies.jsonld
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{
"@context": "http://obofoundry.github.io/registry/context.jsonld",
"ontologies": [
{
"contact": {
"email": "David Blackburn",
"label": "[email protected]"
},
"homepage": "http://github.com/seger/aao",
"id": "aao",
"is_obsolete": true,
"layout": "ontology_detail",
"replaced_by": "uberon",
"taxon": {
"id": "NCBITaxon:8292",
"label": "Amphibia"
},
"title": "Amphibian gross anatomy"
},
{
"contact": {
"email": "Animal Diversity Web technical staff",
"label": "[email protected]"
},
"homepage": "http://www.animaldiversity.org",
"id": "adw",
"is_obsolete": true,
"layout": "ontology_detail",
"title": "Animal natural history and life history"
},
{
"build": {
"checkout": "git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git",
"method": "vcs",
"path": "src/ontology",
"system": "git"
},
"contact": {
"email": "[email protected]",
"label": "Jonathan Bard"
},
"description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology",
"domain": "anatomy",
"homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology/",
"id": "aeo",
"layout": "ontology_detail",
"ontology_purl": "http://purl.obolibrary.org/obo/aeo.owl",
"products": [
{
"id": "aeo.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/aeo.owl"
}
],
"title": "Anatomical Entity Ontology"
},
{
"build": {
"method": "owl2obo",
"source_url": "http://purl.obolibrary.org/obo/aero.owl"
},
"contact": {
"email": "[email protected]",
"label": "Melanie Courtot"
},
"description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events",
"domain": "health",
"homepage": "http://purl.obolibrary.org/obo/aero",
"id": "aero",
"layout": "ontology_detail",
"ontology_purl": "http://purl.obolibrary.org/obo/aero.owl",
"products": [
{
"id": "aero.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/aero.owl"
}
],
"title": "Adverse Event Reporting Ontology"
},
{
"build": {
"method": "obo2owl",
"source_url": "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/ascomycete_phenotype.obo"
},
"contact": {
"email": "[email protected]",
"label": "Maria Costanza"
},
"description": "A structured controlled vocabulary for the phenotypes of Ascomycete fungi",
"domain": "phenotype",
"homepage": "http://www.yeastgenome.org/",
"id": "apo",
"layout": "ontology_detail",
"ontology_purl": "http://purl.obolibrary.org/obo/apo.owl",
"products": [
{
"id": "apo.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/apo.owl"
}
],
"taxon": {
"id": "NCBITaxon:4890",
"label": "Ascomycota"
},
"title": "Ascomycete phenotype ontology"
},
{
"contact": {
"email": "David Blackburn",
"label": "[email protected]"
},
"homepage": "http://www.amphibanat.org",
"id": "ato",
"is_obsolete": true,
"layout": "ontology_detail",
"taxon": {
"id": "NCBITaxon:8292",
"label": "Amphibia"
},
"title": "Amphibian taxonomy"
},
{
"contact": {
"email": "[email protected]",
"label": "Jie Zheng"
},
"description": "An application ontology built for beta cell genomics studies.",
"homepage": "https://github.com/obi-bcgo/bcgo",
"id": "bcgo",
"in_foundry": false,
"layout": "ontology_detail",
"license": {
"label": "CC-BY",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "http://creativecommons.org/licenses/by/3.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/bcgo.owl",
"products": [
{
"id": "bcgo.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/bcgo.owl"
}
],
"title": "Beta Cell Genomics Ontology",
"tracker": "https://github.com/obi-bcgo/bcgo/issues"
},
{
"contact": {
"email": "[email protected]",
"label": "Ramona Walls"
},
"description": "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.",
"homepage": "https://github.com/tucotuco/bco",
"id": "bco",
"in_foundry": false,
"layout": "ontology_detail",
"ontology_purl": "http://purl.obolibrary.org/obo/bco.owl",
"products": [
{
"id": "bco.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/bco.owl"
}
],
"title": "Biological Collections Ontology",
"tracker": "https://github.com/tucotuco/bco/issues"
},
{
"browsers": [
{
"label": "BioPortal",
"title": "BioPortal Browser",
"url": "http://bioportal.bioontology.org/ontologies/BFO?p=classes"
}
],
"contact": {
"email": "[email protected]",
"label": "Barry Smith"
},
"depicted_by": "https://avatars2.githubusercontent.com/u/12972134?v=3&s=200",
"description": "The upper level ontology upon which OBO Foundry ontologies are built.",
"domain": "upper",
"homepage": "http://ifomis.org/bfo/",
"id": "bfo",
"layout": "ontology_detail",
"license": {
"label": "CC-BY",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "http://creativecommons.org/licenses/by/3.0/"
},
"mailing_list": "https://groups.google.com/forum/#!forum/bfo-discuss",
"ontology_purl": "http://purl.obolibrary.org/obo/bfo.owl",
"products": [
{
"id": "bfo.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/bfo.owl"
},
{
"id": "bfo.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/bfo.obo"
}
],
"title": "Basic Formal Ontology",
"tracker": "https://github.com/BFO-ontology/BFO/issues"
},
{
"build": {
"method": "obo2owl",
"source_url": "http://4dx.embl.de/4DXpress_4d/edocs/bilateria_mrca.obo"
},
"contact": {
"email": "[email protected]",
"label": "Thorsten Heinrich"
},
"domain": "anatomy",
"homepage": "http://4dx.embl.de/4DXpress",
"id": "bila",
"is_obsolete": true,
"layout": "ontology_detail",
"products": [
{
"id": "bila.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/bila.owl"
}
],
"replaced_by": "uberon",
"taxon": {
"id": "NCBITaxon:33213",
"label": "Bilateria"
},
"title": "Bilateria anatomy"
},
{
"contact": {
"email": "Vivian Lee",
"label": "[email protected]"
},
"homepage": "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html",
"id": "bootstrep",
"is_obsolete": true,
"layout": "ontology_detail",
"replaced_by": "molecular_function",
"title": "Gene Regulation Ontology"
},
{
"build": {
"checkout": "git clone https://github.com/obophenotype/biological-spatial-ontology.git",
"infallible": 1,
"method": "vcs",
"path": "src/ontology",
"system": "git"
},
"contact": {
"email": "[email protected]",
"label": "Chris Mungall"
},
"description": "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces",
"domain": "anatomy",
"homepage": "https://github.com/obophenotype/biological-spatial-ontology",
"id": "bspo",
"layout": "ontology_detail",
"license": {
"label": "CC-BY",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "http://creativecommons.org/licenses/by/3.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/bspo.owl",
"products": [
{
"id": "bspo.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/bspo.owl"
}
],
"publications": [
{
"id": "http://www.ncbi.nlm.nih.gov/pubmed/25140222",
"title": "Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology."
}
],
"title": "Biological Spatial Ontology",
"tracker": "https://github.com/obophenotype/biological-spatial-ontology/issues"
},
{
"build": {
"method": "obo2owl",
"source_url": "http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO"
},
"contact": {
"email": "[email protected]",
"label": "Antje Chang"
},
"description": "A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.",
"domain": "anatomy",
"homepage": "http://www.brenda-enzymes.info",
"id": "bto",
"layout": "ontology_detail",
"license": {
"alert": "Restricted",
"label": "BRENDA license",
"url": "http://www.brenda-enzymes.org/copy.php"
},
"ontology_purl": "http://purl.obolibrary.org/obo/bto.owl",
"page": "https://en.wikipedia.org/wiki/BRENDA_tissue_ontology",
"products": [
{
"id": "bto.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/bto.owl"
}
],
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/21030441",
"title": "The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources"
}
],
"title": "BRENDA tissue / enzyme source"
},
{
"build": {
"method": "obo2owl",
"notes": "moving to owl soon",
"source_url": "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro.obo"
},
"contact": {
"email": "[email protected]",
"label": "Melissa Haendel"
},
"description": "An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species",
"domain": "anatomy",
"homepage": "https://github.com/obophenotype/caro/",
"id": "caro",
"layout": "ontology_detail",
"ontology_purl": "http://purl.obolibrary.org/obo/caro.owl",
"products": [
{
"id": "caro.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/caro.owl"
}
],
"title": "Common Anatomy Reference Ontology",
"tracker": "https://github.com/obophenotype/caro/issues"
},
{
"build": {
"method": "owl2obo",
"source_url": "http://purl.obolibrary.org/obo/cdao.owl"
},
"contact": {
"email": "[email protected]",
"label": "Jim Balhoff"
},
"description": "a formalization of concepts and relations relevant to evolutionary comparative analysis",
"homepage": "http://sourceforge.net/apps/mediawiki/cdao/index.php?title=Main_Page",
"id": "cdao",
"layout": "ontology_detail",
"ontology_purl": "http://purl.obolibrary.org/obo/cdao.owl",
"products": [
{
"id": "cdao.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/cdao.owl"
}
],
"title": "Comparative Data Analysis Ontology"
},
{
"build": {
"checkout": "git clone https://github.com/obophenotype/cephalopod-ontology.git",
"method": "vcs",
"path": "src/ontology",
"system": "git"
},
"contact": {
"email": "[email protected]",
"label": "Chris Mungall"
},
"description": "An anatomical and developmental ontology for cephalopods",
"domain": "anatomy",
"homepage": "https://github.com/obophenotype/cephalopod-ontology",
"id": "ceph",
"layout": "ontology_detail",
"license": {
"label": "CC-BY",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "http://creativecommons.org/licenses/by/3.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/ceph.owl",
"products": [
{
"id": "ceph.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/ceph.owl"
}
],
"taxon": {
"id": "NCBITaxon:6605",
"label": "Cephalopod"
},
"title": "Cephalopod Ontology",
"tracker": "https://github.com/obophenotype/cephalopod-ontology/issues"
},
{
"alternatePrefix": "ChEBI",
"browsers": [
{
"label": "CHEBI",
"title": "EBI CHEBI Browser",
"url": "http://www.ebi.ac.uk/chebi/chebiOntology.do?treeView=true&chebiId=CHEBI:24431#graphView"
}
],
"build": {
"infallible": 1,
"method": "archive",
"path": "archive/main",
"source_url": "http://build.berkeleybop.org/job/build-chebi/lastSuccessfulBuild/artifact/*zip*/archive.zip"
},
"contact": {
"email": "[email protected]",
"label": "Janna Hastings"
},
"description": "A structured classification of chemical compounds of biological relevance.",
"domain": "biochemistry",
"homepage": "http://www.ebi.ac.uk/chebi",
"id": "chebi",
"in_foundry_order": 1,
"layout": "ontology_detail",
"ontology_purl": "http://purl.obolibrary.org/obo/chebi.owl",
"page": "http://www.ebi.ac.uk/chebi/init.do?toolBarForward=userManual",
"products": [
{
"id": "chebi.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/chebi.owl"
},
{
"id": "chebi.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/chebi.obo"
}
],
"title": "Chemical entities of biological interest",
"tracker": "https://sourceforge.net/p/chebi/curator-requests/",
"twitter": "chebit"
},
{
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