obofoundry.obofoundry.registry.json Maven / Gradle / Ivy
{
"@context": "http://obofoundry.github.io/registry/context.jsonld",
"ontologies": [
{
"activity_status": "active",
"browsers": [
{
"label": "BioPortal",
"title": "BioPortal Browser",
"url": "http://bioportal.bioontology.org/ontologies/BFO?p=classes"
}
],
"contact": {
"email": "[email protected]",
"github": "phismith",
"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",
"in_foundry_order": 1,
"layout": "ontology_detail",
"license": {
"label": "CC-BY",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "http://creativecommons.org/licenses/by/4.0/"
},
"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",
"usages": [
{
"description": "BFO is imported by multiple OBO ontologies to standardize upper level structure",
"type": "owl_import",
"user": "http://obofoundry.org"
}
]
},
{
"activity_status": "active",
"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": "obo2owl",
"source_url": "ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo"
},
"contact": {
"email": "[email protected]",
"github": "G-Owen",
"label": "Gareth Owen"
},
"description": "A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds.",
"domain": "biochemistry",
"homepage": "http://www.ebi.ac.uk/chebi",
"id": "chebi",
"in_foundry_order": 1,
"layout": "ontology_detail",
"license": {
"label": "CC-BY 4.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/4.0/"
},
"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"
},
{
"id": "chebi.owl.gz",
"ontology_purl": "http://purl.obolibrary.org/obo/chebi.owl.gz",
"title": "chebi, compressed owl"
},
{
"id": "chebi/chebi_lite.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/chebi/chebi_lite.obo",
"title": "chebi_lite, no syns or xrefs"
},
{
"id": "chebi/chebi_core.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/chebi/chebi_core.obo",
"title": "chebi_core, no xrefs"
}
],
"title": "Chemical Entities of Biological Interest",
"tracker": "https://github.com/ebi-chebi/ChEBI/issues",
"twitter": "chebit"
},
{
"DO wiki": "http://diseaseontology.sourceforge.net/",
"activity_status": "active",
"browsers": [
{
"label": "DO",
"title": "DO Browser",
"url": "http://www.disease-ontology.org/"
}
],
"build": {
"infallible": 1,
"method": "obo2owl",
"source_url": "https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid.obo"
},
"contact": {
"email": "[email protected]",
"github": "lschriml",
"label": "Lynn Schriml"
},
"description": "An ontology for describing the classification of human diseases organized by etiology.",
"domain": "disease",
"facebook": "https://www.facebook.com/diseaseontology",
"homepage": "http://www.disease-ontology.org",
"id": "doid",
"in_foundry_order": 1,
"layout": "ontology_detail",
"license": {
"label": "CC0 1.0 Universal",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png",
"url": "https://creativecommons.org/publicdomain/zero/1.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/doid.owl",
"products": [
{
"id": "doid.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/doid.owl",
"title": "Disease Ontology, OWL format. This file contains DO's is_a asserted hierarchy plus equivalent axioms to other OBO Foundry ontologies."
},
{
"id": "doid.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/doid.obo",
"title": "Disease Ontology, OBO format. This file omits the equivalent axioms."
}
],
"publications": [
{
"id": "http://www.ncbi.nlm.nih.gov/pubmed/?term=25348409",
"title": "Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data"
}
],
"taxon": {
"id": "NCBITaxon:9606",
"label": "Homo sapiens"
},
"title": "Human Disease Ontology",
"tracker": "https://github.com/DiseaseOntology/HumanDiseaseOntology/issues",
"twitter": "diseaseontology",
"usages": [
{
"description": "MGI disease model annotations use DO",
"examples": [
{
"description": "Human genes and mouse homology associated with nail diseases",
"url": "http://www.informatics.jax.org/disease/DOID:4123"
}
],
"user": "http://www.informatics.jax.org/disease"
}
]
},
{
"activity_status": "active",
"browsers": [
{
"label": "AmiGO",
"title": "Gene Ontology AmiGO 2 Browser",
"url": "http://amigo.geneontology.org/amigo/term/GO:0008150#display-lineage-tab"
}
],
"contact": {
"email": "[email protected]",
"github": "ukemi",
"label": "David Hill"
},
"dependencies": [
{
"id": "uberon",
"subset": "go/extensions/uberon_import.owl"
},
{
"id": "cl",
"subset": "go/extensions/cl_import.owl"
},
{
"id": "ncbitaxon",
"subset": "go/extensions/ncbitaxon_import.owl"
},
{
"id": "ro",
"subset": "go/extensions/ro_import.owl"
},
{
"connects": [
{
"id": "nifstd"
},
{
"id": "go"
}
],
"description": "Bridging axioms between nifstd and go",
"id": "go/extensions/go-bridge-to-nifstd.owl",
"publications": [
{
"id": "http://www.ncbi.nlm.nih.gov/pubmed/24093723",
"title": "The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments."
}
],
"title": "GO bridge to NIFSTD",
"type": "BridgeOntology"
}
],
"depicted_by": "http://geneontology.org/sites/default/files/go-logo-icon.mini__0.png",
"description": "An ontology for describing the function of genes and gene products",
"domain": "biology",
"facebook": "https://www.facebook.com/Gene-Ontology-305908656519/",
"homepage": "http://geneontology.org/",
"id": "go",
"in_foundry_order": 1,
"integration_server": "http://build.berkeleybop.org/view/GO",
"label": "GO",
"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/go.owl",
"products": [
{
"description": "The main ontology in OWL. This is self contained and does not have connections to other OBO ontologies",
"id": "go.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/go.owl",
"page": "http://geneontology.org/page/download-ontology",
"title": "GO (OWL edition)"
},
{
"description": "Equivalent to go.owl, in obo format",
"id": "go.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/go.obo",
"page": "http://geneontology.org/page/download-ontology",
"title": "GO (OBO Format edition)"
},
{
"description": "Equivalent to go.owl, in obograph json format",
"id": "go.json",
"ontology_purl": "http://purl.obolibrary.org/obo/go.json",
"page": "https://github.com/geneontology/obographs/",
"title": "GO (JSON edition)"
},
{
"description": "The main ontology plus axioms connecting to select external ontologies",
"id": "go/extensions/go-plus.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/go/extensions/go-plus.owl",
"page": "http://geneontology.org/page/download-ontology",
"title": "GO-Plus"
},
{
"description": "As go-plus.owl, in obographs json format",
"id": "go/extensions/go-plus.json",
"ontology_purl": "http://purl.obolibrary.org/obo/go/extensions/go-plus.json",
"page": "https://github.com/geneontology/obographs/",
"title": "GO-Plus"
},
{
"description": "The main ontology plus axioms connecting to select external ontologies",
"id": "go/go-basic.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/go/go-basic.obo",
"page": "http://geneontology.org/page/download-ontology",
"title": "GO-Basic, Filtered, for use with legacy tools"
},
{
"description": "As go-basic.obo, in json format",
"id": "go/go-basic.json",
"ontology_purl": "http://purl.obolibrary.org/obo/go/go-basic.json",
"page": "http://geneontology.org/page/download-ontology",
"title": "GO-Basic, Filtered, for use with legacy tools (JSON)"
},
{
"description": "Classes added to ncbitaxon for groupings such as prokaryotes",
"id": "go/extensions/go-taxon-groupings.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/go/extensions/go-taxon-groupings.owl",
"page": "http://geneontology.org/page/download-ontology",
"title": "GO Taxon Groupings"
},
{
"description": "Equivalent to go.owl, but released daily. Note the snapshot release is not archived.",
"id": "snapshot/go.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/snapshot/go.owl",
"page": "http://geneontology.org/page/download-ontology",
"title": "GO (OWL edition), daily snapshot release"
},
{
"description": "Equivalent to go.owl, but released daily. Note the snapshot release is not archived.",
"id": "snapshot/go.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/snapshot/go.obo",
"page": "http://geneontology.org/page/download-ontology",
"title": "GO (OBO Format edition), daily snapshot release"
}
],
"taxon": {
"id": "NCBITaxon:1",
"label": "All life"
},
"termgenie": "http://go.termgenie.org",
"title": "Gene Ontology",
"tracker": "https://github.com/geneontology/go-ontology/issues/",
"twitter": "news4go",
"usages": [
{
"description": "The GO ontology is used by the GO consortium for functional annotation of genes",
"examples": [
{
"description": "annotations to transmembrane transport",
"url": "http://amigo.geneontology.org/amigo/term/GO:0055085"
}
],
"type": "annotation",
"user": "http://geneontology.org"
}
]
},
{
"activity_status": "active",
"browsers": [
{
"label": "BioPortal",
"title": "BioPortal Browser",
"url": "http://bioportal.bioontology.org/ontologies/OBI?p=classes"
}
],
"build": {
"source_url": "http://purl.obofoundry.org/obo/obi/repository/trunk/src/ontology/branches/"
},
"contact": {
"email": "[email protected]",
"label": "Bjoern Peters"
},
"depicted_by": "https://svn.code.sf.net/p/obi/code/trunk/web/htdocs/images/obi-lotext.png",
"description": "An integrated ontology for the description of life-science and clinical investigations",
"domain": "experiments",
"homepage": "http://obi-ontology.org",
"id": "obi",
"in_foundry_order": 1,
"integration_server": "http://build.berkeleybop.org/job/build-obi/",
"layout": "ontology_detail",
"license": {
"label": "CC-BY 3.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/3.0/"
},
"mailing_list": "http://groups.google.com/group/obi-users",
"ontology_purl": "http://purl.obolibrary.org/obo/obi.owl",
"products": [
{
"id": "obi.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/obi.owl",
"title": "OBI"
},
{
"id": "obi/obi_core.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/obi/obi_core.owl",
"title": "OBI Core"
}
],
"title": "Ontology for Biomedical Investigations",
"tracker": "http://purl.obolibrary.org/obo/obi/tracker"
},
{
"activity_status": "active",
"browsers": [
{
"label": "BioPortal",
"title": "BioPortal Ontology Browser",
"url": "https://bioportal.bioontology.org/ontologies/PATO"
}
],
"build": {
"infallible": 1,
"method": "obo2owl",
"source_url": "https://raw.githubusercontent.com/pato-ontology/pato/master/pato.obo"
},
"contact": {
"email": "[email protected]",
"github": "gkoutos",
"label": "George Gkoutos"
},
"description": "An ontology of phenotypic qualities (properties, attributes or characteristics)",
"domain": "phenotype",
"homepage": "https://github.com/pato-ontology/pato/",
"id": "pato",
"in_foundry_order": 1,
"jobs": [
{
"id": "https://travis-ci.org/pato-ontology/pato",
"type": "travis-ci"
}
],
"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/pato.owl",
"products": [
{
"id": "pato.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/pato.owl"
},
{
"id": "pato.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/pato.obo"
},
{
"id": "pato.json",
"ontology_purl": "http://purl.obolibrary.org/obo/pato.json"
},
{
"description": "Includes axioms linking to other ontologies, but no imports of those ontologies",
"id": "pato-base.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/pato-base.owl"
}
],
"repository": "https://github.com/pato-ontology/pato/",
"title": "Phenotype And Trait Ontology",
"tracker": "https://github.com/pato-ontology/pato/issues"
},
{
"activity_status": "active",
"browsers": [
{
"label": "Planteome",
"title": "Planteome browser",
"url": "http://browser.planteome.org/amigo"
}
],
"build": {
"checkout": "git clone https://github.com/Planteome/plant-ontology.git",
"infallible": 1,
"method": "vcs",
"system": "git"
},
"contact": {
"email": "[email protected]",
"github": "jaiswalp",
"label": "Pankaj Jaiswal"
},
"description": "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.",
"domain": "anatomy and development",
"homepage": "http://browser.planteome.org/amigo",
"id": "po",
"in_foundry_order": 1,
"jobs": [
{
"id": "https://travis-ci.org/Planteome/plant-ontology",
"type": "travis-ci"
}
],
"layout": "ontology_detail",
"license": {
"label": "CC-BY 4.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/4.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/po.owl",
"page": "https://github.com/Planteome/plant-ontology",
"products": [
{
"id": "po.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/po.owl"
},
{
"id": "po.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/po.obo"
}
],
"publications": [
{
"id": "http://www.ncbi.nlm.nih.gov/pubmed/23220694",
"title": "The plant ontology as a tool for comparative plant anatomy and genomic analyses."
},
{
"id": "https://doi.org/10.1093/nar/gkx1152",
"title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics."
}
],
"taxon": {
"id": "NCBITaxon:33090",
"label": "Viridiplantae"
},
"title": "Plant Ontology",
"tracker": "https://github.com/Planteome/plant-ontology/issues",
"twitter": "planteome",
"usages": [
{
"description": "Planteome uses PO to describe location of tissue expression for genes in viridiplantae",
"examples": [
{
"description": "Genes and proteins annotate to leaf",
"url": "http://browser.planteome.org/amigo/term/PO:0025034"
}
],
"user": "http://planteome.org/"
},
{
"description": "Maize CELL genomics DB uses PO to annotate images",
"examples": [
{
"url": "http://maize.jcvi.org/cellgenomics/geneDB_list.php?filter=3"
}
],
"user": "http://maize.jcvi.org/"
},
{
"description": "MaizeGDB uses PO for annotation of genes",
"examples": [
{
"url": "http://maizegdb.org/gene_center/gene/GRMZM5G863962"
}
],
"user": "http://maizegdb.org/"
},
{
"description": "Gramene uses PO for the annotation of plant genes",
"examples": [
{
"description": "Gramene annotations to leaf from Arabidopsis",
"url": "http://archive.gramene.org/db/ontology/search?id=PO:0025034"
}
],
"user": "http://gramene.org/"
}
]
},
{
"activity_status": "active",
"browsers": [
{
"label": "BioPortal",
"title": "BioPortal Browser",
"url": "http://bioportal.bioontology.org/ontologies/PR?p=classes&conceptid=http://purl.obolibrary.org/obo/PR_000000001"
},
{
"label": "PRO",
"title": "PRO Home",
"url": "http://proconsortium.org"
}
],
"build": {
"infallible": 0,
"method": "obo2owl",
"oort_args": "--no-reasoner",
"source_url": "https://proconsortium.org/download/current/pro_nonreasoned.obo"
},
"contact": {
"email": "[email protected]",
"label": "Darren Natale"
},
"depicted_by": "https://raw.githubusercontent.com/PROconsortium/logo/master/PROlogo_small.png",
"description": "An ontological representation of protein-related entities",
"development": {
"id_policy": "https://pir17.georgetown.edu/confluence/display/PROWIKI/PRO+PURLs"
},
"documentation": "https://proconsortium.org/download/current/pro_readme.txt",
"domain": "proteins",
"homepage": "http://proconsortium.org",
"id": "pr",
"in_foundry_order": 1,
"layout": "ontology_detail",
"license": {
"label": "CC-BY",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "http://creativecommons.org/licenses/by/4.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/pr.owl",
"products": [
{
"description": "PRO after reasoning has been applied, OWL format.",
"id": "pr.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/pr.owl",
"title": "pro_reasoned.owl"
},
{
"description": "PRO after reasoning has been applied, OBO format.",
"id": "pr.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/pr.obo",
"title": "pro_reasoned.obo"
}
],
"publications": [
{
"id": "https://proconsortium.org/pro_dsmnt.shtml#publication",
"title": "Publications & Dissemination"
}
],
"title": "PRotein Ontology (PRO)",
"tracker": "http://purl.obolibrary.org/obo/pr/tracker"
},
{
"activity_status": "active",
"build": {
"infallible": 0,
"method": "obo2owl",
"source_url": "https://raw.githubusercontent.com/xenopus-anatomy/xao/master/xenopus_anatomy.obo"
},
"contact": {
"email": "[email protected]",
"github": "seger",
"label": "Erik Segerdell"
},
"description": "Anatomy and development of the African clawed frog (Xenopus laevis).",
"domain": "anatomy",
"homepage": "http://www.xenbase.org/anatomy/xao.do?method=display",
"id": "xao",
"in_foundry_order": 1,
"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/xao.owl",
"products": [
{
"id": "xao.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/xao.owl"
},
{
"id": "xao.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/xao.obo"
}
],
"publications": [
{
"id": "http://www.ncbi.nlm.nih.gov/pubmed/18817563",
"title": "An ontology for Xenopus anatomy and development."
},
{
"id": "http://www.ncbi.nlm.nih.gov/pubmed/24139024",
"title": "Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase."
}
],
"taxon": {
"id": "NCBITaxon:8353",
"label": "Xenopus"
},
"title": "Xenopus Anatomy Ontology",
"tracker": "https://github.com/xenopus-anatomy/xao/issues"
},
{
"activity_status": "active",
"build": {
"infallible": 1,
"method": "obo2owl",
"notes": "may be ready to switch to vcs soon",
"source_url": "https://raw.githubusercontent.com/cerivs/zebrafish-anatomical-ontology/master/src/zebrafish_anatomy.obo"
},
"contact": {
"email": "[email protected]",
"github": "cerivs",
"label": "Ceri Van Slyke"
},
"description": "A structured controlled vocabulary of the anatomy and development of the Zebrafish",
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