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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": [
{
"activity_status": "active",
"browsers": [
{
"label": "BioPortal",
"title": "BioPortal Browser",
"url": "http://bioportal.bioontology.org/ontologies/BFO?p=classes"
}
],
"contact": {
"email": "phismith@buffalo.edu",
"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"
}
],
"review": {
"date": 2016,
"document": {
"label": "PDF",
"link": "https://drive.google.com/open?id=0B81h9ah4tAM_RnNTRUZnVGRyWXM"
}
},
"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": "amalik@ebi.ac.uk",
"github": "amalik01",
"label": "Adnan Malik"
},
"depicted_by": "https://www.ebi.ac.uk/chebi/images/ChEBI_logo.png",
"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"
}
],
"publications": [
{
"id": "http://europepmc.org/article/MED/26467479",
"title": "ChEBI in 2016: Improved services and an expanding collection of metabolites."
}
],
"review": {
"date": 2010
},
"title": "Chemical Entities of Biological Interest",
"tracker": "https://github.com/ebi-chebi/ChEBI/issues",
"twitter": "chebit",
"usages": [
{
"description": "Rhea uses CHEBI to annotate reaction participants",
"examples": [
{
"description": "Query for all usages of CHEBI:29748 (chorismate)",
"url": "https://www.rhea-db.org/searchresults?q=CHEBI:29748"
}
],
"user": "https://www.rhea-db.org/"
},
{
"description": "ZFIN uses CHEBI to annotate experiments",
"examples": [
{
"description": "A curated zebrafish experiment involving exposure to (5Z,8Z,14Z)-11,12-dihydroxyicosatrienoic acid (CHEBI:63969)",
"url": "http://zfin.org/action/expression/experiment?id=ZDB-EXP-190627-10"
}
],
"user": "http://zfin.org"
}
]
},
{
"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": "lynn.schriml@gmail.com",
"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"
}
],
"review": {
"date": 2015,
"document": {
"label": "PDF",
"link": "https://drive.google.com/open?id=0B8vqEgF1N0NIZ082U2JETHlSTGs"
}
},
"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": "suzia@stanford.edu",
"label": "Suzi Aleksander"
},
"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/assets/go-logo-icon.mini.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 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/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, with subsets of those 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": "The main ontology plus axioms connecting to select external ontologies, excluding the external ontologies themselves",
"id": "go/go-base.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/go/go-base.owl",
"page": "http://geneontology.org/page/download-ontology",
"title": "GO Base Module"
},
{
"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": "Basic version of the GO, filtered such that the graph is guaranteed to be acyclic and annotations can be propagated up the graph. The relations included are is a, part of, regulates, negatively regulates and positively regulates. This version excludes relationships that cross the 3 GO hierarchies.",
"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": "go/snapshot/go.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/go/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": "go/snapshot/go.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/go/snapshot/go.obo",
"page": "http://geneontology.org/page/download-ontology",
"title": "GO (OBO Format edition), daily snapshot release"
}
],
"review": {
"date": 2010
},
"taxon": {
"id": "NCBITaxon:1",
"label": "All life"
},
"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": "bpeters@lji.org",
"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 4.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/4.0/"
},
"mailing_list": "http://groups.google.com/group/obi-users",
"ontology_purl": "http://purl.obolibrary.org/obo/obi.owl",
"products": [
{
"description": "The full version of OBI in OWL format",
"id": "obi.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/obi.owl",
"title": "OBI"
},
{
"description": "The OBO-format version of OBI",
"id": "obi.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/obi.obo",
"title": "OBI in OBO"
},
{
"description": "A collection of important high-level terms and their relations from OBI and other ontologies",
"id": "obi/obi_core.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/obi/obi_core.owl",
"title": "OBI Core"
}
],
"review": {
"date": 2013,
"document": {
"label": "PDF",
"link": "https://drive.google.com/open?id=0B8vqEgF1N0NIMFlSM3RvdUxGTnc"
}
},
"title": "Ontology for Biomedical Investigations",
"tracker": "http://purl.obolibrary.org/obo/obi/tracker",
"usages": [
{
"description": "PennTURBO accelerates the processes of finding and connecting key information from clinical records, via semantic modeling of the processes that generated the data. This makes the discovery of previously unappreciated relations between the data possible for research and for operational tasks.",
"example": [
{
"description": "CYP2C1*2/*2 MI patient taking Clopidogrel",
"url": "https://github.com/PennTURBO/Turbo-Documentation/blob/master/IBI_CIC_TURBO_MAM_20190102.pdf"
}
],
"user": "http://upibi.org/turbo/"
},
{
"description": "The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the biological research domain. ECO uses OBI to logically describe how the evidence arises from an investigation.",
"example": [
{
"description": "rapid amplification of cDNA ends polymerase chain reaction evidence",
"url": "http://purl.obolibrary.org/obo/ECO_0001820"
}
],
"user": "http://evidenceontology.org/"
}
]
},
{
"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": "g.gkoutos@gmail.com",
"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/pato-base.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/pato/pato-base.owl"
}
],
"repository": "https://github.com/pato-ontology/pato/",
"review": {
"date": 2010
},
"title": "Phenotype And Trait Ontology",
"tracker": "https://github.com/pato-ontology/pato/issues",
"usages": [
{
"description": "PATO is used by the Human Phenotype Ontology (HPO) for logical definitions of phenotypes that facilitate cross-species integration.",
"examples": [
{
"url": "https://www.ebi.ac.uk/ols/ontologies/hp/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHP_0011017&viewMode=All&siblings=false"
}
],
"reference": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324074/",
"type": "annotation",
"user": "https://hpo.jax.org/app/"
}
]
},
{
"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": "jaiswalp@science.oregonstate.edu",
"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."
}
],
"review": {
"date": 2013,
"document": {
"label": "PDF",
"link": "https://drive.google.com/open?id=0B8vqEgF1N0NIV1o0N21UOHlLSmc"
}
},
"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": "dan5@georgetown.edu",
"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"
}
],
"review": {
"date": 2010
},
"title": "PRotein Ontology (PRO)",
"tracker": "https://github.com/PROconsortium/PRoteinOntology/issues",
"usages": [
{
"description": "Colorado Richly Annotated Full-Text (CRAFT) Corpus; PRO is used for entity tagging and annotation",
"examples": [
{
"description": "Tagged entities (requires download)",
"url": "https://github.com/UCDenver-ccp/CRAFT/releases/tag/v4.0.1"
}
],
"user": "https://github.com/UCDenver-ccp/CRAFT"
},
{
"description": "Cell Ontology is a structured controlled vocabulary for cell types in animals; PRO is used for cell type definitions",
"examples": [
{
"description": "A B cell that is CD19-positive (uses the PRO term for non-species-specific CD19 molecule, PR:000001002)",
"url": "http://purl.obolibrary.org/obo/CL_0001201"
}
],
"user": "http://www.obofoundry.org/ontology/cl.html"
}
]
},
{
"activity_status": "active",
"build": {
"infallible": 0,
"method": "obo2owl",
"source_url": "https://raw.githubusercontent.com/xenopus-anatomy/xao/master/xenopus_anatomy.obo"
},
"contact": {
"email": "esegerd3@gmail.com",
"github": "seger",
"label": "Erik Segerdell"
},
"description": "XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis.",
"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."
}
],
"review": {
"date": 2010
},
"taxon": {
"id": "NCBITaxon:8353",
"label": "Xenopus"
},
"title": "Xenopus Anatomy Ontology",
"tracker": "https://github.com/xenopus-anatomy/xao/issues",
"usages": [
{
"description": "Xenbase uses XAO to annotate gene expression.",
"examples": [
{
"description": "Xenopus genes expressed in the pronephric kidney.",
"url": "http://www.xenbase.org/anatomy/showanatomy.do?method=displayAnatomySummary&anatomyId=463"
}
],
"user": "http://www.xenbase.org"
}
]
},
{
"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": "van_slyke@zfin.org",
"github": "cerivs",
"label": "Ceri Van Slyke"
},
"description": "A structured controlled vocabulary of the anatomy and development of the Zebrafish",
"domain": "anatomy",
"homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources",
"id": "zfa",
"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/zfa.owl",
"products": [
{
"id": "zfa.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/zfa.owl"
},
{
"id": "zfa.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/zfa.obo"
}
],
"publications": [
{
"id": "http://www.ncbi.nlm.nih.gov/pubmed/24568621",
"title": "The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio."
}
],
"review": {
"date": 2010
},
"taxon": {
"id": "NCBITaxon:7954",
"label": "Danio"
},
"title": "Zebrafish anatomy and development ontology",
"tracker": "https://github.com/cerivs/zebrafish-anatomical-ontology/issues",
"usages": [
{
"description": "ZFIN uses ZFA to annotate gene expression and phenotype",
"examples": [
{
"description": "zebrafish genes expressed in hindbrain and genotypes with hindbrain phenotype",
"url": "http://zfin.org/ZFA:0000029"
}
],
"user": "http://zfin.org"
}
]
},
{
"activity_status": "active",
"build": {
"checkout": "git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git",
"method": "vcs",
"path": "src/ontology",
"system": "git"
},
"contact": {
"email": "J.Bard@ed.ac.uk",
"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",
"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/aeo.owl",
"products": [
{
"id": "aeo.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/aeo.owl"
}
],
"title": "Anatomical Entity Ontology",
"tracker": "https://github.com/obophenotype/human-developmental-anatomy-ontology/issues"
},
{
"activity_status": "active",
"build": {
"checkout": "git clone https://github.com/AgriculturalSemantics/agro.git",
"infallible": 1,
"method": "vcs",
"path": ".",
"system": "git"
},
"contact": {
"email": "m.a.laporte@cgiar.org",
"github": "marieALaporte",
"label": "Marie-Ang\u00e9lique Laporte"
},
"dependencies": [
{
"id": "envo"
},
{
"id": "uo"
},
{
"id": "ro"
},
{
"id": "pato"
},
{
"id": "chebi"
},
{
"id": "iao"
},
{
"id": "ncbitaxon"
},
{
"id": "po"
},
{
"id": "peco"
}
],
"description": "Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments",
"domain": "agronomy",
"homepage": "https://github.com/AgriculturalSemantics/agro",
"id": "agro",
"jobs": [
{
"id": "https://travis-ci.org/AgriculturalSemantics/agro",
"type": "travis-ci"
}
],
"layout": "ontology_detail",
"license": {
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"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/4.0/"
},
"mailing_list": "https://groups.google.com/group/agronomyOntology",
"ontology_purl": "http://purl.obolibrary.org/obo/agro.owl",
"products": [
{
"id": "agro.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/agro.owl"
}
],
"title": "Agronomy Ontology",
"tracker": "https://github.com/AgriculturalSemantics/agro/issues/"
},
{
"activity_status": "active",
"build": {
"checkout": "git clone https://github.com/EBISPOT/amphx_ontology.git",
"path": ".",
"system": "git"
},