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{
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{
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"url": "https://www.alliancegenome.org/disease/DOID:0080599"
}
],
"user": "https://www.alliancegenome.org"
},
{
"description": "MGI disease model annotations use DO",
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{
"description": "physical disorder",
"url": "http://www.informatics.jax.org/disease/DOID:0080015"
}
],
"user": "http://www.informatics.jax.org/disease"
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{
"description": "Immune Epitope Database",
"examples": [
{
"description": "Antibody and T cell epitopes associated with human diseases",
"url": "https://www.iedb.org"
}
],
"user": "https://www.iedb.org"
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]
},
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"activity_status": "active",
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}
],
"build": {
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"email": "cp390@cam.ac.uk",
"github": "Clare72",
"label": "Clare Pilgrim",
"orcid": "0000-0002-1373-1705"
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"label": "CC BY 4.0",
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"title": "The Drosophila phenotype ontology."
}
],
"repository": "https://github.com/FlyBase/drosophila-phenotype-ontology",
"taxon": {
"id": "NCBITaxon:7227",
"label": "Drosophila"
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"title": "Drosophila Phenotype Ontology",
"tracker": "https://github.com/FlyBase/drosophila-phenotype-ontology/issues",
"usages": [
{
"description": "FlyBase uses dpo for phenotype data annotation in Drosophila",
"examples": [
{
"description": "alleles and constructs annotated to pupal lethal in FlyBase",
"url": "http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBcv:0002030"
}
],
"user": "http://flybase.org"
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},
{
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"contact": {
"email": "hoganwr@gmail.com",
"github": "hoganwr",
"label": "William Hogan",
"orcid": "0000-0002-9881-1017"
},
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"id": "dron",
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"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
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"title": "Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request"
}
],
"repository": "https://github.com/ufbmi/dron",
"title": "The Drug Ontology",
"tracker": "https://github.com/ufbmi/dron/issues",
"usages": [
{
"description": "DrOn is used for the classification of Drugs, in particular, based on RxNorm codes, in the PennTURBO project.",
"examples": [
{
"description": "From the documentation: For example, the text `500 mg Tylenol po tabs` might be mapped to http://purl.obolibrary.org/obo/DRON_00073395, with the label `Acetaminophen 500 MG Oral Tablet [Tylenol]`. DrOn knows that this is a subclass of `Acetaminophen 500 MG Oral Tablet` (through its logical axiomatisation).",
"url": "https://pennturbo.github.io/Turbo-Documentation/medication_text_to_terms_to_roles.html"
}
],
"type": "annotation",
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}
]
},
{
"activity_status": "active",
"contact": {
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"github": "mcourtot",
"label": "Melanie Courtot",
"orcid": "0000-0002-9551-6370"
},
"dependencies": [
{
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},
{
"id": "iao"
}
],
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"domain": "information",
"homepage": "https://github.com/EBISPOT/DUO",
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"layout": "ontology_detail",
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"label": "CC BY 4.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
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"ontology_purl": "http://purl.obolibrary.org/obo/duo.owl"
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],
"repository": "https://github.com/EBISPOT/DUO",
"title": "Data Use Ontology",
"tracker": "https://github.com/EBISPOT/DUO/issues"
},
{
"activity_status": "active",
"build": {
"checkout": "git clone https://github.com/echinoderm-ontology/ecao_ontology.git",
"path": ".",
"system": "git"
},
"contact": {
"email": "ettensohn@cmu.edu",
"github": "ettensohn",
"label": "Charles Ettensohn",
"orcid": "0000-0002-3625-0955"
},
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{
"id": "cl"
},
{
"id": "ro"
},
{
"id": "uberon"
}
],
"description": "An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586).",
"domain": "anatomy and development",
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"layout": "ontology_detail",
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"preferredPrefix": "ECAO",
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{
"id": "ecao.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/ecao.obo"
}
],
"repository": "https://github.com/echinoderm-ontology/ecao_ontology",
"title": "The Echinoderm Anatomy and Development Ontology",
"tracker": "https://github.com/echinoderm-ontology/ecao_ontology/issues"
},
{
"activity_status": "active",
"browsers": [
{
"label": "ECO",
"title": "ECO Browser",
"url": "https://www.evidenceontology.org/browse"
}
],
"contact": {
"email": "mgiglio@som.umaryland.edu",
"github": "mgiglio99",
"label": "Michelle Giglio",
"orcid": "0000-0001-7628-5565"
},
"depicted_by": "https://avatars1.githubusercontent.com/u/12802432",
"description": "An ontology for experimental and other evidence statements.",
"domain": "investigations",
"funded_by": [
{
"id": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=1458400",
"title": "NSF ABI-1458400"
}
],
"homepage": "https://www.evidenceontology.org",
"id": "eco",
"layout": "ontology_detail",
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"label": "CC0 1.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png",
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}
],
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"preferred": true,
"title": "ECO: the Evidence and Conclusion Ontology, an update for 2022."
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/30407590",
"title": "ECO, the Evidence & Conclusion Ontology: community standard for evidence information."
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{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/25052702",
"title": "Standardized description of scientific evidence using the Evidence Ontology (ECO)"
}
],
"repository": "https://github.com/evidenceontology/evidenceontology",
"title": "Evidence and Conclusion Ontology",
"tracker": "https://github.com/evidenceontology/evidenceontology/issues",
"usages": [
{
"description": "ECO is used by the GO consortium for evidence on GO associations",
"examples": [
{
"description": "annotations to transmembrane transport",
"url": "http://amigo.geneontology.org/amigo/term/GO:0055085"
}
],
"type": "annotation",
"user": "http://geneontology.org"
},
{
"description": "ECO is used by the Monarch Initiative for evidence types for disease to phenotype annotations.",
"examples": [
{
"description": "Parkinsonism: Characteristic neurologic anomaly resulting form degeneration of dopamine-generating cells in the substantia nigra, a region of the midbrain, characterized clinically by shaking, rigidity, slowness of movement and difficulty with walking and gait.",
"url": "https://monarchinitiative.org/phenotype/HP%3A0001300#disease"
}
],
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{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/27899636",
"title": "The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species"
}
],
"type": "annotation",
"user": "https://monarchinitiative.org/"
}
]
},
{
"activity_status": "active",
"contact": {
"email": "p.buttigieg@gmail.com",
"github": "pbuttigieg",
"label": "Pier Luigi Buttigieg",
"orcid": "0000-0002-4366-3088"
},
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{
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{
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"description": "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.",
"domain": "environment",
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"id": "ecocore",
"layout": "ontology_detail",
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],
"repository": "https://github.com/EcologicalSemantics/ecocore",
"tags": [
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"ecological interactions"
],
"title": "An ontology of core ecological entities",
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},
{
"activity_status": "active",
"contact": {
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"github": "diatomsRcool",
"label": "Anne Thessen",
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{
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}
],
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"domain": "environment",
"homepage": "https://github.com/EnvironmentOntology/environmental-exposure-ontology",
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],
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"title": "Environmental conditions, treatments and exposures ontology",
"tracker": "https://github.com/EnvironmentOntology/environmental-exposure-ontology/issues"
},
{
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"notes": "new url soon",
"source_url": "ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAPA.obo"
},
"contact": {
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"github": "tfhayamizu",
"label": "Terry Hayamizu",
"orcid": "0000-0002-0956-8634"
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"description": "An ontology for mouse anatomy covering embryonic development and postnatal stages.",
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"homepage": "http://www.informatics.jax.org/expression.shtml",
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"id": "https://www.ncbi.nlm.nih.gov/pubmed/23972281",
"title": "EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update"
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{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/26208972",
"title": "Mouse Anatomy Ontologies: Enhancements and Tools for Exploring and Integrating Biomedical Data"
},
{
"id": "https://doi.org/10.1016/B978-0-12-800043-4.00023-3",
"title": "Textual Anatomics: the Mouse Developmental Anatomy Ontology and the Gene Expression Database for Mouse Development (GXD)"
}
],
"repository": "https://github.com/obophenotype/mouse-anatomy-ontology",
"taxon": {
"id": "NCBITaxon:10088",
"label": "Mus"
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"title": "Mouse Developmental Anatomy Ontology",
"tracker": "https://github.com/obophenotype/mouse-anatomy-ontology/issues",
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"description": "GXD",
"seeAlso": "https://doi.org/10.25504/FAIRsharing.q9neh8",
"user": "http://www.informatics.jax.org/expression.shtml"
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},
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"github": "pbuttigieg",
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},
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{
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{
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{
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],
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"description": "An ontology of environmental systems, components, and processes.",
"domain": "environment",
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},
{
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"ontology_purl": "http://purl.obolibrary.org/obo/envo.obo",
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},
{
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},
{
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"ontology_purl": "http://purl.obolibrary.org/obo/envo/subsets/envoEmpo.owl",
"title": "Earth Microbiome Project subset"
},
{
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"ontology_purl": "http://purl.obolibrary.org/obo/envo/subsets/EnvO-Lite-GSC.obo",
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}
],
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"id": "https://doi.org/10.1186/2041-1480-4-43",
"preferred": true,
"title": "The environment ontology: contextualising biological and biomedical entities"
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{
"id": "https://doi.org/10.1186/s13326-016-0097-6",
"title": "The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation"
}
],
"repository": "https://github.com/EnvironmentOntology/envo",
"title": "Environment Ontology",
"tracker": "https://github.com/EnvironmentOntology/envo/issues/",
"usages": [
{
"description": "describing species habitats",
"examples": [
{
"description": "Pseudobarbus burchelli (Tradou Redfin) is a species of bony fishes in the family Cyprinidae. They are associated with freshwater habitat. Individuals can grow to 13.5 cm. They have sexual reproduction.",
"url": "http://eol.org/pages/211700/data"
}
],
"type": "data-annotation",
"user": "http://eol.org"
},
{
"description": "describing stomach contents",
"type": "data-annotation",
"user": "http://globalbioticinteractions.org"
},
{
"description": "annotating datasets in data repositories",
"seeAlso": "http://blogs.nature.com/scientificdata/2015/12/17/isa-explorer/",
"type": "dataset-description",
"user": "http://www.nature.com/sdata/"
},
{
"description": "Samples collected during Tara Oceans expedition are annotated with ENVO",
"examples": [
{
"description": "Sample collected during the Tara Oceans expedition (2009-2013) at station TARA_004 (latitudeN=36.5533, longitudeE=-6.5669)",
"url": "https://www.ebi.ac.uk/metagenomics/projects/ERP001736/samples/ERS487899"
}
],
"user": "http://oceans.taraexpeditions.org/en/"
},
{
"description": "Annotation of habitats of microbes",
"examples": [
{
"description": "Annotation of habitat of Pseudovibrio sp. FO-BEG1 to marine environment",
"url": "https://www.ncbi.nlm.nih.gov/nuccore/NC_016642"
}
],
"user": "https://www.ncbi.nlm.nih.gov/"
},
{
"description": "Annotation and semantic search over microbial data sets",
"examples": [
{
"description": "Example metadata of a sample of marine water near Lisboa, taken as part of the Ocean Sampling Day Project (https://www.microb3.eu/osd.html). ENVO is used for the fields environmental feature, material, and biome.",
"url": "https://www.planetmicrobe.org/project/#/samples/200"
}
],
"user": "https://www.planetmicrobe.org/project/"
}
]
},
{
"activity_status": "active",
"contact": {
"email": "alpha.tom.kodamullil@scai.fraunhofer.de",
"github": "akodamullil",
"label": "Alpha Tom Kodamullil",
"orcid": "0000-0001-9896-3531"
},
"dependencies": [
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"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/fypo.owl",
"preferredPrefix": "FYPO",
"products": [
{
"id": "fypo.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/fypo.owl"
},
{
"id": "fypo.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/fypo.obo"
}
],
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/23658422",
"title": "FYPO: The Fission Yeast Phenotype Ontology."
}
],
"repository": "https://github.com/pombase/fypo",
"taxon": {
"id": "NCBITaxon:4896",
"label": "S. pombe"
},
"title": "Fission Yeast Phenotype Ontology",
"tracker": "https://github.com/pombase/fypo/issues",
"usages": [
{
"description": "Pombase uses fypo for phenotype data annotation in fission yeast",
"examples": [
{
"description": "genotypes annotated to abnormal mitotic cell cycle in fission yeast",
"url": "https://www.pombase.org/term/FYPO:0000059"
}
],
"user": "https://www.pombase.org"
}
]
},
{
"activity_status": "active",
"contact": {
"email": "adeans@psu.edu",
"github": "adeans",
"label": "Andy Deans",
"orcid": "0000-0002-2119-4663"
},
"dependencies": [
{
"id": "caro"
},
{
"id": "flopo"
},
{
"id": "ncbitaxon"
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{
"id": "obi"
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{
"id": "pato"
},
{
"id": "po"
},
{
"id": "poro"
},
{
"id": "ro"
}
],
"description": "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls.",
"domain": "phenotype",
"homepage": "https://adeans.github.io/gallont/",
"id": "gallont",
"layout": "ontology_detail",
"license": {
"label": "CC0 1.0",
"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/gallont.owl",
"preferredPrefix": "GALLONT",
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{
"id": "gallont.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/gallont.owl"
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{
"id": "gallont.json",
"ontology_purl": "http://purl.obolibrary.org/obo/gallont.json"
},
{
"id": "gallont.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/gallont.obo"
}
],
"repository": "https://github.com/adeans/gallont",
"title": "Plant Gall Ontology",
"tracker": "https://github.com/adeans/gallont/issues"
},
{
"activity_status": "active",
"contact": {
"email": "rbca.jackson@gmail.com",
"github": "beckyjackson",
"label": "Rebecca Jackson",
"orcid": "0000-0003-4871-5569"
},
"description": "An ontology to represent genomics cohort attributes",
"domain": "organisms",
"homepage": "https://github.com/IHCC-cohorts/GECKO",
"id": "gecko",
"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/gecko.owl",
"preferredPrefix": "GECKO",
"products": [
{
"id": "gecko.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/gecko.owl"
}
],
"repository": "https://github.com/IHCC-cohorts/GECKO",
"tags": [
"cohort studies"
],
"title": "Genomics Cohorts Knowledge Ontology",
"tracker": "https://github.com/IHCC-cohorts/GECKO/issues",
"usages": [
{
"description": "IHCC uses GECKO to standardize data from various cohorts for the IHCC cohort browser",
"user": "https://ihccglobal.org/"
}
]
},
{
"activity_status": "active",
"contact": {
"email": "damion_dooley@sfu.ca",
"github": "ddooley",
"label": "Damion Dooley",
"orcid": "0000-0002-8844-9165"
},
"dependencies": [
{
"id": "chebi"
},
{
"id": "ncbitaxon"
},
{
"id": "po"
},
{
"id": "ro"
},
{
"id": "uberon"
}
],
"description": "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.",
"domain": "health",
"homepage": "http://genepio.org/",
"id": "genepio",
"layout": "ontology_detail",
"license": {
"label": "CC BY 3.0",
"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/genepio.owl",
"page": "https://github.com/GenEpiO/genepio",
"preferredPrefix": "GENEPIO",
"products": [
{
"homepage": "http://genepio.github.io/genepio/",
"id": "genepio.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/genepio.owl"
}
],
"repository": "https://github.com/GenEpiO/genepio",
"title": "Genomic Epidemiology Ontology",
"tracker": "https://github.com/GenEpiO/genepio/issues/"
},
{
"activity_status": "active",
"build": {
"checkout": "git clone https://github.com/monarch-initiative/GENO-ontology.git",
"path": "src/ontology",
"system": "git"
},
"contact": {
"email": "mhb120@gmail.com",
"github": "mbrush",
"label": "Matthew Brush",
"orcid": "0000-0002-1048-5019"
},
"description": "An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases.",
"domain": "biological systems",
"homepage": "https://github.com/monarch-initiative/GENO-ontology/",
"id": "geno",
"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/geno.owl",
"preferredPrefix": "GENO",
"products": [
{
"id": "geno.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/geno.owl",
"title": "GENO"
}
],
"repository": "https://github.com/monarch-initiative/GENO-ontology",
"tags": [
"genotype-to-phenotype associations"
],
"title": "Genotype Ontology",
"tracker": "https://github.com/monarch-initiative/GENO-ontology/issues"
},
{
"activity_status": "active",
"contact": {
"email": "hoganwr@gmail.com",
"github": "hoganwr",
"label": "Bill Hogan",
"orcid": "0000-0002-9881-1017"
},
"description": "An ontology of geographical entities",
"domain": "environment",
"homepage": "https://github.com/ufbmi/geographical-entity-ontology/wiki",
"id": "geo",
"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/geo.owl",
"preferredPrefix": "GEO",
"products": [
{
"id": "geo.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/geo.owl"
}
],
"repository": "https://github.com/ufbmi/geographical-entity-ontology",
"title": "Geographical Entity Ontology",
"tracker": "https://github.com/ufbmi/geographical-entity-ontology/issues"
},
{
"activity_status": "active",
"browsers": [
{
"label": "Structure Browser",
"title": "GNOme Glycan Structure Browser",
"url": "https://gnome.glyomics.org/StructureBrowser.html?HexNAc=4&Hex=5&dHex=1&NeuAc=2"
},
{
"label": "Composition Browser",
"title": "GNOme Glycan Composition Browser",
"url": "https://gnome.glyomics.org/CompositionBrowser.html?HexNAc=4&Hex=5&dHex=1&NeuAc=2"
}
],
"build": {
"checkout": "git clone https://github.com/glygen-glycan-data/GNOme.git",
"path": ".",
"system": "git"
},
"contact": {
"email": "nje5@georgetown.edu",
"github": "edwardsnj",
"label": "Nathan Edwards",
"orcid": "0000-0001-5168-3196"
},
"description": "GlyTouCan provides stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations). GNOme organizes these stable accessions for interative browsing, for text-based searching, and for automated reasoning with well-defined characterization levels.",
"domain": "chemistry and biochemistry",
"homepage": "https://gnome.glyomics.org/",
"id": "gno",
"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/gno.owl",
"preferredPrefix": "GNO",
"products": [
{
"description": "Glycan Naming and Subsumption Ontology, OWL format (primary)",
"id": "gno.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/gno.owl"
},
{
"description": "Glycan Naming and Subsumption Ontology, OBO format (automated conversion from OWL)",
"id": "gno.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/gno.obo"
},
{
"description": "Glycan Naming and Subsumption Ontology, JSON format (automated conversion from OWL)",
"id": "gno.json",
"ontology_purl": "http://purl.obolibrary.org/obo/gno.json"
}
],
"publications": [
{
"id": "https://doi.org/10.5281/zenodo.6678278",
"title": "GNOme - Glycan Naming and Subsumption Ontology"
}
],
"repository": "https://github.com/glygen-glycan-data/GNOme",
"tags": [
"glycan structure"
],
"title": "Glycan Naming and Subsumption Ontology (GNOme)",
"tracker": "https://github.com/glygen-glycan-data/GNOme/issues",
"usages": [
{
"description": "GlyGen - Computational and Informatics Resources for Glycoscience",
"examples": [
{
"description": "GNOme attributes and related glycans on glycan pages",
"url": "https://www.glygen.org/glycan/G00028MO"
}
],
"user": "https://www.glygen.org/"
},
{
"description": "PRO - Protein Ontology",
"examples": [
{
"description": "example of PRO use of GNO terms",
"url": "http://purl.obolibrary.org/obo/PR_000059585"
}
],
"user": "https://proconsortium.org/"
},
{
"description": "ChEBI - Chemical Entities of Biological Interest",
"examples": [
{
"description": "example of ChEBI use of GNO terms",
"url": "http://purl.obolibrary.org/obo/CHEBI_167503"
}
],
"user": "https://www.ebi.ac.uk/chebi/init.do"
}
]
},
{
"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",
"github": "suzialeksander",
"label": "Suzi Aleksander",
"orcid": "0000-0001-6787-2901"
},
"dependencies": [
{
"id": "cl",
"subset": "go/extensions/cl_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"
},
{
"id": "ncbitaxon",
"subset": "go/extensions/ncbitaxon_import.owl"
},
{
"id": "ro",
"subset": "go/extensions/ro_import.owl"
},
{
"id": "uberon",
"subset": "go/extensions/uberon_import.owl"
}
],
"depicted_by": "/images/go_logo.png",
"description": "An ontology for describing the function of genes and gene products",
"domain": "biological systems",
"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",
"preferredPrefix": "GO",
"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"
}
],
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/10802651",
"title": "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/33290552",
"title": "The Gene Ontology resource: enriching a GOld mine"
}
],
"repository": "https://github.com/geneontology/go-ontology",
"tags": [
"biology"
],
"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"
},
{
"description": "Uniprot uses GO to show the function of proteins",
"examples": [
{
"description": "functional annotations of human Sonic hedgehog protein",
"url": "https://www.uniprot.org/uniprot/Q15465#function"
}
],
"type": "annotation",
"user": "https://www.uniprot.org"
},
{
"description": "Reactome annotates activities, pathways, and cellular localization using GO",
"examples": [
{
"description": "protein tyrosine kinase activity of an EGFR complex",
"url": "https://reactome.org/content/detail/R-HSA-177934"
}
],
"type": "annotation",
"user": "https://reactome.org"
},
{
"description": "The Alliance of Genome Resources uses GO for model organism gene function annotation",
"examples": [
{
"description": "Functional summary of C elegans nsy-1 gene",
"url": "https://www.alliancegenome.org/gene/WB:WBGene00003822#function---go-annotations"
},
{
"description": "Gene Ontology Causal Activity Models for C elegans nsy-1 gene",
"url": "https://www.alliancegenome.org/gene/WB:WBGene00003822#pathways"
}
],
"type": "annotation",
"user": "https://www.alliancegenome.org"
},
{
"description": "Rhea uses GO to describe individual biochemical reactions",
"examples": [
{
"description": "Glutamine scyllo-inositol transaminase reaction and associated GO term",
"url": "https://www.rhea-db.org/rhea/22920"
}
],
"type": "mapping",
"user": "https://www.rhea-db.org"
}
]
},
{
"activity_status": "active",
"contact": {
"email": "dwelter.ontologist@gmail.com",
"github": "daniwelter",
"label": "Danielle Welter",
"orcid": "0000-0003-1058-2668"
},
"description": "The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies.",
"domain": "organisms",
"homepage": "https://ebispot.github.io/hancestro/",
"id": "hancestro",
"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/hancestro.owl",
"preferredPrefix": "HANCESTRO",
"products": [
{
"description": "The full version of HANCESTRO in OWL format, with BFO upper hierarchy for easier integration with other ontologies",
"id": "hancestro.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/hancestro.owl",
"title": "HANCESTRO"
},
{
"description": "Base version of HANCESTRO",
"id": "hancestro-base.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/hancestro-base.owl",
"title": "HANCESTRO Base"
}
],
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/29448949",
"title": "A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog"
}
],
"repository": "https://github.com/EBISPOT/hancestro",
"tags": [
"ancestry"
],
"title": "Human Ancestry Ontology",
"tracker": "https://github.com/EBISPOT/hancestro/issues",
"usages": [
{
"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.",
"examples": [
{
"description": "Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data",
"url": "https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHANCESTRO_0004&viewMode=All&siblings=false"
}
],
"user": "http://www.ebi.ac.uk/efo"
},
{
"description": "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.",
"examples": [
{
"description": "Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data",
"url": "https://www.ebi.ac.uk/ols/ontologies/genepio/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHANCESTRO_0004&viewMode=All&siblings=false"
}
],
"user": "https://genepio.org/"
},
{
"description": "FoodOn (http://foodon.org) is a consortium-driven project to build a comprehensive and easily accessible global farm-to-fork ontology about food, that accurately and consistently describes foods commonly known in cultures from around the world.",
"examples": [
{
"description": "Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data",
"url": "https://www.ebi.ac.uk/ols/ontologies/foodon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHANCESTRO_0004&viewMode=All&siblings=false"
}
],
"user": "http://foodon.org"
}
]
},
{
"activity_status": "active",
"build": {
"checkout": "git clone https://github.com/hymao/hao.git",
"system": "git"
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"description": "Bgee is a database to retrieve and compare gene expression patterns between animal species. Bgee in using Uberon to annotate the site of expression, and Bgee curators one the major contributors to the ontology.",
"examples": [
{
"description": "Uberon terms used to annotate expression of human hemoglobin subunit beta",
"url": "http://bgee.org/?page=gene&gene_id=ENSG00000244734"
}
],
"seeAlso": "https://doi.org/10.25504/FAIRsharing.x6d6sx",
"type": "annotation",
"user": "http://bgee.org/"
},
{
"description": "The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The ENCODE DCC users Uberon to annotate samples",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/25776021",
"title": "Ontology application and use at the ENCODE DCC"
}
],
"seeAlso": "https://doi.org/10.25504/FAIRsharing.v0hbjs",
"type": "annotation",
"user": "https://www.encodeproject.org/"
},
{
"description": "FANTOM5 is using Uberon and CL to annotate samples allowing for transcriptome analyses with cell-type and tissue-level specificity.",
"examples": [
{
"description": "FANTOM5 samples annotated to telencephalon or its parts",
"url": "http://fantom.gsc.riken.jp/5/sstar/UBERON:0001893"
}
],
"type": "annotation",
"user": "http://fantom5-collaboration.gsc.riken.jp/"
},
{
"description": "Querying expression and phenotype data",
"type": "query",
"user": "https://monarchinitiative.org/"
},
{
"description": "GO Database is used for querying for functional annotations relevant to a tissue",
"examples": [
{
"description": "GO annotations relevant to the uberon class for brain",
"url": "http://amigo.geneontology.org/amigo/term/UBERON:0000955"
}
],
"type": "query",
"user": "https://geneontology.org/"
},
{
"description": "The Phenoscape project is both a major driver of and contributor to Uberon, contibuting thousands of terms. The teleost (bony fishes) component of Uberon was derived from the Teleost Anatomy Ontology, developed by the Phenoscape group. Most of the high level design of the skeletal system comes from the Vertebrate Skeletal Anatomy Ontology (VSAO), also created by the Phenoscape group. Phenoscape curators continue to extend the ontology, covering a wide variety of tetrapod structures, with an emphasis on the appendicular system.",
"user": "http://phenoscape.org"
},
{
"description": "Searchable collection of neuroscience data and ontology for neuroscience",
"type": "Database",
"user": "https://neuinfo.org/"
},
{
"description": "cooperative data platform to be used by diverse communities in making data more FAIR.",
"type": "Database",
"user": "https://scicrunch.org/"
},
{
"description": "SCPortalen",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/29045713",
"title": "SCPortalen: human and mouse single-cell centric database"
}
],
"type": "Database",
"user": "http://single-cell.clst.riken.jp/"
},
{
"description": "ChEMBL uses Uberon to describe organ/tissue information in assays",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/30398643",
"title": "ChEMBL: towards direct deposition of bioassay data"
}
],
"type": "Database",
"user": "https://www.ebi.ac.uk/chembl/"
}
],
"wikidata_template": "https://en.wikipedia.org/wiki/Template:Uberon"
},
{
"activity_status": "active",
"build": {
"method": "obo2owl",
"source_url": "https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"
},
"contact": {
"email": "g.gkoutos@gmail.com",
"github": "gkoutos",
"label": "George Gkoutos",
"orcid": "0000-0002-2061-091X"
},
"description": "Metrical units for use in conjunction with PATO",
"domain": "phenotype",
"homepage": "https://github.com/bio-ontology-research-group/unit-ontology",
"id": "uo",
"in_foundry": false,
"layout": "ontology_detail",
"license": {
"label": "CC BY 3.0",
"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/uo.owl",
"preferredPrefix": "UO",
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{
"id": "uo.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/uo.owl"
},
{
"id": "uo.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/uo.obo"
}
],
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/23060432",
"title": "The Units Ontology: a tool for integrating units of measurement in science"
}
],
"repository": "https://github.com/bio-ontology-research-group/unit-ontology",
"title": "Units of measurement ontology",
"tracker": "https://github.com/bio-ontology-research-group/unit-ontology/issues"
},
{
"activity_status": "active",
"build": {
"method": "archive",
"path": "archive/ontology",
"source_url": "http://build.berkeleybop.org/job/build-pheno-ontologies/lastSuccessfulBuild/artifact/*zip*/archive.zip"
},
"contact": {
"email": "jmcl@ebi.ac.uk",
"github": "jamesamcl",
"label": "James McLaughlin",
"orcid": "0000-0002-8361-2795"
},
"description": "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.",
"domain": "phenotype",
"homepage": "https://github.com/obophenotype/upheno",
"id": "upheno",
"layout": "ontology_detail",
"license": {
"label": "CC0 1.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png",
"url": "https://creativecommons.org/publicdomain/zero/1.0/"
},
"mailing_list": "https://groups.google.com/forum/#!forum/phenotype-ontologies-editors",
"ontology_purl": "http://purl.obolibrary.org/obo/upheno.owl",
"preferredPrefix": "UPHENO",
"products": [
{
"description": "uPheno 1 is no longer actively maintained, please start using uPheno 2 (see below).",
"id": "upheno.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/upheno.owl",
"page": "https://github.com/obophenotype/upheno",
"title": "uPheno 1 (inactive)"
},
{
"description": "No longer actively maintained.",
"id": "upheno/mp-hp-view.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/upheno/mp-hp-view.owl",
"page": "https://github.com/obophenotype/upheno/tree/master/hp-mp",
"title": "uPheno MP-HP equivalence axioms"
},
{
"description": "The new version of uPheno, along with species independent phenotypes and additional phenotype relations. The ontology is still in Beta status, but we recommend users to migrate their infrastructures to uPheno 2 as uPheno 1 is no longer actively maintained.",
"id": "upheno/v2/upheno.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/upheno/v2/upheno.owl",
"page": "https://github.com/obophenotype/upheno-dev",
"title": "uPheno 2"
}
],
"publications": [
{
"id": "https://doi.org/10.1101/2024.09.18.613276",
"title": "The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics"
},
{
"id": "https://zenodo.org/record/2382757",
"title": "Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species"
},
{
"id": "https://zenodo.org/record/3352149",
"title": "Phenotype Ontologies Traversing All The Organisms (POTATO) workshop: 2nd edition"
}
],
"repository": "https://github.com/obophenotype/upheno",
"title": "Unified Phenotype Ontology (uPheno)",
"tracker": "https://github.com/obophenotype/upheno/issues",
"usages": [
{
"description": "uPheno is used by the Monarch Initiative for cross-species inference.",
"examples": [
{
"description": "Characteristic neurologic anomaly resulting form degeneration of dopamine-generating cells in the substantia nigra, a region of the midbrain, characterized clinically by shaking, rigidity, slowness of movement and difficulty with walking and gait.",
"url": "https://monarchinitiative.org/phenotype/HP:0001300#disease"
}
],
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/27899636",
"title": "The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species "
}
],
"type": "analysis",
"user": "https://monarchinitiative.org/"
}
]
},
{
"activity_status": "active",
"contact": {
"email": "Sabrina@tislab.org",
"github": "sabrinatoro",
"label": "Sabrina Toro",
"orcid": "0000-0002-4142-7153"
},
"dependencies": [
{
"id": "ncbitaxon"
}
],
"description": "Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.",
"domain": "organisms",
"homepage": "https://github.com/monarch-initiative/vertebrate-breed-ontology",
"id": "vbo",
"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/vbo.owl",
"preferredPrefix": "VBO",
"products": [
{
"id": "vbo.owl",
"name": "Vertebrate Breed Ontology main release in OWL format",
"ontology_purl": "http://purl.obolibrary.org/obo/vbo.owl"
},
{
"id": "vbo.obo",
"name": "Vertebrate Breed Ontology additional release in OBO format",
"ontology_purl": "http://purl.obolibrary.org/obo/vbo.obo"
},
{
"id": "vbo.json",
"name": "Vertebrate Breed Ontology additional release in OBOJSon format",
"ontology_purl": "http://purl.obolibrary.org/obo/vbo.json"
},
{
"id": "vbo/vbo-base.owl",
"name": "Vertebrate Breed Ontology main release in OWL format",
"ontology_purl": "http://purl.obolibrary.org/obo/vbo/vbo-base.owl"
},
{
"id": "vbo/vbo-base.obo",
"name": "Vertebrate Breed Ontology additional release in OBO format",
"ontology_purl": "http://purl.obolibrary.org/obo/vbo/vbo-base.obo"
},
{
"id": "vbo/vbo-base.json",
"name": "Vertebrate Breed Ontology additional release in OBOJSon format",
"ontology_purl": "http://purl.obolibrary.org/obo/vbo/vbo-base.json"
}
],
"repository": "https://github.com/monarch-initiative/vertebrate-breed-ontology",
"title": "Vertebrate Breed Ontology",
"tracker": "https://github.com/monarch-initiative/vertebrate-breed-ontology/issues",
"usages": [
{
"description": "VBO is used in the Online Mendelian Inheritance in Animals (OMIA) for breed annotations.",
"examples": [
{
"description": "Urticaria pigmentosa affects the Sphynx (Cat) (VBO:0100230) breed.",
"url": "https://www.omia.org/OMIA001289/9685/"
}
],
"type": "annotation",
"user": "https://omia.org/home/"
}
]
},
{
"activity_status": "active",
"build": {
"source_url": "https://raw.githubusercontent.com/vaccineontology/VO/master/src/VO_merged.owl"
},
"contact": {
"email": "yongqunh@med.umich.edu",
"github": "yongqunh",
"label": "Yongqunh He",
"orcid": "0000-0001-9189-9661"
},
"description": "VO is a biomedical ontology in the domain of vaccine and vaccination.",
"domain": "health",
"homepage": "https://violinet.org/vaccineontology",
"id": "vo",
"layout": "ontology_detail",
"license": {
"label": "CC BY 4.0",
"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/vo.owl",
"preferredPrefix": "VO",
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"ontology_purl": "http://purl.obolibrary.org/obo/vo.owl"
}
],
"publications": [
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"id": "https://www.ncbi.nlm.nih.gov/pubmed/23256535",
"title": "Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/21624163",
"title": "Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology"
}
],
"repository": "https://github.com/vaccineontology/VO",
"title": "Vaccine Ontology",
"tracker": "https://github.com/vaccineontology/VO/issues",
"usages": [
{
"description": "VIOLIN uses VO to standardize vaccine information",
"examples": [
{
"description": "VIOLIN using VO grouped all SARS-CoV-2 vaccines",
"url": "https://violinet.org/canvaxkb/vaccine_detail.php?c_vaccine_id=5339"
},
{
"description": "A specific vaccine ‘Allogeneic Tumor Cell Vaccine’ curated in VO for VIOLIN vaccine record",
"url": "https://violinet.org/vaxquery/query_detail.php?c_pathogen_id=321#vaccine_5878"
}
],
"user": "https://violinet.org"
},
{
"description": "Vaccine Adjuvant Compendium (VAC) uses Vaccine Ontology to standard vaccine adjuvants developed by NIH",
"examples": [
{
"description": "A specific vaccine adjuvant, such as CaPNP (CaPtivant)(TM), in Vaccine Adjuvant Compendium, uses VO_0005295 ‘CaPNP (CaPtivant)(TM) vaccine adjuvant’",
"url": "https://vac.niaid.nih.gov/view?id=11"
}
],
"user": "https://www.niaid.nih.gov/research/vaccine-adjuvant-compendium-vac"
},
{
"description": "ImmPort uses Vaccine Ontology to standardize vaccine recorded collected in NIH funded ImmPort studies",
"examples": [
{
"description": "ImmPort data used VO for annotation shown in its dataModel",
"url": "https://www.immport.org/shared/dataModel"
}
],
"user": "https://www.immport.org/"
},
{
"description": "Human Immunology Project Consortium (HIPC) uses VO to standardize vaccine records",
"examples": [
{
"description": "Influenza Vaccine Live, Intranasal used VO_0000044",
"url": "http://www.hipc-dashboard.org/#vaccine/vo-0000044"
}
],
"user": "https://immunespace.org/"
}
]
},
{
"activity_status": "active",
"build": {
"checkout": "svn co http://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/vt",
"method": "vcs",
"system": "svn"
},
"contact": {
"email": "caripark@iastate.edu",
"github": "caripark",
"label": "Carissa Park",
"orcid": "0000-0002-2346-5201"
},
"description": "An ontology of traits covering vertebrates",
"domain": "phenotype",
"homepage": "https://github.com/AnimalGenome/vertebrate-trait-ontology",
"id": "vt",
"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/vt.owl",
"preferredPrefix": "VT",
"products": [
{
"id": "vt.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/vt.owl"
}
],
"repository": "https://github.com/AnimalGenome/vertebrate-trait-ontology",
"title": "Vertebrate trait ontology",
"tracker": "https://github.com/AnimalGenome/vertebrate-trait-ontology/issues",
"usages": [
{
"description": "The Animal Quantitative Trait Loci (QTL) Database (Animal QTLdb) annotates trait mapping data for livestock animals using the VTO",
"examples": [
{
"description": "Links to cattle QTL associated with the VTO term gastrointestinal system morphology trait or its descendants",
"url": "https://www.animalgenome.org/cgi-bin/QTLdb/BT/traitsrch?tword=Gastrointestinal%20tract%20weight"
}
],
"user": "https://www.animalgenome.org/cgi-bin/QTLdb/index"
},
{
"description": "The Rat Genome Database (RGD) uses the VTO to annotate rat QTL",
"examples": [
{
"description": "Annotations of rat QTL associated with the VTO term cholesterol amount or its descendants",
"url": "https://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=VT:0003947&species=Rat"
}
],
"user": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=VT:0000001"
},
{
"description": "The Mouse Phenome Database (MPD) uses the VTO to annotate mouse strain traits",
"examples": [
{
"description": "Studies in the MPD database that have measurements related to the VTO term spleen size trait or its descendants",
"url": "https://phenome.jax.org/ontologies/VT:0002224"
}
],
"user": "https://phenome.jax.org/ontologies/navigate/VT:0000001"
}
]
},
{
"activity_status": "active",
"contact": {
"email": "balhoff@renci.org",
"github": "balhoff",
"label": "Jim Balhoff",
"orcid": "0000-0002-8688-6599"
},
"description": "Comprehensive hierarchy of extinct and extant vertebrate taxa.",
"domain": "organisms",
"homepage": "https://github.com/phenoscape/vertebrate-taxonomy-ontology",
"id": "vto",
"layout": "ontology_detail",
"license": {
"label": "CC0 1.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png",
"url": "http://creativecommons.org/publicdomain/zero/1.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/vto.owl",
"preferredPrefix": "VTO",
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{
"id": "vto.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/vto.owl"
},
{
"id": "vto.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/vto.obo"
}
],
"publications": [
{
"id": "https://doi.org/10.1186/2041-1480-4-34",
"title": "The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes"
}
],
"repository": "https://github.com/phenoscape/vertebrate-taxonomy-ontology",
"title": "Vertebrate Taxonomy Ontology",
"tracker": "https://github.com/phenoscape/vertebrate-taxonomy-ontology/issues",
"usages": [
{
"description": "Phenoscape uses VTO to annotate systematics data",
"user": "http://phenoscape.org"
}
]
},
{
"activity_status": "active",
"build": {
"checkout": "git clone https://github.com/obophenotype/c-elegans-gross-anatomy-ontology.git",
"path": ".",
"system": "git"
},
"contact": {
"email": "raymond@caltech.edu",
"github": "raymond91125",
"label": "Raymond Lee",
"orcid": "0000-0002-8151-7479"
},
"description": "A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.",
"domain": "anatomy and development",
"homepage": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology",
"id": "wbbt",
"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/wbbt.owl",
"preferredPrefix": "WBbt",
"products": [
{
"id": "wbbt.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/wbbt.owl"
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{
"id": "wbbt.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/wbbt.obo"
}
],
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/18629098",
"title": "Building a cell and anatomy ontology of Caenorhabditis elegans"
}
],
"repository": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology",
"taxon": {
"id": "NCBITaxon:6237",
"label": "Caenorhabditis"
},
"title": "C. elegans Gross Anatomy Ontology",
"tracker": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/issues",
"usages": [
{
"description": "WormBase uses WBbt to curate anatomical expression patterns and anatomy function annotations, and to allow search and indexing on the WormBase site",
"examples": [
{
"description": "Expression for gene daf-16 with WormBase ID WBGene00000912",
"url": "http://www.wormbase.org/db/get?name=WBGene00000912;class=Gene;widget=expression"
}
],
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/31642470",
"title": "WormBase: a modern Model Organism Information Resource"
}
],
"type": "annotation",
"user": "https://www.wormbase.org/"
}
]
},
{
"activity_status": "active",
"build": {
"checkout": "git clone https://github.com/obophenotype/c-elegans-development-ontology.git",
"path": ".",
"system": "git"
},
"contact": {
"email": "cgrove@caltech.edu",
"github": "chris-grove",
"label": "Chris Grove",
"orcid": "0000-0001-9076-6015"
},
"description": "A structured controlled vocabulary of the development of Caenorhabditis elegans.",
"domain": "anatomy and development",
"homepage": "https://github.com/obophenotype/c-elegans-development-ontology",
"id": "wbls",
"layout": "ontology_detail",
"license": {
"label": "CC BY 4.0",
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"url": "https://creativecommons.org/licenses/by/4.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/wbls.owl",
"preferredPrefix": "WBls",
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{
"id": "wbls.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/wbls.owl"
},
{
"id": "wbls.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/wbls.obo"
}
],
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/31642470",
"title": "WormBase: a modern Model Organism Information Resource"
}
],
"repository": "https://github.com/obophenotype/c-elegans-development-ontology",
"tags": [
"developemental life stage"
],
"taxon": {
"id": "NCBITaxon:6237",
"label": "Caenorhabditis"
},
"title": "C. elegans development ontology",
"tracker": "https://github.com/obophenotype/c-elegans-development-ontology/issues",
"usages": [
{
"description": "WormBase uses WBls to curate temporal expression patterns, and to allow search and indexing on the WormBase site",
"examples": [
{
"description": "Expression for daf-16 gene with WormBase ID WBGene00000912.",
"url": "http://www.wormbase.org/db/get?name=WBGene00000912;class=Gene;widget=expression"
}
],
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/31642470",
"title": "WormBase: a modern Model Organism Information Resource"
}
],
"type": "annotation",
"user": "https://www.wormbase.org/"
}
]
},
{
"activity_status": "active",
"build": {
"checkout": "git clone https://github.com/obophenotype/c-elegans-phenotype-ontology.git",
"path": ".",
"system": "git"
},
"contact": {
"email": "cgrove@caltech.edu",
"github": "chris-grove",
"label": "Chris Grove",
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{
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{
"description": "Egg long: The fertilized oocytes have a greater than standard length measured end to end compared to control.",
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