ontologies.jsonld

{"ontologies": [{"layout": "ontology_detail", "contact": {"email": "J.Bard@ed.ac.uk", "label": "Jonathan Bard"}, "products": [{"id": "aeo.owl"}], "id": "aeo", "domain": "anatomy", "description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology", "title": "Anatomical Entity Ontology", "homepage": "http://www.obofoundry.org/wiki/index.php/AEO:Main_Page"}, {"layout": "ontology_detail", "contact": {"email": "mcourtot@gmail.com", "label": "Melanie Courtot"}, "products": [{"id": "aero.owl"}], "id": "aero", "domain": "health", "description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events", "title": "Adverse Event Reporting Ontology", "homepage": "http://purl.obolibrary.org/obo/aero"}, {"layout": "ontology_detail", "contact": {"email": "maria@genome.stanford.edu", "label": "Maria Costanza"}, "products": [{"id": "apo.owl"}], "id": "apo", "domain": "phenotype", "taxon": {"label": "Ascomycota", "id": "NCBITaxon:4890"}, "description": "A structured controlled vocabulary for the phenotypes of Ascomycete fungi", "title": "Ascomycete phenotype ontology", "homepage": "http://www.yeastgenome.org/ "}, {"layout": "ontology_detail", "id": "bcgo", "description": "The Beta Cell Genomics Ontology (BCGO) is an application ontology built for the beta cell genomics studies aiming to support database annotation, complicated semantic queries, and automated cell type classification.", "products": [{"id": "bcgo.owl"}], "title": "Beta Cell Genomics Ontology", "homepage": "http://code.google.com/p/bcgo-ontology/", "tracker": "http://code.google.com/p/bcgo-ontology/issues/list"}, {"contact": {"email": "rwalls2008@gmail.com", "label": "Ramona Walls"}, "id": "bco", "description": "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.", "products": [{"id": "bco.owl"}], "title": "Biological Collections Ontology", "homepage": "https://github.com/tucotuco/bco", "tracker": "https://github.com/tucotuco/bco/issues"}, {"layout": "ontology_detail", "contact": {"email": "phismith@buffalo.edu", "label": "Barry Smith"}, "products": [{"id": "bfo.owl"}], "page": "http://ifomis.org/bfo/", "id": "bfo", "domain": "upper", "description": "The upper level ontology upon which OBO Foundry ontologies are built.", "title": "Basic Formal Ontology", "homepage": "http://ifomis.org/bfo/"}, {"layout": "ontology_detail", "contact": {"email": "henrich@embl.de", "label": "Thorsten Heinrich"}, "products": [{"id": "bila.owl"}], "id": "bila", "domain": "anatomy", "taxon": {"label": "Bilateria", "id": "NCBITaxon:33213"}, "title": "Bilateria anatomy", "homepage": "http://4dx.embl.de/4DXpress"}, {"layout": "ontology_detail", "contact": {"email": "cjmungall@lbl.gov", "label": "Chris Mungall"}, "products": [{"id": "bspo.owl"}], "id": "bspo", "domain": "anatomy", "publications": [{"title": "Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.", "id": "http://www.ncbi.nlm.nih.gov/pubmed/25140222"}], "description": "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces", "title": "Biological Spatial Ontology", "homepage": "https://github.com/obophenotype/biological-spatial-ontology", "tracker": "https://github.com/obophenotype/biological-spatial-ontology/issues"}, {"layout": "ontology_detail", "contact": {"email": "a.chang@tu-bs.de", "label": "Antje Chang"}, "products": [{"id": "bto.owl"}], "page": "http://www.brenda-enzymes.info", "id": "bto", "domain": "anatomy", "description": "A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.", "title": "BRENDA tissue / enzyme source", "homepage": "http://www.brenda-enzymes.info"}, {"layout": "ontology_detail", "contact": {"email": "haendel@ohsu.edu", "label": "Melissa Haendel"}, "products": [{"id": "caro.owl"}], "id": "caro", "domain": "anatomy", "description": "An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species", "title": "Common Anatomy Reference Ontology", "homepage": "https://github.com/obophenotype/caro/", "tracker": "https://github.com/obophenotype/caro/issues"}, {"layout": "ontology_detail", "contact": {"email": "balhoff@nescent.org", "label": "Jim Balhoff"}, "id": "cdao", "description": "a formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types).", "products": [{"id": "cdao.owl"}], "title": "Comparative Data Analysis Ontology", "homepage": "http://sourceforge.net/apps/mediawiki/cdao/index.php?title=Main_Page"}, {"layout": "ontology_detail", "contact": {"email": "hastings@ebi.ac.uk", "label": "Janna Hastings"}, "products": [{"id": "chebi.owl"}, {"id": "chebi.obo"}], "page": "http://www.ebi.ac.uk/chebi/init.do?toolBarForward=userManual", "id": "chebi", "domain": "biochemistry", "in_foundry": true, "alternatePrefix": "ChEBI", "description": "A structured classification of chemical compounds of biological relevance.", "title": "Chemical entities of biological interest", "homepage": "http://www.ebi.ac.uk/chebi", "tracker": "https://sourceforge.net/p/chebi/curator-requests/"}, {"layout": "ontology_detail", "contact": {"email": "hastings@ebi.ac.uk", "label": "Janna Hastings"}, "products": [{"id": "cheminf.owl"}], "id": "cheminf", "domain": "biochemistry", "description": "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.", "title": "Chemical Information Ontology", "homepage": "http://code.google.com/p/semanticchemistry/"}, {"layout": "ontology_detail", "contact": {"email": "batchelorc@rsc.org", "label": "Colin Batchelor"}, "products": [{"id": "chmo.owl"}], "id": "chmo", "domain": "health", "description": "CHMO, the chemical methods ontology, describes methods used to", "title": "Chemical Methods Ontology", "homepage": "http://code.google.com/p/rsc-cmo/", "tracker": "http://code.google.com/p/rsc-cmo/issues/list"}, {"layout": "ontology_detail", "label": "Cell Ontology", "products": [{"id": "cl.owl"}, {"id": "cl.obo"}, {"id": "cl/cl-basic.obo"}], "id": "cl", "domain": "cells", "taxon": {"label": "Metazoa", "id": "NCBITaxon:33208"}, "canonical": "cl.owl", "termgenie": "http://cl.termgenie.org", "mailing_list": "https://lists.sourceforge.net/lists/listinfo/obo-cell-type", "description": "The Cell Ontology is a structured controlled vocabulary for cell types in animals.", "dependencies": [{"id": "uberon"}, {"id": "go"}], "integration_server": "http://build.berkeleybop.org/job/build-cl/", "title": "Cell Ontology", "tracker": "https://code.google.com/p/cell-ontology/issues/list"}, {"layout": "ontology_detail", "contact": {"email": "Sirarat.Sarntivijai@fda.hhs.gov", "label": "Sirarat Sarntivijai"}, "id": "clo", "description": "The Cell Line Ontology (CLO) is a community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning.", "products": [{"id": "clo.owl"}], "title": "Cell Line Ontology", "homepage": "http://www.clo-ontology.org"}, {"domain": "clinical", "layout": "ontology_detail", "contact": {"email": "shimoyama@mcw.edu", "label": "Mary Shimoyama"}, "description": "The Clinical Measurement Ontology is designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs.", "products": [{"id": "cmo.owl"}], "title": "Clinical measurement ontology", "id": "cmo"}, {"layout": "ontology_detail", "contact": {"email": "cjmungall@lbl.gov", "label": "Chris Mungall"}, "products": [{"id": "cteno.owl"}], "id": "cteno", "domain": "anatomy", "taxon": {"label": "Ctenophore", "id": "NCBITaxon:10197"}, "description": "An anatomical and developmental ontology for ctenophores (Comb Jellies)", "title": "Ctenophore Ontology", "homepage": "https://github.com/obophenotype/ctenophore-ontology", "tracker": "https://github.com/obophenotype/ctenophore-ontology/issues"}, {"layout": "ontology_detail", "contact": {"email": "adrien.barton@gmail.com", "label": "Adrien Barton"}, "products": [{"id": "cvdo.owl"}], "id": "cvdo", "domain": "health", "description": "An ontology to describe entities related to cardiovascular diseases (including the diseases themselves, the underlying disorders, and the related pathological processes)", "title": "Cardiovascular Disease Ontology", "homepage": "https://code.google.com/p/cvdo/", "tracker": "https://code.google.com/p/cvdo/issues/list"}, {"layout": "ontology_detail", "contact": {"email": "r-chisholm@northwestern.edu", "label": "Rex Chisholm"}, "products": [{"id": "ddanat.owl"}], "id": "ddanat", "domain": "anatomy", "taxon": {"label": "Dictyostelium discoideum", "id": "NCBITaxon:44689"}, "description": "A structured controlled vocabulary of the anatomy of the slime-mould <i>Dictyostelium discoideum</i>.", "title": "Dictyostelium discoideum anatomy", "homepage": "http://dictybase.org/", "tracker": "http://sourceforge.net/tracker/?group_id=76834&atid=974664"}, {"layout": "ontology_detail", "contact": {"email": "lynn.schriml@gmail.com", "label": "Lynn Schriml"}, "products": [{"id": "doid.owl"}], "page": "http://diseaseontology.sourceforge.net/", "id": "doid", "domain": "health", "taxon": {"label": "Homo sapiens", "id": "NCBITaxon:9606"}, "description": "Creating a comprehensive hierarchical controlled vocabulary for human disease representation.", "title": "Human disease ontology", "homepage": "http://diseaseontology.sourceforge.net/", "tracker": "http://sourceforge.net/tracker/?func=add&group_id=79168&atid=555739"}, {"layout": "ontology_detail", "contact": {"email": "djs93@gen.cam.ac.uk", "label": "David Osumi-Sutherland"}, "preferredPrefix": "FBcv", "products": [{"id": "dpo.owl"}], "id": "dpo", "description": "An ontology of commonly encountered and/or high level Drosophila phenotypes.  It has significant formalisation - utilising terms from GO, CL, PATO and the Drosophila anatomy ontology.  It has been used by FlyBase for > 159000 annotations of phenotype", "title": "Drosophila Phenotype Ontology", "homepage": "http://www.flybase.org/"}, {"layout": "ontology_detail", "contact": {"email": "hoganwr@gmail.com", "label": "William Hogan"}, "products": [{"id": "dron.owl"}], "id": "dron", "domain": "health", "description": "An ontology to support comparative effectiveness researchers studying claims data.", "title": "The Drug Ontology", "homepage": "http://code.google.com/p/dr-on", "tracker": "https://code.google.com/p/dr-on/issues/list"}, {"layout": "ontology_detail", "products": [{"id": "eco.owl"}], "id": "eco", "domain": "experiments", "description": "An ontology for experimental and other evidence statements.", "title": "Evidence codes", "homepage": "https://github.com/evidenceontology/evidenceontology/", "tracker": "https://github.com/evidenceontology/evidenceontology/issues"}, {"layout": "ontology_detail", "contact": {"email": "J.Bard@ed.ac.uk", "label": "Jonathan Bard"}, "products": [{"id": "ehdaa2.owl"}, {"id": "ehdaa2.obo"}], "id": "ehdaa2", "domain": "anatomy", "taxon": {"label": "Homo sapiens", "id": "NCBITaxon:9606"}, "description": "A structured controlled vocabulary of stage-specific anatomical structures of the developing human.", "title": "Human developmental anatomy, abstract", "homepage": "http://genex.hgu.mrc.ac.uk/", "tracker": "https://github.com/obophenotype/human-developmental-anatomy-ontology/issues"}, {"layout": "ontology_detail", "contact": {"email": "Terry.Hayamizu@jax.org", "label": "Terry Hayamizu"}, "products": [{"id": "emap.owl"}], "page": "http://www.obofoundry.org/wiki/index.php/EMAPA:Main_Page", "id": "emap", "domain": "anatomy", "taxon": {"label": "Mus", "id": "NCBITaxon:10088"}, "description": "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).", "title": "Mouse gross anatomy and development, timed", "homepage": "http://emouseatlas.org"}, {"layout": "ontology_detail", "contact": {"email": "p.buttigieg@googlemail.com", "label": "Pier Luigi Buttigieg"}, "products": [{"id": "envo.owl"}], "page": "https://github.com/EnvironmentOntology/envo", "id": "envo", "domain": "environment", "publications": [{"title": "The environment ontology: contextualising biological and biomedical entities", "id": "http://www.dx.doi.org/10.1186/2041-1480-4-43"}], "description": "Ontology of environmental features and habitats", "title": "Environment Ontology", "homepage": "http://environmentontology.org/", "tracker": "https://github.com/EnvironmentOntology/envo/issues/"}, {"contact": {"email": "jaiswalp@science.oregonstate.edu", "label": "Pankaj Jaiswal"}, "products": [{"id": "eo.owl"}], "page": "http://www.gramene.org/plant_ontology/index.html#eo", "id": "eo", "domain": "environment", "description": "A structured, controlled vocabulary for the representation of plant environmental conditions.", "title": "Plant Environmental Conditions", "homepage": "http://www.gramene.org"}, {"description": "An ontology designed to support the semantic annotation of epidemiology resources", "products": [{"id": "epo.owl"}], "homepage": "https://code.google.com/p/epidemiology-ontology/", "id": "epo", "title": "Epidemiology Ontology"}, {"layout": "ontology_detail", "contact": {"email": "carlotorniai@gmail.com", "label": "Carlo Torniai"}, "products": [{"id": "ero.owl"}], "id": "ero", "title": "eagle-i resource ontology", "domain": "resources", "description": "ERO models research resources such instruments. protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project  (http://eagle-i.net/).", "documentation": "http://code.google.com/p/eagle-i/wiki/Documentation", "homepage": "http://code.google.com/p/eagle-i/", "tracker": "http://code.google.com/p/eagle-i/issues/list"}, {"layout": "ontology_detail", "products": [{"id": "exo.owl"}], "page": "http://ctdbase.org/downloads/#exposures", "id": "exo", "domain": "health", "description": "ExO is designed to facilitate centralization and integration of exposure data to inform understanding of environmental health.", "title": "Exposure ontology", "homepage": "http://ctdbase.org/downloads/#exposures"}, {"layout": "ontology_detail", "contact": {"email": "maria@genome.stanford.edu", "label": "Maria Costanzo"}, "products": [{"id": "fao.owl"}], "page": "http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/#description", "id": "fao", "domain": "anatomy", "taxon": {"label": "Fungal", "id": "NCBITaxon:4751"}, "description": "A structured controlled vocabulary for the anatomy of fungi.", "title": "Fungal gross anatomy", "homepage": "http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/"}, {"layout": "ontology_detail", "contact": {"email": "dorloff@ncmir.ucsd.edu", "label": "David Orloff"}, "products": [{"id": "fbbi.owl"}], "id": "fbbi", "domain": "experiments", "description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.", "title": "Biological imaging methods", "homepage": "http://cellimagelibrary.org/"}, {"layout": "ontology_detail", "contact": {"email": "djs93@gen.cam.ac.uk", "label": "David Osumi-Sutherland"}, "preferredPrefix": "FBbt", "products": [{"id": "fbbt.owl"}], "id": "fbbt", "domain": "anatomy", "taxon": {"label": "Drosophila", "id": "NCBITaxon:7227"}, "description": "A structured controlled vocabulary of the anatomy of Drosophila melanogaster", "title": "Drosophila gross anatomy", "homepage": "http://purl.obolibrary.org/obo/fbbt", "tracker": "http://purl.obolibrary.org/obo/fbbt/tracker"}, {"contact": {"email": "djs93@gen.cam.ac.uk", "label": "David Osumi-Sutherland"}, "products": [{"id": "fbdv.owl"}], "id": "fbdv", "domain": "anatomy", "taxon": {"label": "Drosophila", "id": "NCBITaxon:7227"}, "description": "A structured controlled vocabulary of the development of Drosophila melanogaster", "title": "Drosophila development", "homepage": "http://www.flybase.org/", "tracker": "https://cedar.bio.indiana.edu/trac/env/ontologies/wiki/PublicWikiStart"}, {"layout": "ontology_detail", "contact": {"email": "ma11@gen.cam.ac.uk", "label": "Michael Ashburner"}, "products": [{"id": "fbsp.owl"}], "id": "fbsp", "domain": "taxonomy", "taxon": {"label": "Drosophila", "id": "NCBITaxon:7227"}, "description": "The taxonomy of the family <i>Drosophilidae</i> (largely after Baechli) and of other taxa referred to in FlyBase.", "title": "Fly taxonomy", "homepage": "http://www.flybase.org/", "tracker": "https://cedar.bio.indiana.edu/trac/env/ontologies/wiki/PublicWikiStart"}, {"description": "FIX consists of two ontologies: methods and properties (but not objects, which are subject of the chemical ontology). The methods are applied to study the properties.", "products": [{"id": "fix.owl"}], "title": "Physico-chemical methods and properties", "id": "fix", "contact": {"email": "hastings@ebi.ac.uk", "label": "Janna Hastings"}}, {"domain": "health", "contact": {"email": "burkesquires@gmail.com", "label": "Burke Squires"}, "id": "flu", "products": [{"id": "flu.owl"}], "title": "Influenza Ontology", "homepage": "http://purl.obolibrary.org/obo/flu/", "tracker": "http://purl.obolibrary.org/obo/flu/tracker"}, {"layout": "ontology_detail", "contact": {"email": "mejino@comcast.net", "label": "Onard Mejino"}, "products": [{"id": "fma.owl"}], "page": "http://en.wikipedia.org/wiki/Foundational_Model_of_Anatomy", "id": "fma", "domain": "anatomy", "taxon": {"label": "Homo sapiens", "id": "NCBITaxon:9606"}, "publications": [{"id": "http://www.ncbi.nlm.nih.gov/pubmed/18688289"}, {"id": "http://www.ncbi.nlm.nih.gov/pubmed/18360535"}, {"id": "http://www.ncbi.nlm.nih.gov/pubmed/16779026"}], "description": "Obo format translation of the FMA, omitting all relationships other than is_a, part_of and has_part. 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