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_config.yml
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_config.yml
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name: OBO Foundry
title: The OBO Foundry
markdown: redcarpet
pygments: true
baseurl: /
imgurl: /images
author:
name: OBO Technical WG
ontologies:
- build: {checkout: 'git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git',
method: vcs, path: src/ontology, system: git}
contact: {email: [email protected], label: Jonathan Bard}
description: AEO is an ontology of anatomical structures that expands CARO, the
Common Anatomy Reference Ontology
domain: anatomy
homepage: http://www.obofoundry.org/wiki/index.php/AEO:Main_Page
id: aeo
layout: ontology_detail
products:
- {id: aeo.owl}
title: Anatomical Entity Ontology
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/aero.owl'}
contact: {email: [email protected], label: Melanie Courtot}
description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at
supporting clinicians at the time of data entry, increasing quality and accuracy
of reported adverse events
domain: health
homepage: http://purl.obolibrary.org/obo/aero
id: aero
layout: ontology_detail
products:
- {id: aero.owl}
title: Adverse Event Reporting Ontology
- build: {method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/ascomycete_phenotype.obo'}
contact: {email: [email protected], label: Maria Costanza}
description: A structured controlled vocabulary for the phenotypes of Ascomycete
fungi
domain: phenotype
homepage: 'http://www.yeastgenome.org/ '
id: apo
layout: ontology_detail
products:
- {id: apo.owl}
taxon: {id: 'NCBITaxon:4890', label: Ascomycota}
title: Ascomycete phenotype ontology
- contact: {email: [email protected], label: Jie Zheng}
description: An application ontology built for beta cell genomics studies.
homepage: https://github.com/obi-bcgo/bcgo
id: bcgo
in_foundry: false
layout: ontology_detail
products:
- {id: bcgo.owl}
title: Beta Cell Genomics Ontology
tracker: https://github.com/obi-bcgo/bcgo/issues
- contact: {email: [email protected], label: Ramona Walls}
description: An ontology to support the interoperability of biodiversity data, including
data on museum collections, environmental/metagenomic samples, and ecological
surveys.
homepage: https://github.com/tucotuco/bco
id: bco
products:
- {id: bco.owl}
title: Biological Collections Ontology
tracker: https://github.com/tucotuco/bco/issues
- contact: {email: [email protected], label: Barry Smith}
depicted_by: https://code.google.com/p/bfo/logo?cct=1426583016
description: The upper level ontology upon which OBO Foundry ontologies are built.
domain: upper
homepage: http://ifomis.org/bfo/
id: bfo
layout: ontology_detail
page: http://ifomis.org/bfo/
products:
- {id: bfo.owl}
title: Basic Formal Ontology
- build: {method: obo2owl, source_url: 'http://4dx.embl.de/4DXpress_4d/edocs/bilateria_mrca.obo'}
contact: {email: [email protected], label: Thorsten Heinrich}
domain: anatomy
homepage: http://4dx.embl.de/4DXpress
id: bila
is_obsolete: true
layout: ontology_detail
products:
- {id: bila.owl}
replaced_by: uberon
taxon: {id: 'NCBITaxon:33213', label: Bilateria}
title: Bilateria anatomy
- build: {checkout: 'git clone https://github.com/obophenotype/biological-spatial-ontology.git',
infallible: 1, method: vcs, path: src/ontology, system: git}
contact: {email: [email protected], label: Chris Mungall}
description: An ontology for respresenting spatial concepts, anatomical axes, gradients,
regions, planes, sides, and surfaces
domain: anatomy
homepage: https://github.com/obophenotype/biological-spatial-ontology
id: bspo
layout: ontology_detail
products:
- {id: bspo.owl}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/25140222', title: 'Nose to tail, roots
to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial
Ontology.'}
title: Biological Spatial Ontology
tracker: https://github.com/obophenotype/biological-spatial-ontology/issues
- build: {method: obo2owl, source_url: 'http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO'}
contact: {email: [email protected], label: Antje Chang}
description: A structured controlled vocabulary for the source of an enzyme comprising
tissues, cell lines, cell types and cell cultures.
domain: anatomy
homepage: http://www.brenda-enzymes.info
id: bto
layout: ontology_detail
license: {alert: Restricted, label: BRENDA license, url: 'http://www.brenda-enzymes.org/copy.php'}
page: https://en.wikipedia.org/wiki/BRENDA_tissue_ontology
products:
- {id: bto.owl}
publications:
- {id: 'https://www.ncbi.nlm.nih.gov/pubmed/21030441', title: 'The BRENDA Tissue
Ontology (BTO): the first all-integrating ontology of all organisms for enzyme
sources'}
title: BRENDA tissue / enzyme source
- build: {method: obo2owl, notes: moving to owl soon, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro.obo'}
contact: {email: [email protected], label: Melissa Haendel}
description: An upper level ontology to facilitate interoperability between existing
anatomy ontologies for different species
domain: anatomy
homepage: https://github.com/obophenotype/caro/
id: caro
layout: ontology_detail
products:
- {id: caro.owl}
title: Common Anatomy Reference Ontology
tracker: https://github.com/obophenotype/caro/issues
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/cdao.owl'}
contact: {email: [email protected], label: Jim Balhoff}
description: a formalization of concepts and relations relevant to evolutionary
comparative analysis
homepage: http://sourceforge.net/apps/mediawiki/cdao/index.php?title=Main_Page
id: cdao
layout: ontology_detail
products:
- {id: cdao.owl}
title: Comparative Data Analysis Ontology
- build: {checkout: 'git clone https://github.com/obophenotype/cephalopod-ontology.git',
method: vcs, path: src/ontology, system: git}
contact: {email: [email protected], label: Chris Mungall}
description: An anatomical and developmental ontology for cephalopods
domain: anatomy
homepage: https://github.com/obophenotype/cephalopod-ontology
id: ceph
layout: ontology_detail
license: {label: CC-BY, url: 'https://creativecommons.org/licenses/by/3.0/'}
products:
- {id: ceph.owl}
taxon: {id: 'NCBITaxon:6605', label: Cephalopod}
title: Cephalopod Ontology
tracker: https://github.com/obophenotype/cephalopod-ontology/issues
- alternatePrefix: ChEBI
build: {infallible: 1, method: archive, path: archive/main, source_url: 'http://build.berkeleybop.org/job/build-chebi/lastSuccessfulBuild/artifact/*zip*/archive.zip'}
contact: {email: [email protected], label: Janna Hastings}
description: A structured classification of chemical compounds of biological relevance.
domain: biochemistry
homepage: http://www.ebi.ac.uk/chebi
id: chebi
in_foundry_order: 1
layout: ontology_detail
page: http://www.ebi.ac.uk/chebi/init.do?toolBarForward=userManual
products:
- {id: chebi.owl}
- {id: chebi.obo}
title: Chemical entities of biological interest
tracker: https://sourceforge.net/p/chebi/curator-requests/
- build: {method: owl2obo, source_url: 'http://semanticchemistry.googlecode.com/svn/trunk/ontology/cheminf.owl'}
contact: {email: [email protected], label: Janna Hastings}
description: Includes terms for the descriptors commonly used in cheminformatics
software applications and the algorithms which generate them.
domain: biochemistry
homepage: http://code.google.com/p/semanticchemistry/
id: cheminf
layout: ontology_detail
products:
- {id: cheminf.owl}
title: Chemical Information Ontology
- contact: {email: [email protected], label: Colin Batchelor}
description: CHMO, the chemical methods ontology, describes methods used to
domain: health
homepage: http://code.google.com/p/rsc-cmo/
id: chmo
layout: ontology_detail
products:
- {id: chmo.owl}
title: Chemical Methods Ontology
tracker: http://code.google.com/p/rsc-cmo/issues/list
- build: {checkout: 'git clone https://github.com/obophenotype/cell-ontology.git',
email_cc: [email protected], infallible: 1, method: vcs, system: git}
canonical: cl.owl
dependencies:
- {id: uberon}
- {id: go}
description: The Cell Ontology is a structured controlled vocabulary for cell types
in animals.
domain: cells
id: cl
integration_server: http://build.berkeleybop.org/job/build-cl/
label: Cell Ontology
layout: ontology_detail
mailing_list: https://lists.sourceforge.net/lists/listinfo/obo-cell-type
products:
- {id: cl.owl}
- {id: cl.obo}
- {id: cl/cl-basic.obo}
taxon: {id: 'NCBITaxon:33208', label: Metazoa}
termgenie: http://cl.termgenie.org
title: Cell Ontology
tracker: https://code.google.com/p/cell-ontology/issues/list
- build: {checkout: 'svn --ignore-externals co http://clo-ontology.googlecode.com/svn/trunk/src/ontology',
method: vcs, post_processing_command: owltools --use-catalog clo.owl --merge-imports-closure
--ni -o -f obo --no-check clo.obo, system: svn}
contact: {email: [email protected], label: Sirarat Sarntivijai}
description: An ontology to standardize and integrate cell line information and
to support computer-assisted reasoning.
homepage: http://www.clo-ontology.org
id: clo
layout: ontology_detail
products:
- {id: clo.owl}
title: Cell Line Ontology
- build: {method: obo2owl, source_url: 'ftp://rgd.mcw.edu/pub/ontology/clinical_measurement/clinical_measurement.obo'}
contact: {email: [email protected], label: Mary Shimoyama}
description: Morphological and physiological measurement records generated from
clinical and model organism research and health programs.
domain: clinical
id: cmo
layout: ontology_detail
products:
- {id: cmo.owl}
- {id: cmo.obo}
title: Clinical measurement ontology
- build: {checkout: 'git clone https://github.com/obophenotype/ctenophore-ontology.git',
method: vcs, path: src/ontology, system: git}
contact: {email: [email protected], label: Chris Mungall}
description: An anatomical and developmental ontology for ctenophores (Comb Jellies)
domain: anatomy
homepage: https://github.com/obophenotype/ctenophore-ontology
id: cteno
layout: ontology_detail
license: {label: CC-BY, url: 'https://creativecommons.org/licenses/by/3.0/'}
products:
- {id: cteno.owl}
taxon: {id: 'NCBITaxon:10197', label: Ctenophore}
title: Ctenophore Ontology
tracker: https://github.com/obophenotype/ctenophore-ontology/issues
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/cvdo.owl'}
contact: {email: [email protected], label: Adrien Barton}
description: An ontology to describe entities related to cardiovascular diseases
domain: health
homepage: https://code.google.com/p/cvdo/
id: cvdo
layout: ontology_detail
products:
- {id: cvdo.owl}
title: Cardiovascular Disease Ontology
tracker: https://code.google.com/p/cvdo/issues/list
- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/dictyBase/migration-data/master/ontologies/dicty_anatomy.obo'}
contact: {email: [email protected], label: Rex Chisholm}
description: A structured controlled vocabulary of the anatomy of the slime-mould
<i>Dictyostelium discoideum</i>.
domain: anatomy
homepage: http://dictybase.org/
id: ddanat
layout: ontology_detail
products:
- {id: ddanat.owl}
taxon: {id: 'NCBITaxon:44689', label: Dictyostelium discoideum}
title: Dictyostelium discoideum anatomy
tracker: http://sourceforge.net/tracker/?group_id=76834&atid=974664
twitter: dictybase
- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/dictyBase/migration-data/master/ontologies/dicty_phenotypes.obo'}
contact: {email: [email protected], label: Rex Chisholm}
description: A structured controlled vocabulary of phenotypes of the slime-mould
<i>Dictyostelium discoideum</i>.
domain: anatomy
homepage: http://dictybase.org/
id: ddpheno
layout: ontology_detail
products:
- {id: ddpheno.owl}
taxon: {id: 'NCBITaxon:44689', label: Dictyostelium discoideum}
title: Dictyostelium discoideum phenotype
twitter: dictybase
- browsers:
- {label: DO, title: DO Browser, url: 'http://www.disease-ontology.org/'}
- {label: Monarch, title: Monarch Phenotype Page, url: 'http://monarchinitiative.org/phenotype/DOID:4'}
build: {infallible: 1, method: obo2owl, source_url: 'http://sourceforge.net/p/diseaseontology/code/HEAD/tree/trunk/HumanDO.obo?format=raw'}
contact: {email: [email protected], label: Lynn Schriml}
description: Creating a comprehensive hierarchical controlled vocabulary for human
disease representation.
domain: health
homepage: http://diseaseontology.sourceforge.net/
id: doid
layout: ontology_detail
page: http://diseaseontology.sourceforge.net/
products:
- {id: doid.owl}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/25348409', title: 'Disease Ontology 2015
update: an expanded and updated database of human diseases for linking biomedical
knowledge through disease data.'}
taxon: {id: 'NCBITaxon:9606', label: Homo sapiens}
title: Human disease ontology
tracker: http://sourceforge.net/tracker/?func=add&group_id=79168&atid=555739
twitter: diseaseontology
- build: {infallible: 0, method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/fbcv/dpo.owl'}
contact: {email: [email protected], label: David Osumi-Sutherland}
description: An ontology of commonly encountered and/or high level Drosophila phenotypes.
homepage: http://www.flybase.org/
id: dpo
layout: ontology_detail
preferredPrefix: FBcv
products:
- {id: dpo.owl}
title: Drosophila Phenotype Ontology
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/dron.owl'}
contact: {email: [email protected], label: William Hogan}
description: An ontology to support comparative effectiveness researchers studying
claims data.
domain: health
homepage: http://code.google.com/p/dr-on
id: dron
layout: ontology_detail
products:
- {id: dron.owl}
title: The Drug Ontology
tracker: https://code.google.com/p/dr-on/issues/list
- build: {infallible: 1, method: obo2owl, notes: switch to vcs, source_url: 'https://raw.githubusercontent.com/evidenceontology/evidenceontology/master/eco.obo'}
description: An ontology for experimental and other evidence statements.
domain: experiments
homepage: https://github.com/evidenceontology/evidenceontology/
id: eco
layout: ontology_detail
products:
- {id: eco.owl}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/25052702', title: Standardized description
of scientific evidence using the Evidence Ontology (ECO)}
title: Evidence codes
tracker: https://github.com/evidenceontology/evidenceontology/issues
- build: {checkout: 'git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git',
method: vcs, path: src/ontology, system: git}
contact: {email: [email protected], label: Jonathan Bard}
description: A structured controlled vocabulary of stage-specific anatomical structures
of the developing human.
domain: anatomy
homepage: http://genex.hgu.mrc.ac.uk/
id: ehdaa2
layout: ontology_detail
products:
- {id: ehdaa2.owl}
- {id: ehdaa2.obo}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/22973865', title: A new ontology (structured
hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages
1-20).}
taxon: {id: 'NCBITaxon:9606', label: Homo sapiens}
title: Human developmental anatomy, abstract
tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues
- build: {method: obo2owl, notes: new url soon, source_url: 'ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAP_combined.obo'}
contact: {email: [email protected], label: Terry Hayamizu}
description: A structured controlled vocabulary of stage-specific anatomical structures
of the mouse (Mus).
domain: anatomy
homepage: http://emouseatlas.org
id: emap
layout: ontology_detail
page: http://www.obofoundry.org/wiki/index.php/EMAPA:Main_Page
products:
- {id: emap.owl}
taxon: {id: 'NCBITaxon:10088', label: Mus}
title: Mouse gross anatomy and development, timed
- build: {method: obo2owl, notes: new url soon, source_url: 'ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAPA.obo'}
contact: {email: [email protected], label: Terry Hayamizu}
description: Abstract (i.e. non-stage specific) stage-specific anatomical structures
of the mouse.
domain: anatomy
homepage: http://emouseatlas.org
id: emapa
layout: ontology_detail
page: http://www.obofoundry.org/wiki/index.php/EMAPA:Main_Page
products:
- {id: emap.owl}
taxon: {id: 'NCBITaxon:10088', label: Mus}
title: Mouse gross anatomy and development, timed
- build: {checkout: 'git clone https://github.com/EnvironmentOntology/envo.git', email_cc: [email protected],
infallible: 1, method: vcs, path: src/envo, system: git}
contact: {email: [email protected], label: Pier Luigi Buttigieg}
description: Ontology of environmental features and habitats
domain: environment
homepage: http://environmentontology.org/
id: envo
layout: ontology_detail
page: https://github.com/EnvironmentOntology/envo
products:
- {id: envo.owl}
publications:
- {id: 'http://www.dx.doi.org/10.1186/2041-1480-4-43', title: 'The environment ontology:
contextualising biological and biomedical entities'}
title: Environment Ontology
tracker: https://github.com/EnvironmentOntology/envo/issues/
- build: {method: obo2owl, source_url: 'http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/plant_environment/environment_ontology.obo'}
contact: {email: [email protected], label: Pankaj Jaiswal}
description: A structured, controlled vocabulary for the representation of plant
environmental conditions.
domain: environment
homepage: http://www.gramene.org
id: eo
layout: ontology_detail
page: http://www.gramene.org/plant_ontology/index.html#eo
products:
- {id: eo.owl}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/22847540', title: Ontologies as integrative
tools for plant science.}
title: Plant Environmental Conditions
tracker: https://github.com/Planteome/plant-environment-ontology/issues
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/epo.owl'}
description: An ontology designed to support the semantic annotation of epidemiology
resources
homepage: https://code.google.com/p/epidemiology-ontology/
id: epo
products:
- {id: epo.owl}
title: Epidemiology Ontology
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/ero.owl'}
contact: {email: [email protected], label: Carlo Torniai}
description: An ontology of research resources such as instruments. protocols, reagents,
animal models and biospecimens.
documentation: http://code.google.com/p/eagle-i/wiki/Documentation
domain: resources
homepage: http://code.google.com/p/eagle-i/
id: ero
layout: ontology_detail
products:
- {id: ero.owl}
title: eagle-i resource ontology
tracker: http://code.google.com/p/eagle-i/issues/list
- build: {method: obo2owl, source_url: 'http://ctdbase.org/reports/CTD_exposure_ontology.obo'}
description: ExO is designed to facilitate centralization and integration of exposure
data to inform understanding of environmental health.
domain: health
homepage: http://ctdbase.org/downloads/#exposures
id: exo
layout: ontology_detail
page: http://ctdbase.org/downloads/#exposures
products:
- {id: exo.owl}
title: Exposure ontology
- build: {method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/microbial_gross_anatomy/fungi/fungal_anatomy.obo'}
contact: {email: [email protected], label: Maria Costanzo}
description: A structured controlled vocabulary for the anatomy of fungi.
domain: anatomy
homepage: http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/
id: fao
layout: ontology_detail
page: http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/#description
products:
- {id: fao.owl}
taxon: {id: 'NCBITaxon:4751', label: Fungal}
title: Fungal gross anatomy
- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/dosumis/fbbi/master/src/ontology/fbbi.obo'}
contact: {email: [email protected], label: David Orloff}
description: A structured controlled vocabulary of sample preparation, visualization
and imaging methods used in biomedical research.
domain: experiments
homepage: http://cellimagelibrary.org/
id: fbbi
layout: ontology_detail
products:
- {id: fbbi.owl}
title: Biological imaging methods
- browsers:
- {label: FB, title: FlyBase Browser, url: 'http://flybase.org/.bin/cvreport.html?cvterm=FBbt:10000000'}
- {label: VFB, title: Virtual Fly Brain, url: 'http://www.virtualflybrain.org/site/stacks/index.htm?add=FBbt:00007401'}
- {label: BioPortal, title: BioPortal Browser, url: 'http://bioportal.bioontology.org/ontologies/FB-BT?p=classes'}
build: {infallible: 1, method: owl2obo, source_url: 'http://svn.code.sf.net/p/fbbtdv/code/fbbt/releases/fbbt.owl'}
contact: {email: [email protected], label: Marta Costa}
description: An ontology representing the anatomy of Drosophila melanogaster
domain: anatomy
homepage: http://purl.obolibrary.org/obo/fbbt
id: fbbt
layout: ontology_detail
preferredPrefix: FBbt
products:
- {id: fbbt.owl}
- {id: fbbt/fbbt-simple.owl}
- {id: fbbt/fbbt-simple.obo}
taxon: {id: 'NCBITaxon:7227', label: Drosophila}
title: Drosophila gross anatomy
tracker: http://purl.obolibrary.org/obo/fbbt/tracker
- build: {method: obo2owl, source_url: 'http://sourceforge.net/p/fbcv/code-0/HEAD/tree/src/trunk/ontologies/fbcv-edit.obo?format=raw'}
contact: {email: [email protected], label: David Osumi-Sutherland}
description: A structured controlled vocabulary used for various aspects of annotation
by FlyBase.
homepage: http://www.flybase.org/
id: fbcv
is_obsolete: true
layout: ontology_detail
preferredPrefix: FBcv
products:
- {id: fbcv.owl}
title: FlyBase Controlled Vocabulary
- build: {infallible: 0, method: obo2owl, source_url: 'http://svn.code.sf.net/p/fbbtdv/code/fbdv/releases/latest/fbdv.obo'}
contact: {email: [email protected], label: David Osumi-Sutherland}
description: A structured controlled vocabulary of the development of Drosophila
melanogaster
domain: anatomy
homepage: http://www.flybase.org/
id: fbdv
products:
- {id: fbdv.owl}
taxon: {id: 'NCBITaxon:7227', label: Drosophila}
title: Drosophila development
tracker: https://cedar.bio.indiana.edu/trac/env/ontologies/wiki/PublicWikiStart
- build: {method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/fly_taxonomy.obo'}
contact: {email: [email protected], label: Michael Ashburner}
description: The taxonomy of the family <i>Drosophilidae</i> (largely after Baechli)
and of other taxa referred to in FlyBase.
domain: taxonomy
homepage: http://www.flybase.org/
id: fbsp
layout: ontology_detail
products:
- {id: fbsp.owl}
taxon: {id: 'NCBITaxon:7227', label: Drosophila}
title: Fly taxonomy
tracker: https://cedar.bio.indiana.edu/trac/env/ontologies/wiki/PublicWikiStart
- contact: {email: [email protected], label: Janna Hastings}
description: An ontology of physico-chemical methods and properties.
id: fix
products:
- {id: fix.owl}
title: Physico-chemical methods and properties
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/flu.owl'}
contact: {email: [email protected], label: Burke Squires}
domain: health
homepage: http://purl.obolibrary.org/obo/flu/
id: flu
products:
- {id: flu.owl}
title: Influenza Ontology
tracker: http://purl.obolibrary.org/obo/flu/tracker
- build: {infallible: 1, method: obo2owl, source_url: 'http://svn.code.sf.net/p/obo/svn/fma-conversion/trunk/fma2_obo.obo'}
contact: {email: [email protected], label: Onard Mejino}
description: This is currently a slimmed down version of FMA
domain: anatomy
homepage: http://sig.biostr.washington.edu/projects/fm/index.html
id: fma
layout: ontology_detail
page: http://en.wikipedia.org/wiki/Foundational_Model_of_Anatomy
products:
- {id: fma.owl}
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'}
taxon: {id: 'NCBITaxon:9606', label: Homo sapiens}
title: Foundational Model of Anatomy (subset)
tracker: https://sourceforge.net/p/obo/foundational-model-of-anatomy-fma-requests/
- build: {infallible: 1, method: obo2owl, source_url: 'https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/releases/latest/fypo.obo?format=raw'}
contact: {email: [email protected], label: Midori Harris}
description: FYPO is a formal ontology of phenotypes observed in fission yeast.
domain: phenotype
homepage: https://github.com/pombase/fypo
id: fypo
layout: ontology_detail
products:
- {id: fypo.owl}
taxon: {id: 'NCBITaxon:4896', label: S. pombe}
title: Fission Yeast Phenotype Ontology
tracker: https://github.com/pombase/fypo/issues
- build: {method: archive, path: archive, source_url: 'http://build.berkeleybop.org/job/build-gaz/lastSuccessfulBuild/artifact/*zip*/archive.zip'}
contact: {email: [email protected], label: Michael Ashburner}
homepage: http://gensc.org/gc_wiki/index.php/GAZ_Project
id: gaz
layout: ontology_detail
products:
- {id: gaz.owl}
title: Gazetteer
tracker: http://sourceforge.net/tracker/?func=browse&group_id=76834&atid=1014856
- contact: {email: [email protected], label: Mathias Brochhausen}
description: An ontology of geographical entities implemented in Web Ontology Language
2 (OWL2) and based on Basic Formal Ontology (BFO). The developers aim to adhere
to the OBO Foundry principles.
homepage: https://code.google.com/p/ge-ontology/
id: geo
layout: ontology_detail
products:
- {id: geo.owl}
title: Geographical Entity Ontology
tracker: https://ontology.atlassian.net/browse/GEO#selectedTab=com.atlassian.jira.plugin.system.project%3Aissues-panel
- browsers:
- {label: AmiGO, title: Gene Ontology AmiGO 2 Browser, url: 'http://amigo.geneontology.org/amigo/term/GO:0008150#display-lineage-tab'}
build: {checkout: 'svn --ignore-externals co svn://ext.geneontology.org/trunk/ontology',
infallible: 1, method: vcs, system: svn}
dependencies:
- {id: uberon, subset: go/extensions/uberon_import.owl}
- {id: cl, subset: go/extensions/cl_import.owl}
- {id: ncbitaxon, subset: go/extensions/ncbitaxon_import.owl}
- {id: ro, subset: go/extensions/ro_import.owl}
- connects:
- {id: nifstd}
- {id: go}
description: Bridging axioms between nifstd and go
id: go/extensions/go-bridge-to-nifstd.owl
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/24093723', title: 'The Gene Ontology
(GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy
Ontology) and other recent developments.'}
title: GO bridge to NIFSTD
type: BridgeOntology
depicted_by: http://geneontology.org/sites/default/files/go-logo-icon.mini__0.png
description: An ontology for describing the function of genes and gene products
domain: biology
id: go
in_foundry_order: 1
integration_server: http://build.berkeleybop.org/view/GO
label: GO
layout: ontology_detail
license: {label: CC-BY, url: 'https://creativecommons.org/licenses/by/3.0/'}
products:
- {id: go.owl}
- {description: The core ontology plus axioms connecting to select external ontologies,
id: go/extensions/go-plus.owl, title: GO-Plus}
- {description: Classes added to ncbitaxon for groupings such as prokaryotes, id: go/extensions/go-taxon-groupings.owl,
title: GO Taxon Groupings}
taxon: {id: 'NCBITaxon:1', label: All life}
termgenie: http://go.termgenie.org
title: Gene Ontology
tracker: https://github.com/geneontology/go-ontology/issues/
twitter: news4go
- build: {checkout: 'svn co http://obo.svn.sourceforge.net/svnroot/obo/ontologies/trunk/HAO',
method: vcs, system: svn}
contact: {email: [email protected], label: Matt Yoder}
description: A structured controlled vocabulary of the anatomy of the Hymenoptera
(bees, wasps, and ants)
domain: anatomy
homepage: http://hymao.org
id: hao
layout: ontology_detail
s:
- {id: hao.owl}
taxon: {id: 'NCBITaxon:7399', label: Hymenoptera}
title: Hymenoptera Anatomy Ontology
- build: {checkout: 'git clone https://github.com/BgeeDB/homology-ontology.git', method: vcs,
system: git}
contact: {email: [email protected], label: ''}
description: This ontology represents concepts related to homology, as well as other
concepts used to describe similarity and non-homology.
homepage: http://bioinfo.unil.ch
id: hom
layout: ontology_detail
products:
- {id: hom.owl}
title: homology_ontology
- alternativePrefix: HPO
browsers:
- {label: HPO, title: Charite HPO Browser, url: 'http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000118'}
- {label: Monarch, title: Monarch Phenotype Page, url: 'http://monarchinitiative.org/phenotype/HP:0000118'}
build: {method: obo2owl, source_url: 'http://compbio.charite.de/svn/hpo/trunk/src/ontology/human-phenotype-ontology.obo'}
contact: {email: [email protected], label: Peter Robinson}
description: A structured and controlled vocabulary for the phenotypic features
encountered in human hereditary and other disease.
domain: phenotype
homepage: http://www.human-phenotype-ontology.org/
id: hp
layout: ontology_detail
products:
- {id: hp.owl}
- {id: hp.obo}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/18950739', title: 'The Human Phenotype
Ontology: a tool for annotating and analyzing human hereditary disease.'}
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/26119816', title: 'The Human Phenotype
Ontology: Semantic Unification of Common and Rare Disease.'}
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/24217912', title: 'The Human Phenotype
Ontology project: linking molecular biology and disease through phenotype data.'}
taxon: {id: 'NCBITaxon:9606', label: Homo sapiens}
termgenie: http://hp.termgenie.org
title: human phenotype ontology
tracker: https://sourceforge.net/p/obo/human-phenotype-requests/
twitter: hp_ontology
- build: {infallible: 1, method: obo2owl, source_url: 'https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/hsapdv/hsapdv.obo'}
description: Life cycle stages for Human
homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv
id: hsapdv
layout: ontology_detail
page: https://github.com/obophenotype/developmental-stage-ontologies
title: Human Developmental Stages
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/iao.owl'}
contact: {email: [email protected], label: Alan Ruttenberg}
depicted_by: https://avatars0.githubusercontent.com/u/13591168?v=3&s=200
description: An ontology of information entities.
domain: information
homepage: http://purl.obolibrary.org/obo/iao
id: iao
layout: ontology_detail
page: http://code.google.com/p/information-artifact-ontology/
products:
- {id: iao.owl}
- contact: {email: [email protected], label: Mathias Brochhausen}
description: An ontology based on a theory of document acts describing what people
can do with documents
id: iao/d-acts.owl
title: ontology of document acts
title: Information Artifact Ontology
tracker: http://code.google.com/p/information-artifact-ontology/issues/list
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/ido.owl'}
contact: {email: [email protected], label: Lindsay Cowell}
domain: health
homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology
id: ido
layout: ontology_detail
products:
- {id: ido.owl}
taxon: {id: 'NCBITaxon:9606', label: Homo sapiens}
title: Infectious disease
tracker: http://code.google.com/p/infectious-disease-ontology/issues/list
- build: {method: obo2owl, source_url: 'http://anobase.vectorbase.org/idomal/IDOMAL.obo'}
contact: {email: [email protected], label: Pantelis Topalis}
description: An application ontology to cover all aspects of malaria as well as
the intervention attempts to control it.
domain: health
homepage: http://anobase.vectorbase.org
id: idomal
layout: ontology_detail
products:
- {id: idomal.owl}
title: Malaria Ontology
- build: {method: obo2owl, source_url: 'http://biomodels.net/kisao/KISAO'}
contact: {email: [email protected], label: Nicolas Le Novere}
description: A classification of algorithms available for the simulation of models
in biology.
domain: algorithms
homepage: http://biomodels.net/kisao
id: kisao
layout: ontology_detail
products:
- {id: kisao.owl}
title: Kinetic Simulation Algorithm Ontology
tracker: https://sourceforge.net/tracker/?group_id=293617
- build: {method: owl2obo, source_url: 'http://www.lipidprofiles.com/LipidOntology'}
contact: {email: [email protected], label: Christipher Baker}
description: An ontology representation of the LIPIDMAPS nomenclature classification.
domain: lipids
id: lipro
products:
- {id: lipro.owl}
title: Lipid Ontology
- build: {infallible: 1, method: obo2owl, source_url: 'ftp://ftp.informatics.jax.org/pub/reports/adult_mouse_anatomy.obo'}
contact: {email: [email protected], label: Terry Hayamizu}
description: A structured controlled vocabulary of the adult anatomy of the mouse
(Mus).
domain: anatomy
homepage: https://github.com/obophenotype/mouse-anatomy-ontology
id: ma
layout: ontology_detail
page: http://www.informatics.jax.org/searches/AMA_form.shtml
products:
- {id: ma.owl}
taxon: {id: 'NCBITaxon:10088', label: Mus}
title: Mouse adult gross anatomy
tracker: https://github.com/obophenotype/mouse-anatomy-ontology/issues
- contact: {email: [email protected], label: Nicolas Le Novere}
description: The Mathematical Modelling Ontology (MAMO) is a classification of the
types of mathematical models used mostly in the life sciences, their variables,
relationships and other relevant features.
homepage: http://sourceforge.net/projects/mamo-ontology/
id: mamo
layout: ontology_detail
products:
- {id: mamo.owl}
title: Mathematical modeling ontology
tracker: http://sourceforge.net/p/mamo-ontology/tickets/
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/mf.owl'}
contact: {email: [email protected], label: Janna Hastings}
homepage: https://code.google.com/p/mental-functioning-ontology/
id: mf
layout: ontology_detail
products:
- {id: mf.owl}
title: Mental Functioning Ontology
tracker: https://code.google.com/p/mental-functioning-ontology/issues/list
- contact: {email: [email protected], label: Robert Druzinsky}
dependencies:
- {id: uberon}
description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the
muscles of the head and neck that participate in feeding, swallowing, and other
oral-pharyngeal behaviors.
domain: anatomy
homepage: http://feedexp.org
id: mfmo
layout: ontology_detail
license: {label: CC-BY, url: 'https://creativecommons.org/licenses/by/3.0/'}
repository: https://github.com/RDruzinsky/feedontology
taxon: {id: 'NCBITaxon:40674', label: Mammalian}
title: Mammalian Feeding Muscle Ontology
tracker: https://github.com/RDruzinsky/feedontology/issues
- build: {method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/medaka_ontology.obo'}
contact: {email: [email protected], label: Thorsten Henrich}
description: A structured controlled vocabulary of the anatomy and development of
the Japanese medaka fish, <i>Oryzias latipes</i>.
domain: anatomy
id: mfo
layout: ontology_detail
products:
- {id: mfo.owl}
taxon: {id: 'NCBITaxon:8089', label: Oryzias}
title: Medaka fish anatomy and development
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/mfoem.owl'}
contact: {email: [email protected], label: Janna Hastings}
description: An ontology of affective phenomena such as emotions, moods, appraisals
and subjective feelings.
domain: health
homepage: https://code.google.com/p/emotion-ontology/
id: mfoem
layout: ontology_detail
products:
- {id: mfoem.owl}
title: Emotion Ontology
tracker: https://code.google.com/p/emotion-ontology/issues/list
- build: {method: obo2owl, source_url: 'http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/mi/rel25/data/psi-mi25.obo'}
contact: {email: [email protected], label: Henning Hermjakob}
description: A structured controlled vocabulary for the annotation of experiments
concerned with protein-protein interactions.
domain: experiments
homepage: http://psidev.sf.net
id: mi
layout: ontology_detail
page: http://psidev.sourceforge.net/mi/xml/doc/user/index.html
products:
- {id: mi.owl}
title: Protein-protein interaction
- contact: {email: [email protected], label: Hilamr Lapp}
description: An application ontology to formalize annotation of phylogenetic data.
homepage: http://www.evoio.org/wiki/MIAPA
id: miapa
layout: ontology_detail
s:
- {id: miapa.owl}
title: MIAPA Ontology
tracker: https://github.com/miapa/miapa/issues
- contact: {email: [email protected], label: Vicky Dritsou}
description: An application ontology for use with miRNA databases.
homepage: http://code.google.com/p/mirna-ontology/
id: mirnao
layout: ontology_detail
products:
- {id: mirnao.owl}
title: microRNA Ontology
- build: {method: obo2owl, source_url: 'http://anobase.vectorbase.org/miro/miro_release.obo'}
contact: {email: [email protected], label: C. Louis}
description: Application ontology for entities related to insecticide resistance
in mosquitos
domain: environment
homepage: http://anobase.vectorbase.org
id: miro
layout: ontology_detail
products:
- {id: miro.owl}
taxon: {id: 'NCBITaxon:44484', label: Anopheles}
title: Mosquito insecticide resistance
- build: {method: obo2owl, source_url: 'ftp://rgd.mcw.edu/pub/ontology/measurement_method/measurement_method.obo'}
contact: {email: [email protected], label: Mary Shimoyama}
description: 'A representation of the variety of methods used to make clinical and
phenotype measurements. '
domain: clinical
id: mmo
layout: ontology_detail
products:
- {id: mmo.owl}
title: Measurement method ontology
- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/mmusdv/mmusdv.obo'}
description: Life cycle stages for Mus Musculus
homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv
id: mmusdv
layout: ontology_detail
page: https://github.com/obophenotype/developmental-stage-ontologies
title: Mouse Developmental Stages
- contact: {email: [email protected], label: Chris Stoeckert}
description: A standardized description of a microarray experiment in support of
MAGE v.1.
domain: experiments
homepage: http://mged.sourceforge.net/ontologies/MGEDontology.php
id: mo
is_obsolete: true
layout: ontology_detail
page: http://mged.sourceforge.net/software/downloads.php
products:
- {id: mo.owl}
replaced_by: obi
title: Microarray experimental conditions
- build: {method: obo2owl, source_url: 'http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mod/data/PSI-MOD.obo'}
contact: {email: [email protected], label: Henning Hermjakob}
description: PSI-MOD is an ontology consisting of terms that describe protein chemical
modifications
domain: proteins
homepage: http://psidev.info/index.php?q=node/104
id: mod
layout: ontology_detail
products:
- {id: mod.owl}
title: Protein modification
- browsers:
- {label: MGI, title: MGI MP Browser, url: 'http://www.informatics.jax.org/searches/MP_form.shtml'}
- {label: Monarch, title: Monarch Phenotype Page, url: 'http://monarchinitiative.org/phenotype/MP:0000001'}
build: {infallible: 1, method: obo2owl, source_url: 'ftp://ftp.informatics.jax.org/pub/reports/MPheno_OBO.ontology'}
contact: {email: [email protected], label: JAX phenotype list}
description: Standard terms for annotating mammalian phenotypic data.
domain: phenotype
homepage: http://www.informatics.jax.org/searches/MP_form.shtml
id: mp
jobs:
- {id: 'http://build.berkeleybop.org/job/build-mp-edit', type: DryRunBuild}
layout: ontology_detail
products:
- {id: mp.owl}
- {id: mp.obo}
taxon: {id: 'NCBITaxon:10088', label: Mus}
termgenie: http://mp.termgenie.org
title: Mammalian phenotype
tracker: https://sourceforge.net/p/obo/mammalian-phenotype-requests/
- build: {method: obo2owl, source_url: 'http://mpath.googlecode.com/svn/trunk/mpath.obo'}
contact: {email: [email protected], label: Paul Schofield}
description: A structured controlled vocabulary of mutant and transgenic mouse pathology
phenotypes
domain: health
homepage: http://www.pathbase.net
id: mpath
layout: ontology_detail
products:
- {id: mpath.owl}
taxon: {id: 'NCBITaxon:10088', label: Mus}
title: Mouse pathology
- build: {method: obo2owl, source_url: 'http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo'}
contact: {email: [email protected], label: Luisa Montecchi}
description: A structured controlled vocabulary for the annotation of experiments
concerned with proteomics mass spectrometry.
domain: experiments
homepage: http://www.psidev.info/index.php?q=node/257
id: ms
layout: ontology_detail
page: http://www.psidev.info/index.php?q=node/257
products:
- {id: ms.owl}
title: Mass spectrometry
- build: {checkout: 'svn co http://behavior-ontology.googlecode.com/svn/trunk', method: vcs,
system: svn}
contact: {email: [email protected], label: George Gkoutos}
domain: behavior
homepage: http://code.google.com/p/behavior-ontology
id: nbo
layout: ontology_detail
products:
- {id: nbo.owl}
title: Neuro Behavior Ontology
tracker: http://code.google.com/p/behavior-ontology/issues/list
- browsers:
- {label: NCBI, title: NCBI Taxonomy Browser, url: 'http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi'}
build: {infallible: 0, method: archive, path: archive/src/ontology, source_url: 'http://build.berkeleybop.org/job/build-ncbitaxon/lastSuccessfulBuild/artifact/*zip*/archive.zip'}
contact: {email: [email protected], label: obo-taxonomy-list}
createdWith: http://owltools.googlecode.com/
description: An ontology representation of the NCBI organismal taxonomy
domain: taxonomy
homepage: http://www.obofoundry.org/wiki/index.php/NCBITaxon:Main_Page
id: ncbitaxon
jobs:
- {id: 'http://build.berkeleybop.org/job/build-ncbitaxon/', type: ReleaseBuild}
layout: ontology_detail
page: http://www.ncbi.nlm.nih.gov/taxonomy
preferredPrefix: NCBITaxon
products:
- {id: ncbitaxon.owl}
- {id: ncbitaxon/subsets/taxslim.owl, title: taxslim}
source: http://www.ncbi.nlm.nih.gov/taxonomy
title: NCBI organismal classification
wasDerivedFrom: ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat
- build: {method: owl2obo, source_url: 'https://msi-workgroups.svn.sourceforge.net/svnroot/msi-workgroups/ontology/NMR.owl'}
contact: {email: [email protected], label: Schober Daniel}
description: Descriptors relevant to the experimental conditions of the Nuclear
Magnetic Resonance (NMR) component in a metabolomics investigation.
domain: experiments
homepage: http://msi-ontology.sourceforge.net/
id: nmr
layout: ontology_detail
page: http://msi-ontology.sourceforge.net/ontology/NMR.owlDocument.doc
products:
- {id: nmr.owl}
title: NMR-instrument specific component of metabolomics investigations
- build: {method: owl2obo, source_url: 'http://svn.code.sf.net/p/oae/code/trunk/src/ontology/oae.owl'}
contact: {email: [email protected], label: Yongqunh He}