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_config.yml
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author: {name: OBO Technical WG}
baseurl: /
imgurl: /images
markdown: redcarpet
name: OBO Foundry
ontologies:
- 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
- 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
- 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
- contact: {email: [email protected], label: Thorsten Heinrich}
domain: anatomy
homepage: http://4dx.embl.de/4DXpress
id: bila
layout: ontology_detail
products:
- {id: bila.owl}
taxon: {id: 'NCBITaxon:33213', label: Bilateria}
title: Bilateria anatomy
- 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
- 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
- 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
- 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
- alternatePrefix: ChEBI
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/
- 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
- 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
- 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
- contact: {email: [email protected], 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.
domain: clinical
id: cmo
layout: ontology_detail
products:
- {id: cmo.owl}
title: Clinical measurement ontology
- 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
- 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
- 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
- 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'}
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
- 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
- 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
- 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
- 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
- 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
- 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/
- 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
- 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
- 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
- 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
- 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
- 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'}
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
- 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
- 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
- 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
- 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
- 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/
- 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/issues
id: fypo
products:
- {id: fypo.owl}
taxon: {id: 'NCBITaxon:4896', label: S Pombe}
title: Fission Yeast Phenotype Ontology
tracker: https://github.com/pombase/fypo/issues
- 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'}
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
- 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
- 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'}
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
- 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
- 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
- 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
- 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
- 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
- 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/
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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'}
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
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/
- 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
- 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
- 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'}
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
- 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
- contact: {email: [email protected], label: Yongqunh He}
description: A biomedical ontology in the domain of adverse events
domain: adverse events, health
homepage: http://www.oae-ontology.org
id: oae
layout: ontology_detail
products:
- {id: oae.owl}
title: Ontology of Adverse Events
- contact: {email: [email protected], label: Chris Mungall}
description: A collection of biological attributes (traits) covering all kingdoms
of life.
domain: phenotype
homepage: https://github.com/obophenotype/bio-attribute-ontology
id: oba
layout: ontology_detail
page: http://wiki.geneontology.org/index.php/Extensions/x-attribute
products:
- {id: oba.owl}
title: Ontology of Biological Attributes
tracker: https://github.com/obophenotype/bio-attribute-ontology/issues
- contact: {email: [email protected], label: Jie Zheng}
description: A biomedical ontology in the domain of biological and clinical statistics.
domain: statistics
homepage: https://github.com/obcs/obcs
id: obcs
in_foundry: false
layout: ontology_detail
products:
- {id: obcs.owl}
title: Ontology of Biological and Clinical Statistics
tracker: https://github.com/obcs/obcs/issues
- contact: {email: [email protected], label: Bjoern Peters}
description: An integrated ontology for the description of life-science and clinical
investigations
domain: experiments
homepage: http://purl.obofoundry.org/obo/obi
id: obi
in_foundry_order: 1
layout: ontology_detail
license: {label: CC-BY, url: 'https://creativecommons.org/licenses/by/3.0/'}
page: http://obi-ontology.org/page/Technical_Reports
products:
- {id: obi.owl}
title: Ontology for Biomedical Investigations
tracker: http://sourceforge.net/p/obi/obi-terms/
- contact: {email: [email protected], label: Yongqun Oliver He}
description: A formal ontology of genes and genomes of biological organisms.
homepage: http://ogg.googlecode.com/
id: ogg
products:
- {id: ogg.owl}
title: The Ontology of Genes and Genomes
tracker: https://code.google.com/p/ogg/issues/list
- description: An ontology that formalizes the genomic element by defining an upper
class genetic interval
homepage: https://code.google.com/p/ontology-for-genetic-interval/
id: ogi
layout: ontology_detail
products:
- {id: ogi.owl}
title: Ontology for genetic interval
tracker: https://code.google.com/p/ontology-for-genetic-interval/issues/list
- contact: {email: [email protected], label: Albert Goldfain}
description: An ontology for representing treatment of disease and diagnosis and
on carcinomas and other pathological entities
domain: medicine
homepage: http://code.google.com/p/ogms/
id: ogms
page: http://code.google.com/p/ogms/
products:
- {id: ogms.owl}
taxon: {id: 'NCBITaxon:9606', label: Homo sapiens}
title: Ontology for General Medical Science
tracker: http://code.google.com/p/ogms/issues/list
- description: An application ontology to represent genetic susceptibility to a specific
disease, adverse event, or a pathological process.
homepage: https://code.google.com/p/ogsf/
id: ogsf
layout: ontology_detail
products:
- {id: ogsf.owl}
title: Ontology of Genetic Susceptibility Factor
tracker: https://code.google.com/p/ogsf/issues/list
- contact: {email: [email protected], label: 'Huang, Jingshan'}
homepage: http://omit.cis.usouthal.edu/
id: omit
page: http://omit.cis.usouthal.edu/
products:
- {id: omit.owl}
title: Ontology for MIRNA Target Prediction
- contact: {email: [email protected], label: Bill Hogan}
description: This ontology covers the domain of social entities that are related
to health care, such as demographic information and the roles of various individuals
and organizations.
domain: medicine
id: omrse
layout: ontology_detail
page: http://code.google.com/p/omrse/
products:
- {id: omrse.owl}
taxon: {id: 'NCBITaxon:9606', label: Homo sapiens}
title: Ontology of Medically Related Social Entities
- contact: {email: [email protected], label: Priti Parikh}
description: A reference ontology for parasite life cycle stages.
homepage: https://github.com/OPL-ontology/OPL
id: opl
layout: ontology_detail
title: Ontology for Parasite LifeCycle
tracker: https://github.com/OPL-ontology/OPL/issues
ts:
- {id: opl.owl}
- contact: {email: [email protected], label: Yongqunh He}
description: A biomedical ontology in the domain of vaccine adverse events. OVAE
is an extension of the Ontology of Adverse Event (OAE) and uses the vaccine information
imported from the Vaccine Ontology (VO)
homepage: http://www.violinet.org/ovae/
id: ovae
layout: ontology_detail
products:
- {id: ovae.owl}
title: Ontology of Vaccine Adverse Events
- id: ovao
layout: ontology_detail
products:
- {id: ovao.owl}
tracker: https://code.google.com/p/ovae/issues/list
- contact: {email: [email protected], label: George Gkoutos}
description: An ontology of phenotypic qualities (properties, attributes or characteristics)
domain: phenotype
homepage: https://github.com/pato-ontology/pato/
id: pato
in_foundry_order: 1
jobs:
- {id: 'http://build.berkeleybop.org/job/build-pato', type: DryRunBuild}
layout: ontology_detail