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ontologies.yml
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ontologies:
- alternatePrefix: ChEBI
browsers:
- {label: CHEBI, title: EBI CHEBI Browser, url: 'http://www.ebi.ac.uk/chebi/chebiOntology.do?treeView=true&chebiId=CHEBI:24431#graphView'}
build: {infallible: 1, method: archive, path: archive/main, source_url: 'http://build.berkeleybop.org/job/build-chebi/lastSuccessfulBuild/artifact/*zip*/archive.zip'}
contact: {email: [email protected], label: Gareth Owen}
description: A structured classification of molecular entities of biological interest
focusing on 'small' chemical compounds.
domain: biochemistry
homepage: http://www.ebi.ac.uk/chebi
id: chebi
in_foundry_order: 1
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/chebi.owl
page: http://www.ebi.ac.uk/chebi/init.do?toolBarForward=userManual
products:
- {id: chebi.owl, ontology_purl: 'http://purl.obolibrary.org/obo/chebi.owl'}
- {id: chebi.obo, ontology_purl: 'http://purl.obolibrary.org/obo/chebi.obo'}
title: Chemical Entities of Biological Interest
tracker: https://sourceforge.net/p/chebi/curator-requests/
twitter: chebit
- browsers:
- {label: DO, title: DO Browser, url: 'http://www.disease-ontology.org/'}
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: An ontology for describing the classification of human diseases organized
by etiology.
domain: disease
facebook: https://www.facebook.com/diseaseontology
homepage: http://diseaseontology.sourceforge.net/
id: doid
in_foundry_order: 1
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/doid.owl
page: http://diseaseontology.sourceforge.net/
products:
- {id: doid.owl, ontology_purl: 'http://purl.obolibrary.org/obo/doid.owl'}
- {id: doid.obo, ontology_purl: 'http://purl.obolibrary.org/obo/doid.obo'}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/?term=25348409', title: 'Disease Ontology
2015 update: an expanded and updated database of human diseases for linking
biomedical knowledge through disease data'}
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
- 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
facebook: https://www.facebook.com/Gene-Ontology-305908656519/
id: go
in_foundry_order: 1
integration_server: http://build.berkeleybop.org/view/GO
label: GO
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/go.owl
products:
- {id: go.owl, ontology_purl: 'http://purl.obolibrary.org/obo/go.owl'}
- {description: The core ontology plus axioms connecting to select external ontologies,
id: go/extensions/go-plus.owl, ontology_purl: 'http://purl.obolibrary.org/obo/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,
ontology_purl: 'http://purl.obolibrary.org/obo/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
- browsers:
- {label: BioPortal, title: BioPortal Browser, url: 'http://bioportal.bioontology.org/ontologies/OBI?p=classes'}
build: {source_url: 'http://purl.obofoundry.org/obo/obi/repository/trunk/src/ontology/branches/'}
contact: {email: [email protected], label: Bjoern Peters}
depicted_by: https://svn.code.sf.net/p/obi/code/trunk/web/htdocs/images/obi-lotext.png
description: An integrated ontology for the description of life-science and clinical
investigations
domain: experiments
homepage: http://obi-ontology.org
id: obi
in_foundry_order: 1
integration_server: http://build.berkeleybop.org/job/build-obi/
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
mailing_list: http://groups.google.com/group/obi-users
ontology_purl: http://purl.obolibrary.org/obo/obi.owl
products:
- {id: obi.owl, ontology_purl: 'http://purl.obolibrary.org/obo/obi.owl', title: OBI}
- {id: obi/obi_core.owl, ontology_purl: 'http://purl.obolibrary.org/obo/obi/obi_core.owl',
title: OBI Core}
title: Ontology for Biomedical Investigations
tracker: http://purl.obofoundry.org/obo/obi/tracker
- browsers:
- {label: BioPortal, title: BioPortal Ontology Browser, url: 'https://bioportal.bioontology.org/ontologies/PATO'}
build: {infallible: 1, method: obo2owl, source_url: 'https://raw.githubusercontent.com/pato-ontology/pato/master/pato.obo'}
contact: {email: [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: 'https://travis-ci.org/pato-ontology/pato', type: travis-ci}
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/pato.owl
products:
- {id: pato.owl, ontology_purl: 'http://purl.obolibrary.org/obo/pato.owl'}
- {id: pato.obo, ontology_purl: 'http://purl.obolibrary.org/obo/pato.obo'}
repository: https://github.com/pato-ontology/pato/
title: Phenotypic quality
tracker: https://github.com/pato-ontology/pato/issues
- build: {checkout: 'git clone https://github.com/Planteome/plant-ontology.git', infallible: 1,
method: vcs, system: git}
contact: {email: [email protected], label: Pankaj Jaiswal}
description: The Plant Ontology is a structured vocabulary and database resource
that links plant anatomy, morphology and growth and development to plant genomics
data.
domain: anatomy and development
homepage: http://www.plantontology.org
id: po
in_foundry_order: 1
jobs:
- {id: 'https://travis-ci.org/Planteome/plant-ontology', type: travis-ci}
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/po.owl
page: http://www.plantontology.org/amigo/go.cgi
products:
- {id: po.owl, ontology_purl: 'http://purl.obolibrary.org/obo/po.owl'}
- {id: po.obo, ontology_purl: 'http://purl.obolibrary.org/obo/po.obo'}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/23220694', title: The plant ontology
as a tool for comparative plant anatomy and genomic analyses.}
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/22847540', title: Ontologies as integrative
tools for plant science.}
taxon: {id: 'NCBITaxon:33090', label: Viridiplantae}
title: Plant Ontology
tracker: https://github.com/Planteome/plant-ontology/issues
twitter: planteome
- build: {infallible: 0, method: obo2owl, oort_args: --no-reasoner, source_url: 'ftp://ftp.pir.georgetown.edu/databases/ontology/pro_obo/pro.obo'}
contact: {email: [email protected], label: Darren Natale}
description: an ontological representation of protein-related entities
development: {id_policy: 'https://pir17.georgetown.edu/confluence/display/PROWIKI/PRO+URI+policy'}
documentation: ftp://ftp.pir.georgetown.edu/databases/ontology/pro_obo/pro_readme.txt
domain: proteins
homepage: http://proconsortium.org
id: pr
in_foundry_order: 1
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/pr.owl
products:
- {id: pr.owl, ontology_purl: 'http://purl.obolibrary.org/obo/pr.owl'}
title: PRotein Ontology (PRO)
tracker: http://sourceforge.net/tracker/?group_id=266825&atid=1135711
- build: {infallible: 0, method: obo2owl, source_url: 'https://raw.githubusercontent.com/xenopus-anatomy/xao/master/xenopus_anatomy.obo'}
description: Anatomy and development of the African clawed frog (<i>Xenopus laevis</i>).
domain: anatomy
homepage: http://www.xenbase.org/anatomy/xao.do?method=display
id: xao
in_foundry_order: 1
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/xao.owl
products:
- {id: xao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/xao.owl'}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/18817563', title: An ontology for Xenopus
anatomy and development.}
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/24139024', title: 'Enhanced XAO: the
ontology of Xenopus anatomy and development underpins more accurate annotation
of gene expression and queries on Xenbase.'}
taxon: {id: 'NCBITaxon:8353', label: Xenopus}
title: Xenopus anatomy and development
tracker: https://github.com/xenopus-anatomy/xao/issues
- build: {infallible: 1, method: obo2owl, notes: may be ready to switch to vcs soon,
source_url: 'https://raw.githubusercontent.com/cerivs/zebrafish-anatomical-ontology/master/src/zebrafish_anatomy.obo'}
contact: {email: [email protected], label: ZFIN administrators}
description: A structured controlled vocabulary of the anatomy and development of
the Zebrafish
domain: anatomy
homepage: http://zfin.org/zf_info/anatomy/dict/sum.html
id: zfa
in_foundry_order: 1
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/zfa.owl
products:
- {id: zfa.owl, ontology_purl: 'http://purl.obolibrary.org/obo/zfa.owl'}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/24568621', title: 'The zebrafish anatomy
and stage ontologies: representing the anatomy and development of Danio rerio.'}
taxon: {id: 'NCBITaxon:7954', label: Danio}
title: Zebrafish anatomy and development
tracker: https://github.com/cerivs/zebrafish-anatomical-ontology/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: AEO is an ontology of anatomical structures that expands CARO, the
Common Anatomy Reference Ontology
domain: anatomy
homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/
id: aeo
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/aeo.owl
products:
- {id: aeo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/aeo.owl'}
title: Anatomical Entity Ontology
- 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
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/aero.owl
products:
- {id: aero.owl, ontology_purl: 'http://purl.obolibrary.org/obo/aero.owl'}
title: Adverse Event Reporting Ontology
- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.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
ontology_purl: http://purl.obolibrary.org/obo/apo.owl
products:
- {id: apo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/apo.owl'}
- {id: apo.obo, ontology_purl: 'http://purl.obolibrary.org/obo/apo.obo'}
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
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/bcgo.owl
products:
- {id: bcgo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/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
in_foundry: false
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/bco.owl
products:
- {id: bco.owl, ontology_purl: 'http://purl.obolibrary.org/obo/bco.owl'}
title: Biological Collections Ontology
tracker: https://github.com/tucotuco/bco/issues
- browsers:
- {label: BioPortal, title: BioPortal Browser, url: 'http://bioportal.bioontology.org/ontologies/BFO?p=classes'}
contact: {email: [email protected], label: Barry Smith}
depicted_by: https://avatars2.githubusercontent.com/u/12972134?v=3&s=200
description: The upper level ontology upon which OBO Foundry ontologies are built.
domain: upper
homepage: http://ifomis.org/bfo/
id: bfo
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
mailing_list: https://groups.google.com/forum/#!forum/bfo-discuss
ontology_purl: http://purl.obolibrary.org/obo/bfo.owl
products:
- {id: bfo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/bfo.owl'}
- {id: bfo.obo, ontology_purl: 'http://purl.obolibrary.org/obo/bfo.obo'}
title: Basic Formal Ontology
tracker: https://github.com/BFO-ontology/BFO/issues
- 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
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/bspo.owl
products:
- {id: bspo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/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: {insert_ontology_id: true, 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'}
ontology_purl: http://purl.obolibrary.org/obo/bto.owl
page: https://en.wikipedia.org/wiki/BRENDA_tissue_ontology
products:
- {id: bto.owl, ontology_purl: 'http://purl.obolibrary.org/obo/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
ontology_purl: http://purl.obolibrary.org/obo/caro.owl
products:
- {id: caro.owl, ontology_purl: 'http://purl.obolibrary.org/obo/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
ontology_purl: http://purl.obolibrary.org/obo/cdao.owl
products:
- {id: cdao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/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, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/ceph.owl
products:
- {id: ceph.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ceph.owl', title: main
version}
- {id: ceph.obo, ontology_purl: 'http://purl.obolibrary.org/obo/ceph.obo', title: oboformat
edition}
taxon: {id: 'NCBITaxon:6605', label: Cephalopod}
title: Cephalopod Ontology
tracker: https://github.com/obophenotype/cephalopod-ontology/issues
- build: {method: owl2obo, source_url: 'http://semanticchemistry.googlecode.com/svn/trunk/ontology/cheminf.owl'}
contact: {email: [email protected], label: Egon Willighagen}
description: Includes terms for the descriptors commonly used in cheminformatics
software applications and the algorithms which generate them.
domain: biochemistry
homepage: https://github.com/egonw/semanticchemistry
id: cheminf
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/cheminf.owl
products:
- {id: cheminf.owl, ontology_purl: 'http://purl.obolibrary.org/obo/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
ontology_purl: http://purl.obolibrary.org/obo/chmo.owl
products:
- {id: chmo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/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}
- {id: ro}
- {id: chebi}
- {id: pato}
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/
jobs:
- {id: 'https://travis-ci.org/obophenotype/cell-ontology', type: travis-ci}
label: Cell Ontology
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
mailing_list: https://lists.sourceforge.net/lists/listinfo/obo-cell-type
ontology_purl: http://purl.obolibrary.org/obo/cl.owl
products:
- description: Complete ontology, plus inter-ontology axioms, and imports modules
format: owl-rdf/xml
id: cl.owl
is_canonical: true
ontology_purl: http://purl.obolibrary.org/obo/cl.owl
title: Main CL OWL edition
uses: [uberon, chebi, go, pr, pato]
- {derived_from: cl.owl, description: 'Complete ontology, plus inter-ontology axioms,
and imports modules merged in', format: obo, id: cl.obo, ontology_purl: 'http://purl.obolibrary.org/obo/cl.obo',
title: CL obo format edition}
- {description: 'Basic version, no inter-ontology axioms', format: obo, id: cl/cl-basic.obo,
ontology_purl: 'http://purl.obolibrary.org/obo/cl/cl-basic.obo', title: Basic
CL}
taxon: {id: 'NCBITaxon:33208', label: Metazoa}
termgenie: http://cl.termgenie.org
title: Cell Ontology
tracker: https://github.com/obophenotype/cell-ontology/issues
- 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}
dependencies:
- {id: uberon}
- {id: cl}
- {id: doid}
- {id: ncbitaxon}
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
ontology_purl: http://purl.obolibrary.org/obo/clo.owl
products:
- {id: clo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/clo.owl'}
title: Cell Line Ontology
- contact: {email: Michael Grove, label: [email protected]}
homepage: https://code.google.com/p/craniomaxillofacial-ontology/
id: cmf
layout: ontology_detail
title: CranioMaxilloFacial ontology
- browsers:
- {label: RGD, title: RGD Ontology Browser, url: 'http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=CMO:0000000'}
build: {method: obo2owl, source_url: 'ftp://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
homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
id: cmo
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/cmo.owl
page: ftp://ftp.rgd.mcw.edu/pub/ontology/clinical_measurement/
products:
- {id: cmo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/cmo.owl'}
- {id: cmo.obo, ontology_purl: 'http://purl.obolibrary.org/obo/cmo.obo'}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/22654893', title: Three ontologies to
define phenotype measurement data.}
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/24103152', title: 'The clinical measurement,
measurement method and experimental condition ontologies: expansion, improvements
and new applications.'}
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}
dependencies:
- {id: uberon}
- {id: ro}
description: An anatomical and developmental ontology for ctenophores (Comb Jellies)
domain: anatomy
homepage: https://github.com/obophenotype/ctenophore-ontology
id: cteno
jobs:
- {id: 'https://travis-ci.org/obophenotype/ctenophore-ontology', type: travis-ci}
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/cteno.owl
products:
- {id: cteno.owl, ontology_purl: 'http://purl.obolibrary.org/obo/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
ontology_purl: http://purl.obolibrary.org/obo/cvdo.owl
products:
- {id: cvdo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/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
ontology_purl: http://purl.obolibrary.org/obo/ddanat.owl
products:
- {id: ddanat.owl, ontology_purl: 'http://purl.obolibrary.org/obo/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: {insert_ontology_id: true, 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
ontology_purl: http://purl.obolibrary.org/obo/ddpheno.owl
products:
- {id: ddpheno.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ddpheno.owl'}
taxon: {id: 'NCBITaxon:44689', label: Dictyostelium discoideum}
title: Dictyostelium discoideum phenotype
twitter: dictybase
- contact: {email: [email protected], label: Mathias Brochhausen}
description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction
Evidence Ontology
homepage: https://github.com/DIDEO/DIDEO
id: dideo
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/dideo.owl
products:
- {id: dideo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/dideo.owl'}
title: Drug Interaction and Evidence Ontology
tracker: https://github.com/DIDEO/DIDEO/issues
- contact: {email: [email protected], label: Maria Herrero}
description: A formal represention for drug-drug interactions knowledge.
domain: health
homepage: https://github.com/labda/DINTO
id: dinto
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'https://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/dinto.owl
products:
- {id: dinto.owl, ontology_purl: 'http://purl.obolibrary.org/obo/dinto.owl'}
publications:
- {id: 'http://pubs.acs.org/doi/10.1021/acs.jcim.5b00119', title: "DINTO: Using\
\ OWL Ontologies and SWRL Rules to Infer Drug\u2013Drug Interactions and Their\
\ Mechanisms."}
title: The Drug-drug Interaction Ontology
tracker: https://github.com/labda/DINTO/issues
- browsers:
- {label: FB, title: FlyBase Browser, url: 'http://flybase.org/.bin/cvreport.html?cvterm=FBcv:0000347'}
build: {infallible: 0, method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/fbcv/dpo.owl'}
contact: {email: [email protected], label: Marta Costa}
description: An ontology of commonly encountered and/or high level Drosophila phenotypes.
domain: phenotype
homepage: http://purl.obolibrary.org/obo/fbcv
id: dpo
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/dpo.owl
preferredPrefix: FBcv
products:
- {id: fbcv/dpo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fbcv/dpo.owl'}
publications:
- {id: 'http://dx.doi.org/10.1186/2041-1480-4-30', title: The Drosophila phenotype
ontology.}
taxon: {id: 'NCBITaxon:7227', label: Drosophila}
title: Drosophila Phenotype Ontology
tracker: http://purl.obolibrary.org/obo/fbcv/tracker
- 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: https://bitbucket.org/uamsdbmi/dron.git
id: dron
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/dron.owl
products:
- {id: dron.owl, ontology_purl: 'http://purl.obolibrary.org/obo/dron.owl'}
title: The Drug Ontology
tracker: https://ontology.atlassian.net/browse/DRON
- build: {infallible: 1, method: obo2owl, notes: switch to vcs, source_url: 'https://raw.githubusercontent.com/evidenceontology/evidenceontology/master/eco.obo'}
contact: {email: [email protected], label: 'Chibucos, Marcus'}
description: An ontology for experimental and other evidence statements.
domain: experiments
funded_by: ['http://www.nsf.gov/awardsearch/showAward?AWD_ID=1458400']
homepage: https://github.com/evidenceontology/evidenceontology/
id: eco
jobs:
- {id: 'https://travis-ci.org/evidenceontology/evidenceontology', type: travis-ci}
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/eco.owl
products:
- {id: eco.owl, ontology_purl: 'http://purl.obolibrary.org/obo/eco.owl'}
- {id: eco.obo, ontology_purl: 'http://purl.obolibrary.org/obo/eco.obo'}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/25052702', title: Standardized description
of scientific evidence using the Evidence Ontology (ECO)}
title: Evidence ontology
tracker: https://github.com/evidenceontology/evidenceontology/issues
- build: {checkout: 'git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git',
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contact: {email: [email protected], label: Jonathan Bard}
dependencies:
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- {id: caro}
- {id: cl}
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
ontology_purl: http://purl.obolibrary.org/obo/ehdaa2.owl
products:
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publications:
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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
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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
ontology_purl: http://purl.obolibrary.org/obo/emap.owl
page: http://www.obofoundry.org/wiki/index.php/EMAPA:Main_Page
products:
- {id: emap.owl, ontology_purl: 'http://purl.obolibrary.org/obo/emap.owl'}
taxon: {id: 'NCBITaxon:10088', label: Mus}
title: Mouse gross anatomy and development, timed
used_by:
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- 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
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domain: anatomy
homepage: http://emouseatlas.org
id: emapa
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/emapa.owl
page: http://www.obofoundry.org/wiki/index.php/EMAPA:Main_Page
products:
- {id: emap.owl, ontology_purl: 'http://purl.obolibrary.org/obo/emap.owl'}
taxon: {id: 'NCBITaxon:10088', label: Mus}
title: Mouse gross anatomy and development, timed
used_by:
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- build: {checkout: 'git clone https://github.com/EnvironmentOntology/envo.git', email_cc: [email protected],
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contact: {email: [email protected], label: Pier Luigi Buttigieg}
dependencies:
- {id: uberon}
- {id: pco}
- {id: ro}
- {id: chebi}
- {id: ncbitaxon}
description: Ontology of environmental features and habitats
domain: environment
homepage: http://environmentontology.org/
id: envo
jobs:
- {id: 'https://travis-ci.org/EnvironmentOntology/envo', type: travis-ci}
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/envo.owl
page: https://github.com/EnvironmentOntology/envo
products:
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- {id: envo.obo, ontology_purl: 'http://purl.obolibrary.org/obo/envo.obo'}
- {id: subsets/envo-basic.obo, ontology_purl: 'http://purl.obolibrary.org/obo/subsets/envo-basic.obo',
title: OBO-Basic edition of ENVO}
- {homepage: 'http://environmentontology.org/downloads', id: subsets/EnvO-Lite-GSC.obo,
ontology_purl: 'http://purl.obolibrary.org/obo/subsets/EnvO-Lite-GSC.obo', title: GSC
Lite subset of ENVO}
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: 'https://github.com/Planteome/plant-environment-ontology/blob/master/plant-environment-ontology.obo.owl'}
contact: {email: [email protected], label: Pankaj Jaiswal}
description: "A structured, controlled vocabulary which \u2260\u2260describes the\
\ treatments, growing conditions, and/or study types used in various types of\
\ plant biology experiments."
domain: environment
homepage: http://planteome.org/
id: eo
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'https://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/eo.owl
page: http://planteome.org/amigo/cgi-bin/crop_amigo/term_details?term=EO:0007359&session_id=815amigo1442021959
products:
- {id: eo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/eo.owl'}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/22847540', title: Ontologies as integrative
tools for plant science.}
title: Plant Environment Ontology
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
in_foundry: false
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/epo.owl
products:
- {id: epo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/epo.owl'}
title: Epidemiology Ontology
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/ero.owl'}
contact: {email: [email protected], label: Tenille Johnson}
description: An ontology of research resources such as instruments. protocols, reagents,
animal models and biospecimens.
documentation: https://open.med.harvard.edu/wiki/display/eaglei/Ontology
domain: resources
homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology
id: ero
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/ero.owl
products:
- {id: ero.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ero.owl'}
title: eagle-i resource ontology
tracker: null
- build: {method: obo2owl, source_url: 'http://ctdbase.org/reports/CTD_exposure_ontology.obo'}
description: Vocabularies for describing exposure data to inform understanding of
environmental health.
domain: health
homepage: http://ctdbase.org/downloads/#exposures
id: exo
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/exo.owl
page: http://ctdbase.org/downloads/#exposures
products:
- {id: exo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/exo.owl'}
title: Exposure ontology
- build: {insert_ontology_id: true, 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
ontology_purl: http://purl.obolibrary.org/obo/fao.owl
page: http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/#description
products:
- {id: fao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/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
ontology_purl: http://purl.obolibrary.org/obo/fbbi.owl
preferredPrefix: FBbi
products:
- {id: fbbi.owl, ontology_purl: 'http://purl.obolibrary.org/obo/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 gross anatomy of Drosophila melanogaster.
domain: anatomy
homepage: http://purl.obolibrary.org/obo/fbbt
id: fbbt
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/fbbt.owl
preferredPrefix: FBbt
products:
- {id: fbbt.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fbbt.owl'}
- {id: fbbt/fbbt-simple.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fbbt/fbbt-simple.owl'}
- {id: fbbt/fbbt-simple.obo, ontology_purl: 'http://purl.obolibrary.org/obo/fbbt/fbbt-simple.obo'}
publications:
- {id: 'http://dx.doi.org/10.1186/2041-1480-4-32', title: 'The Drosophila anatomy
ontology. [Journal of Biomedical Semantics'}
- {id: 'http://dx.doi.org/10.1093/bioinformatics/bts113', title: A strategy for
building neuroanatomy ontologies}
- {id: 'http://dx.doi.org/10.1093/bioinformatics/btr677', title: The Virtual Fly
Brain Browser and Query Interface}
- {id: 'http://dx.doi.org/10.1093/nar/gkj068', title: 'FlyBase: anatomical data,
images and queries'}
taxon: {id: 'NCBITaxon:7227', label: Drosophila}
title: Drosophila gross anatomy
tracker: http://purl.obolibrary.org/obo/fbbt/tracker
- browsers:
- {label: FB, title: FlyBase Browser, url: 'http://flybase.org/.bin/cvreport.html?cvterm=FBcv:0000013'}
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: Marta Costa}
description: A structured controlled vocabulary used for various aspects of annotation
by FlyBase.
domain: null
homepage: http://purl.obolibrary.org/obo/fbcv
id: fbcv
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/fbcv.owl
preferredPrefix: FBcv
products:
- {id: fbcv.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fbcv.owl'}
title: FlyBase Controlled Vocabulary
tracker: http://purl.obolibrary.org/obo/fbbt/tracker
- browsers:
- {label: FB, title: FlyBase Browser, url: 'http://flybase.org/.bin/cvreport.html?cvterm=FBdv:00007008'}
build: {infallible: 0, method: obo2owl, source_url: 'http://svn.code.sf.net/p/fbbtdv/code/fbdv/releases/fbdv.obo'}
contact: {email: [email protected], label: Marta Costa}
description: A structured controlled vocabulary of the development of Drosophila
melanogaster.
domain: development
homepage: http://purl.obolibrary.org/obo/fbdv
id: fbdv
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/fbdv.owl
preferredPrefix: FBdv
products:
- {id: fbdv.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fbdv.owl'}
- {id: fbdv/fbdv-simple.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fbdv/fbdv-simple.owl'}
- {id: fbdv/fbbt-simple.obo, ontology_purl: 'http://purl.obolibrary.org/obo/fbdv/fbbt-simple.obo'}
taxon: {id: 'NCBITaxon:7227', label: Drosophila}
title: Drosophila development
tracker: http://purl.obolibrary.org/obo/fbdv/tracker
- contact: {email: [email protected], label: Janna Hastings}
description: An ontology of physico-chemical methods and properties.
id: fix
in_foundry: false
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/fix.owl
products:
- {id: fix.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fix.owl'}
title: Physico-chemical methods and properties
- contact: {email: [email protected], label: Robert Hoehndorf}
description: Traits and phenotypes of flowering plants occurring in digitized Floras
domain: phenotype
homepage: https://github.com/flora-phenotype-ontology/flopoontology
id: flopo
layout: ontology_detail
license: {url: 'https://creativecommons.org/about/cc0'}
ontology_purl: http://purl.obolibrary.org/obo/flopo.owl
products:
- {id: flopo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/flopo.owl'}
taxon: {id: 'NCBITaxon:33090', label: Viridiplantae}
title: Flora Phenotype Ontology
tracker: https://github.com/flora-phenotype-ontology/flopoontology/issues
- 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
in_foundry: false
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/flu.owl
products:
- {id: flu.owl, ontology_purl: 'http://purl.obolibrary.org/obo/flu.owl'}
title: Influenza Ontology
tracker: http://purl.obolibrary.org/obo/flu/tracker
- build: {insert_ontology_id: true, 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
ontology_purl: http://purl.obolibrary.org/obo/fma.owl
page: http://en.wikipedia.org/wiki/Foundational_Model_of_Anatomy
products:
- {id: fma.owl, ontology_purl: 'http://purl.obolibrary.org/obo/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}
depicted_by: http://www.pombase.org/sites/pombase.org/files/images/fypo_logo_tiny.png
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
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/fypo.owl
products:
- {id: fypo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/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}
description: A gazetteer constructed on ontological principles
homepage: http://gensc.org/gc_wiki/index.php/GAZ_Project
id: gaz
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/gaz.owl
products:
- {id: gaz.owl, ontology_purl: 'http://purl.obolibrary.org/obo/gaz.owl'}
- {id: gaz.obo, ontology_purl: 'http://purl.obolibrary.org/obo/gaz.obo'}
title: Gazetteer
tracker: https://github.com/EnvironmentOntology/envo/issues/
- contact: {email: [email protected], label: Mathias Brochhausen}
description: An ontology of geographical entities
homepage: https://code.google.com/p/ge-ontology/
id: geo
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/geo.owl
products:
- {id: geo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/geo.owl'}
title: Geographical Entity Ontology
tracker: https://ontology.atlassian.net/browse/GEO#selectedTab=com.atlassian.jira.plugin.system.project%3Aissues-panel
- 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
ontology_purl: http://purl.obolibrary.org/obo/hao.owl
products:
- {id: hao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/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,
path: src/ontology, system: git}
contact: {email: [email protected], label: BgeeDB}
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
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/hom.owl