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_config.yml
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name: OBO Foundry
title: The OBO Foundry
markdown: kramdown
highlighter: rouge
baseurl: /
imgurl: /images
repo: https://github.com/OBOFoundry/OBOFoundry.github.io/
repo_src: https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/
author:
name: OBO Technical WG
## --Anything above this line can be edited in _config_header.yml --
## --Everything below this line automatically generated in _config.yml --
ontologies:
- browsers:
- {label: BioPortal, title: BioPortal Browser, url: 'http://bioportal.bioontology.org/ontologies/BFO?p=classes'}
contact: {email: phismith@buffalo.edu, 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
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/'}
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
- 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: obo2owl, source_url: 'ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo'}
contact: {email: gowen@ebi.ac.uk, 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://github.com/ebi-chebi/ChEBI/issues
twitter: chebit
- DO wiki: http://diseaseontology.sourceforge.net/
browsers:
- {label: DO, title: DO Browser, url: 'http://www.disease-ontology.org/'}
build: {infallible: 1, method: obo2owl, source_url: 'https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid-non-classified.obo'}
contact: {email: lynn.schriml@gmail.com, 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://www.disease-ontology.org
id: doid
in_foundry_order: 1
layout: ontology_detail
license: {label: CC0 1.0 Universal, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png',
url: 'https://creativecommons.org/publicdomain/zero/1.0/'}
ontology_purl: http://purl.obolibrary.org/obo/doid.owl
products:
- {id: doid.owl, ontology_purl: 'http://purl.obolibrary.org/obo/doid.owl', title: 'Disease
Ontology inferred hierarchy that includes anatomy, cell of origin, infectious
agent and phenotype axioms'}
- {id: doid.obo, ontology_purl: 'http://purl.obolibrary.org/obo/doid.obo', title: Disease
Ontology asserted is_a hierarchy (this file is equivalent to DO's previous HumanDO.obo
file)}
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: https://github.com/DiseaseOntology/HumanDiseaseOntology/issues
twitter: diseaseontology
- 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
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: bpeters@liai.org, 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: g.gkoutos@gmail.com, 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
- browsers:
- {label: Planteome, title: Planteome browser, url: 'http://browser.planteome.org/amigo'}
build: {checkout: 'git clone https://github.com/Planteome/plant-ontology.git', infallible: 1,
method: vcs, system: git}
contact: {email: jaiswalp@science.oregonstate.edu, 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://browser.planteome.org/amigo
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 4.0, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'https://creativecommons.org/licenses/by/4.0/'}
ontology_purl: http://purl.obolibrary.org/obo/po.owl
page: https://github.com/Planteome/plant-ontology
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: dan5@georgetown.edu, label: Darren Natale}
depicted_by: https://raw.githubusercontent.com/PROconsortium/logo/master/PROlogo_small.png
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
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/4.0/'}
ontology_purl: http://purl.obolibrary.org/obo/pr.owl
products:
- {description: 'PRO after reasoning has been applied, OWL format.', id: pr.owl,
ontology_purl: 'http://purl.obolibrary.org/obo/pr.owl', title: pro_reasoned.owl}
- {description: 'PRO after reasoning has been applied, OBO format.', id: pr.obo,
ontology_purl: 'http://purl.obolibrary.org/obo/pr.obo', title: pro_reasoned.obo}
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'}
- {id: xao.obo, ontology_purl: 'http://purl.obolibrary.org/obo/xao.obo'}
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: zfinadmin@zfin.org, 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'}
- {id: zfa.obo, ontology_purl: 'http://purl.obolibrary.org/obo/zfa.obo'}
publications:
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title: Zebrafish anatomy and development
tracker: https://github.com/cerivs/zebrafish-anatomical-ontology/issues
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description: AEO is an ontology of anatomical structures that expands CARO, the
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domain: anatomy
homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/
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title: Anatomical Entity Ontology
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contact: {email: mcourtot@gmail.com, 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',
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contact: {email: m.a.laporte@cgiar.org, github: marieALaporte, label: "Marie-Ang\xE9\
lique Laporte"}
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- {id: iao}
description: Ontology of agronomic practices, agronomic techniques, and agronomic
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domain: agronomy
homepage: https://github.com/AgriculturalSemantics/agro
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products:
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title: Agronomy Ontology
tracker: https://github.com/AgriculturalSemantics/agro/issues/
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contact: {email: sgd-helpdesk@lists.stanford.edu, label: sgd-helpdesk}
description: A structured controlled vocabulary for the phenotypes of Ascomycete
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homepage: http://www.yeastgenome.org/
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taxon: {id: 'NCBITaxon:4890', label: Ascomycota}
title: Ascomycete phenotype ontology
- contact: {email: jiezheng@upenn.edu, label: Jie Zheng}
description: An application ontology built for beta cell genomics studies.
homepage: https://github.com/obi-bcgo/bcgo
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layout: ontology_detail
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title: Beta Cell Genomics Ontology
tracker: https://github.com/obi-bcgo/bcgo/issues
- contact: {email: rwalls2008@gmail.com, 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
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title: Biological Collections Ontology
tracker: https://github.com/tucotuco/bco/issues
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contact: {email: cjmungall@lbl.gov, label: Chris Mungall}
description: An ontology for respresenting spatial concepts, anatomical axes, gradients,
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domain: anatomy
homepage: https://github.com/obophenotype/biological-spatial-ontology
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layout: ontology_detail
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publications:
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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
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contact: {email: a.chang@tu-bs.de, 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'}
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sources'}
title: BRENDA tissue / enzyme source
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contact: {email: haendel@ohsu.edu, 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: balhoff@nescent.org, 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
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- {id: cdao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/cdao.owl'}
title: Comparative Data Analysis Ontology
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contact: {email: cjmungall@lbl.gov, label: Chris Mungall}
description: An anatomical and developmental ontology for cephalopods
domain: anatomy
homepage: https://github.com/obophenotype/cephalopod-ontology
id: ceph
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taxon: {id: 'NCBITaxon:6605', label: Cephalopod}
title: Cephalopod Ontology
tracker: https://github.com/obophenotype/cephalopod-ontology/issues
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contact: {email: egon.willighagen@gmail.com, 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
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title: Chemical Information Ontology
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description: CHMO, the chemical methods ontology, describes methods used to
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homepage: https://github.com/rsc-ontologies/rsc-cmo
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title: Chemical Methods Ontology
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contact: {email: frederic.bastian@unil.ch, label: Frederic Bastian}
description: An ontology to capture confidence information about annotations.
homepage: https://github.com/BgeeDB/confidence-information-ontology
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layout: ontology_detail
mailing_list: null
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title: Confidence Information Ontology
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dependencies:
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- {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:
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mailing_list: https://lists.sourceforge.net/lists/listinfo/obo-cell-type
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ontology_purl: http://purl.obolibrary.org/obo/cl.owl
title: Main CL OWL edition
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taxon: {id: 'NCBITaxon:33208', label: Metazoa}
termgenie: http://cl.termgenie.org
title: Cell Ontology
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- contact: {email: Sirarat.Sarntivijai@fda.hhs.gov, label: Sirarat Sarntivijai}
dependencies:
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description: An ontology to standardize and integrate cell line information and
to support computer-assisted reasoning.
homepage: http://www.clo-ontology.org
id: clo
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title: Cell Line Ontology
- contact: {email: Michael Grove, label: grovmi@ohsu.edu}
homepage: https://code.google.com/p/craniomaxillofacial-ontology/
id: cmf
layout: ontology_detail
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build: {method: obo2owl, source_url: 'ftp://ftp.rgd.mcw.edu/pub/ontology/clinical_measurement/clinical_measurement.obo'}
contact: {email: shimoyama@mcw.edu, 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
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publications:
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measurement method and experimental condition ontologies: expansion, improvements
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title: Clinical measurement ontology
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method: vcs, path: ., system: git}
contact: {email: cjmungall@lbl.gov, label: Chris Mungall}
dependencies:
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description: An anatomical and developmental ontology for ctenophores (Comb Jellies)
domain: anatomy
homepage: https://github.com/obophenotype/ctenophore-ontology
id: cteno
jobs:
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contact: {email: adrien.barton@gmail.com, label: Adrien Barton}
description: An ontology to describe entities related to cardiovascular diseases
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contact: {email: r-chisholm@northwestern.edu, label: Rex Chisholm}
description: A structured controlled vocabulary of the anatomy of the slime-mould
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homepage: http://dictybase.org/
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homepage: http://dictybase.org/
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\ Mechanisms."}
title: The Drug-Drug Interactions Ontology
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contact: {email: mmc46@cam.ac.uk, label: Marta Costa}
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publications:
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taxon: {id: 'NCBITaxon:7227', label: Drosophila}
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contact: {email: hoganwr@gmail.com, label: William Hogan}
description: An ontology to support comparative effectiveness researchers studying
claims data.
domain: health
homepage: https://bitbucket.org/uamsdbmi/dron.git
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layout: ontology_detail
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products:
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jobs:
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title: The Data Use Ontology
tracker: https://github.com/EBISPOT/DUO/issues
- build: {infallible: 1, method: obo2owl, notes: switch to vcs, source_url: 'https://raw.githubusercontent.com/evidenceontology/evidenceontology/master/eco.obo'}
contact: {email: MChibucos@som.umaryland.edu, 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'}
- {id: eco/gaf-eco-mapping.txt, ontology_purl: 'http://purl.obolibrary.org/obo/eco/gaf-eco-mapping.txt',
title: Mapping between ECO classes and Gene Ontology codes, type: Mapping}
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',
method: vcs, path: src/ontology, system: git}
contact: {email: J.Bard@ed.ac.uk, label: Jonathan Bard}
dependencies:
- {id: aeo}
- {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:
- {id: ehdaa2.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ehdaa2.owl'}
- {id: ehdaa2.obo, ontology_purl: 'http://purl.obolibrary.org/obo/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: {insert_ontology_id: true, method: obo2owl, notes: new url soon, source_url: 'ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAP_combined.obo'}
contact: {email: Terry.Hayamizu@jax.org, 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:
- {label: GXD, url: 'https://www.biosharing.org/biodbcore-000659'}
- build: {method: obo2owl, notes: new url soon, source_url: 'ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAPA.obo'}
contact: {email: Terry.Hayamizu@jax.org, 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
ontology_purl: http://purl.obolibrary.org/obo/emapa.owl
page: http://www.obofoundry.org/wiki/index.php/EMAPA:Main_Page
products:
- {id: emapa.owl, ontology_purl: 'http://purl.obolibrary.org/obo/emapa.owl'}
- {id: emapa.obo, ontology_purl: 'http://purl.obolibrary.org/obo/emapa.obo'}
taxon: {id: 'NCBITaxon:10088', label: Mus}
title: Mouse gross anatomy and development, timed
used_by:
- {label: GXD, url: 'https://www.biosharing.org/biodbcore-000659'}
- build: {checkout: 'git clone https://github.com/EnvironmentOntology/envo.git', email_cc: cjmungall@lbl.gov,
infallible: 1, method: vcs, path: ., system: git}
contact: {email: p.buttigieg@googlemail.com, 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:
- {id: envo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/envo.owl'}
- {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'}
- {id: 'http://doi.org/10.1186/s13326-016-0097-6', title: 'The environment ontology
in 2016: bridging domains with increased scope, semantic density, and interoperation'}
title: Environment Ontology
tracker: https://github.com/EnvironmentOntology/envo/issues/
usages:
- description: describing species habitats
examples: {url: 'http://eol.org/pages/211700/data'}
resources: {label: EOL, url: 'http://eol.org'}
type: data-annotation
- datasets: {url: 'https://s3.amazonaws.com/globi/snapshot/target/data/taxa/interactions.csv.gz'}
description: describing stomach contents
resources: {label: GloBI, url: 'http://globalbioticinteractions.org'}
type: data-annotation
- description: annotating datasets in data repositories
resources: {label: Nature Scientific Data, url: 'http://www.nature.com/sdata/'}
search: http://scientificdata.isa-explorer.org/
seeAlso: http://blogs.nature.com/scientificdata/2015/12/17/isa-explorer/
type: dataset-description
- build: {method: obo2owl, source_url: 'https://github.com/Planteome/plant-environment-ontology/blob/master/plant-environment-ontology.obo.owl'}
contact: {email: jaiswalp@science.oregonstate.edu, label: Pankaj Jaiswal}
description: A structured, controlled vocabulary which describes the treatments,
growing conditions, and/or study types used in plant biology experiments.
domain: environment
homepage: http://planteome.org/
id: eo
layout: ontology_detail
license: {label: CC-BY 4.0, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'https://creativecommons.org/licenses/by/4.0/'}
ontology_purl: http://purl.obolibrary.org/obo/eo.owl
page: http://browser.planteome.org/amigo/term/EO:0007359
products:
- {id: eo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/eo.owl'}
- {id: eo.obo, ontology_purl: 'http://purl.obolibrary.org/obo/eo.obo'}
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: tenille_johnson@hms.harvard.edu, 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'}
- {id: exo.obo, ontology_purl: 'http://purl.obolibrary.org/obo/exo.obo'}
title: Exposure ontology
- build: {checkout: 'git clone https://github.com/obophenotype/fungal-anatomy-ontology.git',
infallible: 1, method: vcs, system: git}
contact: {email: dinglis@stanford.edu, label: Diane Inglis}
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'}
- {id: fao.obo, ontology_purl: 'http://purl.obolibrary.org/obo/fao.obo'}
taxon: {id: 'NCBITaxon:4751', label: Fungal}
title: Fungal gross anatomy
tracker: https://github.com/obophenotype/fungal-anatomy-ontology/issues
- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/dosumis/fbbi/master/src/ontology/fbbi.obo'}
contact: {email: dorloff@ncmir.ucsd.edu, 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: 'https://raw.githubusercontent.com/FlyBase/drosophila-anatomy-developmental-ontology/master/fbbt/releases/fbbt.owl'}
contact: {email: mmc46@cam.ac.uk, 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: 'https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/releases/fbcv.owl'}
contact: {email: mmc46@cam.ac.uk, 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: 'https://raw.githubusercontent.com/FlyBase/drosophila-anatomy-developmental-ontology/master/fbdv/releases/fbdv.owl'}
contact: {email: mmc46@cam.ac.uk, 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: hastings@ebi.ac.uk, label: Janna Hastings}
description: An ontology of physico-chemical methods and properties.