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_config.yml
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_config.yml
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name: OBO Foundry
title: The OBO Foundry
markdown: kramdown
highlighter: rouge
baseurl: /
imgurl: /images
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:
- 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: 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: 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
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: 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'}
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: 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
- 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://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: 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:
- {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: 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'}
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: J.Bard@ed.ac.uk, 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: 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',
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: {checkout: 'git clone https://github.com/AgriculturalSemantics/agro.git',
infallible: 1, method: vcs, path: ., system: git}
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description: An ontology to support the interoperability of biodiversity data, including
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surveys.
homepage: https://github.com/tucotuco/bco
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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: 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: {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'}
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 \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: 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: {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: maria@genome.stanford.edu, 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: 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.
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
- build: {method: owl2obo, source_url: 'https://github.com/flora-phenotype-ontology/flopoontology/raw/master/ontology/flopo.owl'}
contact: {email: robert.hoehndorf@kaust.edu.sa, 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: {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/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: burkesquires@gmail.com, 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: mejino@u.washington.edu, 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