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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:
- activity_status: active
browsers:
- label: BioPortal
title: BioPortal Browser
url: http://bioportal.bioontology.org/ontologies/BFO?p=classes
contact:
email: [email protected]
github: phismith
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/4.0/
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
review:
date: 2016
document:
label: PDF
link: https://drive.google.com/open?id=0B81h9ah4tAM_RnNTRUZnVGRyWXM
title: Basic Formal Ontology
tracker: https://github.com/BFO-ontology/BFO/issues
usages:
- description: BFO is imported by multiple OBO ontologies to standardize upper level
structure
type: owl_import
user: http://obofoundry.org
- activity_status: active
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: [email protected]
github: amalik01
label: Adnan Malik
depicted_by: https://www.ebi.ac.uk/chebi/images/ChEBI_logo.png
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
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/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
- id: chebi.owl.gz
ontology_purl: http://purl.obolibrary.org/obo/chebi.owl.gz
title: chebi, compressed owl
- id: chebi/chebi_lite.obo
ontology_purl: http://purl.obolibrary.org/obo/chebi/chebi_lite.obo
title: chebi_lite, no syns or xrefs
- id: chebi/chebi_core.obo
ontology_purl: http://purl.obolibrary.org/obo/chebi/chebi_core.obo
title: chebi_core, no xrefs
publications:
- id: http://europepmc.org/article/MED/26467479
title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites.'
review:
date: 2010
title: Chemical Entities of Biological Interest
tracker: https://github.com/ebi-chebi/ChEBI/issues
twitter: chebit
usages:
- description: Rhea uses CHEBI to annotate reaction participants
examples:
- description: Query for all usages of CHEBI:29748 (chorismate)
url: https://www.rhea-db.org/searchresults?q=CHEBI:29748
user: https://www.rhea-db.org/
- description: ZFIN uses CHEBI to annotate experiments
examples:
- description: A curated zebrafish experiment involving exposure to (5Z,8Z,14Z)-11,12-dihydroxyicosatrienoic
acid (CHEBI:63969)
url: http://zfin.org/action/expression/experiment?id=ZDB-EXP-190627-10
user: http://zfin.org
- DO wiki: http://diseaseontology.sourceforge.net/
activity_status: active
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.obo
contact:
email: [email protected]
github: lschriml
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, OWL format. This file contains DO's is_a asserted hierarchy
plus equivalent axioms to other OBO Foundry ontologies.
- id: doid.obo
ontology_purl: http://purl.obolibrary.org/obo/doid.obo
title: Disease Ontology, OBO format. This file omits the equivalent axioms.
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'
review:
date: 2015
document:
label: PDF
link: https://drive.google.com/open?id=0B8vqEgF1N0NIZ082U2JETHlSTGs
taxon:
id: NCBITaxon:9606
label: Homo sapiens
title: Human Disease Ontology
tracker: https://github.com/DiseaseOntology/HumanDiseaseOntology/issues
twitter: diseaseontology
usages:
- description: MGI disease model annotations use DO
examples:
- description: Human genes and mouse homology associated with nail diseases
url: http://www.informatics.jax.org/disease/DOID:4123
user: http://www.informatics.jax.org/disease
- activity_status: active
browsers:
- label: AmiGO
title: Gene Ontology AmiGO 2 Browser
url: http://amigo.geneontology.org/amigo/term/GO:0008150#display-lineage-tab
contact:
email: [email protected]
label: Suzi Aleksander
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/assets/go-logo-icon.mini.png
description: An ontology for describing the function of genes and gene products
domain: biology
facebook: https://www.facebook.com/Gene-Ontology-305908656519/
homepage: http://geneontology.org/
id: go
in_foundry_order: 1
integration_server: http://build.berkeleybop.org/view/GO
label: GO
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/go.owl
products:
- description: The main ontology in OWL. This is self contained and does not have
connections to other OBO ontologies
id: go.owl
ontology_purl: http://purl.obolibrary.org/obo/go.owl
page: http://geneontology.org/page/download-ontology
title: GO (OWL edition)
- description: Equivalent to go.owl, in obo format
id: go.obo
ontology_purl: http://purl.obolibrary.org/obo/go.obo
page: http://geneontology.org/page/download-ontology
title: GO (OBO Format edition)
- description: Equivalent to go.owl, in obograph json format
id: go.json
ontology_purl: http://purl.obolibrary.org/obo/go.json
page: https://github.com/geneontology/obographs/
title: GO (JSON edition)
- description: The main ontology plus axioms connecting to select external ontologies,
with subsets of those ontologies
id: go/extensions/go-plus.owl
ontology_purl: http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
page: http://geneontology.org/page/download-ontology
title: GO-Plus
- description: The main ontology plus axioms connecting to select external ontologies,
excluding the external ontologies themselves
id: go/go-base.owl
ontology_purl: http://purl.obolibrary.org/obo/go/go-base.owl
page: http://geneontology.org/page/download-ontology
title: GO Base Module
- description: As go-plus.owl, in obographs json format
id: go/extensions/go-plus.json
ontology_purl: http://purl.obolibrary.org/obo/go/extensions/go-plus.json
page: https://github.com/geneontology/obographs/
title: GO-Plus
- description: Basic version of the GO, filtered such that the graph is guaranteed
to be acyclic and annotations can be propagated up the graph. The relations
included are is a, part of, regulates, negatively regulates and positively regulates.
This version excludes relationships that cross the 3 GO hierarchies.
id: go/go-basic.obo
ontology_purl: http://purl.obolibrary.org/obo/go/go-basic.obo
page: http://geneontology.org/page/download-ontology
title: GO-Basic, Filtered, for use with legacy tools
- description: As go-basic.obo, in json format
id: go/go-basic.json
ontology_purl: http://purl.obolibrary.org/obo/go/go-basic.json
page: http://geneontology.org/page/download-ontology
title: GO-Basic, Filtered, for use with legacy tools (JSON)
- 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
page: http://geneontology.org/page/download-ontology
title: GO Taxon Groupings
- description: Equivalent to go.owl, but released daily. Note the snapshot release
is not archived.
id: go/snapshot/go.owl
ontology_purl: http://purl.obolibrary.org/obo/go/snapshot/go.owl
page: http://geneontology.org/page/download-ontology
title: GO (OWL edition), daily snapshot release
- description: Equivalent to go.owl, but released daily. Note the snapshot release
is not archived.
id: go/snapshot/go.obo
ontology_purl: http://purl.obolibrary.org/obo/go/snapshot/go.obo
page: http://geneontology.org/page/download-ontology
title: GO (OBO Format edition), daily snapshot release
review:
date: 2010
taxon:
id: NCBITaxon:1
label: All life
title: Gene Ontology
tracker: https://github.com/geneontology/go-ontology/issues/
twitter: news4go
usages:
- description: The GO ontology is used by the GO consortium for functional annotation
of genes
examples:
- description: annotations to transmembrane transport
url: http://amigo.geneontology.org/amigo/term/GO:0055085
type: annotation
user: http://geneontology.org
- activity_status: active
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 4.0
logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png
url: https://creativecommons.org/licenses/by/4.0/
mailing_list: http://groups.google.com/group/obi-users
ontology_purl: http://purl.obolibrary.org/obo/obi.owl
products:
- description: The full version of OBI in OWL format
id: obi.owl
ontology_purl: http://purl.obolibrary.org/obo/obi.owl
title: OBI
- description: The OBO-format version of OBI
id: obi.obo
ontology_purl: http://purl.obolibrary.org/obo/obi.obo
title: OBI in OBO
- description: A collection of important high-level terms and their relations from
OBI and other ontologies
id: obi/obi_core.owl
ontology_purl: http://purl.obolibrary.org/obo/obi/obi_core.owl
title: OBI Core
review:
date: 2013
document:
label: PDF
link: https://drive.google.com/open?id=0B8vqEgF1N0NIMFlSM3RvdUxGTnc
title: Ontology for Biomedical Investigations
tracker: http://purl.obolibrary.org/obo/obi/tracker
usages:
- description: PennTURBO accelerates the processes of finding and connecting key
information from clinical records, via semantic modeling of the processes that
generated the data. This makes the discovery of previously unappreciated relations
between the data possible for research and for operational tasks.
example:
- description: CYP2C1*2/*2 MI patient taking Clopidogrel
url: https://github.com/PennTURBO/Turbo-Documentation/blob/master/IBI_CIC_TURBO_MAM_20190102.pdf
user: http://upibi.org/turbo/
- description: The Evidence & Conclusion Ontology (ECO) describes types of scientific
evidence within the biological research domain. ECO uses OBI to logically describe
how the evidence arises from an investigation.
example:
- description: rapid amplification of cDNA ends polymerase chain reaction evidence
url: http://purl.obolibrary.org/obo/ECO_0001820
user: http://evidenceontology.org/
- activity_status: active
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]
github: gkoutos
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
- id: pato.json
ontology_purl: http://purl.obolibrary.org/obo/pato.json
- description: Includes axioms linking to other ontologies, but no imports of those
ontologies
id: pato/pato-base.owl
ontology_purl: http://purl.obolibrary.org/obo/pato/pato-base.owl
repository: https://github.com/pato-ontology/pato/
review:
date: 2010
title: Phenotype And Trait Ontology
tracker: https://github.com/pato-ontology/pato/issues
usages:
- description: PATO is used by the Human Phenotype Ontology (HPO) for logical definitions
of phenotypes that facilitate cross-species integration.
examples:
- url: https://www.ebi.ac.uk/ols/ontologies/hp/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHP_0011017&viewMode=All&siblings=false
reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324074/
type: annotation
user: https://hpo.jax.org/app/
- activity_status: active
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: [email protected]
github: jaiswalp
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: https://doi.org/10.1093/nar/gkx1152
title: 'The Planteome database: an integrated resource for reference ontologies,
plant genomics and phenomics.'
review:
date: 2013
document:
label: PDF
link: https://drive.google.com/open?id=0B8vqEgF1N0NIV1o0N21UOHlLSmc
taxon:
id: NCBITaxon:33090
label: Viridiplantae
title: Plant Ontology
tracker: https://github.com/Planteome/plant-ontology/issues
twitter: planteome
usages:
- description: Planteome uses PO to describe location of tissue expression for genes
in viridiplantae
examples:
- description: Genes and proteins annotate to leaf
url: http://browser.planteome.org/amigo/term/PO:0025034
user: http://planteome.org/
- description: Maize CELL genomics DB uses PO to annotate images
examples:
- url: http://maize.jcvi.org/cellgenomics/geneDB_list.php?filter=3
user: http://maize.jcvi.org/
- description: MaizeGDB uses PO for annotation of genes
examples:
- url: http://maizegdb.org/gene_center/gene/GRMZM5G863962
user: http://maizegdb.org/
- description: Gramene uses PO for the annotation of plant genes
examples:
- description: Gramene annotations to leaf from Arabidopsis
url: http://archive.gramene.org/db/ontology/search?id=PO:0025034
user: http://gramene.org/
- activity_status: active
browsers:
- label: BioPortal
title: BioPortal Browser
url: http://bioportal.bioontology.org/ontologies/PR?p=classes&conceptid=http://purl.obolibrary.org/obo/PR_000000001
- label: PRO
title: PRO Home
url: http://proconsortium.org
build:
infallible: 0
method: obo2owl
oort_args: --no-reasoner
source_url: https://proconsortium.org/download/current/pro_nonreasoned.obo
contact:
email: [email protected]
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+PURLs
documentation: https://proconsortium.org/download/current/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
publications:
- id: https://proconsortium.org/pro_dsmnt.shtml#publication
title: Publications & Dissemination
review:
date: 2010
title: PRotein Ontology (PRO)
tracker: https://github.com/PROconsortium/PRoteinOntology/issues
usages:
- description: Colorado Richly Annotated Full-Text (CRAFT) Corpus; PRO is used for
entity tagging and annotation
examples:
- description: Tagged entities (requires download)
url: https://github.com/UCDenver-ccp/CRAFT/releases/tag/v4.0.1
user: https://github.com/UCDenver-ccp/CRAFT
- description: Cell Ontology is a structured controlled vocabulary for cell types
in animals; PRO is used for cell type definitions
examples:
- description: A B cell that is CD19-positive (uses the PRO term for non-species-specific
CD19 molecule, PR:000001002)
url: http://purl.obolibrary.org/obo/CL_0001201
user: http://www.obofoundry.org/ontology/cl.html
- activity_status: active
build:
infallible: 0
method: obo2owl
source_url: https://raw.githubusercontent.com/xenopus-anatomy/xao/master/xenopus_anatomy.obo
contact:
email: [email protected]
github: seger
label: Erik Segerdell
description: XAO represents the anatomy and development of the African frogs Xenopus
laevis and tropicalis.
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.'
review:
date: 2010
taxon:
id: NCBITaxon:8353
label: Xenopus
title: Xenopus Anatomy Ontology
tracker: https://github.com/xenopus-anatomy/xao/issues
usages:
- description: Xenbase uses XAO to annotate gene expression.
examples:
- description: Xenopus genes expressed in the pronephric kidney.
url: http://www.xenbase.org/anatomy/showanatomy.do?method=displayAnatomySummary&anatomyId=463
user: http://www.xenbase.org
- activity_status: active
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]
github: cerivs
label: Ceri Van Slyke
description: A structured controlled vocabulary of the anatomy and development of
the Zebrafish
domain: anatomy
homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
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:
- id: http://www.ncbi.nlm.nih.gov/pubmed/24568621
title: 'The zebrafish anatomy and stage ontologies: representing the anatomy and
development of Danio rerio.'
review:
date: 2010
taxon:
id: NCBITaxon:7954
label: Danio
title: Zebrafish anatomy and development ontology
tracker: https://github.com/cerivs/zebrafish-anatomical-ontology/issues
usages:
- description: ZFIN uses ZFA to annotate gene expression and phenotype
examples:
- description: zebrafish genes expressed in hindbrain and genotypes with hindbrain
phenotype
url: http://zfin.org/ZFA:0000029
user: http://zfin.org
- activity_status: active
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
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/aeo.owl
products:
- id: aeo.owl
ontology_purl: http://purl.obolibrary.org/obo/aeo.owl
title: Anatomical Entity Ontology
tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues
- activity_status: active
build:
checkout: git clone https://github.com/AgriculturalSemantics/agro.git
infallible: 1
method: vcs
path: .
system: git
contact:
email: [email protected]
github: marieALaporte
label: "Marie-Ang\xE9lique Laporte"
dependencies:
- id: envo
- id: uo
- id: ro
- id: pato
- id: chebi
- id: iao
- id: ncbitaxon
- id: po
- id: peco
description: Ontology of agronomic practices, agronomic techniques, and agronomic
variables used in agronomic experiments
domain: agronomy
homepage: https://github.com/AgriculturalSemantics/agro
id: agro
jobs:
- id: https://travis-ci.org/AgriculturalSemantics/agro
type: travis-ci
layout: ontology_detail
license:
label: CC-BY
logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png
url: https://creativecommons.org/licenses/by/4.0/
mailing_list: https://groups.google.com/group/agronomyOntology
ontology_purl: http://purl.obolibrary.org/obo/agro.owl
products:
- id: agro.owl
ontology_purl: http://purl.obolibrary.org/obo/agro.owl
title: Agronomy Ontology
tracker: https://github.com/AgriculturalSemantics/agro/issues/
- activity_status: active
build:
checkout: git clone https://github.com/EBISPOT/amphx_ontology.git
path: .
system: git
contact:
email: [email protected]
label: Hector Escriva
dependencies:
- id: uberon
description: An ontology for the development and anatomy of Amphioxus (Branchiostoma
lanceolatum).
domain: anatomy
homepage: https://github.com/EBISPOT/amphx_ontology
id: amphx
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/amphx.owl
products:
- id: amphx.owl
ontology_purl: http://purl.obolibrary.org/obo/amphx.owl
- id: amphx.obo
ontology_purl: http://purl.obolibrary.org/obo/amphx.obo
title: The Amphioxus Development and Anatomy Ontology
tracker: https://github.com/EBISPOT/amphx_ontology/issues
- activity_status: active
build:
method: obo2owl
source_url: https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo
contact:
email: [email protected]
github: srengel
label: Stacia R Engel
description: A structured controlled vocabulary for the phenotypes of Ascomycete
fungi
domain: phenotype
homepage: http://www.yeastgenome.org/
id: apo
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/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
tracker: https://github.com/obophenotype/ascomycete-phenotype-ontology/issues
- activity_status: active
contact:
email: [email protected]
label: Mathias Brochhausen
description: Defines terms and relations necessary for interoperation between epidemic
models and public health application software that interface with these models
domain: health
homepage: https://github.com/ApolloDev/apollo-sv
id: apollo_sv
layout: ontology_detail
license:
label: CC-BY 3.0
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/apollo_sv.owl
products:
- id: apollo_sv.owl
ontology_purl: http://purl.obolibrary.org/obo/apollo_sv.owl
title: Apollo Structured Vocabulary
tracker: https://github.com/ApolloDev/apollo-sv/issues
- activity_status: active
contact:
email: [email protected]
github: raphenya
label: CARD
description: Antibiotic resistance genes and mutations
homepage: https://github.com/arpcard/aro
id: aro
layout: ontology_detail
license:
label: CC-BY
logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png
url: https://creativecommons.org/licenses/by/4.0/
mailing_list: https://mailman.mcmaster.ca/mailman/listinfo/card-l
ontology_purl: http://purl.obolibrary.org/obo/aro.owl
products:
- id: aro.owl
ontology_purl: http://purl.obolibrary.org/obo/aro.owl
title: Antibiotic Resistance Ontology
tracker: https://github.com/arpcard/aro/issues
- activity_status: active
contact:
email: [email protected]
github: ramonawalls
label: Ramona Walls
description: An ontology to support the interoperability of biodiversity data, including
data on museum collections, environmental/metagenomic samples, and ecological
surveys.
domain: biodiversity collections
homepage: https://github.com/tucotuco/bco
id: bco
in_foundry: false
layout: ontology_detail
license:
label: CC-0
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/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
- activity_status: active
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]
github: cmungall
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
- id: bspo.obo
ontology_purl: http://purl.obolibrary.org/obo/bspo.obo
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
- activity_status: active
build:
checkout: git clone https://github.com/BRENDA-Enzymes/BTO.git
path: .
system: git
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.org
id: bto
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/bto.owl
page: https://en.wikipedia.org/wiki/BRENDA_tissue_ontology
products:
- id: bto.owl
ontology_purl: http://purl.obolibrary.org/obo/bto.owl
- id: bto.obo
ontology_purl: http://purl.obolibrary.org/obo/bto.obo
- id: bto.json
ontology_purl: http://purl.obolibrary.org/obo/bto.json
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
tracker: https://github.com/BRENDA-Enzymes/BTO/issues
- activity_status: active
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]
github: mellybelly
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
license:
label: CC-BY 3.0
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/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
- activity_status: active
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: https://github.com/evoinfo/cdao
id: cdao
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/cdao.owl
products:
- id: cdao.owl
ontology_purl: http://purl.obolibrary.org/obo/cdao.owl
title: Comparative Data Analysis Ontology
tracker: https://github.com/evoinfo/cdao/issues
- activity_status: active
build:
method: owl2obo
source_url: https://raw.githubusercontent.com/semanticchemistry/semanticchemistry/master/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/semanticchemistry/semanticchemistry
id: cheminf
layout: ontology_detail
license:
label: CC BY 4.0
logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png
url: http://creativecommons.org/licenses/by/4.0/
mailing_list: https://groups.google.com/forum/#!forum/cheminf-ontology
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
tracker: https://github.com/semanticchemistry/semanticchemistry/issues
- activity_status: active
build:
checkout: git clone https://github.com/obophenotype/chiro.git
path: .
system: git
contact:
email: [email protected]
github: nicolevasilevsky
label: Nicole Vasilevsky
dependencies:
- id: chebi
- id: mp
- id: hp
- id: go
- id: pr
- id: uberon
- id: ncbitaxon
description: CHEBI provides a distinct role hierarchy. Chemicals in the structural
hierarchy are connected via a 'has role' relation. CHIRO provides links from these
roles to useful other classes in other ontologies. This will allow direct connection
between chemical structures (small molecules, drugs) and what they do. This could
be formalized using 'capable of', in the same way Uberon and the Cell Ontology
link structures to processes.
domain: biochemistry
homepage: https://github.com/obophenotype/chiro
id: chiro
jobs:
- id: https://travis-ci.org/obophenotype/chiro
type: travis-ci
layout: ontology_detail
license:
label: CC-0
logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png
url: http://creativecommons.org/publicdomain/zero/1.0/
ontology_purl: http://purl.obolibrary.org/obo/chiro.owl
products:
- id: chiro.owl
name: CHEBI Integrated Role Ontology main release in OWL format
ontology_purl: http://purl.obolibrary.org/obo/chiro.owl
- id: chiro.obo
name: CHEBI Integrated Role Ontology additional release in OBO format
ontology_purl: http://purl.obolibrary.org/obo/chiro.obo
title: CHEBI Integrated Role Ontology
tracker: https://github.com/obophenotype/chiro/issues
- activity_status: active
contact: