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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
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
orcid: 0000-0003-1384-116X
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 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/bfo-discuss
ontology_purl: http://purl.obolibrary.org/obo/bfo.owl
preferredPrefix: BFO
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
repository: https://github.com/BFO-ontology/BFO
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
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
orcid: 0000-0001-8123-5351
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: chemistry and 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
preferredPrefix: CHEBI
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: https://www.ncbi.nlm.nih.gov/pubmed/26467479
title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites.'
repository: https://github.com/ebi-chebi/ChEBI
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
- 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
orcid: 0000-0001-8910-9851
depicted_by: http://www.disease-ontology.org/media/images/DO_logo.jpg
description: An ontology for describing the classification of human diseases organized
by etiology.
domain: health
homepage: http://www.disease-ontology.org
id: doid
in_foundry_order: 1
layout: ontology_detail
license:
label: CC0 1.0
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/doid.owl
preferredPrefix: DOID
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: https://www.ncbi.nlm.nih.gov/pubmed/25348409
title: 'Disease Ontology 2015 update: an expanded and updated database of human
diseases for linking biomedical knowledge through disease data'
- id: https://www.ncbi.nlm.nih.gov/pubmed/34755882
title: The Human Disease Ontology 2022 update
repository: https://github.com/DiseaseOntology/HumanDiseaseOntology
review:
date: 2015
document:
label: PDF
link: https://drive.google.com/open?id=0B8vqEgF1N0NIZ082U2JETHlSTGs
tags:
- disease
taxon:
id: NCBITaxon:9606
label: Homo sapiens
title: Human Disease Ontology
tracker: https://github.com/DiseaseOntology/HumanDiseaseOntology/issues
twitter: diseaseontology
usages:
- description: Alliance of Genome Resources - MGD, RGD, SGD, FlyBase, WormBase,
ZFIN use DO
examples:
- description: Human diseases annotated to over 190,000 MOD genes, alleles, disease
models and human genes
url: https://www.alliancegenome.org/search?category=disease
- description: The landing page for Coronavirus Infectious Disease
url: https://www.alliancegenome.org/disease/DOID:0080599
user: https://www.alliancegenome.org
- description: MGI disease model annotations use DO
examples:
- description: physical disorder
url: http://www.informatics.jax.org/disease/DOID:0080015
user: http://www.informatics.jax.org/disease
- description: Immune Epitope Database
examples:
- description: Antibody and T cell epitopes associated with human diseases
url: https://www.iedb.org
user: https://www.iedb.org
- 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]
github: suzialeksander
label: Suzi Aleksander
orcid: 0000-0001-6787-2901
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: biological systems
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
preferredPrefix: GO
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
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/10802651
title: 'Gene ontology: tool for the unification of biology. The Gene Ontology
Consortium'
- id: https://www.ncbi.nlm.nih.gov/pubmed/33290552
title: 'The Gene Ontology resource: enriching a GOld mine'
repository: https://github.com/geneontology/go-ontology
review:
date: 2010
tags:
- biology
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
- description: Uniprot uses GO to show the function of proteins
examples:
- description: functional annotations of human Sonic hedgehog protein
url: https://www.uniprot.org/uniprot/Q15465#function
type: annotation
user: https://www.uniprot.org
- description: Reactome annotates activities, pathways, and cellular localization
using GO
examples:
- description: protein tyrosine kinase activity of an EGFR complex
url: https://reactome.org/content/detail/R-HSA-177934
type: annotation
user: https://reactome.org
- description: The Alliance of Genome Resources uses GO for model organism gene
function annotation
examples:
- description: Functional summary of C elegans nsy-1 gene
url: https://www.alliancegenome.org/gene/WB:WBGene00003822#function---go-annotations
- description: Gene Ontology Causal Activity Models for C elegans nsy-1 gene
url: https://www.alliancegenome.org/gene/WB:WBGene00003822#pathways
type: annotation
user: https://www.alliancegenome.org
- description: Rhea uses GO to describe individual biochemical reactions
examples:
- description: Glutamine scyllo-inositol transaminase reaction and associated
GO term
url: https://www.rhea-db.org/rhea/22920
type: mapping
user: https://www.rhea-db.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]
github: bpeters42
label: Bjoern Peters
orcid: 0000-0002-8457-6693
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: investigations
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
preferredPrefix: OBI
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
- description: Base module for OBI
id: obi/obi-base.owl
ontology_purl: http://purl.obolibrary.org/obo/obi/obi-base.owl
title: OBI Base module
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/27128319
title: The Ontology for Biomedical Investigations
repository: https://github.com/obi-ontology/obi
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: The Immune Epitope Database (IEDB) is funded by NIAID that catalogs
experimental data on antibody and T cell epitopes studied in humans, non-human
primates, and other animal species in the context of infectious disease, allergy,
autoimmunity and transplantation.
examples:
- description: A specific assay curated in the IEDB using the OBI:1110180 '3H-thymidine
assay measuring epitope specific proliferation of T cells' ('3H-thymidine')
url: http://www.iedb.org/assay/1505273
user: https://www.iedb.org
- description: ENCODE is a comprehensive parts list of functional elements in the
human genome, including elements that act at the protein and RNA levels, and
regulatory elements that control cells and circumstances in which a gene is
active.
examples:
- description: A specific assay annotated in ENCODE using OBI:0000716 'ChiP-seq'
url: https://www.encodeproject.org/report/?type=Experiment&accession=ENCSR012KGU&accession=ENCSR560MXA&accession=ENCSR803FKU&accession=ENCSR216YPQ&accession=ENCSR115BCB&field=%40id&field=assay_term_name&field=assay_term_id
user: https://www.encodeproject.org/
- description: The NASA GeneLab data repository hosts space biology and space-related
datasets funded by multiple space agencies around the world.
examples:
- description: A specific assay annotated in NASA GeneLab using OBI:0001271 'RNA-seq
assay'
url: https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-464/
user: https://genelab-data.ndc.nasa.gov/genelab/projects
- description: The CFDE is providing a centralized metadata resource to allow search
across data coordination centers from multiple Common Fund programs.
examples:
- description: OBI is used in CFDE to captures types of experiments with assay
terms such as OBI:0003094 'fluorescence in-situ hybridization assay'
url: https://app.nih-cfde.org/chaise/recordset/#1/CFDE:assay_type@sort(nid)
user: https://app.nih-cfde.org/
- description: NIF is a dynamic inventory of Web-based neuroscience resources, data,
and tools accessible via any computer connected to the Internet.
examples:
- description: A specific OBI term used to autocomplete in NIF search OBI:0100026
'organism'
url: https://neuinfo.org/data/search?q=organism&l=organism#all
user: http://www.neuinfo.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
orcid: 0000-0002-2061-091X
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 3.0
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
preferredPrefix: PATO
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
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/28387809
title: 'The anatomy of phenotype ontologies: principles, properties and applications'
- id: https://www.ncbi.nlm.nih.gov/pubmed/15642100
title: Using ontologies to describe mouse phenotypes
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:
- description: An abnormality in a cellular process.
url: https://www.ebi.ac.uk/ols/ontologies/hp/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHP_0011017&viewMode=All&siblings=false
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/30476213
title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources
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
orcid: 0000-0002-1005-8383
depicted_by: http://planteome.org/sites/default/files/garland_logo.PNG
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
preferredPrefix: PO
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: https://www.ncbi.nlm.nih.gov/pubmed/23220694
title: The plant ontology as a tool for comparative plant anatomy and genomic
analyses.
- id: https://www.ncbi.nlm.nih.gov/pubmed/29186578
title: 'The Planteome database: an integrated resource for reference ontologies,
plant genomics and phenomics.'
repository: https://github.com/Planteome/plant-ontology
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:
- description: LhG4 Promoter Drivers
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:
- description: Introduced in gene model set 5b in assembly version RefGen_v2.
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]
github: nataled
label: Darren Natale
orcid: 0000-0001-5809-9523
depicted_by: https://raw.githubusercontent.com/PROconsortium/logo/master/PROlogo_small.png
description: An ontological representation of protein-related entities
documentation: https://proconsortium.org/download/current/pro_readme.txt
domain: chemistry and biochemistry
homepage: http://proconsortium.org
id: pr
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: http://creativecommons.org/licenses/by/4.0/
ontology_purl: http://purl.obolibrary.org/obo/pr.owl
preferredPrefix: PR
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://www.ncbi.nlm.nih.gov/pubmed/27899649
title: 'Protein Ontology (PRO): enhancing and scaling up the representation of
protein entities'
repository: https://github.com/PROconsortium/PRoteinOntology
review:
date: 2010
tags:
- proteins
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
orcid: 0000-0002-9611-1279
description: XAO represents the anatomy and development of the African frogs Xenopus
laevis and tropicalis.
domain: anatomy and development
homepage: http://www.xenbase.org/anatomy/xao.do?method=display
id: xao
in_foundry_order: 1
layout: ontology_detail
license:
label: CC BY 3.0
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
preferredPrefix: XAO
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: https://www.ncbi.nlm.nih.gov/pubmed/18817563
title: An ontology for Xenopus anatomy and development.
- id: https://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.'
repository: https://github.com/xenopus-anatomy/xao
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
orcid: 0000-0002-2244-7917
description: A structured controlled vocabulary of the anatomy and development of
the Zebrafish
domain: anatomy and development
homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
id: zfa
in_foundry_order: 1
layout: ontology_detail
license:
label: CC BY 3.0
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
preferredPrefix: ZFA
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: https://www.ncbi.nlm.nih.gov/pubmed/24568621
title: 'The zebrafish anatomy and stage ontologies: representing the anatomy and
development of Danio rerio.'
repository: https://github.com/cerivs/zebrafish-anatomical-ontology
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/AgriculturalSemantics/agro.git
path: .
system: git
contact:
email: [email protected]
github: marieALaporte
label: Marie-Angélique Laporte
orcid: 0000-0002-8461-9745
dependencies:
- id: envo
- id: go
- id: foodon
- id: ncbitaxon
- id: pato
- id: peco
- id: po
- id: to
- id: ro
- id: bfo
- id: iao
- id: obi
- id: uo
- id: xco
description: Ontology of agronomic practices, agronomic techniques, and agronomic
variables used in agronomic experiments
domain: agriculture
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 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/agro.owl
preferredPrefix: AGRO
products:
- description: Contains all AgrO terms and links to other relavent ontologies.
id: agro.owl
ontology_purl: http://purl.obolibrary.org/obo/agro.owl
title: AgrO
publications:
- id: http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf
title: 'Data-driven Agricultural Research for Development: A Need for Data Harmonization
Via Semantics.'
repository: https://github.com/AgriculturalSemantics/agro
tags:
- agronomy
title: Agronomy Ontology
tracker: https://github.com/AgriculturalSemantics/agro/issues/
usages:
- description: AgroFIMS enables digital collection of agronomic data that is semantically
described a priori with agronomic terms from AgrO.
user: https://agrofims.org/about
- description: AgrO is being used by GARDIAN to facilitate data search within publications
and datasets for use in quantitative analyses.
user: https://gardian.bigdata.cgiar.org/
- activity_status: active
build:
checkout: git clone https://github.com/insect-morphology/aism
path: .
system: git
contact:
email: [email protected]
github: JCGiron
label: Jennifer C. Girón
orcid: 0000-0002-0851-6883
dependencies:
- id: ro
- id: uberon
- id: caro
- id: pato
- id: bfo
- id: bspo
description: The AISM contains terms used in insect biodiversity research for describing
structures of the exoskeleton and the skeletomuscular system. It aims to serve
as the basic backbone of generalized terms to be expanded with order-specific
terminology.
domain: anatomy and development
homepage: https://github.com/insect-morphology/aism
id: aism
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/aism.owl
preferredPrefix: AISM
products:
- id: aism.owl
ontology_purl: http://purl.obolibrary.org/obo/aism.owl
- id: aism.obo
ontology_purl: http://purl.obolibrary.org/obo/aism.obo
- id: aism.json
ontology_purl: http://purl.obolibrary.org/obo/aism.json
repository: https://github.com/insect-morphology/aism
title: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)
tracker: https://github.com/insect-morphology/aism/issues
- activity_status: active
build:
checkout: git clone https://github.com/EBISPOT/amphx_ontology.git
path: .
system: git
contact:
email: [email protected]
github: hescriva
label: Hector Escriva
orcid: 0000-0001-7577-5028
dependencies:
- id: uberon
description: An ontology for the development and anatomy of Amphioxus (Branchiostoma
lanceolatum).
domain: anatomy and development
homepage: https://github.com/EBISPOT/amphx_ontology
id: amphx
layout: ontology_detail
license:
label: CC BY 3.0
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
preferredPrefix: AMPHX
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
repository: https://github.com/EBISPOT/amphx_ontology
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
orcid: 0000-0001-5472-917X
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
preferredPrefix: APO
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
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/20157474
title: New mutant phenotype data curation system in the Saccharomyces Genome Database
repository: https://github.com/obophenotype/ascomycete-phenotype-ontology
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]
github: hoganwr
label: William Hogan
orcid: 0000-0002-9881-1017
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 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/apollo_sv.owl
preferredPrefix: APOLLO_SV
products:
- id: apollo_sv.owl
ontology_purl: http://purl.obolibrary.org/obo/apollo_sv.owl
publications:
- id: https://doi.org/10.1186/s13326-016-0092-y
title: 'The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious
disease epidemiology and population biology for use in epidemic simulation'
repository: https://github.com/ApolloDev/apollo-sv
title: Apollo Structured Vocabulary
tracker: https://github.com/ApolloDev/apollo-sv/issues
- activity_status: active
contact:
email: [email protected]
github: agmcarthur
label: Andrew G. McArthur
orcid: 0000-0002-1142-3063
description: Antibiotic resistance genes and mutations
domain: microbiology
homepage: https://github.com/arpcard/aro
id: aro
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: https://mailman.mcmaster.ca/mailman/listinfo/card-l
ontology_purl: http://purl.obolibrary.org/obo/aro.owl
preferredPrefix: ARO
products:
- id: aro.owl
ontology_purl: http://purl.obolibrary.org/obo/aro.owl
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/31665441
title: 'CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic
resistance database.'
repository: https://github.com/arpcard/aro
title: Antibiotic Resistance Ontology
tracker: https://github.com/arpcard/aro/issues
- activity_status: active
contact:
email: [email protected]
github: ramonawalls
label: Ramona Walls
orcid: 0000-0001-8815-0078
description: An ontology to support the interoperability of biodiversity data, including
data on museum collections, environmental/metagenomic samples, and ecological
surveys.
domain: organisms
homepage: https://github.com/BiodiversityOntologies/bco
id: bco
in_foundry: false
layout: ontology_detail
license:
label: CC0 1.0
logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png
url: https://creativecommons.org/publicdomain/zero/1.0/