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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
plugins:
- jekyll-sitemap
## --Anything above this line can be edited in _config_header.yml --
## --Everything below this line automatically generated in _config.yml --
ontologies:
- activity_status: active
contact:
email: alpha.tom.kodamullil@scai.fraunhofer.de
github: akodamullil
label: Alpha Tom Kodamullil
orcid: 0000-0001-9896-3531
dependencies:
- id: bfo
description: Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses
varieties of concepts related to Alzheimer'S Disease, structured by upper level
Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities
that demonstrate the network of the understanding on Alzheimer's disease and can
be readily applied for text mining.
domain: health
homepage: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO
id: ado
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/ado.owl
preferredPrefix: ADO
products:
- id: ado.owl
ontology_purl: http://purl.obolibrary.org/obo/ado.owl
repository: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO
title: Alzheimer's Disease Ontology
tracker: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO/issues
- activity_status: active
contact:
email: mcmelek@msn.com
github: Melek-C
label: Melek Chaouch
orcid: 0000-0001-5868-4204
description: AfPO is an ontology that can be used in the study of diverse populations
across Africa. It brings together publicly available demographic, anthropological
and genetic data relating to African people in a standardised and structured format.
The AfPO can be employed to classify African study participants comprehensively
in prospective research studies. It can also be used to classify past study participants
by mapping them using a language or ethnicity identifier or synonyms.
domain: organisms
homepage: https://github.com/h3abionet/afpo
id: afpo
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/afpo.owl
preferredPrefix: AfPO
products:
- description: The main ontology in OWL. Contains all MP terms and links to other
OBO ontologies
id: afpo.owl
ontology_purl: http://purl.obolibrary.org/obo/afpo.owl
title: AfPO (OWL edition)
- description: A direct translation of the AfPO (OWL edition) into OBO format
id: afpo.obo
ontology_purl: http://purl.obolibrary.org/obo/afpo.obo
page: https://github.com/h3abionet/afpo
title: AfPO (OBO edition)
- description: A direct translation of the AfPO (OWL edition) into OBOGraph JSON
format
id: afpo.json
ontology_purl: http://purl.obolibrary.org/obo/afpo.json
page: https://github.com/h3abionet/afpo
title: AfPO (obographs JSON edition)
repository: https://github.com/h3abionet/afpo
tags:
- ancestry
title: African Population Ontology
tracker: https://github.com/h3abionet/afpo/issues
- activity_status: active
contact:
email: m.a.laporte@cgiar.org
github: marieALaporte
label: Marie-Angélique Laporte
orcid: 0000-0002-8461-9745
dependencies:
- id: bfo
- id: envo
- id: foodon
- id: go
- id: iao
- id: ncbitaxon
- id: obi
- id: pato
- id: peco
- id: po
- id: ro
- id: to
- 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
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 relevant 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: entiminae@gmail.com
github: JCGiron
label: Jennifer C. Girón
orcid: 0000-0002-0851-6883
dependencies:
- id: bfo
- id: bspo
- id: caro
- id: pato
- id: ro
- id: uberon
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: hescriva@obs-banyuls.fr
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: stacia@stanford.edu
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: hoganwr@gmail.com
github: hoganwr
label: William Hogan
orcid: 0000-0002-9881-1017
description: An OWL2 ontology of phenomena in infectious disease epidemiology and
population biology for use in epidemic simulation.
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
usages:
- description: Apollo-SV terms are used in the new MIDAS portal (https://midasnetwork.us/catalog/)
for making data discoverable.
examples:
- description: A 'hospital stay dataset' reference in the midasnetwork.us resource
url: https://midasnetwork.us/ontology/class-oboapollo_sv_00000600.html
seeAlso: https://midasnetwork.us/catalog/
type: annotation
user: https://midasnetwork.us/
- activity_status: active
contact:
email: mcarthua@mcmaster.ca
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: rlwalls2008@gmail.com
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/
ontology_purl: http://purl.obolibrary.org/obo/bco.owl
preferredPrefix: BCO
products:
- id: bco.owl
ontology_purl: http://purl.obolibrary.org/obo/bco.owl
publications:
- id: https://doi.org/10.1371/journal.pone.0089606
title: 'Semantics in Support of Biodiversity Knowledge Discovery: An Introduction
to the Biological Collections Ontology and Related Ontologies'
repository: https://github.com/BiodiversityOntologies/bco
tags:
- biodiversity collections
title: Biological Collections Ontology
tracker: https://github.com/BiodiversityOntologies/bco/issues
- activity_status: active
browsers:
- label: BioPortal
title: BioPortal Browser
url: http://bioportal.bioontology.org/ontologies/BFO?p=classes
contact:
email: phismith@buffalo.edu
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
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
build:
checkout: git clone https://github.com/obophenotype/biological-spatial-ontology.git
infallible: 1
method: vcs
path: src/ontology
system: git
contact:
email: cjmungall@lbl.gov
github: cmungall
label: Chris Mungall
orcid: 0000-0002-6601-2165
description: An ontology for representing spatial concepts, anatomical axes, gradients,
regions, planes, sides, and surfaces
domain: anatomy and development
homepage: https://github.com/obophenotype/biological-spatial-ontology
id: bspo
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/bspo.owl
preferredPrefix: BSPO
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: https://www.ncbi.nlm.nih.gov/pubmed/25140222
title: 'Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity
in the Biological Spatial Ontology.'
repository: https://github.com/obophenotype/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: c.dudek@tu-braunschweig.de
github: chdudek
label: Christian-Alexander Dudek
orcid: 0000-0001-9117-7909
description: A structured controlled vocabulary for the source of an enzyme comprising
tissues, cell lines, cell types and cell cultures.
domain: anatomy and development
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
preferredPrefix: BTO
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'
repository: https://github.com/BRENDA-Enzymes/BTO
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: haendel@ohsu.edu
github: mellybelly
label: Melissa Haendel
orcid: 0000-0001-9114-8737
description: An upper level ontology to facilitate interoperability between existing
anatomy ontologies for different species
domain: anatomy and development
homepage: https://github.com/obophenotype/caro/
id: caro
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/caro.owl
preferredPrefix: CARO
products:
- id: caro.owl
ontology_purl: http://purl.obolibrary.org/obo/caro.owl
repository: https://github.com/obophenotype/caro
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: balhoff@renci.org
github: balhoff
label: Jim Balhoff
orcid: 0000-0002-8688-6599
description: a formalization of concepts and relations relevant to evolutionary
comparative analysis
domain: organisms
homepage: https://github.com/evoinfo/cdao
id: cdao
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/cdao.owl
preferredPrefix: CDAO
products:
- id: cdao.owl
ontology_purl: http://purl.obolibrary.org/obo/cdao.owl
publications:
- id: https://doi.org/10.4137/EBO.S2320
title: Initial Implementation of a Comparative Data Analysis Ontology
repository: https://github.com/evoinfo/cdao
title: Comparative Data Analysis Ontology
tracker: https://github.com/evoinfo/cdao/issues
- activity_status: active
build:
checkout: git clone https://github.com/CompositionalDietaryNutritionOntology/cdno.git
path: .
system: git
contact:
email: landreshdz@gmail.com
github: LilyAndres
label: Liliana Andres Hernandez
orcid: 0000-0002-7696-731X
dependencies:
- id: bfo
- id: chebi
- id: envo
- id: pato
- id: ro
description: CDNO provides structured terminologies to describe nutritional attributes
of material entities that contribute to human diet.
domain: diet, metabolomics, and nutrition
homepage: https://cdno.info/
id: cdno
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/cdno.owl
preferredPrefix: CDNO
products:
- id: cdno.owl
name: Compositional Dietary Nutrition Ontology main release in OWL format
ontology_purl: http://purl.obolibrary.org/obo/cdno.owl
- id: cdno.obo
name: Compositional Dietary Nutrition Ontology additional release in OBO format
ontology_purl: http://purl.obolibrary.org/obo/cdno.obo
publications:
- id: https://doi.org/10.3389/fnut.2022.928837
title: Establishing a Common Nutritional Vocabulary - From Food Production to
Diet
repository: https://github.com/CompositionalDietaryNutritionOntology/cdno
title: Compositional Dietary Nutrition Ontology
tracker: https://github.com/CompositionalDietaryNutritionOntology/cdno/issues
- 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: amalik@ebi.ac.uk
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
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
build:
method: owl2obo
source_url: https://raw.githubusercontent.com/semanticchemistry/semanticchemistry/master/ontology/cheminf.owl
contact:
email: egon.willighagen@gmail.com
github: egonw
label: Egon Willighagen
orcid: 0000-0001-7542-0286
description: Includes terms for the descriptors commonly used in cheminformatics
software applications and the algorithms which generate them.
domain: chemistry and biochemistry
homepage: https://github.com/semanticchemistry/semanticchemistry
id: cheminf
layout: ontology_detail
license:
label: CC0 1.0
logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png
url: http://creativecommons.org/publicdomain/zero/1.0/
mailing_list: https://groups.google.com/forum/#!forum/cheminf-ontology
ontology_purl: http://purl.obolibrary.org/obo/cheminf.owl
preferredPrefix: CHEMINF
products:
- id: cheminf.owl
ontology_purl: http://purl.obolibrary.org/obo/cheminf.owl
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/21991315
title: 'The chemical information ontology: provenance and disambiguation for chemical
data on the biological semantic web'
repository: https://github.com/semanticchemistry/semanticchemistry
title: Chemical Information Ontology
tracker: https://github.com/semanticchemistry/semanticchemistry/issues
usages:
- description: ChEMBL uses CHEMINF in the RDF download
examples:
- description: The RDF is provided as SPARQL endpoint by Maastricht University.
url: https://chemblmirror.rdf.bigcat-bioinformatics.org/
user: https://www.ebi.ac.uk/chembl/
- description: PubChem uses CHEMINF in their RDF representation
examples:
- description: Physicochemical properties are represented as classes that are
typed with CHEMINF classes
url: https://pubchem.ncbi.nlm.nih.gov/rest/rdf/descriptor/CID161282_Canonical_SMILES
user: https://pubchem.ncbi.nlm.nih.gov/
- activity_status: active
contact:
email: vasilevs@ohsu.edu
github: nicolevasilevsky
label: Nicole Vasilevsky
orcid: 0000-0001-5208-3432
dependencies:
- id: chebi
- id: go
- id: hp
- id: mp
- id: ncbitaxon
- id: pr
- id: uberon
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: chemistry and biochemistry
homepage: https://github.com/obophenotype/chiro
id: chiro
layout: ontology_detail
license:
label: CC0 1.0
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
preferredPrefix: CHIRO
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
publications:
- id: https://doi.org/10.26434/chemrxiv.12591221
title: Extension of Roles in the ChEBI Ontology
repository: https://github.com/obophenotype/chiro
title: CHEBI Integrated Role Ontology
tracker: https://github.com/obophenotype/chiro/issues
- activity_status: active
contact:
email: batchelorc@rsc.org
github: batchelorc
label: Colin Batchelor
orcid: 0000-0001-5985-7429
description: CHMO, the chemical methods ontology, describes methods used to
domain: health
homepage: https://github.com/rsc-ontologies/rsc-cmo
id: chmo
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: chemistry-ontologies@googlegroups.com
ontology_purl: http://purl.obolibrary.org/obo/chmo.owl
preferredPrefix: CHMO
products:
- id: chmo.owl
ontology_purl: http://purl.obolibrary.org/obo/chmo.owl
repository: https://github.com/rsc-ontologies/rsc-cmo
title: Chemical Methods Ontology
tracker: https://github.com/rsc-ontologies/rsc-cmo/issues
- activity_status: active
contact:
email: yongqunh@med.umich.edu
github: yongqunh
label: Yongqun Oliver He
orcid: 0000-0001-9189-9661
description: The Coronavirus Infectious Disease Ontology (CIDO) aims to ontologically
represent and standardize various aspects of coronavirus infectious diseases,
including their etiology, transmission, epidemiology, pathogenesis, diagnosis,
prevention, and treatment.
domain: health
homepage: https://github.com/cido-ontology/cido
id: cido
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: cido-discuss@googlegroups.com
ontology_purl: http://purl.obolibrary.org/obo/cido.owl
preferredPrefix: CIDO
products:
- id: cido.owl
ontology_purl: http://purl.obolibrary.org/obo/cido.owl
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/36271389
title: 'A comprehensive update on CIDO: the community-based coronavirus infectious
disease ontology'
repository: https://github.com/cido-ontology/cido
title: Coronavirus Infectious Disease Ontology
tracker: https://github.com/cido-ontology/cido/issues
- activity_status: active
contact:
email: frederic.bastian@unil.ch
github: fbastian
label: Frédéric Bastian
orcid: 0000-0002-9415-5104
description: An ontology to capture confidence information about annotations.
domain: information
homepage: https://github.com/BgeeDB/confidence-information-ontology
id: cio
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/cio.owl
preferredPrefix: CIO
products:
- id: cio.owl
ontology_purl: http://purl.obolibrary.org/obo/cio.owl
- id: cio.obo
ontology_purl: http://purl.obolibrary.org/obo/cio.obo
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/25957950
title: 'The Confidence Information Ontology: a step towards a standard for asserting
confidence in annotations'
repository: https://github.com/BgeeDB/confidence-information-ontology
title: Confidence Information Ontology
tracker: https://github.com/BgeeDB/confidence-information-ontology
- activity_status: active
canonical: cl.owl
contact:
email: addiehl@buffalo.edu
github: addiehl
label: Alexander Diehl
orcid: 0000-0001-9990-8331
dependencies:
- id: chebi
- id: go
- id: ncbitaxon
- id: pato
- id: pr
- id: ro
- id: uberon
depicted_by: /images/CL-logo.jpg
description: The Cell Ontology is a structured controlled vocabulary for cell types
in animals.
domain: anatomy and development
homepage: https://obophenotype.github.io/cell-ontology/
id: cl
label: Cell Ontology
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/g/cl_edit
ontology_purl: http://purl.obolibrary.org/obo/cl.owl
preferredPrefix: CL
products:
- description: Complete ontology, plus inter-ontology axioms, and imports modules
format: owl-rdf/xml
id: cl.owl
is_canonical: true
ontology_purl: http://purl.obolibrary.org/obo/cl.owl
title: Main CL OWL edition
uses:
- uberon
- chebi
- go
- pr
- pato
- ncbitaxon
- ro
- derived_from: cl.owl
description: Complete ontology, plus inter-ontology axioms, and imports modules
merged in
format: obo
id: cl.obo
ontology_purl: http://purl.obolibrary.org/obo/cl.obo
title: CL obo format edition
- description: Basic version, no inter-ontology axioms
format: obo
id: cl/cl-basic.obo
ontology_purl: http://purl.obolibrary.org/obo/cl/cl-basic.obo
title: Basic CL
- description: complete CL but with no imports or external axioms
id: cl/cl-base.owl
ontology_purl: http://purl.obolibrary.org/obo/cl/cl-base.owl
title: CL base module
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/27377652
title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology
interoperability.'
repository: https://github.com/obophenotype/cell-ontology
tags:
- cells
taxon:
id: NCBITaxon:33208
label: Metazoa
title: Cell Ontology
tracker: https://github.com/obophenotype/cell-ontology/issues
twitter: CellOntology
usages:
- description: The BICCN created a high-resolution atlas of cell types in the primary
motor based on single cell transcriptomics. These cell types are represented
in the brain data standards ontology which anchors to cell types in the cell
ontology.
examples:
- description: cell type card of a cell type linked to a PCL cell type (L2/3 IT
primary motor cortex glutamatergic neuron) which is a subclass of cell types
in CL (CL:4023041)
url: https://knowledge.brain-map.org/celltypes/CCN202002013/CS202002013_193
- description: PCL cell type used in cell type cards linked directly to CL cell
types
url: https://www.ebi.ac.uk/ols/ontologies/pcl/terms?iri=http://purl.obolibrary.org/obo/PCL_0011193
publications:
- id: https://doi.org/10.1101/2021.10.10.463703
title: 'Brain Data Standards Ontology: A data-driven ontology of transcriptomically
defined cell types in the primary motor cortex'
type: annotation
user: https://biccn.org/
- description: HuBMAP develops tools to create an open, global atlas of the human
body at the cellular level. The Cell Ontology is used in annotating cell types
in the tools developed.
examples:
- description: ASCT+B reporter showing CL being used to annotate cell types in
the heart
url: https://hubmapconsortium.github.io/ccf-asct-reporter/vis?selectedOrgans=heart-v1.1&playground=false
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/31597973
title: 'The human body at cellular resolution: the NIH Human Biomolecular Atlas
Program.'
type: annotation
user: https://hubmapconsortium.org/
- description: The Human Cell Atlas (HCA) is an international group of researchers
using a combination of these new technologies to create cellular reference maps.
The HCA use CL to annotate cells in their reference maps.
examples:
- description: HCA collection studies that are related B cell (CL:0000236) that
is filtered through CL annotation
url: https://singlecell.broadinstitute.org/single_cell?type=study&page=1&facets=cell_type%3ACL_0000236&scpbr=human-cell-atlas-main-collection
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/29206104
title: The Human Cell Atlas
type: annotation
user: https://www.humancellatlas.org/
- description: The EBI single cell expression atlas is an extension to EBI expression
atlas that displays gene expression in single cells. Cell types in the single
cell expression atlas linked with terms from the Cell Ontology.
examples:
- description: RNA-Seq CAGE (Cap Analysis of Gene Expression) analysis of mice
cells in RIKEN FANTOM5 project annotated using cell types from CL
url: https://www.ebi.ac.uk/gxa/experiments/E-MTAB-3578/Results
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/31665515
title: 'Expression Atlas update: from tissues to single cells'
type: annotation
user: https://www.ebi.ac.uk/gxa/home
- description: The National Human Genome Research Institute (NHGRI) launched a public
research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September
2003, to carry out a project to identify all functional elements in the human
genome sequence. The ENCODE DCC uses Uberon to annotate samples
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/25776021
title: Ontology application and use at the ENCODE DCC
seeAlso: https://doi.org/10.25504/FAIRsharing.v0hbjs
type: annotation
user: https://www.encodeproject.org/
- description: FANTOM5 is using Uberon and CL to annotate samples allowing for transcriptome
analyses with cell-type and tissue-level specificity.
examples:
- description: FANTOM5 samples annotated to neuron
url: http://fantom.gsc.riken.jp/5/sstar/CL:0000540
type: annotation
user: http://fantom5-collaboration.gsc.riken.jp/
- activity_status: active
build:
checkout: git clone https://github.com/luis-gonzalez-m/Collembola.git
path: .
system: git
contact:
email: lagonzalezmo@unal.edu.co
github: luis-gonzalez-m
label: Luis González-Montaña
orcid: 0000-0002-9136-9932
dependencies:
- id: ro
description: 'CLAO is an ontology of anatomical terms employed in morphological
descriptions for the Class Collembola (Arthropoda: Hexapoda).'
domain: anatomy and development
homepage: https://github.com/luis-gonzalez-m/Collembola
id: clao
layout: ontology_detail
license:
label: CC0 1.0
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/clao.owl
preferredPrefix: CLAO
products:
- id: clao.owl
ontology_purl: http://purl.obolibrary.org/obo/clao.owl
- id: clao.obo
ontology_purl: http://purl.obolibrary.org/obo/clao.obo
pull_request_added: 1337
repository: https://github.com/luis-gonzalez-m/Collembola
title: Collembola Anatomy Ontology
tracker: https://github.com/luis-gonzalez-m/Collembola/issues
- activity_status: active
contact:
email: zhengj2007@gmail.com
github: zhengj2007
label: Jie Zheng
orcid: 0000-0002-2999-0103
dependencies:
- id: cl
- id: doid
- id: ncbitaxon
- id: uberon
description: An ontology to standardize and integrate cell line information and
to support computer-assisted reasoning.
domain: anatomy and development
homepage: https://github.com/CLO-Ontology/CLO
id: clo
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/clo.owl
preferredPrefix: CLO
products:
- id: clo.owl
ontology_purl: http://purl.obolibrary.org/obo/clo.owl
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/25852852
title: 'CLO: The Cell Line Ontology'
repository: https://github.com/CLO-Ontology/CLO