Registry Open Biological and Biomedical Ontologies

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The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies.

Prefix: obo
Preferred Prefix: obo
Keywords: artificial intelligence biomedical science earth science health science infectious disease medicine informatics knowledge representation life science microbiology nutritional science omics ontology/terminology/nomenclature plant cell biology registry
License: CC-BY-4.0
Links: Homepage
Publications: 2021 OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies; 2007 The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration; https://bioregistry.io/pubmed:17321117; https://bioregistry.io/pubmed:16964349; https://bioregistry.io/pubmed:16564748; https://bioregistry.io/pubmed:16549013; https://bioregistry.io/pubmed:16442850; https://bioregistry.io/pubmed:16435295; https://bioregistry.io/pubmed:16360342
References: GitHub PR https://github.com/biopragmatics/bioregistry/pull/913; GitHub Issue https://github.com/biopragmatics/bioregistry/issues/910

Identifier Standards

Pattern for Local Unique Identifiers: Missing LUI pattern
Example Local Unique Identifiers: uberon Resolve
go Resolve
uberon.owl Resolve
Example CURIEs: obo:uberon
obo:go
obo:uberon.owl
Format String for RDF URIs: http://purl.obolibrary.org/obo/$1
Example RDF URI: http://purl.obolibrary.org/obo/uberon

Contacts

Contact: Nicolas Matentzoglu 0000-0002-7356-1779 matentzn
Contributor: creator Charles Tapley Hoyt 0000-0003-4423-4370 cthoyt

Ontology

A summary of the relations in the Semantic Farm schema can be found here.

In Collection (1): WikiPathways Resources

Mappings to External Registries

Mappings from records in Semantic Farm to external registries comprises the metaregistry. This resource has 4 mappings to external registries with 4 unique external prefixes.

Registry Name	Registry Metaprefix	External Prefix
BARTOC	`bartoc`	`1737`
BioContext	`biocontext`	`OBO`
FAIRsharing	`fairsharing`	`FAIRsharing.847069`
Integbio	`integbio`	`nbdc00305`

Providers

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A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier uberon is used to demonstrate the providers available for Open Biological and Biomedical Ontologies. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.

Provider Name	Provider Code	URI
Open Biological and Biomedical Ontologies	`obo`	http://purl.obolibrary.org/obo/uberon
Open Biological and Biomedical Ontologies (RDF)	`rdf`	http://purl.obolibrary.org/obo/uberon
Bioregistry	`bioregistry`	https://bioregistry.io/obo:uberon

This name annotation was originally annotated in Bioregistry and is redistributed under the CC0-1.0 license.

Get the name:

>>> import bioregistry as br
>>> br.get_name("obo")
'Open Biological and Biomedical Ontologies'

Get the license:

>>> import bioregistry as br
>>> br.get_license("obo")
'CC-BY-4.0'

Get the homepage:

>>> import bioregistry as br
>>> br.get_homepage("obo")
'http://www.obofoundry.org'

Get the contact's name:

>>> import bioregistry as br
>>> br.get_contact_name("obo")
'Nicolas Matentzoglu'

Get the contact's email:

>>> import bioregistry as br
>>> br.get_contact_email("obo")
'nicolas.matentzoglu@gmail.com'

Get the contact's GitHub handle:

>>> import bioregistry as br
>>> br.get_contact_github("obo")
'matentzn'

Get the contact's ORCiD identifier:

>>> import bioregistry as br
>>> br.get_contact_orcid("obo")
'0000-0002-7356-1779'