Registry BioLink Model

A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations.

Prefix: biolink
Preferred Prefix: biolink
Keywords: ontology
Version: 4.4.4
License: CC0-1.0
Links: Homepage Repository OWL RDF

Identifier Standards

Pattern for Local Unique Identifiers: Local unique identifiers in BioLink Model should match this regular expression:
^\S+$
Example Local Unique Identifier: PathologicalProcessOutcome Resolve
Pattern for CURIES: Compact URIs (CURIEs) constructed from BioLink Model should match this regular expression:
^biolink:\S+$
Example CURIE: biolink:PathologicalProcessOutcome
Format String for RDF URIs: https://w3id.org/biolink/vocab/$1
Example RDF URI: https://w3id.org/biolink/vocab/PathologicalProcessOutcome

Contacts

Contact: Chris Mungall 0000-0002-6601-2165 cmungall
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): GHGA Collection

Mappings to External Registries

Mappings from records in Semantic Farm to external registries comprises the metaregistry. This resource has 5 mappings to external registries with 1 unique external prefixes.

Registry Name	Registry Metaprefix	External Prefix
AberOWL	`aberowl`	`BIOLINK`
Biolink	`biolink.resource`	`biolink`
BioPortal	`bioportal`	`BIOLINK`
Identifiers.org namespace	`miriam`	`biolink`
OLS	`ols`	`biolink`

Providers

Suggest

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 PathologicalProcessOutcome is used to demonstrate the providers available for BioLink Model. 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
BioLink Model	`biolink`	https://biolink.github.io/biolink-model/PathologicalProcessOutcome
BioLink Model (RDF)	`rdf`	https://w3id.org/biolink/vocab/PathologicalProcessOutcome
Bioregistry	`bioregistry`	https://bioregistry.io/biolink:PathologicalProcessOutcome
Identifiers.org namespace	`miriam`	https://identifiers.org/biolink:PathologicalProcessOutcome
EBI Ontology Lookup Service	`ols`	https://www.ebi.ac.uk/ols/ontologies/biolink/terms?iri=https://w3id.org/biolink/vocab/PathologicalProcessOutcome
BioPortal	`bioportal`	https://bioportal.bioontology.org/ontologies/BIOLINK/?p=classes&conceptid=https://w3id.org/biolink/vocab/PathologicalProcessOutcome

Get the version:

>>> import bioregistry as br
>>> br.get_version("biolink")
'4.4.4'

This name annotation was originally annotated in Identifiers.org namespace and is redistributed under the CC-BY-4.0 license.

Get the name:

>>> import bioregistry as br
>>> br.get_name("biolink")
'BioLink Model'

Get the license:

>>> import bioregistry as br
>>> br.get_license("biolink")
'CC0-1.0'

Get the homepage:

>>> import bioregistry as br
>>> br.get_homepage("biolink")
'https://biolink.github.io/biolink-model'

Get the repository:

>>> import bioregistry as br
>>> br.get_repository("biolink")
'https://github.com/biolink/biolink-model'

Get the OWL download link:

>>> import bioregistry as br
>>> br.get_owl_download("biolink")
'https://w3id.org/biolink/biolink-model.owl.ttl'

Get the RDF download link:

>>> import bioregistry as br
>>> br.get_rdf_download("biolink")
'https://w3id.org/biolink/biolink-model.owl.ttl'

Get the contact's name:

>>> import bioregistry as br
>>> br.get_contact_name("biolink")
'Chris Mungall'

Get the contact's email:

>>> import bioregistry as br
>>> br.get_contact_email("biolink")
'cjmungall@lbl.gov'

Get the contact's GitHub handle:

>>> import bioregistry as br
>>> br.get_contact_github("biolink")
'cmungall'

Get the contact's ORCiD identifier:

>>> import bioregistry as br
>>> br.get_contact_orcid("biolink")
'0000-0002-6601-2165'