The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.
- Prefix
pharmgkb.gene- Keywords
- gene ontology organism-specific databases pharmacogenomics
- License
- CC-BY-SA-4.0
- Links
- Homepage OBO OWL OBO JSON
- Publications
- https://bioregistry.io/pubmed:34216021
- 2011 From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource
- 2005 PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base
Identifier Standards
- Pattern for Local Unique Identifiers
-
Local identifiers in PharmGKB Gene should match this regular expression:
^PA\w+$ - Example Local Unique Identifier
- PA131 Resolve
- Pattern for CURIES
-
Compact URIs (CURIEs) constructed from PharmGKB Gene should match this regular expression:
^pharmgkb\.gene:PA\w+$ - Example CURIE
- pharmgkb.gene:PA131
Contacts
- Contact
-
Teri E Klein
0000-0001-5527-6475
TeriKlein
- Group Contact
- Mailing List
Ontology
A summary of the relations in the Bioregistry schema can be found here.
-
Part Of (
bfo:0000050) - pharmgkb
- In Collection (3)
- FHIR External Terminologies Global Biodata Coalition - Global Core Biodata Resources Synapse.org external links
Mappings to External Registries
Mappings from records in Bioregistry to external registries comprises the metaregistry. This resource has 8 mappings to external registries with 3 unique external prefixes.
| Registry Name | Registry Metaprefix | External Prefix | Curate |
|---|---|---|---|
| BioContext | biocontext |
PHARMGKB.GENE
|
|
Biolink
|
biolink |
PHARMGKB.GENE
|
|
BioPortal
|
bioportal |
PHARMGKB
|
|
GO
|
go |
PharmGKB
|
|
Identifiers.org
|
miriam |
pharmgkb.gene
|
|
N2T
|
n2t |
pharmgkb.gene
|
|
Prefix Commons
|
prefixcommons |
pharmgkb.gene
|
|
UniProt
|
uniprot |
DB-0285
|
Providers
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 PA131 is used to demonstrate the providers
available for PharmGKB Gene. 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 |
|---|---|---|
| PharmGKB Gene | pharmgkb.gene |
http://www.pharmgkb.org/gene/PA131 |
| Bioregistry | bioregistry |
https://bioregistry.io/pharmgkb.gene:PA131 |
| Identifiers.org | miriam |
https://identifiers.org/pharmgkb.gene:PA131 |
| Name-to-Thing | n2t |
https://n2t.net/pharmgkb.gene:PA131 |
Extra Providers
Additional providers curated in the Bioregistry are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.
| Provider Name | Provider Code | URL |
|---|---|---|
| Bio2RDF | bio2rdf |
http://bio2rdf.org/pharmgkb.gene:PA131 |