What is PharmGKB?
What is it?
The
PharmGKB database stores data on the DNA sequence variability (particularly SNPs) of
Homo sapiens genes and associated phenotypic manifestations, focusing on how variant sequences affect the pharmacodynamics and pharmacokinetics of drugs, as well as other non-pharmacological aspects of phenotype, including susceptibility to disease.
In short, it addresses the genotype-phenotype problem in
Homo sapiens with respect to compounds, especially therapeutic drugs.
What is it for?
- Identifying the sequence variants of a gene
- Understanding how the sequence variants of a gene influence phenotype
- Identifying drugs whose metabolism or effect is known to be influenced by gene sequence variants
- Identifying diseases whose presentation is known to be influenced by gene sequence variants
- Understanding the genomic structure and transcripts of a gene
- Obtaining marker information
- Obtaining information about the function of the gene products
What's in it?
- All data pertain to Homo sapiens
- Genetic sequence variability data
- Genomic structure of genes
- Molecular and cellular phenotype data
- Clinical information regarding participants in pharmacogenomics research studies, including clinical and basic pharmacokinetic and pharmacogenomic data
Click for
example record.
Where to get it
In general, no user account is required to access pooled and/or summary data. However, an account is required for viewing data associated with individual identifiers (in order to protect the confidentiality of subjects) and for submitting data. In addition, certain resources may be restricted to users affiliated with specific projects. You can request one
here.
Programmatic access
In addition to providing point-and-clik access, PharmGKB also makes available various forms of programmatic interactions, i.e., the ability for a user's program to talk to the PharmGKB database directly without human intervention. This capability is particularly useful when analyzing large datasets or performing data mining.
Different languages are supported (e.g.,
Perl and Python), as well as different types of queries, described
here.
Key references
- Klein TE, Chang JT, Cho MK, Easton KL, Fergerson R, Hewett M, Lin Z, Liu Y, Liu S, Oliver DE, Rubin DL, Shafa F, Stuart JM, Altman RB (2001)
Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base, Pharmacogenomics J. 1:167-170.
- All PubMed references pertaining to PharmGKB and published by the PharmGKB group.
Source
Lane Librarian
Record created 5/18/2006.
ypouliot, September 16, 2009