PharmGKB / CPIC¶
Pharmacogenomic workflows often need two things at once: actionable guidance and supporting annotation context. That is why BioMCP treats this page as a combined source guide instead of splitting the user-facing workflow into two nearly identical entry points.
In BioMCP, CPIC supplies the core get pgx <gene_or_drug> card plus recommendations, frequencies, and guidelines, while PharmGKB supplies the annotations enrichment section. That split matters because the main recommendations users act on come from CPIC even when PharmGKB adds broader clinical annotation context.
What BioMCP exposes¶
| Command | What BioMCP gets from this source | Integration note |
|---|---|---|
search pgx |
PGx matches for genes and drugs | Search is aligned to the CPIC-backed workflow |
get pgx <gene_or_drug> |
Core PGx card for a gene or drug | CPIC-backed base view |
get pgx <gene_or_drug> recommendations |
Dosing and action recommendations | CPIC recommendations section |
get pgx <gene_or_drug> frequencies |
Allele frequency context | CPIC frequencies section |
get pgx <gene_or_drug> guidelines |
Guideline references and summaries | CPIC guidelines section |
get pgx <gene_or_drug> annotations |
Clinical annotations and enrichment | PharmGKB-backed section |
Example commands¶
Returns PGx search matches for a gene-oriented query.
Returns the base PGx card for the requested gene or drug.
Returns CPIC recommendations for the requested PGx target.
Returns the PharmGKB-backed annotations section.
Returns a combined PGx view with recommendations and frequency context for codeine.
API access¶
No BioMCP API key required.
Official source¶
PharmGKB is the public pharmacogenomics knowledgebase paired with CPIC in BioMCP's PGx workflow.