PGX¶

Use PGX commands to query pharmacogenomic guidelines and annotations from CPIC and PharmGKB.

Search PGX¶

By gene:

biomcp search pgx -g CYP2D6

By drug:

biomcp search pgx -d codeine

With evidence and CPIC level filters:

biomcp search pgx -g CYP2D6 --cpic-level A --evidence --limit 10

Key flags: -g/--gene for the gene symbol, -d/--drug for the therapy, --cpic-level for CPIC levels A|B|C|D, --pgx-testing for testing-related guidance, and --evidence when you want evidence summaries alongside the main results. Use --limit and --offset for bounded paging.

Get PGX records¶

biomcp get pgx CYP2D6

The base PGX card summarizes affected drugs and the guideline context tied to the gene or drug you queried.

Request PGX sections¶

Retrieve detailed PGX data for a gene-drug pair by section.

Dosing recommendations:

biomcp get pgx CYP2D6 recommendations

Allele frequency data:

biomcp get pgx CYP2D6 frequencies

Clinical guidelines:

biomcp get pgx CYP2D6 guidelines

PharmGKB annotations:

biomcp get pgx CYP2D6 annotations

All sections at once:

biomcp get pgx CYP2D6 all

Available sections¶

Section	Content
`recommendations`	CPIC dosing recommendations
`frequencies`	Allele frequency data
`guidelines`	Published clinical guidelines
`annotations`	PharmGKB clinical annotations
`all`	All sections combined

Helper commands¶

PGX does not expose a separate helper family. Start with search pgx when you need to find the right anchor, then switch to get pgx <gene_or_drug> for the base card or section-level follow-up.

JSON mode¶

biomcp --json search pgx -g CYP2D6
biomcp --json get pgx CYP2D6 recommendations

Practical tips¶

Start with search pgx when you only know the gene or drug and need the matching guideline rows first.
Use section-specific get pgx calls when you need only recommendations, frequencies, guidelines, or annotations.
Keep CPIC level filters tight when you want high-confidence dosing guidance.