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 guideline-name and CPIC level filters:

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

Key flags: -g/--gene for the gene symbol, -d/--drug for the therapy, --cpic-level for CPIC levels A|B|C|D, and --pgx-testing for Actionable PGx, Informative PGx, No Clinical PGx, Testing Recommended, or Testing Required. --evidence remains a best-effort free-text match over guideline names or CPIC levels. Use --limit and --offset for bounded paging.

Get PGX records¶

biomcp get pgx CYP2D6

The default card returns only the first 10 CPIC interactions. Use --limit (1-50) and --offset to page that bounded list.

Request PGX sections¶

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

Interactions explicitly:

biomcp get pgx CYP2D6 interactions --limit 10 --offset 10

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, capped at 50 rows per section:

biomcp get pgx CYP2D6 --full

Available sections¶

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

A named section returns only identity, provenance, and that section. Multiple sections may be requested together at offset zero. To follow a continuation, request its section alone with the advertised --offset; nonzero offsets with multiple sections or --full are rejected before provider work.

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

Requested frequencies and annotations are also represented in section_outcomes. CPIC frequency aggregation is degraded when some additive lookups fail but usable rows remain, and unavailable when no usable rows survive. PharmGKB annotation failures are unavailable; healthy no-results are empty.

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 interactions, recommendations, frequencies, guidelines, or annotations.
Keep CPIC level filters tight when you want high-confidence dosing guidance.