PharmGKB / ClinPGx Query Skill

Queries two complementary APIs:

• ClinPGx API (api.clinpgx.org/v1) — gene, chemical, variant detail
• CPIC API (api.cpicpgx.org/v1) — gene-drug pairs, CPIC guideline levels (PostgREST)

Auto-detects input entity type by pattern:

Input Pattern	Detected As	Data Sources
PA128	ClinPGx accession	gene or chemical detail + CPIC pairs
rs4244285	dbSNP rsID	variant lookup
CYP2D6	gene symbol (uppercase, 2-15 chars)	gene detail + CPIC pairs
anything else	drug / free text	chemical detail + CPIC pairs

API

Function	Input	Returns
search(entity)	single entity string	dict with genes, chemicals, variants, cpic_pairs, related
search_batch(entities)	list of entity strings	dict[str → search result]
summarize(result, entity)	search result + label	compact text (one line per hit)
to_json(result)	search result	indented JSON string
search_gene(symbol)	gene symbol	list of gene dicts (ClinPGx)
search_drug(name)	drug name	list of chemical dicts (ClinPGx)
search_variant(rsid)	rsID string	list of variant dicts (ClinPGx)
get_cpic_pairs_by_gene(symbol)	gene symbol	list of pair dicts (CPIC pair_view)
get_cpic_pairs_by_drug(name)	drug name	list of pair dicts (CPIC pair_view)

Usage

See if __name__ == "__main__" block in 49_PHARMGKB_CLINPGX.py for runnable examples covering: gene symbol, drug name, rsID, ClinPGx accession, batch search, and JSON output.

Key Fields

Gene (ClinPGx): id, symbol, name, hasCpicGuideline

Chemical (ClinPGx): id, name, types

Variant (ClinPGx): id, symbol, genes, location

CPIC Pair (pair_view): genesymbol, drugname, cpiclevel (A/B/C/D), clinpgxlevel (evidence), pgxtesting, guidelinename

Data Sources

• ClinPGx (Stanford / NIH) — https://www.clinpgx.org/ — REST JSON, no key, ≤2 req/s, CC BY-SA 4.0
• CPIC API — https://api.cpicpgx.org/ — PostgREST, no key — gene-drug guideline pairs
• Note: PharmGKB was subsumed by ClinPGx (July 2025). CPIC API remains at api.cpicpgx.org.