clinpgx-term-lookup 0.1.0

Fuzzy term lookup for ClinPGx/PharmGKB: drugs and variants, via the PharmGKB and RxNorm APIs

clinpgx-term-lookup

Fuzzy term lookup for ClinPGx / PharmGKB: take a free-text drug or variant term and resolve it to its ClinPGx record.

It is API-only — no local data files to download. Lookups are served by the public PharmGKB and RxNorm APIs, so results stay current and the package stays small. An internet connection is required at lookup time.

Installation

pip install clinpgx-term-lookup

Usage

Drugs

from clinpgx_term_lookup import DrugLookup

results = DrugLookup().search("warfarin")
for r in results:
    print(r.name, r.id, r.url, r.score, r.source)

The drug lookup:

1. Tries an exact PharmGKB chemical name match.
2. On a miss, fuzzy-matches the term with RxNorm's approximateTerm endpoint, resolves it to its ingredient (so brand names like Tylenol map to acetaminophen), and re-queries PharmGKB by that name.
3. On a miss, returns the RxNorm result itself as a fallback (with source="rxnorm").

So misspellings (warfarn) and trade names (tylenol) both resolve to the right PharmGKB chemical.

Variants

from clinpgx_term_lookup import VariantLookup

VariantLookup().search("rs1234")        # rsID  -> variant endpoint
VariantLookup().search("CYP2C19*2")     # star allele -> haplotype endpoint

Terms starting with rs are looked up as rsIDs; everything else is treated as a star allele.

Result objects

Both lookups return a list of Pydantic models with these fields:

Field	Description
raw_input	The original query string
id	PharmGKB accession ID (or RXN<rxcui>)
name	The matched name
url	Link to the ClinPGx (or RxNorm) record
score	0–1 fuzzy similarity to the query
source	"pharmgkb" or "rxnorm"

Command line

clinpgx-term-lookup warfarin --type drug
clinpgx-term-lookup rs1234 --type variant

Output is JSON. Use --top-k and --threshold to tune results.

License

MIT. Note that lookups query the PharmGKB and RxNorm APIs; their data is subject to their respective terms of use.