ClawBio PharmGx Reporter skill

Qualified idclawbio/pharmgx-reporter@0.1.0

Generates a CPIC-guideline pharmacogenomic report (12 genes, 31 SNPs, 51 drugs) from a 23andMe or AncestryDNA raw genotype export.

Unsigned
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Overview

The pharmgx-reporter skill from ClawBio, a bioinformatics-native AI agent skill library. Parses a 23andMe or AncestryDNA raw genotype file (either GRCh37 or GRCh38, detected automatically), calls star-allele diplotypes for 12 pharmacogenes, maps each to a metaboliser phenotype (poor/intermediate/normal/rapid/ultra-rapid), and returns CPIC-guideline drug recommendations across 51 medications -- a real, named, clinically used pharmacogenomics standard, not generic genotyping. Its own SKILL.md states every recommendation 'traces to a published star-allele -> phenotype -> drug mapping', which this entry records as the skill's provenance-logging behaviour. Verified live via direct fetch of the skill's SKILL.md, its evals/ directory, and the repository's own skills/catalog.json, which records this skill at maturity_tier: ci-validated (ci_tested: true, has_tests: true, has_demo: true) -- ClawBio's escalating maturity-tier system functioning as the closest analogue to a certification ladder found in this seeding pass. A sibling skill in the same repository, clinical-variant-reporter (ACMG classification from VCF/BCF), was considered but not seeded here: the same catalog.json records its status as planned and maturity_tier: cli-registered with benchmark_validated: false, i.e. not yet validated against the Genome in a Bottle truth sets an earlier research pass attributed to it, so this entry deliberately picks the more mature sibling instead of describing an aspirational capability as current state. Terms check: the repository's root LICENSE is MIT (confirmed by direct fetch), and this specific skill's own SKILL.md frontmatter and catalog.json entry both independently declare license: MIT with empty model_license/data_license fields, i.e. no divergent third-party licence applies to this particular skill (the repository does warn that other skills wrapping third-party models or data may declare stricter terms). No slug collision with any existing entry in this registry.

Details

Licence
MIT
Version
0.1.0
Category
Variant interpretation
Homepage
https://github.com/ClawBio/ClawBio/tree/main/skills/pharmgx-reporter
Repository
https://github.com/ClawBio/ClawBio
Maintainers
Susheel Varma (@susheel, GA4GH AI Workstream / Sage Bionetworks)
Keywords
pharmacogenomicscpicclawbio23andmedrug-gene-interaction

Publisher

Published by
ClawBio (GitHub organisation) profile ↗
Upstream name
pharmgx-reporter
Upstream version
0.1.0 (Manifest)

Safety classification

No safety classification has been submitted for this entry.

What the safety levels mean

Skill

Human oversight
required
Provenance logging
Yes
Evaluation criteria
https://github.com/ClawBio/ClawBio/tree/main/skills/pharmgx-reporter/evals
Source
https://github.com/ClawBio/ClawBio.git (skills/pharmgx-reporter)

Inputs

  • genotype_file (file) — A 23andMe or AncestryDNA raw genotype export (.txt or .txt.gz), GRCh37 or GRCh38.
  • drug (string) — Optional single-drug mode: restrict the report to one medication.

Outputs

  • pharmacogenomic_report (object) — Per-gene star-allele/diplotype calls, metaboliser phenotype, and CPIC-guideline drug recommendations across up to 51 medications and 12 genes, each traced to a published star-allele-to-drug mapping.

Provenance

Created
Updated
Last verified