ClinPGx (PharmGKB) (Claude Skill)

Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations, FDA/EMA drug labels, and PGx pathways.

   
Type Claude Skill
Supplier jaechang-hits (community OSS, CC BY 4.0)
Availability GA — part of the BixBench-evaluated SciAgent-Skills collection
Pricing Free / OSS (CC-BY-SA-4.0)
Capabilities Read/Write — Claude runs the skill’s Python locally (Bash), not as an MCP tool

How to install

SciAgent-Skills is not an npm package — skills are plain markdown read directly by the agent (no npx/npm).

  • Claude Code — clone and load as a plugin: 
    git clone https://github.com/jaechang-hits/SciAgent-Skills

    Then inside Claude Code run /plugin install sciagent-skills (verify it appears under /plugin → Installed). Clone into your project directory so Claude Code picks the skills up via CLAUDE.md.

  • Manual / other agents — point the agent at the skill file directly: 
    cp -r SciAgent-Skills/skills/genomics-bioinformatics/databases/clinpgx-database ~/.claude/skills/

    The skill declares its own Python dependencies in its SKILL.md; install them when prompted on first use.

What it does

Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations, FDA/EMA drug labels, and PGx pathways. Two-host architecture: api.clinpgx.org for annotation records, api.cpicpgx.org for genotype→recommendation lookups. No auth. For germline pathogenicity use clinvar-database; for somatic cancer PGx use cosmic-database or opentargets-database; for drug bioactivity use chembl-database-bioactivity.

Primary use cases: Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations, FDA/EMA drug labels, and PGx pathways.

Notes

Distributed as a SKILL.md (plus code examples) in the SciAgent-Skills collection — Claude executes it locally via Bash/Python rather than as an MCP server. Upstream license: CC-BY-SA-4.0. The skill directory upstream is skills/genomics-bioinformatics/databases/clinpgx-database.

Sources

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