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skill CX Codex GP ChatGPT official · OpenAI

pharmgkb-skill — Codex skill: what it does, how to install

Submits compact requests to the PharmGKB API and returns brief summaries for genes, variants, and drug dosing.

Install into Codex · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add openai/plugins --skill pharmgkb-skill -a codex
Open on GitHub

What pharmgkb-skill does

This skill queries the PharmGKB API using the bundled scripts/rest_request.py script. It accepts a JSON payload from standard input with a base URL and an endpoint path, then formats the output into markdown summaries.

It works with endpoints for genes, variants, clinical annotations, and dosing guidelines. List and search queries use max_items=10 to keep model context small. When complete server responses are required, setting save_raw=true writes the raw payload to disk and returns the file path.

You need Python installed alongside the local script. Install this if you frequently look up pharmacogenomics data inside your coding assistant; skip it if you only make occasional lookups in a browser.

What it helps with

  • Fetch details for a gene or variant by accession identifier
  • Retrieve clinical annotations for linked chemicals
  • Query pharmacogenomic dosing guidelines
  • Save raw PharmGKB API payloads directly to disk

Example prompts for the agent

  • Look up clinical annotations for chemical PA449726 in PharmGKB
  • Fetch gene data for PA36679 using pharmgkb-skill
  • Get dosing guidelines for variant PA166158545 and save the raw response

How to install pharmgkb-skill

1Skills CLI (Vercel)

npx skills add openai/plugins --skill pharmgkb-skill -a codex

2Manually: put the files in place

.agents/skills/pharmgkb-skill/SKILL.md

For all projects use ~/.agents/skills/

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Questions about pharmgkb-skill

How to install pharmgkb-skill in Codex?

Run npx skills add openai/plugins --skill pharmgkb-skill -a codex.

What does pharmgkb-skill do?

It queries the PharmGKB REST API via a Python script and outputs compact summaries for genes, variants, and drug guidelines.

What are the runtime requirements for this skill?

It requires a local Python environment and the scripts/rest_request.py script provided with the package.

See also

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