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skill CX Codex GP ChatGPT official · OpenAI

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

Queries ClinVar Clinical Tables and NCBI Variation to look up genetic variants, identifiers, and summary records.

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

What clinvar-variation-skill does

The skill sends structured requests to ClinVar Clinical Tables and NCBI Variation endpoints via scripts/clinvar_variation.py. It returns concise markdown summaries for variant lookups and identifier mappings. Raw output is omitted by default.

Execution relies on a Python script reading JSON inputs from standard input. Actions cover search for clinical tables alongside vcv, rcv, scv, and refsnp lookups. When you need the full payload, setting save_raw=true writes data directly to a local file path.

Install this skill if your workflow involves frequent lookups across NCBI records and ClinVar identifiers. If you do not handle genetic variation data, skip this tool.

What it helps with

  • search ClinVar Clinical Tables for variant terms
  • retrieve compact summaries for VCV and RCV records
  • map variant identifiers across NCBI Variation objects
  • save large raw JSON responses directly to disk

Example prompts for the agent

  • Search ClinVar for variant VCV000013080 and summarize the findings
  • Look up the RefSNP identifier and display the summary
  • Fetch details for this SCV record and save the raw JSON to disk

How to install clinvar-variation-skill

1Skills CLI (Vercel)

npx skills add openai/plugins --skill clinvar-variation-skill -a codex

2Manually: put the files in place

.agents/skills/clinvar-variation-skill/SKILL.md

For all projects use ~/.agents/skills/

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Questions about clinvar-variation-skill

How do I install clinvar-variation-skill in Codex?

Run npx skills add openai/plugins --skill clinvar-variation-skill in your terminal.

What does clinvar-variation-skill do?

It queries ClinVar Clinical Tables and NCBI Variation to fetch variant summaries, identifiers, and search results.

What is required to run this skill?

The skill requires Python to execute scripts/clinvar_variation.py, which handles JSON input from stdin.

See also

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