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

This skill sends compact requests to the GWAS Catalog REST API v2 and returns summaries for genomic studies. Use it for focused biomedical data lookups.

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

What gwas-catalog-skill does

gwas-catalog-skill works with GWAS Catalog REST API v2 resources for studies, associations, SNPs, EFO traits, genes, publications, loci, and metadata. An agent can filter records by a trait or gene and return a concise summary instead of the full API response.

All API calls go through scripts/rest_request.py. The script reads JSON with base_url and path, plus optional filters, a record path, and an item limit. Python and access to the GWAS Catalog API v2 are required.

Install it when Codex or ChatGPT needs compact GWAS Catalog summaries. Use save_raw=true when the full HATEOAS payload or pagination links are needed.

What it helps with

  • find studies for an EFO trait
  • filter associations by mapped gene
  • retrieve SNP and locus records
  • summarize GWAS publications
  • query catalog metadata

Example prompts for the agent

  • Find GWAS Catalog studies for the trait asthma and summarize them.
  • Show associations mapped to BRCA1 in a compact response.
  • Query GWAS Catalog metadata with `scripts/rest_request.py`.

How to install gwas-catalog-skill

1Skills CLI (Vercel)

npx skills add openai/plugins --skill gwas-catalog-skill -a codex

2Manually: put the files in place

.agents/skills/gwas-catalog-skill/SKILL.md

For all projects use ~/.agents/skills/

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Questions about gwas-catalog-skill

How do I install gwas-catalog-skill in Codex?

Run npx skills add openai/plugins --skill gwas-catalog-skill or npx skills add openai/plugins --skill gwas-catalog-skill -a codex. The skill file is placed at .agents/skills/gwas-catalog-skill/SKILL.md.

What does gwas-catalog-skill do?

It sends requests to the GWAS Catalog REST API v2 and produces concise summaries for studies, associations, SNPs, EFO traits, genes, publications, loci, and metadata.

What is required to run gwas-catalog-skill?

Python is needed to run scripts/rest_request.py, along with access to the GWAS Catalog REST API v2. Set save_raw=true when the full HATEOAS response is required.

See also

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