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gwas-catalog-skill

Submit compact GWAS Catalog REST API v2 requests for studies, associations, SNPs, EFO traits, genes, publications, loci, and metadata. Use when a user wants concise GWAS Catalog summaries

Stars
1,305
Source
openai/plugins
Updated
2026-05-30
Slug
openai--plugins--gwas-catalog-skill
View on GitHubRaw SKILL.md

// install — copy + paste into any project

mkdir -p .claude/skills && curl -fsSL https://raw.githubusercontent.com/openai/plugins/HEAD/plugins/life-science-research/skills/gwas-catalog-skill/SKILL.md -o .claude/skills/gwas-catalog-skill.md

Drops the SKILL.md into .claude/skills/gwas-catalog-skill.md. Works with Claude Code, Cursor, and any agent that loads SKILL.md files from .claude/skills/.

Operating rules

  • Use scripts/rest_request.py for all GWAS Catalog API calls.
  • Use base_url=https://www.ebi.ac.uk/gwas/rest/api/v2.
  • The script accepts max_items; for collection endpoints, start with API size=10 and max_items=10.
  • Single-resource endpoints such as studies/<accession> generally do not need max_items.
  • Use record_path to target _embedded.<resource> lists.
  • Re-run requests in long conversations instead of relying on older tool output.
  • Treat displayed ... in tool previews as UI truncation, not literal request content.

Execution behavior

  • Return concise markdown summaries from the script JSON by default.
  • Return the script JSON verbatim only if the user explicitly asks for machine-readable output.
  • Prefer these paths: metadata, studies, studies/<accession>, associations, snps, efoTraits, genes, publications, and loci.
  • Use save_raw=true if the user needs the full HATEOAS payload or pagination links.

Input

  • Read one JSON object from stdin.
  • Required fields: base_url, path
  • Optional fields: method, params, headers, json_body, form_body, record_path, response_format, max_items, max_depth, timeout_sec, save_raw, raw_output_path
  • Common GWAS Catalog patterns:
    • {"base_url":"https://www.ebi.ac.uk/gwas/rest/api/v2","path":"metadata"}
    • {"base_url":"https://www.ebi.ac.uk/gwas/rest/api/v2","path":"studies","params":{"efo_trait":"asthma","size":10},"record_path":"_embedded.studies","max_items":10}
    • {"base_url":"https://www.ebi.ac.uk/gwas/rest/api/v2","path":"associations","params":{"mapped_gene":"BRCA1","size":10},"record_path":"_embedded.associations","max_items":10}

Output

  • Success returns ok, source, path, method, status_code, warnings, and either compact records or a compact summary.
  • Use raw_output_path when save_raw=true.
  • Failure returns ok=false with error.code and error.message.

Execution

echo '{"base_url":"https://www.ebi.ac.uk/gwas/rest/api/v2","path":"studies","params":{"efo_trait":"asthma","size":10},"record_path":"_embedded.studies","max_items":10}' | python scripts/rest_request.py

References

  • No additional runtime references are required; keep the import package limited to this file and scripts/rest_request.py.