gwas-catalog-skill

Imported from openai/plugins (plugins/life-science-research/skills/gwas-catalog-skill/SKILL.md). Install upstream with npx skills add openai/plugins --skill gwas-catalog-skill. Copyright stays with the author.

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.