eqtl-catalogue-skill

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

Operating rules

• Use scripts/rest_request.py for all eQTL Catalogue calls.
• Use base_url=https://www.ebi.ac.uk/eqtl/api.
• Prefer targeted association endpoints over broad list endpoints.
• The public API currently appears strict about query validation, and live smoke tests returned intermittent 400/500/timeout failures even with documented parameter sets; treat this source as usable but upstream-fragile.
• For association endpoints, the script now backfills compatibility defaults for quant_method, p_lower, p_upper, and blank filter strings because the live API is currently rejecting omitted optional filters.
• Prefer variant_id in requests; the script mirrors it to the legacy snp query key to accommodate the current server-side validator.
• Re-run requests in long conversations instead of relying on older tool output.

Execution behavior

• Return concise markdown summaries from the script JSON by default.
• Return raw JSON only if the user explicitly asks for machine-readable output.
• Prefer documented versioned paths such as v3/studies, v3/associations, v3/studies/<study_id>/associations, or legacy v1/.../associations routes with explicit filters, and surface upstream 400/500 errors verbatim when they occur.

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 eQTL Catalogue patterns:
  • {"base_url":"https://www.ebi.ac.uk/eqtl/api","path":"v3/studies","max_items":10}
  • {"base_url":"https://www.ebi.ac.uk/eqtl/api","path":"v3/associations","params":{"gene_id":"ENSG00000141510","rsid":"rs7903146","size":10},"max_items":10}
  • {"base_url":"https://www.ebi.ac.uk/eqtl/api","path":"v1/genes/ENSG00000141510/associations","params":{"variant_id":"rs7903146","size":10},"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/eqtl/api","path":"v3/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.