pharmgkb-skill

Operating rules

• Use scripts/rest_request.py for all PharmGKB API calls.
• Use base_url=https://api.pharmgkb.org/v1/data.
• Single object lookups usually do not need max_items; list and search endpoints are better with max_items=10.
• 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.
• Prefer these paths: gene/<id>, variant/<id>, clinicalAnnotation, dosingGuideline, and search endpoints.
• If the user needs the full payload, set save_raw=true and report the saved file path.

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 PharmGKB patterns:
  • {"base_url":"https://api.pharmgkb.org/v1/data","path":"gene/PA36679"}
  • {"base_url":"https://api.pharmgkb.org/v1/data","path":"clinicalAnnotation","params":{"relatedChemicals.accessionId":"PA449726","limit":10},"max_items":10}
  • {"base_url":"https://api.pharmgkb.org/v1/data","path":"variant/PA166158545"}

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://api.pharmgkb.org/v1/data","path":"gene/PA36679"}' | 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.