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pharmgkb-skill

✓ Official★ 4,081

by openai · part of openai/plugins

Submit compact PharmGKB API requests for genes, variants, clinical annotations, dosing guidelines, and search. Use when a user wants concise PharmGKB summaries

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🧩 One of 7 skills in the openai/plugins package — works on its own, and pairs well with its siblings.

This is the playbook your agent receives when the skill activates — you don't need to read it to use the skill, but it's here to audit before installing.

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.