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tpmi-phewas-skill

Look up TPMI associations for a single genetic variant using an rsID or genome coordinates. Get a concise summary showing the queried variant, the total number of associations, and whether the displayed results are incomplete.

한국어 요약은 준비 중입니다. 영어 요약을 표시하고 있습니다.

원문원문 설명 보기

Fetch compact TPMI PheWAS summaries for single variants by accepting rsID, GRCh37, or GRCh38 input and resolving to the required GRCh38 query. Use when a user wants concise TPMI association results for one variant

openai/plugins
설치 방법 보기

이럴 때 유용합니다

  • Check TPMI associations for a variant identified by rsID
  • Look up a variant using GRCh37 genome coordinates
  • Save the full association response to a file

포함된 파일(4)

  • SKILL.md2.3 KB
  • agents/openai.yaml95 B
  • scripts/tpmi_phewas.py7.4 KB
  • scripts/variant_resolution.py11.9 KB

SKILL.md(원문)

설치하기 전에 에이전트에게 전달되는 지시 내용을 확인할 수 있습니다.

Operating rules

  • Use scripts/tpmi_phewas.py for all TPMI PheWAS lookups.
  • Accept exactly one of rsid, grch37, grch38, or variant; resolve to the canonical GRCh38 chr:pos-ref-alt query before calling TPMI.
  • The script accepts max_results; start with max_results=10 and only increase it if the first slice is insufficient.
  • Re-run the lookup in long conversations instead of relying on older tool output.
  • Treat displayed ... in tool previews as UI truncation, not literal request content.
  • If the user needs the full association payload, set save_raw=true and report raw_output_path instead of pasting large arrays into chat.

Execution behavior

  • Return concise markdown summaries from the script JSON by default.
  • Return the JSON verbatim only if the user explicitly asks for machine-readable output.
  • Surface the canonical queried variant, total association count, and whether the results were truncated.
  • Increase max_results gradually instead of asking for large association dumps in one call.

Input

  • Read one JSON object from stdin, or a single JSON string containing the variant.
  • Required input: exactly one of rsid, grch37, grch38, or variant
  • Optional fields: max_results, save_raw, raw_output_path, timeout_sec
  • Common patterns:
    • {"grch38":"6:160540105-T-C","max_results":10}
    • {"grch37":"6:162447146-T-C","max_results":10}
    • {"rsid":"rs9273363","max_results":10}
    • {"variant":"6:160540105:T:C","max_results":25,"save_raw":true}

Output

  • Success returns ok, source, input, query_variant, max_results_applied, association_count, association_count_total, truncated, associations, variant, variant_url, raw_output_path, and warnings.
  • Use raw_output_path when save_raw=true.
  • Failure returns ok=false with error.code and error.message.

Execution

echo '{"grch38":"6:160540105-T-C","max_results":10}' | python scripts/tpmi_phewas.py

References

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

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