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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.

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原文查看原文说明

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

查看安装方法

适用场景

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

包含的文件（4）

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

SKILL.md（原文）

安装前可以查看交给 AI 代理的指令内容。

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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