Agent Skills
› openai/plugins
› finngen-phewas-skill
finngen-phewas-skill
GitHub用于查询FinnGen单变异体PheWAS关联结果的技能。支持rsID或坐标输入，自动解析为GRCh38标准格式，调用脚本获取并返回简洁的汇总摘要或原始数据，适用于遗传学数据分析场景。
Trigger Scenarios
用户询问特定基因变异的疾病关联
需要查询FinnGen数据库中的PheWAS结果
提供rsID或基因组坐标以获取表型关联信息
Install
npx skills add openai/plugins --skill finngen-phewas-skill -g -y
SKILL.md
Frontmatter
{
"name": "finngen-phewas-skill",
"description": "Fetch compact FinnGen 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 FinnGen association results for one variant"
}
Operating rules
- Use
scripts/finngen_phewas.pyfor all FinnGen PheWAS lookups. - Accept exactly one of
rsid,grch37,grch38, orvariant; resolve to the canonical GRCh38chr:pos-ref-altquery before calling FinnGen. - The script accepts
max_results; start withmax_results=10and 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=trueand reportraw_output_pathinstead 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, truncation status, and any returned
regions. - Increase
max_resultsgradually 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, orvariant - Optional fields:
max_results,save_raw,raw_output_path,timeout_sec - Common patterns:
{"grch38":"10:112998590-C-T","max_results":10}{"grch37":"10:114758349-C-T","max_results":10}{"rsid":"rs7903146","max_results":10}{"variant":"10:112998590:C:T","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,regions,variant_url,raw_output_path, andwarnings. - Use
raw_output_pathwhensave_raw=true. - Failure returns
ok=falsewitherror.codeanderror.message.
Execution
echo '{"grch38":"10:112998590-C-T","max_results":10}' | python scripts/finngen_phewas.py
References
- No additional runtime references are required; keep the import package limited to this file and
scripts/finngen_phewas.py.
Version History
- 11c74d6 Current 2026-07-19 09:38
