Agent Skills
› openai/plugins
› biobankjapan-phewas-skill
biobankjapan-phewas-skill
GitHub用于查询日本生物银行（BBJ）PheWAS关联结果。支持rsID或GRCh37/38坐标输入，自动解析并返回简洁的Markdown摘要。默认限制10条结果，支持保存原始数据至文件，避免聊天窗口溢出。
Trigger Scenarios
用户询问特定基因变异的疾病关联
用户提供rsID或基因组坐标请求BBA PheWAS数据
Install
npx skills add openai/plugins --skill biobankjapan-phewas-skill -g -y
SKILL.md
Frontmatter
{
"name": "biobankjapan-phewas-skill",
"description": "Fetch compact BioBank Japan PheWAS summaries for single variants by accepting rsID, GRCh38, or GRCh37 input and resolving to the required GRCh37 query. Use when a user wants concise BBJ association results for one variant"
}
Operating rules
- Use
scripts/biobankjapan_phewas.pyfor all BioBank Japan PheWAS lookups. - Accept exactly one of
rsid,grch37,grch38, orvariant; resolve to the canonical GRCh37chr:pos-ref-altquery before calling BioBank Japan. - 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, and whether the results were truncated.
- 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:
{"grch37":"10:114758349-C-T","max_results":10}{"grch38":"10:112998590-C-T","max_results":10}{"rsid":"rs7903146","max_results":10}{"variant":"10:114758349: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,variant_url,raw_output_path, andwarnings. - Use
raw_output_pathwhensave_raw=true. - Failure returns
ok=falsewitherror.codeanderror.message.
Execution
echo '{"grch37":"10:114758349-C-T","max_results":10}' | python scripts/biobankjapan_phewas.py
References
- No additional runtime references are required; keep the import package limited to this file and
scripts/biobankjapan_phewas.py.
Version History
- 11c74d6 Current 2026-07-19 09:37
