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genebass-gene-burden-skill

Retrieve concise Genebass summaries linking a selected gene's variant group to traits across a broad association scan. Specify one Ensembl gene ID, choose a variant group, and control result counts, with optional JSON output.

中文简介正在准备中。当前显示英语简介。

原文查看原文说明

Submit compact Genebass gene burden requests for one Ensembl gene ID and one burden set. Use when a user wants concise Genebass PheWAS summaries

查看安装方法

适用场景

  • Review trait associations for a single gene
  • Request associations for a chosen variant group
  • Expand the number of associations returned
  • Get results as JSON for further processing

包含的文件(3)

  • SKILL.md1.7 KB
  • agents/openai.yaml110 B
  • scripts/genebass_gene_burden.py9.5 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/genebass_gene_burden.py for all Genebass calls.
  • This skill accepts one Ensembl gene ID per invocation.
  • max_results is flexible; start around 25 for broad summaries and increase only if the user explicitly wants more associations.
  • 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.
  • Return raw JSON only if the user explicitly asks for machine-readable output.
  • Supported burden sets are pLoF, missense|LC, and synonymous, with the aliases already handled by the script.
  • If the user needs the full result set, increase max_results deliberately instead of dumping everything by default.

Input

  • Read JSON from stdin as either a string Ensembl ID or an object.
  • String form:
    • "ENSG00000173531"
  • Object form:
    • {"ensembl_gene_id":"ENSG00000173531","burden_set":"pLoF","max_results":25}

Output

  • Success returns ok, source, input metadata, gene, association counts, truncated, and compact associations.
  • Failure returns ok=false with error.code and error.message.

Execution

echo '{"ensembl_gene_id":"ENSG00000173531","burden_set":"pLoF","max_results":25}' | python scripts/genebass_gene_burden.py

References

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

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