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bgee-skill

Query Bgee for healthy wild-type gene expression metadata and receive concise summaries. The skill supports lookups that account for relationships between biological terms, keeps requests small, and saves raw results only when requested.

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原文查看原文说明

Submit compact Bgee SPARQL requests for healthy wild-type expression metadata and ontology-aware lookup patterns. Use when a user wants concise Bgee summaries; save raw results only on request.

查看安装方法

适用场景

  • Looking up healthy wild-type expression metadata
  • Searching with relationships between biological terms
  • Checking whether matching data exists
  • Saving raw query results when needed

包含的文件(3)

  • SKILL.md1.7 KB
  • agents/openai.yaml89 B
  • scripts/sparql_request.py7.4 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/sparql_request.py for all Bgee SPARQL work.
  • Start with small SELECT or ASK queries and add LIMIT early.
  • Prefer ontology-aware, healthy wild-type expression questions over broad triple dumps.
  • Use query_path for longer SPARQL documents instead of pasting large inline queries.
  • Re-run requests in long conversations instead of relying on older tool output.

Execution behavior

  • Return concise markdown summaries from the SPARQL JSON by default.
  • Return raw results only if the user explicitly asks for machine-readable output.
  • Default to JSON result format unless the user explicitly asks for text output.

Input

  • Read one JSON object from stdin.
  • Required field: query or query_path
  • Optional fields: method, params, response_format, max_items, max_depth, timeout_sec, save_raw, raw_output_path
  • Common Bgee patterns:
    • {"query":"ASK {}"}
    • {"query":"SELECT * WHERE { ?s ?p ?o } LIMIT 3","max_items":3}

Output

  • Success returns ok, source, a compact summary, and raw_output_path when save_raw=true.
  • Failure returns ok=false with error.code such as invalid_json, invalid_input, network_error, or invalid_response.

Execution

echo '{"query":"ASK {}"}' | python scripts/sparql_request.py

References

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

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