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bgee-skill

✓ Official★ 4,081

by openai · part of openai/plugins

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.

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🧩 One of 7 skills in the openai/plugins package — works on its own, and pairs well with its siblings.

This is the playbook your agent receives when the skill activates — you don't need to read it to use the skill, but it's here to audit before installing.

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.