Bgee Skill

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.