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Skill v1.0.0
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PublishedApril 26, 2026 at 05:57 AM
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version: "1.0.0" name: bgee-skill description: 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.
Operating rules
- Use
scripts/sparql_request.pyfor all Bgee SPARQL work. - Start with small
SELECTorASKqueries and addLIMITearly. - Prefer ontology-aware, healthy wild-type expression questions over broad triple dumps.
- Use
query_pathfor 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:
queryorquery_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 compactsummary, andraw_output_pathwhensave_raw=true. - Failure returns
ok=falsewitherror.codesuch asinvalid_json,invalid_input,network_error, orinvalid_response.
Execution
bash
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.