Update to Life Sciences Databases

{
  "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.",
  "included_files": [
    {
      "relative_path": "scripts/sparql_request.py",
      "size_in_bytes": 8445
    }
  ],
  "skill_md_contents": "---\nname: bgee-skill\ndescription: 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.\n---\n\n## Source presentation\n<!-- source-presentation-contract:v2 -->\n- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.\n- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.\n- Use the `bgee-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.\n\n## Operating rules\n- Use `scripts/sparql_request.py` for all Bgee SPARQL work.\n- Start with small `SELECT` or `ASK` queries and add `LIMIT` early.\n- Prefer ontology-aware, healthy wild-type expression questions over broad triple dumps.\n- Use `query_path` for longer SPARQL documents instead of pasting large inline queries.\n- Re-run requests in long conversations instead of relying on older tool output.\n\n## Execution behavior\n- Return concise markdown summaries from the SPARQL JSON by default.\n- Return raw results only if the user explicitly asks for machine-readable output.\n- Default to JSON result format unless the user explicitly asks for text output.\n\n## Input\n- Read one JSON object from stdin.\n- Required field: `query` or `query_path`\n- Optional fields: `method`, `params`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`\n- Common Bgee patterns:\n  - `{\"query\":\"ASK {}\"}`\n  - `{\"query\":\"SELECT * WHERE { ?s ?p ?o } LIMIT 3\",\"max_items\":3}`\n\n## Output\n- Success returns `ok`, `source`, a compact `summary`, and `raw_output_path` when `save_raw=true`.\n- Failure returns `ok=false` with `error.code` such as `invalid_json`, `invalid_input`, `network_error`, or `invalid_response`.\n\n## Execution\n```bash\necho '{\"query\":\"ASK {}\"}' | python scripts/sparql_request.py\n```\n"
}