Update to Life Sciences Databases

{
  "name": "rhea-skill",
  "description": "Submit compact Rhea reaction search requests for biochemical reactions and reaction IDs. Use when a user wants concise Rhea summaries",
  "included_files": [
    {
      "relative_path": "scripts/rest_request.py",
      "size_in_bytes": 1097
    }
  ],
  "skill_md_contents": "---\nname: rhea-skill\ndescription: Submit compact Rhea reaction search requests for biochemical reactions and reaction IDs. Use when a user wants concise Rhea summaries\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 `rhea-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.\n\n## Operating rules\n- Use `scripts/rest_request.py` for all Rhea calls.\n- Use Rhea's official `base_url=https://sparql.rhea-db.org` SPARQL endpoint for compact JSON reaction records.\n- The website search API supports TSV, not `format=json`; avoid website requests that fail with Cloudflare HTTP 403.\n- Keep queries narrow by reaction ID, compound name, EC number, or free-text reaction term.\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 script JSON by default.\n- Return raw JSON only if the user explicitly asks for machine-readable output.\n- Prefer a targeted SPARQL reaction identifier, `LIMIT 1`, `format=json`, and `record_path=results.bindings`.\n\n## Input\n- Read one JSON object from stdin.\n- Required fields: `base_url`, `path`\n- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`\n- Common Rhea patterns:\n  - `{\"base_url\":\"https://sparql.rhea-db.org\",\"path\":\"sparql\",\"params\":{\"query\":\"PREFIX rh: <http://rdf.rhea-db.org/> SELECT ?accession ?equation WHERE { <http://rdf.rhea-db.org/47148> rh:accession ?accession ; rh:equation ?equation . } LIMIT 1\",\"format\":\"json\"},\"headers\":{\"Accept\":\"application/sparql-results+json\"},\"record_path\":\"results.bindings\",\"max_items\":5}`\n\n## Output\n- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records` or a compact `summary`.\n- Use `raw_output_path` when `save_raw=true`.\n- Failure returns `ok=false` with `error.code` and `error.message`.\n\n## Execution\n```bash\necho '{\"base_url\":\"https://sparql.rhea-db.org\",\"path\":\"sparql\",\"params\":{\"query\":\"PREFIX rh: <http://rdf.rhea-db.org/> SELECT ?accession ?equation WHERE { <http://rdf.rhea-db.org/47148> rh:accession ?accession ; rh:equation ?equation . } LIMIT 1\",\"format\":\"json\"},\"headers\":{\"Accept\":\"application/sparql-results+json\"},\"record_path\":\"results.bindings\",\"max_items\":5}' | python scripts/rest_request.py\n```\n"
}