Update to Life Science Research

{
  "name": "hmdb-skill",
  "description": "Submit compact HMDB search requests for metabolites, proteins, diseases, and pathways. Use when a user wants concise HMDB summaries",
  "included_files": [
    {
      "relative_path": "agents/openai.yaml",
      "size_in_bytes": 89
    },
    {
      "relative_path": "scripts/rest_request.py",
      "size_in_bytes": 10728
    }
  ],
  "skill_md_contents": "---\nname: hmdb-skill\ndescription: Submit compact HMDB search requests for metabolites, proteins, diseases, and pathways. Use when a user wants concise HMDB summaries\n---\n\n## Operating rules\n- Use `scripts/rest_request.py` for all HMDB calls.\n- Use `base_url=https://hmdb.ca`.\n- Search endpoints are better with `per_page=10` and `max_items=10`.\n- Keep category-specific requests narrow instead of broad searches across multiple categories at once.\n- Re-run requests in long conversations instead of relying on older tool output.\n- Treat displayed `...` in tool previews as UI truncation, not literal request content.\n\n## Execution behavior\n- Return concise markdown summaries from the script JSON by default.\n- Prefer `unearth/q` with explicit `query`, `category`, and `format=json`.\n- If the user needs the full payload, set `save_raw=true` and report the saved file path.\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 HMDB patterns:\n  - `{\"base_url\":\"https://hmdb.ca\",\"path\":\"unearth/q\",\"params\":{\"query\":\"serotonin\",\"category\":\"metabolites\",\"format\":\"json\",\"per_page\":10},\"record_path\":\"metabolites\",\"max_items\":10}`\n  - `{\"base_url\":\"https://hmdb.ca\",\"path\":\"unearth/q\",\"params\":{\"query\":\"glycolysis\",\"category\":\"pathways\",\"format\":\"json\",\"per_page\":10},\"max_items\":10}`\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://hmdb.ca\",\"path\":\"unearth/q\",\"params\":{\"query\":\"serotonin\",\"category\":\"metabolites\",\"format\":\"json\",\"per_page\":10},\"record_path\":\"metabolites\",\"max_items\":10}' | python scripts/rest_request.py\n```\n\n## References\n- No additional runtime references are required; keep the import package limited to this file and `scripts/rest_request.py`.\n"
}