Update to Life Science Research

{
  "name": "chebi-skill",
  "description": "Submit compact ChEBI 2.0 API requests for chemical search, compound lookup, ontology traversal, and structure metadata. Use when a user wants concise ChEBI 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: chebi-skill\ndescription: Submit compact ChEBI 2.0 API requests for chemical search, compound lookup, ontology traversal, and structure metadata. Use when a user wants concise ChEBI summaries\n---\n\n## Operating rules\n- Use `scripts/rest_request.py` for all ChEBI calls.\n- Use `base_url=https://www.ebi.ac.uk`.\n- Prefer the documented public routes under `chebi/backend/api/public/`.\n- Start with `es_search/` for free-text lookup and use `compound/<CHEBI:id>/` for targeted records.\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 these paths: `chebi/backend/api/public/es_search/`, `chebi/backend/api/public/compound/<CHEBI:id>/`, and ontology child or parent routes.\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 ChEBI patterns:\n  - `{\"base_url\":\"https://www.ebi.ac.uk\",\"path\":\"chebi/backend/api/public/es_search/\",\"params\":{\"query\":\"caffeine\",\"size\":10},\"record_path\":\"results\",\"max_items\":10}`\n  - `{\"base_url\":\"https://www.ebi.ac.uk\",\"path\":\"chebi/backend/api/public/compound/CHEBI:27732/\"}`\n  - `{\"base_url\":\"https://www.ebi.ac.uk\",\"path\":\"chebi/backend/api/public/ontology/children/CHEBI:27732/\"}`\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://www.ebi.ac.uk\",\"path\":\"chebi/backend/api/public/es_search/\",\"params\":{\"query\":\"caffeine\",\"size\":10},\"record_path\":\"results\",\"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"
}