Update to Life Sciences Databases

{
  "name": "chembl-skill",
  "description": "Submit compact ChEMBL API requests for activity, molecule, target, mechanism, and text-search endpoints. Use when a user wants concise ChEMBL summaries",
  "included_files": [
    {
      "relative_path": "scripts/rest_request.py",
      "size_in_bytes": 1097
    }
  ],
  "skill_md_contents": "---\nname: chembl-skill\ndescription: Submit compact ChEMBL API requests for activity, molecule, target, mechanism, and text-search endpoints. Use when a user wants concise ChEMBL 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 `chembl-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 ChEMBL API calls.\n- Use `base_url=https://www.ebi.ac.uk/chembl/api/data`.\n- The script accepts `max_items`; for activity, mechanism, and text-search collections, start with API `limit=10` and `max_items=10`.\n- Single molecule or target lookups usually do not need `max_items`.\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- Return the script JSON verbatim only if the user explicitly asks for machine-readable output.\n- Prefer these paths: `activity.json`, `molecule/<id>.json`, `target/<id>.json`, `mechanism.json`, and `molecule/search.json`.\n- Use `record_path` to target list fields like `activities`, `mechanisms`, or `molecules`.\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 ChEMBL patterns:\n  - `{\"base_url\":\"https://www.ebi.ac.uk/chembl/api/data\",\"path\":\"activity.json\",\"params\":{\"molecule_chembl_id\":\"CHEMBL25\",\"limit\":10},\"record_path\":\"activities\",\"max_items\":10}`\n  - `{\"base_url\":\"https://www.ebi.ac.uk/chembl/api/data\",\"path\":\"molecule/CHEMBL25.json\"}`\n  - `{\"base_url\":\"https://www.ebi.ac.uk/chembl/api/data\",\"path\":\"molecule/search.json\",\"params\":{\"q\":\"imatinib\",\"limit\":10},\"record_path\":\"molecules\",\"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://www.ebi.ac.uk/chembl/api/data\",\"path\":\"activity.json\",\"params\":{\"molecule_chembl_id\":\"CHEMBL25\",\"limit\":10},\"record_path\":\"activities\",\"max_items\":10}' | python scripts/rest_request.py\n```\n"
}