Update to Life Sciences Databases

{
  "name": "cbioportal-skill",
  "description": "Submit compact cBioPortal API requests for studies, molecular profiles, mutations, clinical data, and samples. Use when a user wants concise cBioPortal summaries",
  "included_files": [
    {
      "relative_path": "scripts/rest_request.py",
      "size_in_bytes": 1097
    }
  ],
  "skill_md_contents": "---\nname: cbioportal-skill\ndescription: Submit compact cBioPortal API requests for studies, molecular profiles, mutations, clinical data, and samples. Use when a user wants concise cBioPortal 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 `cbioportal-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 cBioPortal API calls.\n- Use `base_url=https://www.cbioportal.org/api`.\n- Collection endpoints are better with `pageSize=10` and `max_items=10`; single study or profile lookups usually do not need `max_items`.\n- Use `method=POST` plus `json_body` for fetch-style endpoints such as mutation fetches.\n- Send `Accept: application/json` in `headers`.\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 these paths: `studies`, `studies/<studyId>/molecular-profiles`, `molecular-profiles/<profileId>/mutations/fetch`, and study-level clinical or sample endpoints.\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 cBioPortal patterns:\n  - `{\"base_url\":\"https://www.cbioportal.org/api\",\"path\":\"studies\",\"params\":{\"keyword\":\"breast\",\"projection\":\"SUMMARY\",\"pageSize\":10},\"headers\":{\"Accept\":\"application/json\"},\"max_items\":10}`\n  - `{\"base_url\":\"https://www.cbioportal.org/api\",\"path\":\"molecular-profiles/brca_tcga_mutations/mutations/fetch\",\"method\":\"POST\",\"json_body\":{\"sampleListId\":\"brca_tcga_all\",\"entrezGeneIds\":[7157]},\"headers\":{\"Accept\":\"application/json\"},\"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.cbioportal.org/api\",\"path\":\"studies\",\"params\":{\"keyword\":\"breast\",\"projection\":\"SUMMARY\",\"pageSize\":10},\"headers\":{\"Accept\":\"application/json\"},\"max_items\":10}' | python scripts/rest_request.py\n```\n"
}