Update to Life Sciences Databases

{
  "name": "ipd-skill",
  "description": "Submit compact IPD REST requests for HLA allele and cell-level metadata using the public IPD query API. Use when a user wants concise IPD summaries; save raw JSON or text only on request.",
  "included_files": [
    {
      "relative_path": "scripts/rest_request.py",
      "size_in_bytes": 1097
    }
  ],
  "skill_md_contents": "---\nname: ipd-skill\ndescription: Submit compact IPD REST requests for HLA allele and cell-level metadata using the public IPD query API. Use when a user wants concise IPD summaries; save raw JSON or text only on request.\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 `ipd-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 IPD calls.\n- Use `base_url=https://www.ebi.ac.uk/cgi-bin/ipd/api`.\n- The most stable public routes are `allele` and `cell`.\n- For HLA allele browsing, pass `project=HLA` and keep `limit` modest.\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 or text only if the user explicitly asks for machine-readable output.\n- Prefer these paths: `allele`, `cell`, and `allele/download`.\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 IPD patterns:\n  - `{\"base_url\":\"https://www.ebi.ac.uk/cgi-bin/ipd/api\",\"path\":\"allele\",\"params\":{\"project\":\"HLA\",\"limit\":10},\"record_path\":\"data\",\"max_items\":10}`\n  - `{\"base_url\":\"https://www.ebi.ac.uk/cgi-bin/ipd/api\",\"path\":\"allele\",\"params\":{\"project\":\"HLA\",\"query\":\"contains(name,\\\"A*01\\\")\",\"limit\":10},\"record_path\":\"data\",\"max_items\":10}`\n  - `{\"base_url\":\"https://www.ebi.ac.uk/cgi-bin/ipd/api\",\"path\":\"cell\",\"params\":{\"limit\":10},\"record_path\":\"data\",\"max_items\":10}`\n\n## Output\n- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records`, a compact `summary`, or `text_head`.\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/cgi-bin/ipd/api\",\"path\":\"allele\",\"params\":{\"project\":\"HLA\",\"limit\":10},\"record_path\":\"data\",\"max_items\":10}' | python scripts/rest_request.py\n```\n"
}