Update to Life Sciences Databases

{
  "name": "human-protein-atlas-skill",
  "description": "Submit compact Human Protein Atlas requests for gene JSON, search downloads, and page-level tissue or cell-line lookups. Use when a user wants concise Human Protein Atlas summaries; save raw JSON or HTML only on request.",
  "included_files": [
    {
      "relative_path": "scripts/rest_request.py",
      "size_in_bytes": 1097
    }
  ],
  "skill_md_contents": "---\nname: human-protein-atlas-skill\ndescription: Submit compact Human Protein Atlas requests for gene JSON, search downloads, and page-level tissue or cell-line lookups. Use when a user wants concise Human Protein Atlas summaries; save raw JSON or HTML 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 `human-protein-atlas-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 Human Protein Atlas calls.\n- Use `base_url=https://www.proteinatlas.org`.\n- The script accepts `max_items`; single gene entry lookups usually do not need it, while search and download endpoints are better with `max_items=10`.\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- If the user asks for full HTML or JSON, set `save_raw=true` and report the saved file path instead of pasting large payloads into chat.\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: `<ENSG>.json`, `api/search_download.php`, `search/tissue/<symbol>`, and `search/cellline/<symbol>`.\n- For page-level search endpoints, prefer `response_format=text` so the script returns only `text_head` unless raw output is requested.\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 HPA patterns:\n  - `{\"base_url\":\"https://www.proteinatlas.org\",\"path\":\"ENSG00000141510.json\"}`\n  - `{\"base_url\":\"https://www.proteinatlas.org\",\"path\":\"api/search_download.php\",\"params\":{\"search\":\"TP53\",\"format\":\"json\",\"columns\":\"g,gs,tissue\",\"compress\":\"no\"},\"max_items\":10}`\n  - `{\"base_url\":\"https://www.proteinatlas.org\",\"path\":\"search/tissue/TP53\",\"response_format\":\"text\"}`\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.proteinatlas.org\",\"path\":\"ENSG00000141510.json\"}' | python scripts/rest_request.py\n```\n"
}