Update to Life Science Research

{
  "name": "proteomexchange-skill",
  "description": "Submit compact ProteomeXchange PROXI requests for datasets, libraries, peptidoforms, proteins, PSMs, spectra, and USI examples. Use when a user wants concise PROXI summaries",
  "included_files": [
    {
      "relative_path": "agents/openai.yaml",
      "size_in_bytes": 106
    },
    {
      "relative_path": "scripts/rest_request.py",
      "size_in_bytes": 10728
    }
  ],
  "skill_md_contents": "---\nname: proteomexchange-skill\ndescription: Submit compact ProteomeXchange PROXI requests for datasets, libraries, peptidoforms, proteins, PSMs, spectra, and USI examples. Use when a user wants concise PROXI summaries\n---\n\n## Operating rules\n- Use `scripts/rest_request.py` for all ProteomeXchange PROXI calls.\n- Use `base_url=https://proteomecentral.proteomexchange.org/api/proxi/v0.1`.\n- Collection endpoints are better with `max_items=10`; targeted identifier lookups usually do not need `max_items`.\n- Keep requests narrow by identifier, spectrum, or dataset whenever possible.\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: `datasets`, `datasets/<identifier>`, `libraries`, `peptidoforms`, `proteins`, `psms`, `spectra`, and `usi_examples`.\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 PROXI patterns:\n  - `{\"base_url\":\"https://proteomecentral.proteomexchange.org/api/proxi/v0.1\",\"path\":\"datasets\",\"max_items\":10}`\n  - `{\"base_url\":\"https://proteomecentral.proteomexchange.org/api/proxi/v0.1\",\"path\":\"datasets/PXD000001\"}`\n  - `{\"base_url\":\"https://proteomecentral.proteomexchange.org/api/proxi/v0.1\",\"path\":\"usi_examples\",\"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://proteomecentral.proteomexchange.org/api/proxi/v0.1\",\"path\":\"datasets\",\"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"
}