Update to Life Science Research

{
  "name": "ncbi-clinicaltables-skill",
  "description": "Submit compact Clinical Tables NCBI Gene requests for human gene lookup, pagination, and field selection. Use when a user wants concise autocomplete-style human gene search results",
  "included_files": [
    {
      "relative_path": "agents/openai.yaml",
      "size_in_bytes": 117
    },
    {
      "relative_path": "scripts/ncbi_gene_clinicaltables.py",
      "size_in_bytes": 5559
    }
  ],
  "skill_md_contents": "---\nname: ncbi-clinicaltables-skill\ndescription: Submit compact Clinical Tables NCBI Gene requests for human gene lookup, pagination, and field selection. Use when a user wants concise autocomplete-style human gene search results\n---\n\n## Operating rules\n- Use `scripts/ncbi_gene_clinicaltables.py` for all Clinical Tables gene searches.\n- The script accepts `max_items`; for search pages, start with `count=10` and `max_items=10`.\n- Use `params` for endpoint options like `df`, `ef`, `sf`, `q`, `offset`, and `count`.\n- Prefer `ncbi-entrez-skill` when the user wants general Entrez Gene records rather than autocomplete/search rows.\n- Page with `offset` instead of asking for large pulls.\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 the full payload, set `save_raw=true` and report the saved file path instead of pasting large response arrays into chat.\n\n## Execution behavior\n- Return concise markdown summaries from the script JSON by default.\n- Return the JSON verbatim only if the user explicitly asks for machine-readable output.\n- Use `terms` for the primary search text.\n- Keep `count` modest and page with `offset` instead of pulling large result sets at once.\n\n## Input\n- Read one JSON object from stdin.\n- Required field: `terms`\n- Optional fields: `params`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`\n- Common NCBI Gene patterns:\n  - `{\"terms\":\"TP53\",\"params\":{\"df\":\"GeneID,Symbol,description\"}}`\n  - `{\"terms\":\"BRCA\",\"params\":{\"count\":10,\"df\":\"chromosome,GeneID,Symbol,description,type_of_gene\"},\"max_items\":10}`\n  - `{\"terms\":\"kinase\",\"params\":{\"count\":10,\"offset\":10,\"df\":\"GeneID,Symbol,description\"},\"max_items\":10}`\n\n## Output\n- Success returns `ok`, `source`, `terms`, `total`, `codes`, `display_rows`, `extra_fields`, and truncation metadata.\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 '{\"terms\":\"TP53\",\"params\":{\"count\":10,\"df\":\"GeneID,Symbol,description\"},\"max_items\":10}' | python scripts/ncbi_gene_clinicaltables.py\n```\n\n## References\n- No additional runtime references are required; keep the import package limited to this file and `scripts/ncbi_gene_clinicaltables.py`.\n"
}