Update to Life Science Research

{
  "name": "ncbi-entrez-skill",
  "description": "Submit compact NCBI Entrez E-Utilities requests for PubMed, Gene, Protein, Nucleotide, PMC metadata, and GEO metadata workflows. Use when a user wants concise Entrez search, fetch, summary, or link results; save raw JSON or XML only on request.",
  "included_files": [
    {
      "relative_path": "agents/openai.yaml",
      "size_in_bytes": 112
    },
    {
      "relative_path": "references/geo.md",
      "size_in_bytes": 930
    },
    {
      "relative_path": "scripts/ncbi_entrez.py",
      "size_in_bytes": 10830
    }
  ],
  "skill_md_contents": "---\nname: ncbi-entrez-skill\ndescription: Submit compact NCBI Entrez E-Utilities requests for PubMed, Gene, Protein, Nucleotide, PMC metadata, and GEO metadata workflows. Use when a user wants concise Entrez search, fetch, summary, or link results; save raw JSON or XML only on request.\n---\n\n## Operating rules\n- Use `scripts/ncbi_entrez.py` for all Entrez calls in this package.\n- Use explicit `endpoint` values such as `esearch`, `esummary`, `efetch`, `elink`, or `einfo`.\n- Search-style Entrez calls are better with `retmax=10` and `max_items=10`.\n- GEO is nested under this skill. Use `db=gds` or `db=geoprofiles` for GEO metadata and load `references/geo.md` only when the user is specifically asking about GEO.\n- BLAST workflows belong in `ncbi-blast-skill`. PMC Open Access workflows belong in `ncbi-pmc-skill`. Datasets v2 workflows belong in `ncbi-datasets-skill`.\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 output by default.\n- In final user-facing summaries, never display a bare PMID or DOI. Render every PMID as a Markdown link in the form `[PMID <PMID>](https://pubmed.ncbi.nlm.nih.gov/<PMID>/)` and every DOI as `[<DOI>](https://doi.org/<DOI>)`, including in tables, bullets, parentheticals, and source lists.\n- Return raw JSON or XML only if the user explicitly asks for machine-readable output.\n- Prefer targeted endpoint calls instead of broad unfiltered dumps.\n- If the user needs the full raw response, set `save_raw=true` and report the saved file path.\n\n## Input\n- Read one JSON object from stdin.\n- Required field: `endpoint`\n- Optional fields: `params`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`\n- Common Entrez patterns:\n  - `{\"endpoint\":\"esearch\",\"params\":{\"db\":\"pubmed\",\"term\":\"KRAS AND colorectal cancer\",\"retmode\":\"json\",\"retmax\":10},\"max_items\":10}`\n  - `{\"endpoint\":\"esummary\",\"params\":{\"db\":\"gene\",\"id\":\"7157\",\"retmode\":\"json\"},\"max_items\":10}`\n  - `{\"endpoint\":\"efetch\",\"params\":{\"db\":\"protein\",\"id\":\"NP_000537.3\",\"retmode\":\"xml\"},\"response_format\":\"xml\",\"max_items\":10}`\n  - `{\"endpoint\":\"elink\",\"params\":{\"dbfrom\":\"gds\",\"db\":\"pubmed\",\"id\":\"200000001\",\"retmode\":\"json\"},\"max_items\":10}`\n\n## Output\n- Success returns `ok`, `source`, endpoint metadata, 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 '{\"endpoint\":\"esearch\",\"params\":{\"db\":\"gene\",\"term\":\"TP53[gene] AND human[orgn]\",\"retmode\":\"json\",\"retmax\":10},\"max_items\":10}' | python scripts/ncbi_entrez.py\n```\n\n## References\n- Load `references/geo.md` only when the user specifically needs GEO query patterns.\n- Keep the import package limited to this file, `references/geo.md`, and `scripts/ncbi_entrez.py`.\n"
}