ncbi-entrez-skill

## Operating rules - Use `scripts/ncbi_entrez.py` for all Entrez calls in this package. - Use explicit `endpoint` values such as `esearch`, `esummary`, `efetch`, `elink`, or `einfo`. - Search-style Entrez calls are better with `retmax=10` and `max_items=10`. - 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. - BLAST workflows belong in `ncbi-blast-skill`. PMC Open Access workflows belong in `ncbi-pmc-skill`. Datasets v2 workflows belong in `ncbi-datasets-skill`. - Re-run requests in long conversations instead of relying on older tool output. - Treat displayed `...` in tool previews as UI truncation, not literal request content. ## Execution behavior - Return concise markdown summaries from the script output by default. - 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. - Return raw JSON or XML only if the user explicitly asks for machine-readable output. - Prefer targeted endpoint calls instead of broad unfiltered dumps. - If the user needs the full raw response, set `save_raw=true` and report the saved file path. ## Input - Read one JSON object from stdin. - Required field: `endpoint` - Optional fields: `params`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path` - Common Entrez patterns: - `{"endpoint":"esearch","params":{"db":"pubmed","term":"KRAS AND colorectal cancer","retmode":"json","retmax":10},"max_items":10}` - `{"endpoint":"esummary","params":{"db":"gene","id":"7157","retmode":"json"},"max_items":10}` - `{"endpoint":"efetch","params":{"db":"protein","id":"NP_000537.3","retmode":"xml"},"response_format":"xml","max_items":10}` - `{"endpoint":"elink","params":{"dbfrom":"gds","db":"pubmed","id":"200000001","retmode":"json"},"max_items":10}` ## Output - Success returns `ok`, `source`, endpoint metadata, and either compact `records`, a compact `summary`, or `text_head`. - Use `raw_output_path` when `save_raw=true`. - Failure returns `ok=false` with `error.code` and `error.message`. ## Execution ```bash echo '{"endpoint":"esearch","params":{"db":"gene","term":"TP53[gene] AND human[orgn]","retmode":"json","retmax":10},"max_items":10}' | python scripts/ncbi_entrez.py ``` ## References - Load `references/geo.md` only when the user specifically needs GEO query patterns. - Keep the import package limited to this file, `references/geo.md`, and `scripts/ncbi_entrez.py`.