ncbi-entrez-skill

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. 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 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 .