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.
• 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