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.
- 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.
By