Operating rules
- Use
scripts/ncbi_gene_clinicaltables.py for all Clinical Tables gene searches.
- The script accepts
max_items; for search pages, start with count=10 and max_items=10.
- Use
params for endpoint options like df, ef, sf, q, offset, and count.
- Prefer
ncbi-entrez-skill when the user wants general Entrez Gene records rather than autocomplete/search rows.
- Page with
offset instead of asking for large pulls.
- 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.
- If the user asks for the full payload, set
save_raw=true and report the saved file path instead of pasting large response arrays into chat.
Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return the JSON verbatim only if the user explicitly asks for machine-readable output.
- Use
terms for the primary search text.
- Keep
count modest and page with offset instead of pulling large result sets at once.
Input
- Read one JSON object from stdin.
- Required field:
terms
- Optional fields:
params, max_items, max_depth, timeout_sec, save_raw, raw_output_path
- Common NCBI Gene patterns:
{"terms":"TP53","params":{"df":"GeneID,Symbol,description"}}{"terms":"BRCA","params":{"count":10,"df":"chromosome,GeneID,Symbol,description,type_of_gene"},"max_items":10}{"terms":"kinase","params":{"count":10,"offset":10,"df":"GeneID,Symbol,description"},"max_items":10}
Output
- Success returns
ok, source, terms, total, codes, display_rows, extra_fields, and truncation metadata.
- Use
raw_output_path when save_raw=true.
- Failure returns
ok=false with error.code and error.message.
Execution
echo '{"terms":"TP53","params":{"count":10,"df":"GeneID,Symbol,description"},"max_items":10}' | python scripts/ncbi_gene_clinicaltables.py
References
- No additional runtime references are required; keep the import package limited to this file and
scripts/ncbi_gene_clinicaltables.py.
