ncbi-clinicaltables-skill

Imported from openai/plugins (plugins/life-science-research/skills/ncbi-clinicaltables-skill/SKILL.md). Install upstream with npx skills add openai/plugins --skill ncbi-clinicaltables-skill. Copyright stays with the author.

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.