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ncbi-clinicaltables-skill

Submit compact Clinical Tables NCBI Gene requests for human gene lookup, pagination, and field selection. Use when a user wants concise autocomplete-style human gene search results

Stars
1,305
Source
openai/plugins
Updated
2026-05-30
Slug
openai--plugins--ncbi-clinicaltables-skill
View on GitHubRaw SKILL.md

// install — copy + paste into any project

mkdir -p .claude/skills && curl -fsSL https://raw.githubusercontent.com/openai/plugins/HEAD/plugins/life-science-research/skills/ncbi-clinicaltables-skill/SKILL.md -o .claude/skills/ncbi-clinicaltables-skill.md

Drops the SKILL.md into .claude/skills/ncbi-clinicaltables-skill.md. Works with Claude Code, Cursor, and any agent that loads SKILL.md files from .claude/skills/.

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.