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clinvar-variation-skill

Submit compact ClinVar Clinical Tables and NCBI Variation requests for search, VCV, RCV, SCV, and RefSNP lookups. Use when a user wants variant-level summaries or identifier mapping

Stars
1,305
Source
openai/plugins
Updated
2026-05-30
Slug
openai--plugins--clinvar-variation-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/clinvar-variation-skill/SKILL.md -o .claude/skills/clinvar-variation-skill.md

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

Operating rules

  • Use scripts/clinvar_variation.py for all ClinVar and NCBI Variation work.
  • The script accepts max_items; for action=search, start around max_items=10.
  • For vcv, rcv, scv, and refsnp, omit max_items unless you need to trim nested arrays in the summary.
  • Re-run requests in long conversations instead of relying on prior tool output.
  • Treat displayed ... in tool previews as UI truncation, not literal request content.
  • If the user asks for full JSON, set save_raw=true and report the saved file path instead of pasting large payloads 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 action=search for the Clinical Tables endpoint.
  • Use action=vcv|rcv|scv|refsnp for NCBI Variation beta objects.

Input

  • Read one JSON object from stdin.
  • Required field: action
  • Action-specific required fields:
    • search: terms
    • vcv: vcv
    • rcv: rcv
    • scv: scv
    • refsnp: refsnp
  • Optional fields: params, max_items, max_depth, timeout_sec, save_raw, raw_output_path

Output

  • search returns total, identifiers, display_rows, extra_fields, and truncation metadata.
  • vcv|rcv|scv|refsnp return a compact summary and optional top_keys.
  • Use raw_output_path when save_raw=true.
  • Failures return ok=false with error.code and error.message.

Execution

echo '{"action":"search","terms":"VCV000013080","max_items":10}' | python scripts/clinvar_variation.py

References

  • No additional runtime references are required; keep the import package limited to this file and scripts/clinvar_variation.py.