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Clinvar Variation Skill for Codex

by openai

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

2k tokens
context cost
the whole folder, loaded on every use
3
files
ships runnable scripts
0
copies elsewhere
how many repositories repackaged it
4915
stars on the repo
on the repository, not the skill itself

Install

one command, takes just this skill from the repository 
npx skills add https://github.com/openai/plugins --skill clinvar-variation-skill

What comes with it

7 955 bytes besides the instruction
agents/openai.yaml
scripts/clinvar_variation.py

The instruction itself

6 sections, as written by the author

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.

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How to use it

Copy the folder

Take openai/clinvar-variation-skill from the repository into ~/.claude/skills for personal use, or into .claude/skills inside a project.

Check the name does not clash

The agent identifies a skill by the name field in its header. Two skills with the same name cannot sit side by side — one of them will be ignored.