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skill CX Codex GP ChatGPT official · OpenAI

civic-skill — Codex skill: what it does, how to install

Runs targeted GraphQL queries against CIViC to inspect schemas and extract cancer variant evidence. Fits life science research workflows in Codex.

Install into Codex · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add openai/plugins --skill civic-skill -a codex
Open on GitHub

What civic-skill does

The skill handles CIViC GraphQL interactions via scripts/civic_graphql.py. It inspects schema types and fetches targeted clinical interpretation records for cancer variants. Narrow selection sets prevent heavy graph dumps from cluttering the agent context.

Execution relies on piped JSON input from stdin. A query string or a query_path file reference is required. Optional parameters include variables, max_items, max_depth, timeout_sec, and save_raw. By default, the script outputs a compact markdown summary. It provides raw JSON only when explicitly requested.

This skill fits researchers and developers who query CIViC data regularly and want structured summaries without writing manual GraphQL wrappers.

What it helps with

  • Inspect types and root fields in the CIViC GraphQL schema
  • Extract targeted cancer variant evidence without broad graph dumps
  • Save raw GraphQL response payloads to disk using save_raw
  • Execute long GraphQL documents via query_path files

Example prompts for the agent

  • Inspect the CIViC GraphQL schema and list the top 20 query fields
  • Run a targeted variant evidence search using scripts/civic_graphql.py
  • Execute the GraphQL document at query.graphql and save raw output

How to install civic-skill

1Skills CLI (Vercel)

npx skills add openai/plugins --skill civic-skill -a codex

2Manually: put the files in place

.agents/skills/civic-skill/SKILL.md

For all projects use ~/.agents/skills/

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Questions about civic-skill

How to install civic-skill in Codex?

Run npx skills add openai/plugins --skill civic-skill in your terminal. The configuration writes to .agents/skills/civic-skill/SKILL.md.

What does civic-skill do?

It runs compact GraphQL queries against the CIViC database using a local Python script. Results come back as concise markdown summaries or raw saved files.

What inputs does scripts/civic_graphql.py accept?

The script reads a single JSON object from stdin requiring query or query_path. Optional keys include variables, max_items, max_depth, timeout_sec, save_raw, and raw_output_path.

See also

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