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skill CX Codex GP ChatGPT official · OpenAI

ukb-topmed-phewas-skill — Codex skill: what it does, install

Fetch a compact UKB-TOPMed PheWAS summary for one variant. Useful when the input arrives as an rsID or GRCh37/GRCh38 coordinates.

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

What ukb-topmed-phewas-skill does

The skill accepts exactly one variant input through rsid, grch37, grch38, or variant. It resolves that value to the canonical GRCh38 query, then runs scripts/ukb_topmed_phewas.py with JSON on standard input. The returned summary includes the queried variant, association counts, and whether the result slice was truncated.

The default lookup starts with max_results=10; increase it gradually when the first slice is too short. Set save_raw=true when the complete association payload is needed. The script then reports raw_output_path instead of putting large arrays in the chat. Check that the request contains one variant and that Python is available before running it.

What it helps with

  • fetch a PheWAS summary for one variant
  • resolve GRCh37 coordinates to a GRCh38 query
  • look up associations by rsID
  • check whether the result slice was truncated
  • save the full JSON response to a file

Example prompts for the agent

  • Fetch a compact UKB-TOPMed PheWAS summary for `rs7903146`.
  • Look up associations for `{"grch38":"10:112998590-C-T","max_results":10}` and report the canonical variant.
  • Save the full response for `{"variant":"10:112998590:C:T","max_results":25,"save_raw":true}` and return `raw_output_path`.

How to install ukb-topmed-phewas-skill

1Skills CLI (Vercel)

npx skills add openai/plugins --skill ukb-topmed-phewas-skill -a codex

2Manually: put the files in place

.agents/skills/ukb-topmed-phewas-skill/SKILL.md

For all projects use ~/.agents/skills/

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Questions about ukb-topmed-phewas-skill

How do I install ukb-topmed-phewas-skill in Codex?

Run npx skills add openai/plugins --skill ukb-topmed-phewas-skill, then run npx skills add openai/plugins --skill ukb-topmed-phewas-skill -a codex. The skill file is at .agents/skills/ukb-topmed-phewas-skill/SKILL.md.

What does ukb-topmed-phewas-skill do?

It accepts one rsID or GRCh37/GRCh38 variant, resolves it to a canonical GRCh38 query, and returns a compact UKB-TOPMed association summary.

How can I retrieve the full association payload?

Set save_raw=true. The skill saves the full response and reports raw_output_path; use max_results to control the returned slice.

See also

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